昆明犬群体遗传结构及受选择基因分析

doi:10.11843/j.issn.0366-6964.2022.05.013

Abstract

Abstract: The objective of this study was to explore genetic diversity and population structure of Kunming dog, which is the only domesticated and widely used as working dog in China.The blood samples of 16 Kunming dogs (3 strains), 4 Malinois dogs and 4 German Shepherds were collected and genomic DNA was extracted. The genetic population structure of the 3 breeds of police dogs was analyzed using principal component analysis (PCA), STRUCTURE and neighboring (NJ) trees by Illumina Caninehd Beadchip chip. Genomic selection footprints analysis was used to identify candidate genes that were selected during domestication and improvement of Kunming dog. The results showed that 86 270 SNPs were selected for analysis according to the quality control standards of chip data. Population STRUCTURE analysis showed that German Shepherd was completely distinguishable from other breeds when k=2. Malinois could be distinguished from other breeds when k=3, but there were some heterozygous German Shepherds in Kunming dogs. Three police dog breeds could be clearly separated by PCA analysis and NJ tree analysis. After setting a sliding window of 500 kb on the autosomes and annotating these regions, 22 candidate genes that may be selected during the domestication and improvement of Kunming dog.The first category was the genes and proteins which participated in adenylate cyclase-activating G-protein coupled receptor signaling pathway.Another type of gene had the function of polymerizing and stabilizing microtubules in the growth cones of neuronal axons, and affecting the growth of axons and leading protrusions. The results of this study investigated the genetic relationship between Kunming dog and other police dogs.It provide an important reference for exploring the adaptive mechanisms of Kunming dogs, such as learning, memory and stress stimulation, which are produced by strong artificial selection.

Key words: domestic dog, Kunming dog, SNP chip, population structure, selection signature

CLC Number:

S829.2

LI Jing, CHENG Luguang, WAN Jiusheng, CHEN Chao, DENG Weidong, ZHANG Zhenghong, ZHANG Zhi, LI Liguang. A Study of Genetic Population Structure Analysis and Selection Signatures in Kunming Dog[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(5): 1455-1464.

References 28

[1]	黎立光,强京宁,宋兴国,等.昆明犬的研究综述[J].中国工作犬业,2007(1):13-15.LI L G,QIANG J N,SONG X G,et al.Research review of Kunming dogs[J].China Working Dog,2007(1):13-15.(in Chinese)
[2]	WANG G D,CHENG L G,FAN R X,et al.Signature of balancing selection at the MC1R gene in Kunming Dog populations[J].PLoS One,2013,8(2):e55469.
[3]	黄庆国,李居东,汪斌,等.中系马里努阿犬家系选育模式探索与实践[J].中国畜禽种业,2019,15(4):71-73.HUANG Q G,LI J D,WANG B,et al.Exploration and practice of breeding model of malinua lineages[J].The Chinese Livestock and Poultry Breeding,2019,15(4):71-73.(in Chinese)
[4]	WANG G D,ZHAI W W,YANG H C,et al.Out of southern East Asia:the natural history of domestic dogs across the world[J].Cell Res,2016,26(1):21-33.
[5]	MACLEAN E L,SNYDER-MACKLER N,VONHOLD B M,et al.Highly heritable and functionally relevant breed differences in dog behaviour[J].Proc Biol Sci,2019,286(1912):20190716.
[6]	WU C I,WANG G D,XU S H.Convergent adaptive evolution-how common,or how rare?[J].Natl Sci Rev,2020,7(6):945-946.
[7]	YANG Q Y,CHEN H,YE J H,et al.Genetic diversity and signatures of selection in 15 Chinese indigenous dog breeds revealed by genome-wide SNPs[J].Front Genet,2019,10:1174.
[8]	SLAVNEY A J,KAWAKAMI T,JENSEN M K,et al.Five genetic variants explain over 70% of hair coat pheomelanin intensity variation in purebred and mixed breed domestic dogs[J].PLoS One,2021,16(5):e0250579.
[9]	SUTTER N B,BUSTAMANTE C D,CHASE K,et al.A single IGF1 allele is a major determinant of small size in dogs[J].Science,2007,316(5821):112-115.
[10]	QUIGNON P,SCHOENEBECK J J,CHASE K,et al.Fine mapping a locus controlling leg morphology in the domestic dog[J].Cold Spring Harb Symp Quant Biol,2009,74:327-333.
[11]	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.
[12]	VILELLA A J,SEVERIN J,URETA-VIDAL A,et al.EnsemblCompara GeneTrees:complete,duplication-aware phylogenetic trees in vertebrates[J].Genome Res,2009,19(2):327-335.
[13]	SAITOU N,NEI M.The neighbor-joining method:a new method for reconstructing phylogenetic trees[J].Mol Biol Evol,1987, 4(4):406-425.
[14]	SELZER P M,MARHOFER R J,ROHWER A.DAVID bioinformatics resource[Z].2008.
[15]	WU Q F,YANG L,LI S,et al.Fibroblast growth factor 13 is a microtubule-stabilizing protein regulating neuronal polarization and migration[J].Cell,2012,149(7):1549-1564.
[16]	ZHANG M,SUN G P,REN L L,et al.Ancient DNA evidence from china reveals the expansion of pacific dogs[J].Mol Biol Evol, 2020, 37(5):1462-1469.
[17]	ZHANG S J,WANG G D,MA P C,et al.Genomic regions under selection in the feralization of the dingoes[J].Nat Commun, 2020,11(1):671.
[18]	PARKER H G,DREGER D L,RIMBAULT M,et al.Genomic analyses reveal the influence of geographic origin,migration,and hybridization on modern dog breed development[J].Cell Rep,2017,19(4):697-708.
[19]	潘寿文,颜泽清.中国地方狼犬与德国牧羊犬杂交育种毛色遗传规律的研究[J].中国畜牧兽医,2009,36(1):80-82.PAN S W,YAN Z Q.The research on cross-breeding genetic laws of hair color between China local wolf-dog and German shepherd dog[J].China Animal Husbandry & Veterinary Medicine,2009,36(1):80-82.(in Chinese)
[20]	BARROSO I.ADCY3,neuronal primary cilia and obesity[J].Nat Genet,2018,50(1):166-167.
[21]	SANABRA C,MENGOD G.Neuroanatomical distribution and neurochemical characterization of cells expressing adenylyl cyclase isoforms in mouse and rat brain[J].J Chem Neuroanat,2011,41(1):43-54.
[22]	STENGEL D,PARMA J,GANNAGÉ M H,et al.Different chromosomal localization of two adenylyl cyclase genes expressed in human brain[J].Hum Genet,1992,90(1-2):126-130.
[23]	WOLF E J,RASMUSSON A M,MITCHELL K S,et al.A genome-wide association study of clinical symptoms of dissociation in a trauma-exposed sample[J].Depress Anxiety,2014,31(4):352-360.
[24]	DAROLES L,GRIBAUDO S,DOULAZMI M,et al.FMRP and dendritic local translation of αCaMKII mRNA are required for the structural plasticity underlying olfactory learning[J].Biol Psychiatry,2015, 80(2):149-159.
[25]	LUO W,FANG M X,XU H P,et al.Transcriptome comparison in the pituitary-adrenal axis between beagle and Chinese Field dogs after chronic stress exposure[J].Anim Genet,2015,46(5):522-534.
[26]	PAN X Y,WU Q F,YANG L,et al.Roles of FGF13 in the regulation of neuronal spine development in mouse brain[C]//Proceedings of the 10th Biennial Conference of the Chinese Neuroscience Society.Beijing:Chinese Society of Neuroscience, 2013:468.
[27]	FRY A E,MARRA C,DERRICK A V.et al.Missense variants in the N-terminal domain of the A isoform of FHF2/FGF13 cause an X-linked developmental and epileptic encephalopathy[J].Am J Hum Genet,2021,108(1):176-185.
[28]	YUNA B,CHENG T L,YANG K,et al.Autism-related protein MeCP2 regulates FGF13 expression and emotional behaviors[J].J Genet Genomics,2017,44(1):63-66.

A Study of Genetic Population Structure Analysis and Selection Signatures in Kunming Dog

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References 28

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	SONG Kelin, YAN Zunqiang, WANG Pengfei, CHENG Wenhao, LI Jie, BAI Yaqin, SUN Guohu, GUN Shuangbao. Analysis on Genetic Diversity and Genetic Structure Based on SNP Chips of Huixian Qingni Black Pig [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(3): 995-1006.
[2]	ZHANG Renbao, ZHOU Donghui, ZHOU Lisheng, GAO Xiaoxiao, LIU Nan, HE Jianning. Analysis of Genetic Structure of Conservation Population in Jining Gray Goats Based on 70 K SNP Chip [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2836-2847.
[3]	ZHAO Zhenjian, WANG Shujie, CHEN Dong, JI Xiang, SHEN Qi, YU Yang, CUI Shengdi, WANG Junge, CHEN Ziyang, TANG Guoqing. Population Structure and Genetic Diversity Analysis of Neijiang Pigs Based on Low-coverage Whole Genome Sequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2297-2307.
[4]	TAO Xuan, YANG Xuemei, LIANG Yan, LIU Yihui, WANG Yong, KONG Fanjing, LEI Yunfeng, YANG Yuekui, WANG Yan, AN Rui, YANG Kun, Lü Xuebin, HE Zhiping, GU Yiren. Analysis of Genetic Structure of Conservation Population in Yacha Pig Based on SNP Chip [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2308-2319.
[5]	LONG Xi, CHEN Li, WU Pingxian, ZHANG Tinghuan, PAN Hongmei, ZHANG Liang, WANG Jinyong, GUO Zongyi, CHAI Jie. Evaluation of the Genetic Structure and Selection Signatures in Hechuan Black Pigs Conserved Population [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1854-1867.
[6]	MA Keyan, HAN Jintao, BAI Yaqin, LI Taotao, MA Youji. Genetic Diversity Analysis of Yongdeng Qishan Sheep Based on Specific-Locus Amplified Fragment Sequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1939-1950.
[7]	GAO Chaoqun, CAO Ranran, DU Wenping, HU Xiaoyu, LEI Yanru, LI Wenting, KANG Xiangtao. Genetic Diversity and Population Structure Analysis of Chinese Native Chicken Breeds using Genome-wide SNPs [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 554-562.
[8]	QI Lina, LU Xuelin, YANG Kaixuan, ZHOU Jin, LI Xianyu, LIU Ke, ZHANG Wengang, GU Xin, ZHANG Weijian. Analysis of Genetic Diversity and Genetic Structure of New Pudong Chicken Based on SNP Chips [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 4962-4971.
[9]	HU Ziping, WANG Ligang, ZONG Wencheng, HOU Renda, SU Yanfang, NIU Naiqi, WANG Lixian, WANG Yuan, ZHNAG Longchao. Genetic Structure Analysis of Jianbai Xiang Pig Population Based on Genomic SNP and ROH [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4117-4125.
[10]	MA Haoran, ZHANG Lupei, JIN Shengyun, BAO Jinshan, LI Hongyan, GAO Huijiang, XU Lingyang, WANG Zezhao, LI Junya. Assessment of the Genomic Relationships for Chinese Indigenous Beef Cattle Using High-density SNP Chip [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4174-4185.
[11]	LIU Chenlong, LU Dan, ZHOU Quanyong, WAN Mingchun, HAO Xiaodong, ZHANG Xianhe, ZHENG Ruiqiang, JI Huayuan. Analysis of Population Genetic Structure of Hang Pigs by High Density SNP Chip [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(8): 2502-2513.
[12]	YUAN Jiao, XU Guoqiang, ZHOU Xiang, XU Sanping, LI Sheng, LI Wangming, LIU Bang. SNP Chip-Based Monitoring of Population Conservation Effect of Tongcheng Pigs [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(8): 2514-2523.
[13]	LIU Hongxiang, SHEN Yongjie, ZHANG Lihua, ZHANG Shuangjie, WANG Jing, ZHU Jie, CHEN Yuzhe, ZHU Chunhong, SONG Weitao, ZHANG Dan, TAO Zhiyun, XU Wenjuan, LIU Honglin, LI Huifang. Genetic Diversity Evaluation of Loumen Duck Based on Reduced-Representation Genome Sequencing [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(6): 1735-1748.
[14]	FENG Xueyan, DIAO Shuqi, LIU Yuqiang, XU Zhiting, WEI Chen, YUAN Xiaolong, LI Jiaqi, ZHANG Zhe. Analysis of Selection Signatures for Hainan Pigs across the Whole Genome Based on SNP BeadChips [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(2): 349-359.
[15]	LEI Zhihui, ZHANG Liping, ZHAO Hongchang, ZHU Shaohua, LU Zengkui, GUO Tingting, SUN Weibo, HE Xue, YUE Yaojing. Genome-wide Selection Signals Reveal Candidate Genes Associated with the Sheep of Hair Follicle Development and Depilation Traits [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(2): 381-390.