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Genome-wide association study of heading and flowering dates and construction of its prediction equation in Chinese common wheat

Theoretical and Applied Genetics volume 131, pages 2271–2285 (2018)Cite this article

Abstract

Heading date is one of the most important traits in wheat breeding as it affects adaptation and yield potential. A genome-wide association study (GWAS) using the 90 K iSelect SNP genotyping assay indicated that a total of 306 loci were significantly associated with heading and flowering dates in 13 environments in Chinese common wheat from the Yellow and Huai wheat region. Of these, 105 loci were significantly correlated with both heading and flowering dates and were found in clusters on chromosomes 2, 5, 6, and 7. Based on differences in distribution of the vernalization and photoperiod genes among chromosomes, arms, or block regions, 13 novel, environmentally stable genetic loci were associated with heading and flowering dates, including RAC875_c41145_189 on 1DS, RAC875_c50422_299 on 2BL, and RAC875_c48703_148 on 2DS, that accounted for more than 20% phenotypic variance explained (PVE) of the heading/flowering date in at least four environments. GWAS and t test of a combination of SNPs and vernalization and photoperiod alleles indicated that the Vrn-B1, Vrn-D1, and Ppd-D1 genes significantly affect heading and flowering dates in Chinese common wheat. Based on the association of heading and flowering dates with the vernalization and photoperiod alleles at seven loci and three significant SNPs, optimal linear regression equations were established, which show that of the seven loci, the Ppd-D1 gene plays the most important role in modulating heading and flowering dates in Chinese wheat, followed by Vrn-B1 and Vrn-D1. Additionally, three novel genetic loci (RAC875_c41145_189, Excalibur_c60164_137, and RAC875_c50422_299) also show important effect on heading and flowering dates. Therefore, Ppd-D1, Vrn-B1, Vrn-D1, and the novel genetic loci should be further investigated in terms of improving heading and flowering dates in Chinese wheat. Further quantitative analysis of an F10 recombinant inbred lines population identified a major QTL that controls heading and flowering dates within the Ppd-D1 locus with PVEs of 28.4% and 34.0%, respectively; this QTL was also significantly associated with spike length, peduncle length, fertile spikelets number, cold resistance, and tiller number.

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Acknowledgements

This project was funded by the National Key Research and Development Program (2016YFD0101802), Henan Major Science and Technology Projects (181100110200), and Henan Science and Technology Innovation Outstanding Youth Funding (174100510001) of China.

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  1. Agronomy College, National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, People’s Republic of China

    Xiangfen Zhang, Jianhui Chen, Yan Yan, Xuefang Yan, Chaonan Shi, Lei Zhao & Feng Chen

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  1. Xiangfen Zhang
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  2. Jianhui Chen
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  3. Yan Yan
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Correspondence to Feng Chen.

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Communicated by Peter Langridge.

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Fig. S1A

Distribution frequency of heading date (1A) and flowering date (1B) of Chinese wheat cultivars in 13 environments (PNG 778 kb)

Fig. S1B

Supplementary material 2 (PNG 814 kb)

Fig. S2

Population structure of the selected 163 cultivars based on unlinked SNP markers. (A) Plot of delta K against putative K ranging from 1 to 10. (B) Stacked bar plot of ancestry relationship of 163 cultivars. (JPEG 68 kb)

Fig. S3A

Manhattan plots and Quantile–Quantile (Q–Q) plots for heading (3A) and flowering dates (3B). (JPEG 6025 kb)

Fig. S3B

Supplementary material 5 (JPEG 6157 kb)

Table S1

Heading and flowering dates in Chinese winter cultivars in 13 environments (XLSX 212 kb)

Table S2

Significant SNPs detected for heading and flowering dates through GWAS (A); Significant SNPs detected for heading date through GWAS (B); Significant SNPs detected for flowering date through GWAS (C); Significant SNPs detected for both heading and flowering dates through GWAS (D) (XLSX 77 kb)

Table S3

PCR primers used in this study (XLSX 13 kb)

Table S4

Allelic variations of the vernalization and photoperiod genes and heading and flowering dates in 2012-2013 and 2014-2015 years of 254 landraces. (XLSX 30 kb)

Table S5

The partial regression coefficient and P value in multiple regression equations in three populations (AMP, CWG, and CL) (XLSX 12 kb)

Table S6

Phenotype of seven traits of a PC population with 97 lines (XLSX 14 kb)

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Zhang, X., Chen, J., Yan, Y. et al. Genome-wide association study of heading and flowering dates and construction of its prediction equation in Chinese common wheat. Theor Appl Genet 131, 2271–2285 (2018). https://doi.org/10.1007/s00122-018-3181-8

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