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

Author
item LI, GENQIAO - Oklahoma State University
item Bai, Guihua
item CARVER, BRETT - Oklahoma State University
item Elliott, Norman - Norm
item Bennett, Rebecca
item WU, YANQI - Oklahoma State University
item HUNGER, ROBERT - Oklahoma State University
item Bonman, John
item Xu, Xiangyang

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/27/2016
Publication Date: 1/26/2017
Citation: Li, G., Bai, G., Carver, B.F., Elliott, N.C., Bennett, R.S., Wu, Y., Hunger, R., Bonman, J.M., Xu, X. 2017. Genome-wide association study reveals genetic architecture of coleoptile length in wheat. Theoretical and Applied Genetics. 130(2):391-401.

Interpretive Summary: The wheat coleoptile length is critical for crop establishment in the low-precipitation dryland regions, where wheat cultivars with long coleoptiles are preferred. The objective of this study was to identify quantitative trait loci (QTL) for coleoptile length using genome-wide association study (GWAS), and find germplasm combining desirable traits for wheat breeding. A set of 893 landraces and historical cultivars was genotyped with 5,011 single nucleotide polymorphism (SNP) markers, and used in the GWAS. Eight QTLs for coleoptile length were identified in two years, and three of them are likely novel loci for coleoptile length. The coleoptile length was significantly associated with QTL number in each accession, suggesting that QTL pyramiding is an effective approach to increase wheat coleoptile length. Germplasm combining greater coleoptile length and shorter plant height were also identified, and these accessions can be used in wheat breeding.

Technical Abstract: Wheat cultivars with long coleoptiles are preferred in wheat growing regions where deep planting is practiced, whereas the wide use in wheat cultivars of GA-insensitive dwarfing genes, Rht-B1b and Rht-D1b, makes it a challenging task to breed dwarf wheat cultivars with long coleoptiles. To understand the genetic basis underlying coleoptile length, we performed a genome-wide association study on a set of 893 landraces and historical cultivars using 5,011 single nucleotide polymorphism (SNP) markers. Structure analysis revealed four subgroups in the association panel. Association analysis using a mixed linear model identified eight quantitative trait loci (QTLs) for coleoptile length, which explained 1.45 – 3.18% and 1.36 – 3.11% of the phenotypic variation in 2015 and 2016, respectively. The allelic substitution effects of these loci ranged from 0.31 to 1.75 cm in 2015, and 0.63 – 1.55 cm in 2016. Of these, three QTLs, including QCL.stars-2DS1, QCL.stars-1BS1 and QCL.stars-5BL1, are likely novel loci for coleoptile length. The favorable alleles in each accession ranged from 2 to 8 with an average of 5.8 at 8 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. Germplasm combining long coleoptile length and short plant height were also identified, and can be used in wheat breeding.