水稻全基因组测序揭示的粳稻与籼稻亚种内品种间多态性研究  

Study on polymorphism between japonica and indica rice subspecies revealed by whole genome sequencing

作　　者：陈喜娜 袁泽科 杜彦修[1] 李俊周[1] 张静[1] 彭廷[1] 赵全志[1] 孙红正[1] CHEN Xi’na;YUAN Zeke;DU Yanxiu;LI Junzhou;ZHANG Jing;PENG Ting;ZHAO Quanzhi;SUN Hongzheng(College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China)

机构地区：[1]河南农业大学农学院,河南郑州450046

出　　处：《河南农业大学学报》2020年第6期913-920,共8页Journal of Henan Agricultural University

基　　金：河南省现代农业产业技术体系项目(S2012-04-G02)

摘　　要：为了评价亚种内杂交进行基因图位克隆的亚种内分子标记多态性水平,从水稻3K测序数据中选取了16份籼稻和16份粳稻种质资源,在全基因组水平对亚种内和亚种间的多态性进行了比较。结果表明,全基因组水平的亚种内多态性只有亚种间多态性的1/2~1/3,但是,由于整个基因组上多态性标记数量极大,亚种内的多态性标记仍较为丰富。在所选取的种质资源中,籼稻亚种内不同的种质资源间平均含有108850个InDels和650797个SNP,每Mb区间内SNP/InDel的密度达到280~2614个。粳稻亚种内不同种质资源间平均含有57384个InDels和639927个SNP,每Mb区间内SNP/InDel的密度达到520~3201个。这样的标记密度对于基因克隆来说足够丰富,增加了亚种内杂交构建分离群体克隆基因的可能性。Segregate population construction by rice inter-subspecies cross was the usual practice in rice map-based gene cloning.Intra-subspecies cross was deemed to be lack of available polymorphic markers.In order to evaluate the possibility of intra-subspecies cross mapping population,inter-and intra-subspecies polymorphic sites between 16 indica accessions and 16 japonica accessions from the rice 3K genome project were compared.The results showed that the intra-subspecies diversity was one third to two third that of inter-subspecies diversity,but the density on the whole chromosome was still relatively high.In the selected accessions,the intra-indica accessions pairs contained 10^8850 InDels and 650797 SNPs on average,the SNP/InDel density varied from 280 to 2614 SNP/InDels per Mb.The intra-japonica accessions pairs contained 57384 InDels and 639927 SNPs between two genomes on average,and density of japonica accessions varied from 520 to 3201 SNP/InDels per Mb.The polymorphic sites were abundant and increased the possibility of map-based gene cloning by intra-subspecies cross population.

关 键 词：水稻 QTL定位 亚种间 亚种内 多态性标记 

分 类 号：S511[农业科学—作物学]