|
|
|
| Detection of Genetic Structure of Conservation Population in Wannanhua Pig (Sus scrofa domesticus) Based on SNPs Chip |
| WANG Jing-Lin1, WU Xu-Dong2, HE Zhi-Bing1, LIU Yang-Guang1, WANG Xiao-Fen1, DING Yue-Yun1, ZHENG Xian-Rui1, ZHANG Xiao-Dong1,*, YIN Zong-Jun1,* |
1 College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China;
2 Anhui Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Medicine, Hefei 230031, China |
|
|
|
|
Abstract The Wannanhua pig (Sus scrofa domesticus) is an indispensable valuable pig breed resource in Anhui province and even in China. Studying the genetic diversity, kinship relationships, and pedigree structure of the Wannanhua pig population is crucial for revealing the current population status. The SNP of 32 Wannanhua pigs was detected using Chinese Chip-1 BeadChip. PLINK software was used to calculate the observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content (PIC), and to analyse the runs of homozygosity (ROH) of the Wannanhua pig population; Constructing G-matrix using GCTA software to analyze the genetic relationship of Wannanhua pig population. A colony evolutionary tree was built using MEGA X software to analyze the family structure of the Wannanhua pig population. The findings indicated that 42 662 SNP loci were identified, with 21 317 of them passing the quality control assessment; The polymorphism marker ratio (PN) was 0.500; The effective population size (Ne) was 3, the observed heterozygosity (Ho) was 0.372, the expected heterozygosity (He) was 0.348. The average relationship coefficient was 0.11. The G matrix results all indicated that most of the Wannanhua pigs were moderately related. There were 884 ROH fragments in the results, the average ROH length of (12.35±2.17) Mb and the individual ROH length of (341.19±139.58) Mb; The mean inbreeding coefficient based on ROH was 0.139±0.056, indicating that the inbreeding degree of the conserved population was not severe; The results of the cluster analysis showed that the Wannanhua pigs were derived from 5 bloodlines. In summary, the population of the Wannanhua pig conservancy herd had a low effective content, medium genetic diversity, medium degree of inbreeding, and might contain a small amount of foreign blood. This study provides scientific basis for the conservation and utilization of genetic resources of the southern Wannanhua pig.
|
|
Received: 28 February 2023
|
|
|
|
Corresponding Authors:
* yinzongjun@ahau.edu.cn; xdzhang1983@163.com
|
|
|
|
[1] 蔡春波, 张雪莲, 张万峰, 等. 2021. 运用SNP芯片评估马身猪保种群体的遗传结构[J]. 畜牧兽医学报, 52(04): 920-931.
(Cai C B, Zhang X L, Zhang W F, et al.2021. Evaluation of genetic structure in Mashen pigs conserved population based on SNP chip[J]. Acta Veterinaria et Zootechnica Sinica, 52(04): 920-931.)
[2] 程智中, 谢艳霞. 2020. 安徽畜禽遗传资源保护利用情况和发展对策[J]. 中国畜禽种业, 16(12): 10-11.
(Cheng Z Z, Xie Y X.2020. Conservation and utilization of livestock and poultry genetic resources in Anhui province and development countermeasures[J]. The Chinese Livestock and Poultry Breeding. 16(12): 10-11.)
[3] 戴丽荷, 褚晓红, 陈晓宇, 等. 2021. 利用SNP标记分析淳安花猪群体遗传多样性和群体结构[J]. 养猪, (06): 59-64.
(Dai L H, Chu X H,Chen X Y, et al. 2021. Analysis of genetic diversity and genetic structure in Chun'an Spotted Pigs conserved population based on SNP chip[J]. Swine Production, (06): 59-64.)
[4] 邓俊, 刘艺端, 许文坤, 等 . 2022. 基于 SNP芯片撒坝猪保种群体的遗传结构分析[J]. 中国饲料, 1(17): 7-11.
(Deng J, Liu Y D, Xu W K, et al.2022. Genetic structure analy‐sis of a conserved population of Saba pigs based onSNP chips[J]. China Feed, 1(17): 7-11.)
[5] 丁勇. 2019. 安徽地方猪遗传多样性分析及安庆六白猪肉质特性研究[D]. 硕士毕业论文, 安徽农业大学, 导师: 殷宗俊, pp. 65.
(Ding Y.2019. Analysis of genetic diversity of Anhui local pig and characteristics of pork quality of Anqing six-end-white pig[D]. Thesis for M.S., Animal Husbandry and Veterinary, Supervisor: Yin Z J, pp. 65.)
[6] 郝鑫宇, 冯健, 孙延晓, 等. 2020. 保种猪场系谱记录、管理及群体遗传结构分析—以莱芜猪为例[J]. 中国畜牧杂志, 56(04): 60-65.
(Hao X Y, Feng J, Sun Y X, et al.2020. Pedigree record, management and population genetic structure analysis of preserved pig farms—A case study of Laiwu pig[J]. Chinese Journal of Animal Science, 56(04): 60-65.)
[7] 胡亮, 孙伟, 马月辉. 2019. 藏系绵羊群体遗传多样性及遗传结构分析[J]. 畜牧兽医学报, 50(06): 1145-1153.
(Hu L, Sun W, Ma Y H.2019. Study on genetic diversity and genetic structure of tibetan sheep populations[J].Chinese Journal of Animal and Veterinary Sciences, 50(06): 1145-1153.)
[8] 蒋模有, 赵瑞莲, 徐民族, 等. 1987. 皖南花猪的品系繁育[J].东北养猪, (03): 9-12.
(Jiang M Y, Zhao R L, Xu M Z, et al. 1987. Breeding of Wannanhua pigs[J]. Swine Production, (03): 9-12.)
[9] 李庆岗, 王重龙, 杨家军, 等. 2018. 5个安徽地方猪种和5个引进猪种微卫星标记遗传多样性分析[J]. 养猪, (03): 67-72.
(Li Q G, Wang C L, Yang J J, et al. 2018. Genetic diversity analysis based on microsatellite markers in five Anhui local and five introduced pig breeds[J]. Swine Production, (03): 67-72.)
[10] 李小金, 钱坤, 刘林清, 等. 2016. 基于RNA-seq技术对不同品种猪背最长肌差异表达基因的筛选与注释[J]. 西北农林科技大学学报(自然科学版), 44(06): 1-8.
(Li X J, Qian K, Liu L Q, et al.2016.Screening and annotation of differentially expressed genes in longissimus muscle of different pig breeds based on RNA-seq technology[J]. Journal of Northwest A & F University (Natural Science Edition), 44(06): 1-8.)
[11] 刘彬, 沈林園, 陈映. 2020. 基于SNP芯片分析青峪猪保种群体的遗传结构[J]. 畜牧兽医学报, 51(02): 260-269.
(Liu B, Shen L Y, Chen Y.2020. Analysis of genetic structure of conservation population in Qingyu pig based on SNP chip[J]. Chinese Journal of Animal and Veterinary Sciences, 51(02): 260-269.)
[12] 刘彬. 2023. 两个西南山地型猪种跨世代过程中群体遗传结构变化研究[D]. 硕士毕业论文, 四川农业大学, 导师: 朱砺, 李强, pp. 63.
(Liu B.2023. Study on the population genetic structure changes in the process of cross-generation of two southwestern mountain type pig breeds[D].Thesis for M.S., Sichuan Agricultural Univerity. Supervisor: Zhu L, Li Q, pp. 63)
[13] 路玉洁, 莫家远, 綦文晶, 等. 2022. 几个中国地方猪群体遗传结构和产仔数性状选择信号分析[J]. 畜牧兽医学报, 53(02): 360-369.
(Lu Y J, Mo J Y, Qi W J, et al.2022. Population genetic structure and selection signatures associated with litter size trait in several Chinese indigenous pig breeds[J]. Acta Veterinaria et Zootechnica Sinica, 53(02): 360-369.)
[14] 罗元宇. 2016. 华南地方猪连锁不平衡分析及有效群体大小估计[D]. 硕士毕业论文, 华南农业大学, 导师: 陈赞谋. pp. 77.
(Luo Y Y.2016. Analysis of lingkage disequilibrium and estimation of effective population size in southern chinese indigenous pig breeds[D]. Thesis for M.S., South China Agricultural University, Supervisor: Chen Z M, pp. 77.)
[15] 马丽娜, 马青. 2020. 利用高密度基因芯片开展滩羊群体亲缘关系遗传分析[J]. 黑龙江畜牧兽医,(03): 65-69, 153-154.
(Ma L N, Ma Q.2020. Genetic analyses of population relatedness in beach goats using high-density gene microarrays[J]. Heilongjiang Animal Science and Veterinary Medicine,(03): 65-69, 153-154.)
[16] 时坤鹏, 刘莹, 张志勇, 等. 2022. 基于SNP芯片分析安庆六白猪群体遗传结构[J]. 中国畜牧杂志, 58(08): 136-140.
(Shi K P, Liu Y, Zhang Z Y, et al.2022. Analysis of population genetic structure of Anqing Liubai pig based on SNP chip[J].Chinese Journal of Animal Science, 58(08): 136-140.)
[17] 陶璇, 何志平, 梁艳, 等. 2022. 不同地方猪重要经济性状关联位点SNP芯片分型及群体遗传结构研究[J]. 畜牧兽医学报, 53(10): 3358-3367.
(Tao X, He Z P, Liang Y, et al.2022. SNP Genotyping of important economic traits, and population genetic structure in different local pig breeds[J]. Chinese Journal of Animal and Veterinary Sciences, 53(10): 3358-3367.)
[18] 陶璇, 杨雪梅, 梁艳, 等. 2023. 基于SNP芯片的丫杈猪保种群体遗传结构研究[J]. 畜牧兽医学报, 54(06): 2308-2319.
(Tao X, Yang X M, Lang Y, et al.2023. Analysis of genetic structure of conservation in Yacha pig based on SNP chip[J]. Chinese Journal of Animal and Veterinary Sciences, 54(06): 2308-2319.)
[19] 王余北, 肖莲梅, 何帅涵, 等. 2022. 基于50k SNP芯片信息的枣庄黑盖猪群体遗传结构分析[J]. 中国畜牧杂志, 58(09): 168-171, 178.
(Wang Y B, Xiao L M, He S H, et al.2022. Analysis of genetic structure of Zaozhuang black-covered pig population based on 50k SNP chip information[J]. Chinese Journal of Animal Science, 58(09): 168-171, 178.)
[20] 吴林慧, 孙琦, 王荔茹, 等. 2019. 恩施黑猪基因组群体遗传学参数的估计与选择信号研究[J]. 畜牧兽医学报, 50(03): 485-494.
(Wu L H, Sun Q, Wang L R, 2019. et al. A study of the population genetics parameters and selection signatures in Enshi black pig[J]. Chinese Journal of Animal and Veterinary Sciences, 50(03): 485-494.)
[21] 殷宗俊, 刘彩霞, 姜润深, 等. 2001.皖南花猪肌肉品质及其变化规律[J]. 安徽农业大学学报, 28(1): 4.
(Yin Z J, Liu C X, Jang R S,et al.2001. Study on meat quality and its change pattern of Wannanhua pig[J]. Journal of Anhui Agricultural University, 28(1): 4.)
[22] 袁娇, 徐国强, 周翔, 等. 2022. 基于SNP芯片监测通城猪的保种效果[J]. 畜牧兽医学报, 53(08): 2514-2523.
(Yuan J, Xu G Q, Zhou X, et al.2022. SNP chip-based moni‐toring of population conservation effect of Tongcheng pigs[J]. Chinese Journal of Animal and Veterinary Sciences, 53(08): 2514-2523.)
[23] 张雪莲. 2020. 基于SNP芯片分析马身猪保种群体的遗传结构[D]. 硕士毕业论文, 山西农业大学, 导师: 曹果清, 李步高, pp. 48.
(Zhang X L.2020. Analysis of genetic structure of conservation population of Mashen pig based on SNP chip[D]. Thesis for M.S., Shanxi Agricultural University, Supervisor: Cao G Q, Li B G. pp. 48.)
[24] Aslanyan L, Avagyan H, Karalyan Z.2020. Whole-genome-based phylogeny of African swine fever virus[J]. Veterinary World, 13(10): 2118-2125.
[25] Cheng Z, Li S, Deng L L, et al.2017. Transcriptome analysis reveals long intergenic noncoding RNAs contributed to growth and meat quality differences between Yorkshire and Wannanhua pig[J]. Genes, 8(8): 203.
[26] Lee S H, Seo D W, Cho E S, et al.2020.Genetic diversity and ancestral study for Korean native pigs using 60k SNP Chip[J]. Animals (Basel), 10(5): 760.
[27] Lencz T, Lambert C, DeRosse P, et al.2007. Runs of homozygosity reveal highly penetrant recessive loci in schizophrenia[J]. Proceedings of the National Academy of Sciences of the USA, 104(50): 19942-19947.
[28] Li M Z, Tian S L, Jin L, et al.2013. Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars[J]. Nature Genetics, 45(12): 1431-1438.
[29] Li X J, Zhou J, Liu L Q,et al.2016. Identification of genes in longissimus dorsi muscle differentially expressed between Wannanhua and Yorkshire pigs using RNA-sequencing[J]. Animal Genetics, 47(3): 324-333.
[30] Li X J, Liu L Q, Dong H, e al.2020. Comparative genome-wide methylation analysis of longissimus dorsi muscles in Yorkshire and Wannanhua pigs[J]. Animal Genetics,52(1): 78-89.
[31] Liu L Q, Qian K, Wang C L.2017. Discovery of porcine miRNA-196a/b may influence porcine adipogenesis in longissimus dorsi muscle by miRNA sequencing[J]. Animal Genetics, 48(2): 175-181.
[32] Martínez-Montes A M, Muiños-Bühl A, Fernández A, et al.2017. Deciphering the regulation of porcine genes influencing growth, fatness and yield-related traits through genetical genomics[J]. Mamm Genome, 28(3-4): 130-142.
[33] Panda S, Kumar A, Gaur G K, et al.2022. Genome wide copy number variations using Porcine 60K SNP Beadchip in Landlly pigs[J]. Anim Biotechnol, 1-9.
[34] Park H B, Han S H, Lee J B, et al.2017. Rapid communication: High-resolution quantitative trait loci analysis identifies LTBP2 encoding latent transforming growth factor beta binding protein 2 associated with thoracic vertebrae number in a large F2 intercross between Landrace and Korean native pigs[J]. Journal of Animal Science, 95(5): 1957-1962.
[35] Purcell S, Neale B, Todd-Brown K, et al.2007. PLINK: A tool set for whole-genome association and population-based linkage analyses[J]. American Journal of Human Genetics, 81(3): 559-575.
[36] Silió L, Rodríguez M C, Fernández A, et al.2013. Measuring inbreeding and inbreeding depression on pig growth from pedigree or SNP-derived metrics[J]. Journal of Animal Breeding & Genetics, 130(5): 349-360.
[37] Suwannasing R, Duangjinda M, Boonkum W, et al.2018.The identification of novel regions for reproduction trait in Landrace and Large White pigs using a single step genome-wide association study[J]. Asian-Australasian Journal of Animal Sciences, 31(12): 1852-1862.
[38] Sved J. A.1971. Linkage disequilibrium and homozygosity of chromosome segments in finite populations[J]. Theoretical Population Biology, 2(2): 125-141.
[39] Timpson N J, Greenwood C M T, Soranzo N, et al.2018. Genetic architecture: The shape of the genetic contribution to human traits and disease[J]. Nature Reviews. Genetics, 19(2): 110-124.
[40] VanRaden P M.2008. Efficient methods to compute genomic predictions[J]. Journal of Dairy Science, 91(11): 4414-4423.
[41] Yang J, Huang L S, Yang M, et al.2016. Possible introgression of the VRTN mutation increasing vertebral number, carcass length and teat number from Chinese pigs into European pigs[J]. Scientific Reports, 6: 19240. |
|
|
|
