摘要
简单重复序列标记(simple sequence repeats,SSR)和单核苷酸多态性标记(single nucleotide polymorphism,SNP)具有高灵敏度和高特异性特征,挖掘不同类型橄榄果实性状相关分子标记可为其分子辅助育种提供参考。本研究以充分成熟的长营和惠圆橄榄果实为材料,经总RNA提取和cDNA文库构建后采用Illumina Novaseq平台进行转录组测序,并采用MISA 1.0和GATK3软件分析转录组的SSR、SNP和插入缺失标记(Indel)位点特征。结果在橄榄果实转录组的10124条unigenes上鉴定到13935个SSR位点,发生频率为22.98%,平均每1 kb序列出现0.25个SSR位点,平均长度为14.34 bp;其中,单碱基重复基元类型的SSR位点数量最多(占比66.80%),长度为10~64 bp,平均长度为12.85 bp,重复基元的重复次数集中在9~12次,频率最高的基元为A/T(占比66.67%);六碱基重复基元类型的SSR位点数量最少(占比0.47%),长度为30~54 bp,平均长度31.76 bp,基元重复次数集中在5~8次,频率最高的基元为AGATGG/ATCTCC(占0.04%)。在橄榄果实转录组中共检测到284992个SNP位点,平均每1 kb序列含有5.21个;其中,转换类型的SNP位点数量为166162,包括C/T和A/G两种;颠换类型的SNP位点数量为118830,包括A/T、A/C、T/G和C/G四种。此外,橄榄果实转录组中共挖掘到18548个InDel位点,平均每1 kb序列存在2.95个,其中含有1个InDel位点的unigenes数量最多(7853条);通过比对预测发现,含有最多InDel位点的unigene可能是胼胝质合成酶基因。研究结果表明,通过转录组测序可有效开发橄榄SSR和SNP/InDel标记,不同性状橄榄果实中存在丰富多样的SSR位点且广泛分布SNP/InDel位点。该研究结果为橄榄果实性状鉴定标记的开发提供数据基础。
Simple sequence repeats(SSR)and single nucleotide polymorphism(SNP)markers have been confirmed to be high sensitivity and specificity.Development of molecular markers related to different types of fruit quality traits of Canarium album(Lour.)Raeusch.can provide reference for its molecular assisted breeding to a considerable extent.The fully mature fruits of C.album cv.Changying and Huiyuan were collected to use as materials.After total RNA extrac-tion and cDNA library construction,the transcriptome was sequenced on the Illumina Novaseq platform,and the SSR,SNP and InDel loci characteristics of the transcriptome were analyzed by MISA 1.0 and GATK3 software.Results showed that a total of 13935 SSR loci were identified from 10124 unigenes of C.album fruit transcriptome,the aver-age 1 kb sequence appeared 0.25 SSR loci,the frequency and average length was 22.98%and 14.34 bp,respectively.Among them,the single base repeat type had the largest number of SSR loci(accounting for 66.80%),with a length of 10–64 bp,and an average length of 12.85 bp,the repeat times of repeat motifs were concentrated in 9–12,and the motif with the highest frequency was A/T(accounting for 66.67%).The number of SSR loci of six base repeat motif type was the least(0.47%),the length was 30-54 bp,which average length was 31.76 bp,the number of motif repeats was con-centrated in 5-8 times,and the motif with the highest frequency was AGATGG/ATCTCC(0.04%).A total of 284992 SNP loci were detected in the transcriptome of C.album fruit,the average 1 kb sequence contained 5.21 SNP loci;Among them,the number of SNP loci of transformation type was 166162,including C/T and A/G.The number of SNP loci of transversion type was 118830,including A/T,A/C,T/G and C/G.In addition,18548 InDel loci were found in the transcriptome of C.album fruit,the average 1 kb sequence existed 2.95 InDel loci.The number of unigenes containing one InDel locus was the largest.It was predicted that the unigene containing the most InDel loci might be the callose synthase gene.These results showed that SSR and SNP/InDel markers could be effectively developed through RNA-seq.The SSR loci and SNP/InDel loci were widely distributed in C.album fruits with different quality traits.The results would provide a data basis for the development of identification markers of C.album fruit traits.
作者
赖瑞联
沈朝贵
冯新
陈义挺
韦晓霞
吴如健
LAI Ruilian;SHEN Chaogui;FENG Xin;CHEN Yiting;WEI Xiaoxia;WU Rujian(Fruit Research Institute,Fujian Academy of Agricultural Sciences,Fuzhou,Fujian 350013,China)
出处
《热带作物学报》
CSCD
北大核心
2023年第4期681-688,共8页
Chinese Journal of Tropical Crops
基金
福建省属公益类科研院所基本科研专项(No.2021R1028003,No.2022R1028003)
农业农村部物种品种资源保护(热带作物)项目(No.18220025)。
关键词
橄榄
转录组
简单重复序列
单核苷酸多态性
插入缺失标记
Canarium album
transcriptome
simple sequence repeats
single nucleotide polymorphism
InDel
