基于重测序技术的塔河马鹿特异性SNP位点筛选

doi:10.16431/j.cnki.1671-7236.2022.04.023

Abstract

Abstract: :【Objective】 To screen high quality single nucleotide polymorphic site (SNP) of Tahe red deer,construct specific molecular genetic markers, provide reference for pure breed identification of Tahe red deer. 【Method】 The whole genome of 32 blood DNA samples of Tahe red deer collected by the National Special Economic Animal Resource Sharing Platform in 1999 was re-sequenced. Compared with the chromosome-level reference genome of sika deer, the alignment rate, coverage and sequencing depth were counted. SNPEff was used to count the distribution of SNP on each chromosome, SNPhylo was used to construct a molecular evolutionary tree based on the sites, VCFTOOLS was used to calculate the genetic differentiation index(Fst), and the Fst value was sorted in descending order and the threshold was settet as Fst≥0.25 to eliminate the unqualified loci. R language was used for principal component analysis, the top 1 500 SNPs of 33 chromosomes was counted, the eigenvalues of the top 100 SNPs was extracted, and the PCA cluster diagrams were drew respectively. 【Result】 The results of whole-genome resequencing showed that the effective data volume of the blood genomic DNA of 32 Tahe red deer that passed the quality inspection was 868 791 354 600 bp, and the sequencing quality met the requirements of subsequent data analysis. The average comparison rate of the 32 samples sequencing data was 98.06%, the average coverage was 97.66%, and the average depth was 6.787. After filtering, 20 139 122 high-quality SNPs were obtained, of which SNPs were the most distributed on chromosome 4, and more than 90% of the mutations were located in the intergenic and exon regions. The number of candidate specific SNP sites after establishment was 12 050 781. 544 717 SNPs were selected by VCFTOOLS. The top 1 500 SNPs of each chromosome were selected for PCA, the PCA results showed that when the number of SNP was decreased from 49 500 to 100, the discrimination efficiency was not decreased. Finally, 100 SNPs with strong specificity and high stability were screened out.【Conclusion】 100 Tahe red deer-specific SNPs were obtained through whole-genome resequencing technology and bioinformatics analysis, which provided a theoretical basis for the identification of purebred Tahe red deer and the screening of core germplasm.

Key words: Tahe red deer; resequencing technology; SNPs; screening

CLC Number:

S825

DENG Yihua, WANG Tianjiao, WANG Hongliang, DONG Yimeng, LIU Xin, XING Xiumei. Screening of Specific SNP Sites in Tahe Red Deer Based on Resequencing Technology[J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(4): 1413-1421.

References

[1] 马合木提·哈力克,吾玛尔·阿布力孜,艾尼瓦尔·吐米尔,等.新疆马鹿塔里木亚种的现状与保护[J].兽类学报,2004,4:329-332. HALIK M,ABLIZ U,TUMUR A,et al.The present living status of Tarim red deer (Cervus elaphus yarkandensis) and its protective countermeasures[J].Acta Theriologica Sinica,2004,4:329-332.(in Chinese)
[2] 帕尔哈提·萨依提.塔里木马鹿遗传资源调查情况[J].当代畜禽养殖业,2015,6:37-38. SAYITI P.Investigation on genetic resources of Tarim red deer[J].Modern Animal Husbandry,2015,6:37-38.(in Chinese)
[3] 陈长明,吐逊汗·牙合甫,冷朝升,等.浅淡塔里木马鹿的品种选育与结构调整[J].畜牧兽医科技信息,2008,4:116. CHEN C M,TUXUNHAN Y,LENG C S,et al.The breeding and structure adjustment of Tarim red deer[J].Chinese Journal of Animal Husbandry and Veterinary Medicine,2008,4:116.(in Chinese)
[4] RABBANI B,TEKIN M,MAHDIEH N.The promise of whole-exome sequencing in medical genetics[J].Journal of Human Genetics,2014,59(1):5-15.
[5] BENTLEY D R.Whole-genome re-sequencing[J].Current Opinion in Genetics and Development,2006,16(6):545-552.
[6] GAO Q,YUE G D,LI W Q,et al.Recent progress using high-throughput sequencing technologies in plant molecular breeding[J].Journal of Integrative Plant Biology,2012,54(4):215-227.
[7] LEE K T,CHUNG W H,LEE S Y,et al.Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity[J].BMC Genomics,2013,14(1):519.
[8] HOUSTON R D,DAVEY J W,BISHOP S C,et al.Characterisation of QTL-linked and genome-wide restriction site-associated DNA (RAD) markers in farmed Atlantic salmon[J].BMC Genomics,2012,13(1):244.
[9] MOON S J,KIM T H,LEE K T,et al.A genome-wide scan for signatures of directional selection in domesticated pigs[J].BMC Genomics,2015,16(1):130.
[10] ZHOU X M,WANG B S,PAN Q,et al.Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history[J].Nature Genetics,2014,46(12):1303-1310.
[11] 汪文强,赵生国,马利青,等.动物基因组学重测序的应用研究进展[J].畜牧兽医学报,2016,47(10):1947-1953. WANG W Q,ZHAO S G,MA L Q,et al.The research progress and application of resequencing based onanimal genomics[J].Acta Veterinaria et Zootechnica Sinica,2016,47(10):1947-1953.(in Chinese)
[12] BA H X,LI Z P,YANG Y F,et al.Development of diagnostic SNP markers to monitor hybridization between sika deer (Cervus nippon) and Wapiti (Cervus elaphus)[J].G3,2018,8(7):2173-2179.
[13] 董世武,王天骄,刘华淼,等.基于GBS技术对梅花鹿、马鹿及其杂交后代基因组SNP特征的分析[J].畜牧兽医学报,2019,50(12):2422-2430. DONG S W,WANG T J,LIU H M,et al.Analysis of genomic SNP characteristics of sika deer,red deer and their hybrid progenies based on GBS technology[J].Acta Veterinaria et Zootechnica Sinica,2019,50(12):2422-2430.(in Chinese)
[14] 塔依尔江·麦麦提,苏比奴尔·艾力,布威海丽且姆·阿巴拜科日,等.塔里木马鹿干旱环境适应相关基因的筛选、克隆及生物信息学分析[J].中国畜牧兽医,2021,48(6):1906-1917. MAMAT T,ELI S,ABABAIKERI B,et al.Screening,cloning and bioinformatics analysis of drought adaptation related genes in Tarim red deer[J].China Animal Husbandry & Veterinary Medicine,2021,48(6):1906-1917.(in Chinese)
[15] FAN H H,WANG T J,LI Y,et al.Development and validation of a 1K sika deer (Cervus nippon) SNP chip[J].BMC Genomic Data,2021,22(1):35.
[16] LI H,DURBIN R.Fast and accurate short read alignment with burrows-wheeler transform[J].Bioinformatics,2009,25(14):1754-1760.
[17] LI H,HANDSAKER B,WYSOKER A,et al.The sequence alignment/map format and SAMtools[J].Bioinformatics,2009,25(16):2078-2079.
[18] DANECEK P,AUTON A,ABECASIS G,et al.The variant call format and VCFtools[J].Bioinformatics,2011,27(15):2156-2158.
[19] DORGIVAL M D L J,ADRIANO H D N R,GUILHERME F D C L,et al.Phenotypic evaluation of trait types in Guzerá cows of different calving orders[J].Semina:Ciências Agrárias,2017,38(4Supl1):2755.
[20] THONGDA W,ZHAO H G,ZHANG D D,et al.Development of SNP panels as a new tool to assess the genetic diversity,population structure,and parentage analysis of the Eastern oyster (Crassostrea virginica)[J].Marine Biotechnology,2018,20(3):385-395.
[21] 何俊,钱长嵩,Richard G,等.SNP芯片数据估计动物个体基因组品种构成的方法及应用[J].遗传,2018,40(4):305-314. HE J,QIAN C S,RICHARD G,et al.Estimating genomic breed composition of individual animals using selected SNPs[J].Hereditas,2018,40(4):305-314.(in Chinese)
[22] 朱涛,谷洪昌,张泽宾,等.鸭不同品种特异性分子标记SNP的筛选与鉴定[J].中国家禽,2018,40(15):7-10. ZHU T,GU H C,ZHANG Z B,et al.SNP identificationfor specific molecular markers of different duck breeds[J].China Poultry,2018,40(15):7-10.(in Chinese)
[23] 岳阳,张哲,徐忠,等.基于单核苷酸多态性鉴别小梅山猪及其制品[J].农业生物技术学报,2018,26(12):2168-2175. YUE Y,ZHANG Z,XU Z,et al.Identification of small Meishan pig (Sus scrofa) and its products based on single nucleotide polymorphism[J].Journal of Agricultural Biotechnology,2018,26(12):2168-2175.(in Chinese)
[24] WANG R,SUN J L,HAN H,et al.Whole-genome resequencing reveals genetic characteristics of different duck breeds from the Guangxi region in China[J].G3,2021,11(4):jkab054.
[25] LI D,LI Y,LI M,et al.Population genomics identifies patterns of genetic diversity and selection in chicken[J].BMC Genomics,2019,20(1):263.
[26] CHEN H,XIE W,HE H,et al.A high-density SNP genotyping array for rice biology and molecular breeding[J].Molecular Plant,2014,7(3):541-553.
[27] 苏莹,邢秀梅,邵元臣,等.利用Y染色体AMELY基因分析中国马鹿的遗传多样性[J].中国畜牧兽医,2016,43(3):761-767. SU Y,XING X M,SHAO Y C,et al.Genetic diversity analysis of cervus elephus using AMELY gene in Y chromosome[J].China Animal Husbandry & Veterinary Medicine,2016,43(3):761-767.(in Chinese)
[28] SHAO Y C,SU W L,LIU H M,et al.Complete mitochondrial genome sequence of northeastern red deer (Cervus elaphus xanthopygus)[J].Mitochondrial DNA:The Journal of DNA Mapping,Sequencing & Analysis,2016,27(1):547-8.
[29] 王小鹏.基于60K芯片的中国地方猪种品种特异性遗传标签构建[D].南昌:江西农业大学,2016. WANG X P.Construction of specific genetic label for Chinese indigenous pig breeds based on 60K chip[D].Nanchang:Jiangxi Agricultural University.2016.(in Chinese)
[30] 刘月丽,覃锡忠,贺三刚,等.PCA与随机森林相结合筛选高信息量SNP位点——应用于羊的品种鉴别[J].计算机工程与应用,2018,54(16):235-240. LIU Y L,QIN X Z,HE S G,et al.Combined use of PCA and random forests to identify high informative SNP loci:Application in sheep population identification[J].Computer Engineering and Applications,2018,54(16):235-240.(in Chinese)

Screening of Specific SNP Sites in Tahe Red Deer Based on Resequencing Technology

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	LIU Xinyue, LI Lifang, WANG Zhenbao, ZHANG Wenliang, ZHANG Xin, ZHAO Hongtao, LI Pengyu, ZHENG Haotian, XIAO Jin, QI Peng. Adjuvants Screening and Immune Protection of Porcine Circovirus Type 2 Synthetic Peptide Vaccine [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(3): 1068-1080.
[2]	MENG Yingwen, LI Yuehua, SHA Zhou, LI Chenyu, GONG Youquan, DONG Yaqin, WEI Rong, ZOU Fengcai, NI Bo. Screening of the Natural Products Against Senecavirus A and Study on Its Mechanism of Antagonism [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(2): 734-744.
[3]	FENG Xiaopin, LI Yinxia, ZHANG Chenjian, ZHANG Jun, MENG Chunhua, QIAN Yong, CAO Shaoxian. Coning and Polymorphism Identification of PLAG1 Gene and Its Association Analysis with Birth Weight and Body Size Traits in Boer Goats [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(9): 3465-3474.
[4]	LI Tianxi, DANG Meng, LONG Miao. Identification of an Antagonistic Strain of Aspergillus flavus and Preliminary Analysis of Its Antibacterial Components [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(5): 1828-1839.
[5]	ZHOU Ya, ZHANG Heyang, LIU Linling, LI Haodong, ZHENG Junjun, WANG Guiwu. Polymorphism of MSRB3 Gene and Its Association Analysis with Antler Weight Traits in Sika Deer [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(11): 4279-4287.
[6]	WANG Xiangyan, XIN Guoqin, XU Haiyan, GU Wei, LAN Jianghua, HAO Muqiang, FENG Gang. Screening of a Strain of Pediococcus pentosus with High Antioxidant Activity [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(1): 179-187.
[7]	XI Li, QIN Xinxi, SUN Xinfeng, SONG Yumin, LI Zhiqiang. Screening and Application of Campylobacter Bacteriophage in Broilers [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(9): 3273-3282.
[8]	LIU Pengcheng, ZHANG Ji, QIU Ganyuan, GONG Yu, LI Xuesong, LI Wei, ZHANG Yiyu, LIU Ruoyu. Polymorphism of Bovine TBC1D Gene and Its Association with Growth Traits in Guanling Cattle [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(8): 2853-2863.
[9]	MIAO Manning, GUO Yiwen, HU Debao, ZENG Yuhan, LI Xin, ZHANG Linlin, DING Xiangbin, GUO Hong. Transcriptome Sequencing and Bioinformatics Analysis of MSTN Gene-edited Bovine Muscles [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(7): 2271-2281.
[10]	DAI Guodong, YAN Hongbin, LI Li, FU Baoquan, JIA Wanzhong. Research Progress on Screening Methods for Candidate Vaccine Molecules Against Parasitic Zoonoses [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(6): 2177-2187.
[11]	FAN Huanhuan, WANG Tianjiao, DONG Yimeng, LI Yang, LIU Huitao, XING Xiumei. Verification of Red Deer Specific Molecular Marker SNP [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(4): 1313-1322.
[12]	ZHOU Zhinan, WU Yu, CHEN Xiang, SONG Rumou, CHEN Wei. Genetic Variation and Function Prediction of GHR Gene and Correlation Analysis with Growth Traits in Guizhou Local Yellow Cattle [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(3): 932-945.
[13]	ZHANG Fan, XU Jie, LI Gang, ZHOU Yongshun, HE Ying, HAN Kai, CHEN Fulong, GAO Jianfeng. Correlation Analysis of iNOS Gene Polymorphism and Brucellosis in Kazakh Sheep [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(3): 1102-1111.
[14]	SUN Lingzhu, RAN Xueqin, LIU Chang, NIU Xi, HUANG Shihui, WANG Jiafu. Detection of Genome Exon SNPs and Analysis of Candidate Genes for Reproduction and Body Type Traits in Xiang Pig [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(2): 537-553.
[15]	ZHENG Haiying, YANG Chunyan, ZHENG Wei, YU Nongqi, WEN Chongli, WEI Kelong, LI Lingyu, HUANG Chunli, HUANG Jiaxiang, SHANG Jianghua. Association Analysis Between PRKAA2 Gene Polymorphisms and Growth Traits in Murrah Buffalo [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(3): 789-798.