庆阳驴mtDNA D-loop区遗传多样性及起源分析

doi:10.16431/j.cnki.1671-7236.2024.02.017

Abstract

Abstract: 【Objective】 This study was aimed to explore the genetic diversity and maternal origin of Qingyang donkey breeding population, understand its genetic information, and provide theoretical basis for protecting germplasm resources, breeding, and genetic improvement in Qingyang donkey.【Method】 133 Qingyang donkeys were randomly selected, the mitochondrial DNA (mtDNA) D-loop region sequences were analyzed by PCR amplification, sequencing and alignment, and the genetic diversity and maternal origin of Qingyang donkey were explored.【Result】 520 bp D-loop base sequence were obtained, the AT content (57.3%) was higher than GC content (42.8%), indicating there was bias in base composition.There were 38 SNPs of D-loop region, including 8 conversions.The nucleotide diversity (Pi), haplotype diversity (Hd) and average nucleotide difference (K) were 0.01591, 0.895 and 8.274, respectively, which was lower than the average of European and Chinese domestic donkey studies, indicating that the nucleotide variation of Qingyang donkey breed was relatively poor.The genetic distances of 35 haplotypes of D-loop region in Qingyang donkey ranged from 0.002 to 0.042.Phylogenetic results showed that there were two mitochondrial lineages, indicating that there were two mitochondrial maternal origins, and the genetic distance between Qingyang donkey and Croatian domestic donkey was relatively close.【Conclusion】 The experiment preliminarily revealed the nucleotide variation of Qingyang donkey was poor from the molecular level, the degree of hybridization was high, and the mtDNA genetic polymorphism was gradually lost, so the protection of genetic resources of Qingyang donkey breed should be strengthened.

Key words: Qingyang donkey; mtDNA; D-loop region; genetic diversity; origin

CLC Number:

S813.3

SHI Haina, WANG Yongjie, LIANG Wanpeng, GENG Zhiguang, LI Shien, XU Zhenfei, LIU Gang, LIU Zhe. Genetic Diversity and Origin Evolution Analysis of Qingyang Donkey Based on mtDNA D-loop Region Sequence[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(2): 601-613.

References

[1] 付胜勇,汤青萍,穆春宇,等.8个鸽品种资源线粒体DNA遗传多态性与系统进化分析[J].中国家禽,2021,43(2):28-31. FU S Y,TANG Q P,MU C Y,et al.Genetic polymorphism and phylogenetic analysis of mitochondrial DNA among 8 pigeon breeding resources[J].China Poultry,2021,43(2):28-31.(in Chinese)
[2] 刘春盛.基于线粒体DNA Cytb和D-loop序列分析象洞鸡遗传多样性[J].特产研究,2022,44(6):40-43. LIU C S.Genetic diversity of Xiangdong chicken species based on mitochondrial DNA Cytb and D-loop region[J].Special Wild Economic Animal and Plant Research,2022,44(6):40-43.(in Chinese)
[3] 国家畜禽遗传资源委员会组.中国畜禽遗传资源志--马驴驼志[M].北京:中国农业出版社,2011. CHINA NATIONAL COMMISSION OF ANIMAL GENETIC RESOURCES.Animal Genetic Resources in China-Horses Donkeys Camels[M].Beijing:China Agriculture Press,2011.(in Chinese)
[4] 施海娜,刘哲,梁万鹏,等.庆阳驴体尺指标的相关性、聚类和主成分分析[J].中国草食动物科学,2023,43(5):29-35. SHI H N,LIU Z,LIANG W P,et al.Correlation,cluster and principle components analysis on body size of Qingyang donkeys[J].China Herbivore Science,2023,43(5):29-35.(in Chinese)
[5] 夏晶晶,贾羽晴,税斐,等.淮北灰驴mtDNA D-loop区遗传多样性及起源分析[J].安徽农业大学学报,2022,49(4):578-582. XIA J J,JIA Y Q,SHUI F,et al.Analysis on genetic diversity and origin evolution analysis of Huaibei Grey donkey base on mtDNA D-loop region sequence[J].Journal of Anhui Agricultural University,2022,49(4):578-582.(in Chinese)
[6] 李慧锋,赵婧微,陈员玉,等.晋南驴mtDNA D-loop区部分序列系统进化分析与体型测定[J].山西农业大学学报(自然科学版),2020,40(4):121-128. LI H F,ZHAO J W,CHEN Y Y,et al.Phylogenetic analysis of partial mtDNA D-loop sequence in Jinnan donkey and their body size measurement[J].Journal of Shanxi Agricultural University (Natural Science Edition),2020,40(4):121-128.(in Chinese)
[7] 陈建兴,宋振华,荣美洁,等.三个品种家驴中Cytb多态与生长性状的相关分析(英文)[A].中国畜牧业协会首届(2015)中国驴业发展大会高层论坛[C].2015. CHEN J X,SONG Z H,RONG M J,et al.The association analysis between Cytb polymorphism and growth traits in three Chinese donkey breeds[A].China Animal Husbandry Association,The first (2015) China Donkey Industry Development Conference High-level Forum[C].2015.(in Chinese)
[8] 郑立,刘延鑫,赵绪永,等.河南3个驴种mtDNA D-loop区序列多态性及起源进化分析[J].西北农林科技大学学报(自然科学版),2011,39(4):29-34. ZHENG L,LIU Y X,ZHAO X Y,et al.Analysis of phylogenetic relationship and genetic diversity of mtDNA D-loop in three Henan donkey breeds[J].Journal of Northwest A&F University (Natural Science Edition),2011,39(4):29-34.(in Chinese)
[9] 赵朝霞,刘文忠,朱文进,等.六个家驴品种mtDNA D-loop部分序列的遗传多样性分析[J].中国草食动物,2008,28(4):3-5. ZHAO Z X,LIU W Z,ZHU W J,et al.Analysis on the genetic diversity of partial sequences in mitochondrial DNA D-loop of six donkey breeds[J].China Herbivores,2008,28(4):3-5.(in Chinese)
[10] SUN Y,JIANG Q,YANG C H,et al.Characterization of complete mitochondrial genome of Dezhou donkey (Equus asinus) and evolutionary analysis[J].Current Genetics, 2016,62(2):383-390.
[11] 刘建斌,杨博辉,郎侠,等.中国9个家驴品种mtDNA D-loop部分序列分析与系统进化研究[J].中国畜牧杂志,2010,46(3):1-6. LIU J B,YANG B H,LANG X,et al.Study on some fragment analysis of mtDNA D-loop and phylogenesis for nine domestic donkey breeds in China[J].Chinese Journal of Animal Science,2010,46(3):1-6.(in Chinese)
[12] 张云生,王小斌,雷初朝,等.中国5个家驴品种mtDNA Cytb基因遗传多样性及起源[J].西北农业学报,2009,18(9):9-11. ZHANG Y S,WANG X B,LEI C Z,et al.mtDNA Cytb gene genetic diversity and origin of five donkey breeds in China[J].Acta Agriculturae Boreali-occidentalis Sinica,2009,18(9):9-11.(in Chinese)
[13] 孙伟丽,杨博辉,曹学亮,等.中国四个地方驴品种mtDNA D-loop部分序列分析与系统进化研究[J].中国草食动物,2007,27(2):7-10. SUN W L,YANG B H,CAO X L,et al.Phylogenetic relationship and genetic diversity of Chinese four domestic donkeys using mtDNA D-loop[J].China Herbivores,2007,27(2):7-10.(in Chinese)
[14] 葛庆兰,雷初朝,蒋永青,等.中国家驴mtDNA D-loop遗传多样性与起源研究[J].畜牧兽医学报,2007,38(7):641-645. GE Q L,LEI C Z,JIANG Y Q,et al.Mitochondrial DNA D-loop genetic diversity and origin of Chinese domestic donkeys[J].Acta Veterinaria et Zootechnica Sinica,2007,38(7):641-645.(in Chinese)
[15] 雷初朝,陈宏,杨公社,等.中国驴种线粒体DNA D-loop多态性研究[J].遗传学报,2005,32(5):481-486. LEI C Z,CHEN H,YANG G S,et al.Study on mitochondrial DNA D-loop polymorphismin chinese donkeys[J].Acta Genetica Sinica,2005,32(5):481-486.(in Chinese)
[16] WANG Y H,HUA X P,SHI X Y,et al.Origin,evolution,and research development of donkeys[J].Genes,2022,13(11):1945.
[17] 梁佳轩.基于Cytb和D-loop区序列分析太白山溪鲵的谱系地理学[D].西安:陕西师范大学,2010. LIANG J X.Phylogeography of B.taibaiensis based on Cytb and D-loop sequences[D].Xi'an:Shaanxi Normal University,2010.(in Chinese)
[18] 朱文进,张美俊,葛慕湘,等.中国8个地方驴种遗传多样性和系统发生关系的微卫星分析[J].中国农业科学,2006,12(2):398-405. ZHU W J,ZHANG M J,GE M X,et al.Microsatellite analysis of genetic diversity and phylogenetic relationship of eight donkey breeds in china[J].Scientia Agricultura Sinica,2006,12(2):398-405.(in Chinese)
[19] 高雪.中国驴种来源的遗传学研究[D].杨凌:西北农林科技大学,2001. GAO X.Studies on genetics of Chinese ass breed's originalty[D].Yangling:Northwest A&F University,2001.(in Chinese)
[20] 李双,夏小婷,李付强,等.温岭高峰牛线粒体DNA全基因组遗传多样性分析[J].中国牛业科学,2022,48(2):28-32. LI S,XIA X T,LI F Q,et al.Genetic diversity of mitochondrial DNA genome of Wenling Humped cattle[J].China Cattle Science,2022,48(2):28-32.(in Chinese)
[21] 贾晓旭,陆俊贤,张静,等.清远麻鸡线粒体DNA细胞色素b基因遗传多样性分析[J].畜牧与兽医,2023,55(2):1-4. JIA X X,LU J X,ZHANG J,et al.Genetic diversity of the mitochondrial DNA Cytb gene in Qingyuan partridge chickens[J].Animal Husbandry&Vetetinary Medicine,2023,55(2):1-4.(in Chinese)
[22] 赵祥,郑建,高天翔,等.基于线粒体DNA控制区的黄姑鱼养殖群体与野生群体比较研究[J].中国海洋大学学报,2021,51(8):11-19. ZHAO X,ZHENG J,GAO T X,et al.Comparative analysis of genetic variation between culrured and wild populations of Nibea albifora base on mitochondrial DNA control region[J].Periodical of Ocean Universitry of China,2021,51(8):11-19.(in Chinese)
[23] 卞玉玲,刘士力,刘一诺,等.湖州河川沙塘鳢群体线粒体DNA cytb基因序列的遗传多样性分析[J].水产学杂志,2023,36(1):22-28. BIAN Y L,LIU S L,LIU Y N,et al.Genetic diversity analysis of mitochondrial DNA Cytb gene sequence of Odontobutis potamophila population in Huzhou[J].Chinese Journal of Fisheries,2023,36(1):22-28.(in Chinese)
[24] IVANKOVIC A,KAVAR T,CAPUT P,et al.Genetic diversity of three donkey populations in the Croatian coastal region[J].Animal Genetics,2002,33(3):169-177.
[25] 雷初朝,葛庆兰,蒋永青,等.中国家驴mtDNA遗传多样性与起源研究[A].中国畜牧兽医学会,第十次全国畜禽遗传标记研讨会论文集[C].2006. LEI C Z,GE Q L,JIANG Y Q,et al.mtDNA genetic diversity and origin of chinese domestic donkeys[A].Chinese Association of Animal Science and Veterinary Medicine,Proceedings of the 10th National Symposium on Genetic Markers of Livestock and Poultry[C].2006.(in Chinese)
[26] BEJA-PEREIRA A,ENGLAND P R,FERRAND N,et al.African origins of the domestic donkey[J].Science,2004,304(5678):1781.
[27] ÖZKAN VNAL E,ÖZDIL F,KAPLAN S,et al.Phylogenetic relationships of turkish indigenous donkey populations determined by mitochondrial DNA D-loop region[J].Animals,2020,10(11):1970.
[28] COZZI C M,VALIATI P,CHERCHI R,et al.Mitochondrial DNA genetic diversity in six Italian donkey breeds (Equus asinus)[J].Mitochondrial DNA,2018,29(3):409-418.
[29] LIU Y,LI H J,WANG M,et al.Genetic architectures and selection signatures of body height in Chinese indigenous donkeys revealed by next-generation sequencing[J].Animal Genetics,2022,53(4):487-497.

Genetic Diversity and Origin Evolution Analysis of Qingyang Donkey Based on mtDNA D-loop Region Sequence

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	YUE Yunfeng, HUANG Weiping, LIU Min, JIN Suyu, HUANG Lin, ZHENG Yucai. Genetic Diversity Analysis of Liangshan Black Sheep Population Based on Mitochondrial Cytb Gene [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(9): 3671-3679.
[2]	LUO Shimin, LI Zhongbo. Genetic Diversity and Genetic Evolution of H and F genes of Canine Distemper Virus in Huaihua District [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(8): 3248-3257.
[3]	HAN Dayong, ZHOU Chunbao, NI Ligang, CHEN Zhangyan, ZHAO Jinming. Genetic Diversity of mtDNA D-loop Sequence in Sujiang Pig [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(4): 1472-1479.
[4]	ZHUANG Mingliang, LI Jianfei, GE Peng, WANG Qi, WANG Zhi, QI Jingwen, NIU Qingsheng, LI Zhiyong. Genetic Diversity Study of Changbaishan Chinese Bee [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(12): 4992-4999.
[5]	YE Wen, SUN Dongxiao, HAN Bo. Application Progress on Whole Genome Resequencing in Farm Animals [J]. China Animal Husbandry and Veterinary Medicine, 2023, 50(10): 4125-4132.
[6]	XIONG Chenyong, YIN Yanwen, SHI Kaichuang, LI Jun, ZHENG Min, WEI Xiankai, FENG Shuping, LONG Feng, QU Sujie, LU Wenjun, ZHOU Hongjin, HUANG Hailian, XIE Shouyu, LI Zongqiang. Genetic Diversity Analysis of Duck Tembusu Virus in Guangxi During 2019-2021 [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(8): 3099-3111.
[7]	PENG Caichun, LI Binqiang, WANG Yeying, SU Haijun. Genetic Diversity Analysis of Sus scrofa Population in Guizhou Based on Mitochondrial CytbGene [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(7): 2601-2612.
[8]	ZHANG Qiang, LUOSANG Dunzhu, BASANG Wangdui, PENG Yangyang, E Guangxin, NIMA Ciren, SUOLANG Duoji, BA Duo, DAN Ba, XIAN Lili, DANBA Jiacan, ZHI Zhang, PINGCUO Zhandui. Estimation of Genetic Diversity and Population Structure of Five Tibet Yak Populations Using Microsatellites Markers [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(6): 2228-2238.
[9]	GUO Luanying, LI Jialei, JIN Qinqin, MA Jun, LIU Quan. Research Progress on Bovine Hepacivirus [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(5): 1994-2000.
[10]	LIU Xiaowei, LI Ruixiang, WANG Xinglong, LI Xiao. Genetic Diversity Analysis of Shaanxi Moschus berezovskii Based on mtDNA Cytb Gene and D-loop Region Sequence [J]. China Animal Husbandry and Veterinary Medicine, 2022, 49(4): 1352-1363.
[11]	LI Zhongbo, HOU Qianghong. Sequencing and Sequence Analysis of Ribosomal 18S rRNA and Mitochondrial cox1 Gene of Aedes albopictus in Huaihua District,Hunan Province [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(8): 2736-2745.
[12]	FANG Ruixin, TIAN Xueqi, ZOU Chen, DONG Yimeng, LI Yang, XING Xiumei, LIU Xin. Analysis of Genetic Diversity and Paternal Type of Red Deer Using SRY Gene in Y Chromosome [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(7): 2457-2466.
[13]	LI Guangzhen, MA Zhijie, CHEN Shengmei, GA Buzang, LI Ruizhe. Genetic Difference Between Menyuan White Yaks and Tianzhu White Yaks Based on mtDNA D-loop Sequences [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(5): 1647-1654.
[14]	XIAO Yi, WANG Mengwen, ZHANG Xiuying, GULZAR Abdukerim, HAN Jianlin, WANG Yutao. Genetic Diversity,Origin and Evolution Analysis of Ovis ammon polii Based on mtDNA Cytb Gene [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(5): 1681-1690.
[15]	FANG Ruixin, TIAN Xueqi, ZOU Chen, DONG Yimeng, LIU Xin, XING Xiumei. Research Advances on the Origin, Evolution and Genetic Diversity of Red Deer (Cervus elaphus) [J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(12): 4575-4587.