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Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding

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Abstract

Key message

Genetic diversity, population structure, LD decay, and selective sweeps in 687 wheat accessions were analyzed, providing relevant guidelines to facilitate the use of the germplasm in wheat breeding.

Abstract

Common wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Landraces were subjected to strong human-mediated selection in developing high-yielding, good quality, and widely adapted cultivars. To investigate the genome-wide patterns of allelic variation, population structure and patterns of selective sweeps during modern wheat breeding, we tested 687 wheat accessions, including landraces (148) and cultivars (539) mainly from China and Pakistan in a wheat 90 K single nucleotide polymorphism array. Population structure analysis revealed that cultivars and landraces from China and Pakistan comprised three relatively independent genetic clusters. Cultivars displayed lower nucleotide diversity and a wider average LD decay across whole genome, indicating allelic erosion and a diversity bottleneck due to the modern breeding. Analysis of genetic differentiation between landraces and cultivars from China and Pakistan identified allelic variants subjected to selection during modern breeding. In total, 477 unique genome regions showed signatures of selection, where 109 were identified in both China and Pakistan germplasm. The majority of genomic regions were located in the B genome (225), followed by the A genome (175), and only 77 regions were located in the D genome. EigenGWAS was further used to identify key selection loci in modern wheat cultivars from China and Pakistan by comparing with global winter wheat and spring wheat diversity panels, respectively. A few known functional genes or loci found within these genome regions corresponded to known phenotypes for disease resistance, vernalization, quality, adaptability and yield-related traits. This study uncovered molecular footprints of modern wheat breeding and explained the genetic basis of polygenic adaptation in wheat. The results will be useful for understanding targets of modern wheat breeding, and in devising future breeding strategies to target beneficial alleles currently not pursued.

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Abbreviations

CL:

Chinese landraces

CMC:

Chinese modern cultivars

FMC:

Foreign modern cultivars

F ST :

F-statistics

GWAS:

Genome-wide association study

IWGSC:

International Wheat Genome Sequencing Consortium

LD:

Linkage disequilibrium

MAF:

Minor allele frequency

MAS:

Marker-assisted selection

NJ:

Neighbor-joining

PCA:

Principal components analysis

PL:

Pakistan landraces

PMC:

Pakistan modern cultivars

SNP:

Single nucleotide polymorphism

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Acknowledgements

We thank Prof. R. A. McIntosh, at Plant Breeding Institute, University of Sydney, for reviewing this manuscript. We are grateful to Dr. Huihui Li, at CAAS, for the help in statistical analysis. We acknowledge the Triticeae Toolbox (http://triticeaetoolbox.org; T3) for 90K data availability used in this manuscript. This work was funded by the National Natural Science Foundation of China (31461143021, 31550110212), the National Key Research and Development Program of China (2016YFD0101802, 2016YFE0108600, 2014BAD01B05), and CAAS Science and Technology Innovation Program.

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Author notes

  1. Jindong Liu and Awais Rasheed contributed equally to this work.

Authors and Affiliations

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

    Jindong Liu, Awais Rasheed, Zhonghu He, Weie Wen & Xianchun Xia

  2. Department of Plant Genetics and Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China

    Jindong Liu & Chaojie Xie

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

    Awais Rasheed & Zhonghu He

  4. Quaid-i-Azam University, Islamabad, Pakistan

    Awais Rasheed & Tariq Mahmood

  5. International Maize and Wheat Improvement Center (CIMMYT) Pakistan Office, c/o National Agriculture Research Center (NARC), Islamabad, Pakistan

    Muhammad Imtiaz

  6. National Institute of Agriculture and Biology (NIAB), Faisalabad, Pakistan

    Anjuman Arif

  7. Bio-resources Conservation Institute (BCI), National Agriculture Research Center (NARC), Islamabad, Pakistan

    Abdul Ghafoor, Sadar Uddin Siddiqui & Muhammad Kashif Ilyas

  8. Crop Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, China

    Fengmei Gao

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  1. Jindong Liu
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Correspondence to Xianchun Xia.

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Communicated by Gary Muehlbauer.

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Liu, J., Rasheed, A., He, Z. et al. Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding. Theor Appl Genet 132, 2509–2523 (2019). https://doi.org/10.1007/s00122-019-03367-4

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