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A 55 K SNP array-based genetic map and its utilization in QTL mapping for productive tiller number in common wheat

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A high-density genetic map constructed with a wheat 55 K SNP array was highly consistent with the physical map of this species and it facilitated the identification of a novel major QTL for productive tiller number.

Abstract

Productive tiller number (PTN) plays a key role in wheat grain yield. In this study, a recombinant inbred line population with 199 lines derived from a cross between ‘20828’ and ‘Chuannong16’ was used to construct a high-density genetic map using wheat 55 K single nucleotide polymorphism (SNP) array. The constructed genetic map contains 12,109 SNP markers spanning 3021.04 cM across the 21 wheat chromosomes. The orders of the genetic and physical positions of these markers are generally in agreement, and they also match well with those based on the 660 K SNP array from which the one used in this study was derived. The ratios of SNPs located in each of the wheat deletion bins were similar among the wheat 9 K, 55 K, 90 K, 660 K and 820 K SNP arrays. Based on the constructed maps, a novel major quantitative trait locus QPtn.sau-4B for PTN was detected across multi-environments in a 0.55 cM interval on 4B and it explained 17.23–45.46% of the phenotypic variance. Twenty common genes in the physical interval between the flanking markers were identified on chromosome 4B of ‘Chinese Spring’ and wild emmer. These results indicate that wheat 55 K SNP array could be an ideal tool in primary mapping of target genes and the identification of QPtn.sau-4B laid a foundation for the following fine mapping and cloning work.

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Acknowledgements

This work is supported by the National Natural Science Foundation of China (31570335 and 31601292), the International Science and Technology Cooperation and Exchanges Program of Science and Technology Department of Sichuan Province (2017HH0076), the Applied Basic Research Programs of Science and Technology Department of Sichuan Province (2016JY0010). We thank the International Wheat Genome Sequencing Consortium (IWGSC) for allowing us to access to the online data. We thanks Yujie Yang for technical support in figure drawing.

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  1. Jiajun Liu and Wei Luo have contributed equally to this paper.

Authors and Affiliations

  1. Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China

    Jiajun Liu, Wei Luo, Nana Qin, Puyang Ding, Han Zhang, Congcong Yang, Yang Mu, Huaping Tang, Yaxi Liu, Qiantao Jiang, Guoyue Chen, Yuming Wei, Youliang Zheng, Xiujin Lan & Jian Ma

  2. College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China

    Wei Li

  3. Commonwealth Scientific and Industrial Research Organization Agriculture and Food, St Lucia, QLD, 4067, Australia

    Chunji Liu

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  1. Jiajun Liu
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Correspondence to Xiujin Lan or Jian Ma.

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All experiments and data analyses were conducted in Sichuan, and the 55 K SNP genotype was done in Beijing, China. All authors have contributed to the study and approved the version for submission. The manuscript has not been submitted to any other journal.

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Communicated by Peter Langridge.

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Liu, J., Luo, W., Qin, N. et al. A 55 K SNP array-based genetic map and its utilization in QTL mapping for productive tiller number in common wheat. Theor Appl Genet 131, 2439–2450 (2018). https://doi.org/10.1007/s00122-018-3164-9

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