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Journal articles on the topic 'Plant genome mapping'

Author: Grafiati

Published: 4 June 2021

Last updated: 31 July 2024

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1

Chaney, Lindsay, Aaron R. Sharp, Carrie R. Evans, and Joshua A. Udall. "Genome Mapping in Plant Comparative Genomics." Trends in Plant Science 21, no. 9 (September 2016): 770–80. http://dx.doi.org/10.1016/j.tplants.2016.05.004.

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2

Doležel, Jaroslav, Marie Kubaláková, Jan Bartoš, and Jiří Macas. "Flow cytogenetics and plant genome mapping." Chromosome Research 12, no. 1 (2004): 77–91. http://dx.doi.org/10.1023/b:chro.0000009293.15189.e5.

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3

Lapitanz, Nora L. V. "Organization and evolution of higher plant nuclear genomes." Genome 35, no. 2 (April 1, 1992): 171–81. http://dx.doi.org/10.1139/g92-028.

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The knowledge gained from studies on eukaryotic genome organization is important for understanding how genomes function and evolve, and it provides the basis for designing strategies for manipulating genomes. Hence, numerous studies on this subject have been conducted over the years, utilizing a variety of methods. In the recent decade, several techniques have been developed that allow the study of eukaryotic genome organization at different levels. Molecular techniques including molecular cloning, DNA sequencing, restriction fragment length polymorphism mapping, in situ hybridization, and pul

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4

Ovesná, J., K. Poláková, and L. Leišová. "DNA analyses and their applications in plant breeding." Czech Journal of Genetics and Plant Breeding 38, No. 1 (July 30, 2012): 29–40. http://dx.doi.org/10.17221/6108-cjgpb.

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In recent years, molecular markers have been developed based on the more detailed knowledge of genome structure. Considerable emphasis has been laid on the use of molecular markers in practical breeding and genotype identification. This review attempts to give an account of different molecular markers currently available for genome mapping and for tagging different traits &ndash; restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs) and microsatellites. Other markers, expressed sequence tags (ESTs) and

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5

Staňková, Helena, Alex R. Hastie, Saki Chan, Jan Vrána, Zuzana Tulpová, Marie Kubaláková, Paul Visendi, et al. "BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes." Plant Biotechnology Journal 14, no. 7 (January 23, 2016): 1523–31. http://dx.doi.org/10.1111/pbi.12513.

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6

Hou, Yuze, Li Wang, and Weihua Pan. "Comparison of Hi-C-Based Scaffolding Tools on Plant Genomes." Genes 14, no. 12 (November 27, 2023): 2147. http://dx.doi.org/10.3390/genes14122147.

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De novo genome assembly holds paramount significance in the field of genomics. Scaffolding, as a pivotal component within the genome assembly process, is instrumental in determining the orientation and arrangement of contigs, ultimately facilitating the generation of a chromosome-level assembly. Scaffolding is contingent on supplementary linkage information, including paired-end reads, bionano, physical mapping, genetic mapping, and Hi-C (an abbreviation for High-throughput Chromosome Conformation Capture). In recent years, Hi-C has emerged as the predominant source of linkage information in s

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7

Vlk, D., and J. Řepková. "Application of next-generation sequencing in plant breeding." Czech Journal of Genetics and Plant Breeding 53, No. 3 (September 13, 2017): 89–96. http://dx.doi.org/10.17221/192/2016-cjgpb.

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In the past decade, next-generation sequencing (NGS) platforms have changed the impact of sequencing on our knowledge of crop genomes and gene regulation. These techniques are today acquiring a great potential in metagenomic and agrigenomic research while showing prospects for their utilization in plant breeding. We can now obtain new and beneficial information about gene regulation on the cellular as well as whole-plant level through RNA-sequencing and subsequent expression analyses of genes participating in plant defence reactions to pathogens and in abiotic stress tolerance. NGS has facilit

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8

Wu, Xing, Wei Jiang, Christopher Fragoso, Jing Huang, Geyu Zhou, Hongyu Zhao, and Stephen Dellaporta. "Prioritized candidate causal haplotype blocks in plant genome-wide association studies." PLOS Genetics 18, no. 10 (October 17, 2022): e1010437. http://dx.doi.org/10.1371/journal.pgen.1010437.

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Genome wide association studies (GWAS) can play an essential role in understanding genetic basis of complex traits in plants and animals. Conventional SNP-based linear mixed models (LMM) that marginally test single nucleotide polymorphisms (SNPs) have successfully identified many loci with major and minor effects in many GWAS. In plant, the relatively small population size in GWAS and the high genetic diversity found in many plant species can impede mapping efforts on complex traits. Here we present a novel haplotype-based trait fine-mapping framework, HapFM, to supplement current GWAS methods

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9

Lindeberg, Magdalen, Christopher R. Myers, Alan Collmer, and David J. Schneider. "Roadmap to New Virulence Determinants in Pseudomonas syringae: Insights from Comparative Genomics and Genome Organization." Molecular Plant-Microbe Interactions® 21, no. 6 (June 2008): 685–700. http://dx.doi.org/10.1094/mpmi-21-6-0685.

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Systematic comparison of the current repertoire of virulence-associated genes for three Pseudomonas syringae strains with complete genome sequences, P. syringae pv. tomato DC3000, P. syringae pv. phaseolicola 1448A, and P. syringae pv. syringae B728a, is prompted by recent advances in virulence factor identification in P. syringae and other bacteria. Among these are genes linked to epiphytic fitness, plant- and insect-active toxins, secretion pathways, and virulence regulators, all reflected in the recently updated DC3000 genome annotation. Distribution of virulence genes in relation to P. syr

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10

Foolad, Majid R. "Genome Mapping and Molecular Breeding of Tomato." International Journal of Plant Genomics 2007 (August 22, 2007): 1–52. http://dx.doi.org/10.1155/2007/64358.

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The cultivated tomato, Lycopersicon esculentum, is the second most consumed vegetable worldwide and a well-studied crop species in terms of genetics, genomics, and breeding. It is one of the earliest crop plants for which a genetic linkage map was constructed, and currently there are several molecular maps based on crosses between the cultivated and various wild species of tomato. The high-density molecular map, developed based on an L. esculentum×L. pennellii cross, includes more than 2200 markers with an average marker distance of less than 1 cM and an average of 750 kbp per cM. Different ty

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11

Yazaki, Junshi, Brian D. Gregory, and Joseph R. Ecker. "Mapping the genome landscape using tiling array technology." Current Opinion in Plant Biology 10, no. 5 (October 2007): 534–42. http://dx.doi.org/10.1016/j.pbi.2007.07.006.

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12

Dutta, Anik, Bruce A. McDonald, and Daniel Croll. "Combined reference-free and multi-reference based GWAS uncover cryptic variation underlying rapid adaptation in a fungal plant pathogen." PLOS Pathogens 19, no. 11 (November 16, 2023): e1011801. http://dx.doi.org/10.1371/journal.ppat.1011801.

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Microbial pathogens often harbor substantial functional diversity driven by structural genetic variation. Rapid adaptation from such standing variation threatens global food security and human health. Genome-wide association studies (GWAS) provide a powerful approach to identify genetic variants underlying recent pathogen adaptation. However, the reliance on single reference genomes and single nucleotide polymorphisms (SNPs) obscures the true extent of adaptive genetic variation. Here, we show quantitatively how a combination of multiple reference genomes and reference-free approaches captures

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13

Jiang, Jiming, and Bikram S. Gill. "Nonisotopic in situ hybridization and plant genome mapping: the first 10 years." Genome 37, no. 5 (October 1, 1994): 717–25. http://dx.doi.org/10.1139/g94-102.

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Nonisotopic in situ hybridization (ISH) was introduced in plants in 1985. Since then the technique has been widely used in various areas of plant genome mapping. ISH has become a routine method for physical mapping of repetitive DNA sequences and multicopy gene families. ISH patterns on somatic metaphase chromosomes using tandemly repeated sequences provide excellent physical markers for chromosome identification. Detection of low or single copy sequences were also reported. Genomic in situ hybridization (GISH) was successfully used to analyze the chromosome structure and evolution of allopoly

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14

Schmidt, Renate. "Physical mapping of the Arabidopsis thaliana genome." Plant Physiology and Biochemistry 36, no. 1-2 (January 1998): 1–8. http://dx.doi.org/10.1016/s0981-9428(98)80086-7.

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15

Tuberosa, Roberto. "Principles and practices of plant penomics. Volume 1. Genome mapping." Annals of Botany 102, no. 5 (November 2008): 879–80. http://dx.doi.org/10.1093/aob/mcn169.

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16

Krishna, Thumadath P. A., Maharajan Theivanayagam, Gurusunathan V. Roch, Veeramuthu Duraipandiyan, and Savarimuthu Ignacimuthu. "Microsatellite Marker: Importance and Implications of Cross-genome Analysis for Finger Millet (Eleusine coracana (L.) Gaertn)." Current Biotechnology 9, no. 3 (December 21, 2020): 160–70. http://dx.doi.org/10.2174/2211550109999200908090745.

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Finger millet is a superior staple food for human beings. Microsatellite or Simple Sequence Repeat (SSR) marker is a powerful tool for genetic mapping, diversity analysis and plant breeding. In finger millet, microsatellites show a higher level of polymorphism than other molecular marker systems. The identification and development of microsatellite markers are extremely expensive and time-consuming. Only less than 50% of SSR markers have been developed from microsatellite sequences for finger millet. Therefore, it is important to transfer SSR markers developed for related species/genus to fing

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17

Wixon, Jo. "UK CropNet." Yeast 1, no. 3 (January 1, 2000): 244–54. http://dx.doi.org/10.1155/2000/124868.

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This review explores the UK CropNet site. The project is aimed at aiding the comparative mapping of cereal and other crop genomes. The site provides software tools for use by those working on genome mapping, and access to an array of databases that will be of interest to all members of the plant genomics research community, using several ACeDB interfaces. All screen views from the website are reproduced with the kind permission of Dr Sean May, Director, Nottingham Arabidopsis Stock Centre (NASC).

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18

Wixon, Jo. "UK CropNet." Yeast 1, no. 3 (2000): 244–54. http://dx.doi.org/10.1002/1097-0061(20000930)17:3<244::aid-yea38>3.0.co;2-p.

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This review explores the UK CropNet site. The project is aimed at aiding the comparative mapping of cereal and other crop genomes. The site provides software tools for use by those working on genome mapping, and access to an array of databases that will be of interest to all members of the plant genomics research community, using several ACeDB interfaces. All screen views from the website are reproduced with the kind permission of Dr Sean May, Director, NottinghamArabidopsisStock Centre (NASC).

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19

Zhang, Hong-Bin, Yaning Li, Baohua Wang, and Peng W. Chee. "Recent Advances in Cotton Genomics." International Journal of Plant Genomics 2008 (January 23, 2008): 1–20. http://dx.doi.org/10.1155/2008/742304.

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Genome research promises to promote continued and enhanced plant genetic improvement. As a world's leading crop and a model system for studies of many biological processes, genomics research of cottons has advanced rapidly in the past few years. This article presents a comprehensive review on the recent advances of cotton genomics research. The reviewed areas include DNA markers, genetic maps, mapped genes and QTLs, ESTs, microarrays, gene expression profiling, BAC and BIBAC libraries, physical mapping, genome sequencing, and applications of genomic tools in cotton breeding. Analysis of the cu

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20

Soundararajan, Prabhakaran, So Youn Won, and Jung Sun Kim. "Insight on Rosaceae Family with Genome Sequencing and Functional Genomics Perspective." BioMed Research International 2019 (February 19, 2019): 1–12. http://dx.doi.org/10.1155/2019/7519687.

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Rosaceae is one of the important families possessing a variety of diversified plant species. It includes many economically valuable crops that provide nutritional and health benefits for the human. Whole genome sequences of valuable crop plants were released in recent years. Understanding of genomics helps to decipher the plant physiology and developmental process. With the information of cultivating species and its wild relative genomes, genome sequence-based molecular markers and mapping loci for economically important traits can be used to accelerate the genome assisted breeding. Identifica

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21

Lin, Jing-Zhong, and Kermit Ritland. "Construction of a genetic linkage map in the wild plant Mimulus using RAPD and isozyme markers." Genome 39, no. 1 (February 1, 1996): 63–70. http://dx.doi.org/10.1139/g96-009.

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As a first step to mapping quantitative trait loci for mating system differences, a genetic linkage map was generated from an interspecific backcross between Mimulus guttatus and Mimulus platycalyx. The linkage map consists of 99 RAPD and two isozyme markers. Eighty-one of these markers were mapped to 15 linkage groups, spanning 1437 contiguous centiMorgans, and covering 58% of the estimated genome. The genome length of Mimulus is estimated at 2474 ± 35 cM; bootstrapping indicates that only ca. 40 markers are needed to give an accurate estimate of genome length. Further statistical analyses in

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22

Mascher, Martin, Thomas Wicker, Jerry Jenkins, Christopher Plott, Thomas Lux, Chu Shin Koh, Jennifer Ens, et al. "Long-read sequence assembly: a technical evaluation in barley." Plant Cell 33, no. 6 (March 12, 2021): 1888–906. http://dx.doi.org/10.1093/plcell/koab077.

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Abstract Sequence assembly of large and repeat-rich plant genomes has been challenging, requiring substantial computational resources and often several complementary sequence assembly and genome mapping approaches. The recent development of fast and accurate long-read sequencing by circular consensus sequencing (CCS) on the PacBio platform may greatly increase the scope of plant pan-genome projects. Here, we compare current long-read sequencing platforms regarding their ability to rapidly generate contiguous sequence assemblies in pan-genome studies of barley (Hordeum vulgare). Most long-read

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23

Hanson, Anthony A., Aaron J. Lorenz, Louis S. Hesler, Siddhi J. Bhusal, Raman Bansal, Andy P. Michel, Guo‐Liang Jiang, and Robert L. Koch. "Genome‐Wide Association Mapping of Host‐Plant Resistance to Soybean Aphid." Plant Genome 11, no. 3 (November 2018): 180011. http://dx.doi.org/10.3835/plantgenome2018.02.0011.

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24

Darzentas, N., A. Bousios, V. Apostolidou, and A. S. Tsaftaris. "MASiVE: Mapping and Analysis of SireVirus Elements in plant genome sequences." Bioinformatics 26, no. 19 (August 9, 2010): 2452–54. http://dx.doi.org/10.1093/bioinformatics/btq454.

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25

Chang, Caren, and Elliot M. Meyerowitz. "Plant genome studies: Restriction fragment length polymorphism and chromosome mapping information." Current Opinion in Biotechnology 2, no. 2 (April 1991): 178–83. http://dx.doi.org/10.1016/0958-1669(91)90007-r.

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26

Chang, Caren, and Elliot M. Meyerowitz. "Plant genome studies: restriction fragment length polymorphism and chromosome mapping information." Current Opinion in Genetics & Development 1, no. 1 (June 1991): 112–18. http://dx.doi.org/10.1016/0959-437x(91)80051-m.

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27

Dey, T., and P. D. Ghosh. "Application of molecular markers in plant genome study." NBU Journal of Plant Sciences 4, no. 1 (2010): 1–9. http://dx.doi.org/10.55734/nbujps.2010.v04i01.001.

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The development of molecular techniques for genetic analysis has led to a great increase in our knowledge of plant genetics and our understanding of the structure and behaviour of plant genome. During last three decades, several powerful DNA based marker technologies have been developed for the assessment of genetic diversities and molecular marker assisted breeding technology. In plant systems, the prospects of DNA profiling and fingerprinting is becoming indispensable in the context of establishment of molecular phylogeny, assessment of somaclonal variants, characterization of plant genomics

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28

Dey, T., and P. D. Ghosh. "Application of molecular markers in plant genome study." NBU Journal of Plant Sciences 4, no. 1 (2010): 1–9. http://dx.doi.org/10.55734/nbujps.2010.v04i01.001.

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The development of molecular techniques for genetic analysis has led to a great increase in our knowledge of plant genetics and our understanding of the structure and behaviour of plant genome. During last three decades, several powerful DNA based marker technologies have been developed for the assessment of genetic diversities and molecular marker assisted breeding technology. In plant systems, the prospects of DNA profiling and fingerprinting is becoming indispensable in the context of establishment of molecular phylogeny, assessment of somaclonal variants, characterization of plant genomics

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29

Dodeweerd, Anne-Marie van, Caroline R. Hall, Elisabeth G. Bent, Samantha J. Johnson, Michael W. Bevan, and Ian Bancroft. "Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana." Genome 42, no. 5 (October 1, 1999): 887–92. http://dx.doi.org/10.1139/g99-033.

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Using contiguous genomic DNA sequences of Arabidopsis thaliana, we were able to identify a region of conserved structure in the genome of rice. The conserved, and presumptive homoeologous segments, are 194 kb and 219-300 kb in size in Arabidopsis and rice, respectively. They contain five homologous genes, distinguished in order by a single inversion. These represent the first homoeologous segments identified in the genomes of a dicot and a monocot, demonstrating that fine-scale conservation of genome structure exists and is detectable across this major divide in the angiosperms. The conserved

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30

Yu, Li, Yanshen Nie, Jinxia Jiao, Liufang Jian, and Jie Zhao. "The Sequencing-Based Mapping Method for Effectively Cloning Plant Mutated Genes." International Journal of Molecular Sciences 22, no. 12 (June 9, 2021): 6224. http://dx.doi.org/10.3390/ijms22126224.

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A forward genetic approach is a powerful tool for identifying the genes underlying the phenotypes of interest. However, the conventional map-based cloning method is lengthy, requires a large mapping population and confirmation of many candidate genes in a broad genetic region to clone the causal variant. The whole-genome sequencing method clones the variants with a certain failure probability for multiple reasons, especially for heterozygotes, and could not be used to clone the mutation of epigenetic modifications. Here, we applied the highly complementary characteristics of these two methods

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31

Kikuchi, Shinji, Raju Bheemanahalli, Krishna S. V. Jagadish, Etsushi Kumagai, Yusuke Masuya, Eiki Kuroda, Chitra Raghavan, Michael Dingkuhn, Akira Abe, and Hiroyuki Shimono. "Genome-wide association mapping for phenotypic plasticity in rice." Plant, Cell & Environment 40, no. 8 (June 2, 2017): 1565–75. http://dx.doi.org/10.1111/pce.12955.

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32

Gardiner, Susan E., Ji Mei Zhu, Heather C. M. Whitehead, and Charlotte Madie. "The New Zealand apple genome mapping project." Euphytica 77, no. 1-2 (February 1994): 77–81. http://dx.doi.org/10.1007/bf02551465.

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33

Uceda-Campos, Guillermo, Oseias R. Feitosa-Junior, Caio R. N. Santiago, Paulo M. Pierry, Paulo A. Zaini, Wesley O. de Santana, Joaquim Martins-Junior, et al. "Comparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems." Microorganisms 10, no. 5 (April 27, 2022): 914. http://dx.doi.org/10.3390/microorganisms10050914.

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Xylella fastidiosa causes diseases in many plant species. Originally confined to the Americas, infecting mainly grapevine, citrus, and coffee, X. fastidiosa has spread to several plant species in Europe causing devastating diseases. Many pathogenicity and virulence factors have been identified, which enable the various X. fastidiosa strains to successfully colonize the xylem tissue and cause disease in specific plant hosts, but the mechanisms by which this happens have not been fully elucidated. Here we present thorough comparative analyses of 94 whole-genome sequences of X. fastidiosa strains

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34

Zhang, Taifeng, Jiajun Liu, Sikandar Amanullah, Zhuo Ding, Haonan Cui, Feishi Luan, and Peng Gao. "Fine Mapping of Cla015407 Controlling Plant Height in Watermelon." Journal of the American Society for Horticultural Science 146, no. 3 (May 2021): 196–205. http://dx.doi.org/10.21273/jashs04934-20.

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The plant compact and dwarf growth habit is an important agronomic trait when breeding watermelon (Citrullus lanatus) cultivars because of their reduced vine length, high-density planting, and better land utilization; however, the genetic basis of the dwarf growth habit is not well-known. In this study, the plant population of six generations, P1, P2, F1, F2, BC1P1, and BC1P2, were studied. A genetic segregation analysis demonstrated that dwarfism is mainly controlled by a single recessive Cldw gene. Furthermore, whole-genome sequencing of two distinct watermelon cultivars, W1-1 (P1) and 812 (

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35

Benchimol-Reis, Luciana L. "Molecular Markers in Plant Breeding." Journal of Agricultural Science 15, no. 3 (February 15, 2023): 58. http://dx.doi.org/10.5539/jas.v15n3p58.

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Molecular markers are an important tool for plant breeding. Since the 1980s, in response to the technology development, molecular marker approaches have been further diversified. The establishment of new-generation sequencing and high-throughput plant phenotyping has greatly decreased the time to genotype large numbers of individuals. For breeders who are not very familiar with molecular techniques and want to catch up with the advances in the field, this review offers basic knowledge. Each molecular marker technology has specific advantages as well as limitations. Molecular marker types, dive

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36

Kumar, Ajay, Kristin Simons, Muhammad J. Iqbal, Monika de Jiménez, Filippo M. Bassi, Farhad Ghavami, Omar Al-Azzam, et al. "Physical mapping resources for large plant genomes: radiation hybrids for wheat D-genome progenitor Aegilops tauschii." BMC Genomics 13, no. 1 (2012): 597. http://dx.doi.org/10.1186/1471-2164-13-597.

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37

Sher, Muhammad Ali, Abdus Salam Khan, Zulfiqar Ali, and Sultan Habibullah Khan. "Association Mapping of Agronomic traits in Bread Wheat using a high Density 90k SNP Array." Pakistan Journal of Biochemistry and Biotechnology 2, no. 2 (December 31, 2021): 236–47. http://dx.doi.org/10.52700/pjbb.v2i2.91.

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A genome-wide association study (GWAS) was performed using a high-density infinium 90K SNP array. We identified a total markers traits associations (MTAs) (p ?0.000) for the following plant traits; days taken to 50% heading(DH), days to 50% maturity (DM), plant height (Ph) cm, flag leaf area cm2 (FLA), tillers number per plant, spike length (SL) cm and grain yield per plant (GP) g. Most of the SNPs were identified in the A and B genome as compared to the D genome. The significant associated SNPs were mainly distributed on the chromosome 2B, 3B, 5A, and 5B. Nine SNPs on chromosome 5A, 2B and 2D

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38

Ling, Maurice H. T., Roel C. Rabara, Prateek Tripathi, Paul J. Rushton, and Xijin Ge. "Extending MapMan Ontology to Tobacco for Visualization of Gene Expression." Dataset Papers in Biology 2013 (February 20, 2013): 1–7. http://dx.doi.org/10.7167/2013/706465.

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Microarrays are a large-scale expression profiling method which has been used to study the transcriptome of plants under various environmental conditions. However, manual inspection of microarray data is difficult at the genome level because of the large number of genes (normally at least 30 000) and the many different processes that occur within any given plant. MapMan software, which was initially developed to visualize microarray data for Arabidopsis, has been adapted to other plant species by mapping other species onto MapMan ontology. This paper provides a detailed procedure and the relev

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39

Yang, Fangping, Jindong Liu, Ying Guo, Zhonghu He, Awais Rasheed, Ling Wu, Shiqin Cao, Hai Nan, and Xianchun Xia. "Genome-Wide Association Mapping of Adult-Plant Resistance to Stripe Rust in Common Wheat (Triticum aestivum)." Plant Disease 104, no. 8 (August 2020): 2174–80. http://dx.doi.org/10.1094/pdis-10-19-2116-re.

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Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a globally devastating disease of common wheat (Triticum aestivum L.), resulting in substantial economic losses. To identify effective resistance genes, a genome-wide association study was conducted on 120 common wheat lines from different wheat-growing regions of China using the wheat 90K iSelect SNP array. Seventeen loci were identified, explaining 9.5 to 21.8% of the phenotypic variation. Most of these genes were detected in the A (seven) and B (seven) genomes, with only three in the D genome. Among them, 11 loci were colocated

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40

Mandal, Lincoln, Sunil Kumar Verma, Saugata Sasmal, Anju Rani Ekka, Jawahar Lal Katara, and Anil S. Kotasthane. "Multi-Parent Advanced Generation Intercross (Magic) Population for Genome Mapping in Plant." International Journal of Genetics 10, no. 2 (March 30, 2018): 343. http://dx.doi.org/10.9735/0975-2862.10.2.343-345.

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41

Thoen, Manus P. M., Nelson H. Davila Olivas, Karen J. Kloth, Silvia Coolen, Ping-Ping Huang, Mark G. M. Aarts, Johanna A. Bac-Molenaar, et al. "Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping." New Phytologist 213, no. 3 (October 4, 2016): 1346–62. http://dx.doi.org/10.1111/nph.14220.

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42

Gupta, S. K., and T. Gopalakrishna. "Advances in genome mapping in orphan grain legumes of genusVigna." Indian Journal of Genetics and Plant Breeding (The) 73, no. 1 (2013): 1. http://dx.doi.org/10.5958/j.0019-5200.73.1.001.

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43

Weir, Bruce S. "Statistical genetic issues for genome-wide association studiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”." Genome 53, no. 11 (November 2010): 869–75. http://dx.doi.org/10.1139/g10-062.

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Genotyping technology now allows the rapid and affordable generation of million-SNP profiles for humans, leading to considerable activity in association mapping. Similar activity is anticipated for many plant species, including Brassica . These plant association mapping activities will require the same care in quality control and quality assurance as for humans. The subsequent analyses may draw upon the same body of theory that is described here in the language of quantitative genetics.

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44

Kudryavtseva, Natalya, Aleksey Ermolaev, Gennady Karlov, Ilya Kirov, Masayoshi Shigyo, Shusei Sato, and Ludmila Khrustaleva. "A Dual-Color Tyr-FISH Method for Visualizing Genes/Markers on Plant Chromosomes to Create Integrated Genetic and Cytogenetic Maps." International Journal of Molecular Sciences 22, no. 11 (May 30, 2021): 5860. http://dx.doi.org/10.3390/ijms22115860.

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In situ imaging of molecular markers on a physical chromosome is an indispensable tool for refining genetic maps and validation genome assembly at the chromosomal level. Despite the tremendous progress in genome sequencing, the plant genome assembly at the chromosome level remains a challenge. Recently developed optical and Hi-C mapping are aimed at assistance in genome assembly. For high confidence in the genome assembly at chromosome level, more independent approaches are required. The present study is aimed at refining an ultrasensitive Tyr-FISH technique and developing a reliable and simpl

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Siezen, Roland J., Marjo J. C. Starrenburg, Jos Boekhorst, Bernadet Renckens, Douwe Molenaar, and Johan E. T. van Hylckama Vlieg. "Genome-Scale Genotype-Phenotype Matching of Two Lactococcus lactis Isolates from Plants Identifies Mechanisms of Adaptation to the Plant Niche." Applied and Environmental Microbiology 74, no. 2 (November 26, 2007): 424–36. http://dx.doi.org/10.1128/aem.01850-07.

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ABSTRACT Lactococcus lactis is a primary constituent of many starter cultures used for the manufacturing of fermented dairy products, but the species also occurs in various nondairy niches such as (fermented) plant material. Three genome sequences of L. lactis dairy strains (IL-1403, SK11, and MG1363) are publicly available. An extensive molecular and phenotypic diversity analysis was now performed on two L. lactis plant isolates. Diagnostic sequencing of their genomes resulted in over 2.5 Mb of sequence for each strain. A high synteny was found with the genome of L. lactis IL-1403, which was

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Zhang, Guobin, Chunxia Ge, Pingping Xu, Shukai Wang, Senan Cheng, Yanbin Han, Yancui Wang, et al. "The reference genome of Miscanthus floridulus illuminates the evolution of Saccharinae." Nature Plants 7, no. 5 (May 2021): 608–18. http://dx.doi.org/10.1038/s41477-021-00908-y.

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AbstractMiscanthus, a member of the Saccharinae subtribe that includes sorghum and sugarcane, has been widely studied as a feedstock for cellulosic biofuel production. Here, we report the sequencing and assembly of the Miscanthus floridulus genome by the integration of PacBio sequencing and Hi-C mapping, resulting in a chromosome-scale, high-quality reference genome of the genus Miscanthus. Comparisons among Saccharinae genomes suggest that Sorghum split first from the common ancestor of Saccharum and Miscanthus, which subsequently diverged from each other, with two successive whole-genome dup

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Wischnitzki, Elisabeth, Eva Maria Sehr, Karin Hansel-Hohl, Maria Berenyi, Kornel Burg, and Silvia Fluch. "How to Isolate a Plant’s Hypomethylome in One Shot." BioMed Research International 2015 (2015): 1–12. http://dx.doi.org/10.1155/2015/570568.

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Genome assembly remains a challenge for large and/or complex plant genomes due to their abundant repetitive regions resulting in studies focusing on gene space instead of the whole genome. Thus, DNA enrichment strategies facilitate the assembly by increasing the coverage and simultaneously reducing the complexity of the whole genome. In this paper we provide an easy, fast, and cost-effective variant of MRE-seq to obtain a plant’s hypomethylome by an optimized methyl filtration protocol followed by next generation sequencing. The method is demonstrated on three plant species with knowingly larg

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Jiang, Jiming, and Bikram S. Gill. "Current status and the future of fluorescence in situ hybridization (FISH) in plant genome research." Genome 49, no. 9 (September 2006): 1057–68. http://dx.doi.org/10.1139/g06-076.

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Fluorescence in situ hybridization (FISH), which allows direct mapping of DNA sequences on chromosomes, has become the most important technique in plant molecular cytogenetics research. Repetitive DNA sequence can generate unique FISH patterns on individual chromosomes for karyotyping and phylogenetic analysis. FISH on meiotic pachytene chromosomes coupled with digital imaging systems has become an efficient method to develop physical maps in plant species. FISH on extended DNA fibers provides a high-resolution mapping approach to analyze large DNA molecules and to characterize large genomic l

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King, Graham J. "Progress in mapping agronomic genes in apple (The European Apple Genome Mapping Project)." Euphytica 77, no. 1-2 (February 1994): 65–69. http://dx.doi.org/10.1007/bf02551463.

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Bellinger, M. Renee, Roshan Paudel, Steven Starnes, Lukas Kambic, Michael B. Kantar, Thomas Wolfgruber, Kurt Lamour, et al. "Taro Genome Assembly and Linkage Map Reveal QTLs for Resistance to Taro Leaf Blight." G3: Genes|Genomes|Genetics 10, no. 8 (June 16, 2020): 2763–75. http://dx.doi.org/10.1534/g3.120.401367.

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Taro (Colocasia esculenta) is a food staple widely cultivated in the humid tropics of Asia, Africa, Pacific and the Caribbean. One of the greatest threats to taro production is Taro Leaf Blight caused by the oomycete pathogen Phytophthora colocasiae. Here we describe a de novo taro genome assembly and use it to analyze sequence data from a Taro Leaf Blight resistant mapping population. The genome was assembled from linked-read sequences (10x Genomics; ∼60x coverage) and gap-filled and scaffolded with contigs assembled from Oxford Nanopore Technology long-reads and linkage map results. The hapl

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