The evolution of common bean (Phaseolus vulgaris) using pooled DNA re-sequencing data
Abstract
Domestication of plants has is correlated with the transition from hunter-gatherer societies to agricultural-based societies. The understanding of genes involved in the domestication process can reveal aspects of plant evolution and as well as beneficiate crop improvement. With the new era of DNA sequencing technologies, the data gathering can be done much ore quickly and efficiently to better understand plant genome evolution. Using a pooled DNA re-sequencing approach, more individual can be sequenced and genetic variation and rare alleles can be determined. Here, we evaluated re-sequencing data derived from nine subpopulation of common bean (Phaseolus vulgaris) corresponding to wild undomesticated relatives and domesticated landraces. Common bean is one of the most important legumes worldwide and was domesticated independently both in Central America/Mexico and South America. These two independent domestication events resulted in two distinct genetic pools (Andean and Mesoamerican). To better understand domestication and evolution of this important crop, we targeted chloroplast genome sequences and sequences of genes related to seed development and flavonoid pathway-plant secondary metabolites. In general wild relative pools showed higher sequence diversity than their respective landraces pools. Nearly 490 SNPs were found the chloroplast of which 49% were specific to either Andean or Mesoamerican pools for an average genetic density of one SNP every 254 bp. Seed development genes showed higher genetic diversity in Mesoamerican pools (π = 0.00213) than Andean pools (π = 0.00058). Multiples copies of genes in the flavonoid pathway were annotated and our data suggests that they have followed different patterns of evolution. These results contribute to a better understanding of evolution, domestication and genetic diversity in common bean that can be exploited for future breeding and crop improvement.
Degree
Ph.D.
Advisors
Ma, Purdue University.
Subject Area
Agronomy|Genetics
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