Investigating Drought Tolerance in Chickpea Using Genome-Wide Association Mapping and Genomic Selection Based on Whole-Genome Resequencing Data.

Yongle Li,Tim Sutton,Jiayin Pang,Jacqueline Batley,Timothy D. Colmer,Pradeep Ruperao,David Edwards,Tanveer Khan,Kadambot H. M. Siddique

doi:10.3389/fpls.2018.00190

Abstract

Drought tolerance is a complex trait that involves numerous genes. Identifying key causal genes or linked molecular markers can facilitate the fast development of drought tolerant varieties. Using a whole-genome resequencing approach, we sequenced 132 chickpea varieties and advanced breeding lines and found more than 144,000 single nucleotide polymorphisms (SNPs). We measured 13 yield and yield-related traits in three drought-prone environments of Western Australia. The genotypic effects were significant for all traits, and many traits showed highly significant correlations, ranging from 0.83 between grain yield and biomass to -0.67 between seed weight and seed emergence rate. To identify candidate genes, the SNP and trait data were incorporated into the SUPER genome-wide association study (GWAS) model, a modified version of the linear mixed model. We found that several SNPs from auxin-related genes, including auxin efflux carrier protein (PIN3), p-glycoprotein, and nodulin MtN21/EamA-like transporter, were significantly associated with yield and yield-related traits under drought-prone environments. We identified four genetic regions containing SNPs significantly associated with several different traits, which was an indication of pleiotropic effects. We also investigated the possibility of incorporating the GWAS results into a genomic selection (GS) model, which is another approach to deal with complex traits. Compared to using all SNPs, application of the GS model using subsets of SNPs significantly associated with the traits under investigation increased the prediction accuracies of three yield and yield-related traits by more than twofold. This has important implication for implementing GS in plant breeding programs.

Highlights

Chickpea (Cicer arietinum L.) is ranked second after soybean in terms of global legume production, reaching ∼13 million tons in 2014 (FAOSTAT 2017)
The extent of Linkage disequilibrium (LD) on each chromosome ranged from 4,000 kb on Ca3 to 150 kb on Ca6 with an average of 700 kb (Table 3 and Supplementary Figure S2)
This study showed that some India-derived genotypes with early podding trait aborted early onset pods in the Australian environments due to low temperatures in early spring

Summary

Introduction

Chickpea (Cicer arietinum L.) is ranked second after soybean in terms of global legume production, reaching ∼13 million tons in 2014 (FAOSTAT 2017). Consisting of 25% of the total exports worldwide, Australia was the second-largest producer and the largest exporter of chickpea in 2014 (FAOSTAT 2017). Drought is one of the most important constraints limiting yield potential in cereal and legume crops. Transient drought is a short-term water deficit that can be relieved by precipitation and can occur at any stages of the growing season. Terminal drought is very common in semi-arid tropics (South Asia, north-east Australia) and Mediterranean-type climates such as southern Australia. More than 80% of the world chickpea production is located in South Asia and north-east Australia. Australia has experienced severe drought events from the late 1990s to mid 2000s known as “the Millennium drought.” As a consequence, the total production of irrigated rice and cotton fell by 99 and 84% during 2002 and 2009, respectively (van Dijk et al, 2013)

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