Genome‐wide association mapping for pre‐harvest sprouting in European winter wheat detects novel resistance QTL, pleiotropic effects, and structural variation in multiple genomes

Abstract

Pre‐harvest sprouting (PHS), germination of seeds before harvest, is a major problem in global wheat (Triticum aestivum L.) production, and leads to reduced bread‐making quality in affected grain. Breeding for PHS resistance can prevent losses under adverse conditions. Selecting resistant lines in years lacking pre‐harvest rain, requires challenging of plants in the field or in the laboratory or using genetic markers. Despite the availability of a wheat reference and pan‐genome, linking markers, genes, allelic, and structural variation, a complete understanding of the mechanisms underlying various sources of PHS resistance is still lacking. Therefore, we challenged a population of European wheat varieties and breeding lines with PHS conditions and phenotyped them for PHS traits, grain quality, phenological and agronomic traits to conduct genome‐wide association mapping. Furthermore, we compared these marker‐trait associations to previously reported PHS loci and evaluated their usefulness for breeding. We found markers associated with PHS on all chromosomes, with strong evidence for novel quantitative trait locus/loci (QTL) on chromosome 1A and 5B. The QTL on chromosome 1A lacks pleiotropic effect, for the QTL on 5B we detected pleiotropic effects on phenology and grain quality. Multiple peaks on chromosome 4A co‐located with the major resistance locus Phs‐A1, for which two causal genes, TaPM19 and TaMKK3, have been proposed. Mapping markers and genes to the pan‐genome and chromosomal alignments provide evidence for structural variation around this major PHS‐resistance locus. Although PHS is controlled by many loci distributed across the wheat genome, Phs‐A1 on chromosome 4A seems to be the most effective and widely deployed source of resistance, in European wheat varieties.

Assessing Falling Number Stability Increases the Genomic Prediction Ability of Pre-Harvest Sprouting Resistance in Common Winter Wheat

“…Similar effects were observed for FN2, but the average FN in each haplotype class changed across the seasons ( Figure S5 ), and the effects for these two markers diminished in the prediction model due to a lower number of field trials with PHS-conducive conditions in the season 2015/2016 ( Figure 4 ). This is in accordance with previous studies where Phs-A1 appeared as one of the major QTL explaining up to 50% of the phenotypic variation for PHS-related traits [ 44 , 45 ]. Our results from weighting Phs-A1 as a fixed effect in the prediction model clearly underline the importance of this locus.…”

“…Therefore, our study aimed at increasing the predictive accuracies by improving heritability through a better trait assessment independent of the weather conditions. In a recent study [ 44 ], PHS was assessed with the falling numbers after artificial rain and delayed harvest (FN2). Therefore, we compared FN2 with our in-house-established falling number stability test (FNS).…”

Exploring the genomics of abiotic stress tolerance and crop resilience to climate change

“…Despite the existence of a wheat reference and pangenome, a comprehensive understanding of the mechanisms governing different sources of PHS resistance remains limited. In this special section, Dallinger et al (2023) conducted a GWAS analysis and identified compelling evidence for novel QTLs associated with PHS resistance on chromosomes 1A and 5B. Several peaks on chromosome 4A were found to co-localize with the prominent resistance locus Phs-A1, containing causal genes TaPM19 and TaMKK3.…”

“…In this special section, Dallinger et al. (2023) conducted a GWAS analysis and identified compelling evidence for novel QTLs associated with PHS resistance on chromosomes 1A and 5B. Several peaks on chromosome 4A were found to co‐localize with the prominent resistance locus Phs‐A1 , containing causal genes TaPM19 and TaMKK3 .…”