TY - JOUR
T1 - Genomic selection in wheat breeding using genotyping-by-sequencing
AU - Poland, Jesse
AU - Endelman, Jeffrey
AU - Dawson, Julie
AU - Rutkoski, Jessica
AU - Wu, Shuangye
AU - Manes, Yann
AU - Dreisigacker, Susanne
AU - Crossa, José
AU - Sánchez-Villeda, Héctor
AU - Sorrells, Mark
AU - Jannink, Jean Luc
N1 - Generated from Scopus record by KAUST IRTS on 2022-09-13
PY - 2012/12/1
Y1 - 2012/12/1
N2 - 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. WiThGBS 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 signifi cant differences were observed in the accuracy of genomic-estimated breeding values (GEBVs) among imputation methods. Genomic-estimated breeding value prediction accuracies wiThGBS 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-bysequencing 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. © Crop Science Society of America.
AB - 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. WiThGBS 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 signifi cant differences were observed in the accuracy of genomic-estimated breeding values (GEBVs) among imputation methods. Genomic-estimated breeding value prediction accuracies wiThGBS 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-bysequencing 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. © Crop Science Society of America.
UR - https://onlinelibrary.wiley.com/doi/10.3835/plantgenome2012.06.0006
UR - http://www.scopus.com/inward/record.url?scp=84878537188&partnerID=8YFLogxK
U2 - 10.3835/plantgenome2012.06.0006
DO - 10.3835/plantgenome2012.06.0006
M3 - Article
SN - 1940-3372
VL - 5
SP - 103
EP - 113
JO - Plant Genome
JF - Plant Genome
IS - 3
ER -