Genome-Wide Association Study Reveals Candidate Genes for Flowering Time Variation in Common Bean (Phaseolus vulgaris L.).

Lorenzo Raggi,Leonardo Caproni,Valeria Negri,Andrea Carboni

doi:10.3389/fpls.2019.00962

Abstract

The common bean is one of the most important staples in many areas of the world. Extensive phenotypic and genetic characterization of unexplored bean germplasm are still needed to unlock the breeding potential of this crop. Dissecting genetic control of flowering time is of pivotal importance to foster common bean breeding and to develop new varieties able to adapt to changing climatic conditions. Indeed, flowering time strongly affects yield and plant adaptation ability. The aim of this study was to investigate the genetic control of days to flowering using a whole genome association approach on a panel of 192 highly homozygous common bean genotypes purposely developed from landraces using Single Seed Descent. The phenotypic characterization was carried out at two experimental sites throughout two growing seasons, using a randomized partially replicated experimental design. The same plant material was genotyped using double digest Restriction-site Associated DNA sequencing producing, after a strict quality control, a dataset of about 50 k Single Nucleotide Polymorphisms (SNPs). The Genome-Wide Association Study revealed significant and meaningful associations between days to flowering and several SNP markers; seven genes are proposed as the best candidates to explain the detected associations.

Highlights

Achieving food security is one of the most important challenges to face in the three decades
For all these reasons the use of legumes as a key ingredient for Genome Wide Association Studies (GWAS) for Bean Flowering Control a sustainable agricultural production system is at the core of agricultural policy debates in different countries (Zander et al, 2016)
In particular: (i) Single Nucleotide Polymorphisms (SNPs) loci characterized by values of missingness higher than 10%, (ii) individuals with more than 10% missing loci, and (iii) markers with a Minor Allele Frequency (MAF) lower than 5% were filtered

Summary

Introduction

Achieving food security is one of the most important challenges to face in the three decades. The demand of food will increase, especially in the areas of the world where most of the developing countries are located, mainly in the African continent (Jensen et al, 2012). In this context, grain legumes are generally regarded as key commodities for improving food security as they are a relatively inexpensive source of amino acids and other important nutrients such as minerals, when compared to livestock and dairy products (Jensen et al, 2012). For all these reasons the use of legumes as a key ingredient for GWAS for Bean Flowering Control a sustainable agricultural production system is at the core of agricultural policy debates in different countries (Zander et al, 2016)

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Results