Crop genome‐wide association study: a harvest of biological relevance

Abstract

Summary With the advent of rapid genotyping and next‐generation sequencing technologies, genome‐wide association study (GWAS) has become a routine strategy for decoding genotype–phenotype associations in many species. More than 1000 such studies over the last decade have revealed substantial genotype–phenotype associations in crops and provided unparalleled opportunities to probe functional genomics. Beyond the many ‘hits’ obtained, this review summarizes recent efforts to increase our understanding of the genetic architecture of complex traits by focusing on non‐main effects including epistasis, pleiotropy, and phenotypic plasticity. We also discuss how these achievements and the remaining gaps in our knowledge will guide future studies. Synthetic association is highlighted as leading to false causality, which is prevalent but largely underestimated. Furthermore, validation evidence is appealing for future GWAS, especially in the context of emerging genome‐editing technologies.

The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition

“…In arabidopsis ( Arabidopsis thaliana ) these genes are involved in calcium transport, which corresponds with evidence that Ca 2+ plays an important role in storage‐induced increases in common bean's required cooking time (Jones & Boulter, ). Similar to major crops (Liu & Yan, ), there is clearly high future potential for the further application of genome‐wide association scans to dissect quantitative traits for new and orphan crops, if appropriate resources are allocated to phenotyping.…”

“…that Ca 2+ plays an important role in storage-induced increases in common bean's required cooking time (Jones & Boulter, 1983). Similar to major crops (Liu & Yan, 2019), there is clearly high future potential for the further application of genome-wide association scans to dissect quantitative traits for new and orphan crops, if appropriate resources are allocated to phenotyping. Genomic selection (Meuwissen et al, 2001) uses phenotypic and genomic data collected from training populations to predict the breeding value of genome-characterised but unphenotyped breeding materials (known as genomic estimated breeding values).…”

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

“…The first article in this collection, by Liu and Yan (), reviews the advances that GWAS has played in illuminating the genotype–phenotype associations of several crop species. The article highlights aspects from more than 1000 GWAS in crops that have been published within the last decade – revealing both advantages and limitations of the approach, as well as emphasizing the importance of phenotypic plasticity and epistasis.…”

A global barley panel revealing genomic signatures of breeding in modern cultivars

“…Underlying population structure is known to be a confounding factor in GWASs, particularly for adaptive traits such as flowering time [16]. Known sources of population structure in domesticated barley varieties include the separation of two-row and six-row barleys, which occurred early in domestication (∼8,000 years ago), as well as the separation of spring and winter barleys, which accelerated the migration of barley through the modification of the vernalisation requirement and photoperiod response [17, 18].…”