Genome-wide association study and quantitative trait loci mapping of seed dormancy in common wheat (Triticum aestivum L.)

Abstract

Main conclusion

Totally, 23 and 26 loci for the first count germination ratio and the final germination ratio were detected by quantitative trait loci (QTL) mapping and association mapping, respectively, which could be used to facilitate wheat pre-harvest sprouting breeding.

Abstract

Weak dormancy can cause pre-harvest sprouting in seeds of common wheat which significantly reduces grain yield. In this study, both quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) were used to identify loci controlling seed dormancy. The analyses were based on a recombinant inbred line population derived from Zhou 8425B/Chinese Spring cross and 166 common wheat accessions. Inclusive composite interval mapping detected 8 QTL, while 45 loci were identified in the 166 wheat accessions by GWAS. Among these, four loci (Qbifcgr.cas-3AS/Qfcgr.cas-3AS, Qbifcgr.cas-6AL.1/Qfcgr.cas-6AL.1, Qbifcgr.cas-7BL.2/Qfcgr.cas-7BL.2, and Qbigr.cas-3DL/Qgr.cas-3DL) were detected in both QTL mapping and GWAS. In addition, 41 loci co-located with QTL reported previously, whereas 8 loci (Qfcgr.cas-5AL, Qfcgr.cas-6DS, Qfcgr.cas-7AS, Qgr.cas-3DS.1, Qgr.cas-3DS.2, Qbigr.cas-3DL/Qgr.cas-3DL, Qgr.cas-4B, and Qgr.cas-5A) were likely to be new. Linear regression showed the first count germination ratio or the final germination ratio reduced while multiple favorable alleles increased. It is suggested that QTL pyramiding was effective to reduce pre-harvest sprouting risk. This study could enrich the research on pre-harvest sprouting and provide valuable information of marker exploration for wheat breeding programs.

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Fig. 1
Fig. 2

Abbreviations

FCGR:

First count germination ratio

GR:

Final germination ratio

GWAS:

Genome-wide association study

LD:

Linkage disequilibrium

MLM:

Mixed linear model

QTL:

Quantitative trait loci (locus)

RIL:

Recombinant inbred line

SNP:

Single nucleotide polymorphism

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Acknowledgements

The authors gratefully thank Xianchun Xia from the National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, for providing the wheat seeds of the RIL population and 166 common wheat accessions. This work was supported by the National Key Research and Development Program of China (2018YFD0100901), Chinese Academy of Sciences grant (XDA08010303) and the National Natural Science Foundation of China (31371242).

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Supplementary material 1 (DOCX 1404 kb) Table S1 QTL identified for first count germination ratio and final germination ratio in R17 environment in the RIL population comparing with previous reported pre-harvest sprouting-related QTL or genes. Table S2 Loci associated with first count germination ratio in the natural population comparing with previous reported pre-harvest sprouting-related QTL or genes.Table S3 Loci associated with final germination ratio in the natural population comparing with previous reported pre-harvest sprouting-related QTL or genes. Table S5 Putative candidate genes corresponding to the QTL associated with first count germination ratio. Table S6 Putative candidate genes corresponding to the QTL associated with final germination ratio. Fig. S1 Boxplot of t-test for comparing the first count germination ratio of fresh dormancy seed (SD) and after-ripened seeds (CK) of the RIL population (a) and 166 common wheat accessions (b). FCGR, first count germination ratio. Fig. S2 Frequency distributions of the RIL population for first count germination ratio (a) and final germination ratio (b) in R17 environment. FCGR, first count germination ratio; GR, final germination ratio; R17, Beijing 2017 of RIL population. Fig. S3 Frequency distributions of 166 common wheat accessions for first count germination ratio in G16 (a), first count germination ratio in G17 (b), final germination ratio in G16 (c) and final germination ratio in G17 (d) environments. FCGR, first count germination ratio; GR, final germination ratio. G16, Beijing 2016 of association panel; G17, Beijing 2017 of association panel. Fig. S4 Population structure and kinship analysis of 166 wheat accessions. (a) Three subgroups inferred by structure analysis; (b) principal components analysis (PCA) plots; (c) kinship plots for 166 wheat accessions. Fig. S5 Allele effects of QTL for wheat dormancy-related trait first count germination ratio in Zhou 8425B/Chinese Spring RIL population. FCGR, first count germination ratio. Fig. S6 Allele effects of QTL for wheat dormancy-related trait final germination ratio in Zhou 8425B/Chinese Spring RIL population. GR, final germination ratio. Fig. S7 Allele effects of loci for wheat dormancy-related trait first count germination ratio in 166 common wheat accessions. FCGR, first count germination ratio; A, pre-harvest sprouting-sensitive genotype; B, pre-harvest sprouting-resistant genotype. Fig. S8 Allele effects of loci for wheat dormancy-related trait germination ratio in 166 common wheat accessions. GR, final germination ratio; A, pre-harvest sprouting-sensitive genotype; B, pre-harvest sprouting-resistant genotype. Fig. S9 Linear regression between the number of favorable or unfavorable alleles in 166 common wheat accessions. a unfavorable alleles of first count germination ratio. b favorable alleles of first count germination ratio. c unfavorable alleles of final germination ratio. d favorable alleles of final germination ratio. FCGR, first count germination ratio; GR, final germination ratio

Supplementary material 2 (XLSX 17 kb) Table S4 The sequences of the markers closely linked or significantly associated with seed dormancy related traits

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Zuo, J., Lin, C., Cao, H. et al. Genome-wide association study and quantitative trait loci mapping of seed dormancy in common wheat (Triticum aestivum L.). Planta 250, 187–198 (2019). https://doi.org/10.1007/s00425-019-03164-9

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Keywords

  • 90K SNP array
  • Dormancy
  • Genome-wide association study (GWAS)
  • Quantitative trait loci (QTL) mapping
  • Pre-harvest sprouting