基于线粒体DNA D-loop区的肉鸡品种遗传多样性和起源分析

doi:10.3864/j.issn.0578-1752.2021.24.012

Abstract

Abstract:

【Objective】 The purpose of this study was to investigate the genetic diversity and origin characteristics of the whole sequence of mitochondrial DNA D-loop region in chicken breeds (complete set line) with different growth rates, so as to provide a theoretical basis for breeding and traceability of broiler breeds. 【Method】 15 broiler breeds with different growth rates were used as research materials, including eight yellow-feathered broiler lines (5 medium-fast and 3 slow lines), two local chicken breeds (Gushi chicken and Tibetan chicken), two introduced chicken breeds (Recessive White and Anka), one white-feathered broiler (Ross 308), 817 hybrid broiler and one commercial layer line (Dawu Brown Eggshell Hens). Chicken blood was collected, and DNA was PCR amplified. The full sequences of mtDNA D-loop region of 683 individuals from 15 chicken breeds were sequenced, and the genetic diversity and haplotype characteristics of each chicken breed were analyzed using DnaSP 5.10 software. The genetic distance between breeds was calculated using MEGA 4.0 software, and then a phylogenetic tree was constructed between different haplotypes and the red original chicken. 【Result】The full sequence size of the D-loop region of 15 chicken breeds ranged from 1 231 to 1 232 bp, and individuals with sequence length of 1 231 bp had C-base deletion at 859 bp. 45 variant loci were detected in 683 individuals, which were combined into 53 haplotypes and could be divided into four haplotype groups, including A, B, C and E. Among them, the medium-fast broilers, 817 hybrid broilers and high-yielding laying hens were all haplotype E as the dominant haplotype (≥48.89%); the dominant haplotypes were B haplotypes for Hongguang black chickens, A haplotypes for Jinghai yellow chickens, and four haplotypes were relatively balanced for Xueshan chickens (the proportion of E haplotypes ≤38.46% for three chicken breeds); the haplotypes of local chicken breeds were A and C haplotypes for Gushi chickens and A and B haplotypes for Tibetan chickens. The genetic diversity of the 15 chicken breeds ranged from 0.496 to 0.853 for Hd and from 0.00146 to 0.00673 for Pi. The relatively rich genetic diversity was found in the Xinxing Dwarf Yellow Chicken, Xueshan Chicken, Jinghai Yellow Chicken and Ross 308; the relatively low genetic diversity was found in the Tibetan Chicken, the High Laying Chicken, the Anka Chicken, the Xinxing partridge Chicken No. 4 and the Xugang Yellow Chicken No. 1. The range of Kiumura two-parameter distance of 15 chicken breeds was 0.0016-0.0113, among which the intra-breed genetic distance of Ross 308 was the largest while the intra-breed genetic distance of 817 hybrid broiler and high-yielding chicken was the smallest; the inter-breed genetic distance was the largest between high-yielding chicken and Tibetan chicken, and the smallest between high-yielding chicken and 817 hybrid broiler; the genetic distance between medium-fast broiler was relatively small while the genetic distance between medium-fast broiler, slow-fast and local chicken breeds was relatively large; the genetic distance between Jinghai and local chicken breeds was relatively large. Cluster analysis showed that the haplotypes A, B, and gallus gallus spadiceus were clustered in one group. Haplotype E and gallus gallus murghi were clustered in another group. Haplotype C was clustered with four subspecies of jungle fowl, including gallus gallus murghi, gallus gallus spadiceus, gallus gallus gallus and gallus gallus bankiva. 【Conclusion】The genetic diversity of mitochondrial D-loop region varied among different chicken breeds; E haplotypes were strongly correlated with broiler growth rate, and E haplotypes were the dominant haplotypes in all medium and fast populations, while the proportion of E haplotypes in slow populations was less than 40%; the national chicken population had multiple red proto-chicken maternal origins, indicating that it was domesticated under neutral selection. The results of the study provided a theoretical basis for broiler breed selection and tracing as well as resource exploitation.

Key words: chicken, mitochondrial DNA, D-loop region, genetic diversity, genetic origin

TANG XiuJun,FAN YanFeng,JIA XiaoXu,GE QingLian,LU JunXian,TANG MengJun,HAN Wei,GAO YuShi. Genetic Diversity and Origin Characteristics of Chicken Species Based on Mitochondrial DNA D-loop Region[J].Scientia Agricultura Sinica, 2021, 54(24): 5302-5315.

Figures/Tables 8

Table 1

The place of origin and sample size of 15 chicken breeds"

品种 Breed	文中简称 Abbreviation	来源 Source	采样数 Sampling number
墟岗黄鸡1号 Xugang yellow chicken No.1	XGH	广东省鹤山市墟岗黄畜牧有限公司 Guangdong Heshan Xuganghuang Animal Husbandry Co. LTD	45
新广铁脚麻鸡 Xinguang tiejiaoma chicken	XGT	佛山市高明区新广农牧有限公司 Foshan Gaoming Xinguang Agriculture and Animal Husbandry Co. LTD	38
新兴麻鸡4号 Xinxing partridge chicken No.4	XXM	广东温氏南方家禽育种有限公司 Guangdong Wenshi South Poultry Breeding Co. LTD	55
良凤花鸡 Liangfeng hua chicken	LFH	广西南宁市良凤农牧有限责任公司 Guangxi Nanning Liangfeng Agriculture and Animal Husbandry Co. LTD	53
新兴矮脚黄鸡 Xinxing dwarf yellow chicken	XXA	广东温氏食品集团有限公司 Guangdong Wens Food Group Co. LTD	46
雪山鸡 Xueshan chicken	XS	江苏立华牧业股份有限公司 Jiangsu Lihua Animal Husbandry Co. LTD	39
京海黄鸡 Jinghai yellow chicken	JHH	江苏京海禽业集团有限公司 Jiangsu Jinghai Poultry Industry Group Co. LTD	40
鸿光黑鸡 Hongguang black chicken	HGH	广西鸿光农牧有限公司 Guangxi Hongguang Agriculture and Animal Husbandry Co. LTD	77
固始鸡 Gushi chicken	GS	国家级地方鸡种基因库（江苏） National Local Chicken Gene Bank (Jiangsu)	73
藏鸡 Tibetan chicken	Z	国家级地方鸡种基因库（江苏） National Local Chicken Gene Bank (Jiangsu)	38
隐性白羽鸡 Recessive White	YXB	国家级地方鸡种基因库（江苏） National Local Chicken Gene Bank (Jiangsu)	45
安卡鸡 Anka chicken	AK	国家级地方鸡种基因库（江苏） National Local Chicken Gene Bank (Jiangsu)	29
罗斯308 Rose 308	LS	国家家禽生产性能测定站 National Poultry production performance testing station	34
817杂交肉鸡 817 hybrid broiler	817	国家家禽生产性能测定站 National Poultry production performance testing station	32
高产蛋鸡 High-yielding layer	E	国家家禽生产性能测定站 National Poultry production performance testing station	39

Table 1

Table 2

The number of mtDNA D-loop region haplotypes in 15 chicken breeds"

单倍型 Haplotype	突变位点 Variable sites (bp)	总计 Total	单倍型类别 Haplotype category	品种 (个数) Breeds (number)
111
1112222222 2222222222 2333333333 3333344677 89022
3691112233 4444555688 9011234566 6669914819 42511
3791272589 0236269113 6605102401 2371976612 60245
D-NC007237 TTTAGTACGA CGCCACATGA CCTCGCGTTA CCTCGCCGGG CCTCG
Hap_1..C..C............A..T....A.........T......T.		82	E1	XGH(6), XGT(11), XXM(8), LFH(17), XXA(3), XS(9), JHH(3),AK(10),LS(15)
Hap_2.....C............A..T....A.........T......T.		159	E2	XGH(30), XGT(14),XXM(36),LFH(14), XXA(13), XS(6),YXB(19), AK(16), LS(1), 817(6), E(4)
Hap_3...........A.....C...T.........TC............		85	C1	XGH(5), XGT(12), XXM(5), LFH(2), XXA(7), XS(11),GS(28),YXB(14), LS(1)
Hap_4....A.......TT.T.CA..TCT..A..........A.A....A		27	B1	XGH(4), LFH(4), XXA(5), XS(4), YXB(2), AK(1), LS(7)
Hap_5....A.......TT.TGCA...CT..A.................A		1	B2	XGT(1)
Hap_6.C.....T.G..T..T.CA..TC...A..................		13	A1	XXM(3), LFH(2),XXA(7),AK(1)
Hap_7.....C............A..T....A.........TA.....T.		5	E3	XXM(3),YXB(2)
Hap_8..C..C............A..T....A........TT......T.		4	E4	LFH(4)
Hap_9.....C...........CA..T...TA.........T......T.		6	E5	LFH(6)
Hap_10....A.......TT.T.CA..TCT..A..........A.A...T.		4	B3	LFH(4)
Hap_11..C..C............A..T....A.........T..A...T.		6	E6	XXA(6)
Hap_12.C.....T....T..T.CA..TC...A..................		52	A2	XXA(4),XS(9),JHH(2),GS(37)
Hap_13.....C............A..T...TA.........T......T.		7	E7	XXA(1),817(6)
Hap_14 CC.....T....T..T.CA..TC...A..................		16	A3	JHH(3),Z(13)
Hap_15....A.......TTTT.CA..TCT..A.................A		3	B4	JHH(3)
单倍型 Haplotype	突变位点 Variable sites（bp）	总计 Total	单倍型类别 Haplotype category	品种 (个数) Breeds (number)
Hap_16.C.....T....T..T.CA..TC...A..........A.......		13	A4	JHH(13)
Hap_17....A.......TT.T.CA..T.T..A..........A......A		2	B5	JHH(2)
Hap_18....A.......TT.T.CA..TCT..A............A....A		7	B6	JHH(7)
Hap_19...........A.........T.........TC............		3	C2	JHH(3)
Hap_20.C..A..T....T..T.CA..TC...A..................		2	A5	JHH(2)
Hap_21.......... TA.....C...T.........TC............		2	C3	JHH(2)
Hap_22....A.......TT.T.CA..TCT..A............A T...A		20	B7	HGH(20)
Hap_23....A.......TT.T.CA..TCT..A............. T...A		23	B8	HGH(23)
Hap_24....A.......TT.T.CA..TCT..A..........A.. T...A		1	B9	HGH(1)
Hap_25.C.....T....T..T.CA..TC...A... T......... T....		4	A6	HGH(4)
Hap_26...........A.....C...T.........TC....... T....		7	C4	HGH(3),GS(4)
Hap_27....A.......TT.T.CAG.TCT..A............. T...A		2	B10	HGH(2)
Hap_28....A.......TT.TGCA...CT..A............A T...A		2	B11	HGH(2)
Hap_29....A.......TT.T.CA. TTCT..A............A T...A		3	B12	HGH(3)
Hap_30....A.......TT.T.CA..TCT..A.C..........A T...A		2	B13	HGH(2)
Hap_31....A........T.T.CA..TCT..A............A T...A		1	B14	HGH(1)
Hap_32.....C............A..T....AC........T... T..T.		1	E8	HGH(1)
Hap_33....A.......TT.T.CA..TCT..A..........A.A T...A		3	B15	HGH(3)
Hap_34...........A.....C...T.........TC....A.. T....		2	C5	HGH(2)
Hap_35....A.......TT.T.CA..TCT..A...........AA T...A		1	B16	HGH(1)
Hap_36.....C............A..T....A.........T... T..T.		4	E9	HGH(4)
Hap_37.C.....TA...T..T.CA..TC...A..........A.. T....		1	A7	HGH(1)
Hap_38....A.......TT.T.CA..TCT..A......T...... T...A		1	B17	HGH(1)
Hap_39.....C............A..T....A......A..T... T..T.		1	E10	HGH(1)
Hap_40.....C............A..T....A.........TA.. T..T.		2	E11	HGH(2)
Hap_41...G.......A.....C...T..A......TC............		1	C6	GS(1)
Hap_42...........A.....C...T.........TC........T...		2	C7	GS(1),AK(1)
Hap_43.C.....T....T..T.CA..TC...A..T...............		8	A8	GS(2),YXB(6)
Hap_44....A.......TT.T.CA. TTCT..A............A....A		24	B18	Z(24)
Hap_45....A.......TT.T.CA..TCT..A.................A		1	B19	Z(1)
Hap_46.C.....T....T..T.CA..TC...A................T.		1	A9	YXB(1)
Hap_47.....C............A..T....A.........T........		1	E12	YXB(1)
Hap_48.C.....T.G..T..T.CA..TC...A...............C..		7	A10	LS(7)
Hap_49....A.......TT.T.CA..TCT..A.......A..A.A....A		1	B20	LS(1)
Hap_50..C..C............A..T....A.......A.T......T.		1	E13	LS(1)
Hap_51.C.....T.G..T..T.CA..TC...A.......A.......C..		1	A11	LS(1)
Hap_52.....C............A..T..............TA.....T.		24	E14	817(13),E（11）
Hap_53.....CG...........A..T...TA.........T......T.		31	E15	817(7),E（24）

Table 2

Table 3

Table 4

Table 5

Fig. 1

Fig. 2

Fig. 3

References 30

[2]	ARMSTRONG E, IRIARTE A, MARTINEZ A M, FEIJOO M, VEGA-PLA J L, DELGADO J V, POSTIGLIONI A. Genetic diversity analysis of the Uruguayan Creole cattle breed using microsatellites and mtDNA markers. Genetics and molecular research, 2013, 12(2):1119-1131. doi: 10.4238/2013.April.10.7
[3]	ASATO Y, OSHIRO M, MYINT C K, YAMAMOTO Y I, KATO H, MARCO J D, MIMORI T, GOMEZ E A L, HASHIGUCHI Y, UEZATO H. Phylogenic analysis of the genus Leishmania by cytochrome b gene sequencing. Experimental Parasitology, 2009, 121(4):352-361. doi: 10.1016/j.exppara.2008.12.013 doi: 10.1016/j.exppara.2008.12.013
[4]	李雪娟, 黄原, 雷富民. 山鹧鸪属鸟类线粒体基因组的比较及系统发育研究. 遗传, 2014(9):912-920.
	LI X J, HUANG Y, LEI F M. Comparative and phylogenomic analyses on mitochondrial genomes of Arborophila species. Hereditas, 2014(9):912-920.(in Chinese)
[5]	MALTSEV A N, STAKHEEV V V, BOGDANOV A S, FOMINA E S, KOTENKOVA E V. Phylogenetic relationships of intraspecific forms of the house mouse Mus musculus: Analysis of variability of the control region (D-loop) of mitochondrial DNA. Doklady Biological Sciences, 2015, 465(1):285-288. doi: 10.1134/S0012496615060058
[6]	TAKASU M, ISHIHARA N, TOZAKI T, KAKOI H, MAEDA M, MUKOYAMA H. Genetic diversity of maternal lineage in the endangered kiso horse based on polymorphism of the mitochondrial DNA D-loop region. Journal of Veterinary Medical Science, 2014, 76(11):1451-1456. doi: 10.1292/jvms.14-0231
[7]	张涛, 路宏朝. 宁强矮马线粒体DNA D-loop区的遗传多样性. 中国农业科学, 2012, 45(8):1587-1594.
	ZHANG T, LU H Z. Genetic diversity of mitochondrial DNA D-loop sequences in Ningqiang pony. Scientia Agricultura Sinica, 2012, 45(8):
[8]	齐国强, 昝林森, 张桂香, 王志刚, 王均辉, 韩旭. 中国部分地方水牛品种mtDNA D-loop区遗传多样性与起源研究. 畜牧兽医学报, 2008(1):7-11.
	QI G Q, ZAN L S, ZHANG G X, WANG Z G, WANG J H, HAN X. Mitochondrial DNA D-loop genetic diversity and origin of some Chinese domestic buffalo breeds. Chinese Journal of Animal and Veterinary Sciences, 2008(1):7-11. (in Chinese)
[9]	武艳平, 关伟军, 赵倩君, 何晓红, 浦亚斌, 霍俊宏, 敖红, 李奎, 马月辉. 山羊线粒体DNA D-loop区部分序列变异位点分析. 畜牧兽医学报, 2008, 39(8):1137-1141. doi: 10.3321/j.issn:0366-6964.2008.08.023. doi: 10.3321/j.issn:0366-6964.2008.08.023
	WU Y P, GUAN W J, ZHAO Q J, HE X H, PU Y B, HUO J H, AO H, LI K, MA Y H. Analysis on partial sequence of mitochondrial DNA D-loop region variation position of goat. Acta Veterinaria et Zootechnica Sinica, 2008, 39(8):1137-1141. doi: 10.3321/j.issn:0366-6964.2008.08.023. (in Chinese) doi: 10.3321/j.issn:0366-6964.2008.08.023
[1]	赵华, 范梅华. 活鸡向冰鲜鸡消费转型亟需解决的六大问题. 中国畜牧杂志, 2015(16):8-10, 14.
	ZHAO H, FAN M H. Six problems need to solve during the consumption of chilled chicken replacing live chicken. Chinese Journal of Animal Science, 2015(16):8-10, 14. (in Chinese)
[10]	郑立, 刘延鑫, 赵绪永, 靳双星, 邓红雨, 刘太宇. 河南3个驴种mtDNA D-loop区序列多态性及起源进化分析. 西北农林科技大学学报(自然科学版), 2011(4):29-34.
	ZHENG L, LIU Y X, ZHAO X Y, JIN S X, DENG H Y, LIU T Y. Analysis of phylogenetic relationship and genetic diversity of mtDNA D-loop in three Henan donkey breeds. Journal of Northwest A & F University (Natural Science Edition), 2011(4):29-34. (in Chinese)
[11]	LEE J C, TSAI L C, LIAO S P, LINACRE A, HSIEH H M. Evaluation of the polymorphic D-loop of Columba livia in forensic applications. Electrophoresis, 2010, 31(23/24):3889-3894. doi: 10.1002/elps.201000414. doi: 10.1002/elps.201000414
[12]	李慧芳, 朱文奇, 杨宁, 宋卫涛, 王继文, 徐文娟, 王强, 陈宽维. 家鸭、媒鸭和野鸭mtDNA D-loop区的遗传变异. 畜牧兽医学报, 2011, 42(9):1213-1219.
	LI H F, ZHU W Q, YANG N, SONG W T, WANG J W, XU W J, WANG Q, CHEN K W. The genetic variation of the mtDNA D-loop region in domestic ducks, Mei ducks and wild ducks. Acta Veterinaria et Zootechnica Sinica, 2011, 42(9):1213-1219. (in Chinese)
[13]	周蓉, 李佳琦, 李铀, 刘迺发, 房峰杰, 施丽敏, 王莹. 基于线粒体DNA的大石鸡种群遗传变异. 生物多样性, 2012, 20(4):451-459. doi: 10.3724/SP.J.1003.2012.09221. doi: 10.3724/SP.J.1003.2012.09221
	ZHOU R, LI J Q, LI Y, LIU N F, FANG F J, SHI L M, WANG Y. Genetic variation in rusty-necklaced partridge (Alectoris magna) detected by mitochondrial DNA. Biodiversity Science, 2012, 20(4):451-459. doi: 10.3724/SP.J.1003.2012.09221. (in Chinese) doi: 10.3724/SP.J.1003.2012.09221
[14]	赵倩君, 关伟军, 郭军, 乔海云, 何晓红, 浦亚斌, 傅宝玲, 敖红, 李奎, 马月辉. 中国7个绵羊品种mtDNA D-loop区序列的系统发育与起源研究. 畜牧兽医学报, 2008(4):417-422.
	ZHAO Q J, GUAN W J, GUO J, QIAO H Y, HE X H, PU Y B, FU B L, AO H, LI K, MA Y H. Origin and phylogenetics of seven Chinese sheep breeds based on D-loop sequence. Chinese Journal of Animal and Veterinary Sciences, 2008(4):417-422. (in Chinese)
[15]	高玉时, 贾晓旭, 唐修君, 唐梦君, 樊艳凤, 陆俊贤, 顾荣, 葛庆联, 苏一军. 基于线粒体基因组D-loop区全序列分析安义瓦灰鸡遗传多样性及其起源进化关系. 农业生物技术学报, 2015, 23(7):940-944. doi: 10.3969/j.issn.1674-7968.2015.07.011. doi: 10.3969/j.issn.1674-7968.2015.07.011
	GAO Y S, JIA X X, TANG X J, TANG M J, FAN Y F, LU J X, GU R, GE Q L, SU Y J. The genetic diversity and origin analysis of Anyi tile-like chickens (Gallus gallus domestiaus) based on mitochondrial DNAD-loop sequence. Journal of Agricultural Biotechnology, 2015, 23(7):940-944. doi: 10.3969/j.issn.1674-7968.2015.07.011. (in Chinese) doi: 10.3969/j.issn.1674-7968.2015.07.011
[16]	LIU Y P, WU G S, YAO Y G, MIAO Y W, LUIKART G, BAIG M, BEJA-PEREIRA A, DING Z L, PALANICHAMY M G, ZHANG Y P. Multiple maternal origins of chickens: out of the Asian jungles. Molecular Phylogenetics and Evolution, 2006, 38(1):12-19. doi: 10.1016/j.ympev.2005.09.014
[17]	MIAO Y W, PENG M S, WU G S, OUYANG Y N, YANG Z Y, YU N, LIANG J P, PIANCHOU G, BEJA-PEREIRA A, MITRA B, PALANICHAMY M G, BAIG M, CHAUDHURI T K, SHEN Y Y, KONG Q P, MURPHY R W, YAO Y G, ZHANG Y P. Chicken domestication: an updated perspective based on mitochondrial genomes. Heredity, 2013, 110(3):277-282. doi: 10.1038/hdy.2012.83
[18]	萨姆布鲁克J, 拉塞尔 D W. 分子克隆实验指南: 第三版. 北京: 科学出版社, 2002, 461-512.
	SAMBROOK J, RUSSELL D W. Molecular cloning：a laboratory manual: the third edition. Science Press. Beijing. 2002, 461-512. (in Chinese)
[19]	ROZAS J, SÁNCHEZ-DELBARRIO J C, MESSEGUER X, ROZAS R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics (Oxford, England), 2003, 19(18):2496-2497. doi: 10.1093/bioinformatics/btg359. doi: 10.1093/bioinformatics/btg359
[20]	TAMURA K, DUDLEY J, NEI M, KUMAR S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 2007, 24(8):1596-1599. doi: 10.1093/molbev/msm092. doi: 10.1093/molbev/msm092
[21]	包文斌, 束婧婷, 王存波, 张红霞, Steffen Weigend, 陈国宏. 中国家鸡和红色原鸡mtDNA控制区遗传多态性及系统进化分析. 畜牧兽医学报, 2008, 39(11):1449-1459. doi: 10.3321/j.issn:0366-6964.2008.11.001. doi: 10.3321/j.issn:0366-6964.2008.11.001
	BAO W B, SHU J T, WANG C B, ZHANG H X, WEIGEND S, CHEN G H. Investigation on genetic diversity and systematic evolution in Chinese domestic fowls and red jungle fowls by analyzing the mtDNA control region. Acta Veterinaria et Zootechnica Sinica, 2008, 39(11):1449-1459. doi: 10.3321/j.issn:0366-6964.2008.11.001. (in Chinese) doi: 10.3321/j.issn:0366-6964.2008.11.001
[22]	DANA N, MEGENS H J, CROOIJMANS R P M A, HANOTTE O, MWACHARO J, GROENEN M A M, ARENDONK J A M V. East Asian contributions to Dutch traditional and western commercial chickens inferred from mtDNA analysis. Animal Genetics, 2010, 42, 125-133. doi: 10.1111/age.2011.42.issue-2
[23]	LYIMO C M, WEIGEND A, MSOFFE P L, HOCKING P M, SIMIANER H, WEIGEND S. Maternal genealogical patterns of chicken breeds sampled in Europe. Animal Genetics, 2015, 46(4):447-451. doi: 10.1111/age.2015.46.issue-4
[24]	OSMAN S A M, YONEZAWA T, NISHIBORI M. Origin and genetic diversity of Egyptian native chickens based on complete sequence of mitochondrial DNA D-loop region. Poultry Science, 2016, 95(6):1248-1256. doi: 10.3382/ps/pew029
[25]	SMITH M A, WOODLEY N E, JANZEN D H, HALLWACHS W, HEBERT P D. DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). Proceedings of the National Academy of Sciences of the United States of America, 2006, 103(10):3657-3662. doi: 10.1073/pnas.0511318103. doi: 10.1073/pnas.0511318103
[26]	潘建飞, 史兆国, 成述儒, 王川, 赵生国. 甘肃主要马群体遗传多样性及系统发育研究. 农业生物技术学报, 2014, 22(2):210-218. doi: 10.3969/j.issn.1674-7968.2014.02.010. doi: 10.3969/j.issn.1674-7968.2014.02.010
	PAN J F, SHI Z G, CHENG S R, WANG C. The study of genetic diversity and phylogenetic evolution in indigenous horses (Equus caballus) of Gansu. Journal of Agricultural Biotechnology, 2014, 22(2):210-218. doi: 10.3969/j.issn.1674-7968.2014.02.010. (in Chinese) doi: 10.3969/j.issn.1674-7968.2014.02.010
[27]	中国畜禽遗传资源志家禽志. 北京: 中国农业出版社, 2011, 331-333.
	Animal genetic resources in China Poultry. China agriculture press. Beijing. 2011, 331-333. (in Chinese)
[28]	FUMIHITO A, MIYAKE T, SUMI S, TAKADA M, OHNO S, KONDO N. One subspecies of the red junglefowl (Gallus gallus gallus) suffices as the matriarchic ancestor of all domestic breeds. Proceedings of the National Academy of Sciences, USA. 1994, 91, 12505-12509.
[29]	KANGINAKUDRU S, METTA M, JAKATI R D, NAGARAJU J. Genetic evidence from Indian red jungle fowl corroborates multiple domestication of modern day chicken. BMC Evolutionary Biology, 2008, 8:174. doi: 10.1186/1471-2148-8-174. doi: 10.1186/1471-2148-8-174
[30]	贾晓旭, 唐修君, 樊艳凤, 陆俊贤, 黄胜海, 葛庆联, 高玉时, 韩威. 华东地区地方鸡品种mtDNA控制区遗传多样性. 生物多样性, 2017, 25(5):540-548. doi: 10.17520/biods.2017012. doi: 10.17520/biods.2017012
	JIA X X, TANG X J, FAN Y F, LU J X, HUANG S H, GE Q L, GAO Y S, HAN W. Genetic diversity of local chicken breeds in East China based on mitochondrial DNA D-loop region. Biodiversity Science, 2017, 25(5):540-548. doi: 10.17520/biods.2017012. (in Chinese) doi: 10.17520/biods.2017012

Metrics

Viewed

Full text

Abstract

Cited

Shared

Discussed

Comments

Recommended 0

No Suggested Reading articles found!

鸡种 Breed	总数 Total	单倍型个数Number of haplotypes (%)
鸡种 Breed	总数 Total	A	B	C	E
XGH	45	—	4(8.89%)	5(11.11%)	36(80.00%)
XGT	38	—	1(2.63%)	12(31.58%)	25(65.79%)
XXM	55	3(5.45%)	—	5(9.09%)	47(85.45%)
LFH	53	2(3.77%)	8(15.09%)	2(3.77%)	41(77.36%)
XXA	46	11(23.91%)	5(10.87%)	7(15.22%)	23(50.00%)
XS	39	9(23.08%)	4(10.26%)	11(28.21%)	15(38.46%)
JHH	40	20(50.00%)	12(30.00%)	5(12.50%)	3(7.50%)
HGH	77	5(6.49%)	59(76.62%)	5(6.49%)	8(10.39%)
GS	73	39(53.42%)	—	34(46.58%)	—
Z	38	13(34.21%)	25(65.79%)	—	—
YXB	45	7(15.56%)	2(4.44%)	14(31.11%)	22(48.89%)
AK	29	1(3.45%)	1(3.45%)	1(3.45%)	26(89.66%)
LS	34	8(23.53%)	8(23.53%)	1(2.94%)	17(50.00%)
817	32	—	—	—	32(100%)
E	39	—	—	—	39(100%)

品种 Breed	变异位点数 No. of variable sites	单倍型数 No. of haplotype	平均核苷酸差异 Average number of nucleotide differences (K)	核苷酸多样度 Nucleotide diversity (Pi)	单倍型多样度 Haplotype diversity (Hd)
XGH	19	4	4.0465	0.00329±0.00078	0.529±0.078
XGT	19	4	4.9644	0.00403±0.00053	0.698±0.026
XXM	17	5	2.8431	0.00231±0.00057	0.546±0.072
LFH	24	8	5.2438	0.00426±0.00066	0.810±0.032
XXA	23	8	7.4899	0.00608±0.00043	0.851±0.026
XS	21	5	7.6167	0.00619±0.00036	0.800±0.024
JHH	24	10	6.9372	0.00564±0.00057	0.853±0.039
HGH	30	19	5.1490	0.00418±0.00056	0.840±0.029
GS	15	6	5.2870	0.00429±0.00013	0.600±0.034
Z	9	3	4.1920	0.00340±0.00036	0.496±0.054
YXB	21	7	6.5920	0.00535±0.00045	0.718±0.043
AK	23	5	2.6700	0.00217±0.00088	0.594±0.065
LS308	24	8	8.2820	0.00673±0.00047	0.738±0.055
817	4	4	1.8468	0.00150±0.00009	0.740±0.041
E	4	3	1.8030	0.00146±0.00016	0.545±0.063
总Total	45	53	7.9552	0.00646±0.00011	0.901±0.006

品种 Breed	种内 Within breeds	XGH	XGT	XXM	LFH	XXA	XS	JHH	HGH	GS	Z	YXB	AK	LS308	817
XGH	0.0033	—
XGT	0.0041	0.0039	—
XXM	0.0023	0.0028	0.0035	—
LFH	0.0043	0.0039	0.0046	0.0035	—
XXA	0.0061	0.0052	0.0056	0.0049	0.0056	—
XS	0.0062	0.0056	0.0056	0.0054	0.0060	0.0062	—
JHH	0.0057	0.0079	0.0082	0.0079	0.0079	0.0071	0.0071	—
HGH	0.0042	0.0091	0.0098	0.0095	0.0090	0.0086	0.0086	0.0068	—
GS	0.0043	0.0074	0.0068	0.0072	0.0079	0.0067	0.0061	0.0061	0.0083	—
Z	0.0034	0.0094	0.0101	0.0098	0.0092	0.0083	0.0084	0.0058	0.0053	0.0075	—
YXB	0.0054	0.0048	0.0049	0.0045	0.0055	0.0059	0.0058	0.0074	0.0091	0.0062	0.0091	—
AK	0.0022	0.0028	0.0036	0.0023	0.0033	0.0050	0.0055	0.0080	0.0094	0.0076	0.0098	0.0047	—
LS308	0.0068	0.0060	0.0066	0.0058	0.0061	0.0066	0.0069	0.0073	0.0083	0.0077	0.0080	0.0069	0.0056	—
817	0.0015	0.0029	0.0038	0.0024	0.0036	0.0054	0.0060	0.0088	0.0104	0.0083	0.0110	0.0050	0.0023	0.0063	—
E	0.0015	0.0032	0.0042	0.0027	0.0039	0.0058	0.0064	0.0092	0.0107	0.0087	0.0113	0.0053	0.0026	0.0067	0.0016

Genetic Diversity and Origin Characteristics of Chicken Species Based on Mitochondrial DNA D-loop Region

RichHTML

PDF

Abstract

Cite this article

share this article

Figures/Tables 8

References 30

Related Articles 15

Metrics

Comments

Recommended 0

[1]	ZHAO QingYao, WANG XiaoMing, XING Tong, LI LingYun, XU XingLian, ZHAO Xue. Extraction Optimization, Structural Characterization, and Anticoagulant Activity of Intestinal Polysaccharides from Yellow-Feathered Chickens [J]. Scientia Agricultura Sinica, 2026, 59(6): 1317-1332.
[2]	YANG LiJuan, CHEN SiYu, ZHAO Wei, ZHU Ling, GUO Lei, MA LiNa, MA RuiMin, ZHANG Juan. Whole-Genome Resequencing Reveals the Genetic Mechanisms Underlying Feather Coloration in Jingyuan Chicken [J]. Scientia Agricultura Sinica, 2026, 59(6): 1348-1360.
[3]	WANG ShaoHua, FAN QiuLi, YANG JinChang, SUN YuJie, YU Niu, JIANG ShouQun. Effects of Different Levels of Mytilaria laosensis Leaves Feeding on Growth Performance, Immune Function, Antioxidant Capacity, Carcass Quality and Meat Quality of Yellow-Feathered Chickens [J]. Scientia Agricultura Sinica, 2026, 59(5): 1111-1127.
[4]	HE ZhiLin, SUN CuiXia, YUE HongLi, TAN YueXia, ZHANG YaoHai, WANG FuSheng, LIU SiTao, JIANG Dong. Genetic Diversity Analysis and GWAS of Alloocimene Based on Resequencing of Citron, Lemon Germplasm Resources [J]. Scientia Agricultura Sinica, 2026, 59(2): 386-401.
[5]	LI Yun, ZHANG Fan, ZHOU YongQi, QIAO ZhiHao, LIU YanLi. Analysis of Body Size Traits During Growth and Development and Comparison of Meat Quality and Flavor Between 13 and 16 Weeks Lueyang Black-Bone Chickens [J]. Scientia Agricultura Sinica, 2026, 59(2): 427-440.
[6]	YAO Hong, SHI ShouRong, ZHAO RuQian. The Potential and Mechanism of Chlorogenic Acid to Alleviate Intestinal Inflammation in Chickens Based on Network Pharmacology and Molecular Docking [J]. Scientia Agricultura Sinica, 2025, 58(3): 600-616.
[7]	XU YuJuan, ZHANG Jie, WANG TianYi, CHEN HaoYang, ZHAO JiaJia, WU BangBang, HAO YuQiong, LI XiaoHua, ZHENG XingWei, ZUO JingJing, ZHENG Jun. Identification of Glu-A3 and Glu-B3 of Low-Molecular-Weight Glutenin in Shanxi Wheat and Its Effect on Quality [J]. Scientia Agricultura Sinica, 2025, 58(24): 5110-5127.
[8]	CHEN CaiJin, MA Lin, JIANG QingXue, LIU JinHui, MIAO Tong, ZHANG ZhiPeng, MENG Xiang, MA XiaoRan, ZHOU XinYue, ZHANG Jian, LIU WenHui, WANG XueMin. Genetic Diversity Analysis of Phenotypic Traits of 244 Forage Oat Germplasm Resources [J]. Scientia Agricultura Sinica, 2025, 58(23): 4825-4836.
[9]	HUANG HuaYun, SUI YuLe, KONG Yi, LIANG Zhong, YANG MiaoMiao, LIU Xing, HAN Wei. Regulatory Effect of FTO Gene on Lipid Deposition in Chicken Intramuscular Adipocytes [J]. Scientia Agricultura Sinica, 2025, 58(22): 4786-4796.
[10]	WEI YiMin, ZHOU MeiLiang, TANG Yu. Origin, Evolution and Spread of Crop Buckwheat [J]. Scientia Agricultura Sinica, 2025, 58(21): 4305-4316.
[11]	LIU XiaoXu, ZHONG ZeXin, QIU JiaRen, YANG ChunXiao, ZHANG YongJun, XIE Wen, ZHANG YouJun, PAN HuiPeng. GENETIC DIVERSITY OF MTCO1 IN DIFFERENT GEOGRAPHICAL POPULATIONS OF MEGALUROTHRIPS USITATUS [J]. Scientia Agricultura Sinica, 2025, 58(21): 4361-4371.
[12]	GUO MengZe, ZHANG Lei, SUN PingPing, JIANG Biao, YAN JinQiang, LI ZhengNan. Molecular Characterization and Evolutionary Dynamics of Tomato Leaf Curl New Delhi Virus Isolate from Wax Gourd (Benincasa hispida) in Guangdong [J]. Scientia Agricultura Sinica, 2025, 58(19): 3890-3904.
[13]	LI XueFeng, WANG Hui, ZHANG NingBo, JIN TaiHua, ZHANG ShuEr, ZHENG QuanSheng, TAO JiaShu, LI QingKe, LÜ ShenJin, LI YongZhu. Prediction and Analysis of Feeding Density on Production Performance, Cecal Flora Diversity, Short-Chain Fatty Acid Content and Microbial Differential Function of Langya Chickens [J]. Scientia Agricultura Sinica, 2025, 58(17): 3544-3560.
[14]	LIU PengPeng, LI JiangBo, XU HongJun, NIE YingBin, HAN XinNian, KONG DeZhen, SANG Wei. Genetic Diversity Analysis of Protein Fractions and Quality in Xinjiang Winter Wheat Cultivar Resources [J]. Scientia Agricultura Sinica, 2025, 58(15): 2948-2959.
[15]	HUANG HuaYun, LIU Xing, WANG QianBao, LI RuiRui, YANG MiaoMiao, LI ChunMiao, WU ZhaoLin, KONG LingLin, ZHAO ZhenHua. Expression Pattern of gga-miR-30a-5p and Its Regulation of Abdominal Fat and Intramuscular Fat Deposition in Chicken [J]. Scientia Agricultura Sinica, 2025, 58(15): 3134-3144.