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Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers

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Abstract

Key message

We identified 21 new and stable QTL, and 11 QTL clusters for yield-related traits in three bread wheat populations using the wheat 90 K SNP assay.

Abstract

Identification of quantitative trait loci (QTL) for yield-related traits and closely linked molecular markers is important in order to identify gene/QTL for marker-assisted selection (MAS) in wheat breeding. The objectives of the present study were to identify QTL for yield-related traits and dissect the relationships among different traits in three wheat recombinant inbred line (RIL) populations derived from crosses Doumai × Shi 4185 (D × S), Gaocheng 8901 × Zhoumai 16 (G × Z) and Linmai 2 × Zhong 892 (L × Z). Using the available high-density linkage maps previously constructed with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, 65, 46 and 53 QTL for 12 traits were identified in the three RIL populations, respectively. Among them, 34, 23 and 27 were likely to be new QTL. Eighteen common QTL were detected across two or three populations. Eleven QTL clusters harboring multiple QTL were detected in different populations, and the interval 15.5–32.3 cM around the Rht-B1 locus on chromosome 4BS harboring 20 QTL is an important region determining grain yield (GY). Thousand-kernel weight (TKW) is significantly affected by kernel width and plant height (PH), whereas flag leaf width can be used to select lines with large kernel number per spike. Eleven candidate genes were identified, including eight cloned genes for kernel, heading date (HD) and PH-related traits as well as predicted genes for TKW, spike length and HD. The closest SNP markers of stable QTL or QTL clusters can be used for MAS in wheat breeding using kompetitive allele-specific PCR or semi-thermal asymmetric reverse PCR assays for improvement of GY.

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Abbreviations

BLUE:

Best linear unbiased estimation

FLL:

Flag leaf length

FLW:

Flag leaf width

GY:

Grain yield

GWAS:

Genome-wide association study

h 2 :

Broad-sense heritability

HD:

Heading date

KASP:

Kompetitive allele-specific PCR

KL:

Kernel length

KNS:

Kernel number per spike

KW:

Kernel width

LOD:

Logarithm of odds

MAS:

Marker-assisted selection

PH:

Plant height

QTL:

Quantitative trait loci

R 2 :

Phenotypic variance explained

RIL:

Recombinant inbred line

SDW:

Spike dry weight

SL:

Spike length

SN:

Spike number per unit area

SNP:

Single nucleotide polymorphism

STARP:

Semi-thermal asymmetric reverse PCR

TKW:

Thousand-kernel weight

UIL:

Uppermost internode length

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Acknowledgements

The authors are grateful to Prof. R. A. McIntosh, Plant Breeding Institute, University of Sydney, for critical review of this manuscript. This work was funded by the National Natural Science Foundation of China (31461143021), National Key Research and Development Programs of China (2016YFD0101802, 2016YFD0100502, 2016YFE0108600), and CAAS Science and Technology Innovation Program.

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Author notes

  1. Faji Li and Weie Wen have contributed equally to this work.

Authors and Affiliations

  1. College of Agronomy, Xinjiang Agricultural University, Ürümqi, 830052, Xinjiang, China

    Faji Li, Weie Wen & Hongwei Geng

  2. Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China

    Faji Li, Weie Wen, Zhonghu He, Jindong Liu, Hui Jin, Shuanghe Cao & Xianchun Xia

  3. International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China

    Zhonghu He

  4. Sino-Russia Agricultural Scientific and Technological Cooperation Center, Heilongjiang Academy of Agricultural Sciences, 368 Xuefu Street, Harbin, 150086, Heilongjiang, China

    Hui Jin

  5. Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), 38 Huanghe Street, Anyang, 455000, Henan, China

    Jun Yan

  6. Crop Research Institute, Anhui Academy of Agricultural Sciences, 40 Nongke South Street, Hefei, 230001, Anhui, China

    Pingzhi Zhang & Yingxiu Wan

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  1. Faji Li
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  2. Weie Wen
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Contributions

FL performed the experiment and wrote the paper; WW participated in the field trials and constructed the linkage maps; JL, HJ, JY, PZ and YW participated in the field trials; SC and HG assisted in writing the paper; ZH and XX designed the experiment and wrote the paper. All authors read the final version of the manuscript and approved for publication.

Corresponding author

Correspondence to Xianchun Xia.

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Conflict of interest

All authors declare that they have no conflict of interests.

Ethical standards

We declare that these experiments complied with the ethical standards in China.

Additional information

Communicated by Susanne Dreisigacker.

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Li, F., Wen, W., He, Z. et al. Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers. Theor Appl Genet 131, 1903–1924 (2018). https://doi.org/10.1007/s00122-018-3122-6

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  • DOI: https://doi.org/10.1007/s00122-018-3122-6

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