儋州鸡体尺性状全基因组关联分析

doi:10.16431/j.cnki.1671-7236.2022.02.021

摘要/Abstract

摘要： 【目的】挖掘影响地方鸡体尺性状的有效SNP位点及功能基因, 给儋州鸡育种工作提供有效的数据基础和理论支撑。【方法】共采集200只儋州鸡血样并提取基因组DNA, 利用10×全基因组重测序技术获得全基因组SNP标记并对试验个体基因型进行分型。使用EMMAX软件基于混合线性模型对70日龄的儋州鸡体尺性状(胫长、胫围、体斜长、胸宽、髋骨宽、胸深、龙骨长)进行全基因组关联分析。【结果】共发现与胫长性状和胫围性状基因组水平显著相关的SNPs位点有12和8个, 与胫长性状相关SNPs分别定位于1、2、4和8号染色体上; 与胫围性状相关的SNPs定位于2、4、8和13号染色体上。预测与胫长相关的候选基因为KCNA1、TPK1、EZH2、FSTL5和AMY2A基因, 与胫围相关的候选基因为TPK1、FSTL5、AMY2A、TGFBI、LECT2和IL-9。通过KEGG通路分析和GO注释发现, 8个基因参与钾离子跨膜转运、硫胺素新陈代谢、细胞增殖、钙离子结合、骨骼肌卫星细胞维持与骨骼肌再生、细胞受体相互作用、生长因子活性等生物学进程。【结论】本研究发现了20个与儋州鸡体尺性状关联的SNPs位点, 并筛选到8个目标性状候选基因, 为儋州鸡育种提供候选的分子标记, 为地方鸡标记辅助选择提供新的思路。

关键词: 儋州鸡; 全基因组关联分析(GWAS); SNP; 体尺性状

Abstract: 【Objective】 This experiment was aimed to explore the effective SNP and functional genes related to body size traits in chickens, and provide effective theoretical support for Danzhou chickens.【Method】 Blood samples of 200 Danzhou chickens were collected and used to extract genomic DNA.Genome-wide SNP markers were obtained by using a depth of 10× whole genome resequencing, and analyzed the genotypes of individuals.Genome-wide association study (GWAS) was performed using a mixed-effects model and linear regression approach for body size traits (shank length, shank circumference, body slope length, breast width, pelvis width, breast depth, and fossil bone length) of 70-day-old Danzhou chickens by EMMAX.【Result】 The results showed that 12 and 8 SNPs were significantly related to the shank length and the shank circumference.SNPs associated with shank length traits were located on chromosomes 1, 2, 4 and 8.SNPs associated with shank circumference traits were located on chromosomes 2, 4, 8 and 13.The experiment predicted that the candidate genes associated with shank length were KCNA1, TPK1, EZH2, FSTL5 and AMY2A, and the candidate genes associated with shank circumference were TPK1, FSTL5, AMY2A, TGFBI, LECT2 and IL-9.Through KEGG pathway analysis and GO annotation, it was found that 8 genes were involved in biological processes such as potassium ion transmembrane transport, thiamine metabolism, cell proliferation, calcium binding, skeletal muscle satellite cell maintenance and skeletal muscle regeneration, cell receptor interaction, growth factor activity and so on.【Conclusion】 In this experiment, 20 SNPs associated with body size traits were found, and 8 candidate genes for the target traits were screened, which provided candidate molecular markers for Danzhou chickens breeding and new ideas for marker assisted selection of local.

Key words: Danzhou chickens; genome wide association study (GWAS); SNP; body size traits

中图分类号:

S831.2

姜宏正, 杨德智, 马中华, 荀文娟, 施力光, 侯冠彧. 儋州鸡体尺性状全基因组关联分析[J]. 中国畜牧兽医, 2022, 49(2): 598-607.

JIANG Hongzheng, YANG Dezhi, MA Zhonghua, XUN Wenjuan, SHI Liguang, HOU Guanyu. Genome-wide Association Study of Body Size Traits in Danzhou Chickens[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(2): 598-607.

参考文献

[1] HUANG S, HE Y, YE S, et al. Genome-wide association study on chicken carcass traits using sequence data imputed from SNP array[J]. Journal of Applied Genetics, 2018, 59(3): 335-344.
[2] BAI H, SUN Y, LIU N, et al. Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600.
SNP arrays[J]. BMC Genomics, 2018, 19(1): 1-10.
[3] LIU Z, SUN C, YAN Y, et al. Genetic variations for egg quality of chickens at late laying period revealed by genome-wide association study[J]. Scientific Reports, 2018, 8(1): 1-11.
[4] 张建丰, 王小立, 孙妍妍, 等. 鸡体尺性状和屠宰性状对繁殖性状的影响[J]. 黑龙江畜牧兽医, 2016, 18: 72-74.
ZHANG J F, WANG X L, SUN Y Y, et al. Influence of body size traits and slaughter traits on reproductive traits in chickens[J]. Heilongjiang Animal Science and Veterinary Medicine, 2016, 18: 72-74. (in Chinese)
[5] 李万贵, 张依裕, 潘兰兵, 等. 兴义鸭体尺性状及屠宰性能的相关性分析[J]. 中国畜牧兽医, 2014, 41(12): 215-219.
LI W G, ZHANG Y Y, PAN L B, et al. Correlation analysis between body size traits and slaughter performances on Xingyi ducks[J]. China Animal Husbandry & Veterinary Medicine, 2014, 41(12): 215-219. (in Chinese)
[6] 徐明明, 彭灿阳, 曲湘勇, 等. 雪峰乌骨鸡体重、体尺性状及产肉性能的相关分析[J]. 经济动物学报, 2017, 21(4): 228-232.
XU M M, PENG C Y, QU X Y, et al. Correlative analysis on body weight, body size and meat productivity of Xuefeng Black-boned chicken[J]. Journal of Economic Animal, 2017, 21(4): 228-232. (in Chinese)
[7] 中华人民共和国农业部. 中华人民共和国农业行业标准——鸡饲养标准: NY/T 33—2004[S]. 北京: 中国标准出版社, 2004.
MINISTRY OF AGRICULTURE OF THE PEOPLE'S REPUBLIC OF CHINA. Agricultural industry standards of the People's Republic of China——Feeding standard of chicken: NY/T 33—2004[S]. Beijing: Standards Press of China, 2004. (in Chinese)
[8] 中华人民共和国农业部. 中华人民共和国农业行业标准——家禽生产性能名词术语和度量统计方法: NY/T 823—2004[S]. 北京: 中国标准出版社, 2004.
MINISTRY OF AGRICULTURE OF THE PEOPLE'S REPUBLIC OF CHINA. Agricultural standards of the People's Republic of China——Performance terminology and measurements for poultrye: NY/T 823—2004[S]. Beijing: Standards Press of China, 2004. (in Chinese)
[9] KANG H M, SUL J H, SERVICE S K, et al. Variance component model to account for sample structure in genome-wide association studies[J]. Nature Genetics, 2010, 42(4): 348-354.
[10] EMRANI H, MASOUDI A A, VAEZ TORSHIZI R, et al. Genome-wide association study of shank length and diameter at different developmental stages in chicken F2 resource population[J]. Animal Genetics, 2020, 51(5): 722-730.
[11] 孙艳发, 刘冉冉, 郑麦青, 等. 鸡胫长和胫围的全基因组关联分析[J]. 畜牧兽医学报, 2013, 44(3): 358-365.
SUN Y F, LIU R R, ZHENG M Q, et al. Genome-wide association study on shank length and shank girth in chicken[J]. Acta Veterinaria et Zootechnica Sinica, 2013, 44(3): 358-365. (in Chinese)
[12] TAM V, PATEL N, TURCOTTE M, et al. Benefits and limitations of genome-wide association studies[J]. Nature Reviews Genetics, 2019, 20(8): 467-484.
[13] ZHANG H, SHEN L Y, XU Z C, et al. Haplotype-based genome-wide association studies for carcass and growth traits in chicken[J]. Poultry Science, 2020, 99(5): 2349-2361.
[14] ENDO T, TAKIZAWA S, TANAKA S, et al. Amylase alpha-2A autoantibodies: Novel marker of autoimmune pancreatitis and fulminant type 1 diabetes[J]. Diabetes, 2009, 58(3): 732-737.
[15] LORDA-DIEZ C I, MONTERO J A, DIAZ-MENDOZA M J, et al. βig-h3 potentiates the profibrogenic effect of TGFβ signaling on connective tissue progenitor cells through the negative regulation of master chondrogenic genes[J]. Tissue Engineering Part A, 2013, 19(3-4): 448-457.
[16] XU Z, HE J, ZHOU X, et al. Down-regulation of LECT2 promotes osteogenic differentiation of MSCs via activating Wnt/beta-Catenin pathway[J]. Biomedicine & Pharmacotherapy, 2020, 130: 110593.
[17] BISCARINI F, BOVENHUIS H, VAN DER POEL J, et al. Across-line SNP association study for direct and associative effects on feather damage in laying hens[J]. Behavior Genetics, 2010, 40(5): 715-727.
[18] AKIZU N, GARCIA M A, ESTARAS C, et al. EZH2 regulates neuroepithelium structure and neuroblast proliferation by repressing p21[J]. Open Biology, 2016, 6(4): 150227.
[19] KISLIOUK T, YOSEFI S, MEIRI N. miR-138 inhibits EZH2 methyltransferase expression and methylation of histone H3 at lysine 27, and affects thermotolerance acquisition[J]. European Journal of Neuroscience, 2011, 33(2): 224-235.
[20] 刘立东, 温康, 顾旺, 等. 卵泡抑素样蛋白5基因在鹅肥肝形成中表达调控的研究[J]. 中国家禽, 2019, 41(13): 6-10.
LIU L D, WEN K, GU W, et al. Study on the expression and regulation of Follistatin-like 5 gene during goose fatty liver formation[J]. China Poultry, 2019, 41(13): 6-10. (in Chinese)
[21] ZHANG D, MA X, SUN W, et al. Down-regulated FSTL5 promotes cell proliferation and survival by affecting Wnt/β-Catenin signaling in hepatocellular carcinoma[J]. International Journal of Clinical and Experimental Pathology, 2015, 8(3): 386-394.
[22] 刘丽. KCNA1在宫颈癌中的表达及与宫颈癌发生发展的关系及机制研究[D]. 济南: 山东大学, 2020.
LIU L. Expression and mechanism of KCNA1 in occurrence and development of cervical cancer[D]. Jinan: Shandong University, 2020. (in Chinese)
[23] OUADID-AHIDOUCH H, CHAUSSADE F, ROUDBARAKI M, et al. KV1.1 K⁺ channels identification in human breast carcinoma cells: Involvement in cell proliferation[J]. Biochemical and Biophysical Research Communications, 2000, 278(2): 272-277.
[24] WENG Z P, PAN X Y, CUI N, et al. Voltage-gated K⁺ channels are associated with cell proliferation and cell cycle of ovarian cancer cell[J]. Gynecologic Oncology, 2007, 104(2): 455-460.
[25] FRADIN D, BOUGNERES P. Three common intronic variants in the maternal and fetal thiamine pyrophosphokinase gene (TPK1) are associated with birth weight[J]. Annals of Human Genetics, 2007, 71(5): 578-585.