Molecular Breeding

, 38:91 | Cite as

Genome-wide association and validation of key loci for yield-related traits in wheat founder parent Xiaoyan 6

  • Feifei Ma
  • Yunfeng Xu
  • Zhengqiang Ma
  • Lihui Li
  • Diaoguo AnEmail author


Xiaoyan 6, one of the most important founder parents in wheat, possesses many superior agronomic traits and has played a crucial role in Chinese wheat breeding programs. In this study, a panel of 66 elite wheat accessions derived from Xiaoyan 6 was planted in four growing seasons; genome-wide association study (GWAS) was performed for six yield-related traits using the wheat 90K genotyping assay. A total of 803 significant marker-trait associations (MTAs) that explained up to 35.0% of the phenotypic variation were detected. Of these, the locus QTkw-5B which contains 19 MTAs for thousand kernel weight (TKW) was consistently detected in three growing seasons and confirmed in a recombinant inbred line (RIL) population by developing simple sequence repeats (SSR) and kompetitive allele-specific PCR (KASP) markers. The locus QPh-3A containing eight repetitive MTAs for plant height (PH) was consistently identified in all the four growing seasons and validated in a RIL population by developing SSR markers. The transmission of Xiaoyan 6 allele indicated that the favorite allele of QPh-3A was strongly selected in breeding programs. Comparing with previous studies, QTkw-5B and QPh-3A should be novel QTL. The locus QFss-2D for fertile spikelet number per spike (FSS) was identified and then validated in three bi-parental populations. This locus controlled various spike-related traits and may be a key spike polymorphic locus. This study could provide insight into dissecting yield-related traits in the breeding population and reliable molecular markers that might be valuable for marker-assisted selection in wheat high-yield breeding programs.


Founder parent GWAS Wheat 90K SNP assay Yield-related traits KASP markers Common wheat 



We are grateful to Prof. Aimin Zhang from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and Prof. Sishen Li from Shandong Agricultural University, for providing the XJ-RIL and ChSh-RIL populations, respectively. This research was financially supported by the National Key Research and Development Program of China (no. 2016YFD0100102), the National Natural Science Foundation of China (no. 31771787), and the National Basic Research Program of China (no. 2011CB100100).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

All of the authors have read and have abided by the statement of ethical standards for manuscripts submitted to Molecular Breeding.

Supplementary material

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Authors and Affiliations

  1. 1.Key Laboratory of Agricultural Water Resources & Hebei Key Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental BiologyChinese Academy of SciencesShijiazhuangChina
  2. 2.University of Chinese Academy of SciencesBeijingChina
  3. 3.The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural SciencesNanjing Agricultural UniversityNanjingChina
  4. 4.The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina

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