Academic literature on the topic 'Marker-assisted backcross breeding'

The efficiency of marker-assisted introgression in backcross populations derived from inbred lines was investigated by simulation. Background genotypes were simulated assuming that a genetic model of many genes of small effects in coupling phase explains the observed breed difference and variance in backcross populations. Markers were efficient in introgression backcross programs for simultaneously introgressing an allele and selecting for the desired genomic background. Using a marker spacing of 10–20 cM gave an advantage of one to two backcross generations selection relative to random or phenotypic selection. When the position of the gene to be introgressed is uncertain, for example because its position was estimated from a trait gene mapping experiment, a chromosome segment should be introgressed that is likely to include the allele of interest. Even for relatively precisely mapped quantitative trait loci, flanking markers or marker haplotypes should cover ∼10–20 cM around the estimated position of the gene, to ensure that the allele frequency does not decline in later backcross generations.

Submergence is a major threat in rice growing areas of South and South-East Asia. Identification of a major QTL, Sub1 and advancements in marker-assisted backcrossing strategy enabled breeders to develop submergence tolerant versions of popular rice cultivars. In the present study, a marker-assisted backcross breeding (MABB) approach was used to introgress the Sub1 locus from the tolerant FR13A variety into CO 43, one of the popular rice varieties of southern India. Evaluation of early generation segregating progenies derived from the cross of CO 43 and FR13A revealed the introgression of Sub1, leading to increased tolerance to submergence and better revival ability after it. Genotyping and phenotyping of BC₃F₃ generation resulted in elite NILs of CO 43 harbouring Sub1 the locus and possessing 94.37% and 95.78% of the recurrent parental CO 43 genome. Selected NILs performed equal as the recurrent parent CO 43 under normal conditions, but were more tolerant to submergence and revived better, afterwards. Under flooding NILs yielded about 25–30% higher than the recurrent parent CO 43.

Abiotic and biotic constraints have widespread yield reducing effects on maize and should receive high priority for maize breeding research. Molecular Breeding offers opportunities for plant breeders to develop cultivars with resilience to such diseases with precision and in less time duration. The term molecular breeding is used to describe several modern breeding strategies, including marker-assisted selection, marker-assisted backcrossing, marker-assisted recurrent selection and genomic selection. Recent advances in maize breeding research have made it possible to identify and map precisely many genes associated with DNA markers which include genes governing resistance to biotic stresses and genes responsible for tolerance to abiotic stresses. Marker assisted selection (MAS) allows monitoring the presence, absence of these genes in breeding populations whereas marker assisted backcross breeding effectively integrates major genes or quantitative trait loci (QTL) with large effect into widely grown adapted varieties. For complex traits where multiple QTLs control the expression, marker assisted recurrent selection (MARS) and genomic selection (GS) are employed to increase precision and to reduce cost of phenotyping and time duration. The biparental mapping populations used in QTL studies in MAS do not readily translate to breeding applications and the statistical methods used to identify target loci and implement MAS have been inadequate for improving polygenic traits controlled by many loci of small effect. Application of GS to breeding populations using high marker densities is emerging as a solution to both of these deficiencies. Hence, molecular breeding approaches offers ample opportunities for developing stress resilient and high-yielding maize cultivars.

Due to the fact that blast (causative agent – Pyricularia oryzae Cav.) is considered to be one of the harmful diseases of rice around the world, weeds compete with the crop for light, mineral nutrition and space, the accelerated development of resistant genotypes for these stressors is very relevant. The use of modern biotechnological approaches (molecular marking) is promising and especially in demand in breeding rice varieties of a new generation. This article presents the results on the introduction and pyramiding in the same genotype blast resistance genes Pi-1, Pi-2, Pi-33, Pi-ta, Pi-b, Pi-40 and the gene for tolerance to prolonged flooding Sub 1A, as a weed control factor, based on domestic rice varieties Flagman, Snezhinka, Novator, Boyarin, as well as large-grain lines, with a short growing season VNIIR5242, KP-25-14, KP-163 and VNIIR9678. As a result of the volumetric work using marker control of target genes in the genotypes of hybrid plants, 4 modern varietal samples and more than 400 backcross self-pollinated rice lines with introduced and pyramided blast resistance genes, as well as backcross self-pollinated lines with Pi and Sub1A genes, were obtained. These plants are adapted for cultivation in the south of Russia, have a duration of 115-117 days, a height of 87-100 cm, a mass of 1000 grains – 30 or more grams, a yield of 8.5 – 11 t/ha, which is significantly higher than that of the standard variety Flagman.

Resistance to cucumber mosaic virus (CMV) in Capsicum from two sources is being transferred into three commercial types (bell, jalapeno, and Anaheim) using a backcross breeding scheme. We have optimized our CMV seedling screening protocol, which involves multiple inoculations beginning at the cotyledon stage with a severe CMV serogroup I isolate. Both sources of resistance, C. annuum `French Perennial' and a C. frutescens accession (BG2814-6), exhibit oligogenic recessive inheritance and share some but not all resistance alleles. Selection for type in the BCF1 generation had no effect on the frequency of resistant individuals in the BCF2 generation. We have determined that it is necessary to self-pollinate every other backcross generation to screen for resistance. Occasionally disease symptoms appear in adult plants that were initially resistant to multiple inoculations at the seedling stage, and we are investigating the correlation between seedling resistance and adult plant resistance. We are also exploring the extent to which the different sources of resistance behave differently as a function of genetic background. Additionally, we are mapping quantitative trait loci (QTLs) for CMV resistance in pepper with the goal of converting RFLP and/or RAPD markers into PCR-based markers to facilitate molecular marker-assisted selection for CMV resistance.

Sunflower (Helianthus annuus L.) high oleic acid content lines differ from conventional sunflower by an increase in oleic acid (C18:1) content of more than 60%. The current sunflower cultivars under production in South Africa are standard sunflower with high levels of linoleic acid (C18:2). The aim of this study was to improve the quality of oil produced by local sunflower germplasm with respect to oleic acid through employing a marker-assisted breeding technique to facilitate and speed up the recovery of the high oleic acid allele into the background of the recurrent parent genome. Eleven sunflower breeding genotypes with high and low oleic acid traits were obtained from the Agricultural Research Council-Grain Crops Institute (ARC-GCI) in Potchefstroom. The breeding genotypes were phenotypically characterised based on their oleic and linoleic acid levels using gas chromatography. Results demonstrated that the average mean of oleic and linoleic acid contents in high oleic acid genotypes were 72% and 17% respectively, while the average mean of oleic acid and linoleic acid contents in wild type lines were 33.5 % and 54 % respectively. These results indicated a perfect negative correlation between the amount of oleic and linoleic acids possessed in high and low oleic acid genotypes (R2 = -99.16%). Sequence characterised amplified region (SCAR) markers were tested to ascertain if any of the ten available dominant FAD2-1 markers was segregating with the high oleic acid allele. Four dominant SCAR markers (FAD2-1F4/R1; FAD2-1F4/R2; FAD2-1F13/R1; FAD2-1F14/R2) were strongly associated with the high oleic acid trait (P< 0.001). With regard to the inheritance of the high oleic acid trait, 143 plants of the F2 segregating population derived from a cross between the high oleic acid parent (AP901-95-3-4-1) and low oleic acid parent (H55-9-2-1-1) were genotyped with the four SCAR markers to determine the genetic state concerning the high oleic acid gene (Ol). Results from a Chi square analysis of the observed frequencies of each dominant FAD2-1 marker locus in 143 F2 individuals indicated that the deviation from the expected ratio of 3:1 (high to low oleic acid) was not statistically significant (P< 0.95) from the observed segregation ratio. These results were consistent with the previous finding that an incomplete dominant gene governs sunflower high oleic acid. A multiplex assay of 78 Simple sequence repeat (SSR) markers was optimised and evaluated on 143 plants of the F2 population to determine suitable SSR markers that can be used in a marker-assisted background selection. Only 14 markers were suitable for marker-assisted background selection based on their high polymorphic information content, allele frequency and maximum allele numbers. In conclusion, this study demonstrated the potential of using SSR and SCAR marker systems as a breeding tool to characterise and speed up the selection process in marker-assisted backcross breeding.
Thesis (MSc (Botany))--North-West University, Potchefstroom Campus, 2013.

Thesis (MScAgric)--Stellenbosch University, 2011.
ENGLISH ABSTRACT: Research into markers for the detection of genetic diversity and cultivar identification has become an important component of the genetic improvement of crops. However, the incorporation of marker assisted selection (MAS) as a tool for the identification and characterization of breeding material has not been fully implemented in the breeding of spring triticale at Stellenbosch University’s Plant Breeding laboratory (SU-PBL). The present study served as a case study in order to achieve this. The first part of the study concerned the detection of genetic diversity in 101 newly sourced triticale cultivars, from a USDA germplasm bank, together with five local control cultivars, in order to identify possible crossing parents. Eight SSR markers, including five derived from rye and three from wheat, and five agronomic characteristics were used to assess diversity. In seedling screening the foreign cultivars showed resistance towards the stem rust isolate used, but were mostly susceptible to the leaf rust isolate. Out of the 8 SSR markers tested, 7 markers were polymorphic and revealed 140 alleles varying from 12 to 26 with an average of 17.5 alleles per locus. The observed polymorphic information content (PIC) value ranged from 0.39 to 0.88 with an average of 0.70, indicative of the good discriminatory ability of the SSR markers. The data revealed that the South African cultivars were genetically closely related to cultivars from the USA and Canada. The second part of the study focused on the introgression of a blue aleurone layer gene (Ba), carried by a wheat cultivar, ‘Cltr1202STR’, and purple pericarp genes (Pp1; Pp3) also carried by a wheat cultivar, ‘Amethyst’, into a triticale background. Unfortunately the introgression of the purple pericarp genes failed. Two lines containing the blue aleurone layer, 11T023 and 11T028, were however successfully created. Molecular typing of these lines with SSR markers were able to show that BC4F1 line 11T023 (Ba) B was genetically similar to the recurrent parent ‘Agbeacon’; and that the BC4F1 11T028 line (Ba) A was closest to the ‘US2007’ recurrent parent. The study illustrated that MAS was a reliable tool for detecting genetic diversity in newly sourced germplasm, and assisted in making a backcross breeding effort more effective. The data generated from MAS could therefore clearly assist in making the SU-PBL breeding program more effective by moving, better informed, decision making toward data based partly on the genotype, thereby minimizing the risks associated with purely phenotypic based decisions.
AFRIKAANSE OPSOMMING: Navorsing rondom die gebruik van merkers vir die bepaling van genetiese-diversiteit en kultivar identifikasie is ‘n toenemend belangriker komponent vir die genetiese verbetering van gewasse. Die inkorporering van merker-bemiddelde-seleksie (MBS) as gereedskap vir die identifikasie en karaktarisering van telingsmateriaal is nog nie ten volle geïmplimenteer in die lente korogtelingsprogram van die Stellenbosch Universiteit Planteteeltlaboratorium (SU-PTL). Die studie het gedien as gevallestudie ten einde dit te bereik. Die eerste gedeelte van die studie het gehandel oor die tipering van die genetiese diversiteit van ‘n 101 kultivars verkry vanaf ‘n USDA kiemplasmabank saam met 5 plaaslike kontroles. Dit was gedien ten einde moontlike kruisings-ouers te kon identifiseer. Agt SSR merkers, insluitend vyf afkomstig van rog en drie vanaf koring, asook vyf agronomiese kenmerke is aangewend om die materiaal se diversiteit te tipeer. Saailingtoetsing is ook gedoen en het aangetoon dat die meeste kultivars weerstandig was vir die stamroes-isolaat, maar nie die blaarroes-isolaat nie. Van die agt SSR merkers getoets het sewe getoon om polimorfies te wees en het ‘n 140 allele gegee wat gewissel het vanaf 12 tot 26 per lokus met ‘n gemiddeld van 17.5. Die waargenome polimorfiese inligtings inhoud (PII) waarde het gewissel vanaf 0.39 tot 0.88 met ‘n gemiddeld van 0.70. Die merkers kon dus suksesvol diskrimineer. Die data het aangetoon dat die Suid-Afrikaanse kultivars genetiese die naaste verwant was aan die kultivars afkomstig vanaf die VSA en Kanada. Die tweede gedeelte van die studie het gefokus op die introgressie van ‘n blou aleuron-laag geen (Ba), afkomstig vanaf die koringkultivar ‘Cltr1202STR’, en twee pers-perikarp gene (Pp1; Pp3), afkomstig vanaf die koringkultivar ‘Amethyst’, na ‘n korog agtergrond. Ongelukkig het die oordrag van die pers-perikarp gene gefaal. Twee lyne wat die blou aleuron- laag bevat, 11T023 en 11T028, is egter suksesvol geskep. Tipering van die lyne met die SSR merkers het aangetoon dat die BC4F1 lyn 11T023 (Ba) B genetiese baie na aan die herhalende ouers ‘Agbeacon’ is en dat die BC4F1 11T028 lyn (Ba) A nader is aan die herhalende ouer ‘US2007’. Die studie het dus geïllustreer dat MBS gebruik kan word as ‘n betroubare manier om genetiese diversiteit te bepaal en by te dra tot die sukses van ‘n terugkruisingsprogram. Die data wat dus voortspruit uit MBS kan dus help om die SU-PTL se telingsprogram te assisteer in die besluitnemingsproses tydens teling deur beter genotipe gebaseerde besluite te neem wat die riskio van fenotipe gebaseerde besluite kan help verminder.

碩士
國立臺灣大學
農藝學研究所
105
To fit for the rotation system in central and southern Taiwan, rice farmers prefer growing early maturing variety. Although there is an early maturing local variety available, Da-lu-xian, its grains need to be stored more than six months before procession. Thus, the purpose of this study was to transfer low gelatinization temperature (alk), high spikelet number (SPIKE), and glutinous (wx) genes from Taikeng Waxy No.1 variety to Da-lu-xian with marker-assisted backcross selection method and to select early maturing, suitable for processing, and glutinous lines of indica type rice. In this study, we successfully developed three SSR markers closely linked with target genes, alk, SPIKE and wx, respectively. Correspondingly genetic distances between markers and genes are 0.12 cM, 0.26 cM and 3.66 cM. We screened 49 polymorphic markers from 252 SSR markers and at least four markers for genetic background analysis were distributed on each chromosome. At first, we confirmed F1 hybrids with markers of two target genes and then performed foreground selection and phenotypic selection based on days to heading and plant height, for 87 BC1F1 plants. Then, we carried out foreground selection and phenotypic selection according to days to heading, plant height, spike number and grain number of principal spike, for 278 BC2F1 plants. Eventually, we selected ten superior BC2F1 plants to produce BC2F2 seeds. Besides possessing three target genes, these superior plants have normal fertility rates close to the recurrent parent. No decrease in fertility rate was found which often occurred in a cross between indica and japonica type rice. Furthermore, nine out of the ten selected plants had similarity less than 85% of genetic background in the recurrent parent providing qualification for plant variety right without the limit of essentially derived variety. In this study, we adopted a new breeding method of backcross recombinant lines. That is backcrossing twice and selecting lines superior to recurrent parent in terms of important traits. The effectiveness of the method has preliminarily proved according to the result of this study.

Abstract This chapter provides information on the various molecular breeding strategies to enhance abiotic stress tolerance and yield improvement in wheat, maize and sorghum, such as marker-assisted selection, marker-assisted backcross breeding, marker-assisted recurrent selection and genome-wide selection.

Abstract This chapter presents the status of molecular breeding, especially marker-assisted backcross breeding (MABB), followed in each of the nutritional traits of maize. It focuses on breeding and improvement of protein quality, lysine and tryptophan, provitamin A, vitamin E, phytate, glycaemic index, amylose, and biofortification of maize for human and animal use.

Rice (Oryza sativa L.) is the staple food of the majority of Indians, and India is both the major producer and consumer of rice. Rice cultivation in India is confronted with diverse agro-climatic conditions, varying soil types, and several biotic and abiotic constraints. Among major fungal diseases of Rice in India, the blast caused by Magnaporthe oryzae is the most devastating disease, with the neck blast being the most destructive form. Most of the blast epidemic areas in India have been identified with a mixture of races blast fungus resulting in the resistance breakdown in a short period. At present, a more significant number of the rice varieties cultivated in India were bred by conventional breeding methods with blast resistance conferred by a single resistance gene. Therefore, the blast disease in India is predominantly addressed by the use of ecologically toxic fungicides. In line with the rest of the world, the Indian scientific community has proven its role by identifying several blast resistance genes and successfully pyramiding multiple blast resistance genes. Despite the wealth of information on resistance genes and the availability of biotechnology tools, not a great number of rice varieties in India harbor multiple resistance genes. In the recent past, a shift in the management of blast disease in India has been witnessed with a greater focus on basic research and modern breeding tools such as marker-assisted selection, marker-assisted backcross breeding, and gene pyramiding.