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

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (9): 3925-3935.doi: 10.11843/j.issn.0366-6964.2024.09.017

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

范广轩¹(), 王天骄¹, 董依萌¹, 王洪亮¹, 丁宁², 王莘皓³, 邢秀梅¹^,*()

1. 中国农业科学院特产研究所农业农村部特种经济动物遗传育种与繁殖重点实验室，长春 130112
2. 东北林业大学野生动物与自然保护地学院，哈尔滨 150006
3. 广东长隆集团有限公司，珠海 519000

收稿日期:2024-02-19 出版日期:2024-09-23 发布日期:2024-09-27
通讯作者: 邢秀梅 E-mail:2362416222@qq.com;xingxiumei2004@126.com
作者简介:范广轩(1997-)，男，河南卫辉人，硕士生，主要从事动物遗传资源研究，E-mail: 2362416222@qq.com
基金资助:
茸用梅花鹿新品种(品系)示范推广(202300801-05);中国农业科学院科技;创新工程-特种动物遗传资源科技创新团队(CAAS-ASTIP-2021-ISAPS);50K梅花鹿育种专用基因芯片研制(2022C038-2)

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

Guangxuan FAN¹(), Tianjiao WANG¹, Yimeng DONG¹, Hongliang WANG¹, Ning DING², Xinhao WANG³, Xiumei XING¹^,*()

1. Key Laboratory of Genetics, Breeding and Reproduction of Special Economic Animals of Ministry of Agriculture and Rural Affairs, Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun 130112, China
2. College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150006, China
3. Guangdong Chimelong Group, Zhuhai 519000, China

Received:2024-02-19 Online:2024-09-23 Published:2024-09-27
Contact: Xiumei XING E-mail:2362416222@qq.com;xingxiumei2004@126.com

摘要/Abstract

摘要：

旨在利用全基因重测序技术获得的SNP位点为吉林梅花鹿保种群构建分子系谱，并对其遗传结构进行分析。本研究在锯茸期采集保种群的吉林梅花鹿血液10 mL(n=425)，其中成年公鹿132只、成年母鹿208只、仔鹿85只，提取DNA后进行全基因重测序。通过计算血源同源系数(IBD)分析吉林梅花鹿亲缘关系；基于观测杂合度(Ho)、期望杂合度(He)、多态信息含量(PIC)、系统发育树和群体分化指数(Fst)等对吉林梅花鹿保种群遗传结构进行分析。通过全基因重测序筛选出25 548 601个高质量SNPs，425个样本共组成了90 100对亲缘关系，平均亲缘系数为0.435 1，得出195对父子关系与143对母子关系，占到采样群体原始系谱记录的92%，检出原始系谱错误率为2.2%，纠正了原始记录错误8处，具有较高的准确性和可靠性；分析群体分化指数(Fst)，东丰型吉林梅花鹿与伊通型距离较远；绘制系统发育树，将吉林梅花鹿保种群划分为17个家系；采用的SNP标记平均观测杂合度为0.456，平均期望杂合度为0.277，平均多态信息含量为0.627，吉林梅花鹿保种群平均近交系数为0.078，存在较弱的近交。本研究建立了吉林梅花鹿保种群的分子系谱并对其群体遗传结构进行了分析，这对于保护吉林梅花鹿遗传多样性和规划保种群后续选育计划至关重要。

关键词: 吉林梅花鹿, SNP, 分子系谱

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

中图分类号:

S829.9

范广轩, 王天骄, 董依萌, 王洪亮, 丁宁, 王莘皓, 邢秀梅. 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[J]. 畜牧兽医学报, 2024, 55(9): 3925-3935.

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.

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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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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

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