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Genome-wide association study of phosphorus-deficiency-tolerance traits in Aegilops tauschii

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Abstract

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Using GWAS, 13 significant SNPs distributed on six of the seven Aegilops tauschii chromosomes (all but 5D) were identified, and several candidate P-deficiency-responsive genes were proposed from searches of public databases.

Abstract

Aegilops tauschii, the wheat (Triticum aestivum) D-genome progenitor, possesses numerous genes for stress resistance, including genes for tolerance of phosphorus (P) deficiency. Investigation of the genetic architecture of A. tauschii will help in developing P-deficiency-tolerant varieties of wheat. We evaluated nine traits in a population of 380 A. tauschii specimens under conditions with and without P application, and we performed genome-wide association studies for these traits using single nucleotide polymorphism (SNP) chips containing 7185 markers. Using a general linear model, we identified 119 SNPs that were significantly associated with all nine traits, and a mixed linear model revealed 18 SNPs associated with all traits. Both models detected 13 significant markers distributed on six of the seven A. tauschii chromosomes (all but 5D). Searches of public databases revealed several candidate/flanking genes related to P-deficiency tolerance. These genes were grouped in five categories by the types of proteins they encoded: defense response proteins, enzymes, promoters and transcription factors, storage proteins, or proteins triggered by P deficiency. The identified SNPs and genes contain essential information for cloning genes related to P-deficiency tolerance in A. tauschii and wheat, and they provide a foundation for breeding P-deficiency tolerant wheat cultivars.

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Abbreviations

AM:

Association mapping

AP:

Applied phosphorus

BLAST:

Basic local alignment search tool

CV:

Coefficient of variation

DH:

Double haploid

DNA:

Deoxyribose nucleic acid

GLM:

General linear model

GWAS:

Genome wide association study

IWGSC:

International Wheat Genome Sequencing Consortium

LD:

Linkage disequilibrium

MAF:

Minor allele frequency

MCMC:

Markov Chain Monte Carlo

MLM:

Mixed linear model

MTAs:

Marker trait associations

NAP:

No-applied phosphorus

NCBI:

National Center for Biotechnology Information

P:

Phosphorus

PDTI:

Phosphorus deficiency tolerance index

PTs:

Phosphate transporters

QTL:

Quantitative trait loci R/S, root to shoot ratio

RDM:

Root diameter

RDW:

Root dry weight

RF:

Root forks

RIL:

Recombinant inbred line

RL:

Root length

RSA:

Root surface area

RT:

Root tips

SDW:

Shoot dry weight

SNP:

Single nucleotide polymorphism

TDW:

Total dry weight

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Acknowledgments

We thank Assad Siham (ICARDA, Syria), Jon W. Raupp (Kansas State University, USA), Shuhei Nasuda (Komugi, Japan) and Harold Bockelman (USDA, USA) for plant materials. This work was supported by the International Science and Technology Cooperation Program of China (No. 2015DFA30600), the National Basic Research Program of China (2014CB147200), and the National Natural Science Foundation of China (31301317, 31171555).

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

      Yaxi Liu, Lang Wang, Mei Deng, Zhanyi Li, Jirui Wang, Yuming Wei & Youliang Zheng

    2. Maize Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China

      Yanli Lu

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    1. Yaxi Liu
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    2. Lang Wang
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    3. Mei Deng
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    4. Zhanyi Li
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    Correspondence to Youliang Zheng.

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    Communicated by M. J. Sillanpaa.

    Y. Liu and L. Wang contributed equally to this work.

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    Liu, Y., Wang, L., Deng, M. et al. Genome-wide association study of phosphorus-deficiency-tolerance traits in Aegilops tauschii . Theor Appl Genet 128, 2203–2212 (2015). https://doi.org/10.1007/s00122-015-2578-x

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