Linkage drag constrains the roots of modern wheat

Abstract

Roots, the hidden half of crop plants, are essential for resource acquisition. However, knowledge about the genetic control of below-ground plant development in wheat, one of the most important small-grain crops in the world, is very limited. The molecular interactions connecting root and shoot development and growth, and thus modulating the plant's demand for water and nutrients along with its ability to access them, are largely unexplored. Here, we demonstrate that linkage drag in European bread wheat, driven by strong selection for a haplotype variant controlling heading date, has eliminated a specific combination of two flanking, highly conserved haplotype variants whose interaction confers increased root biomass. Reversing this inadvertent consequence of selection could recover root diversity that may prove essential for future food production in fluctuating environments. Highly conserved synteny to rice across this chromosome segment suggests that adaptive selection has shaped the diversity landscape of this locus across different, globally important cereal crops. By mining wheat gene expression data, we identified root-expressed genes within the region of interest that could help breeders to select positive variants adapted to specific target soil environments.

Applying the latest advances in genomics and phenomics for trait discovery in polyploid wheat

“…Thus, we can benefit from years of available phenotypic data and selection to assess haplotype × environment interactions. This retrospective approach has highlighted, for example, how strong selection for flowering time has eliminated haplotypes for increased root biomass, a desirable trait (Voss‐Fels et al ., ). We can now use this knowledge to break these negative correlations by purposely generating haplotypes that combine both beneficial traits.…”

Linkage and association mapping reveals the genetic basis of brown fibre (Gossypium hirsutum)

“…A genomic inversion event around Lc 1 has been reported previously (Hinchliffe et al, 2016), which might cause the lower recombination rate. Such a long cosegregating region could easily cause linkage drag, which is disadvantageous in the modification of a target trait because of the unfavourable QTLs linked with the favourable gene (Voss-Fels et al, 2017). This finding will allow us to avoid genetic drag in the genetic improvement of brown fibre.…”

Association mapping and haplotype analysis of the pre-harvest sprouting resistance locusPhs-A1reveals a causal role ofTaMKK3-Ain global germplasm

“…Understanding haplotypes structure across genes of agronomic interest is increasingly possible with the latest advances in wheat genomics (Clavijo et al, 2017;Uauy, 2017). It is also increasingly relevant given potential negative linkage drag associated with major phenology traits (Voss-Fels et al, 2017). The markers and knowledge generated in this study should facilitate the choice of parental genotypes for the deployment of TaMKK3 in commercial cultivars.…”