The validation of QTL for pod quality and domestication traits through association mapping and genomics in snap beans (Phaseolus vulgaris l.)

Pod quality traits of the snap bean are important characteristics in commercial production and processing industry, where standards for pod quality are required in order to fit the processing equipment (Myers and Baggett, 1999). The overall objective of this dissertation was to validate the QTL for pod quality and domestication traits of the snap bean that were identified in the Eagle x Puebla 152 recombinant inbred line (EP RIL) population. Several approaches have been performed to validate the QTL, which were through i) single marker analysis in biparental populations, ii) association mapping in a non-biparental population, and iii) in silico searches for candidate genes in the common bean reference genome. All objectives were addressed in three separate chapters of this dissertation.;Single marker analyses using two-sample t-test and Mann Whitney U test have validated six and four markers for pod quality traits in the EPE and EPH populations, respectively. In addition, association mapping in these populations identified similar markers reported previously in the EP RIL population and revealed several new markers. Association mapping in a non-biparental BeanCAP snap bean panel using 73 genotypes revealed a total of 23 SNP markers associated with fiber, pod length, pod shape and suture string in both 2014 and 2015. However, none of these markers were reported in the EP RIL population suggesting different genetic structure between the EP RIL (biparental population) and BeanCAP snap bean panel (non-biparental population). In silico gene searches in the reference genome based on the location of QTL revealed mostly genes associated with plant growth and defense mechanisms. In addition, a total of four genes of the MADS box protein family which is known as controlling the flower and silique development in Arabidopsis were identified within 2 Mbp region of the QTL for pod length on chromosomes 1 and 3. This study provides some insights regarding the genetic variation between different population structures and genes near the QTL affecting pod quality traits. The accuracy of QTL is primarily important in molecular breeding for crop improvement through marker assisted selection or gene editing such as CRISPR/Cas technology.