Graduate Thesis Or Dissertation
 

Development of a multi-parent advanced generation inter-cross (MAGIC) population and analysis of a nested association mapping (NAM) population for improvement of genetic resistance to white mold in snap bean

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  • Common bean (Phaseolus vulgaris L.) comes in a huge assortment of fresh and dried varieties, including snap beans, kidney beans, and pinto beans. Together, these and other market classes provide a third of the daily dietary protein in some cultures, particularly in Africa, Asia, and developing nations in the Americas. White mold (WM) (Sclerotinia sclerotiorum Lib. de Bary) is one of the most harmful diseases of snap bean in the United States, with yield losses of up to 100% under conditions that favor the disease. Selective breeding for WM resistance, which is a measurable quantitative trait in beans, presents a big challenge because multiple genes within the same genotype control the phenotype. Multiparent populations are an important tool for plant breeding and genetics studies because they result in greater genetic gain than biparental populations. Eight distinct bean lines showing resistance in the field and greenhouse were selected as founders for the MAGIC (multi-parent advanced generation intercross) snap bean population. Six snap beans (Banga, Flo, Stayton, Top Crop, Unidor, US Refugee 5) were selected based on gene pool diversity, and genomic estimated breeding values (GEBV), and A195 and USPT-WM-12 were selected as dry bean parents. All the parents carry different quantitative trait loci (QTL) alleles contributing to WM resistance. The research aimed to combine as many QTLs as possible into a bean line by intercrossing all the parents. The resulting population can be used to identify new and previously reported regions associated with the WM resistance and those lines with the most favorable combination of QTL. The seedling straw test method was used to identify resistant lines from remnant F2 seeds. This modified version of the straw test can be used to detect significant QTLs related to WM resistance in snap beans. Among 622 progenies, 284 genotypes were resistant based on their response when inoculated with WM isolate 1980. In the summer of 2022, The F3 generation of the MAGIC Snap bean population was grown at Oregon State University Vegetable Research Farm, and 622 lines derived from the population were evaluated based on its agricultural traits such as growth habit, flower color, pod stringiness, market class (dry or snap bean). At the end of the season, single-seed descent was employed at harvest. Single seeds from each pod were mixed to represent each plant in the population. In the winter of 2022, one thousand fifty F4 seeds were advanced in the greenhouse. The greenhouse population was divided into two groups based on their pod qualities as dry and snap beans. The remaining seeds were bulked separately in a separate bag as backup seeds. The F5 generation will be grown in the field in 2023 for generation advance, and the population will be genotyped and phenotyped during the fall and winter of 2023. In the snap bean Nested Association Mapping (NAM) project, four bi-parental snap bean populations were developed with the common parent WMG904-20-03, which was derived from a backcross population developed by introgressing WM resistance from P. coccineus. The common bean parents were selected for their known QTLs that confer partial resistance to WM. The NAM population was screened for WM reaction in the field in 2017 and 2018, and subsequently genotyped using the Illumina Infinium Gene Chip BARCBEAN12K_3 array of single nucleotide polymorphisms (SNPs). The bean NAM population was evaluated for various agronomic traits in the summer of 2020 and 2021, including one-hundred-seed weight, whole-plot weight, seed emergence, vigor, leaf heliotropism ratio, number of germinated plants, maturity, leaf color, degree of pod curvature, and shape of pod curvature. Linkage maps were generated for four populations of F5-derived recombinant inbred lines in 2022, and QTL analysis was performed for both years of WM and field data using Interval Mapping and Multiple-QTL Mapping (MQM) functions of MapQTL 6.0. The results of interval mapping and MQM analysis showed the potential presence of QTLs in all four populations, with a total of 22 QTLs for WM present on nine chromosomes detected by analyzing the NAM population. Notably, the most abundant QTLs were found on chromosome Pv03 (a total of 10). Additionally, 54 QTLs were found on all 11 chromosomes for agronomic traits, and 16 SNPs located on 9 chromosomes were associated with leaf color. Three QTLs were found on Pv02, Pv03, and Pv04 associated with leaf heliotropism ability. Seedrelated traits such as one-hundred seed weight, and whole plot weight had large additive effects from donor parents. The WM-MAGIC snap and dry bean population developed in this study offer advantages over traditional bi-parental populations, providing a wider range of genetic diversity in terms of white mold resistance, plant architecture, and bean market class. Similarly, the WM-NAM population, created by combining four different bi-parental populations, has the potential to increase mapping resolution and identify novel white mold-associated QTLs.
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  • The project was supported by National Sclerotinia Initiative.
  • The author supported with a scholarship from Turkish Ministry of Education.
  • The project was supported by USDA.
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  • 2023-03-27 to 2023-04-06

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