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

Abstract

Summary Improving traits in wheat has historically been challenging due to its large and polyploid genome, limited genetic diversity and in‐field phenotyping constraints. However, within recent years many of these barriers have been lowered. The availability of a chromosome‐level assembly of the wheat genome now facilitates a step‐change in wheat genetics and provides a common platform for resources, including variation data, gene expression data and genetic markers. The development of sequenced mutant populations and gene‐editing techniques now enables the rapid assessment of gene function in wheat directly. The ability to alter gene function in a targeted manner will unmask the effects of homoeolog redundancy and allow the hidden potential of this polyploid genome to be discovered. New techniques to identify and exploit the genetic diversity within wheat wild relatives now enable wheat breeders to take advantage of these additional sources of variation to address challenges facing food production. Finally, advances in phenomics have unlocked rapid screening of populations for many traits of interest both in greenhouses and in the field. Looking forwards, integrating diverse data types, including genomic, epigenetic and phenomics data, will take advantage of big data approaches including machine learning to understand trait biology in wheat in unprecedented detail.

Identification of Transcription Factors Regulating Senescence in Wheat through Gene Regulatory Network Modelling

“…This adds further weight to the hypothesis that the RWP-RK TFs may play a role in senescence, in addition to their known role in nitrogen responses (Chardin et al, 2014). The roles of these identified TFs can now be directly tested in wheat to determine whether they regulate senescence using gene editing and TILLING (Borrill et al, 2019).…”

From genome to phenome: genome‐wide association studies and other approaches that bridge the genotype to phenotype gap

“…Borrill et al . () review how the discovery of traits in crops with challenging complex genomes, such as hexaploidy wheat, has been significantly improved by recent advances in comparative genomics (Dvorak et al ., ) and in‐field phenotyping. They describe how the development of sequenced mutant populations and targeted gene‐editing (Gil‐Humanes et al ., ) is enabling the rapid assessment of gene function in these species.…”

Variance heterogeneity genome-wide mapping for cadmium in bread wheat reveals novel genomic loci and epistatic interactions

“…Further, we observed a potential vQTL region on 2D from the DGLM and HGLM analyses. This region was slightly below the significance threshold level but may have an implication on Cd variation given that the allopolyploid nature of wheat and the role of homoeologous gene sets on phenotypic variation (Borrill et al, 2019).…”

“…This also indicates that genetic complexity of Cd phenotype is not only controlled by multiple genes but may be affected by the multiple homoeologs of the individual genes which warrants further investigation. Presence of multiple copies of homoeologous genes may have consequence on phenotypic variation due to dosage effects and or functional redundancy (Borrill et al, 2019). Dosage effect, in which the phenotypic variation is amplified by the addition of each gene copies can act additively (e.g., genes controlling grain protein content (Avni et al, 2014) and grain size (Wang et al, 2018)) or non-additively (e.g., genes controlling amylopectin content in wheat (Kim et al, 2003)).…”