Quantitative trait locus analysis for spikelet shape-related traits in wild wheat progenitor Aegilops tauschii: Implications for intraspecific diversification and subspecies differentiation

Abstract

Wild diploid wheat Aegilops tauschii, the D-genome progenitor of common wheat, carries large genetic variation in spikelet and grain morphology. Two differentiated subspecies of Ae. tauschii, subspecies tauschii and strangulata, have been traditionally defined based on differences in spikelet morphology. Here, we first assessed six spikelet shape-related traits among 199 Ae. tauschii accessions, and found that the accessions belonging to TauL1major lineage produced significantly longer spikes, higher spikelet density, and shorter, narrower spikelets than another major lineage, TauL2, in which the strangulata accessions are included. Next, we performed quantitative trait locus (QTL) analysis of the spikelet and grain shape using three mapping populations derived from interlineage crosses between TauL1 and TauL2 to identify the genetic loci for the morphological variations of the spikelet and grain shape in Ae. tauschii. Three major QTL regions for the examined traits were detected on chromosomes 3D, 4D and 7D. The 3D and 4D QTL regions for several spikelet shape-related traits were conserved in the three mapping populations, which indicated that the 3D and 4D QTLs contribute to divergence of the two major lineages. The 7D QTLs were found only in a mapping population from a cross of the two subspecies, suggesting that these 7D QTLs may be closely related to subspecies differentiation in Ae. tauschii. Thus, QTL analysis for spikelet and grain morphology may provide useful information to elucidate the evolutionary processes of intraspecific differentiation.

Dissection of Pleiotropic QTL Regions Controlling Wheat Spike Characteristics Under Different Nitrogen Treatments Using Traditional and Conditional QTL Mapping

“…On the right of each chromosomal region: the blue and green rectangles represent the QTL with positive alleles from KN9204 and J411, respectively; the letter C after parentheses represents the expression of QTL induced by N deficiency, and among them, C * represents the QTL (qFsn-7D) is a completely LN-stress induced QTL. Reference 1: (Nishijima et al, 2017); Reference 2: (Cuthbert et al, 2008); Reference 3: (Cui et al, 2017); Reference 4: (Heidari et al, 2011); Reference 5: (Zhang et al, 2017); Reference 6: (Fan et al, 2015); Reference 7: (Zhai et al, 2016); Reference 8: (Xu et al, 2014).…”

Genetic mapping of a novel recessive allele for non-glaucousness in wild diploid wheat Aegilops tauschii: implications for the evolution of common wheat

“…The subspecies strangulata accessions, defined by markedly moniliform spikes, are distributed only in a TauL2b and TauL2 admixture, and only one QTL region determining the distinct spikelet and grain morphology of the two Ae. tauschii subspecies, tauschii and strangulata, was mainly associated with the spikelet morphological divergence in TauL2 (Nishijima et al 2017). Therefore, Ae.…”

RNA-seq analysis reveals considerable genetic diversity and provides genetic markers saturating all chromosomes in the diploid wild wheat relative Aegilops umbellulata

“…The power of indel detection with RNA-seq is not as high as that of SNPs, because indels in exons often have functionally deleterious effects on proteins and are purged from the genome by purifying selection. Notwithstanding this disadvantage, RNA-seq still provides useful indel markers for genetic mapping [ 47 ]. The indel markers were effective for validating detection of F 1 alleles between Ae.…”