Abstract
SummaryTo feed an ever‐increasing population we must leverage advances in genomics and phenotyping to harness the variation in wheat breeding populations for traits like photosynthetic capacity which remains unoptimized. Here we survey a diverse set of wheat germplasm containing elite, introgression and synthetic derivative lines uncovering previously uncharacterized variation. We demonstrate how strategic integration of exotic material alleviates the D genome genetic bottleneck in wheat, increasing SNP rate by 62% largely due to Ae. tauschii synthetic wheat donors. Across the panel, 67% of the Ae. tauschii donor genome is represented as introgressions in elite backgrounds. We show how observed genetic variation together with hyperspectral reflectance data can be used to identify candidate genes for traits relating to photosynthetic capacity using association analysis. This demonstrates the value of genomic methods in uncovering hidden variation in wheat and how that variation can assist breeding efforts and increase our understanding of complex traits.
Highlights
Bread wheat occurred through hybridisation of domesticated emmer with diploid goat grass, Ae
We developed a 12-Mb target sequence using the MyBaits system based on that described by Gardiner et al, 20183, where underperforming baits were replaced with baits targeting genes associated with photosynthesis and biomass accumulation
A T-test comparing the elite and exotic subpopulation showed no significant differences between the number of reads nor the number of bp that were mapped to ≥5x coverage between populations
Summary
Bread wheat occurred through hybridisation of domesticated emmer with diploid goat grass, Ae. This event is thought to have occurred very few times in nature, integrating very few Tauschii donors and resulting in a genetic bottleneck in D genome diversity[2] This lack of diversity has been identified in multiple populations, using capture enrichment[3] and whole genome resequencing[4] where variation rate in the A/B genomes was >4-fold higher than the D genome. In addition to providing diversity for wheat breeders, this genetic diversity can be used to unpick the genetic basis of the traits measured at CIMMYT year on year We demonstrate this by investigating phenotypic variation in spectral indices that are related to three classes of traits: (i) thermal/hydration properties measured in the infrared part of the electromagnetic spectrum, (ii) pigment related indices assessed in visible bands[18] and (iii) photosynthesis related indices derived from the whole spectra[19,20] in the High Biomass Association Panel (HiBAP). Previous work has uncovered multiple marker trait associations (MTAs) related to RUE and biomass accumulation at various phenological stages 22 and demonstrated a link between RUE and photoprotection
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