Identification of eight QTL controlling multiple yield components in a German multi-parental wheat population, including Rht24, WAPO-A1, WAPO-B1 and genetic loci on chromosomes 5A and 6A

Abstract

Quantitative trait locus (QTL) mapping of 15 yield component traits in a German multi-founder population identified eight QTL each controlling ≥2 phenotypes, including the genetic loci Rht24, WAPO-A1 and WAPO-B1. Grain yield in wheat (Triticum aestivum L.) is a polygenic trait representing the culmination of many developmental processes and their interactions with the environment. Toward maintaining genetic gains in yield potential, 'reductionist approaches' are commonly undertaken by which the genetic control of yield components, that collectively determine yield, are established. Here we use an eight-founder German multi-parental wheat population to investigate the genetic control and phenotypic trade-offs between 15 yield components. Increased grains per ear was significantly positively correlated with the number of fertile spikelets per ear and negatively correlated with the number of infertile spikelets. However, as increased grain number and fertile spikelet number per ear were significantly negatively correlated with thousand grain weight, sink strength limitations were evident. Genetic mapping identified 34 replicated quantitative trait loci (QTL) at two or more test environments, of which 24 resolved into eight loci each controlling two or more traits-termed here 'multi-trait QTL' (MT-QTL). These included MT-QTL associated with previously cloned genes controlling semi-dwarf plant stature, and with the genetic locus Reduced height 24 (Rht24) that further modulates plant height. Additionally, MT-QTL controlling spikelet number traits were located to chromosome 7A encompassing the gene WHEAT ORTHOLOG OF APO1 (WAPO-A1), and to its homoeologous location on chromosome 7B containing WAPO-B1. The genetic loci identified in this study, particularly those that potentially control multiple yield components, provide future opportunities for the targeted investigation of their underlying genes, gene networks and phenotypic trade-offs, in order to underpin further genetic gains in yield.

Fig. 1

Correlations between the 15 traits measured in the BMWpop grown in field trials undertaken in the United Kingdom in 2017 and 2018 (UK17 and UK 18) and in Germany in 2018 (DE18). Trait abbreviations: EL (ear length), EW (ear width), NFSP (number of fertile spikelets per ear), NISP (number of infertile spikelets per ear), totNSP (total number of spikelets per ear), NS.NE (number of seeds per ear), WS.EW (seed weight/ear weight ratio), SA (seed area), SWI (seed width), SL (seed length), FFD (factor form density), SL.SWI (seed length/seed width ratio), FT (flowering time), HT (plant height)

Fig. 2

The genetic map locations of quantitative trait loci (QTL) identified in the BMWpop grown in field trials undertaken in the United Kingdom in 2017 and 2018 (UK17 and UK 18) and in Germany in 2018 (DE18) using interval mapping and composite interval mapping. Multi-trait QTL (MT-QTL) are also included, and are shown in red. ‘Strong’ QTL, classified as those with -log10p-values higher than the trait-specific p = 0.05 significance thresholds determined by permutation are indicated by solid bars. ‘Weak’ QTL, classified as those with -log₁₀p-values less than the permutated p = 0.05 significance threshold but with -log₁₀p > 3 and which explain ≥ 5% of the phenotypic variation, are indicated by bars with diagonal lines. The BMWpop genetic map is previously published (Stadlmeier et al. 2018)

Fig. 3

Analysis of the effects of haplotypes WAPO-A1.hap1 WAPO-A1.hap2 at the multi-trait QTL QMtqtl.lfl-7A.1controlling spikelet number traits on chromosome 7A. Allelic state at SNP wsnp_JD_c20555_18262317, located six gene models from WAPO-A1 in the wheat reference genome (RefSeq v1.0, gene model build RefSeq v1.2; IWGSC 2018), was found to be in phase with the two WAPO-A1 haplotypes present in the eight BMWpop founders. This SNP was therefore used group the BMWpop recombinant inbred lines (RILs) for each of the three traits for which QTL co-located at QMtqtl.lfl-7A.1: (a) ‘number of fertile spikelets’, (b) ‘number of infertile spikelets’, and (c) ‘ear length’. For each of these traits, the meta-analysis best linear unbiased estimates (BLUEs) were used for haplotype analysis. The trait values for all 394 BMWpop RILs are shown on the left in red. The significance of the differences between haplotypes was determined by Wilcoxon test (p < 0.05)

Fig. 4

The BMWpop multi-trait QTL QMtqtl.lfl-7B.1 and details of the underlying candidate gene, WAPO-B1. (a) QTL on chromosome 7B identified in trials conducted in the United Kingdom in 2017 (UK17) and 2018 (UK18) for the trait ‘total number of spikelets’, one of the three traits with co-locating QTL at QMtqtl.lfl-7B.1. Results of composite interval mapping with five covariates are shown (note, while the significance of the QTL is inflated relative to the results of interval mapping without the inclusion of covariates shown in Supplementary Table 6, the definition of the QTL intervals is improved and so is used here). (b) Location on the chromosome 7B physical map (RefSeq v1.0; IWGSC 2018) of the peak SNP marker (AX.94949800, in gene model TraesCS7B02G386400) identified at QTL for ‘total number of spikelets’ in trials UK17 and UK18. (c) the location WAPO-B1 (TraesCS7B02G384000) on the physical map, 24 high-confidence gene models from the peak SNP identified by QTL mapping. (d) WAPO-B1 haplotypes, based on the DNA variants identified by comparing sequences from the wheat reference genome assembly (IWGSC 2018) with those from 15 additional hexaploid wheat lines with sequenced genomes (Walkowiak et al. 2020). The positions of the 17 DNA variants that define the haplotypes are as detailed in Supplementary Table 8b, with changes in the DNA and amino acid sequences from that of the reference sequence of cv. Chinese Spring indicated in red. The 5 bp insertion (1) / deletion (d) in exon-1 present in WAPO-B1.hap3 is indicated, and leads to a frame shift (grey) that spans the F-box domain and a subsequent premature stop codon (red asterisk). Sequencing the 1,893 bp region indicated by the dashed horizontal black line in seven of the eight BMWpop founders allowed allocation as WAPO-B1.hap1 (Ambition, Bussard, Event, Format and BAY4535, all of which carried the low spikelet number allele, designated here WAPO-B1a) or WAPO-B1.hap2 (Julius and Potenzial, allele WAPO-B1b); WAPO-B1 haplotype in the founder Firl3565 is currently undetermined as we were unable to amplify the gene. Of the five SNPs that differentiated the two WAPO-B1 haplotypes in the seven BMWpop founders, two lead to alterations of the predicted protein in WAPO-B1.hap2. The first was an A + 140/G SNP that results in a H/47R amino acid substitution in a highly non-conserved region of the protein (alignment shown in Supplementary Fig. 6). The second was a G + 517/T SNP resulting in an A173/S amino acid substitution, (e) located in a highly conserved region of the protein, based on alignment of 56 proteins from 53 plant species. (f) Haplotype analysis at the QMtqtl.lfl-7B.1 locus in the BMWpop recombinant inbred lines (RILs). Haplotypes were constructed using three SNPs: Tdurum_contig81911_179, Kukri_c12901_706 and AX.94949800 (the peak marker from the meta-analyses for ‘number of fertile spikelets’ and ‘total number of spikelets’), located at RefSeq v1.0 positions 646,037,877, 646,063,954 and 651,340,580 bp, respectively. Haplotype `000’ (representing the combination of the allele calls at each of the three SNPs) tags the low spikelet WAPO-B1a allele (Ambition, Bussard, Event, Format, BAYP4535) while haplotype `222′ tags the high spikelet WAPO-B1b allele (Julius and Potenzial, as well as Firl3565). All BMWpop RILs carried haplotypes `000′ or `222′, except for two lines carrying haplotype ‘002′ which were excluded for the purposes of the analysis presented here. (g) WAPO-A1, -B1 and -D1 gene expression in the apical meristem at different stages of development, measured as transcripts per million reads (TPM), sourced from Li et al. (2018b). Apical meristem developmental stages included are numbered in developmental order: 1 = vegetative, 2 = elongation, 3 = single ridge, 4 = double ridge, 5 = glume primordium, 6 = floret differentiation. At stage 4, the meristem has transitioned from the vegetative to reproductive stage