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.

Genome-Wide Association Study Uncovers Novel Genomic Regions Associated With Coleoptile Length in Hard Winter Wheat

“…Based on the threshold value of -log10 (p-value) > 3, we identified 14, 1, 1, 2, 18, 6, and 4 significant SNPs on chromosomes 2A (QCL.sdsu-2AS), 2B (QCL.sdsu-2BS), 2D (QCL.sdsu-2DS), 3B (QCL.sdsu-3BS), 4B (QCL.sdsu-4BS and QCL.sdsu-4BL), 5B (QCL.sdsu-5BL), and 6B (QCL.sdsu-6BL), respectively ( Figure 2). Like previous studies (Rebetzke et al, 2007a;Rebetzke et al, 2014;Li et al, 2017), we also found Rht-B1, a Gibberelin (GA) insensitive dwarf allele to be associated with coleoptile length. Out of 298 genotypes, 201 (67.4%) carried the dwarf allele (allele 2) and 84 (28.2%) carried the tall allele (allele 1) of Rht-B1.…”

“…Molecular markers linked to genes or quantitative trait loci (QTLs) can facilitate simultaneous marker-assisted breeding and pyramiding for several traits, avoiding laborious and timeconsuming phenotyping. Recently, a few QTL mapping studies in spring wheat have mapped several QTLs that control coleoptile length on chromosomes 1A, 1B, 1D, 2B, 2D, 3A, 3B, 3D, 4A, 4BS (Rht-B1b), 4DS (Rht-D1b), 5A, 5B, 5D, 6A, 6B, and 7B (Rebetzke et al, 2007a;Spielmeyer et al, 2007;Yu and Bai, 2010;Rebetzke et al, 2014;Singh et al, 2015;Li et al, 2017) However, linkage mapping studies have lower power in identifying QTLs with smaller effect and typically demarcate the QTLs to large genomic regions of 15-20 cM (Tuberosa et al, 2002;Korte and Farlow, 2013).…”

“…Nearly all previous studies (Spielmeyer et al, 2007;Yu and Bai, 2010;Rebetzke et al, 2014;Singh et al, 2015) consistently mapped QTLs close to Rht-B1b and Rht-D1b, however, the diverse populations used in those studies led to the identification of distinct novel loci; on chromosomes 1B, 3D, 4DL, and 5AS using a Chinese wheat variety (Yu and Bai, 2010); on chromosomes 1D, 3A, 6A, and 7B using a population derived from Australian cultivars (Spielmeyer et al, 2007;Rebetzke et al, 2014); on chromosomes 3BS and 3BL using Indian cultivars (Singh et al, 2015); and on chromosomes 1BS, 2DS, 4BS, and 5BL using diverse 893 accessions collected from around the world (Li et al, 2017). This suggests that there are a number of QTLs for coleoptile length and therefore, the potential of utilizing these distinct loci in the development of varieties suitable to specific regions.…”

“…Further, GWAS can effectively identify many natural allelic variations in a large set of unrelated individuals as compared to the traditional QTL mapping (Huang and Han, 2014). Li et al (2017) conducted GWAS using a global wheat collection of 893 accessions and identified two major QTLs for coleoptile length. These two QTLs are present on chromosome 4B and 4D, independent of Rht-B1b and Rht-D1b respectively, but their physical locations are unknown.…”

Exploring natural diversity of Medicago truncatula reveals physiotypes and loci associated with the response of seedling performance to nitrate supply

“…Most QTL (quantitative trait locus) studies on seedling heterotrophic performance were based on traditional linkage mapping using bi‐parental populations either in crop species (Bettey et al 2000, Lee et al 2001, Limami et al 2002, Finch‐Savage et al 2010, Rebetzke et al 2014), or in our previous studies in M. truncatula (Dias et al 2011, Vandecasteele et al 2011, Youssef et al 2016). Few were based on GWAS analyses (Li et al 2016, in wheat). Despite the potential of plant natural diversity, it is an underused resource for physiological and genetic (QTL) studies regarding seedling establishment.…”