title: Genomic and pedigree-based prediction for leaf, stem, and stripe rust resistance in wheat.
abstract: Genomic prediction for seedling and adult plant resistance to wheat rusts was compared to prediction using few markers as fixed effects in a least-squares approach and pedigree-based prediction. The unceasing plant-pathogen arms race and ephemeral nature of some rust resistance genes have been challenging for wheat (Triticum aestivum L.) breeding programs and farmers. Hence, it is important to devise strategies for effective evaluation and exploitation of quantitative rust resistance. One promising approach that could accelerate gain from selection for rust resistance is 'genomic selection' which utilizes dense genome-wide markers to estimate the breeding values (BVs) for quantitative traits. Our objective was to compare three genomic prediction models including genomic best linear unbiased prediction (GBLUP), GBLUP A that was GBLUP with selected loci as fixed effects and reproducing kernel Hilbert spaces-markers (RKHS-M) with least-squares (LS) approach, RKHS-pedigree (RKHS-P), and RKHS markers and pedigree (RKHS-MP) to determine the BVs for seedling and/or adult plant resistance (APR) to leaf rust (LR), stem rust (SR), and stripe rust (YR). The 333 lines in the 45th IBWSN and the 313 lines in the 46th IBWSN were genotyped using genotyping-by-sequencing and phenotyped in replicated trials. The mean prediction accuracies ranged from 0.31-0.74 for LR seedling, 0.12-0.56 for LR APR, 0.31-0.65 for SR APR, 0.70-0.78 for YR seedling, and 0.34-0.71 for YR APR. For most datasets, the RKHS-MP model gave the highest accuracies, while LS gave the lowest. GBLUP, GBLUP A, RKHS-M, and RKHS-P models gave similar accuracies. Using genome-wide marker-based models resulted in an average of 42% increase in accuracy over LS. We conclude that GS is a promising approach for improvement of quantitative rust resistance and can be implemented in the breeding pipeline.
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Philomin
authors.initials: P
authors.lastname: Juliana
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, DF, Mexico.
authors.forename: Ravi P
authors.initials: RP
authors.lastname: Singh
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, DF, Mexico.
authors.forename: Pawan K
authors.initials: PK
authors.lastname: Singh
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, DF, Mexico.
authors.forename: Jose
authors.initials: J
authors.lastname: Crossa
authors.affiliation: Campo Experimental Valle de México INIFAP, 56230, Chapingo, Edo, de México, Mexico.
authors.forename: Julio
authors.initials: J
authors.lastname: Huerta-Espino
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, DF, Mexico.
authors.forename: Caixia
authors.initials: C
authors.lastname: Lan
authors.affiliation: CIMMYT, ICRAF House, United Nations Avenue, Gigiri, Village Market, Nairobi, 00621, Kenya.
authors.forename: Sridhar
authors.initials: S
authors.lastname: Bhavani
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.|International Maize and Wheat Improvement Center (CIMMYT), Apdo, Postal 6-641, 06600, Mexico, DF, Mexico.
authors.forename: Jessica E
authors.initials: JE
authors.lastname: Rutkoski
authors.affiliation: Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Kansas State University, Manhattan, KS, 66506, USA.
authors.forename: Jesse A
authors.initials: JA
authors.lastname: Poland
authors.affiliation: Plant Pathology and Plant-microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA.
authors.forename: Gary C
authors.initials: GC
authors.lastname: Bergstrom
authors.affiliation: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA. mes12@cornell.edu.
authors.forename: Mark E
authors.initials: ME
authors.lastname: Sorrells
mesh_terms: D001487:Basidiomycota; D060467:Disease Resistance / Q000235:genetics*; D005819:Genetic Markers; D023281:Genomics / Q000379:methods; D005838:Genotype; D016014:Linear Models; D008957:Models, Genetic; D010641:Phenotype; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D040641:Quantitative Trait Loci; D014908:Triticum / Q000235:genetics* / Q000382:microbiology
chemical_list: D005819:Genetic Markers