The Haplotype-Based Analysis of Aegilops tauschii Introgression Into Hard Red Winter Wheat and Its Impact on Productivity Traits

Abstract

The introgression from wild relatives have a great potential to broaden the availability of beneficial allelic diversity for crop improvement in breeding programs. Here, we assessed the impact of the introgression from 21 diverse accessions of Aegilops tauschii, the diploid ancestor of the wheat D genome, into 6 hard red winter wheat cultivars on yield and yield component traits. We used 5.2 million imputed D genome SNPs identified by the whole-genome sequencing of parental lines and the sequence-based genotyping of introgression population, including 351 BC₁F_3:5 lines. Phenotyping data collected from the irrigated and non-irrigated field trials revealed that up to 23% of the introgression lines (ILs) produce more grain than the parents and check cultivars. Based on 16 yield stability statistics, the yield of 12 ILs (3.4%) was stable across treatments, years, and locations; 5 of these lines were also high yielding lines, producing 9.8% more grain than the average yield of check cultivars. The most significant SNP- and haplotype-trait associations were identified on chromosome arms 2DS and 6DL for the spikelet number per spike (SNS), on chromosome arms 2DS, 3DS, 5DS, and 7DS for grain length (GL) and on chromosome arms 1DL, 2DS, 6DL, and 7DS for grain width (GW). The introgression of haplotypes from A. tauschii parents was associated with an increase in SNS, which was positively correlated with a heading date (HD), whereas the haplotypes from hexaploid wheat parents were associated with an increase in GW. We show that the haplotypes on 2DS associated with an increase in the spikelet number and HD are linked with multiple introgressed alleles of Ppd-D1 identified by the whole-genome sequencing of A. tauschii parents. Meanwhile, some introgressed haplotypes exhibited significant pleiotropic effects with the direction of effects on the yield component traits being largely consistent with the previously reported trade-offs, there were haplotype combinations associated with the positive trends in yield. The characterized repertoire of the introgressed haplotypes derived from A. tauschii accessions with the combined positive effects on yield and yield component traits in elite germplasm provides a valuable source of alleles for improving the productivity of winter wheat by optimizing the contribution of component traits to yield.

Keywords: Aegilops tauschii; genotype imputation; grain yield; haplotypes; wheat; whole genome sequencing; wild relative introgression; yield component traits.

Figure 1

Boxplots comparing the mean grain yield (GY) between the top-performing introgression lines (ILs) and the controls (parents and checks) across treatments, years, and locations. AS20 refers to Ashland rainfed trial in 2020, CO18 is Colby rainfed trial in 2018, COI18 is Colby irrigated trial in 2018, CO19 is Colby rainfed trial in 2019, and COI19 is Colby irrigated trial in 2019.

Figure 2

Pearson's correlation coefficients between yield and yield component traits at Colby in 2018 rainfed trial (A) and Ashland in 2020 rainfed trial (B). Where HD, heading date; PH, plant height; BM, aboveground dry biomass; SPSF, spikes per square foot; SPB, spikes per bag; SNS, spikelet number per spike; GSW, grain sample weight; HI, harvest index; GN, grain number; TGW, 1,000 grain weight; GA, grain area; GW, grain width; GL, grain length; GY, grain yield.

Figure 3

Relationship between SNS (A,B), GL (C,D), GY (E,F), and the proportion of introgression under non-irrigated conditions at Colby in 2019 (CO19) and Ashland in 2020 (AS20). Here, r is the correlation coefficient and P is the significance of the correlation between introgression size and observed trait phenotype.

Figure 4

Manhattan plots showing the D genome loci with SNPs and haplotypes that are significantly associated with SNS at Ashland in 2020 (AS20) under rainfed conditions (A,B) and GL at Colby in 2018 (COI18) under irrigated conditions (C,D) in the Aegilops tauschii introgression population. The horizontal solid black line shows a threshold of 0.05 significance level for Bonferroni correction, the black arrowheads indicate the SNPs, and haplotypes above the threshold.

Figure 5

Effect of haplotypes introgressed from Ae. tauschii into the chromosome arms 2DS and 4DL of hexaploid wheat on the spikelet number per spike (SNS) and heading date (HD) of the introgression lines and the possible link to Ppd-D1 gene located on 2DS. (A) SNP table showing the haplotype variants at the Ppd-D1 gene locus in winter wheat accessions (top six) and the 21 Ae. tauschii lines. The black rectangle shows SNPs within the coding region of the gene where SN is a synonymous SNP, IN is an intronic SNP and MS is a missense SNP (His16Asn) as reported by snpEff v4.3 software. (B) Unique haplotypes in the introgression population tagging the Ppd-D1 locus and GWAS signal for SNS and HD on chromosome arm 2D, and the associated phenotype. Hap_HW is present in introgression lines that have Hap1 from hexaploid wheat at the Ppd-D1 locus, Hap_AeT includes lines that have Hap3–6 and 8 while Hap_AeT* includes lines that have Hap2 and Hap7 at the Ppd-D1 locus in Ae. tauschii parents. The TT and CA alleles at the GWAS signal have reducing and increasing effects, respectively, on SNS and HD. Phenotype means with the same superscript letters are not significantly different at α = 0.05. (C) Boxplot showing the impact of introgression from Ae. tauschii in chromosome arms 2DS and 4DL on SNS. (D) Boxplot showing the impact of introgression from Ae. tauschii in chromosome arms 2DS and 4DL on HD. (E) A Venn diagram showing the number of introgression lines in the 90th percentile for SNS and HD. Lines in the intersection have the increasing alleles on both 2DS and 4DL loci associated with SNS and HD. *** indicates significant difference between groups with p < 0.001 while NS indicates a nonsignificant difference based on t-test statistics.