GENOME-WIDE ASSOCIATION STUDY OF THERMAL TOLERANCE IN LARGE YELLOW CROAKER LARIMICHTHYS CROCEA BASED ON SLAF-SEQ TECHNOLOGY
-
摘要: 利用Illumina HiSeqTM 2500测序平台, 对通过高温胁迫实验筛选得到的20尾耐高温和20尾不耐高温的大黄鱼(Larimichthys crocea)进行了简化基因组测序(SLAF-seq), 每个样本的平均测序深度达到10.26×, 共获得419211个高质量的群体单核苷酸多态性(SNP)位点 。利用TASSEL软件的混合线性模型(MLM)进行全基因组关联分析(GWAS), 共筛选到38个与大黄鱼耐高温性状显著相关的SNP位点(P<2.39E–08)。利用BLAST程序定位每个SNP位点在大黄鱼基因组中的位置, 并分析其周围的功能基因。结果在38个SNPs附近共找到26个已知的功能基因, 这些基因主要与细胞转录、代谢、免疫等功能相关。研究结果可为下一步大黄鱼耐高温分子机制解析及耐高温品种的选育提供参考。Abstract: Twenty thermal-tolerant and twenty thermal-sensitive individuals of Larimichthys crocea were sequenced using specific-locus amplified fragment (SLAF-seq) technology based on Illumina HiSeqTM2500 platform. 419211 SNPs were identified with an average read depth of 10.26× for each sample. Thirty-eight SNPs (P<2.39E–08) signifi- cantly related with thermal tolerance trait were identified according to association analysis. The SNP locations in large yellow croaker genome were identified using BLAST program, and functional genes around SNP were annotated. Twenty-six genes with known functions were discovered around 38 SNPs, which mainly regulate cell transcription, metabolism and immunity. These results provide basic information to analyze thermal-tolerant molecular mechanism and develop thermal-tolerant lines of Larimichthys crocea in the future.
-
Keywords:
- Larimichthys crocea /
- High temperature /
- SLAF-seq /
- SNP marker /
- GWAS
-
-
![]()
图 3 大黄鱼耐热性状全基因组关联分析的曼哈顿图
Figure 3. Manhttan plot of GWAS of thermal tolerance in large yellow croaker
表 1 20尾耐高温(R)和20尾不耐高温(S)大黄鱼的死亡时间
Table 1 The information of death time of 20-tails thermal-tole-rance (R) and 20-tails thermal-sensitive (S) large yellow croaker
编号Number 33℃后存活时间Elapsed time after 33℃ 编号Number 33℃后存活时间Elapsed time after 33℃ S1 0 R1 199h 15min S2 1h 20min R2 199h 30min S3 1h 58min R3 199h 45min S4 2h 35min R4 200h 5min S5 3h 1min R5 200h 9min S6 3h 12min R6 200h 26min S7 3h 13min R7 200h 52min S8 3h 14min R8 201h 42min S9 3h 55min R9 201h 49min S10 4h R10 201h 53min S11 4h 35min R11 202h 5min S12 4h 45min R12 202h 12min S13 25h 50min R13 202h 25min S14 32h 10min R14 202h 45min S15 32h 22min R15 202h 56min S16 32h 40min R16 203h 35min S17 33h 10min R17 204h 5min S18 36h R18 204h 16min S19 36h 40min R19 204h 20min S20 49h 35min R20 204h 32min 
下载: 导出CSV
表 2 与耐热性状显著关联的SNPs位点
Table 2 SNPs significantly associated with thermal tolerance trait
位点Scaffold 位置Position (bp) P值P value 周围基因Surrounding gene 功能注释Function annotation scf2 839614 1.02E–8 Hypothetical protein EH28_10329 假定蛋白 scf2 1432837 1.25E–8 Trafficking kinesin-binding protein 1 参与核内体到溶酶体运输的调控 scf2 1643308 6.40E–9 Zinc finger protein 292 锌指蛋白 scf2 3088908 9.44E–9 Coiled-coil domain-containing protein 96 细胞骨架及非膜性细胞器细胞组分 scf2 3130802 9.44E–9 Deleted in malignant brain tumors 1 protein 一种糖蛋白 scf2 3207868 9.44E–9 NF-kappa-B-repressing factor 参与转录负调控 scf2 3258294 9.44E–9 未发现 无 scf2 3266727 4.57E–9 Multiple epidermal growth factor-like domains protein 8 多表皮生长因子样结构域蛋白 scf2 3331592 1.45E–9 Gamma-crystallin M2 γ-晶状体蛋白M2 scf2 3443140 9.44E–9 Ryanodine receptor 2 主要存在于心肌组织, 是肌质释放储存钙离子时主要媒介 scf223 463406 8.55E–9 Spectrin beta chain, brain 3 是一种肌动蛋白交联和蛋白质分子支架, 连接细胞膜与肌动蛋白, 决定细胞形状, 安置跨膜蛋白等功能 scf223 909858 5.53E–9 putative voltage-dependent R-type calcium channel subunit alpha-1E 调节钙离子进入兴奋的细胞, 参与依赖钙离子的生物过程 scf257 8308 1.34E–10 GTPase IMAP family member 8 在免疫系统中起到抗凋亡作用、应激感染 scf466 99149 2.69E–11 Suppressor of tumorigenicity 14 protein 降解细胞外基质 scf466 132344 2.11E–8 未发现 无 scf466 337518 2.03E–12 Potassium voltage-gated channel subfamily B member 1 是电压门控钾通道亚家族中一员, 介导兴奋细胞膜的跨膜钾离子运输 scf466 337519 2.03E–12 Potassium voltage-gated channel subfamily B member 1 是电压门控钾通道亚家族中一员, 介导兴奋细胞膜的跨膜钾离子运输 scf466 354360 2.27E–10 NHL repeat-containing protein 2 调节细胞氧化还原内稳态 scf466 357793 1.41E–13 hypothetical protein EH28_01175 假定蛋白 scf466 358008 1.59E–9 hypothetical protein EH28_01175 假定蛋白 scf466 417746 1.13E–8 Nebulin-related-anchoring protein 伴肌动蛋白相关锚定蛋白 scf466 418698 2.27E–10 Nebulin-related-anchoring protein 伴肌动蛋白相关锚定蛋白 scf466 451775 2.21E–8 Dynamin-binding protein 支架蛋白 scf716 33634 3.29E–14 Serine/threonine-protein kinase tousled-like 2 丝氨酸/苏氨酸蛋白激酶, 参与染色质组装, DNA复制、转录及修复等过程 scf716 78112 2.11E–8 未发现 无 scf716 80028 9.44E–9 Low affinity cationic amino acid transporter 2 阳离子氨基酸转运蛋白2, 作为一种透性酶, 参与碱性氨基酸的运输 scf716 89206 1.92E–8 Rho-related GTP-binding protein RhoN 与神经元和肝脏功能相关 scf716 90152 9.44E–9 Rho-related GTP-binding protein RhoN 与神经元和肝脏功能相关 scf716 140280 4.11E–10 Splicing factor 3B subunit 3 剪接因子 scf716 140448 3.06E–11 Centrosomal protein 中心体蛋白 scf716 179863 1.17E–10 Disintegrin and metalloproteinase domain-containing protein 11 解离素和金属蛋白酶 scf716 180588 3.10E–12 Disintegrin and metalloproteinase domain-containing protein 11 解离素和金属蛋白酶 scf716 199932 3.49E–10 Disintegrin and metalloproteinase domain-containing protein 11 解离素和金属蛋白酶 scf716 206908 1.61E–8 Synaptonemal complex protein SC65 联会复合体蛋白 scf716 240491 9.44E–9 ATP-citrate synthase ATP柠檬酸合成酶 scf716 276714 9.44E–9 Nucleoporin Nup37 核孔蛋白 scf716 276720 9.44E–9 Nucleoporin Nup37 核孔蛋白 scf1453 71224 1.39E–9 Potassium voltage-gated channel subfamily H member 4 是电压门控钾通道超家族中一员, 介导兴奋细胞膜的跨膜钾离子运输
下载: 导出CSV
-
[1] 薛彬, 何依娜, 郭远明, 等. 大黄鱼生态养殖系统研究. 现代农业科技, 2014, (16): 244—249 http://www.cnki.com.cn/Article/CJFDTOTAL-ANHE201416153.htm Xue B, He Y N, Guo Y M, et al. Research of ecological culture system of Larimichthys crocea [J]. Modern Agricultural Sciences and Technology, 2014, (16): 244—249
薛彬, 何依娜, 郭远明, 等. 大黄鱼生态养殖系统研究. 现代农业科技, 2014, (16): 244—249 http://www.cnki.com.cn/Article/CJFDTOTAL-ANHE201416153.htm[2] 李佳凯, 王志勇, 刘贤德, 等. 高温对大黄鱼(Larimichthys crocea)幼鱼血清生化指标的影响. 海洋通报, 2015, 34(4): 457—462 doi: 10.11840/j.issn.1001-6392.2015.04.014 Li J K, Wang Z Y, Liu X D, et al. Effects of high tempera-ture on serum biochemical indices of large yellow croa-ker Larimichthys crocea [J]. Marine Science Bulletin, 2015, 34(4): 457—462
李佳凯, 王志勇, 刘贤德, 等. 高温对大黄鱼(Larimichthys crocea)幼鱼血清生化指标的影响. 海洋通报, 2015, 34(4): 457—462 doi: 10.11840/j.issn.1001-6392.2015.04.014[3] Hulata G. Genetic manipulations in aquaculture: a review of stock improvement by classical and modern technologies [J]. Genetica, 2001, 111(1—3): 155—173
[4] 马爱军, 黄智慧, 王新安, 等. 大菱鲆(Scophthalmus maxi-)耐高温品系选育及耐温性能评估. 海洋与湖沼, 2012, 43(4): 797—804 doi: 10.11693/hyhz201204017017 Ma A J, Huang Z H, Wang X A, et al. The selective breeding of thermal tolerance family and appraisal of performance in turbot Scophthalmus maximus [J]. Oceanologia Et Limnologia Sinica, 2012, 43(4): 797—804
马爱军, 黄智慧, 王新安, 等. 大菱鲆(Scophthalmus maxi-)耐高温品系选育及耐温性能评估. 海洋与湖沼, 2012, 43(4): 797—804 doi: 10.11693/hyhz201204017017[5] Xu K, Duan W, Xiao J, et al. Development and application of biological technologies in fish genetic breeding [J]. Science China Life Sciences, 2015, 58(2): 187—201 doi: 10.1007/s11427-015-4798-3
[6] Yue G H. Recent advances of genome mapping and marker-assisted selection in aquaculture [J]. Fish and Fisheries, 2014, 15(3): 376—396 doi: 10.1111/faf.2014.15.issue-3
[7] Vignal A, Milan D, SanCristobal M, et al. A review on SNP and other types of molecular markers and their use in animal genetics [J]. Genetics Selection Evolution, 2002, 34(3): 275—306 doi: 10.1186/1297-9686-34-3-275
[8] Liu Z J, Cordes J F. DNA marker technologies and their applications in aquaculture genetics [J]. Aquaculture, 2004, 238(1): 1—37
[9] 全迎春, 马冬梅, 白俊杰, 等. 大口黑鲈转录组SNPs筛选及其与生长的关联分析. 水生生物学报, 2016, 40(6): 1128-1134 doi: 10.7541/2016.146 Quan Y C, Ma D M, Bai J J, et al. SNPs identification in RNA-seq data of largemouth bass (Micropterus salmoides) fed on formulated feed and association analysis with growth trait [J]. Acta Hydrobiologica Sinica, 2016, 40(6): 1128-1134
全迎春, 马冬梅, 白俊杰, 等. 大口黑鲈转录组SNPs筛选及其与生长的关联分析. 水生生物学报, 2016, 40(6): 1128-1134 doi: 10.7541/2016.146[10] Korte A, Farlow A. The advantages and limitations of trait analysis with GWAS: a review [J]. Plant methods, 2013, 9(1): 29 doi: 10.1186/1746-4811-9-29
[11] Yang J, Jiang H, Yeh C T, et al. Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel [J]. The Plant Journal, 2015, 84(3): 587—596 doi: 10.1111/tpj.2015.84.issue-3
[12] 赵琼一, 李信, 周德贵, 等. 后基因组时代下作物的SNP分型方法. 分子植物育种, 2010, 8(1): 125—133 http://www.cnki.com.cn/Article/CJFDTOTAL-FZZW201001027.htm Zhao Q Y, Li X, Zhou D G, et al. SNP genotyping methods for crops in post-genomic era [J]. Molecular Plant Breeding, 2010, 8(1): 125—133
赵琼一, 李信, 周德贵, 等. 后基因组时代下作物的SNP分型方法. 分子植物育种, 2010, 8(1): 125—133 http://www.cnki.com.cn/Article/CJFDTOTAL-FZZW201001027.htm[13] 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. doi: 10.1371/journal.pone.0058700
[14] Diegane N D, Chen Y Y, Lin Y H, et al. The immune response of tilapia Oreochromis mossambicus and its susceptibility to Streptococcus iniae under stress in low and high temperatures [J]. Fish & Shellfish Immunology, 2007, 22(6): 686—694
[15] Li R, Yu C, Li Y, et al. SOAP2: an improved ultrafast tool for short read alignment [J]. Bioinformatics, 2009, 25(15): 1966—1967 doi: 10.1093/bioinformatics/btp336
[16] Purcell S, Neale B, Todd-Brown K, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses [J]. The American Journal of Human Genetics, 2007, 81(3): 559—575 doi: 10.1086/519795
[17] Bradbury P J, Zhang Z, Kroon D E, et al. TASSEL: software for association mapping of complex traits in diverse samples [J]. Bioinformatics, 2007, 23(19): 2633—2635 doi: 10.1093/bioinformatics/btm308
[18] Alexander D H, Novembre J, Lange K. Fast model-based estimation of ancestry in unrelated individuals [J]. Genome Research, 2009, 19(9): 1655—1664 doi: 10.1101/gr.094052.109
[19] Davey J W, Hohenlohe P A, Etter P D, et al. Genome-wide genetic marker discovery and genotyping using next-generation sequencing [J]. Nature Reviews Genetics, 2011, 12(7): 499—510 doi: 10.1038/nrg3012
[20] Xia C, Chen L, Rong T, et al. Identification of a new maize inflorescence meristem mutant and association analysis using SLAF-seq method [J]. Euphytica, 2015, 202(1): 35—44 doi: 10.1007/s10681-014-1202-5
[21] Zhang P, Zhu Y, Wang L, et al. Mining candidate genes associated with powdery mildew resistance in cucumber via super-BSA by specific length amplified fragment (SLAF) sequencing [J]. BMC Genomics, 2015, 16: 1058. doi: 10.1186/s12864-015-2041-z
[22] Li H, Peng Z, Yang X, et al. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels [J]. Nature Genetics, 2013, 45(1): 43—50
[23] Huang X, Wei X, Sang T, et al. Genome-wide association studies of 14 agronomic traits in rice landraces [J]. Nature Genetics, 2010, 42(11): 961—967 doi: 10.1038/ng.695
计量
- 文章访问数:
- HTML全文浏览量:
- PDF下载量: