Genetic diversity and population structure of indigenous chicken breeds in South China

doi:10.15302/J-FASE-2016102

Front. Agr. Sci. Eng.

0, Vol.

Issue () : 97-101 https://doi.org/10.15302/J-FASE-2016102

LETTER

Genetic diversity and population structure of indigenous chicken breeds in South China

Xunhe HUANG^1,^*(

),Jinfeng ZHANG¹,Danlin HE²,Xiquan ZHANG²,Fusheng ZHONG¹,Weina LI¹,Qingmei ZHENG¹,Jiebo CHEN¹,Bingwang DU³

¹. School of Life Sciences, Jiaying University, Meizhou 514015, China
². College of Animal Sciences, South China Agricultural University, Guangzhou 510642, China
³. College of Agricultural, Guangdong Ocean University, Zhanjiang 524088, China

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Abstract

A total of 587 individuals from 12 indigenous chicken breeds from South China and two commercial breeds were genotyped for 26 microsatellites to investigate the genetic diversity and population structure. All microsatellites were found to be polymorphic. The number of alleles per locus ranged from 5 to 36, with an average of 12.10 ± 7.00 (SE). All breeds, except White Recessive Rock, had high allelic polymorphism (>0.5). Higher genetic diversity was revealed in the indigenous chicken breeds rather than in the commercial breeds. Potential introgression from the commercial breeds into the indigenous chickens was also detected. The population structure of these indigenous chicken breeds could be explained by their geographical distribution, which suggested the presence of independent history of breed formation. Data generated in this study will provide valuable information to the conservation for indigenous chicken breeds in future.

Keywords microsatellites genetic diversity population structure indigenous chicken South China conservation

Corresponding Author(s): Xunhe HUANG

Just Accepted Date: 08 June 2016 Online First Date: 24 June 2016 Issue Date: 05 July 2016

Cite this article:

Xunhe HUANG,Jinfeng ZHANG,Danlin HE, et al. Genetic diversity and population structure of indigenous chicken breeds in South China[J]. Front. Agr. Sci. Eng. , 0, (): 97-101.

URL:

https://academic.hep.com.cn/fase/EN/10.15302/J-FASE-2016102
https://academic.hep.com.cn/fase/EN/Y0/V/I/97

Breed (code)	N	Allelic diversity				Genetic diversity		Proportion of clusters
Breed (code)	N	TNA	MNA±SE	Ar(g)±SE	Ap(g)±SE	H_E±SE	H_O±SE	I/II/III	F_IS
Wenchang (WC)*	34	183	7.04±3.45	5.21±0.37	0.13±0.03	0.70±0.13	0.65±0.15	0.90/0.04/0.06	0.08
Guangxi Yellow (GX)*	32	172	6.62±3.29	4.85±0.40	0.13±0.04	0.65±0.16	0.65±0.21	0.94/0.02/0.04	0.01
Huaixiang (HX)*	78	209	8.04±4.47	5.17±0.41	0.14±0.04	0.67±0.14	0.66±0.16	0.92/0.03/0.05	0.03
Xinghua (XH)*	36	156	6.00±2.79	4.65±0.35	0.06±0.03	0.64±0.16	0.67±0.17	0.85/0.03/0.12	- 0.03
Zhongshan Shalan (SL)*	36	171	6.58±3.26	4.83±0.40	0.11±0.05	0.65±0.14	0.68±0.17	0.96/0.02/0.02	- 0.04
Qingyuan Partridge (QY)*	47	190	7.31±3.25	4.99±0.38	0.11±0.03	0.65±0.15	0.67±0.18	0.94/0.02/0.04	- 0.02
Yangshan (YS)*	36	166	6.38±3.07	4.77±0.35	0.06±0.03	0.65±0.16	0.66±0.20	0.87/0.04/0.09	0.00
Huanglang (HL)*	50	215	8.27±4.53	5.35±0.41	0.24±0.05	0.68±0.14	0.68±0.18	0.89/0.02/0.09	0.02
Huiyang Bearded (HY)*	35	171	6.58±2.73	4.97±0.29	0.15±0.04	0.69±0.09	0.64±0.13	0.05/0.90/0.05	0.08
Wuhua Yellow (WH)	58	191	7.35±3.27	4.95±0.30	0.13±0.03	0.69±0.11	0.65±0.15	0.04/0.92/0.04	0.06
Ningdu Yellow (ND)*	50	181	6.96±3.74	4.94±0.40	0.17±0.06	0.67±0.14	0.61±0.16	0.25/0.02/0.73	0.10
Hetian (HT)*	45	181	6.96±3.90	5.05±0.42	0.16±0.05	0.68±0.14	0.62±0.18	0.04/0.04/0.92	0.10
Lingnan Yellow III (LN)	30	177	6.81±3.74	5.32±0.41	0.14±0.04	0.70±0.13	0.63±0.20	0.59/0.12/0.29	0.11
White Recessive Rock (WR)	20	96	3.69±1.50	3.31±0.24	0.04±0.02	0.48±0.18	0.48±0.20	0.01/0.88/0.11	0.05
Cluster I	349	281	10.81±6.34	8.02±0.84	0.93±0.19	0.68±0.14	0.66±0.15	0.90/0.04/0.06	0.03
Cluster II	93	220	8.46±4.12	7.53±0.66	0.80±0.14	0.71±0.10	0.65±0.13	0.06/0.61/0.33	0.08
Cluster III	95	214	8.23±4.73	7.43±0.80	0.78±0.18	0.69±0.14	0.61±0.15	0.02/0.04/0.94	0.11
Commercial breeds	50	188	7.23±3.81	6.38±0.57	0.97±0.27	0.69±0.11	0.57±0.13	0.32/0.50/0.18	0.17
Indigenous breeds	537	310	11.92±6.77	7.20±0.67	1.80±0.36	0.70±0.13	0.65±0.13	0.60/0.19/0.21	0.07
Overall	587	314	12.10±7.00	–	–	0.71±0.12	0.65±0.13	0.63/0.32/0.05	0.09

Tab.1 Genetic diversity of 12 indigenous chicken breeds from South China and two commercial breeds using 26 microsatellite markers

Fig.1 (a) Substructure of 12 indigenous chicken breeds from South China and commercial breeds as indicated by STRUCTURE analysis. Each individual represented by a single vertical line was assigned to one of three distinct clusters based on clustering result at K = 3. Black bars are separators for breeds;Color codes: green, Cluster I; purple, Cluster II; red, Cluster III ;(b) geographical distribution of 12 indigenous chicken breeds from South China. The shaded area in each pie chart is proportional to the number of individuals in each population observed for each genetic cluster. Color codes: green, Cluster I; purple, Cluster II; red, Cluster III. Breed codes: WC, Wenchang; GX, Guangxi Yellow;HX, Huaixiang;SL, Zhongshan Shalan; XH, Xinghua; QY, Qingyuan Partridge; YS, Yangshan; HL, Huanglang; HY, Huiyang Bearded; WH, Wuhua Yellow; ND, Ningdu Yellow; HT, Hetian; LN, Lingnan Yellow III; WR, White Recessive Rock.

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