Open AccessGenomic Selection in Wheat Breeding using Genotyping‐by‐Sequencing
Author(s) -
Poland Jesse,
Endelman Jeffrey,
Dawson Julie,
Rutkoski Jessica,
Wu Shuangye,
Manes Yann,
Dreisigacker Susanne,
Crossa José,
SánchezVilleda Héctor,
Sorrells Mark,
Jannink JeanLuc
Publication year - 2012
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2012.06.0006
Subject(s) - imputation (statistics) , biology , genotyping , molecular breeding , genomic selection , breeding program , genetics , genomics , marker assisted selection , genome , genetic gain , selection (genetic algorithm) , plant breeding , single nucleotide polymorphism , computational biology , genetic marker , genotype , statistics , missing data , genetic variation , gene , agronomy , computer science , mathematics , machine learning , cultivar
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.