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Genetic diversity and association mapping of agronomic yield traits in eighty six synthetic hexaploid wheat

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Abstract

Association mapping is a method to identify associations between target traits and genetic markers based on linkage disequilibrium (LD) of a quantitative trait locus. Synthetic hexaploid wheat (SHW) is derived from a cross between Triticum durum Desf. and Aegilops tauschii Coss. that enhances genetic diversity and broadens breeding resources. In this study, phenotypic diversity in 110 wheat accessions (86 SHW germplasm specimens and 24 conventional wheat varieties) was evaluated quantitatively for yield characteristics of grains per spike, thousand kernel weight, and spike length. Phenotypic data were collected over two years at two locations, and 1785 alleles were detected (mean 6.59), ranging from 3 to 11 alleles per locus. The average genetic diversity index was 0.749, with a range from 0.239 to 0.923. The polymorphic information content (PIC) ranged from 0.145 to 0.968, with a mean value of 0.695. The genetic diversity index and PIC indicated that genome B > D > A. Accessions were grouped into three subgroups based on STRUCTURE and unweighted pair-group with arithmetic mean clustering. The mean LD decay across the genome was 11.78 cM. Association mapping between traits and simple sequence repeat markers was performed using the generalized linear model approach. Forty-six SSR loci were significantly associated with the measured agronomic traits in two geographic locations. Together, these results broaden our knowledge of how to harness elite genes and genetic diversity in SHW in genomic and marker-assisted selection.

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Abbreviations

AFLP:

Amplified fragment length polymorphisms

AM:

Association mapping

ANOVA:

Analysis of variance

BIC:

Bayesian information criterion

Bp:

Base pair

CIMMYT:

International maize and wheat improvement center

cM:

Centimorgan

CTAB:

Cetyltrimethylammonium bromide

CW:

Conventional wheat

DNA:

Deoxyribonucleic acid

FSS:

No. of fertile spike per spike

Gb:

Giga base pairs

GLM:

Generalized linear model

GPS:

Grains per spike

GW:

Grain weight

GWAS:

Genome-wide association study

K:

Genetic relationship coefficient

Kb:

Kilo base pairs

LD:

Linkage disequilibrium

MLM:

Mixed linear model

PAGE:

Polyacrylamide gel electrophoresis

PCR:

Polymerase chain reaction

PH:

Plant height

PIC:

Polymorphic information content

Q:

Population structure

QTL:

Quantitative trait locus

SHW:

Synthetic hexaploid wheat

SL:

Spike length

SNP:

Single nucleotide polymorphism

SSR:

Simple sequence repeat

TKW:

Thousand kernel weight

UPGMA:

Unweighted pair-group with arithmetic mean

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Acknowledgements

This study was funded by the “948” program (2015-Z39) and Science and technology overall plan of Shaanxi Province (2016KTCQ02-02, K3320215198). We thank Dr Minqiang Tang and Xiaopeng Song for their help with data analyses, and Mr Kimberly for advice on manuscript preparation. The authors would like to thank reviewers for their valuable feedback on the manuscript, and Editage for their professional editing service.

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Authors and Affiliations

  1. Agricultural College, Northwest A&F University, Yangling, Shaanxi, China

    Hongxia Zhang, Fangning Zhang, Guidong Li, Sini Zhang, Zigang Zhang & Lingjian Ma

  2. School of Biological Science, University of Western Australia, Perth, Australia

    Fangning Zhang

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  1. Hongxia Zhang
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  2. Fangning Zhang
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  3. Guidong Li
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  4. Sini Zhang
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  5. Zigang Zhang
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Correspondence to Hongxia Zhang, Fangning Zhang or Lingjian Ma.

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Zhang, H., Zhang, F., Li, G. et al. Genetic diversity and association mapping of agronomic yield traits in eighty six synthetic hexaploid wheat. Euphytica 213, 111 (2017). https://doi.org/10.1007/s10681-017-1887-3

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