基于SNP标记的团头鲂、黑尾近红鲌和鲌鲂“先锋2号”群体遗传分析
武汉市农业科学院, 水产研究所, 湖北武汉 430207
| 摘 要： | 研究应用SLAF-seq开发了团头鲂、黑尾近红鲌以及鲌鲂“先锋2号”的SNP标记并研究了群体遗传多样性和群体遗传结构，结果显示Rsa-I的酶切效率为90.11%，三种鱼共得到181.13M reads。通过生物信息学分析，共获得SLAF标签1,339,007个，共得到446,680个SNP，测序平均Q30为93.03%，平均GC含量37.79%，测得观察等位基因数（No）为2.0，期望等位基因数（Ne）为1.63，观察杂合度（Ho）为0.08，期望杂合度（He）为0.36，遗传多样性指数（Genetic diversity index）为0.41，香浓指数（Shnnon Wiener index）为0.54，多态信息含量（PIC）为0.29，次要等位基因型频率（MAF）为0.28，表明三种鱼群体遗传多样处于中等水平，这可能跟三种鱼长期的人工选育有关。三种鱼的遗传距离显示鲌鲂“先锋2号”与团头鲂最近、与黑尾近红鲌次之、团头鲂和黑尾近红鲌最远，这也与形态学基本保持一致。 |
| 关 键 词： | 团头鲂; 黑尾近红鲌; 鲌鲂“先锋2号”; SNP标记; SLAF-seq; 遗传多样性; 遗传结构 |
| DOI： | 10.57237/j.jaf.2023.03.003 |
View:
Downloads:
收稿日期: 2023-08-10
接受日期: 2023-09-20
在线出版日期: 2023-10-09
Genetic Analysis of Megalobrama amblycephala, Ancherythroculter nigrocauda and Bo Fang “Xianfeng No. 2” Based on SNP Markers
Fisheries Research Institute, Wuhan Academy of Agricultural Sciences, Wuhan 430207, China
| Abstract: | The SNP markers of Megalobrama amblycephala, Ancherythroculter nigrocauda and Bo Fang “Xianfeng No. 2” were developed by SLAF-seq in this study. Further analysis on genetic diversity and genetic population were also done in this paper. The results showed that the efficiency of Enzyme digestion was 90.11% and 181.13M reads were obtained from three fishes. 1,339,007 SLAF labels and 446,680 SNP markers were through bioinformatics analysis. And the Q30 of mean sequencing was 93.03%, the mean GC content was 37.79%. The results showed that the observed allele number (No) was 2.0, and the expected allele number (Ne) was 1.63. The observed heterozygosity (Ho) was 0.08, while the expected heterozygosity (He) was 0.36. The genetic diversity index was 0.41, the Shnnon Wiener index was 0.54, and the PIC was 0.29, the MAF was 0.28. These results suggest that the genetic diversity of three populations were in the medium level. It might be related to artificial selection. The nearest genetic distance was between Bo Fang “Xianfeng No. 2” and Megalobrama amblycephala, and the furthest distance between was Megalobrama amblycephala and Ancherythroculter nigrocauda, which were in accordance with their shapes. |
| Keywords: | Megalobrama amblycephala; Ancherythroculter nigrocauda; Bo Fang “Xianfeng No. 2”; SNP Marker; SLAF-seq; Genetic Diversity; Genetic Population |
基金
| 1. | 湖北省科技创新专项 (2018ABA105) |
| 2. | 湖北洪山实验室开放课题 (2021hskf015) |
参考文献
| [1] | Sambrook J, Russell DW. Molecular Cloning: A Laboratory Manual, 3rd ed [M]. Cold Spring Harbor Laboratory Press, New York, 2001: 463-446. |
| [2] | Sun X, Liu D, Zhang X, et al. SLAF-seq: an efficient method of large-scale De novo SNP discovery and genotyping using high-throughput sequencing [J]. PloS one, 2013, 8 (3): e58700. |
| [3] | 李光华, 金方彭, 周睿, 等. 基于SNP标记的短须裂腹鱼自然群体遗传多样性分析 [J]. 水生生物学报, 2018, 42 (2): 271-276. |
| [4] | Alexander D H, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals [J]. Genome Research, 2009, 19 (9): 1655-1664. |
| [5] | Tamura K., Peterson D., Peterson N., et al. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods [J]. Molecular Biology and Evolution, 2011, 28 (10): 2731-2739. |
| [6] | Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences [J]. Journal of Molecular Evolution, 1980, 16: 111-120. |
| [7] | Qiu G F, Xiong L W, Han Z K, et al. 2017. A second generation SNP and SSR integrated linkage map and QTL mapping for the Chinese mitten crab Eriocheir sinensis [J]. Scientific Reports, 2017, 7, 39826. |
| [8] | Yu Y, Zhang X J, Yuan J B, et al. Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific White Shrimp Litopenaeus vannamei [J]. Scientific Reports, 2015, 5, 15612. |
| [9] | 蒋寿佳. 大黄鱼生长性状相关SNP标记的研究 [硕士学位论文]. 舟山: 浙江海洋大学图书馆, 2015. |
| [10] | Sun Y H, Qing Li Q, Wang G Y, et al. Polymorphisms in the Myostatin-1 gene and their association with growth traits in Ancherythroculter nigrocauda. Chinese Joumal of Oceanology and Limnology, 2017, 35: 597-602. |
| [11] | 侯宁, 张研, 鲁翠云, 等. 微卫星DNA标记分析德国镜鲤的遗传潜力 [J]. 遗传, 2007, 29 (12): 1509-1518. |
| [12] | Wright. Evolution and the Genetics of Populations [M]. Chicago: University of Chicago Press. 1978. |
| [13] | Nei M. Estimation of average heterozygosity and genetic distance from a small number of individuals [J]. Genetics, 1978, 89 (3): 583-590. |
| [14] | Nei M, Maruyama T, Chakraborty R. The bottleneck effect and genetic variability in populations [J]. Evolution, 1975, 29 (1): 1-10. |
| [15] | Beardmore J A, Mair G C, Lewis R I. Biodiversity in aquatic systems in relation to aquaculture [J]. Aquaculture Research, 1997, 28 (10): 829-839. |
| [16] | Xu Z, Primavera J P, Pena L D, et al. Genetic diversity of wild and cultured Black Tiger Shrimp (Penaeus monodom) in the Philippines using microsatellites [J]. Aquaculture, 2001, 199 (1-2): 13-40. |
| [17] | 赵广泰, 刘贤德, 王志勇, 等. 大黄鱼连续4代选育群体遗传多样性与遗传结构的微卫星分析 [J]. 水产学报, 2010, 34 (4): 500-507. |
| [18] | 张进, 梁旭芳, 杨敏, 等. 2个鳜鱼选育群体遗传多样性分析 [J]. 水产科学, 2014, 33 (7): 447-450. |
| [19] | 孙艳红，马浩，魏辉杰，等. 基于SSR标记的鲌鲂“先锋2号”、团头鲂及黑尾近红鲌的群体遗传分析 [J]. 淡水渔业，2022, 52 (1): 30-36. |
