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.

Fig 1. Photos of the parental accessions of the mapping populations.

(A) Spike phenotype of each parental accession. (B) Grain shape of the two subspecies.

Fig 2. Box and dot plots for the six spikelet-related traits based on the lineages and sublineages.

Welch’s t-test was conducted for statistical significance (***P < 0.001) of differences between the two lineages, TauL1 and TauL2. Sublineages sharing a common letter were not significantly different (Steel-Dwass test, P < 0.05). The tests were performed excluding TauL3 in the interlineage analyses and TauL1x and TauL2x in the intersublineage analyses because of the lack of statistical power. Red and black dots indicate the accessions of subspecies strangulata and tauschii, respectively.

Fig 3. Graph of the first three and two axes from two principal component analyses based on the six spikelet shape-related (A, B) and four grain shape-related (C) traits.

Fig 4. Box and dot plot comparison of grain shape between lineages and among sublineages of Ae. tauschii.

Welch’s t-test was conducted for statistical significance (***P < 0.001) of differences between the two lineages, TauL1 and TauL2. Multiplex comparison between the four sublineages was excluded because of the lack of statistical power. Red and black dots indicate the accessions of subspecies strangulata and tauschii, respectively.

Fig 5. Comparison of the QTL positions on the chromosomes 3D (A) and 4D (B) linkage maps between the three Ae. tauschii populations.

QTLs with LOD scores above the thresholds are indicated, and genetic distances are given in centimorgans. Gray boxes indicate putative centromeric regions.

Fig 6. Comparison of the QTL positions on the chromosome 7D linkage maps between the three Ae. tauschii populations.

QTLs with LOD scores above the thresholds are indicated, and genetic distances are given in centimorgans. Gray boxes indicate putative centromeric regions.

Fig 7. Genotypic effects of selected QTLs on spikelet-related traits in the KU-2078/PI499262 population.

The genotypes of QTLs were inferred from genotyping data in the marker intervals shown above each graph. Means ± SD with the same letter were not significantly different (P > 0.05, Tukey-Kramer HSD test).

Fig 8. Genotypic effects of selected QTLs on spikelet-related traits in the KU-2003/KU-2124 and PI476874/IG47182 populations.

The genotypes of QTLs were inferred from genotyping data in the marker intervals shown above each graph. Means ± SD with the same letter were not significantly different (P > 0.05, Tukey-Kramer HSD test).

Fig 9. Phenotypic effect of the genotype combinations on spikelet morphology.