Genomic Selection in Wheat Breeding using Genotyping‐by‐Sequencing

TLDR

Genomic selection uses genomewide markers to predict breeding values before phenotyping, and genotyping‑by‑sequencing provides marker discovery and genotyping for large populations without a reference genome, making it well suited for breeding. The study demonstrates that genotyping‑by‑sequencing can be used for de novo genotyping of wheat breeding panels and to develop accurate genomic‑selection models in the large, complex, polyploid wheat genome. Four imputation methods—including random forest regression and a new multivariate‑normal expectation‑maximization algorithm—were evaluated on unmapped markers; the EM algorithm improved marker‑level imputation accuracy, though all methods produced similar genomic‑estimated breeding‑value accuracies. GBS identified 41,371 SNPs in 254 CIMMYT breeding lines and achieved grain‑yield GEBV accuracies of 0.28–0.45, 0.1–0.2 higher than an established marker platform, underscoring its flexibility and low cost as an ideal genomics‑assisted breeding tool.

Abstract

Genomic selection (GS) uses genomewide molecular markers to predict breeding values and make selections of individuals or breeding lines prior to phenotyping. Here we show that genotyping‐by‐sequencing (GBS) can be used for de novo genotyping of breeding panels and to develop accurate GS models, even for the large, complex, and polyploid wheat ( Triticum aestivum L.) genome. With GBS we discovered 41,371 single nucleotide polymorphisms (SNPs) in a set of 254 advanced breeding lines from CIMMYT's semiarid wheat breeding program. Four different methods were evaluated for imputing missing marker scores in this set of unmapped markers, including random forest regression and a newly developed multivariate‐normal expectation‐maximization algorithm, which gave more accurate imputation than heterozygous or mean imputation at the marker level, although no significant differences were observed in the accuracy of genomic‐estimated breeding values (GEBVs) among imputation methods. Genomic‐estimated breeding value prediction accuracies with GBS were 0.28 to 0.45 for grain yield, an improvement of 0.1 to 0.2 over an established marker platform for wheat. Genotyping‐by‐sequencing combines marker discovery and genotyping of large populations, making it an excellent marker platform for breeding applications even in the absence of a reference genome sequence or previous polymorphism discovery. In addition, the flexibility and low cost of GBS make this an ideal approach for genomics‐assisted breeding.