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Genome-wide association study reveals genetic architecture of coleoptile length in wheat

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Abstract

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Eight QTL for coleoptile length were identified in a genome-wide association study on a set of 893 wheat accessions, four of which are novel loci.

Abstract

Wheat cultivars with long coleoptiles are preferred in wheat-growing regions where deep planting is practiced. However, the wide use of gibberellic acid (GA)-insensitive dwarfing genes, Rht-B1b and Rht-D1b, makes it challenging to breed dwarf wheat cultivars with long coleoptiles. To understand the genetic basis of coleoptile length, we performed a genome-wide association study on a set of 893 landraces and historical cultivars using 5011 single nucleotide polymorphism (SNP) markers. Structure analysis revealed four subgroups in the association panel. Association analysis results suggested that Rht-B1b and Rht-D1b genes significantly reduced coleoptile length, and eight additional quantitative trait loci (QTL) for coleoptile length were also identified. These QTL explained 1.45–3.18 and 1.36–3.11% of the phenotypic variation in 2015 and 2016, respectively, and their allelic substitution effects ranged from 0.31 to 1.75 cm in 2015, and 0.63–1.55 cm in 2016. Of the eight QTL, QCL.stars-1BS1, QCL.stars-2DS1, QCL.stars-4BS2, and QCL.stars-5BL1 are likely novel loci for coleoptile length. The favorable alleles in each accession ranged from two to eight with an average of 5.8 at eight loci in the panel, and more favorable alleles were significantly associated with longer coleoptile, suggesting that QTL pyramiding is an effective approach to increase wheat coleoptile length.

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Abbreviations

FDR:

False discovery rate

GWAS:

Genome-wide association study

LD:

Linkage disequilibrium

LnP(D):

Log probability of data

MAGIC:

Multiparent advanced generation intercross

MLM:

Mixed linear model

NSGC:

National Small Grains Collection

PCR:

Polymerase chain reaction

QTL:

Quantitative trait loci

SNP:

Single-nucleotide polymorphism

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Authors and Affiliations

  1. USDA-ARS Wheat, Peanut, and Other Field Crops Research Unit, Stillwater, Oklahoma, USA

    Genqiao Li, Norman C. Elliott, Rebecca S. Bennett & Xiangyang Xu

  2. USDA-ARS Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, USA

    Guihua Bai

  3. Plant and Soil Science Department, Oklahoma State University, Stillwater, Oklahoma, USA

    Genqiao Li, Brett F. Carver & Yanqi Wu

  4. Entomology and Plant Pathology Department, Oklahoma State University, Stillwater, Oklahoma, USA

    Robert Hunger

  5. USDA-ARS Small Grains and Potato Germplasm Research Unit, Aberdeen, Idaho, USA

    J. Michael Bonman

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  1. Genqiao Li
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  2. Guihua Bai
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  4. Norman C. Elliott
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  8. J. Michael Bonman
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  9. Xiangyang Xu
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Correspondence to Xiangyang Xu.

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Communicated by S. Dreisigacker.

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Li, G., Bai, G., Carver, B.F. et al. Genome-wide association study reveals genetic architecture of coleoptile length in wheat. Theor Appl Genet 130, 391–401 (2017). https://doi.org/10.1007/s00122-016-2820-1

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