Genome-based Exploration Of The Genetic Differentiation Of Lowland And Upland Rice

Lowland and upland rice are two different ecological types of cultivated rice,which evolved from wild rice.In-depth research on genetic differentiation of lowland and upland rice can provide theoretical basis for the conservation of its diversity.In this study,we constructed a high-quality reference genome of the upland rice Hanhui15 genome by using the third-generation sequencing data.By combining the existing 21 lowland and 9 upland rice genomes,and using the 3K genome resequencing data of lowland and upland rice,identification of the specific genes and exploration of the genetic differentiation of lowland and upland rice were carried out.At the same time,combined with the information of QTL mapping of droughtresistant traits and drought-resistant genes,the signals of local differentiation of upland rice genome were detected.The main research results are as follows:1.The genome of Hanhui15 was assembled based on Pac Bio CCS reads.Contig N50 was 21.8 Mb,the genome size was 399.4 Mb,the evaluation results of LAI showed that it reached the level of gold reference genome.Comparative analysis of genome showed that the Hanhui15 genome had 1 Mb more base sequences at the end of chromosome 8 and chromosome 11 than other genomes.2.The comparative analysis of 31 genomic showed that no specific base sequences were found in the lowland and upland rice genome.The average differentiation coefficient between the genome and resequencing rice showed that there was no obvious whole genome differentiation between lowland and upland rice.In addition,there was no clustering in the 3K phylogenetic tree of upland rice.However,tropical and subtropical japonica rice in upland rice subpopulation can be clustered in one or adjacent clades respectively.3.There were 12 In Dels and 1218 SNPs between IRAT109 and Hanhui 15 in QTL region of chromosome 2.10 large In Dels and 2686 SNPs were found in the QTL region of chromosome 4.Based on the difference of drought resistance genes in the genomes of Nipponbare,IRAT109 and Hanhui 15,There was a large fragment sequence insertion in the Nipponbare promoter region of Os03g0122500.Os08g0174500 has a large fragment insertion in the promoter region of Hanhui15.Os03g0122600 has 6 large Indels among the three genomes.Based on high-quality genome and population resequencing data,the results are helpful to further understand the differences of lowland and upland rice genomes,and provided new insights into the differentiation of lowland and upland rice.