利用简化基因组测序数据鉴定蚕豆SNP  

SNP Identification of Faba Bean(Vicia faba L.)by using Simplified Genome Sequencing Data

作　　者：刘庭付 李汉美 汪宝根[3] 吴苏淇 李素娟[4] 王琳琳 李国景[3] 吴新义[3] Liu Tingfu;Li Hanmei;Wang Baogen;Wu Suqi;Li Sujuan;Wang Linlin;Li Guojing;Wu Xinyi(Lishui Academy of Agricultural and Forestry Sciences,Lishui,323000;Lishui Vocational and Technical College,Lishui,323000;Institute of Vegetables,Zhejiang Academy of Agricultural Sciences,Hangzhou,310021;Central Laboratory of Zhejiang Academy of Agricultural Sciences,Hangzhou,310021)

机构地区：[1]丽水市农林科学研究院,丽水323000 [2]丽水职业技术学院,丽水323000 [3]浙江省农业科学院蔬菜研究所,杭州310021 [4]浙江省农业科学院公共实验室,杭州310021

出　　处：《分子植物育种》2022年第4期1214-1221,共8页Molecular Plant Breeding

基　　金：浙江省农业科学院地方科技合作项目(LS2017005);浙江省农业新品种选育重大科技专项(2016C02051)共同资助。

摘　　要：蚕豆(Vicia faba L.)是中国一种重要的食用豆类作物。由于蚕豆基因组较大,尚无参考基因组,因而目前蚕豆上SNP标记数量有限。为了开发全基因组范围内的SNP,本研究对8份蚕豆地方品种进行了简化基因组测序,共获得35.47 Gb的数据,每份种质平均测序量为4.77 Gb;生成Reads总数为245443516个,单个Read平均长度为144 bp,单个种质获得的平均Reads数目为30680439.5;Q20和Q30分别大于97.89%和93.83%,GC含量变异幅度为38.05%~40.09%。利用无参考基因组情况下特殊的贝叶斯算法,从中共鉴定到3722个SNP,单个种质上鉴定出的SNP数目变异为3278~3578,其中大部分种质中纯合SNP突变数目大于杂合SNP突变数目。突变类型中,T:A->C:G突变类型所占的比例最大(平均38.8%),其次为C:G->T:A(平均28.0%),出现比例最小的为T:A->A:T(平均7.50%)。本研究选择了31个SNP转化为KASP标记,在46份种质中的扩增成功率为66.7%。本研究所鉴定的SNP为蚕豆种质资源鉴定、基因定位及分子育种提供了有力的遗传工具。Faba bean is an important edible legume crop in China.Due to its huge genome size and no available reference genome,SNP marker is very limited in faba bean.To identify genome-wide SNP markers,we obtained35.47 Gb data from eight landraces by RAD-sequencing,with an average of 4.77 Gb data for each accession.A total of 245443516 reads were generated,the single accession has an average of 30680439.5 reads,and the average length of the reads reaches to 144 bp.The Q20 and Q30 values were over 97.89%and 93.83%,respectively.The GC content between the reads varied from 38.05%to 40.09%.Using a special Bayesian method under the situation of no reference genome,we identified 3722 SNPs among the eight landraces.Regarding the single accession,the detected SNPs varied from 3278 to 3578,and the homozygous SNPs number was larger than that of Heterozygous SNPs for most of accessions.For the SNP types,T:A->C:G type has the largest proportion(38.8%),followed by C:G->T:A(28.0%)and the smallest is T:A->A:T(7.5%).31 SNPs were selected to convert into KASP markers,and they showed a success rate of 66.7%through amplifying on 46 accessions.The SNPs in this study provide a strong genetic tool for germplasm identification,gene mapping and molecular breeding in faba bean.

关 键 词：蚕豆 SNP 简化基因组测序 KASP 

分 类 号：S643.6[农业科学—蔬菜学]