Exploring The Genetic Architecture And Improving Genomic Prediction Accuracy For Yield Mineral Concentration And Canning Quality Traits In Common Bean Phaseolus Vulgaris PDF Download

Drought is the main constraint in common bean (Phaseolus vulgaris) production. Although breeding efforts to increase drought resistance have shown gains in productivity, their full potential remains untapped. Improvements have been limited by the complexity of the trait involved, limited germplasm recombination, and most importantly, the poorly understood genetic basis of tolerance. To gain information about the genetics and mechanism(s) of drought adaptation, I explored the genetic diversity of wild and domesticated Mesoamerican gene pool of the species through genetic analyses in natural, bi-parental, and multi-parental populations. In the first chapter, I evaluated root and shoot traits in a large panel of wild accessions and reference domesticated cultivars, both from the Mesoamerican distribution of common bean, in a greenhouse tube experiment. The domesticated beans were, in general, more vigorous and deeper-rooted than wild beans. Nevertheless, some wild beans were outstanding in their productivity and rooting capacity. A comparison of the measured phenotypic traits with the climatic and soil characteristics of the location of origin of the individual wild bean accessions showed that most traits were significantly associated with mean annual temperature and aridity. The most deeply rooted and productive accessions originated from the driest regions. Each wild accession was genotyped with both a SNP array and a GBS platform; three populations of wild bean accessions were identified, of which the most productive, deeply rooted, and more drought-tolerant population, originating from Central and North-West Mexico and Oaxaca. Through genome-wide association analyses, genomic regions associated with productivity, root depth, and drought adaptation were identified. Some co-located with regions showing signals of selection suggesting that drought stress is a driver of local adaptation in wild common beans.In the second chapter, I investigated the effects of drought stress on the genetic architecture of photosynthate allocation and remobilization in pods, one of the main mechanisms of drought resistance and overall productivity. A bi-parental recombinant inbred line (RIL) population of the Mesoamerican gene pool was evaluated in field conditions under well-watered conditions and terminal and intermittent drought stress in two years. There was a significant effect of the water regime and year on pod harvest index (PHI), a measure of the partition of seed biomass to pod biomass, its components, phenology and grain yield at the phenotypic and QTL level. QTLs for pod harvest index, including a major, stable QTL on chromosome Pv07 was detected. For grain yield, the QTLs were not stable; however, three were detected for the overall mean across environments. There was differential co-localization of the components of PHI, co-localizing mainly with either the pod wall, seed mass, or both. Three of the eight yield QTLs co-localized with PHI QTLs, underlying the importance of photosynthate remobilization in productivity. Epistasis explained a considerable part of the variation, especially for PHI and yield. In the third chapter, to further test the value of wild variation as compared with the domesticated forms, joint linkage mapping of nested populations was carried out in three newly develop domesticated by wild backcrossed recombinant inbred line populations. The populations were developed by crossing three wild accessions representing the extreme range of rainfall of the Mesoamerican wild bean distribution to an elite drought resistant domesticated parent. Grain yield was evaluated under field conditions in two fully irrigated trials in two seasons and a simulated terminal drought in the second season. The highest yielding populations were the populations from the lower part of the rainfall distribution. The populations were genotyped and a consensus map was developed containing 721 SNP markers. Twenty QTLs were found in 13 unique regions on eight chromosomes. At least one wild allele with a significant positive additive effect was found in five of these regions. The additive effects of all the QTLs ranged from -164 to 277 kg ha−1, with some evidence of allelic series. The variation explained by these QTLs ranged from 0.6 to 5.4 % of the total variation. These results underlie the potential of wild variation for bean crop improvement as well the identification of regions for efficient marker-assisted introgression and candidate genes.