Validation of Candidate Gene-Based Markers and Identification of Novel Loci for Thousand-Grain Weight in Spring Bread Wheat.

Deepmala Sehgal,Guillermo Garcia Barrios,Suchismita Mondal,Susanne Dreisigacker,Ravi Singh,Carlos Guzman,Carolina Franco

doi:10.3389/fpls.2019.01189

Deepmala Sehgal, Guillermo Garcia Barrios + Show 5 more

Open Access

https://doi.org/10.3389/fpls.2019.01189

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Abstract

Increased thousand-grain weight (TGW) is an important breeding target for indirectly improving grain yield (GY). Fourteen reported candidate genes known to enhance TGW were evaluated in two independent and existing datasets of wheat at CIMMYT, the Elite Yield Trial (EYT) from 2015 to 2016 (EYT2015-16) and the Wheat Association Mapping Initiative (WAMI) panel, to study their allele effects on TGW and to verify their suitability for marker-assisted selection. Of these, significant associations were detected for only one gene (TaGs3-D1) in the EYT2015-16 and two genes (TaTGW6 and TaSus1) in WAMI. The reported favorable alleles of TaGs3-D1 and TaTGW6 genes decreased TGW in the datasets. A haplotype-based genome wide association study was implemented to identify the genetic determinants of TGW on a large set of CIMMYT germplasm (4,302 lines comprising five EYTs), which identified 15 haplotype blocks to be significantly associated with TGW. Four of them, identified on chromosomes 4A, 6A, and 7A, were associated with TGW in at least three EYTs. The locus on chromosome 6A (Hap-6A-13) had the largest effect on TGW and additionally GY with increases of up to 2.60 g and 258 kg/ha, respectively. Discovery of novel TGW loci described in our study expands the opportunities for developing diagnostic markers and for multi-gene pyramiding to derive new allele combinations for enhanced TGW and GY in CIMMYT wheat.

Highlights

Of all yield components, grain weight is the most stable and heritable trait, an important selection target for the genetic improvement of grain yield (GY) (Cooper et al, 2012; Xiao et al, 2012)
In Wheat Association Mapping Initiative (WAMI), the favorable allele of the gene TaCwi-5D was present in 99% of lines while those of the remaining genes were in low (6.4%) to high (87.7%) frequencies
Opposite and quite variable effects of the alleles on GY were observed. These results reinforce the previous findings that the currently known allelic effects of reported candidate genes (CGs) related to thousand grain weight (TGW) vary with genetic background and/or environment (Sukumaran et al, 2018), and it will be challenging to use the associated single nucleotide polymorphism (SNP) for Mapping for Thousand-Grain Weight selection (MAS) across individual breeding programs

Summary

Introduction

Grain weight is the most stable and heritable trait, an important selection target for the genetic improvement of grain yield (GY) (Cooper et al, 2012; Xiao et al, 2012). Inconclusive results were obtained in a recent study on CIMMYT germplasm, where Hap6A-G was found superior in Mexico and the second allele, i.e., Hap-6A-A, in Nepal and India (Sukumaran et al, 2018) These examples suggest that besides compensatory effects on GY, the genetic effects of the reported CGs can be environment- and/ or germplasm-dependent. The other panel is the well-known WAMI (Wheat Association Mapping Initiative) that includes historical cultivars and synthetic-derived lines (Lopes et al, 2012; Lopes et al, 2015)

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