Genomic prediction of synthetic hexaploid wheat upon tetraploid durum and diploid Aegilops parental pools.

Abstract

Bread wheat (Triticum aestivum L.) is a globally important food crop, which was domesticated about 8-10,000 years ago. Bread wheat is an allopolyploid, and it evolved from two hybridization events of three species. To widen the genetic base in breeding, bread wheat has been re-synthesized by crossing durum wheat (Triticum turgidum ssp. durum) and goat grass (Aegilops tauschii Coss), leading to so-called synthetic hexaploid wheat (SHW). We applied the quantitative genetics tools of "hybrid prediction"-originally developed for the prediction of wheat hybrids generated from different heterotic groups - to a situation of allopolyploidization. Our use-case predicts the phenotypes of SHW for three quantitatively inherited global wheat diseases, namely tan spot (TS), septoria nodorum blotch (SNB), and spot blotch (SB). Our results revealed prediction abilities comparable to studies in 'traditional' elite or hybrid wheat. Prediction abilities were highest using a marker model and performing random cross-validation, predicting the performance of untested SHW (0.483 for SB to 0.730 for TS). When testing parents not necessarily used in SHW, combination prediction abilities were slightly lower (0.378 for SB to 0.718 for TS), yet still promising. Despite the limited phenotypic data, our results provide a general example for predictive models targeting an allopolyploidization event and a method that can guide the use of genetic resources available in gene banks.

Plant phenotyping relevance

遺伝マーカーから作物病害表現型を予測するモデルを中心的に適用・評価しており、植物の病害状態を推定する計算的フェノタイピング手法に該当する。

Code and data availability

The article's data availability statement points to a public CIMMYT repository deposit containing the paper's own phenotypic (tan spot, septoria nodorum blotch, spot blotch) and genotypic datasets, matching the allowed handle URL. No author analysis code or trained model deposit is stated.