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A genome-wide associate study reveals favorable alleles conferring apical and basal spikelet fertility in wheat (Triticum aestivum L.)

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Abstract

Kernel number per spike (KNPS) is one of the key factors affecting wheat yield, which can be significantly reduced by lower fertility or sterility of the apical and basal spikelets. In this study, the spikelet number per spike (SNPS), thousand kernel weight (TKW), KNPS, total grain numbers of the top three apical spikelets (GNAS), and total grain numbers of the bottom three basal spikelets (GNBS) of 212 wheat lines were recorded from five different environmental conditions. These 212 accessions were genotyped using the 9K iSelect SNP Beadchip. A total of 3269 SNP markers were used for genome-wide association analysis (GWAS). One hundred twelve significant marker-trait associations (MTAs) were identified. Twenty-two MTAs were identified in at least two environments and two of them showed association with two or more grain setting properties. Different loci showed an additive effect with both GNAS and GNBS being much higher in the lines with more favorite alleles. Two SNP loci, wsnp_Ex_c31799_40545376 and wsnp_BF293620A_Ta_2_3, showed the largest effects on increasing KNPS through improved fertility of apical and basal spikelets, respectively. These MTAs have the potential to be used in future marker-assisted selection.

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Funding

This work was supported by grants from the National Key R&D Program of China (2017YFD0101000), the National Key R&D Program of Shanxi Province (201703D211007), the Technology Innovation Program of Higher Education of Shanxi Province (2017142), and the Science & Technology Innovation Foundation of Shanxi Agricultural University (2016YJ05).

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Author notes

  1. Weiping Shi, Linqi Yue and Jingye Cheng contributed equally to this work.

Authors and Affiliations

  1. College of Agronomy, Shanxi Agricultural University, Taigu, 030801, China

    Weiping Shi, Linqi Yue, Jingye Cheng, Jiahui Guo, Lulu Li, Kaidi Xie, Jiarui Dong, Jie Guo & Meixue Zhou

  2. College of Agronomy, Yangzhou University, Yangzhou, 225009, China

    Jingye Cheng

  3. Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, 434025, China

    Yanhao Xu & Meixue Zhou

  4. School of Land and Food, University of Tasmania, Hobart, 7250, Australia

    Meixue Zhou

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  1. Weiping Shi
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  2. Linqi Yue
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  3. Jingye Cheng
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  4. Jiahui Guo
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Correspondence to Jie Guo or Meixue Zhou.

Electronic supplementary material

Table S1

Details for 212 wheat accessions included in the germplasm set used in this study. (XLSX 18 kb)

Table S2

Allele number, MAF and PIC of 3778 polymorphic SNP markers detected in the association panel. (XLSX 301 kb)

Table S3

One hundred and twelve significant MTAs involving 88 SNP loci and eleven phenotypic traits. (XLSX 36 kb)

Table S4

Best blast hit of wheat SNP flanking sequence/Genebank against genomic sequence (IWGSC) of Triticum aestivum. (XLSX 10 kb)

Fig. S1

Population structure of 212 cultivars based on 3778 unlinked SNP markers. a: Plot of ΔK against putative K ranging from 1 to 12; b: Stacked bar plot of ancestry relationships of 212 wheat cultivars. (PNG 96 kb)

High Resolution Image (TIF 457 kb)

Fig. S2

The information of overlapping genes ranged from 585.0 Mb to 589.5 Mb on chromosome 5A. (PNG 311 kb)

High Resolution Image (TIF 693 kb)

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Shi, W., Yue, L., Cheng, J. et al. A genome-wide associate study reveals favorable alleles conferring apical and basal spikelet fertility in wheat (Triticum aestivum L.). Mol Breeding 38, 146 (2018). https://doi.org/10.1007/s11032-018-0906-y

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