@article{Wang2023, 
author = {Jinshe Wang and Jianbo He and Jiayin Yang and Junyi Gai},
title = {A novel procedure for identifying a hybrid QTL-allele system for hybrid-vigor improvement, with a case study in soybean (Glycine max) yield},
year = {2023},
journal = {The Crop Journal},
volume = {11},
number = {1},
pages = {177-188},
keywords = {Breeding by design, Diallel hybrid population, PLSRGA (partial least squares regression via genetic algorithm), QTL-allele matrix of additive/dominance effect, Simulation experiment, Soybean [Glycine max (L.) Merr.]},
url = {https://www.sciopen.com/article/10.1016/j.cj.2022.04.019},
doi = {10.1016/j.cj.2022.04.019},
abstract = {"Breeding by design" for pure lines may be achieved by construction of an additive QTL-allele matrix in a germplasm panel or breeding population, but this option is not available for hybrids, where both additive and dominance QTL-allele matrices must be constructed. In this study, a hybrid-QTL identification approach, designated PLSRGA, using partial least squares regression (PLSR) for model fitting integrated with a genetic algorithm (GA) for variable selection based on a multi-locus, multi-allele model is described for additive and dominance QTL-allele detection in a diallel hybrid population (DHP). The PLSRGA was shown by simulation experiments to be superior to single-marker analysis and was then used for QTL-allele identification in a soybean DPH yield experiment with eight parents. Twenty-eight main-effect QTL with 138 alleles and nine QTL × environment QTL with 46 alleles were identified, with respective contributions of 61.8% and 23.5% of phenotypic variation. Main-effect additive and dominance QTL-allele matrices were established as a compact form of the DHP genetic structure. The mechanism of heterosis superior-to-parents (or superior-to-parents heterosis, SPH) was explored and might be explained by a complementary locus-set composed of OD+ (showing positive over-dominance, most often), PD+ (showing positive partial-to-complete dominance, less often) and HA+ (showing positive homozygous additivity, occasionally) loci, depending on the parental materials. Any locus-type, whether OD+, PD + and HA+, could be the best genotype of a locus. All hybrids showed various numbers of better or best genotypes at many but not necessarily all loci, indicating further SPH improvement. Based on the additive/dominance QTL-allele matrices, the best hybrid genotype was predicted, and a hybrid improvement approach is suggested. PLSRGA is powerful for hybrid QTL-allele detection and cross-SPH improvement.}
}