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Development of an integrated linkage map of einkorn wheat and its application for QTL mapping and genome sequence anchoring

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Abstract

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An integrated genetic map was constructed for einkorn wheat A genome and provided valuable information for QTL mapping and genome sequence anchoring.

Abstract

Wheat is one of the most widely grown food grain crops in the world. The construction of a genetic map is a key step to organize biologically or agronomically important traits along the chromosomes. In the present study, an integrated linkage map of einkorn wheat was developed using 109 recombinant inbred lines (RILs) derived from an inter sub-specific cross, KT1-1 (T. monococcum ssp. boeoticum) × KT3-5 (T. monococcum ssp. monococcum). The map contains 926 molecular markers assigned to seven linkage groups, and covers 1,377 cM with an average marker interval of 1.5 cM. A quantitative trait locus (QTL) analysis of five agronomic traits identified 16 stable QTL on all seven chromosomes, except 6A. The total phenotypic variance explained by these stable QTL using multiple regressions varied across environments from 8.8 to 87.1 % for days to heading, 24.4–63.0 % for spike length, 48.2–79.6 % for spikelet number per spike, 13.1–48.1 % for plant architecture, and 12.2–26.5 % for plant height, revealing that much of the RIL phenotypic variation had been genetically dissected. Co-localizations of closely linked QTL for different traits were frequently observed, especially on 3A and 7A. The QTL on 3A, 5A and 7A were closely associated with Eps-A m 3, Vrn1 and Vrn3 loci, respectively. Furthermore, this genetic map facilitated the anchoring of 237 T. urartu scaffolds onto seven chromosomes with a physical length of 26.15 Mb. This map and the QTL data provide valuable genetic information to dissect important agronomic and developmental traits in diploid wheat and contribute to the genetic ordering of the genome assembly.

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Abbreviations

AFLP:

Amplified fragment length polymorphism

ANOVA:

Analysis of variance

BAC:

Bacterial artificial chromosome

CIM:

Composite interval mapping

cM:

CentiMorgan

CTAB:

Hexadecyltrimethylammonium bromide

DArT:

Diversity arrays technology

EST:

Expressed sequence tag

HD:

Days to heading

LOD:

Logarithm of the odds

PA:

Plant architecture

PH:

Plant height

PVE:

Phenotypic variance

QTL:

Quantitative trait locus or loci

RIL:

Recombinant inbred line

RFLP:

Restriction fragment length polymorphism

SNP:

Single nucleotide polymorphism

SPL:

Spike length

SPLN:

Spikelet number per spike

SSR:

Simple sequence repeat

STS:

Sequence-tagged site

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Acknowledgments

We thank Dr. Jorge Dubcovsky and two anonymous reviewers for their helpful comments on this article, Dr. Muḥammad Sajjad (COMSATS Institute of Information Technology, Pakistan; Institute of Genetics and Developmental Biology, China) for reviewing this manuscript, and Chikako Shindo and Tetsuo Sasakuma (Kihara Institute for Biological Research/Graduate School of Integrated Science, Yokohama City University, Japan) for providing experimental materials used in this study. This work was supported by the Chinese Academy of Sciences (XDA08010104), and the Ministry of Science and Technology of China (2014CB138101, 2011AA100104).

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    1. State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, People’s Republic of China

      Kang Yu, Dongcheng Liu, Wenying Wu, Wenlong Yang, Jiazhu Sun, Xin Li, Hongqing Ling & Aimin Zhang

    2. Collaborative Innovation Center for Grain Crops in Henan, Henan Agricultural University, No. 95 Wenhua Road, Zhengzhou, Henan, 450002, People’s Republic of China

      Kehui Zhan, Dangqun Cui & Aimin Zhang

    3. Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Fragrant Hill, Beijing, 100093, People’s Republic of China

      Kang Yu & Chunming Liu

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    1. Kang Yu
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    Communicated by J. Dubcovsky.

    Kang Yu and Dongcheng Liu have contributed equally to this work.

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    Yu, K., Liu, D., Wu, W. et al. Development of an integrated linkage map of einkorn wheat and its application for QTL mapping and genome sequence anchoring. Theor Appl Genet 130, 53–70 (2017). https://doi.org/10.1007/s00122-016-2791-2

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