摘要
[目的]基于三代全长转录组测序数据,开发极边扁咽齿鱼SSR分子标记,积累和丰富该物种遗传信息,为后期指导和优化人工繁殖技术提供理论参考.[方法]基于极边扁咽齿鱼三代全长转录组测序结果(PRJNA792686),分析SSR分布情况,筛选出具有多态性的SSR引物,并对2个流域37尾边扁咽齿鱼的遗传多样性进行分析.[结果]极边扁咽齿鱼单核苷酸重复SSR个数最多,占37.87%,二核苷酸～六核苷酸重复序列依次占31.77%、10.32%、1.29%、0.25%和0.10%;二核苷酸、三核苷酸、四核苷酸和六核苷酸重复序列均以重复次数5～8次居多,分别占各自SSR总数的55.26%、94.90%、70.92%和89.52%;之后随重复次数增加而逐渐减少,当重复次数为21～24次时最低,分别占各自SSR总数的2.63%、0.04%、2.68%和0.单核苷酸重复序列以重复次数9～12次居多,占其SSR总数的71.43%;五核苷酸重复序列的重复次数主要集中在5～8次,占其SSR总数的83.33%;三核苷酸、四核苷酸和五核苷酸重复序列中,排名前5的序列分别是TA(17.07%)、AT(16.95%)、TG(15.29%)、AC(12.51%)和CA(9.71%);TTA(7.53%)、GAT(6.07%)、TAT(5.93%)、CAG(5.50%)和GAG(5.50%);TATC(4.83%)、TTTA(4.32%)、TTCT(3.81%)、TATT(3.56%)和TGTT(3.18%).共设计38对SSR引物,最终筛选得到9对SSR多态性引物.2个流域的极边扁咽齿鱼等位基因数(Na)为3～29,其中,A流域极边扁咽齿鱼的期望杂合度(He)为0.484～0.931,香农指数(H′)为0.677～2.793;B流域极边扁咽齿鱼的He为0.315～0.948,H′为0.578～3.075.[结论]2个流域的极边扁咽齿鱼具有较高的遗传多样性.开发的9个多态性SSR分子标记可用于极边扁咽齿鱼育种和种质保护.
Abstract
[Objective]The purpose of the study was to develop SSR molecular markers for Platypharodon extremus based on three-generation full-length transcriptome sequencing data,in order to accumulate and enrich the genetic infor-mation of this species,and to provide theoretical reference for guiding and optimizing artificial breeding techniques in the later stage.[Method]Based on the three-generation full-length transcriptome sequencing results of P.extremus(PRJNA 792686),the distribution of SSRs was analyzed,and polymorphic SSR primers were selected.The genetic diversity of 37 P.extremus individuals in two watersheds was analyzed.[Result]The results showed that the number of mononucleotide repeat SSRs was the largest in P.extremus,accounting for 37.87%.The dinucleotide-hexanucleotide repeat sequences ac-counted for 31.77%,10.32%,1.29%,0.25%and 0.10%in order.The dinucleotide,trinucleotide,tetranucleotide and hexanucleotide repeat sequences were predominant at 5-8 repeats,accounting for 55.26%,94.90%,70.92%and 89.52%of the total number of their respective SSRs,respectively.After that,they gradually decreased with the increase of repeat number,and they were the lowest when the number of repeats was 21-24,accounting for 2.63%,0.04%,2.68%and 0 of the total number of their respective SSRs,respectively.The mononucleotide repeat sequences were predominantly re-peated 9-12 times,accounting for 71.43%of their total SSRs.The pentanucleotide repeats were mainly concentrated in 5-8 times,accounting for 83.33%of their total SSRs.The top 5 sequences in trinucleotide,tetranucleotide and pentanucleo-tide repeats were TA(17.07%),AT(16.95%),TG(15.29%),AC(12.51%)and CA(9.71%);TTA(7.53%),GAT(6.07%),TAT(5.93%),CAG(5.50%)and GAG(5.50%);TATC(4.83%),TTTA(4.32%),TTCT(3.81%),TATT(3.56%)and TGTT(3.18%),respectively.A total of 38 pairs of SSR primers were designed,and 9 pairs of SSR polymor-phic primers were ultimately screened.The number of alleles(Na)in the two watersheds was 3-29,in which the expected heterozygosity(He)of P.extremus in watershed A was 0.484-0.931 and the Shannon index(H')was 0.677 to 2.793.The He of the watershed B was 0.315-0.948 and H'was 0.578-3.075.[Conclusion]P.extremus in the two watersheds have high genetic diversities.The nine polymorphic SSR molecular markers developed can be used for breeding and germplasm protection of P.extremus.
基金项目
四川省科技计划项目(2021YFYZ0015)
国家现代农业产业技术体系四川淡水鱼创新团队建设专项(2019-2023)()
维普
万方数据