Combining Traditional Mutagenesis with New High-Throughput Sequencing and Genome Editing to Reveal Hidden Variation in Polyploid Wheat

Abstract

Induced mutations have been used to generate novel variation for breeding purposes since the early 1900s. However, the combination of this old technology with the new capabilities of high-throughput sequencing has resulted in powerful reverse genetic approaches in polyploid crops. Sequencing genomes or exomes of large mutant populations can generate extensive databases of mutations for most genes. These mutant collections, together with genome editing, are being used in polyploid species to combine mutations in all copies of a gene (homoeologs), and to expose phenotypic variation that was previously hidden by functional redundancy among homoeologs. This redundancy is more extensive in recently formed polyploids such as wheat, which can now benefit from the deployment of useful recessive mutations previously identified in its diploid relatives. Sequenced mutant populations and genome editing have changed the paradigm of what is possible in functional genetic analysis of wheat.

Identification of phytic acid mutants in oilseed rape (Brassica napus) by large‐scale screening of mutant populations through amplicon sequencing

“…Since transgenic technologies are not available to breeders in many parts of the world due to legal constraints, mutation breeding has become an interesting alternative. Moreover, polyploid B. napus tolerates a high mutation load, which gave rise to numerous mutants with altered agronomical traits (Harloff et al , ; Uauy et al , ).…”

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

“…During domestication and breeding, humans have selected most frequently for dominant gain‐of‐function mutations given their strong, easily identifiable phenotypic effects. These include genes with major effects on phenology and adaptation traits as described above, as well as most disease resistance genes (Uauy et al ., ). In contrast, the effects of recessive loss‐of‐function mutations in a single homoeolog are frequently masked by functional redundancy and dosage effects (Figure ).…”

“…As a result, screening more than one mutation per gene might be necessary as predicting the functional effects of missense mutations is not always easy a priori . Similarly, use of the TILLING lines typically requires multiple iterations of crossing, first to combine mutations across homoeologs of the gene of interest and secondly to reduce background mutations (Krasileva et al ., ; Uauy et al ., ). Typically, for quantitative traits, phenotypes are clearer with successive backcross generations (Simmonds et al ., ).…”

A reductionist approach to dissecting grain weight and yield in wheat

“…While important as an initial step towards defining the commonality across species and for use in breeding, in most cases further functional validation would be warranted. This could be achieved using multiple independent mutants (Uauy et al ), now available in silico (Krasileva et al ), or gene‐edited or transgenic lines with the appropriate modification for each case.…”