青海省青稞主栽品种昆仑14与昆仑15的基因组序列多态性比较OA北大核心CSTPCD

[Objective]At present,Kunlun 14 and Kunlun 15 are the main varieties of the naked barley in Qinghai Province,and also the important backbone parents in the breeding of the naked barley.The genomic sequences of Kunlun 14 and Kunlun 15 were compared to provide references for the trace of important character regions/loci,pedigree analysis and their utilization in molecular design breeding of the naked barley.[Method]In this study,the agronomic and grain traits of Kunlun 14 and Kunlun 15 were investigated in the field,and the whole genome resequencing were performed(sequencing depth≥15×).The sequence differences of copy number variation(CNV),single nucleotide polymorphism(SNP)and insertion/deletion(InDel)were compared between the two varieties.According to the SNP distribution patterns,the polymorphism hotspot and genetic similar regions between them were identified.The mutation types of polymorphism hotspot and genetic similar regions were compared and analyzed.The gene enrichment analysis was carried out in the specific CNV regions and the polymorphism hotspots regions of the two varieties.[Result]In addition to the plant height and peduncle internode length,Kunlun 14 and Kunlun 15 had high similarity in important agronomic and grain traits.Compared with the barley reference genome of Morex,the two varieties had a common CNV variation interval of 83 Mb,and the length of cultivar-specific CNV variation interval in Kunlun 14 and Kunlun 15 was 37 Mb and 38 Mb,respectively.There were 564 genes in the CNV region specific to Kunlun 14,which were significantly enriched in 15 GO terms,while 519 genes were in the CNV region specific to Kunlun 15 and were significantly enriched in 7 GO terms.Based on the SNP distribution patterns,1 706 Mb polymorphism hotspots and 2 411 Mb sequence similarity intervals of Kunlun 14 and Kunlun 15 were identified at the whole genome level,and the polymorphism hotspots were mainly distributed on 3H,6H and 7H.The polymorphism hotspots regions contained 16 768 genes,whose functions were mainly related to plant growth and development.There was no significant difference between polymorphism hotspot regions and genetic similar regions in SNP variation type,InDel length distribution and the proportion of mutations affecting coding function.The SNPs and InDel mutations in polymorphism hotspot and genetic similar regions were mainly missense mutations and followed by synonymy mutations.[Conclusion]The field phenotypes of Kunlun 14 and Kunlun 15 were similar.At the whole genome level,a total of 75 Mb CNV variation regions between them and the polymorphism hotspot regions were mainly distributed at 3H,6H and 7H.