Project Description: "Genome-wide identification of positive selection in regulatory regions of soybean (Glycine max)"
Positive selection refers to the selection for novel variants in DNA sequence. Domestication and further plant breeding are processes which can impose positive selection on a population. Previous studies of positive selection in plant species have focused on coding regions of genes and have conducted candidate gene or genome-wide analyses to identify evidence of positive selection on genes or gene families. In the animal kingdom, genome-wide scans have also been conducted to identify evidence of positive selection within promoter regions; sequence variations related to human neural and nutritional adaption may reside primarily in cis-regulatory sequences, with relatively little variation related to these adaptations in coding regions. Positive selection occurring in the teosinte branched1 gene important in the domestication of maize was only shown in the putative regulatory region and was not detected in the protein-coding region. Consequently, we posit that that many domestication traits are conferred by changes in regulatory elements. The objective of this project is to identify regulatory regions exhibiting evidence of positive selection associated with the domestication of soybean (Glycine max). To achieve this goal, using re-sequencing data from 14 accessions of cultivated soybean and 18 accessions of its nearest wild ancestor G. soja, we will 1) predict promoters and compare the sequence diversity of predicted promoter regions with the related nearby intronic sequences which are theoretically under neutral selection and 2) analyze predicted microRNA target sites by comparing the rates of synonymous substitutions within the target sites and the non-target sites of each gene. The later stages of this project will depend on these initial results and may include genotype-phenotype association analyses, functional analysis of regulatory elements, and additional analysis of regions exhibiting evidence of positive selection during domestication. The proposed research may help identify yield and quality genes which have been critical to the domestication and improvement of cultivated soybean.