龙头鱼SSR和SRAP标记筛选及遗传多样性分析
摘要
龙头鱼(Harpadon nehereus)是我国重要的经济鱼类之一，目前关于龙头鱼的分子遗传学方面的研究报道很少。本文采用SSR和SRAP两种分子标记对不同地理环境的龙头鱼群体进行遗传多样性研究，旨在为龙头鱼种质资源的保护和合理利用提供重要的理论依据。在SSR实验中，本研究首先采用生物素标记的(CA)12寡核苷酸探针，利用磁珠富集法构建了龙头鱼微卫星部分基因组富集文库，从设计的28对微卫星引物中筛选出21对微卫星引物，其中5个为多态的微卫星标记。用筛选的5对微卫星引物对龙头鱼36个个体进行遗传多态性分析。每个位点等位基因数3-4。观测杂合度和期望杂合度分别为0.3500-0.8421和0.5244-0.6244。PIC值0.4403-0.5538，表明这5个微卫星位点在龙头鱼中均有较高的信息含量。5个微卫星多态位点的Hardy-Weinberg平衡检验结果表明，所有位点均处于Hardy-Weinberg平衡（P>0.01）状态。在SRAP实验中，对SRAP引物进行了筛选和优化，分析了SRAP-PCR的影响因子，包括Taq酶、Mg2+、引物、dNTP的浓度对PCR反应的影响，得到了8个重复性好、多态性高的引物组合，对舟山(ZS)，象山(XS)，宁海(NH)，乐清(YQ)，温岭(WL)，温州(WZ)，瑞安(RA)，厦门(XM)，珠海(ZH)和海口(HK)10个龙头鱼群体进行研究，最终确立了适合于龙头鱼SRAP反应体系为：Taq酶1.0U，Mg2+浓度1.5mmol/L，dNTP浓度的为0.20mmol/L，引物浓度为0.20μmol/L。利用筛选出的引物对龙头鱼群体遗传多样性进行了分析，统计结果表明，在292个个体中共检测到98个清晰稳定的多态位点，多态性条带主要分布在100-2000bp之间，多态位点数在55到83之间，平均多态位点数为73.8；多态位点比例在53.06%到84.69%之间，平均多态比例为75.20%，这一结果表明龙头鱼群体存在较高的遗传多样性。10个群体的Nei's基因多样性指数(H)分别为：0.2740，0.2934，0.2126，0.3026，0.2978，0.1657，0.2654，0.2725，0.1540和0.2398，平均Nei's基因多样性指数(H)为0.2478，其中YQ群体最高，ZS群体最低，这表明在10个群体中YQ群体的遗传多样性是最高的，ZS群体的遗传多样性最低；Shannon信息多样性指数(I)在分别为0.4111，0.4345，0.3529，0.4506，0.4426，0.2525，0.4017，0.4077，0.2396和0.3690，平均Shannon信息多样性指数(I)为0.3735，其中YQ和NH群体最高，ZS群体最低，这同样说明YQ群体的遗传多样性最丰富，ZS群体最低。从整体水平上来看，龙头鱼群体的遗传多样性水平还是相对比较高的。分子方差分析结果表明，群体内个体间的变异是总变异的主要来源（71.74%），28.26%的遗传变异来自群体间（Fst=0.2826）。采用MEGA4.0软件计算了群体间的遗传距离，ZS群体和HK群体的遗传距离最远为0.3841，XS群体和RA群体的遗传距离最近为0.0410。根据群体间的遗传距离进行了NJ法聚类分析，结果显示10个龙头鱼群体明显地分为两支，第一分支包括ZS，WZ，XS，WL，RA，YQ和NH；第二分支包括ZH，XM和HK。这一结果显示龙头鱼群体存在显著的地理差异。SRAP分析结果显示，尽管龙头鱼群体具有相对丰富的遗传多样性，但是在HK和ZS群体中，多态位点数为52和55，多态比例、Nei's基因多样性指数(H)和Shannon信息多样性指数与其他群体相比也是最低的，表明这两个群体的遗传多样性与其他群体相比处于较低水平。因而我们应该对HK群体和ZS群体的种质资源进行保护。
Harpadon nehereus is one of the important fisheries resources in China, the moleculargenetics of H. nehereus has not seen so far. This paper investigated the genetic diversity ofthe H. nehereus which was collected from different geographical regions by using SSR andSRAP molecular markers. The results could provide an important theoretical basis for theprotection and sustainable utilization of H. nehereus. In the research of microsatellitemarkers, first of all, we constructed an enriched microsatellite library by a magnetic-beadenrichment method used biotinylated (CA)12probe, twenty-eight primer pairs weredesigned and twenty-one were successfully amplified; five loci were polymorphic. Usingthe five primer pairs to investigated the genetic diversity of36individuals of the H.nehereus. The number of alleles per locus was3or4; the observed and expectedheterozygosity varied from0.3500to0.8421and from0.5244to0.6244, respectively;polymorphism information content (PIC) ranged form0.4403to0.5538, the resultsindicated that the polymorphism information content at five loci of H. nehereus was rich.Hardy-Weinberg equilibrium probability tests showed that all of the five polymorphic lociwere at Hardy-Weinberg equilibrium (adjusted P value>0.01). In the research ofSequence-related amplified polymorphism, the SRAP primers were screened and optimized.In this study, the effect of Taq DNA polymerase, Mg2+concentration, dNTPs, primerconcentration on the SRAP-PCR amplification was analyzed. And the suitable SRAP-PCRreaction system was established, the resulted that the reaction system was as follows: TaqDNA polymerase1.0U, Mg2+1.5mmol/L, dNTPs0.20mmol/L, primer0.20μmol/L. Eightcombinations of primer pairs were chosen to be used in SRAP analysis. These primersamplified good repeatability, and their polymorphism is also very high. Using these primersto studied the genetic diversity of the H. nehereus which were collected from tengeographic locations which locations of Zhoushan (ZS), Xiangshan (XS), Ninghai (NH),Yueqing (YQ), Wenling (WL), Wenzhou (WZ), Ruian (RA), Xiamen (XM), Zhuhai (ZH)and Haikou (HK). The results suggested that a total of98loci ranging from100to2000bpwere produced from292individuals by eight SRAP primers. The number of polymorphicloci (POLs) was spread from55to83, with an average of73.8; the proportion of polymorphic loci (PPB) was varied from53.06%to84.69%, with an average of75.20%.High percentage of polymorphism observed by these markers indicated a high level ofgenetic diversity existed among different populations of H. nehereus. This indicationshowed that the genetic exchanges among these populations were relatively frequent; TheNei's gene diversity (H) of the ten populations was0.2740,0.2934,0.2126,0.3026,0.2978,0.1657,0.2654,0.2725,0.1540, and0.2398, with an average of0.2478. It suggested thatthe YQ population was in the highest level of genetic diversity, and the smallest was ZSpopulation; The Shannon’s information indices (I) of the ten populations were0.4111,0.4345,0.3529,0.4506,0.4426,0.2525,0.4017,0.4077,0.2396and0.3690, with theaverage of0.3735. The results revealed that the genetic diversity of the NH and YQpopulation is rich, and the ZS population is poor; the whole values showed the geneticdiversity is relatively high among all these ten populations. AMOVA showed that most ofthe variation was within populations (71.74%), and only28.26%variations betweenpopulations. The genetic distance calculated by MEGA4.0software between ZS and HKstocks is the greatest at0.3841, while that between XS and RA ones is the smallest at0.0410. The NJ tree based on genetic distance revealed that two main clusters wereidentified. The first cluster is composed of seven populations from ZS, WZ, XS, WL, RA,YQ and NH; the second cluster is composed of three populations from ZH, XM and HK.The result suggested that significant genealogical structure existed throughout the examinedrange of the H. nehereus. Although the results above showed that the genetic diversity of H.nehereus is relatively rich. However, in ZS and HK populations, the number ofpolymorphic loci was52and55severally, which were obviously lower than the other8populations. The percentage of polymorphic loci in HK population was the lowest amongthe ten studied populations, ZS population was followed. The other populations were nearlyat the same level and were higher than the two populations. The results suggested that thegenetic diversity of HK and ZS populations were counter-low. So we should pay moreattention to HK and ZS populations for the further germplasm resources protection.
Harpadon nehereus is one of the important fisheries resources in China, the moleculargenetics of H. nehereus has not seen so far. This paper investigated the genetic diversity ofthe H. nehereus which was collected from different geographical regions by using SSR andSRAP molecular markers. The results could provide an important theoretical basis for theprotection and sustainable utilization of H. nehereus. In the research of microsatellitemarkers, first of all, we constructed an enriched microsatellite library by a magnetic-beadenrichment method used biotinylated (CA)12probe, twenty-eight primer pairs weredesigned and twenty-one were successfully amplified; five loci were polymorphic. Usingthe five primer pairs to investigated the genetic diversity of36individuals of the H.nehereus. The number of alleles per locus was3or4; the observed and expectedheterozygosity varied from0.3500to0.8421and from0.5244to0.6244, respectively;polymorphism information content (PIC) ranged form0.4403to0.5538, the resultsindicated that the polymorphism information content at five loci of H. nehereus was rich.Hardy-Weinberg equilibrium probability tests showed that all of the five polymorphic lociwere at Hardy-Weinberg equilibrium (adjusted P value>0.01). In the research ofSequence-related amplified polymorphism, the SRAP primers were screened and optimized.In this study, the effect of Taq DNA polymerase, Mg2+concentration, dNTPs, primerconcentration on the SRAP-PCR amplification was analyzed. And the suitable SRAP-PCRreaction system was established, the resulted that the reaction system was as follows: TaqDNA polymerase1.0U, Mg2+1.5mmol/L, dNTPs0.20mmol/L, primer0.20μmol/L. Eightcombinations of primer pairs were chosen to be used in SRAP analysis. These primersamplified good repeatability, and their polymorphism is also very high. Using these primersto studied the genetic diversity of the H. nehereus which were collected from tengeographic locations which locations of Zhoushan (ZS), Xiangshan (XS), Ninghai (NH),Yueqing (YQ), Wenling (WL), Wenzhou (WZ), Ruian (RA), Xiamen (XM), Zhuhai (ZH)and Haikou (HK). The results suggested that a total of98loci ranging from100to2000bpwere produced from292individuals by eight SRAP primers. The number of polymorphicloci (POLs) was spread from55to83, with an average of73.8; the proportion of polymorphic loci (PPB) was varied from53.06%to84.69%, with an average of75.20%.High percentage of polymorphism observed by these markers indicated a high level ofgenetic diversity existed among different populations of H. nehereus. This indicationshowed that the genetic exchanges among these populations were relatively frequent; TheNei's gene diversity (H) of the ten populations was0.2740,0.2934,0.2126,0.3026,0.2978,0.1657,0.2654,0.2725,0.1540, and0.2398, with an average of0.2478. It suggested thatthe YQ population was in the highest level of genetic diversity, and the smallest was ZSpopulation; The Shannon’s information indices (I) of the ten populations were0.4111,0.4345,0.3529,0.4506,0.4426,0.2525,0.4017,0.4077,0.2396and0.3690, with theaverage of0.3735. The results revealed that the genetic diversity of the NH and YQpopulation is rich, and the ZS population is poor; the whole values showed the geneticdiversity is relatively high among all these ten populations. AMOVA showed that most ofthe variation was within populations (71.74%), and only28.26%variations betweenpopulations. The genetic distance calculated by MEGA4.0software between ZS and HKstocks is the greatest at0.3841, while that between XS and RA ones is the smallest at0.0410. The NJ tree based on genetic distance revealed that two main clusters wereidentified. The first cluster is composed of seven populations from ZS, WZ, XS, WL, RA,YQ and NH; the second cluster is composed of three populations from ZH, XM and HK.The result suggested that significant genealogical structure existed throughout the examinedrange of the H. nehereus. Although the results above showed that the genetic diversity of H.nehereus is relatively rich. However, in ZS and HK populations, the number ofpolymorphic loci was52and55severally, which were obviously lower than the other8populations. The percentage of polymorphic loci in HK population was the lowest amongthe ten studied populations, ZS population was followed. The other populations were nearlyat the same level and were higher than the two populations. The results suggested that thegenetic diversity of HK and ZS populations were counter-low. So we should pay moreattention to HK and ZS populations for the further germplasm resources protection.
引文
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