Genome-wide association study and quantitative trait loci mapping of seed dormancy in common wheat (Triticum aestivum L.)
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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.
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.
Keywords90K SNP array Dormancy Genome-wide association study (GWAS) Quantitative trait loci (QTL) mapping Pre-harvest sprouting
First count germination ratio
Final germination ratio
Genome-wide association study
Mixed linear model
Quantitative trait loci (locus)
Recombinant inbred line
Single nucleotide polymorphism
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).
Compliance with ethical standards
Conflict of interest
We declare no conflict of interest in regard to this manuscript.
We declare that these experiments comply with the ethical standards in China.
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