title: Genome-wide association study reveals genetic architecture of coleoptile length in wheat.
abstract: 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. 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.
authors.affiliation: USDA-ARS Wheat, Peanut, and Other Field Crops Research Unit, Stillwater, Oklahoma, USA.|Plant and Soil Science Department, Oklahoma State University, Stillwater, Oklahoma, USA.
authors.forename: Genqiao
authors.initials: G
authors.lastname: Li
authors.affiliation: USDA-ARS Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, USA.
authors.forename: Guihua
authors.initials: G
authors.lastname: Bai
authors.affiliation: Plant and Soil Science Department, Oklahoma State University, Stillwater, Oklahoma, USA.
authors.forename: Brett F
authors.initials: BF
authors.lastname: Carver
authors.affiliation: USDA-ARS Wheat, Peanut, and Other Field Crops Research Unit, Stillwater, Oklahoma, USA.
authors.forename: Norman C
authors.initials: NC
authors.lastname: Elliott
authors.affiliation: USDA-ARS Wheat, Peanut, and Other Field Crops Research Unit, Stillwater, Oklahoma, USA.
authors.forename: Rebecca S
authors.initials: RS
authors.lastname: Bennett
authors.affiliation: Plant and Soil Science Department, Oklahoma State University, Stillwater, Oklahoma, USA.
authors.forename: Yanqi
authors.initials: Y
authors.lastname: Wu
authors.affiliation: Entomology and Plant Pathology Department, Oklahoma State University, Stillwater, Oklahoma, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Hunger
authors.affiliation: USDA-ARS Small Grains and Potato Germplasm Research Unit, Aberdeen, Idaho, USA.
authors.forename: J Michael
authors.initials: JM
authors.lastname: Bonman
authors.affiliation: USDA-ARS Wheat, Peanut, and Other Field Crops Research Unit, Stillwater, Oklahoma, USA. xiangyang.xu@ars.usda.gov.
authors.forename: Xiangyang
authors.identifier: http://orcid.org/0000-0002-1364-7941
authors.initials: X
authors.lastname: Xu
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D018548:Cotyledon / Q000254:growth & development*; D056726:Genetic Association Studies; D005828:Genetics, Population; D005838:Genotype; D015810:Linkage Disequilibrium; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D014908:Triticum / Q000235:genetics* / Q000254:growth & development