“酉芯一号”在地方鸡遗传多样性和结构分析中的应用效力研究

doi:10.16288/j.yczz.24-068

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Hereditas(Beijing) ›› 2024, Vol. 46 ›› Issue (8): 640-648.doi: 10.16288/j.yczz.24-068

• Research Article • Previous Articles Next Articles

Application effectiveness of “Youxin-1” in genetic diversity and structure analysis of local chickens

Mengyu Wang¹^,²(), Chenghao Zhou²(), Qian Xue²^,³, Jianmei Yin², Yixiu Jiang², Huiyong Zhang², Guohui Li², Wei Han¹^,²()

1. Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou 225125, China
2. Poultry Institute of Jiangsu Province, Yangzhou 225125, China
3. Science and Technology Innovation Co., Ltd., Poultry Institute of JiangsuProvince, Yangzhou 225125, China

Received:2024-03-14 Revised:2024-06-12 Online:2024-08-20 Published:2024-06-24
Contact: Wei Han E-mail:2664935435@qq.com;604242123@qq.com;hanwei830@163.com
Supported by:
National Key Research and Development Program of China(2021YFD1200302);Seed Industry Revitalization Project of Jiangsu Province(JBGS[2021]029);Natural Science Foundation Project of Jiangsu Province(BK20221285)

Abstract

Abstract:

China’s local chicken breeds are rich in resources, and have formed different germplasm characteristics in the process of long-term selection and evolution. Scientific assessment of population genetic diversity and identification of inter-breed genetic structure are of great value to the protection and innovative utilization of local chicken breed resource. In order to evaluate the application effectiveness of 23K SNP chip “Youxin-1” in the analysis of genetic diversity and genetic structure of local chickens, we used RADseq to identify genomic genetic variation of 21 local chicken breeds and developed 23K chip “Youxin-1”. The genetic statistics of each variety were calculated based on two sets of SNP data, and correlation, fitting and phylogenetic analysis were carried out to evaluate the application effectiveness of the chip. The results showed that the observed heterozygosity (Ho), polymorphism information content (PIC), inbred coefficient (F_ROH) and genetic differentiation coefficient (Fst) calculated based on the two SNP data sets were basically consistent in the 21 local chicken breeds. The genetic diversity of Langya chicken (LA), Piao chicken (PJ) and Wenchang chicken (WC) was relatively rich. The genetic diversity of Bian chickens (BJ), Langshan chickens (LS), Gushi chickens (GS), Dongxiang blue-eggshell chickens (DX) and Beijing fatty chickens (BY) was relatively poor, and the correlation coefficients of Ho, PIC, F_ROH and average Fst in the two groups were 0.794, 0.901, 0.926 and 0.984, respectively, all reaching extremely significant levels (P<0.01) with a high degree of fit (P<0.001) and R²were 0.644, 0.827, 0.916 and 0.927. For the two sets of SNP data, the evolutionary tree constructed by neighbor-joining (NJ) method and maximum likelihood (ML) method was reasonable, and the 21 local chicken breeds were generally divided into six categories, which was consistent with the formation history and geographical distribution of the varieties. The 23K chip also realized reasonable clustering of the five new varieties without individual deviation. There are some differences in the estimation of genetic statistics using SNP with different densities, and data standardization is needed. 23K chip has good efficacy in the analysis of genetic diversity and structure of local chickens.

Key words: RADseq, SNP chip, genetic diversity, genetic structure

Mengyu Wang, Chenghao Zhou, Qian Xue, Jianmei Yin, Yixiu Jiang, Huiyong Zhang, Guohui Li, Wei Han. Application effectiveness of “Youxin-1” in genetic diversity and structure analysis of local chickens[J]. Hereditas(Beijing), 2024, 46(8): 640-648.

Figures/Tables 6

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品种	观察杂合度(Ho)	多态信息含量(PIC)	近交系数 (F_ROH)	平均遗传分化系数 (Fst)
白耳黄鸡(BE)	0.2049	0.2712	0.1562	0.1632
边鸡(BJ)	0.1833	0.2717	0.1697	0.1443
北京油鸡(BY)	0.1887	0.2586	0.2328	0.1781
茶花鸡(CH)	0.2104	0.2844	0.1547	0.1592
大骨鸡(DG)	0.2121	0.2953	0.1373	0.1362
东乡绿壳蛋鸡(DX)	0.1876	0.262	0.1806	0.1614
固始鸡(GS)	0.1901	0.2558	0.2277	0.1715
天津猴鸡(HOU)	0.2214	0.2822	0.2077	0.1785
惠阳胡须鸡(HX)	0.2179	0.3016	0.0972	0.1235
金湖乌凤鸡(JH)	0.2039	0.284	0.169	0.1423
琅琊鸡(LA)	0.2535	0.3182	0.0536	0.1028
狼山鸡(LS)	0.205	0.2691	0.1989	0.1795
鹿苑鸡(LY)	0.2447	0.3202	0.048	0.1026
瓢鸡(PJ)	0.2359	0.3149	0.0181	0.1079
文昌鸡(WC)	0.224	0.2981	0.0732	0.1277
安义瓦灰鸡(WH)	0.2172	0.2879	0.1369	0.1408
汶上芦花鸡(WS)	0.2163	0.2853	0.1703	0.1515
大围山微型鸡(WX)	0.2154	0.2886	0.1264	0.1455
仙居鸡(XJ)	0.2047	0.2816	0.1445	0.1503
萧山鸡(XS)	0.2146	0.2842	0.1657	0.1544
藏鸡(ZZ)	0.2127	0.2979	0.145	0.1396

品种	观察杂合度(Ho)	多态信息含量(PIC)	近交系数 (F_ROH)	平均遗传分化系数 (Fst)
白耳黄鸡(BE)	0.1955	0.2714	0.1543	0.1902
边鸡(BJ)	0.1856	0.2813	0.1787	0.1598
北京油鸡(BY)	0.1735	0.2482	0.1911	0.2001
茶花鸡(CH)	0.2066	0.2867	0.1444	0.1927
大骨鸡(DG)	0.2205	0.2963	0.1364	0.1557
东乡绿壳蛋鸡(DX)	0.1411	0.2413	0.2147	0.1811
固始鸡(GS)	0.1824	0.2577	0.1899	0.1862
天津猴鸡(HOU)	0.1966	0.2644	0.2105	0.2010
惠阳胡须鸡(HX)	0.2096	0.3085	0.1201	0.1438
金湖乌凤鸡(JH)	0.2008	0.3016	0.1724	0.1718
琅琊鸡(LA)	0.2472	0.3156	0.0736	0.1273
狼山鸡(LS)	0.1867	0.2556	0.1609	0.2039
鹿苑鸡(LY)	0.213	0.3102	0.0568	0.1229
瓢鸡(PJ)	0.2242	0.3139	0.0780	0.1282
文昌鸡(WC)	0.2493	0.3174	0.0940	0.1453
安义瓦灰鸡(WH)	0.2135	0.2888	0.1331	0.1615
汶上芦花鸡(WS)	0.2165	0.2862	0.1657	0.1729
大围山微型鸡(WX)	0.2145	0.2912	0.1177	0.1693
仙居鸡(XJ)	0.1834	0.2755	0.1350	0.1735
萧山鸡(XS)	0.2096	0.283	0.1470	0.1779
藏鸡(ZZ)	0.1983	0.2961	0.1413	0.1659

统计量	皮尔逊相关系数	拟合曲线	拟合度R²
杂合度(Ho)	0.794**	y=0.12×15.71^x	0.644***
近交系数(F_ROH)	0.926**	y=0.17-4.69x+50.97x²-132.84x³	0.916***
多态信息含量(PIC)	0.901**	y=0.43-1.79x+4.48x²	0.827***
平均遗传分化系数(Fst)	0.984**	$y={{e}^{-0.88-\frac{0.17}{x}}}$	0.972***

Application effectiveness of “Youxin-1” in genetic diversity and structure analysis of local chickens

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