Analysis Of Genetic Structure In African New Rice (NERICA) Population

African New Rice is composed of land rice and aquatic rice.In this study,African New Rice(NERICA_L)population with 60 varieties were selected as the sample.which were selected from 73 Oryza sativa L population and 110 Oryza glaberrima Steud population as reference samples.Based on SNP genotyping and simplified genome sequencing,the genetic structure of NERICA_L population was analyzed,and the genetic basis of several key agronomic traits was analyzed.The SNP(W-core)was collected from 768 cultivars in 60 African New Rice samples using the illumma Golden Gate SNP gene chip.The results showed that the diversity index of African new rice populations reached 0.230,which was higher than that of Oryza glaberrima Steud and temperate japonica rice,which indicated that the African new rice population had rich genetic diversity.The genetic differentiation coefficient of African new rice population and Oryza glaberrima Steud was 0.475,However,the Genetic relationship of African new rice populations and Oryza sativa L was closer,were the genetic relationship between Asian rice and African rice was similar to that of Asian indica rice.Oryza glaberrima Steud,African new rice and japonica subspecies have higher genetic differentiation coefficient.The results of 25707 SNP markers based on Simplified Genome Sequencing(SLAF-SNP)showed that the genetic differences between African new rice population and TOG5681 were the largest,while the IR64 is fully integrated into the genetic evolutionary tree of the African new rice group.Most of the genomes of the African new rice population originated from the reincarnated indica rice IR64.Only a small number of gene fragments from the African cultivated rice TOG5681 gene fragments are irregularly distributed in 60 African new rice on the 12 chromosomes.In this study,the genetic relationship between African new rice populations and their phylogenetic relationships is not only important for further discovering the genetic contribution and excellent alleles of African new rice,but also for the study of genetical analysis differentiation and inheritance of African new rice,beneficial to further select the parental combination to carry out further genetic breeding work,the information provided for the breeder's choice can provide reference to shorten the breeding period.Based on the W-core SNP,the genetic traits of several important agronomic traits,the results showed that the LOD value and the genetic contribution rate of the main effect amylose content were 14.26 and 83.2%,respectively,and the single marker significant linkage site of amylose content.Overlaps with the reported Waxy position and is the same as the location based on the SLAF-seq single marker analysis.Based on the W-core SNP,we found a response to anoxia-induced germination on chromosome 1,with a LOD of 4.85%ofthe contribution rate of 27.2%.In the SLAF-seq-based single marker assay,we also mapped the locus on the first chromosome,and a significant anoxia-resistant response signal was found on chromosome 7.By the single-label analysis of SLAF-seq,three loci on chromosome 4.chromosome 8 and chromosome 10 were also found to respond to anoxia-tolerant sites This is a good foundation for further genetic improvement in order to discover the genetic resources derived from the new African rice.