Genetic diversity of the Xuefeng black bone chicken based on microsatellite markers

doi:10.3724/SP.J.1003.2008.07320

Abstract

Abstract:

We studied polymorphisms of 23 microsatellite loci from 23 chromosomes in an indigenous breed of Xuefeng black bone chicken from Hunan in order to elucidate its genetic diversity and structure and to propose reasonable measures for its conservation and utilization. Seventy-nine alleles were identified in 50 individuals and the mean number of alleles was 3.435 per locus. Average heterozygosity and polymorphic information content of 23 microsatellite loci were 0.6285 and 0.5496, respectively. These results indicate that this breed of Xuefeng black bone chicken has a high level of genetic diversity and may provide a scientific basis for future conservation and utilization of the Xuefeng black bone chicken.

Key words: Xuefeng black bone chicken, microsatellite markers, polymorphism information content, heterozygosity

Lin Wei, Shenggui Liu, Xianwei Shi. Genetic diversity of the Xuefeng black bone chicken based on microsatellite markers[J]. Biodiv Sci, 2008, 16(5): 503-508.

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URL: https://www.biodiversity-science.net/EN/10.3724/SP.J.1003.2008.07320

https://www.biodiversity-science.net/EN/Y2008/V16/I5/503

Figures/Tables 3

References 21

[1]	ai WL (白文林), Yin RH (尹荣焕), Yang GQ (杨桂芹), Zhao SJ (赵素君), Gong YQ (宫艳秋), Luo GB (罗光彬) (2007) Analysis on population genetic diversity of Bian Chicken breed using microsatellite DNA markers. Acta Agriculturae Universitatis Jiangxiensis (江西农业大学学报), 29,423-428. (in Chinese with English abstract)
[2]	Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32,314-331.
[3]	Chen HJ (陈红菊), Yue YS (岳永生), Fan XZ (樊新忠), Zhang CS (张传生), Du LX (杜立新) (2003) Analysis of genetic diversity of Shandong indigenous chicken breeds using microsatellite markers. Acta Genetica Sinica (遗传学报), 30,855-860. (in Chinese with English abstract)
[4]	Du ZQ (杜志强), Qu LJ (曲鲁江), Li XY (李显耀), Hu XX (胡晓湘), Huang YH (黄银花), Li N (李宁), Yang N (杨宁) (2004) Genetic diversity in Tibetan chicken. Hereditas(Beijing) (遗传), 26,167-171. (in Chinese with English abstract)
[5]	FAO (1998) Measurement of domestic animal diversity (MoDAD): original working group report. Secondary guidelines for development of national farm animal genetic resources management plans (http://dad.Fao.org/en/refer/library/guidelin/workgrp.pdf)
[6]	Gao YS (高玉时), Qian Y (钱勇), Tu YJ (屠云洁), Chen GH (陈国宏), Li HF (李慧芳), Chen KW (陈宽维), Gu R (顾荣) (2005) Analysis of genetic variation of Chinese native chicken breeds using microsatellite and AFLP fingerprintings. Journal of Northwest Sci-Tech University of Agriculture and Forestry (Natural Science Edition) (西北农林科技大学学报(自然科学版)), 33(12),6-12. (in Chinese with English abstract)
[7]	Gao YS (高玉时), Yang N (杨宁), Li HF (李慧芳), Wang KH (王克华), Tong HB (童海兵) (2004) Analysis of genetic diversity of preserved population of native chicken breeds by microsatellite and file foundation of markers. Hereditas (Beijing) (遗传), 26,859-864. (in Chinese with English abstract)
[8]	Hillel J, Groenen MA, Tixier Boichard M, Korol AB, David L, Kirzhner VM, Burke T, Barre-Dirie A, Crooijmans RP, Elo K, Feldman MW, Freidlin PJ, Mäki-Tanila A, Oortwijn M, Thomson P, Vignal A, Wimmers K, Weigend S (2003) Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genetics Selection Evolution, 35,533-557.
[9]	Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89,583-590.
[10]	Romanov MN, Weigend S (2001) Analysis of genetic relationships between various populations of domestic and jungle fowl using microsatellite markers. Poultry Science, 80,1057-1063.
[11]	Sambrook J, Fritsch E F, Maniaatis T (1989) Molecular Cloning, A Laboratory Manual. Cold Spring Harbor-laboratory Press, New York.
[12]	Takahashi H, Nirasawa K, Nagamine Y, Tsudzuli M,YamamotoY (1998) Genetic relationships among Japanese native breeds of chicken based on microsatellite DNA polymorphisms. Journal of Heredity, 89,543-546.
[13]	Tang QP (汤青萍), Chen KW (陈宽维), Li HF (李慧芳), Zhang SJ (章双杰), Zhao DW (赵东伟) (2005) Analysis of genetic differentiation of Chinese game chicken by using microsatellite. Journal of Northwest Sci-Tech University of Agriculture and Forestry (Natural Science Edition) (西北农林科技大学学报(自然科学版)), 33(3),19-23, 28. (in Chinese with English abstract)
[14]	Vanhala T, Tuiskul haavisto M, Elo K, Vilkki J, Maki-Tanila A (1998) Evaluation of genetic variability and genetic distances between eight chicken lines using microsatellite markers. Poultry Science, 77,783-790.
[15]	Wang DQ (王得前), Chen GH (陈国宏), Wu XS (吴信生), Zhang XY (张学余), Wang KH (王克华), Cheng R (成荣), Liu B (刘博), Xu Q (徐琪), Zhou QL (周群兰) (2003) The genetic relationship analysis among Chinese native chicken breeds by microsatellites. Journal of Yangzhou University (Agriculture and Life Sciences Edition) (扬州大学学报(农业与生命科学版)), 24 (2),1-6. (in Chinese with English abstract)
[16]	Wu XS (吴信生), Chen GH (陈国宏), Wang DQ (王得前), Zhang XY (张学余), Wang KH (王克华), Cheng R (成荣), Liu B (刘博), Xu Q (徐琪), Zhou QL (周群兰) (2004) Analysis of genetic relationship among Chinese native chicken breeds using microsatellites markers. Acta Genetica Sinica(遗传学报), 31,43-50. (in Chinese with English abstract)
[17]	Ye LH (叶朗惠), Huo JL (霍金龙), Miao YW (苗永旺), Zhu SQ (朱胜全), Chen T (陈涛), Liu LX (刘丽仙), Pan WR (潘伟荣), Bi BL (毕保良) (2006) Genetic diversity analysis of Nixi Chicken using microsatellite DNA markers. Zoological Research (动物学研究), 27,68-74. (in Chinese with English abstract)
[18]	Ye LH (叶朗惠), Miao YW (苗永旺), Huo JL (霍金龙), Wei HJ (魏红江), Liu JP (刘建平), Liu LX (刘丽仙), Zhu SQ (朱胜全), Chen T (陈涛) (2006) Genetic diversity of Chahua chicken based on microsatellite markers. Chinese Journal of Zoology (动物学杂志), 41(2),37-42. (in Chinese with English abstract)
[19]	Zhang XQ (张细权), Lü XM (吕雪梅), Yang YH (杨玉华), Liu JS (刘敬顺), Yang GF (杨关福), Wu XH (吴显华) (1998) Population genetic variability of microsatellite polymorphisms and RAPDs in Chinese chicken breeds in Guangdong. Acta Genetica Sinica (遗传学报), 25,112-119. (in Chinese with English abstract)
[20]	Zhang YW (张云武), Zhang YP (张亚平) (2001) Microsatellites and its application. Zoological Research (动物学研究), 22,315-320. (in Chinese with English abstract)
[21]	Zhu Q (朱庆), Li L (李亮) (2002) Genetic diversity in Sichuan black bone chicken lines as revealed by microsatellite DNA markers. Sichuan Animal & Veterinary Science (四川畜牧兽医), 29 (8),26-29. (in Chinese)

采集地点 Collection sites	数量 Sample size	采集地点 Collection sites	数量 Sample size
雪峰镇界脚村 Jiejiao Village, Xuefeng Town	3	塘湾镇白羊村 Baiyang Village, Tangwan Town	3
雪峰镇车力溪村 Chelixi Village, Xuefeng Town	2	塘湾镇木兰溪村 Mulanxi Village, Tangwan Town	3
雪峰镇桐溪村 Tongxi Village, Xuefeng Town	2	塘湾镇里木冲村 Limuchong Village, Tangwan Town	3
雪峰镇先峰溪村 Xianfengxi Village, Xuefeng Town	2	安江镇倒水湾村 Daoshuiwan Village, Anjiang Town	3
雪峰镇两溪口村 Liangxikou Village, Xuefeng Town	2	安江镇桃子垅村 Taozilong Village, Anjiang Town	3
雪峰镇龙家田村 Longjiatian Village, Xuefeng Town	2	安江镇油菜园村 Youcaiyuan Village, Anjiang Town	3
雪峰镇兰溪冲村 Lanxichong Village, Xuefeng Town	2	安江镇大沙坪村 Dashaping Village, Anjiang Town	2
雪峰镇青山洞村 Qingshandong Village, Xuefeng Town	2	托口镇王家坳村 Wangjia’ao Village, Tuokou Town	3
雪峰镇笙竹村 Shengzhu Village, Xuefeng Town	2	硖州乡下坪村 Xiaping Village, Xiazhou Town	2
塘湾镇永红村 Yonghong Village, Tangwan Town	4	硖州乡溪边村 Xibian Village, Xiazhou Town	2

采集地点 Collection sites	数量 Sample size	采集地点 Collection sites	数量 Sample size
雪峰镇界脚村 Jiejiao Village, Xuefeng Town	3	塘湾镇白羊村 Baiyang Village, Tangwan Town	3
雪峰镇车力溪村 Chelixi Village, Xuefeng Town	2	塘湾镇木兰溪村 Mulanxi Village, Tangwan Town	3
雪峰镇桐溪村 Tongxi Village, Xuefeng Town	2	塘湾镇里木冲村 Limuchong Village, Tangwan Town	3
雪峰镇先峰溪村 Xianfengxi Village, Xuefeng Town	2	安江镇倒水湾村 Daoshuiwan Village, Anjiang Town	3
雪峰镇两溪口村 Liangxikou Village, Xuefeng Town	2	安江镇桃子垅村 Taozilong Village, Anjiang Town	3
雪峰镇龙家田村 Longjiatian Village, Xuefeng Town	2	安江镇油菜园村 Youcaiyuan Village, Anjiang Town	3
雪峰镇兰溪冲村 Lanxichong Village, Xuefeng Town	2	安江镇大沙坪村 Dashaping Village, Anjiang Town	2
雪峰镇青山洞村 Qingshandong Village, Xuefeng Town	2	托口镇王家坳村 Wangjia’ao Village, Tuokou Town	3
雪峰镇笙竹村 Shengzhu Village, Xuefeng Town	2	硖州乡下坪村 Xiaping Village, Xiazhou Town	2
塘湾镇永红村 Yonghong Village, Tangwan Town	4	硖州乡溪边村 Xibian Village, Xiazhou Town	2

座位 Locus	上游引物序列 Forward primer’s sequences(5’→3’)
ADL0188	CACTTCCAGTATTAACGTGA	GTGGACACAATGAGTTCCTC	54	125-209	1
ADL0190	TCAGCTCTTCAGGCAAAAAG	AACTTGGACCACAATCTTAT	52	220-231	2
MCW0224	ATTACCTTTCTTCATTAACGCC	TTCATAGACTTGAGCGAGGAC	56	291-301	3
MCW0170	TTGTGAAACTCACAGCAGCTG	TTATAGCAGGCTGGCCTGAAG	60	263-267	4
MCW0029	CATGCAATTCAGGACCGTGCA	GTGGACACCCATTTGTACCCTATG	56	149-194	5
MCW0176	AAAGAGAAGTATAAAACATGCC	TCCATTCTTGGCAGTGCATAG	58	257-270	6
MCW0120	CTATGTAAAGCTTGAATCTTCA	ATTCCTGGGTGCTAATTTACC	54	250-287	7
ADL0121	CTGGAACAAGAGGGCTTTGC	GGATGTGAAAAATCTCCTGG	56	125-157	8
MCW0134	GGAGACTTCATTGTGTAGCAC	ACCAAAAGACTGGAGGTCAAC	56	260-284	9
MCW0035	CAGAAACATTTGGACTTGGCTT	TTGCTTCATTTCTAGTCTCCAGTT	60	227-233	10
MCW0097	GGAGAGCATCTGCCTTCCTAG	TGGTCTTCCAGTCTATGGTAG	56	263-309	11
MCW0198	GATCTTTGCTACCATCCACTG	ACCCATCTGGTTGGACTATGC	58	97-152	12
MCW0104	TAGCACAACTCAAGCTGTGAG	AGACTTGCACAGCTGTGTACC	56	189-263	13
LEI0098	AAAAGACAATGCAATTGGTGC	CTGCCACTGATGCTGTCACT	60	147-170	14
MCW0080	GAAATGGTACAGTGCAGTTGG	CCGTGCATTCTTAATTGACAG	58	278-337	15
MCW0330	TGGACCTCATCAGTCTGACAG	AATGTTCTCATAGAGTTCCTGC	56	260-290	17
MCW0217	GATCTTTCTGGAACAGATTTC	CTGCACTTGGTTCAGGTTCTG	56	153-174	18
MCW0094	GGAGCTGGTATTTGTCCTAAG	GCACAGCCTTTTGACATGTAC	60	77-95	19
MCW0165	CAGACATGCATGCCCAGATGA	GATCCAGTCCTGCAGGCTGC	55	125-144	23
MCW0285	AGTTGGAGGTTATATTA CGGG	TATGACATAATCCACGCTGAG	58	156-300	26
MCW0328	ATGGAAACAGATGGAGCTGGC	CTCCAATCCCAGGCTCCAAC	57	262-324	27
ADL0284	CAGAGTTCATCCGCCACTGC	CCTCCCCACTAACATTGGAA	60	137-167	28
LEI0254	AGACCACTGGATCCAACTC	GTCTGGAACTCATCCCTTCATC	55	89-101	Z

座位 Locus	上游引物序列 Forward primer’s sequences(5’→3’)
ADL0188	CACTTCCAGTATTAACGTGA	GTGGACACAATGAGTTCCTC	54	125-209	1
ADL0190	TCAGCTCTTCAGGCAAAAAG	AACTTGGACCACAATCTTAT	52	220-231	2
MCW0224	ATTACCTTTCTTCATTAACGCC	TTCATAGACTTGAGCGAGGAC	56	291-301	3
MCW0170	TTGTGAAACTCACAGCAGCTG	TTATAGCAGGCTGGCCTGAAG	60	263-267	4
MCW0029	CATGCAATTCAGGACCGTGCA	GTGGACACCCATTTGTACCCTATG	56	149-194	5
MCW0176	AAAGAGAAGTATAAAACATGCC	TCCATTCTTGGCAGTGCATAG	58	257-270	6
MCW0120	CTATGTAAAGCTTGAATCTTCA	ATTCCTGGGTGCTAATTTACC	54	250-287	7
ADL0121	CTGGAACAAGAGGGCTTTGC	GGATGTGAAAAATCTCCTGG	56	125-157	8
MCW0134	GGAGACTTCATTGTGTAGCAC	ACCAAAAGACTGGAGGTCAAC	56	260-284	9
MCW0035	CAGAAACATTTGGACTTGGCTT	TTGCTTCATTTCTAGTCTCCAGTT	60	227-233	10
MCW0097	GGAGAGCATCTGCCTTCCTAG	TGGTCTTCCAGTCTATGGTAG	56	263-309	11
MCW0198	GATCTTTGCTACCATCCACTG	ACCCATCTGGTTGGACTATGC	58	97-152	12
MCW0104	TAGCACAACTCAAGCTGTGAG	AGACTTGCACAGCTGTGTACC	56	189-263	13
LEI0098	AAAAGACAATGCAATTGGTGC	CTGCCACTGATGCTGTCACT	60	147-170	14
MCW0080	GAAATGGTACAGTGCAGTTGG	CCGTGCATTCTTAATTGACAG	58	278-337	15
MCW0330	TGGACCTCATCAGTCTGACAG	AATGTTCTCATAGAGTTCCTGC	56	260-290	17
MCW0217	GATCTTTCTGGAACAGATTTC	CTGCACTTGGTTCAGGTTCTG	56	153-174	18
MCW0094	GGAGCTGGTATTTGTCCTAAG	GCACAGCCTTTTGACATGTAC	60	77-95	19
MCW0165	CAGACATGCATGCCCAGATGA	GATCCAGTCCTGCAGGCTGC	55	125-144	23
MCW0285	AGTTGGAGGTTATATTA CGGG	TATGACATAATCCACGCTGAG	58	156-300	26
MCW0328	ATGGAAACAGATGGAGCTGGC	CTCCAATCCCAGGCTCCAAC	57	262-324	27
ADL0284	CAGAGTTCATCCGCCACTGC	CCTCCCCACTAACATTGGAA	60	137-167	28
LEI0254	AGACCACTGGATCCAACTC	GTCTGGAACTCATCCCTTCATC	55	89-101	Z

座位 Locus	等位基因频率 Allele frequencies	等位基因数 No. of allele	杂合度 Heterozygosity	多态信息含量 PIC
座位 Locus	P1	P2	P3	P4	P5	P6
ADL0188	0.3166	0.2167	0.2000	0.2667			4	0.7417	0.6939
ADL0190	0.5167	0.4833					2	0.4994	0.3747
MCW0224	0.5714	0.3878	0.0408				3	0.5214	0.4211
MCW0170	0.1500	0.2167	0.5000	0.1333			4	0.6628	0.5690
MCW0029	0.5000	0.5000					2	0.5000	0.3750
MCW0176	0.2333	0.2167	0.5500				3	0.5961	0.5342
MCW0120	0.2800	0.2400	0.1200	0.1500	0.1500	0.0700	6	0.8026	0.7738
ADL0121	0.2414	0.3793	0.3793				3	0.7110	0.6530
MCW0134	0.3500	0.6500					2	0.4550	0.3515
MCW0035	0.2333	0.4833	0.2833				3	0.6317	0.5434
MCW0097	0.0667	0.2667	0.3176	0.3500			4	0.7016	0.6463
MCW0198	0.2500	0.2667	0.4833				3	0.6328	0.5412
MCW0104	0.2755	0.2245	0.2245	0.2755			4	0.7474	0.7015
LEI0098	0.1167	0.1833	0.7000				3	0.4628	0.3836
MCW0080	0.3167	0.4667	0.2166				3	0.6439	0.5846
MCW0330	0.2245	0.2551	0.2857	0.1837	0.0510		5	0.7666	0.7227
MCW0217	0.1600	0.4000	0.4400				3	0.6208	0.5390
MCW0094	0.4285	0.5715					2	0.4899	0.3700
MCW0165	0.5300	0.0800	0.1600	0.0600	0.1700		5	0.6546	0.5902
MCW0285	0.4500	0.2833	0.2667				3	0.6461	0.5771
MCW0328	0.5000	0.5000					2	0.5000	0.3750
ADL0284	0.2813	0.2604	0.0417	0.0208	0.1875	0.2083	6	0.7723	0.7163
LEI0254	0.1333	0.1333	0.3667	0.3667			4	0.6955	0.6041
群体平均数及标准误 Mean and standard error (Mean±SE)							3.4350±0.2501	0.6285±0.0225	0.5496±0.0276