Interacted QTL Mapping in Partial NCII Design Provides Evidences for Breeding by Design

Abstract

The utilization of heterosis in rice, maize and rapeseed has revolutionized crop production. Although elite hybrid cultivars are mainly derived from the F1 crosses between two groups of parents, named NCII mating design, little has been known about the methodology of how interacted effects influence quantitative trait performance in the population. To bridge genetic analysis with hybrid breeding, here we integrated an interacted QTL mapping approach with breeding by design in partial NCII mating design. All the potential main and interacted effects were included in one full model. If the number of the effects is huge, bulked segregant analysis were used to test which effects were associated with the trait. All the selected effects were further shrunk by empirical Bayesian, so significant effects could be identified. A series of Monte Carlo simulations was performed to validate the new method. Furthermore, all the significant effects were used to calculate genotypic values of all the missing F1 hybrids, and all these F1 phenotypic or genotypic values were used to predict elite parents and parental combinations. Finally, the new method was adopted to dissect the genetic foundation of oil content in 441 rapeseed parents and 284 F1 hybrids. As a result, 8 main-effect QTL and 37 interacted QTL were found and used to predict 10 elite restorer lines, 10 elite sterile lines and 10 elite parental crosses. Similar results across various methods and in previous studies and a high correlation coefficient (0.76) between the predicted and observed phenotypes validated the proposed method in this study.

Development of a multiple-hybrid population for genome-wide association studies: theoretical consideration and genetic mapping of flowering traits in maize

“…Considering all available mating designs that have been used in quantitative genetics, hybrids from a full diallel design with n parents would be one of the best MHPs, as the full set hybrids can be divided into three subsets, two diallels and one NC II, as needed. As such an attempt with a limited number of hybrids, a partial NC II was used for QTL mapping to test effects associated with traits, and the significant effects identified by empirical Bayesian were used to estimate genetic effects for the missing F 1 s with elite parents and hybrids predicted37. The generated hybrids, along with the parental genotype and phenotype, can be used to predict the missing hybrids and the rest hybrids.…”

“…As we calculated in the precious section, genotypes for 4,500 hybrids can be inferred from 100 parental lines genotyped, the former being 45 folds larger. In Brassica napus , 205 SSR markers were used to examine the polymorphisms among 441 parents (298 sterile and 143 restorer lines), and the genotypes for the partial NC II hybrids could be then deduced from their parents37, with 8 main-effect and 37 interacted QTL identified for oil content, which could be used to predict 10 elite restorer lines, 10 elite sterile lines and 10 elite hybrids.…”

“…For ungenerated hybrids (1275–724 = 551), their performance can be predicted using genomic best linear unbiased prediction (GBLUP)108 or empirical Bayesian approach37, and in general Bayes and GBLUP possess high accuracy. With an optimized scheme, we should be able to predict performance for much more hybrids with much less hybrids tested.…”

“…The empirical Bayesian approach was developed and used for a partial NC II mating design in Brassica napus including 284 F 1 hybrids, and 143 restorers and 298 sterile lines were used to predict the phenotypes for missing hybrids, with QTL effects estimated by empirical Bayesian. GCA and SCA would be estimated and elite parents and hybrids could be predicted37. In our following research, the GBLUP approach108 will be used for analysis of the MHP and reported elsewhere.…”

EcoTILLING revealed SNPs in GhSus genes that are associated with fiber- and seed-related traits in upland cotton

“…All the effects in the above model were estimated by empirical Bayes 61 . Results from Monte Carlo simulation studies showed that these estimates were unbiased 61 62 63 . The significance threshold of the logarithm of odds (LOD) score was set at 3, which is equivalent to the significance level of 0.0002 63 .…”