title: An efficient hierarchical generalized linear mixed model for mapping QTL of ordinal traits in crop cultivars.
abstract: Many important phenotypic traits in plants are ordinal. However, relatively little is known about the methodologies for ordinal trait association studies. In this study, we proposed a hierarchical generalized linear mixed model for mapping quantitative trait locus (QTL) of ordinal traits in crop cultivars. In this model, all the main-effect QTL and QTL-by-environment interaction were treated as random, while population mean, environmental effect and population structure were fixed. In the estimation of parameters, the pseudo data normal approximation of likelihood function and empirical Bayes approach were adopted. A series of Monte Carlo simulation experiments were performed to confirm the reliability of new method. The result showed that new method works well with satisfactory statistical power and precision. The new method was also adopted to dissect the genetic basis of soybean alkaline-salt tolerance in 257 soybean cultivars obtained, by stratified random sampling, from 6 geographic ecotypes in China. As a result, 6 main-effect QTL and 3 QTL-by-environment interactions were identified.
authors.affiliation: Section on Statistical Genomics, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Department of Crop Genetics and Breeding, Nanjing Agricultural University, Nanjing, Jiangsu, China.
authors.forename: Jian-Ying
authors.initials: JY
authors.lastname: Feng
authors.forename: Jin
authors.initials: J
authors.lastname: Zhang
authors.forename: Wen-Jie
authors.initials: WJ
authors.lastname: Zhang
authors.forename: Shi-Bo
authors.initials: SB
authors.lastname: Wang
authors.forename: Shi-Feng
authors.initials: SF
authors.lastname: Han
authors.forename: Yuan-Ming
authors.initials: YM
authors.lastname: Zhang
mesh_terms: D000220:Adaptation, Biological; D000465:Algorithms; D000483:Alleles; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D003198:Computer Simulation; D018556:Crops, Agricultural / Q000235:genetics*; D018703:Founder Effect; D059647:Gene-Environment Interaction; D016014:Linear Models; D008957:Models, Genetic; D009010:Monte Carlo Method; D010641:Phenotype; D040641:Quantitative Trait Loci; D011995:Recombination, Genetic; D013025:Glycine max / Q000235:genetics / Q000378:metabolism; D013312:Stress, Physiological