Decreased Nucleotide and Expression Diversity and Modified Coexpression Patterns Characterize Domestication in the Common Bean

Abstract

ORCID ID: 0000-0001-9598-3131 (R.P.)Using RNA sequencing technology and de novo transcriptome assembly, we compared representative sets of wild and domesticated accessions of common bean (Phaseolus vulgaris) from Mesoamerica. RNA was extracted at the first true-leaf stage, and de novo assembly was used to develop a reference transcriptome; the final data set consists of ;190,000 single nucleotide polymorphisms from 27,243 contigs in expressed genomic regions. A drastic reduction in nucleotide diversity (;60%) is evident for the domesticated form, compared with the wild form, and almost 50% of the contigs that are polymorphic were brought to fixation by domestication. In parallel, the effects of domestication decreased the diversity of gene expression (18%). While the coexpression networks for the wild and domesticated accessions demonstrate similar seminal network properties, they show distinct community structures that are enriched for different molecular functions. After simulating the demographic dynamics during domestication, we found that 9% of the genes were actively selected during domestication. We also show that selection induced a further reduction in the diversity of gene expression (26%) and was associated with 5-fold enrichment of differentially expressed genes. While there is substantial evidence of positive selection associated with domestication, in a few cases, this selection has increased the nucleotide diversity in the domesticated pool at target loci associated with abiotic stress responses, flowering time, and morphology.

Genome-wide identification and characterization of aquaporin gene family in common bean (Phaseolus vulgaris L.)

“…These two gene pools were independently domesticated in what is now Mexico and South America (Gepts et al 1986;Bitocchi et al 2013) about 8,000 years ago. The release of a reference P. vulgaris genome sequence (Schmutz et al 2014), together with the development and application of Next Generation Sequencing technologies in plant species (Bräutigam and Gowik 2010) and synteny among plants, such as soybean and Arabidopsis, enabled a genome-wide identification of actual or putative loci involved in the domestication process of this species (Repinski et al 2012;Kwak et al 2012;Bellucci et al 2014;Schmutz et al 2014).…”

Discovering new biology through RNA-Seq

“…For example, it was shown that during the domestication of common bean in Mesoamerica, drastic changes in the pattern and structure of gene expression occurred, with overall lower diversity of gene expression patterns and a general down-regulation of gene expression levels in the domesticated variants as compared with the ancestral species. In this case, the loss of genetic diversity during domestication was directly associated with a reduced diversity of gene expression patterns (Bellucci et al, 2014). Comparative analysis of gene expression during cotton fiber development in four wild and five cultivated accessions of cotton revealed, among other important findings, that human selection during domestication has led to a prolonged duration of fiber elongation.…”

Genomics-based strategies for the use of natural variation in the improvement of crop metabolism

“…[50]). In any case, RNAseq has proved to be a powerful approach to uncover both genetic and expression diversity in a set of related species or accessions [51][52][53].…”