Acta Veterinaria et Zootechnica Sinica ›› 2023, Vol. 54 ›› Issue (5): 1939-1950.doi: 10.11843/j.issn.0366-6964.2023.05.016
• ANIMAL GENETICS AND BREEDING • Previous Articles Next Articles
MA Keyan1, HAN Jintao2, BAI Yaqin3, LI Taotao1, MA Youji1*
Received:
2022-10-24
Online:
2023-05-23
Published:
2023-05-20
CLC Number:
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.
[1] | NOTTER D R.The importance of genetic diversity in livestock populations of the future[J]. J Anim Sci,1999,77(1):61-69. |
[2] | 王世强,王立儒,刘帅,等.基于SSR标记的黄精品种(系)DNA指纹图谱库构建[J].分子植物育种,2018,16(6):1878-1887.WANG S Q,WANG L R,LIU S,et al.Construction of DNA fingerprint database based on SSR marker for polygonatum varieties (Lines)[J]. Molecular Plant Breeding,2018,16(6):1878-1887.(in Chinese) |
[3] | 王统苗,常国斌,白皓,等.利用16个微卫星标记分析6个鸭品种的遗传多样性[J].四川农业大学学报,2019, 37(2):221-226.WANG T M,CHANG G B,BAI H,et al.Analysis of genetic diversity of 6 duck populations using 16 microsatellite markers[J]. Journal of Sichuan Agricultural University,2019,37(2):221-226.(in Chinese) |
[4] | 毛永江,常洪,杨章平,等.青海高原牦牛血液蛋白基因座群体遗传学分析[J].中国畜牧杂志,2008,44(5):8-10.MAO Y J,CHANG H,YANG Z P,et al.Population genetic analysis of blood protein loci in Qinghai plateau yaks[J] Chinese Journal of Animal Science, 2008,44(5):8-10.(in Chinese) |
[5] | 王兴东,郭宪,吴晓云,等.青海高原牦牛mtDNA Cytb 基因和D-loop区遗传多样性及系统进化分析[J].基因组学与应用生物学,2021,40(1):9-17.WANG X D,GUO X,WU X Y,et al.Genetic diversity and phylogenetic analysis of mtDNA Cytb gene and D-loop region in yak of Qinghai plateau[J]. Genomics and Applied Biology,2021,40(1):9-17.(in Chinese) |
[6] | 师方,柴志欣,罗晓林,等.麦洼牦牛的随机扩增多态性DNA遗传多样性分析[J].畜牧与兽医,2015,47(2):5-10.SHI F,CHAI Z X,LUO X L,et al.Polymorphic frequency of genetic variation in Maiwa yak by RAPD[J]. Animal Husbandry & Veterinary Medicine,2015,47(2):5-10.(in Chinese) |
[7] | 姬秋梅,唐懿挺,张成福,等.西藏牦牛mtDNA cytb 基因的序列多态性及其系统进化分析[J].畜牧兽医学报, 2012, 43(11):1723-1732.JI Q M,TANG Y T,ZHANG C F,et al.Genetic diversity and evolution relationship of Tibet yaks inferred from mtDNA cytb[J]. Acta Veterinaria et Zootechnica Sinica,2012,43(11):1723-1732.(in Chinese) |
[8] | 胡亚亚,刘兰服,冀红柳,等.简化基因组测序技术研究进展[J].江苏师范大学学报:自然科学版,2018,36(4):63-68.HU Y Y,LIU L F,JI H L,et al.Research progress on the reduced-representation genome sequencing technique[J]. Journal of Jiangsu Normal University:Natural Science Edition,2018,36(4):63-68.(in Chinese) |
[9] | WANG W M,ZHANG X X,ZHOU X,et al.Deep genome resequencing reveals artificial and natural selection for visual deterioration,plateau adaptability and high prolificacy in Chinese domestic sheep[J]. Front Genet,2019,10:300. |
[10] | CHENG J,ZHAO H Q,CHEN N B,et al.Population structure,genetic diversity,and selective signature of Chaka sheep revealed by whole genome sequencing[J]. BMC Genomics,2020,21(1):520. |
[11] | ZHANG Y Y,XUE X L,LIU Y,et al.Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep[J]. Sci Rep,2021,11(1):2466. |
[12] | HUANG N,ZHAO L H,WANG J P,et al.Signatures of selection in indigenous Chinese cattle genomes reveal adaptive genes and genetic variations to cold climate[J]. J Anim Sci,2023,101:1-11. |
[13] | WEI C H,WANG H H,LIU G,et al.Genome-wide analysis reveals population structure and selection in Chinese indigenous sheep breeds[J]. BMC Genomics,2015,16(1):194. |
[14] | XU L Y,YANG L,ZHU B,et al.Genome-wide scan reveals genetic divergence and diverse adaptive selection in Chinese local cattle[J]. BMC Genomics,2019,20(1):494. |
[15] | BHUIYAN M S A,LEE S H,HOSSAIN S M J,et al.Unraveling the genetic diversity and population structure of Bangladeshi indigenous cattle populations using 50K SNP markers[J]. Animals (Basel),2021,11(8):2381. |
[16] | AMANE A,BELAY G,NASSER Y,et al.Genome-wide insights of Ethiopian indigenous sheep populations reveal the population structure related to tail morphology and phylogeography[J]. Genes Genomics,2020,42(10):1169-1178. |
[17] | EMERSON K J,MERZ C R,CATCHEN J M,et al.Resolving postglacial phylogeography using high-throughput sequencing[J]. Proc Natl Acad Sci U S A,2010,107(37):16196-16200. |
[18] | HOHENLOHE P A,AMISH S J,CATCHEN J M,et al.Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout[J]. Mol Ecol Resour,2011,11(S1):117-122. |
[19] | HOHENLOHE P A,BASSHAM S,ETTER P D,et al.Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags[J]. PLoS Genet,2010,6(2):e1000862. |
[20] | 刘宏祥,沈永杰,张丽华,等.基于简化基因组测序的娄门鸭遗传多样性评价[J].畜牧兽医学报,2022,53(6):1735-1748.LIU H X,SHEN Y J,ZHANG H L,et al.Genetic diversity evaluation of loumen duck based on reduced-representation genome sequencing[J]. Acta Veterinaria et Zootechnica Sinica,2022,53(6):1735-1748.(in Chinese) |
[21] | 马士龙,李小伟,李响,等.基于GBS简化基因组测序评估3个麦洼牦牛保种群的遗传结构研究[J].草业学报,2022, 31(9):183-194.MA S L,LI X W,LI X,et al.Assessment of genetic structure of 3 Maiwa yak preserved populations based on genotyping-by- sequencing technology[J]. Acta Prataculturae Sinica,2022,31(9):183-194.(in Chinese) |
[22] | 尤桂爽,易兴友,蒋美山,等.四川盆地6个地方鸡群体遗传关系研究[J].畜牧兽医学报,2022,53(2):370-380.YOU G S,YI X Y,JIANG M S,et al.Study on the genetic relationship of six local chicken populations from Sichuan basin[J]. Acta Veterinaria et Zootechnica Sinica,2022,53(2):370-380.(in Chinese) |
[23] | 马丽娜,额尔和花,李颖康.基于酶切的简化基因组测序在绵羊品种进化关系研究中的应用[J].畜牧与兽医,2017, 49(9):8-12.MA L N,E E H H,LI Y K.Reduced representation sequencing in evolutional relationship among sheep breeds based on restriction-site associated DNA[J]. Animal Husbandry & Veterinary Medicine,2017,49(9):8-12.(in Chinese) |
[24] | LI H,DURBIN R.Fast and accurate long-read alignment with Burrows-Wheeler transform[J]. Bioinformatics, 2010, 26(5):589-595. |
[25] | MCKENNA A,HANNA M,BANKS E,et al.The genome analysis toolkit:a MapReduce framework for analyzing next- generation DNA sequencing data[J]. Genome Res,2010,20(9):1297-1303. |
[26] | LI H,HANDSAKER B,WYSOKER A,et al.The sequence alignment/map format and SAMtools[J]. Bioinformatics, 2009, 25(16):2078-2079. |
[27] | CINGOLANI P,PLATTS A,WANG L L,et al.A program for annotating and predicting the effects of single nucleotide polymorphisms,SnpEff:SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso -3[J]. Fly,2012,6(2):80-92. |
[28] | PRICE A L,PATTERSON N J,PLENGE R M,et al.Principal components analysis corrects for stratification in genome-wide association studies[J]. Nat Genet,2006,38(8):904-909. |
[29] | KUMAR S,STECHER G,LI M,et al.MEGA X:molecular evolutionary genetics analysis acrosscomputing platforms[J]. Mol Biol Evol, 2018,35(6):1547-1549. |
[30] | YANG J,LEE S H,GODDARD M E,et al.GCTA:a tool for genome-wide complex trait analysis[J]. Am J Hum Genet,2011, 88(1):76-82. |
[31] | LIU F,QU Y K,GENG C,et al.Analysis of the population structure and genetic diversity of the red swamp crayfish (Procambarus clarkii) in China using SSR markers[J]. Electron J Biotechnol,2020,47:59-71. |
[32] | FU Y R,LI S K,GUO Q Q,et al.Genetic diversity and population structure of two endemic Cupressus (Cupressaceae) species on the Qinghai-Tibetan plateau[J]. J Genet,2019,98(1):14. |
[33] | 成述儒,罗玉柱,刘哲,等.甘肃地方绵羊品种微卫星遗传多样性与系统发育分析[J].畜牧与兽医,2009,41(4):19-23.CHENG S R,LUO Y Z,LIU Z,et al.Microsatellite marker analyses on genetic diversity and phylogenetics in Gansu local breeds of sheeps[J]. Animal Husbandry & Veterinary Medicine,2009,41(4):19-23.(in Chinese) |
[34] | AZIMU W,MANATBAY B,LI Y,et al.Genetic diversity and population structure analysis of eight local chicken breeds of Southern Xinjiang[J]. Br Poult Sci,2018,59(6):629-635. |
[35] | KIRIKCI K,CAM M A,MERCAN L.Genetic diversity and relationship among indigenous Turkish Karayaka sheep subpopulations[J]. Arch Anim Breed,2020,63(2):269-275. |
[36] | QIN M,LI C H,LI Z X,et al.Genetic diversities and differentially selected regions between Shandong indigenous pig breeds and western pig breeds[J]. Front Genet,2020,10:1351. |
[37] | LI Z,WEI S J,LI H J,et al.Genome-wide genetic structure and differentially selected regions among Landrace,Erhualian,and Meishan pigs using specific-locus amplified fragment sequencing[J]. Sci Rep,2017,7(1):10063. |
[38] | WEIR B S,COCKERHAM C C.Estimating F -statistics for the analysis of population structure[J]. Evolution, 1984, 38(6):1358-1370. |
[39] | ZHONG T,HAN J L,GUO J,et al.Genetic diversity of Chinese indigenous sheep breeds inferred from microsatellite markers[J]. Small Rumin Res,2010,90(1-3):88-94. |
[40] | 吕潇潇.甘肃省绵羊品种遗传多样性的微卫星分析[D].兰州:甘肃农业大学,2009.LV X X.Analysis on genetic diversity in sheep breeds in Gansu province by microsatellite markers[D].Lanzhou:Gansu Agricultural University,2009.(in Chinese) |
[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] | YANG Qing, GONG Jing, ZHAO Xueyan, ZHU Xiaodong, GENG Liying, ZHANG Chuansheng, WANG Jiying. Comparison of Array and Resequencing in Pig Genetic Structure Studies [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2772-2782. |
[3] | 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. |
[4] | 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. |
[5] | 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. |
[6] | LIU Shuang, HE Lixia, MA Jun, FENG Xue, YANG Mengli, WANG Shuzhe, YANG Runjun, FANG Xibi, XIAN Hailong, WANG Yongkang, ZHANG Lupei, MA Yun. Analysis on Genetic Background and Body Size Indexes and Beef-purpose Index of Guyuan Cattle [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2376-2388. |
[7] | YANG Sukun, DONG Yimeng, WANG Hongliang, ZHAO Xitang, CHEN Xu, XING Xiumei. Genetic Diversity Analysis of Stud Tahe Red Deer Based on the Gene Fragments of mtDNA and Y Chromosome [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2402-2413. |
[8] | 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. |
[9] | LIU Jiankui, XU Ye, LIU Chen, YU Hui, YANG Yuan, HE Le, LI Jiarui, DAN Huijuan, DAI Ailing, YANG Xiaoyan, WEI Chunhua. Genomic Characteristics of Porcine Reproductive and Respiratory Syndrome Virus in Fujian Province from 2017 to 2021 based on Whole Genome [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1579-1589. |
[10] | 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. |
[11] | LI Yinxia, YA Shengjiang·Nasier, SAI Like·Duman, QIAN Yong, CAO Shaoxian, WANG Weilie, MENG Chunhua, ZHANG Jun, ZHANG Jianli. Evaluation of Genetic Diversity and Genetic Structure in Kirgiz Sheep Population Based on SNPs Chip [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(2): 572-583. |
[12] | 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. |
[13] | LI Dengpan, MA Keyan, HAN Jintao, BAI Yaqin, LI Taotao, MA Youji. Detection and Analysis of Whole Genome Selection Signal of Yongdeng Qishan Sheep [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4577-4588. |
[14] | 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. |
[15] | 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. |
Viewed | ||||||
Full text |
|
|||||
Abstract |
|
|||||