| Oat(Avena sativa L.)belongs to the Poaceae family and Avena genus.It is an important cereal crop widely cultivated around the world as a crop used for food,animal feed,and livestock forage.Due to its large genome size and being an allopolyploid,research on genome selection breeding in cultivated oat is challenging,with a weak foundation.This study aims to integrate existing genomic data of the Avena genus and build a platform for oat genomics analysis to provide fundamental data and resources for whole-genome selection breeding.1.Ten Avena species genomes were collected,including two genome diploid A.longiglumis,one genome diploid A.atlantica,one genome diploid A.strigosa,one genome diploid A.eriantha,two genome tetraploid A.insularis,and three genome hexaploid cultivated oat A.sativa.The chromosome nomenclature was unified for the genomes released by different research institutions,and errors in gene structure annotation information were corrected.2.The 780,548 genes in the above-mentioned genomes were functionally annotated using NR,KOG,Uniprot,GO,and KEGG databases.Homologous genes between each genome and model research plants(Arabidopsis thaliana,rice,and wheat)were identified.The Pfam database was used to identify all potential structural domains contained in the genes,providing a foundation for functional studies of oat.3.Based on the genome information,4,730,336 SSR markers and corresponding primer sequences were developed,covering all ten genomes.SNP markers were also developed based on multi-omics data,including high-depth second-generation sequencing data and low-depth GBS sequencing data.A subsequent strategy was proposed to estimate missing genotypes in the low-depth sequencing data using highdepth resequencing data.4.Multi-point trait identification data of core germplasm resources of oat has been collected for many years.Massive genotypic and phenotypic data are necessary prerequisites for constructing whole genome selection breeding of oat.This study has fully integrated the existing oat omics data by constructing a large-scale genomic database based on the previous back-end isolation.The database adopts a highperformance architecture and a scalable database system,which provide a good framework for further collecting massive genotype and phenotypic information needed for whole-genome selection breeding of oats,as well as integrating multiple online tools and databases.5.An initial attempt was made to use phenotypic data on 12 traits from 666 cultivated oat over four years,combined with their genotype data,to construct a singletrait genome selection breeding model for oat.This provides an example for planning an online module for oat whole-genome selection breeding,laying the foundation for future work in this area. |
