Construction of diversity panels of landrace rice collections in Myanmar

Abstract

Abstract To meet the future demand of the global population, new varieties to adapt to regional climate changes such as salinity, drought, and submergence and new race emergence of pest disease and insects are expected to be developed for plant breeders. To facilitate efficient screening of germplasm and gene exploration on bi-parental cross populations and genome-wide association study (GWAS), the construction of a compact and genetically characterized germplasm platform is necessary in the National gene bank. In this study, genetic relationships of the representative core collections (CC) conserved in the National Seedbank of Myanmar were investigated using the genotyping-by-sequencing approach. It was found that the accessions were classified into the three clusters corresponding so-called japonica, indica, and aroma subpopulations. For efficient germplasm screening and gene exploration by GWAS on the indica landrace germplasm in Myanmar, a compact diversity panel designated “G” consisting of the 249 accessions was assembled, and genome-wide nucleotide variants were collected by the whole genome sequencing. The principal component analysis using genome-wide variants revealed that the selected accessions did not have an apparent population structure, but the first and second principal component scores correlated to the latitude and longitude, suggesting that latitude is the more causal factor of the geographical variation within the Myanmar landrace. When the reference genome of the leading variety in Myanmar was used, the mixed model genome-wide association analysis provided higher -log10(p) scores and detected seven peaks of apiculus pigmentation of spikelet. The five peak associations of the seven fall into the linkage disequllibrium blocks or neighbor blocks containing the isolated genes involved in anthocyanin pigmentation in rice. These results demonstrated that the combination of the landrace GWAS of the National seed banks and reference sequences genetically related to the landrace provide better research environments in characterization and gene exploration.