Rescuing fixed deleterious alleles through genomic selection

During the long-term improvement processes in maize, large numbers of deleterious alleles (bad alleles) have been accumulated and fixed in the elite maize lines by chance, creating obstacles for further crop improvement. Fortunately, a portion of the fixed bad alleles are still segregating in traditional cultivated landraces, which provides opportunities to rescue these fixed bad alleles and to enrich the diversity of the germplasm pool for breeding. It will take years, however, to adapt the open pollinated landraces, mainly grown in the tropical areas of the world, to the U.S. corn belt environments. The USDA-ARS GEM (Germplasm Enhancement of Maize) project has brought some of the exotic alleles into temperate lines since 1994. In the lab, we will identify the alternative alleles using publicly available GEM lines and evaluate their phenotypic consequences, emphasizing on the micronutrient composition (collaborating with Waters research lab at UNL) and yield related traits. Eventually, we will develop genomic selection protocols, a method enables rapid selection of the desired gentoypes and hence accelerates the breeding cycle, in collaboration with the Cheng Lab at UC Davis to facilitate the rescuing process.

  • This project is supported by USDA NIFA (2019-67013-29167) to the J. Yang lab.

Genetic mechanisms underlying heterosis

Heterosis or hybrid vigor is a phenomenon that hybrids performance better than both of the inbred parents. Heterosis is of substantial importance to crop improvement but its genetic basis remains controversial. Population genetic theory has long argued that heterosis can be explained largely by complementation of recessive deleterious alleles, but this model is inconsistent with evidence from polyploid hybrids that suggests an important role for gene dosage. Our published work has shown that a model of incomplete dominance both fits predictions of population genetic theory and explains empirical results from polyploids. The long-term interest of the lab is to enhance the heterosis prediction for future breeding.

High throughput phenotyping and GWAS

With extensive genome-wide association study (GWAS) experience, our lab has started to expand to the area of high throughput phenotyping, emphasizing on downstream genotype-phenotype association study. In collobration with the Schnable Lab@UNL and Yufeng Ge Lab, we sought to characterize the phenotypic traits by using machine vision technology, i.e. unmanned aerial system (UAS) and LemnaTec high-throughput phenotyping system in the Greenhouse Innovation Center. We are interested in estimating the genetic parameters, i.e. polygenicity (number of non zero effect SNPs), selection pressure, magnitude of effects, SNP-based heritability etc., in controlling various phenotypic traits extracted from high throughput phenotyping.