Analysis of main effect QTL for thousand grain weight in European winter wheat (Triticum aestivum L.) by genome-wide association mapping.

Christine D Zanke,Erhard Ebmeyer,Andrea Eichhorn,Jie Ling,Felix Neumann,Maike Hinze,Cornelia Jaenecke,Viktor Korzun,Gunther Stiewe,Martin W Ganal,Marion S Röder,Andreas Polley,Jörg Plieske,Sonja Kollers,Odile Argillier

doi:10.3389/fpls.2015.00644

Christine D Zanke, Erhard Ebmeyer + Show 13 more

Open Access

https://doi.org/10.3389/fpls.2015.00644

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Abstract

Grain weight, an essential yield component, is under strong genetic control and at the same time markedly influenced by the environment. Genetic analysis of the thousand grain weight (TGW) by genome-wide association study (GWAS) was performed with a panel of 358 European winter wheat (Triticum aestivum L.) varieties and 14 spring wheat varieties using phenotypic data of field tests in eight environments. Wide phenotypic variations were indicated for the TGW with BLUEs (best linear unbiased estimations) values ranging from 35.9 to 58.2 g with a mean value of 45.4 g and a heritability of H2 = 0.89. A total of 12 candidate genes for plant height, photoperiodism and grain weight were genotyped on all varieties. Only three candidates, the photoperiodism gene Ppd-D1, dwarfing gene Rht-B1and the TaGW-6A gene were significant explaining up to 14.4, 2.3, and 3.4% of phenotypic variation, respectively. For a comprehensive genome-wide analysis of TGW-QTL genotyping data from 732 microsatellite markers and a set of 7769 mapped SNP-markers genotyped with the 90k iSELECT array were analyzed. In total, 342 significant (-log10 (P-value) ≥ 3.0) marker trait associations (MTAs) were detected for SSR-markers and 1195 MTAs (−log10(P-value) ≥ 3.0) for SNP-markers in all single environments plus the BLUEs. After Bonferroni correction, 28 MTAs remained significant for SSR-markers (−log10 (P-value) ≥ 4.82) and 58 MTAs for SNP-markers (−log10 (P-value) ≥ 5.89). Apart from chromosomes 4B and 6B for SSR-markers and chromosomes 4D and 5D for SNP-markers, MTAs were detected on all chromosomes. The highest number of significant SNP-markers was found on chromosomes 3B and 1B, while for the SSRs most markers were significant on chromosomes 6D and 3D. Overall, TGW was determined by many markers with small effects. Only three SNP-markers had R2 values above 6%.

Highlights

Grain size is a yield component and part of the domestication syndrome (Peng et al, 2003) in cereals
Description of Phenotypic Data The means of thousand grain weight (TGW) across 358 winter wheat plus 14 spring wheat varieties in eight field environments ranged from 42.3 g in the environment 10.JAN to 50.2 g in the environment 09.SEL (Figure 1)
The continuous distribution of the TGW phenotype indicated a quantitative mode of inheritance and most spring wheat varieties were found in the second half of the distribution containing the varieties with larger grains (Figure 2A)

Summary

Introduction

Grain size is a yield component and part of the domestication syndrome (Peng et al, 2003) in cereals. Already several genes related to grain size and grain shape have been cloned and characterized (Sakamoto and Matsuoka, 2008; Huang et al, 2013). Syntenic genes were discovered in maize (Li et al, 2010a) and wheat (Zhang et al, 2014), where a QTL for marker TaGS-D1 was described in a recombinant inbred population. GRAIN WIDTH 2 (GW2) is a major QTL for rice grain width and weight and encodes a RING-type E3 ubiquitin ligase (Song et al, 2007). Two syntenic genes in maize had effects on traits related to kernel shape and weight in an association panel (Li et al, 2010b). Significant associations with grain weight were reported for haplotypes of the genes TaGW2-6A and TaGW2-6B (Qin et al, 2014)

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