title: Genomic Prediction of Gene Bank Wheat Landraces.
abstract: This study examines genomic prediction within 8416 Mexican landrace accessions and 2403 Iranian landrace accessions stored in gene banks. The Mexican and Iranian collections were evaluated in separate field trials, including an optimum environment for several traits, and in two separate environments (drought, D and heat, H) for the highly heritable traits, days to heading (DTH), and days to maturity (DTM). Analyses accounting and not accounting for population structure were performed. Genomic prediction models include genotype × environment interaction (G × E). Two alternative prediction strategies were studied: (1) random cross-validation of the data in 20% training (TRN) and 80% testing (TST) (TRN20-TST80) sets, and (2) two types of core sets, "diversity" and "prediction", including 10% and 20%, respectively, of the total collections. Accounting for population structure decreased prediction accuracy by 15-20% as compared to prediction accuracy obtained when not accounting for population structure. Accounting for population structure gave prediction accuracies for traits evaluated in one environment for TRN20-TST80 that ranged from 0.407 to 0.677 for Mexican landraces, and from 0.166 to 0.662 for Iranian landraces. Prediction accuracy of the 20% diversity core set was similar to accuracies obtained for TRN20-TST80, ranging from 0.412 to 0.654 for Mexican landraces, and from 0.182 to 0.647 for Iranian landraces. The predictive core set gave similar prediction accuracy as the diversity core set for Mexican collections, but slightly lower for Iranian collections. Prediction accuracy when incorporating G × E for DTH and DTM for Mexican landraces for TRN20-TST80 was around 0.60, which is greater than without the G × E term. For Iranian landraces, accuracies were 0.55 for the G × E model with TRN20-TST80. Results show promising prediction accuracies for potential use in germplasm enhancement and rapid introgression of exotic germplasm into elite materials.
authors.affiliation: Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico j.crossa@cgiar.org suk.singh@cgiar.org.
authors.forename: José
authors.identifier: 0000-0001-9429-5855
authors.initials: J
authors.lastname: Crossa
authors.affiliation: Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 321 Keim Hall, Lincoln, Nebraska 68583-0915.
authors.forename: Diego
authors.initials: D
authors.lastname: Jarquín
authors.affiliation: Departamento de Biometría, Estadística y Computación, Facultad de Agronomía, Universidad de la República (Udelar), Paysandú, Uruguay.
authors.forename: Jorge
authors.initials: J
authors.lastname: Franco
authors.affiliation: Colegio de Post-Graduados, Montecillos, Edo. de Mexico, 56230 Mexico.
authors.forename: Paulino
authors.initials: P
authors.lastname: Pérez-Rodríguez
authors.affiliation: Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico.
authors.forename: Juan
authors.initials: J
authors.lastname: Burgueño
authors.affiliation: Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico.
authors.forename: Carolina
authors.initials: C
authors.lastname: Saint-Pierre
authors.affiliation: Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico.
authors.forename: Prashant
authors.initials: P
authors.lastname: Vikram
authors.affiliation: Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico.
authors.forename: Carolina
authors.initials: C
authors.lastname: Sansaloni
authors.affiliation: Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico.
authors.forename: Cesar
authors.initials: C
authors.lastname: Petroli
authors.affiliation: Department of Plant Breeding & Genetics, Cornell University, Ithaca, New York 14853.
authors.forename: Deniz
authors.initials: D
authors.lastname: Akdemir
authors.affiliation: Department of Horticulture and Crop Science, Ohio State University, Wooster, Ohio 44691.
authors.forename: Clay
authors.initials: C
authors.lastname: Sneller
authors.affiliation: Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico.
authors.forename: Matthew
authors.initials: M
authors.lastname: Reynolds
authors.affiliation: Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico.
authors.forename: Maria
authors.initials: M
authors.lastname: Tattaris
authors.affiliation: Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico.
authors.forename: Thomas
authors.initials: T
authors.lastname: Payne
authors.affiliation: Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico.
authors.forename: Carlos
authors.initials: C
authors.lastname: Guzman
authors.affiliation: Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico.
authors.forename: Roberto J
authors.initials: RJ
authors.lastname: Peña
authors.affiliation: Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico.
authors.forename: Peter
authors.initials: P
authors.lastname: Wenzl
authors.affiliation: Genetic Resources Program and the Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), 06600, Mexico, DF, Mexico j.crossa@cgiar.org suk.singh@cgiar.org.
authors.forename: Sukhwinder
authors.initials: S
authors.lastname: Singh
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D055864:Droughts; D059647:Gene-Environment Interaction; D018745:Genome, Plant; D005838:Genotype; D006358:Hot Temperature; D007492:Iran; D008800:Mexico; D008957:Models, Genetic; D015233:Models, Statistical; D010641:Phenotype; D019655:Quantitative Trait, Heritable; D012641:Selection, Genetic; D013312:Stress, Physiological; D014908:Triticum / Q000145:classification / Q000235:genetics*
keywords: A × E: accession × environment interaction; GenPred; Gene bank accessions; cross-validations; genomic prediction; genomic selection; reference core subsets; shared data resources