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Journal articles on the topic 'Cotton Molecular genetics'
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1
Farahani, Farah, Masoud Sheidai, and Fahimeh Koohdar. "Genetic finger printing of cotton cultivars by ISSR molecular markers." Genetika 50, no. 2 (2018): 627–34. http://dx.doi.org/10.2298/gensr1802627f.
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Gossypium hirsutum is one of the main tetraploid cotton species that is cultivated throughout the world. Due to continuous selection of cotton cultivars for specific agronomic traits, the genetic variability within the cultivars decrease that lead to genetic erosion. To tackle the problem of reduced genetic variability, we should track all available genetic diversity within cotton germplasm and use them for inter-specific and intra-specific hybridization and produce new elite cotton cultivars. Therefore, the present study used ISSR molecular markers to illustrate genetic variability in 13 tetraploid cotton genotypes (Gossypium hirsutum L.) and to categorize these genotypes based on genetic affinity. 65 cotton plants were studied. The results identified private bands in the studied genotypes, while Network and STRUCTURE analyses of molecular data obtained grouped the genotypes with genetic affinity together. Some of the genotypes differed in their genetic content from the others; therefore, studying the genetic and agronomic variability within available cultivars is very important and produced data to broaden the gene pool for planning further hybridization in cotton.
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Grover, Corrinne E., Mengqiao Pan, Daojun Yuan, Mark A. Arick, Guanjing Hu, Logan Brase, David M. Stelly, et al. "The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution." G3: Genes|Genomes|Genetics 10, no. 5 (March 2, 2020): 1457–67. http://dx.doi.org/10.1534/g3.120.401050.
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Cotton is an important crop that has made significant gains in production over the last century. Emerging pests such as the reniform nematode have threatened cotton production. The rare African diploid species Gossypium longicalyx is a wild species that has been used as an important source of reniform nematode immunity. While mapping and breeding efforts have made some strides in transferring this immunity to the cultivated polyploid species, the complexities of interploidal transfer combined with substantial linkage drag have inhibited progress in this area. Moreover, this species shares its most recent common ancestor with the cultivated A-genome diploid cottons, thereby providing insight into the evolution of long, spinnable fiber. Here we report a newly generated de novo genome assembly of G. longicalyx. This high-quality genome leveraged a combination of PacBio long-read technology, Hi-C chromatin conformation capture, and BioNano optical mapping to achieve a chromosome level assembly. The utility of the G. longicalyx genome for understanding reniform immunity and fiber evolution is discussed.
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Andres, Ryan J., Daryl T. Bowman, Don C. Jones, and Vasu Kuraparthy. "Major Leaf Shapes of Cotton: Genetics and Agronomic Effects in Crop Production." Journal of Cotton Science 20, no. 4 (2016): 330–40. http://dx.doi.org/10.56454/mnrs4737.
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There exist four major leaf shape alleles in tetraploid cotton: normal, sub-okra/Sea-Island, okra, and super-okra. This allelic series has long served as a model genetic locus both in cotton and the broader leaf development research community. Over the years, numerous studies have attributed various production advantages to specific leaf shapes. The objective of this study was to provide a comprehensive review of this literature in order to provide a definitive report on the true benefits of these leaf shapes. In addition, a history of the genetic dissection of the major leaf shape locus was compiled. Leaf shape was found to have consistent effects on boll rot resistance, earliness, flowering rate, chemical spray penetration, lint trash, and yield. Reported effects on various insect resistances, photosynthetic rate, water use efficiency, and fiber quality were not consistent across studies. An ideal cotton cultivar would produce normal leaves up until the point canopy closure is obtained and then it would switch over to an open canopy of okra or super okra. Major leaf shapes of Upland cotton are a multiple allelic series of a single incompletely dominant genetic locus L-D1 on chromosome 15-D1 (Chr15). Genetic analysis studies have precisely mapped the major effect leaf shape genes in cotton and deciphered the causal nucleotide and gene expression changes leading to leaf shape phenotypic diversity in cotton. Recent advances in understanding the molecular processes underlying leaf shape phenotypic changes could help open new avenues for developing cotton cultivars with ideal leaf shape and could enhance sustainable and profitable cotton production.
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Ji, Yuanfu, Dwaine A. Raska, M. Nurul Islam-Faridi, Charles F. Crane, Michael S. Zwick, Robert E. Hanson, H. James Price, David M. Stelly, and Thomas D. McKnight. "Use of meiotic FISH for identification of a new monosome in Gossypium hirsutum L." Genome 40, no. 1 (February 1, 1997): 34–40. http://dx.doi.org/10.1139/g97-005.
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The extensive use of molecular cytogenetics in human genetics and clinical diagnostics indicates that analogous applications in plants are highly feasible. One sort of application would be the identification of new aneuploids, which traditionally involves either direct karyotypic identification, which is feasible in only a few plant species, or tests with markers (cytogenetic, genetic, or molecular), which require sexual hybridization and at least one subsequent seed or plant generation. We have used meiotic fluorescence in situ hybridization (FISH) to analyze a new monosome of cotton (Gossypium hirsutum L., 2n = 4x = 52, 2(AD)1) that had a phenotype which seemed to be distinct from monosomes in the Cotton Cytogenetic Collection. Painting with A2-genome DNA revealed the monosome's D-subgenome origin. DAPI–PI staining showed that the monosome carries a major NOR, delimiting it to the major NOR-bearing chromosomes of the D-subgenome, i.e., 16 or 23. Dual-color FISH with 5S and 18S–28S rDNAs indicated that the monosome contains separate major clusters of each of these two tandemly repeated rDNA elements, thus delimiting the monosome to chromosome 23, for which the Cotton Cytogenetic Collection has previously been devoid of any sort of deficiency. Of the 26 chromosomes in the cotton genome, the Collection now provides coverage for 16 (70%) in the form of monosomy, and 20 (77%) in the form of monosomy and (or) telosomy. Use of molecular cytogenetic methods to identify a new plant aneuploid in cotton exemplifies the fact that a physicochemical karyotypic chromosome identification system is not required a priori for application of new molecular cytogenetic methods, thus indicating their potential applicability to nearly all plant species.Key words: fluorescence in situ hybridization, monosome, aneuploid, Gossypium hirsutum.
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Becerra Lopez-Lavalle, L. A., B. Matheson, and C. L. Brubaker. "A genetic map of an Australian wild Gossypium C genome and assignment of homoeologies with tetraploid cultivated cotton." Genome 54, no. 9 (September 2011): 779–94. http://dx.doi.org/10.1139/g11-037.
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Genetic diversity for traits such as fibre quality or disease resistance to microorganisms is limited in the elite cotton germplasm; consequently, cotton breeders are looking for novel alleles in the secondary or even in the tertiary gene pools. The wild Australian Gossypium species (tertiary gene pool) represent an alternative source of novel alleles. However, to use these species efficiently, enabling tools are required. Chromosome-specific molecular markers are particularly useful tools to track the transmission of this exotic genetic material into the cultivated cotton during introgression. In this study, we report the construction of a genetic linkage map of the Australian wild C-genome species Gossypium sturtianum. The map, based on an F2 population of 114 individuals, contains 291 AFLP loci. The map spans 1697 cM with an average distance of 5.8 cM between markers. To associate C-genome chromosomes with the A and D subgenomes of cultivated cotton, 29 SSR and RFLP–STS markers were assigned to chromosomes using cultivated cotton mapped marker information. Polymorphisms were revealed by 51 AFLP primer combinations and 38 RFLP–STS and 115 SSR cotton mapped markers. The utility of transferring RFLP–STS and SSR cotton mapped markers to other Gossypium species shows the usefulness of a comparative approach as a source of markers and for aligning the genetic map of G. sturtianum with the cultivated species in the future. This also indicates that the overall structure of the G. sturtianum linkage groups is similar to that of the A and D subgenomes of cotton at the gross structural level. Applications of the map for the Australia wild C-genome species and cotton breeding are discussed.
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Ahmed, Haris, Mian Faisal Nazir, Zhoe Pan, Wenfang Gong, Muhammad Shahid Iqbal, Shoupu He, and Xiongming Du. "Genotyping by Sequencing Revealed QTL Hotspots for Trichome-Based Plant Defense in Gossypium hirsutum." Genes 11, no. 4 (March 28, 2020): 368. http://dx.doi.org/10.3390/genes11040368.
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Cotton possesses certain physical features, including leaf and stem trichomes that help plants deter damage caused by insect pests, and to some extent, from abiotic factors as well. Among those features, trichomes (pubescence) hold a special place as a first line of defense and a managemental tool against sucking insect pests of cotton. Different insect pests of cotton (whiteflies, aphids, jassids, and boll weevil) severely damage the yield and quality of the crop. Likewise, whiteflies, aphids, jassids, and other insect pests are considered as potential carriers for cotton leaf curl viruses and other diseases. Genotyping by sequencing (GBS) study was conducted to understand and explore the genomic regions governing hairy (Pubescence) leaves and stem phenotypes. A total of 224 individuals developed from an intraspecific cross (densely haired cotton (Liaoyang duomao mian) × hairless cotton (Zong 128)) and characterized phenotypically for leaf and stem pubescence in different environments. Here we identify and report significant QTLs (quantitative trait loci) associated with leaf and stem pubescence, and the response of plant under pest (aphid) infestation. Further, we identified putative genes colocalized on chromosome A06 governing mechanism for trichome development and host–pest interaction. Our study provides a comprehensive insight into genetic architecture that can be employed to improve molecular marker-assisted breeding programs aimed at developing biotic (insect pests) resilient cotton cultivars.
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Zheng, Juyun, Zeliang Zhang, Yajun Liang, Zhaolong Gong, Nala Zhang, Allah Ditta, Zhiwei Sang, Junduo Wang, and Xueyuan Li. "Whole Transcriptome Sequencing Reveals Drought Resistance-Related Genes in Upland Cotton." Genes 13, no. 7 (June 27, 2022): 1159. http://dx.doi.org/10.3390/genes13071159.
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China, particularly the cotton-growing province of Xinjiang, is experiencing acute agricultural water shortages, stifling the expansion of the cotton sector. Discovering drought resistance genes in cotton and generating high-quality, drought-resistant cotton varieties through molecular breeding procedures are therefore critical to the cotton industry’s success. The drought-resistant cotton variety Xinluzhong No. 82 and the drought-sensitive cotton variety Kexin No. 1 were utilised in this study to uncover a batch of drought-resistant candidate genes using whole transcriptome sequencing. The following are the key research findings: A competing endogenous RNA network (ceRNA) was built using complete transcriptional sequencing to screen the core genes in the core pathway, and two drought-related candidate genes were discovered. It was found that γ-aminobutyric acid aminotransferase (GhGABA-T, Gohir.A11G156000) was upregulated at 0 h vs. 12 h and downregulated at 12 h vs. 24 h. L-Aspartate oxidase (GhAO, Gohir.A07G220600) was downregulated at 0 h vs. 12 h and upregulated at 12 h vs. 24 h. GABA-T is analogous to a pyridoxal phosphate-dependent transferase superfamily protein (POP2) in Arabidopsis thaliana and influences plant drought resistance by controlling γ-aminobutyric acid (GABA) concentration. The analogue of GhAO in A. thaliana is involved in the early steps of nicotinamide adenine dinucleotide (NAD) production as well as in plant antioxidant responses. This study revealed that gene expression regulatory networks can be used for rapid screening of reliable drought resistance genes and then utilised to validate gene function.
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Smith, W. E. "Therese Cotton." Biospectroscopy 5, no. 1 (1999): 1–2. http://dx.doi.org/10.1002/(sici)1520-6343(1999)5:1<1::aid-bspy1>3.0.co;2-6.
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Grover, Corrinne E., Mi-Jeong Yoo, Meng Lin, Matthew D. Murphy, David B. Harker, Robert L. Byers, Alexander E. Lipka, et al. "Genetic Analysis of the Transition from Wild to Domesticated Cotton (Gossypium hirsutum L.)." G3: Genes|Genomes|Genetics 10, no. 2 (December 16, 2019): 731–54. http://dx.doi.org/10.1534/g3.119.400909.
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The evolution and domestication of cotton is of great interest from both economic and evolutionary standpoints. Although many genetic and genomic resources have been generated for cotton, the genetic underpinnings of the transition from wild to domesticated cotton remain poorly known. Here we generated an intraspecific QTL mapping population specifically targeting domesticated cotton phenotypes. We used 466 F2 individuals derived from an intraspecific cross between the wild Gossypium hirsutum var. yucatanense (TX2094) and the elite cultivar G. hirsutum cv. Acala Maxxa, in two environments, to identify 120 QTL associated with phenotypic changes under domestication. While the number of QTL recovered in each subpopulation was similar, only 22 QTL were considered coincident (i.e., shared) between the two locations, eight of which shared peak markers. Although approximately half of QTL were located in the A-subgenome, many key fiber QTL were detected in the D-subgenome, which was derived from a species with unspinnable fiber. We found that many QTL are environment-specific, with few shared between the two environments, indicating that QTL associated with G. hirsutum domestication are genomically clustered but environmentally labile. Possible candidate genes were recovered and are discussed in the context of the phenotype. We conclude that the evolutionary forces that shape intraspecific divergence and domestication in cotton are complex, and that phenotypic transformations likely involved multiple interacting and environmentally responsive factors.
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Li, Shengmei, Shiwei Geng, Bo Pang, Jieyin Zhao, Yajie Huang, Cun Rui, Jinxin Cui, Yang Jiao, Ru Zhang, and Wenwei Gao. "Revealing Genetic Differences in Fiber Elongation between the Offspring of Sea Island Cotton and Upland Cotton Backcross Populations Based on Transcriptome and Weighted Gene Coexpression Networks." Genes 13, no. 6 (May 26, 2022): 954. http://dx.doi.org/10.3390/genes13060954.
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Fiber length is an important indicator of cotton fiber quality, and the time and rate of cotton fiber cell elongation are key factors in determining the fiber length of mature cotton. To gain insight into the differences in fiber elongation mechanisms in the offspring of backcross populations of Sea Island cotton Xinhai 16 and land cotton Line 9, we selected two groups with significant differences in fiber length (long-fiber group L and short-fiber group S) at different fiber development stages 0, 5, 10 and 15 days post-anthesis (DPA) for transcriptome comparison. A total of 171.74 Gb of clean data was obtained by RNA-seq, and eight genes were randomly selected for qPCR validation. Data analysis identified 6055 differentially expressed genes (DEGs) between two groups of fibers, L and S, in four developmental periods, and gene ontology (GO) term analysis revealed that these DEGs were associated mainly with microtubule driving, reactive oxygen species, plant cell wall biosynthesis, and glycosyl compound hydrolase activity. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that plant hormone signaling, mitogen-activated protein kinase (MAPK) signaling, and starch and sucrose metabolism pathways were associated with fiber elongation. Subsequently, a sustained upregulation expression pattern, profile 19, was identified and analyzed using short time-series expression miner (STEM). An analysis of the weighted gene coexpression network module uncovered 21 genes closely related to fiber development, mainly involved in functions such as cell wall relaxation, microtubule formation, and cytoskeletal structure of the cell wall. This study helps to enhance the understanding of the Sea Island–Upland backcross population and identifies key genes for cotton fiber development, and these findings will provide a basis for future research on the molecular mechanisms of fiber length formation in cotton populations.
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Sajid, M., M. A. B. Saddique, M. H. N. Tahir, A. Matloob, Z. Ali, F. Ahmad, Q. Shakil, Z. U. Nisa, and M. Kifayat. "Physiological and molecular response of cotton (Gossypium hirsutum L.) to heat stress at the seedling stage." SABRAO Journal of Breeding and Genetics 54, no. 1 (March 31, 2022): 44–52. http://dx.doi.org/10.54910/sabrao2022.54.1.5.
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The ideal temperature range for the optimal growth and development of cotton is 25 °C–32 °C and high temperature adversely affects the metabolic activities of plant cells. This study was aimed to screen heat-tolerant cotton genotypes based on physiological and molecular parameters. Experiments were carried out during 2019–2020 at the MNS-University of Agriculture, Multan, Pakistan. The research comprised two parts. In the first experiment, 30 cotton genotypes were sown in a completely randomized design with three replications under laboratory conditions for the determination of cell membrane thermostability. Principal component analysis was performed, and four genotypes, i.e., two heat-tolerant (‘CRIS-5A’ and ‘VH-338’) and two heat-sensitive (‘FH-242’ and ‘VH-281’) genotypes, were selected. In the second experiment, the screened cotton genotypes were sown in pots in a factorial complete randomized design with three replications and two treatments (normal and heat treatment). Heat stress was applied at the seedling stage, and eight leaf samples (one from each experimental unit) were collected. Two genes were used for molecular analysis and were amplified in all eight cDNA samples. Molecular analysis indicated the presence of HSP70 and HSP26 genes in the cotton genotypes, and the expression of these genes was measured by using ImageJ software. The gene expression level of HSP70 was very high (16.41%) in ‘VH-281’, which is a heat-sensitive genotype under heat stress. The sensitive genotype ‘FH-242’ exhibited the highest gene expression level of HSP26 (20.32%) under normal conditions. A similar sequence of HSP70 gene of Agave sisalana was amplified for the first time in cotton. It is a good indicator for screening heat tolerant cotton genotypes at the molecular level.
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Lu, Chao, Yunxiao Wei, Zhigang Meng, Yongming Liu, Abid Muhammad Ali, Qinfei Liu, Mubashir Abbas, et al. "Overexpression of LT, an Oncoprotein Derived from the Polyomavirus SV40, Promotes Somatic Embryogenesis in Cotton." Genes 13, no. 5 (May 11, 2022): 853. http://dx.doi.org/10.3390/genes13050853.
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Although genetic transformation has opened up a new era for cotton molecular breeding, it still suffers from the limitation problem of long transformation periods, which slows down the generation of new cotton germplasms. In this study, LT gene (SV40 large T antigen), which promotes the transformation efficiency of animal cells, was codon-optimized. Its overexpression vector was transformed into cotton. It was observed that EC (embryogenic callus) formation period was 33% shorter and transformation efficiency was slightly higher in the LT T0 generation than that of control. RNA-seq data of NEC (non-embryonic callus) and EC from LT and control revealed that more DEGs (differential expression genes) in NEC were identified than that of EC, indicating LT mainly functioned in NEC. Further KEGG, GO, and transcription factor analyses showed that DEGs were significantly enriched in brassinosteroid biosynthesis pathways and that bHLH, MYB, and AP2/ERF were the top three gene families, which are involved in EC formation. In addition, the key genes related to the auxin pathway were differentially expressed only in LT overexpression NEC, which caused early response, biosynthesis, and transportation of the hormone, resulting in EC earlier formation. In summary, the results demonstrated that LT can promote somatic embryogenesis in cotton, which provides a new strategy for improving cotton transformation and shortening EC formation time.
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Qanmber, Ghulam, Faiza Ali, Lili Lu, Huijuan Mo, Shuya Ma, Zhi Wang, and Zuoren Yang. "Identification of Histone H3 (HH3) Genes in Gossypium hirsutum Revealed Diverse Expression During Ovule Development and Stress Responses." Genes 10, no. 5 (May 9, 2019): 355. http://dx.doi.org/10.3390/genes10050355.
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Histone acts as the core for nucleosomes and is a key protein component of chromatin. Among different histone variants, histone H3 (HH3) variants have been reported to play vital roles in plant development. However, biological information and evolutionary relationships of HH3 genes in cotton remain to be elucidated. The current study identified 34 HH3 genes in Gossypium hirsutum. Phylogenetic analysis classified HH3 genes of 19 plant species into eight distinct clades. Sequence logos analysis among Arabidopsis, rice, and G. hirsutum amino acid residues showed higher conservation in amino acids. Using collinearity analysis, we identified 81 orthologous/paralogous gene pairs among the four genomes (A, D, At, and Dt) of cotton. Further, orthologous/paralogous and the Ka/Ks ratio demonstrated that cotton HH3 genes experienced strong purifying selection pressure with restricted functional divergence resulting from segmental and whole genome duplication. Expression pattern analysis indicated that GhHH3 genes were preferentially expressed in cotton ovule tissues. Additionally, GhHH3 gene expression can be regulated by abiotic stresses (cold, heat, sodium chloride (NaCl), and polyethylene glycol (PEG)) and phytohormonal (brassinolide (BL), gibberellic acid (GA), indole-3-acetic acid (IAA), salicylic acid (SA), and methyl jasmonate (MeJA)) treatments, suggesting that GhHH3 genes might play roles in abiotic and hormone stress resistance. Taken together, this work provides important information to decipher complete molecular and physiological functions of HH3 genes in cotton.
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Guo, Huihui, Haixia Guo, Li Zhang, Yijie Fan, Jianfei Wu, Zhengmin Tang, Yao Zhang, Yupeng Fan, and Fanchang Zeng. "Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Genotype-Recalcitrant Somatic Embryogenesis Transdifferentiation in Cotton." Genes 11, no. 5 (May 7, 2020): 519. http://dx.doi.org/10.3390/genes11050519.
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As a notable illustration of totipotency and plant regeneration, somatic embryogenesis (SE) is the developmental reprogramming of somatic cells toward the embryogenesis pathway, the key step for genetic engineering. Investigations examining the totipotency process are of great fundamental and practical importance in crop biotechnology. However, high-frequency regeneration of cotton via SE has been limited due to genotype-dependent response. The molecular basis deciphering SE genotype recalcitrance remains largely unexplored in cotton. In the current study, to comprehensively investigate the dynamic transcriptional profiling and gene regulatory patterns involved in SE process, a genome-wide RNA sequencing analysis was performed in two cotton genotypes with distinct embryogenic abilities, the highly embryogenic genotype Yuzao 1 (YZ) and the recalcitrant genotype Lumian 1 (LM). Three typical developmental staged cultures of early SE—hypocotyls (HY), nonembryogenic calli (NEC) and primary embryogenic calli (PEC)—were selected to establish the transcriptional profiles. Our data revealed that a total of 62,562 transcripts were present amongst different developmental stages in the two genotypes. Of these, 18,394 and 26,514 differentially expressed genes (DEGs) were identified during callus dedifferentiation (NEC-VS-HY) and embryogenic transdifferentiation (PEC-VS-NEC), respectively in the recalcitrant genotype, 21,842 and 22,343 DEGs in the highly embryogenic genotype. Furthermore, DEGs were clustered into six expression patterns during cotton SE process in the two genotypes. Moreover, functional enrichment analysis revealed that DEGs were significantly enriched in fatty acid, tryptophan and pyruvate metabolism in the highly embryogenic genotype and in DNA conformation change otherwise in the recalcitrant genotype. In addition, critical SE-associated expressed transcription factors, as well as alternative splicing events, were notably and preferentially activated during embryogenic transdifferentiation in the highly embryogenic genotype compared with the recalcitrant genotype. Taken together, by systematically comparing two genotypes with distinct embryogenic abilities, the findings in our study revealed a comprehensive overview of the dynamic gene regulatory patterns and uncharacterized complex regulatory pathways during cotton SE genotype-dependent response. Our work provides insights into the molecular basis and important gene resources for understanding the underlying genotype recalcitrance during SE process and plant regeneration, thereby holding great promise for accelerating the application of biotechnology to cotton for improving its breeding efficiency.
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Zhang, Chengwei, Linlin Guo, Xiulan Wang, Hui Zhang, Haiyan Shi, Wenliang Xu, and Xuebao Li. "Molecular Characterization of Four ADF Genes Differentially Expressed in Cotton." Journal of Genetics and Genomics 34, no. 4 (April 2007): 347–54. http://dx.doi.org/10.1016/s1673-8527(07)60037-x.
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Ren, Guangming, Huijuan Mo, and Ruqiang Xu. "Arginine Decarboxylase Gene ADC2 Regulates Fiber Elongation in Cotton." Genes 13, no. 5 (April 28, 2022): 784. http://dx.doi.org/10.3390/genes13050784.
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Cotton is an important agro-industrial crop providing raw material for the textile industry. Fiber length is the key factor that directly affects fiber quality. ADC, arginine decarboxylase, is the key rate-limiting enzyme in the polyamine synthesis pathway; whereas, there is no experimental evidence that ADC is involved in fiber development in cotton yet. Our transcriptome analysis of the fiber initiation material of Gossypium arboreum L. showed that the expression profile of GaADC2 was induced significantly. Here, GhADC2, the allele of GaADC2 in tetraploid upland cotton Gossypium hirsutum L., exhibited up-regulated expression pattern during fiber elongation in cotton. Levels of polyamine are correlated with fiber elongation; especially, the amount of putrescine regulated by ADC was increased. Scanning electron microscopy showed that the fiber length was increased with exogenous addition of an ADC substrate or product putrescine; whereas, the fiber density was decreased with exogenous addition of an ADC specific inhibitor. Next, genome-wide transcriptome profiling of fiber elongation with exogenous putrescine addition was performed to determine the molecular basis in Gossypium hirsutum. A total of 3163 differentially expressed genes were detected, which mainly participated in phenylpropanoid biosynthesis, fatty acid elongation, and sesquiterpenoid and triterpenoid biosynthesis pathways. Genes encoding transcription factors MYB109, WRKY1, and TCP14 were enriched. Therefore, these results suggested the ADC2 and putrescine involvement in the development and fiber elongation of G. hirsutum, and provides a basis for cotton fiber development research in future.
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Wang, Yi, Yuehua Yu, Quanjia Chen, Guanghong Bai, Wenwei Gao, Yanying Qu, and Zhiyong Ni. "Heterologous Expression of GbTCP4, a Class II TCP Transcription Factor, Regulates Trichome Formation and Root Hair Development in Arabidopsis." Genes 10, no. 9 (September 19, 2019): 726. http://dx.doi.org/10.3390/genes10090726.
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Two class I family teosinte branched1/cycloidea/proliferating cell factor1 (TCP) proteins from allotetraploid cotton are involved in cotton fiber cell differentiation and elongation and root hair development. However, the biological function of most class II TCP proteins is unclear. This study sought to reveal the characteristics and functions of the sea-island cotton class II TCP gene GbTCP4 by biochemical, genetic, and molecular biology methods. GbTCP4 protein localizes to nuclei, binding two types of TCP-binding cis-acting elements, including the one in its promoter. Expression pattern analysis revealed that GbTCP4 is widely expressed in tissues, with the highest level in flowers. GbTCP4 is expressed at different fiber development stages and has high transcription in fibers beginning at 5 days post anthesis (DPA). GbTCP4 overexpression increases primary root hair length and density and leaf and stem trichomes in transgenic Arabidopsis relative to wild-type plants (WT). GbTCP4 binds directly to the CAPRICE (CPC) promoter, increasing CPC transcript levels in roots and reducing them in leaves. Compared with WT plants, lignin content in the stems of transgenic Arabidopsis overexpressing GbTCP4 increased, and AtCAD5 gene transcript levels increased. These results suggest that GbTCP4 regulates trichome formation and root hair development in Arabidopsis and may be a candidate gene for regulating cotton fiber elongation.
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Buyyarapu, Ramesh, Ramesh V. Kantety, John Z. Yu, Sukumar Saha, and Govind C. Sharma. "Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species." International Journal of Plant Genomics 2011 (January 17, 2011): 1–9. http://dx.doi.org/10.1155/2011/894598.
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New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps.
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Wang, Weina, Youlu Yuan, Can Yang, Shuaipeng Geng, Quan Sun, Lu Long, Chaowei Cai, et al. "Characterization, Expression, and Functional Analysis of a Novel NAC Gene Associated with Resistance to Verticillium Wilt and Abiotic Stress in Cotton." G3 Genes|Genomes|Genetics 6, no. 12 (December 1, 2016): 3951–61. http://dx.doi.org/10.1534/g3.116.034512.
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Abstract Elucidating the mechanism of resistance to biotic and abiotic stress is of great importance in cotton. In this study, a gene containing the NAC domain, designated GbNAC1, was identified from Gossypium barbadense L. Homologous sequence alignment indicated that GbNAC1 belongs to the TERN subgroup. GbNAC1 protein localized to the cell nucleus. GbNAC1 was expressed in roots, stems, and leaves, and was especially highly expressed in vascular bundles. Functional analysis showed that cotton resistance to Verticillium wilt was reduced when the GbNAC1 gene was silenced using the virus-induced gene silencing (VIGS) method. GbNAC1-overexpressing Arabidopsis showed enhanced resistance to Verticillium dahliae compared to wild-type. Thus, GbNAC1 is involved in the positive regulation of resistance to Verticillium wilt. In addition, analysis of GbNAC1-overexpressing Arabidopsis under different stress treatments indicated that it is involved in plant growth, development, and response to various abiotic stresses (ABA, mannitol, and NaCl). This suggests that GbNAC1 plays an important role in resistance to biotic and abiotic stresses in cotton. This study provides a foundation for further study of the function of NAC genes in cotton and other plants.
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Chee, Peng W., Junkang Rong, Dawn Williams-Coplin, Stefan R. Schulze, and Andrew H. Paterson. "EST derived PCR-based markers for functional gene homologues in cotton." Genome 47, no. 3 (June 1, 2004): 449–62. http://dx.doi.org/10.1139/g04-002.
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We investigated the utility of the Gossypium arboreum EST sequences in the GenBank database for developing PCR-based markers targeting known-function genes in cultivated tetraploid cottons, G. hirsutum and G. barbadense. Four hundred sixty-five randomly selected ESTs from this library were subjected to BLASTn search against all GenBank databases, of which putative function was assigned to 93 ESTs based on high nucleotide homology to previously studied genes. PCR primers were synthesized for 89 of the known-function ESTs. A total of 57 primer pairs amplified G. arboreum genomic DNA, but only 39 amplified in G. hirsutum and G. barbadense, suggesting that sequence divergence may be a factor causing non-amplification for some sites. DNA sequence analysis showed that most primer pairs were targeting the expected homologous loci. While the amplified products that were of larger size than the corresponding EST sequences contain introns, the primer pairs with a smaller amplicon than predicted from the flanking EST sequences did not amplify the expected orthologous gene sequences. Among the 39 primer pairs that amplified tetraploid cotton DNA, 3 detected amplicon size polymorphisms and 10 detected polymorphisms after digestion with one of six restriction enzymes. Ten of the polymorphic loci were subsequently mapped to an anchor RFLP map. Digestion of PCR-amplified sequences offers one means by which cotton genes can be mapped to their chromosomal locations more quickly and economically than by RFLP analysis.Key words: Gossypium arboreum, cotton, expressed sequence tag, PCR, known-function genes.
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Kim, Hee Jin, and Barbara A. Triplett. "Cotton fiber germin-like protein. I. Molecular cloning and gene expression." Planta 219, no. 1 (May 1, 2004): 190. http://dx.doi.org/10.1007/s00425-004-1258-x.
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Multani, D. S., and B. R. Lyon. "Genetic fingerprinting of Australian cotton cultivars with RAPD markers." Genome 38, no. 5 (October 1, 1995): 1005–8. http://dx.doi.org/10.1139/g95-132.
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RAPD (random amplified polymorphic DNA) markers generated by 30 random decamer primers were used to fingerprint 12 released cultivars and a breeding line of Gossypium hirsutum and 1 cultivar of G. barbadense presently under cultivation in Australia. Among a total of 453 developed markers, 69 (15.2%) were only present (unique) in the G. barbadense cultivar Pima S-7. Of the remaining markers, 128 (33.3%) were fixed in all 13 G. hirsutum cultivars. In pairwise comparisons of the degree of band sharing, nine closely-related cultivars showed 92.1–98.9% genetic similarity. Cluster analysis of genetic distance estimates between each of the cultivars revealed phylogenetic relationships in broad agreement with the known lineage of the cultivars. Ten of the G. hirsutum cultivars can be characterized individually based upon cultivar-specific RAPD markers, thus making it possible to differentiate closely related cultivars by molecular markers.Key words: RAPD, DNA fingerprinting, Gossypium hirsutum, Gossypium barbadense, cotton cultivars.
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Gallagher, Joseph P., Corrinne E. Grover, Guanjing Hu, Josef J. Jareczek, and Jonathan F. Wendel. "Conservation and Divergence in Duplicated Fiber Coexpression Networks Accompanying Domestication of the Polyploid Gossypium hirsutum L." G3: Genes|Genomes|Genetics 10, no. 8 (June 25, 2020): 2879–92. http://dx.doi.org/10.1534/g3.120.401362.
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Gossypium hirsutum L. (Upland cotton) has an evolutionary history involving inter-genomic hybridization, polyploidization, and subsequent domestication. We analyzed the developmental dynamics of the cotton fiber transcriptome accompanying domestication using gene coexpression networks for both joint and homoeologous networks. Remarkably, most genes exhibited expression for at least one homoeolog, confirming previous reports of widespread gene usage in cotton fibers. Most coexpression modules comprising the joint network are preserved in each subgenomic network and are enriched for similar biological processes, showing a general preservation of network modular structure for the two co-resident genomes in the polyploid. Interestingly, only one fifth of homoeologs co-occur in the same module when separated, despite similar modular structures between the joint and homoeologous networks. These results suggest that the genome-wide divergence between homoeologous genes is sufficient to separate their co-expression profiles at the intermodular level, despite conservation of intramodular relationships within each subgenome. Most modules exhibit D-homoeolog expression bias, although specific modules do exhibit A-homoeolog bias. Comparisons between wild and domesticated coexpression networks revealed a much tighter and denser network structure in domesticated fiber, as evidenced by its fewer modules, 13-fold increase in the number of development-related module member genes, and the poor preservation of the wild network topology. These results demonstrate the amazing complexity that underlies the domestication of cotton fiber.
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Kottapalli, Pratibha, Mauricio Ulloa, Kameswara Rao Kottapalli, Paxton Payton, and John Burke. "SNP Marker Discovery in Pima Cotton (Gossypium barbadense L.) Leaf Transcriptomes." Genomics Insights 9 (January 2016): GEI.S40377. http://dx.doi.org/10.4137/gei.s40377.
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The objective of this study was to explore the known narrow genetic diversity and discover single-nucleotide polymorphic (SNP) markers for marker-assisted breeding within Pima cotton ( Gossypium barbadense L.) leaf transcriptomes. cDNA from 25-day plants of three diverse cotton genotypes [Pima S6 (PS6), Pima S7 (PS7), and Pima 3-79 (P3-79)] was sequenced on Illumina sequencing platform. A total of 28.9 million reads (average read length of 138 bp) were generated by sequencing cDNA libraries of these three genotypes. The de novo assembly of reads generated transcriptome sets of 26,369 contigs for PS6, 25,870 contigs for PS7, and 24,796 contigs for P3-79. A Pima leaf reference transcriptome was generated consisting of 42,695 contigs. More than 10,000 single-nucleotide polymorphisms (SNPs) were identified between the genotypes, with 100% SNP frequency and a minimum of eight sequencing reads. The most prevalent SNP substitutions were C–-T and A–-G in these cotton genotypes. The putative SNPs identified can be utilized for characterizing genetic diversity, genotyping, and eventually in Pima cotton breeding through marker-assisted selection.
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Anwar, Muhammad, Muhammad Zafar Iqbal, Aamir Ali Abro, Shabana Memon, Liaquat Ali Bhutto, Shamim Ara Memon, and Yan Peng. "Inter-Specific Hybridization in Cotton (Gossypium hirsutum) for Crop Improvement." Agronomy 12, no. 12 (December 13, 2022): 3158. http://dx.doi.org/10.3390/agronomy12123158.
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Interspecific hybridization has contributed significantly to land diversity, species evolution, and crops’ domestication, including upland cotton, the cultivated form of Gossypium hirsutum. Being the world’s most important fiber crop species, Gossypium hirsutum belongs to the allotetraploid Gossypium consisting of six additional tetraploid species. The lint fiber evolved once in diploid parent A-genome species in the Gossypium’s history and passed on during hybridization of the A-genome with the D-genome and was maintained in subsequent evolution. The domestication history of G. hirsutum involved the collection and use of lint fibers by indigenous people for the purpose of making strings and other textile products; hence, spinnable lint fibers were likely to have evolved under domestication. Crossing with G. barbadense has resulted in the development of multiple genetic lines in contemporary upland cotton. However, in later-generation hybrids between G. hirsutum and other polyploid species, reproductive barriers such as reduced fertility, segregation distortion, and hybrid breakdown are frequently observed, complicating the task of introgressing new, stably inherited allelic variation from inter-specific hybridization. Recent efforts in molecular genetics research have provided insights into the location and effects of QTLs from wild species that are associated with traits important to cotton production. These and future research efforts will undoubtedly provide the tools that can be utilized by plant breeders to access novel genes from wild and domesticated allotetraploid Gossypium for upland cotton improvement.
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Jiang, Xiao, Liqiang Fan, Pengtao Li, Xianyan Zou, Zhen Zhang, Senmiao Fan, Juwu Gong, Youlu Yuan, and Haihong Shang. "Co-expression network and comparative transcriptome analysis for fiber initiation and elongation reveal genetic differences in two lines from upland cotton CCRI70 RIL population." PeerJ 9 (July 21, 2021): e11812. http://dx.doi.org/10.7717/peerj.11812.
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Upland cotton is the most widely planted for natural fiber around the world, and either lint percentage (LP) or fiber length (FL) is the crucial component tremendously affecting cotton yield and fiber quality, respectively. In this study, two lines MBZ70-053 and MBZ70-236 derived from G. hirsutum CCRI70 recombinant inbred line (RIL) population presenting different phenotypes in LP and FL traits were chosen to conduct RNA sequencing on ovule and fiber samples, aiming at exploring the differences of molecular and genetic mechanisms during cotton fiber initiation and elongation stages. As a result, 249/128, 369/206, 4296/1198 and 3547/2129 up-/down- regulated differentially expressed genes (DGEs) in L2 were obtained at −3, 0, 5 and 10 days post-anthesis (DPA), respectively. Seven gene expression profiles were discriminated using Short Time-series Expression Miner (STEM) analysis; seven modules and hub genes were identified using weighted gene co-expression network analysis. The DEGs were mainly enriched into energetic metabolism and accumulating as well as auxin signaling pathway in initiation and elongation stages, respectively. Meanwhile, 29 hub genes were identified as 14-3-3ω, TBL35, GhACS, PME3, GAMMA-TIP, PUM-7, etc., where the DEGs and hub genes revealed the genetic and molecular mechanisms and differences during cotton fiber development.
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Shaban, Muhammad, Yuhuan Miao, Abid Ullah, Anam Qadir Khan, Hakim Menghwar, Aamir Hamid Khan, Muhammad Mahmood Ahmed, Muhammad Adnan Tabassum, and Longfu Zhu. "Physiological and molecular mechanism of defense in cotton against Verticillium dahliae." Plant Physiology and Biochemistry 125 (April 2018): 193–204. http://dx.doi.org/10.1016/j.plaphy.2018.02.011.
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Harder, Olivia E., Kathryn M. Emmer, Amanda E. Sparks, Eric J. Miller, Anne J. Gemensky-Metzler, Dondrae J. Coble, Stefan Niewiesk, and Krista M. D. La Perle. "Cause and Treatment of Exophthalmos in Aged Cotton Rats (Sigmodon hispidus)." Comparative Medicine 70, no. 3 (June 1, 2020): 291–99. http://dx.doi.org/10.30802/aalas-cm-19-000107.
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Aged cotton rats (Sigmodon hispidus) from an established breeding colony displayed signs of spontaneous exophthalmos. Of a total of 118 colony animals that were older than 6 mo of age, 37 (31%) displayed signs of exophthalmos. These rats were clinically healthy and had no other signs of disease. Ophthalmic exams, molecular and microbiologic testing, and histopa- thology were performed to determine the cause of the exophthalmos and to provide appropriate treatment. Environmental monitoring records were also reviewed for vivarium rooms in which the cotton rats were housed. Histopathology findings supported that the exophthalmos in these cotton rats was secondary to retro-orbital thrombosis associated with cardiomyopathy. The exophthalmic eyes were treated by either removal of the affected eye (enucleation) or surgical closure of the eyelids (temporary tarsorraphy). Enucleation of the exophthalmic eye was the best intervention for these aged cotton rats. These findings demonstrate the potential for a high incidence of ocular problems occurring secondary to cardiomyopathy in aged cotton rats. Enucleation as a therapeutic intervention for exophthalmic eyes in aged cotton rats prolongs the morbidity-free time span during which these aged animals can be used experimentally.
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Penna, Julio C. Viglioni, Laval M. Verhalen, M. B. Kirkham, and Ronald W. McNew. "Screening cotton genotypes for seedling drought tolerance." Genetics and Molecular Biology 21, no. 4 (December 1998): 545–49. http://dx.doi.org/10.1590/s1415-47571998000400023.
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The objectives of this study were to adapt a screening method previously used to assess seedling drought tolerance in cereals for use in cotton (Gossypium hirsutum L.) and to identify tolerant accessions among a wide range of genotypes. Ninety genotypes were screened in seven growth chamber experiments. Fifteen-day-old seedlings were subjected to four 4-day drought cycles, and plant survival was evaluated after each cycle. Three cycles are probably the minimum required in cotton work. Significant differences (at the 0.05 level or lower) among entries were obtained in four of the seven experiments. A "confirmation test" with entries previously evaluated as "tolerant" (high survival) and "susceptible" (low survival) was run. A number of entries duplicated their earlier performance, but others did not, which indicates the need to reevaluate selections. Germplasms considered tolerant included: `IAC-13-1', `IAC-RM4-SM5', `Minas Sertaneja', `Acala 1517E-1' and `4521'. In general, the technique is simple, though time-consuming, with practical value for screening a large number of genotypes. Results from the screening tests generally agreed with field information. The screening procedure is suitable to select tolerant accessions from among a large number of entries in germplasm collections as a preliminary step in breeding for drought tolerance. This research also demonstrated the need to characterize the internal lack of uniformity in growth chambers to allow for adequate designs of experiments.
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Bertini, Cândida H. C. de Magalhães, Ivan Schuster, Tocio Sediyama, Everaldo Gonçalves de Barros, and Maurílio Alves Moreira. "Characterization and genetic diversity analysis of cotton cultivars using microsatellites." Genetics and Molecular Biology 29, no. 2 (2006): 321–29. http://dx.doi.org/10.1590/s1415-47572006000200021.
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Yasir, Muhammad, Shoupu He, Gaofei Sun, Xiaoli Geng, Zhaoe Pan, Wenfang Gong, Yinhua Jia, and Xiongming Du. "A Genome-Wide Association Study Revealed Key SNPs/Genes Associated With Salinity Stress Tolerance In Upland Cotton." Genes 10, no. 10 (October 21, 2019): 829. http://dx.doi.org/10.3390/genes10100829.
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Millions of hectares of land are too saline to produce economically valuable crop yields. Salt tolerance in cotton is an imperative approach for improvement in response to ever-increasing soil salinization. Little is known about the genetic basis of salt tolerance in cotton at the seedling stage. To address this issue, a genome-wide association study (GWAS) was conducted on a core collection of a genetically diverse population of upland cotton (Gossypium hirsutum L.) comprising of 419 accessions, representing various geographic origins, including China, USA, Pakistan, the former Soviet Union, Chad, Australia, Brazil, Mexico, Sudan, and Uganda. Phenotypic evaluation of 7 traits under control (0 mM) and treatment (150 mM) NaCl conditions depicted the presence of broad natural variation in the studied population. The association study was carried out with the efficient mixed-model association eXpedited software package. A total of 17,264 single-nucleotide polymorphisms (SNPs) associated with different salinity stress tolerance related traits were found. Twenty-three candidate SNPs related to salinity stress-related traits were selected. Final key SNPs were selected based on the r2 value with nearby SNPs in a linkage disequilibrium (LD) block. Twenty putative candidate genes surrounding SNPs, A10_95330133 and D10_61258588, associated with leaf relative water content, RWC_150, and leaf fresh weight, FW_150, were identified, respectively. We further validated the expression patterns of twelve candidate genes with qRT-PCR, which revealed different expression levels in salt-tolerant and salt-sensitive genotypes. The results of our GWAS provide useful knowledge about the genetic control of salt tolerance at the seedling stage, which could assist in elucidating the genetic and molecular mechanisms of salinity stress tolerance in cotton plants.
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Udall, Joshua A., Evan Long, Chris Hanson, Daojun Yuan, Thiruvarangan Ramaraj, Justin L. Conover, Lei Gong, et al. "De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri." G3: Genes|Genomes|Genetics 9, no. 10 (August 28, 2019): 3079–85. http://dx.doi.org/10.1534/g3.119.400392.
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Cotton is an agriculturally important crop. Because of its importance, a genome sequence of a diploid cotton species (Gossypium raimondii, D-genome) was first assembled using Sanger sequencing data in 2012. Improvements to DNA sequencing technology have improved accuracy and correctness of assembled genome sequences. Here we report a new de novo genome assembly of G. raimondii and its close relative G. turneri. The two genomes were assembled to a chromosome level using PacBio long-read technology, HiC, and Bionano optical mapping. This report corrects some minor assembly errors found in the Sanger assembly of G. raimondii. We also compare the genome sequences of these two species for gene composition, repetitive element composition, and collinearity. Most of the identified structural rearrangements between these two species are due to intra-chromosomal inversions. More inversions were found in the G. turneri genome sequence than the G. raimondii genome sequence. These findings and updates to the D-genome sequence will improve accuracy and translation of genomics to cotton breeding and genetics.
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Chen, D., Y. Ding, W. Guo, and T. Zhang. "Molecular mapping of genic male-sterile genesms15,ms5andms6in tetraploid cotton." Plant Breeding 128, no. 2 (April 2009): 193–98. http://dx.doi.org/10.1111/j.1439-0523.2008.01562.x.
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Zhao, Xinping, Rod A. Wing, and Andrew H. Paterson. "Cloning and characterization of the majority of repetitive DNA in cotton (Gossypium L.)." Genome 38, no. 6 (December 1, 1995): 1177–88. http://dx.doi.org/10.1139/g95-156.
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Repetitive DNA elements representing 60–70% of the total repetitive DNA in tetraploid cotton (Gossypium barbadense L.) and comprising 30–36% of the tetraploid cotton genome were isolated from a genomic library of DNA digested with a mixture of four blunt-end cutting restriction enzymes. A total of 313 clones putatively containing nuclear repetitive sequences were classified into 103 families, based on cross hybridization and Southern blot analysis. The 103 families were characterized in terms of genome organization, methylation pattern, abundance, and DNA variation. As in many other eukaryotic genomes, interspersed repetitive elements are the most abundant class of repetitive DNA in the cotton genome. Paucity of tandem repeat families with high copy numbers (>104) may be a unique feature of the cotton genome as compared with other higher plant genomes. Interspersed repeats tend to be methylated, while tandem repeats seem to be largely unmethylated in the cotton genome. Minimal variation in repertoire and overall copy number of repetitive DNA elements among different tetraploid cotton species is consistent with the hypothesis of a relatively recent origin of tetraploid cottons.Key words: genome analysis, genome evolution, tandemly repetitive DNA sequences, interspersed repetitive DNA sequences, polyploid.
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Tao, Xiaoyuan, Menglin Li, Ting Zhao, Shouli Feng, Hailin Zhang, Luyao Wang, Jin Han, et al. "Neofunctionalization of a polyploidization-activated cotton long intergenic non-coding RNA DAN1 during drought stress regulation." Plant Physiology 186, no. 4 (April 19, 2021): 2152–68. http://dx.doi.org/10.1093/plphys/kiab179.
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Abstract The genomic shock of whole-genome duplication (WGD) and hybridization introduces great variation into transcriptomes, for both coding and noncoding genes. An altered transcriptome provides a molecular basis for improving adaptation during the evolution of new species. The allotetraploid cotton, together with the putative diploid ancestor species compose a fine model for study the rapid gene neofunctionalization over the genome shock. Here we report on Drought-Associated Non-coding gene 1 (DAN1), a long intergenic noncoding RNA (lincRNA) that arose from the cotton progenitor A-diploid genome after hybridization and WGD events during cotton evolution. DAN1 in allotetraploid upland cotton (Gossypium hirsutum) is a drought-responsive lincRNA predominantly expressed in the nucleoplasm. Chromatin isolation by RNA purification profiling and electrophoretic mobility shift assay analysis demonstrated that GhDAN1 RNA can bind with DNA fragments containing AAAG motifs, similar to DNA binding with one zinc finger transcription factor binding sequences. The suppression of GhDAN1 mainly regulates genes with AAAG motifs in auxin-response pathways, which are associated with drought stress regulation. As a result, GhDAN1-silenced plants exhibit improved tolerance to drought stress. This phenotype resembles the drought-tolerant phenotype of the A-diploid cotton ancestor species, which has an undetectable expression of DAN1. The role of DAN1 in cotton evolution and drought tolerance regulation suggests that the genomic shock of interspecific hybridization and WGD stimulated neofunctionalization of non-coding genes during the natural evolutionary process.
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Phillips, Sonia M., Ian A. Dubery, and Henriette van Heerden. "Molecular characterisation of two homoeologous elicitor-responsive lipin genes in cotton." Molecular Genetics and Genomics 288, no. 10 (July 30, 2013): 519–33. http://dx.doi.org/10.1007/s00438-013-0770-8.
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Jiao, Yang, Yilei Long, Kaixiang Xu, Fuxiang Zhao, Jieyin Zhao, Shengmei Li, Shiwei Geng, et al. "Weighted Gene Co-Expression Network Analysis Reveals Hub Genes for Fuzz Development in Gossypium hirsutum." Genes 14, no. 1 (January 13, 2023): 208. http://dx.doi.org/10.3390/genes14010208.
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Fuzzless Gossypium hirsutum mutants are ideal materials for investigating cotton fiber initiation and development. In this study, we used the fuzzless G. hirsutum mutant Xinluzao 50 FLM as the research material and combined it with other fuzzless materials for verification by RNA sequencing to explore the gene expression patterns and differences between genes in upland cotton during the fuzz period. A gene ontology (GO) enrichment analysis showed that differentially expressed genes (DEGs) were mainly enriched in the metabolic process, microtubule binding, and other pathways. A weighted gene co-expression network analysis (WGCNA) showed that two modules of Xinluzao 50 and Xinluzao 50 FLM and four modules of CSS386 and Sicala V-2 were highly correlated with fuzz. We selected the hub gene with the highest KME value among the six modules and constructed an interaction network. In addition, we selected some genes with high KME values from the six modules that were highly associated with fuzz in the four materials and found 19 common differential genes produced by the four materials. These 19 genes are likely involved in the formation of fuzz in upland cotton. Several hub genes belong to the arabinogalactan protein and GDSL lipase, which play important roles in fiber development. According to the differences in expression level, 4 genes were selected from the 19 genes and tested for their expression level in some fuzzless materials. The modules, hub genes, and common genes identified in this study can provide new insights into the formation of fiber and fuzz, and provide a reference for molecular design breeding for the genetic improvement of cotton fiber.
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Li, Ximei, Daojun Yuan, Hantao Wang, Xuemei Chen, Bin Wang, Zhongxu Lin, and Xianlong Zhang. "Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP." Genome 55, no. 6 (June 2012): 459–70. http://dx.doi.org/10.1139/g2012-032.
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Simple sequence repeat (SSR) markers are widely used in plant genetics and breeding. However, there are many SSR markers that do not reveal polymorphism in cotton. Traditional SSR genotyping methods only provide information on product sizes. This leaves many marker polymorphism undetected, thus, lowering the utility of SSRs. In the present study, monomorphic SSRs between two mapping parents, ‘Emian22’ and 3-79, were subjected to single-strand conformation polymorphism (SSCP) analysis to reveal polymorphism. Of the 4194 monomorphic SSR primer pairs, 158 pairs (3.77%) showed polymorphism and revealed 174 polymorphic loci. Sequence analysis showed that the differences in PCR products between the mapping parents were solely due to base transition or transversion, which was in agreement with SSCP principles. SSCP also revealed SSRs with motifs of AT/TA and GAA/CTT were more polymorphic in dinucleotides and trinucleotides, respectively. Genetic mapping integrated 160 loci into our interspecific BC1 linkage map, 5 of which associated with QTLs related to cotton fiber quality. The technique discussed in the present study enables us to detect polymorphism of monomorphic SSRs, and increase the utilization efficiency of the existing SSR primers.
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Ma, Lin, Meng-Yue Li, Chun-Yan Chang, Fang-Fang Chen, Yang Hu, and Xiang-Dong Liu. "The host range of Aphis gossypii is dependent on aphid genetic background and feeding experience." PeerJ 7 (September 27, 2019): e7774. http://dx.doi.org/10.7717/peerj.7774.
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Background A polyphagous insect herbivore has a wide range of host plants. However, it has been found that many polyphagous herbivores commonly exhibit a strong preference for a subset of species in their broad host range, and various host biotypes exist in herbivore populations. Nutrition and secondary metabolites in plants affect herbivore preference and performance, but it is still not clear which factors determine the host range and host preference of polyphagous herbivores. Method Cotton-melon aphids, Aphis gossypii Glover, collected from cotton and cucumber crops, were used in this study. The genetic backgrounds of these aphids were detected using microsatellite PCR and six genotypes were evaluated. Performance of these six aphid genotypes on excised leaves and plants of cotton and cucumber seedlings were examined through a reciprocal transplant experiment. In order to detect whether the feeding experience on artificial diet would alter aphid host range, the six genotypes of aphids fed on artificial diet for seven days were transferred onto cotton and cucumber leaves, and then their population growth on these two host plants was surveyed. Results Aphids from cotton and cucumber plants could not colonize the excised leaves and intact plants of cucumber and cotton seedlings, respectively. All six genotypes of aphids collected from cotton and cucumber plants could survive and produce offspring on artificial diet, which lacked plant secondary metabolites. The feeding experience on the artificial diet did not alter the ability of all six genotypes to use their native host plants. However, after feeding on this artificial diet for seven days, two aphid genotypes from cotton and one from cucumber acquired the ability to use both of the excised leaves from cucumber and cotton plants. The two aphid genotypes from cotton conditioned by the feeding experience on artificial diet and then reared on excised cucumber leaves for >12 generations still maintained the ability to use intact cotton plants but did not establish a population on cucumber plants. However, one cucumber genotype conditioned by artificial diet and then reared on excised cotton leaves could use both the intact cotton and cucumber plants, showing that the expansion of host range was mediated by feeding experience. Conclusion Feeding experience on artificial diet induced the expansion of host range of the cucurbit-specialized A. gossypii, and this expansion was genotype-specific. We speculated that feeding on a constant set of host plants in the life cycle of aphids may contribute to the formation of host specialization.
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Song, Xian-Liang, and Tian-Zhen Zhang. "Identification of quantitative trait loci controlling seed physical and nutrient traits in cotton." Seed Science Research 17, no. 4 (December 2007): 243–51. http://dx.doi.org/10.1017/s0960258507834957.
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AbstractCotton (Gossypium spp.) is an important source of edible oil and protein meals. Complex genetics and strong environmental effects hinder progress in seed quality trait breeding in this species. The use of molecular markers can improve an understanding of the genetic factors conditioning seed quality traits, and is expected to assist in selection of superior genotypes. This study was conducted to identify quantitative trail loci (QTL) associated with seed physical and nutrient traits in cotton. To achieve this objective, a population of 140 BC1S1 lines developed from a cross between ‘TM-1’ and ‘Hai7124’ was evaluated in 2003 and 2004. A linkage map consisting of 918 markers from this population was used to identify QTL using QTLNetwork-2.0 software. Eleven single QTL were identified for kernel percentage, kernel oil percentage, kernel protein percentage and seven amino acids (Asp, Ser, Gly, Ile, Leu, Phe and Arg). Phenotypic variation explained by each individual QTL ranged from 10.89 to 46.28%. Two epistatic QTL for Cys and Leu were detected, explaining 9.55 and 4.43% of the phenotypic variation. These QTL detected for seed quality traits in cotton are expected to be useful for further breeding programmes targeting development of cotton with improved nutrient quality.
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Chen, Li-yu, Li-feng Zhang, Zhan-yuan Lu, Feng Xian, Jian-zhong Zhang, Yu-chen Cheng, Xiang-qian Zhang, and Yan Liu. "Effects of Trace Irrigation at Different Depths on Transcriptome Expression Pattern in Cotton (G. hirsutum L.) Leaves." BioMed Research International 2020 (July 27, 2020): 1–12. http://dx.doi.org/10.1155/2020/7248513.
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Drought is a limiting factor for cotton productivity and quality. Irrigation could increase cotton yield. This study is aimed at formulating a proper irrigation depth for cotton at China’ Inner Mongolia and at investigating the molecular mechanism underlying the difference induced by irrigation. Transcriptomic analysis was carried out to reveal the global transcriptome profiles on the leaves of cotton seedlings (G. hirsutum L. cv. “Zhongmian 92”) with trace irrigation tapes at 30 cm (D30) and 50 cm (D50) underground. The differentially expressed genes (DEGs) were identified and clustered by functional enrichment analysis. The results showed that no significant differences were found in the lint percentage. The yields of unpinned and lint cotton were increased by the D30 regime but decreased by the D50 regime. Transcriptomic analysis showed that 4,549 nonoverlapped DEGs were identified by comparative analysis. Transcription factors, including bZIP, WARK, Myb, and NAC, were altered between D50 and D30. The D50 regime induced more DEGs compared with the D30 regime, which was associated with plant tolerance to abiotic stresses and drought. In conclusion, trace irrigation at 30 cm underground was suitable for cotton irrigation at China’s Inner Mongolia, while the D50 irrigation regime influenced the cotton yield via drought stress in cotton plants.
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Salih, Haron, Wenfang Gong, Mtawa Mkulama, and Xiongming Du. "Genome-wide characterization, identification, and expression analysis of the WD40 protein family in cotton." Genome 61, no. 7 (July 2018): 539–47. http://dx.doi.org/10.1139/gen-2017-0237.
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WD40 repeat proteins are largely distributed across the plant kingdom and play an important role in diverse biological activities. In this work, we performed genome-wide identification, characterization, and expression level analysis of WD40 genes in cotton. A total of 579, 318, and 313 WD40 genes were found in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. Based on phylogenetic tree analyses, WD40 genes were divided into 11 groups with high similarities in exon/intron features and protein domains within the group. Expression analysis of WD40 genes showed differential expression at different stages of cotton fiber development (0 and 8 DPA) and cotton stem. A number of miRNAs were identified to target WD40 genes that are significantly involved in cotton fiber development during the initiation and elongation stages. These include miR156, miR160, miR162, miR164, miR166, miR167, miR169, miR171, miR172, miR393, miR396, miR398, miR2950, and miR7505. The findings provide a stronger indication of WD40 gene function and their involvement in the regulation of cotton fiber development during the initiation and elongation stages.
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Ma, Xuexia, Yezhang Ding, Baoliang Zhou, Wangzhen Guo, Yanhui Lv, Xiefei Zhu, and Tianzhen Zhang. "QTL mapping in A-genome diploid Asiatic cotton and their congruence analysis with AD-genome tetraploid cotton in genus Gossypium." Journal of Genetics and Genomics 35, no. 12 (December 2008): 751–62. http://dx.doi.org/10.1016/s1673-8527(08)60231-3.
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Khashimova, Z. S. "Antiproliferative activity of cotton glycoproteins." Biopolymers and Cell 17, no. 3 (May 20, 2001): 212–15. http://dx.doi.org/10.7124/bc.0005ac.
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Wang, Fei, James McD Stewart, and Jinfa Zhang. "Molecular markers linked to the Rf2 fertility restorer gene in cotton." Genome 50, no. 9 (September 2007): 818–24. http://dx.doi.org/10.1139/g07-061.
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Cytoplasmic male sterility (CMS) is a maternally inherited trait in which plants do not produce viable pollen. Fertility in plants with CMS can be recovered by nuclear restorer genes. Most restorer genes cloned so far are members of the pentatricopeptide repeat (PPR) protein family. The objective of our study was to use the CMS-D8 and restoration (Rf2) system of cotton ( Gossypium hirsutum L.) to develop more DNA markers for the Rf2 gene. In a backcross population with 112 plants, segregation of male fertility was 1 fertile : 1 sterile. Three new RAPD markers were identified for Rf2, one of which was converted to a CAPS marker. In addition, 2 AFLP markers and 1 SSR marker were identified to be linked to the fertility restorer gene (Rf2). PPR motif primers were designed based on the conserved PPR motifs and used in combination with AFLP primers to test the mapping population, and 1 PPR-AFLP marker was identified. A linkage map with 9 flanking markers including 1 from a previous study was constructed.
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Yin, Xiaomin, Rulin Zhan, Yingdui He, Shun Song, Lixia Wang, Yu Ge, and Di Chen. "Morphological description of a novel synthetic allotetraploid(A1A1G3G3) of Gossypium herbaceum L.and G.nelsonii Fryx. suitable for disease-resistant breeding applications." PLOS ONE 15, no. 12 (December 3, 2020): e0242620. http://dx.doi.org/10.1371/journal.pone.0242620.
Full textAbstract:
Wild species of Gossypium ssp. are an important source of traits for improving commercial cotton cultivars. Previous reports show that Gossypium herbaceum L. and Gossypium nelsonii Fryx. have better disease resistance characteristics than commercial cotton varieties. However, chromosome ploidy and biological isolation make it difficult to hybridize diploid species with the tetraploid Gossypium hirsutum L. We developed a new allotetraploid cotton genotype (A1A1G3G3) using a process of distant hybridization within wild cotton species to create new germplasms. First of all, G. herbaceum and G. nelsonii were used for interspecific hybridization to obtain F1 generation. Afterwards, apical meristems of the F1 diploid cotton plants were treated with colchicine to induce chromosome doubling. The new interspecific F1 hybrid and S1 cotton plants originated from chromosome duplication, were tested via morphological and molecular markers and confirmed their tetraploidy through flowrometric and cytological identification. The S1 tetraploid cotton plants was crossed with a TM-1 line and fertile hybrid offspring were obtained. These S2 offsprings were tested for resistance to Verticillium wilt and demonstrated adequate tolerance to this fungi. The results shows that the new S1 cotton line could be used as parental material for hybridization with G. hirsutum to produce pathogen-resistant cotton hybrids. This new S1 allotetraploid genotype will contributes to the enrichment of Gossypium germplasm resources and is expected to be valuable in polyploidy evolutionary studies.
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Jana, T. K., N. K. Singh, K. R. Koundal, and T. R. Sharma. "Genetic differentiation of charcoal rot pathogen, Macrophomina phaseolina, into specific groups using URP-PCR." Canadian Journal of Microbiology 51, no. 2 (February 1, 2005): 159–64. http://dx.doi.org/10.1139/w04-122.
Full textAbstract:
Forty isolates of Macrophomina phaseolina, a pathogen causing charcoal dry root rot of soybean, cotton, and chickpea, were genetically characterized with universal rice primers (URP; primers derived from DNA repeat sequences in the rice genome) using polymerase chain reaction (URP-PCR). Out of 12 URPs used in this study, 5 primers were effective in producing polymorphic fingerprint patterns from the DNA of M. phaseolina isolates. Three primers (URP-2F, URP-6R, and URP-30F) were quite informative and produced high levels of polymorphism among the isolates of M. phaseolina. Analysis of the entire fingerprint profiles using unweighted pair-group method with arithmetic averages (UPGMA) clearly differentiated M. phaseolina isolates obtained from soybean, cotton, and chickpea hosts into specific groups. In this study, we found for the first time transferability and use of PCR primers derived from plant genomes to generate host-specific fingerprint profiles of M. phaseolina, a broad host range plant pathogenic fungus. These results demonstrate that URPs are sensitive and technically simple to use for assaying genetic variability in M. phaseolina populations.Key words: Macrophomina phaseolina, molecular variability, soybean, cotton, chickpea.
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Ma, Chenhui, Zibo Zhao, Na Wang, Muhammad Tehseen Azhar, and Xiongming Du. "Genome-Wide Identification and Comparative Analysis of Myosin Gene Family in Four Major Cotton Species." Genes 11, no. 7 (June 30, 2020): 731. http://dx.doi.org/10.3390/genes11070731.
Full textAbstract:
Myosin protein as a molecular motor, binding with Actin, plays a significant role in various physiological activities such as cell division, movement, migration, and morphology; however, there are only a few studies on plant Myosin gene family, particularly in cotton. A total of 114 Myosin genes were found in Gossypium hirsutum, Gossypium barbadense, Gossypium raimondii, and Gossypium arboreum. All Myosins could be grouped into six groups, and for each group of these genes, similar gene structures are found. Study of evolution suggested that the whole genome duplications event occurring about 13–20 MYA (millions of years ago) is the key explanation for Myosins expanse in cotton. Cis-element and qPCR analysis revealed that plant hormones such as abscisic acid, methyl jasmonate, and salicylic acid can control the expression of Myosins. This research provides useful information on the function of Myosin genes in regulating plant growth, production, and fiber elongation for further studies.
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Bolton, James J., Khairy M. Soliman, Thea A. Wilkins, and Johnie N. Jenkins. "Aberrant Expression of Critical Genes during Secondary Cell Wall Biogenesis in a Cotton Mutant, Ligon Lintless-1 (Li-1)." Comparative and Functional Genomics 2009 (2009): 1–8. http://dx.doi.org/10.1155/2009/659301.
Full textAbstract:
Over ninety percent of the value of cotton comes from its fiber; however, the genetic mechanisms governing fiber development are poorly understood. Due to their biochemical and morphological diversity in fiber cells cotton fiber mutants have been useful in examining fiber development; therefore, using the Ligon Lintless (Li-1) mutant, a monogenic dominant cotton mutant with very short fibers, we employed the high throughput approaches of microarray technology and real time PCR to gain insights into what genes were critical during the secondary cell wall synthesis stage. Comparative transcriptome analysis of the normal TM-1 genotype and the near isogenicLi-1 revealed that over 100 transcripts were differentially expressed at least 2-fold during secondary wall biogenesis, although the genetic profile of the expansion phase showed no significant differences in the isolines. Of particular note, we identified three candidate gene families-expansin, sucrose synthase, and tubulin—whose expression inLi-1 deviates from normal expression patterns of its parent, TM-1. These genes may contribute to retarded growth of fibers inLi-1 since they are fiber-expressed structural and metabolic genes. This work provides more details into the mechanisms of fiber development, and suggests theLigene is active during the later stages of fiber development.
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Lu, Quanwei, Yuzhen Shi, Xianghui Xiao, Pengtao Li, Juwu Gong, Wankui Gong, Aiying Liu, et al. "Transcriptome Analysis Suggests That Chromosome Introgression Fragments from Sea Island Cotton (Gossypium barbadense) Increase Fiber Strength in Upland Cotton (Gossypium hirsutum)." G3: Genes|Genomes|Genetics 7, no. 10 (September 5, 2017): 3469–79. http://dx.doi.org/10.1534/g3.117.300108.
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