title: Genomic prediction in biparental tropical maize populations in water-stressed and well-watered environments using low-density and GBS SNPs.
abstract: One of the most important applications of genomic selection in maize breeding is to predict and identify the best untested lines from biparental populations, when the training and validation sets are derived from the same cross. Nineteen tropical maize biparental populations evaluated in multienvironment trials were used in this study to assess prediction accuracy of different quantitative traits using low-density (~200 markers) and genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs), respectively. An extension of the Genomic Best Linear Unbiased Predictor that incorporates genotype × environment (GE) interaction was used to predict genotypic values; cross-validation methods were applied to quantify prediction accuracy. Our results showed that: (1) low-density SNPs (~200 markers) were largely sufficient to get good prediction in biparental maize populations for simple traits with moderate-to-high heritability, but GBS outperformed low-density SNPs for complex traits and simple traits evaluated under stress conditions with low-to-moderate heritability; (2) heritability and genetic architecture of target traits affected prediction performance, prediction accuracy of complex traits (grain yield) were consistently lower than those of simple traits (anthesis date and plant height) and prediction accuracy under stress conditions was consistently lower and more variable than under well-watered conditions for all the target traits because of their poor heritability under stress conditions; and (3) the prediction accuracy of GE models was found to be superior to that of non-GE models for complex traits and marginal for simple traits.
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico.
authors.forename: X
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Colegio de Postgraduados, Montecillo, Estado de Mexico, Mexico.
authors.forename: P
authors.initials: P
authors.lastname: Pérez-Rodríguez
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya.
authors.forename: K
authors.initials: K
authors.lastname: Semagn
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya.
authors.forename: Y
authors.initials: Y
authors.lastname: Beyene
authors.affiliation: CIMMYT-India, c/o ICRISAT, Andhra Pradesh, India.
authors.forename: R
authors.initials: R
authors.lastname: Babu
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico.
authors.forename: M A
authors.initials: MA
authors.lastname: López-Cruz
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico.
authors.forename: F
authors.initials: F
authors.lastname: San Vicente
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico.
authors.forename: M
authors.initials: M
authors.lastname: Olsen
authors.affiliation: USDA Agricultural Research Service, Cornell University, Ithaca, NY, USA.
authors.forename: E
authors.initials: E
authors.lastname: Buckler
authors.affiliation: USDA Agricultural Research Service, Cornell University, Ithaca, NY, USA.
authors.forename: J-L
authors.initials: JL
authors.lastname: Jannink
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya.
authors.forename: B M
authors.initials: BM
authors.lastname: Prasanna
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico.
authors.forename: J
authors.initials: J
authors.lastname: Crossa
mesh_terms: D001947:Breeding; D059647:Gene-Environment Interaction; D023281:Genomics / Q000379:methods*; D005838:Genotype; D008957:Models, Genetic; D015233:Models, Statistical; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D019655:Quantitative Trait, Heritable; D013312:Stress, Physiological; D014867:Water / Q000502:physiology; D003313:Zea mays / Q000235:genetics*
chemical_list: D014867:Water