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

  • Xiangfen Zhang
  • Jianhui Chen
  • Yan Yan
  • Xuefang Yan
  • Chaonan Shi
  • Lei Zhao
  • Feng Chen
Review

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.

Notes

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.

Compliance with ethical standards

Conflict of interest

The authors have no conflict of interest to declare.

Supplementary material

122_2018_3181_MOESM1_ESM.png (779 kb)
Fig. S1A Distribution frequency of heading date (1A) and flowering date (1B) of Chinese wheat cultivars in 13 environments (PNG 778 kb)
122_2018_3181_MOESM2_ESM.png (814 kb)
Fig. S1B Supplementary material 2 (PNG 814 kb)
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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)
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Fig. S3A Manhattan plots and Quantile–Quantile (QQ) plots for heading (3A) and flowering dates (3B). (JPEG 6025 kb)
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Fig. S3B Supplementary material 5 (JPEG 6157 kb)
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Table S1 Heading and flowering dates in Chinese winter cultivars in 13 environments (XLSX 212 kb)
122_2018_3181_MOESM7_ESM.xlsx (77 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)
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Table S3 PCR primers used in this study (XLSX 13 kb)
122_2018_3181_MOESM9_ESM.xlsx (31 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)
122_2018_3181_MOESM10_ESM.xlsx (13 kb)
Table S5 The partial regression coefficient and P value in multiple regression equations in three populations (AMP, CWG, and CL) (XLSX 12 kb)
122_2018_3181_MOESM11_ESM.xlsx (15 kb)
Table S6 Phenotype of seven traits of a PC population with 97 lines (XLSX 14 kb)

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© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Agronomy College, National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain CropsHenan Agricultural UniversityZhengzhouPeople’s Republic of China

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