Identification of novel drought-tolerant-associated SNPs in common bean (Phaseolus vulgaris).

Emiliano Villordo-Pineda,Jorge A. Acosta-Gallegos,Mario M. González-Chavira,Patricia Giraldo-Carbajo,Juan Caballero-Pérez

doi:10.3389/fpls.2015.00546

Abstract

Common bean (Phaseolus vulgaris L.) is a leguminous in high demand for human nutrition and a very important agricultural product. Production of common bean is constrained by environmental stresses such as drought. Although conventional plant selection has been used to increase production yield and stress tolerance, drought tolerance selection based on phenotype is complicated by associated physiological, anatomical, cellular, biochemical, and molecular changes. These changes are modulated by differential gene expression. A common method to identify genes associated with phenotypes of interest is the characterization of Single Nucleotide Polymorphims (SNPs) to link them to specific functions. In this work, we selected two drought-tolerant parental lines from Mesoamerica, Pinto Villa, and Pinto Saltillo. The parental lines were used to generate a population of 282 families (F3:5) and characterized by 169 SNPs. We associated the segregation of the molecular markers in our population with phenotypes including flowering time, physiological maturity, reproductive period, plant, seed and total biomass, reuse index, seed yield, weight of 100 seeds, and harvest index in three cultivation cycles. We observed 83 SNPs with significant association (p < 0.0003 after Bonferroni correction) with our quantified phenotypes. Phenotypes most associated were days to flowering and seed biomass with 58 and 44 associated SNPs, respectively. Thirty-seven out of the 83 SNPs were annotated to a gene with a potential function related to drought tolerance or relevant molecular/biochemical functions. Some SNPs such as SNP28 and SNP128 are related to starch biosynthesis, a common osmotic protector; and SNP18 is related to proline biosynthesis, another well-known osmotic protector.

Highlights

Common bean (Phaseolus vulgaris L.) is the most important leguminous crop species for human nutrition because it is a natural source of essential nutrients and proteins in the diet of ∼500 million people in Latin America and Africa (Broughton et al, 2003)
Even when rain precipitation was variable per cycle, water was not enough and the terminal-stress produced a reduction in production as expected (Supplementary Table 3, Supplementary Figure 1)
We noted differences in the response in both parental lines, this confirms that the parental lines have differences in the way the stress is tolerated as we are validating at the molecular level

Summary

Introduction

Common bean (Phaseolus vulgaris L.) is the most important leguminous crop species for human nutrition because it is a natural source of essential nutrients and proteins in the diet of ∼500 million people in Latin America and Africa (Broughton et al, 2003). The Mesoamerican and Durango races are considered to be a rich genetic source for drought stress resistance (Terán and Singh, 2002b; Singh, 2007). Drought is the most important abiotic stress limiting cultivar productivity. Drought negatively impacts dry-bean cultivars depending on intensity, type and duration of the stress (Terán and Singh, 2002a,b; Muñoz-Perea et al, 2006). We can expect than drought will be increasing in number of events and duration in the principal agriculture regions because of global warming. This will affect negatively the production and food availability (McClean et al, 2011). Drought effects are increased by other biotic or abiotic factors (Polanía et al, 2012)

Methods

Results

Conclusion