基于SNP位点的吉林梅花鹿分子系谱构建及群体遗传结构分析

doi:10.11843/j.issn.0366-6964.2024.09.017

Abstract

Abstract:

The aim of this study was to construct a molecular pedigree for the Jilin sika deer conservation herd using SNP loci obtained by genome resequencing technology, and to analyse the genetic structure of the population. The 10 mL of blood from Jilin sika deer of the conservation herd (n=425) during the antler-sawing period was collected, including 132 adult bucks, 208 adult does and 85 fawns, and extracted the DNA for whole genome resequencing. The kinship relationship of Jilin sika deer was analysed by calculating the blood homology coefficient (IBD), and the genetic structure of the Jilin sika deer conservation population was analysed based on the observed heterozygosity (Ho), the expected heterozygosity (He), the polymorphic information content (PIC), the phylogenetic tree and the population differentiation index (Fst). The 25 548 601 high-quality SNPs were screened by whole genome resequencing, and 425 samples comprised a total of 90 100 pairs of kinship relationships, with an average kinship coefficient of 0.435 1. A total of 195 pairs of paternity and 143 pairs of maternity were derived, which accounted for 92% of the original genealogical records of the sampled populations, and the error rate of the original genealogical records was detected to be 2.2%, and the errors of the original records were corrected to be 8, with a high accuracy and reliability. The group differentiation index (Fst) was calculated, and the Dongfeng-type Jilin sika deer was farther away from the Yitong-type; the phylogenetic tree was drawn, and the Jilin sika deer population was divided into 17 families; the average observed heterozygosity of the SNP markers was 0.456, the average expected heterozygosity was 0.277, and the average polymorphic information content was 0.627. The average inbreeding coefficient was 0.078, and there was weak inbreeding. The present study established the molecular genealogy and analysed the population genetic structure of the Jilin sika deer conservation herd, which is crucial for the conservation of genetic diversity of the Jilin sika deer and for the planning of the subsequent selection and breeding programme of the conservation herd.

Key words: Jilin sika deer, SNP, molecular genealogy

CLC Number:

S829.9

Guangxuan FAN, Tianjiao WANG, Yimeng DONG, Hongliang WANG, Ning DING, Xinhao WANG, Xiumei XING. Molecular Genealogy Construction and Population Genetic Structure Analysis of Jilin Sika Deer Based on SNP Loci[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(9): 3925-3935.

Figures/Tables 9

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References 40

1	WANG I L , HSIAO C Y , SHEN J Y , et al. The effects of Jilin Sika Deer's (Cervus dybowski) tendon liquid supplementation on endurance drop jumps performance, biochemistry profile of free boxing players[J]. J Ethnopharmacol, 2019, 245, 112119. doi: 10.1016/j.jep.2019.112119
2	RADKO A , SMOŁUCHA G , KOSENIUK A . Microsatellite DNA analysis for diversity study, individual identification and parentage control in pig breeds in Poland[J]. Genes (Basel), 2021, 12 (4): 595. doi: 10.3390/genes12040595
3	WOJCIECHOWSKA-KOSZKO I , MNICHOWSKA-POLANOWSKA M , ROSZKOWSKA P , et al. Improved RAPD method for Candida parapsilosis fingerprinting[J]. Genes (Basel), 2023, 14 (4): 868. doi: 10.3390/genes14040868
4	LI J S , WU L Y , ZHANG H , et al. PCR-RFLP for detection of Fusarium graminearum genotypes with resistance to phenamacril[J]. Plant Dis, 2021, 105 (4): 889- 895. doi: 10.1094/PDIS-06-20-1156-RE
5	赵蒙蒙. 用于番鸭亲子鉴定的微卫星分子标记筛选[D]. 广州: 华南农业大学, 2020.
	ZHAO M M. Screening of microsatellite markers for paternity ldentification of muscovy ducks[D]. Guangzhou: South China Agricultural University, 2020. (in Chinese)
6	BROOKES A J . The essence of SNPs[J]. Gene, 1999, 234 (2): 177- 186. doi: 10.1016/S0378-1119(99)00219-X
7	WENG Z Y , YANG Y , WANG X , et al. Parentage analysis in giant grouper (Epinephelus lanceolatus) using microsatellite and SNP markers from genotyping-by-sequencing data[J]. Genes (Basel), 2021, 12 (7): 1042. doi: 10.3390/genes12071042
8	SUN T H , SHAO Y J , MAO C L , et al. A novel quality-control procedure to improve the accuracy of rare variant calling in SNP arrays[J]. Front Genet, 2021, 12, 736390. doi: 10.3389/fgene.2021.736390
9	COOPER D N , SMITH B A , COOKE H J , et al. An estimate of unique DNA sequence heterozygosity in the human genome[J]. Hum Genet, 1985, 69 (3): 201- 205. doi: 10.1007/BF00293024
10	TANG M S , WANG T , ZHANG X F . A review of SNP heritability estimation methods[J]. Brief Bioinform, 2022, 23 (3): bbac067. doi: 10.1093/bib/bbac067
11	KRUGLYAK L . Prospects for whole-genome linkage disequilibrium mapping of common disease genes[J]. Nat Genet, 1999, 22 (2): 139- 144. doi: 10.1038/9642
12	唐修君, 樊艳凤, 贾晓旭, 等. 基于线粒体控制区的鸡不同杂交组合遗传多样性研究[J]. 畜牧兽医学报, 2021, 52 (6): 1523- 1534. doi: 10.11843/j.issn.0366-6964.2021.06.008
	TANG X J , FAN Y F , JIA X X , et al. Study on genetic diversity in different hybrid combinations of chickens based on mitochondrial control region[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52 (6): 1523- 1534. doi: 10.11843/j.issn.0366-6964.2021.06.008
13	董晓宇, 单文娟, 于丽娟, 等. 塔里木马鹿(Cervus elaphus yarkandensis)遗传结构及遗传多样性分析[J]. 生物技术, 2010, 20 (5): 16- 20. doi: 10.3969/j.issn.1004-311X.2010.05.150
	DONG X Y , SHAN W J , YU L J , et al. Structure of the mitochondrial DNA control region and population genetic diversity analysis of Tarim Red Deer (C.·e.·yarkandensis)[J]. Biotechnology, 2010, 20 (5): 16- 20. doi: 10.3969/j.issn.1004-311X.2010.05.150
14	李正杰, 周先坤, 王浥尘, 等. 阿坝藏族羌族自治州若尔盖地区藏猪mtDNA D-loop的遗传多样性分析[J]. 畜牧兽医学报, 2019, 50 (12): 2387- 2399. doi: 10.11843/j.issn.0366-6964.2019.12.003
	LI Z J , ZHOU X K , WANG Y C , et al. Genetic diversity of Tibetan pig mitochondrial DNA D-Loop in Ruoergai Area of A'ba Tibetan and Qiang autonomous prefecture[J]. Acta Veterinaria et Zootechnica Sinica, 2019, 50 (12): 2387- 2399. doi: 10.11843/j.issn.0366-6964.2019.12.003
15	卜李那, 彭业博, 张春媛, 等. 基于祖源分析的猪遗传成分鉴定[J]. 中国畜牧兽医, 2020, 47 (2): 544- 553.
	BU L N , PENG Y B , ZHANG C Y , et al. Ancestry analysis of genetic components of pigs[J]. China Animal Husbandry & Veterinary Medicine, 2020, 47 (2): 544- 553.
16	XING X M , AI C , WANG T J , et al. The first high-quality reference genome of Sika deer provides insights into high-tannin adaptation[J]. Genomics Proteomics Bioinformatics, 2023, 21 (1): 203- 215. doi: 10.1016/j.gpb.2022.05.008
17	卢凯妹, 王天骄, 董世武, 等. 梅花鹿基因组微卫星分布特征研究[J]. 特产研究, 2022, 44 (6): 8-15, 23.
	LU K M , WANG T J , DONG S W , et al. Research on distribution characteristics of microsatellites in Sika deer genome[J]. Special Wild Economic Animal and Plant Research, 2022, 44 (6): 8-15, 23.
18	YUE G D , GAO Q , LUO L H , et al. The application of high-throughput sequencing technology in plant and animal research[J]. Sci Sin Vitae, 2012, 42 (2): 107- 124. doi: 10.1360/052011-634
19	PURCELL S , NEALE B , TODD-BROWN K , et al. PLINK: a tool set for whole-genome association and population-based linkage analyses[J]. Am J Hum Genet, 2007, 81 (3): 559- 575. doi: 10.1086/519795
20	BOTSTEIN D , WHITE R L , SKOLNICK M , et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. Am J Hum Genet, 1980, 32 (3): 314- 331.
21	ALHUSAIN L , HAFEZ A M . Nonparametric approaches for population structure analysis[J]. Human Genomics, 2018, (12): 25.
22	LI R H , WANG X A , BIAN C , et al. Whole-genome sequencing of Sinocyclocheilus maitianheensis reveals phylogenetic evolution and immunological variances in various Sinocyclocheilus fishes[J]. Front Genet, 2021, 12, 736500. doi: 10.3389/fgene.2021.736500
23	CHENG P L , HUANG Y , DU H , et al. Draft genome and complete Hox-cluster characterization of the sterlet (Acipenser ruthenus)[J]. Front Genet, 2019, 10, 776. doi: 10.3389/fgene.2019.00776
24	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]. Genet Sel Evol, 2002, 34 (3): 275. doi: 10.1186/1297-9686-34-3-275
25	YU G C , TANG Q Z , LONG K R , et al. Effectiveness of microsatellite and single nucleotide polymorphism markers for parentage analysis in European domestic pigs[J]. Genet Mol Res, 2015, 14 (1): 1362- 1370. doi: 10.4238/2015.February.13.15
26	HAUSER L , BAIRD M , HILBORN R , et al. An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population[J]. Mol Ecol Resour, 2015, 11 (S1): 150- 161.
27	REVERTER A , HUDSON N J , MCWILLIAM S , et al. Low-density SNP genotyping panel for the accurate prediction of cattle breeds[J]. J Anim Sci, 2020, 98 (11): 337. doi: 10.1093/jas/skaa337
28	ZHU H H , ZHOU X . Statistical methods for SNP heritability estimation and partition: a review[J]. Computat Struct Biotechnol J, 2020, 18, 1557- 1568. doi: 10.1016/j.csbj.2020.06.011
29	ELBLINGER E , BOKOR J , BOKOR Á , et al. Parentage testing and looking for single nucleotide markers associated with antler quality in deer (Cervus elaphus)[J]. J Anim Sci, 2022, 65 (3): 267- 274.
30	CHRISTENSEN L G, MADSEN P, PETERSEN J. The influence of incorrectsire-identification on the estimates of genetic parameters and breeding values[C]//2nd World Congress on Genetics applied to Livestock Production. 1982: 200-208.
31	杨雨婷, 张兴, 牛安然. 基于高密度SNP标记重构猪多品种群体系谱[J]. 畜牧兽医学报, 2022, 53 (12): 4183- 4196. doi: 10.11843/j.issn.0366-6964.2022.12.006
	YANG Y T , ZHANG X , NIU A R . Rebuilding multi-species population genealogies based on high-density SNP markers in pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53 (12): 4183- 4196. doi: 10.11843/j.issn.0366-6964.2022.12.006
32	李玲, 李业芳, 梁奔梦, 等. 基于SNP标记的滩羊亲子鉴定研究[J]. 畜牧兽医学报, 2022, 53 (9): 2912- 2919. doi: 10.11843/j.issn.0366-6964.2022.09.009
	LI L , LI Y F , LIANG B M , et al. Paternity identification of tan sheep based on SNP markers[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53 (9): 2912- 2919. doi: 10.11843/j.issn.0366-6964.2022.09.009
33	YANG H . Livestock development in China: animal production, consumption and genetic resources[J]. J Anim Breed Genet, 2013, 130 (4): 249- 251. doi: 10.1111/jbg.12045
34	孙萍. 大尾寒羊保种群分子系谱的构建及遗传结构分析[D]. 泰安: 山东农业大学, 2020.
	SUN P. Construction of molecular pedigree and analysis of genetic structure of large tailed han sheep population[D]. Taian: Shandong Agricultural University, 2020. (in Chinese)
35	赵志达, 王欣悦, 石田培, 等. 基于微卫星标记鉴定湖羊家系[J]. 中国畜牧兽医, 2020, 47 (11): 3573- 3583.
	ZHAO Z D , WANG X Y , SHI T P , et al. Identification of Hu sheep family based on microsatellite markers[J]. China Animal Husbandry & Veterinary Medicine, 2020, 47 (11): 3573- 3583.
36	WANG X P , ZHANG H , HUANG M , et al. Whole-genome SNP markers reveal conservation status, signatures of selection, and introgression in Chinese Laiwu pigs[J]. Evol Appl, 2021, 14 (2): 383- 398. doi: 10.1111/eva.13124
37	GUERRERO-CÓZAR I , PEREZ-GARCIA C , BENZEKRI H , et al. Development of whole-genome multiplex assays and construction of an integrated genetic map using SSR markers in senegalese sole[J]. Sci Rep, 2020, 10 (1): 21905. doi: 10.1038/s41598-020-78397-w
38	RUNGE J N , KÖNIG B , LINDHOLM A K , et al. Parent-offspring Inference in Inbred Populations[J]. Mol Ecol Resources, 2022, 22 (8): 2981- 2993. doi: 10.1111/1755-0998.13680
39	MACHMOUM M , BOUJENANE I , AZELHAK R , et al. Genetic diversity and population structure of Arabian horse populations using microsatellite markers[J]. J Equine Vet Sci, 2020, 93, 103200. doi: 10.1016/j.jevs.2020.103200
40	KING F J M , BANGA C B , VISSER C . Genetic diversity and population structure of three native cattle populations in mozambique[J]. Trop Anim Health Prod, 2021, 53 (1): 117. doi: 10.1007/s11250-021-02562-0

个体号 Individual number	父本编号 Father’s number	PI_HAT	母本编号 Mother’s number	PI_HAT
21005	D107	0.547 8	D134	0.549 1
21007	D107	0.536 5	D012	0.546 1
21008	D107	0.561 9	D090	0.504 2
21036	SY504	0.548 0	SY758	0.559 0
21037	D133	0.436 2	16006	0.445 2
21038	SY504	0.545 2	SY730	0.564 7
21039	SY504	0.541 3	SY770	0.555 9
21040	SY504	0.553 4	SY830	0.472 0
21041	SY504	0.547 3	SY822	0.542 0
21060	DW031	0.538 3	17736	0.456 0
21062	DW031	0.539 2	18016	0.383 2
22066	16063	0.545 0	17712	0.535 7
22067	SY560	0.543 0	20080	0.510 0
22068	16063	0.553 6	17728	0.489 2
22069	SY560	0.532 0	20074	0.512 2
22070	SY504	0.540 3	SY872	0.552 2
22075	SY560	0.541 5	20078	0.509 0

SNP标记 SNP marker	信息 Information
平均期望杂合度 Mean expected heterozygosity(He)	0.277
平均观测杂合度 Mean observed heterozygosity(Ho)	0.456
平均多态信息含量 Mean polymorphic information content (PIC)	0.627
哈代-温伯格平衡 Hardy-Weinberg equilibrium(HWE)	0.104

类型 Typology	东丰型 Dongfeng	双阳型 Shuangyang	伊通型 Yitong
东丰型 Dongfeng
双阳型 Shuangyang	0.007 663
伊通型 Yitong	0.009 625	0.006 259 971

家系名称 Family name	样本个数 No. of samples	种公鹿数量 Number of bucks	近交系数 Fis
JL1	58	40	0.086 3
JL2	18	5	0.084 4
JL3	18	10	0.075 6
JL4	23	10	0.111 1
JL5	41	16	0.091 4
JL6	19	5	0.073 8
JL7	8	5	0.057 4
JL8	14	2	0.057 4
JL9	13	1	0.081 6
JL10	17	0	0.076 8
JL11	18	4	0.069 8
JL12	30	11	0.082 2
JL13	14	10	0.079 0
JL14	34	14	0.071 5
JL15	24	8	0.075 2
JL16	28	11	0.076 6
JL17	48	14	0.068 8

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Molecular Genealogy Construction and Population Genetic Structure Analysis of Jilin Sika Deer Based on SNP Loci

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出生年份 Year of birth	东丰公鹿/只 Dongfeng buck	东丰母鹿/只 Dongfeng doe	伊通公鹿/只 Yitong buck	伊通母鹿/只 Yitong doe	双阳公鹿/只 Shuangyang buck	双阳母鹿/只 Shuangyang doe
2015	2	4	6	15	3	6
2016	1	1	2	7	0	5
2017	5	5	7	11	5	22
2018	4	2	11	6	2	3
2019	3	3	7	21	3	17
2020	13	8	8	19	11	14
2021	12	5	17	19	6	18
2022	4	3	13	25	20	19
类型合计 Total number	75		196		154