Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs

Yousef Rahimi,Hadi Alipour,Alireza Taleei,Mohammad Reza Bihamta,Pär K Ingvarsson

doi:10.1186/s12870-019-2165-4

Yousef Rahimi, Hadi Alipour + Show 3 more

Open Access

https://doi.org/10.1186/s12870-019-2165-4

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Abstract

BackgroundIdentification of loci for agronomic traits and characterization of their genetic architecture are crucial in marker-assisted selection (MAS). Genome-wide association studies (GWAS) have increasingly been used as potent tools in identifying marker-trait associations (MTAs). The introduction of new adaptive alleles in the diverse genetic backgrounds may help to improve grain yield of old or newly developed varieties of wheat to balance supply and demand throughout the world. Landraces collected from different climate zones can be an invaluable resource for such adaptive alleles.ResultsGWAS was performed using a collection of 298 Iranian bread wheat varieties and landraces to explore the genetic basis of agronomic traits during 2016–2018 cropping seasons under normal (well-watered) and stressed (rain-fed) conditions. A high-quality genotyping by sequencing (GBS) dataset was obtained using either all original single nucleotide polymorphism (SNP, 10938 SNPs) or with additional imputation (46,862 SNPs) based on W7984 reference genome. The results confirm that the B genome carries the highest number of significant marker pairs in both varieties (49,880, 27.37%) and landraces (55,086, 28.99%). The strongest linkage disequilibrium (LD) between pairs of markers was observed on chromosome 2D (0.296). LD decay was lower in the D genome, compared to the A and B genomes. Association mapping under two tested environments yielded a total of 313 and 394 significant (−log10P >3) MTAs for the original and imputed SNP data sets, respectively. Gene ontology results showed that 27 and 27.5% of MTAs of SNPs in the original set were located in protein-coding regions for well-watered and rain-fed conditions, respectively. While, for the imputed data set 22.6 and 16.6% of MTAs represented in protein-coding genes for the well-watered and rain-fed conditions, respectively.ConclusionsOur finding suggests that Iranian bread wheat landraces harbor valuable alleles that are adaptive under drought stress conditions. MTAs located within coding genes can be utilized in genome-based breeding of new wheat varieties. Although imputation of missing data increased the number of MTAs, the fraction of these MTAs located in coding genes were decreased across the different sub-genomes.

Highlights

Identification of loci for agronomic traits and characterization of their genetic architecture are crucial in marker-assisted selection (MAS)
The greatest variation under well-watered conditions was observed for seed number per spike and thousand kernel weight, whereas plant height and peduncle length were more variable under rain-fed conditions (SD 15.55 and 7.26, respectively)
A significant positive association was observed between grain yield, spike weight, seed number, thousand kernel weight, leaf greenness, and grain filling period under well-watered conditions (P < 0.01), whereas phenology traits and canopy temperature were negatively correlated with grain yield (P < 0.01 and 0.05, Additional file 2: Table S4)

Summary

Introduction

Identification of loci for agronomic traits and characterization of their genetic architecture are crucial in marker-assisted selection (MAS). The introduction of new adaptive alleles in the diverse genetic backgrounds may help to improve grain yield of old or newly developed varieties of wheat to balance supply and demand throughout the world. Bread wheat (Triticum aestivum L.) is a staple crop both in developing and developed countries and there is a constant need to balance supply and demand [1]. The projected increase of human population is expected to increase the demand of wheat thereby highlighting the need for plant breeders to utilize all accessible tools to find new ways to sustainably increase the production of bread wheat over the coming decades [1, 2]. Wheat production increased significantly after green revolution in the 1960s and 1970s by better farm management practices and introduction of well-adapted wheat varieties. There are several factors drastically limiting wheat production throughout the world, such as water deficiency, salt and cold stress, resulting in significant losses in both grain and biomass [3, 4]

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