基于RAD-seq简化基因组测序评价鹿苑鸡不同保种群保种现状

doi:10.11843/j.issn.0366-6964.2017.05.005

摘要/Abstract

摘要：

本研究旨在评价基因库与保种场两个鹿苑鸡保种群的保种现状。利用RAD-seq简化基因组测序鉴定基因库与保种场两个鹿苑鸡群体的SNP标记，通过计算遗传统计量，比较分析两个群体的遗传差异。结果，经过两步数据质控，在基因库与保种场两个鹿苑鸡群体中分别鉴定出SNPs标记395 021个和428 314个，两个群体的平均杂合度Ho分别为0.211 1和0.206 8，群体间的遗传分化系数Fst为0.005 6；在Structure模型聚类分析中两个群体始终聚为一类，没有个体分离出来，表明两个鹿苑鸡群体未发生显著遗传分化（P>0.05）。两个群体的近交系数Fis分别为0.178 8和0.193 5，相对较高的近交水平可能是由于起始基础群规模较小（抢救性保护）所导致的。进一步的选择信号分析发现，两个鹿苑鸡群体在1、2、5、Z等染色体区域（位点）上存在一定分化，通过Fst和θπ检验鉴定出58个受选择区域，筛选到96个受选择候选基因。GO和KEGG分析表明，这些差异基因主要富集在能量代谢、信号传递、应激免疫反应等调控通路。利用全基因组SNP标记信息可以更全面地评价保种现状，研究结果为进一步优化鹿苑鸡保种技术方案提供了依据。

Abstract:

This study aimed to evaluate the conservation status of Luyuan chicken breeds which were saved in the national chicken genetic resources and Zhangjiagang Luyuan chicken conservation farm, respectively. The genetic differences of Luyuan chicken populations between national chicken genetic resources and Zhangjiagang Luyuan chicken conservation farm were analyzed by identifying SNP markers and calculating genetic statistics based on RAD-seq simplified genome sequencing technology. The results showed that 395 021 and 428 314 SNP markers were identified in two populations after two steps of data quality control. The average heterozygosity of two Luyuan chicken populations were 0.211 1 and 0.206 8, respectively. The genetic differentiation coefficient of two Luyuan chicken populations was 0.005 6. Results of cluster analysis based on Structure model showed that two Luyuan chicken populations were always clustered together and no individual was separated. These results indicated that the difference between the two populations was not significant(P>0.05). Moreover, the inbreeding coefficient of the two populations were 0.178 8 and 0.193 5, respectively. The relative high inbreeding level could be caused by the smaller scale of the initial population (rescuing conservation). The selection signal analysis found that there were some differentiation between two Luyuan chicken populations on 1, 2, 5, Z chromosomes (locus). 58 selected areas and 96 candidated genes were identified through the Fst and θπ testing. GO and KEGG analysis showed that these candidate genes were mainly enriched in some biological pathways such as energy metabolism, signal transduction, stress and immunity response pathways, and so on. In conclusion, the method of genome-wide SNP marker can more comprehensively evaluate the conservation status. The results provide the basis for further optimizing the conservation solution of Luyuan chickens.

中图分类号:

S831.2

王洪志, 李国辉, 张贤, 张一平, 张会永, 殷建玫, 苏一军, 王克华, 韩威, 邹剑敏. 基于RAD-seq简化基因组测序评价鹿苑鸡不同保种群保种现状[J]. 畜牧兽医学报, 2017, 48(5): 818-825.

WANG Hong-zhi, LI Guo-hui, ZHANG Xian, ZHANG Yi-ping, ZHANG Hui-yong, YIN Jian-mei, SU Yi-jun, WANG Ke-hua, HAN Wei, ZOU Jian-min. Conservation Status Evaluation of Two Luyuan Chicken Populations Based on RAD-seq Simplified Genome Sequencing Technology[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2017, 48(5): 818-825.

参考文献

[1] 陈国宏, 王克华, 王金玉, 等. 中国禽类遗传资源[M]. 上海: 上海科学技术出版社, 2004.
CHEN G H, WANG K H, WANG J Y, et al. Poultry genetic resources in China[M]. Shanghai: Shanghai Science and Technology Press, 2004. (in Chinese)
[2] 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.
[3] 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.
[4] 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.
[5] CHUTIMANITSAKUN Y, NIPPER R W, CUESTA-MARCOS A, et al. Construction and application for QTL analysis of a restriction site associated DNA (RAD) linkage map in barley[J]. BMC Genomics, 2011, 12: 4.
[6] PFENDER W F, SAHA M C, JOHNSON E A, et al. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne[J]. Theor Appl Genet, 2011, 122(8): 1467-1480.
[7] BAXTER S W, DAVEY J W, JOHNSTON J S, et al. Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism[J]. PLoS One, 2011, 6(4): e19315.
[8] 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.
[9] LI H, HANDSAKER B, WYSOKER A, et al. The Sequence alignment/map (SAM) format and SAM tools[J]. Transplant Proc, 1987, 19(1): 1653-1654.
[10] YEH F C, YANG R C, BOYLE J, et al. POPGENE, the user-friendly shareware for population genetic analysis[R]. Alberta, Canada: Molecular Biology and Biotechnology Centre, University of Alberta, 1999: 10.
[11] 李慧芳, 高玉时, 苏一军, 等. 中国地方鸡种资源不同保种方法的分子检测[J]. 云南农业大学学报, 2006, 21(2): 228-230, 245.
LI H F, GAO Y S, SU Y J, et al. Molecular evaluation of different conservation measures of Chinese indigenous chicken breeds[J]. Journal of Yunnan Agricultural University, 2006, 21(2): 228-230, 245. (in Chinese)
[12] 赵振华, 黎寿丰, 吴兆林, 等. 不同保种方法对地方鸡种的保种效果分析[J]. 中国家禽, 2009, 31(14): 23-25.
ZHAO Z H, LI S F, WU Z L, et al. Effect of different conservation measures in domestic chicken[J]. China Poultry, 2009, 31(14): 23-25. (in Chinese)
[13] 曲鲁江, 吴桂琴, 李显耀, 等. 采用微卫星DNA标记分析部分地方鸡种保种场的保种效果[J]. 遗传学报, 2004, 31(6): 591-595.
QU L J, WU G Q, LI X Y, et al. Conservation efficiency of local chicken breeds in different farms as revealed by microsatellite markers[J]. Acta Genetica Sinica, 2004, 31(6): 591-595. (in Chinese)
[14] 段修军, 王丽华, 龚道清, 等. 利用微卫星标记检测金定鸭小群保种效果[J]. 畜牧兽医学报, 2008, 39(9): 1159-1164.
DUAN X J, WANG L H, GONG D Q, et al. Analysis on conserved effect of small population in Jinding duck using microsatellite markers[J]. Acta Veterinaria et Zootechnica Sinica, 2008, 39(9): 1159-1164. (in Chinese)
[15] SIMÓN-SÁNCHEZ J, SCHULTE C, BRAS J M, et al. Genome-wide association study reveals genetic risk underlying Parkinson's disease[J]. Nat Genet, 2009, 41(12): 1308-1312.
[16] RIOUX J D, XAVIER R J, TAYLOR K D, et al. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis[J]. Nat Genet, 2007, 39(5): 596-604.
[17] VAN HEEL D A, FRANKE L, HUNT K A, et al. A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21[J]. Nat Genet, 2007, 39(7): 827-829.
[18] HILL-BURNS E M, CLARK A G. Functional regulatory divergence of the innate immune system in interspecific Drosophila hybrids[J]. Mol Biol Evol, 2010, 27(11): 2596-2605.
[19] HUANG J, ZHANG J H, LI W Z, et al. Genome-wide association analysis of ten chilling tolerance indices at the germination and seedling stages in maize[J]. J Integr Plant Biol, 2013, 55(8): 735-744.
[20] DAVEY J W, BLAXTER M L. RADSeq: next-generation population genetics[J]. Brief Funct Genomics, 2010, 9(5-6): 416-423.
[21] 汪文强, 赵生国, 马利青, 等. 动物基因组学重测序的应用研究进展[J]. 畜牧兽医学报, 2016, 47(10): 1947-1953.
WANG W Q, ZHAO S G, MA L Q, et al. The research progress and application of resequencing based on animal genomics[J]. Acta Veterinaria et Zootechnica Sinica, 2016, 47(10): 1947-1953. (in Chinese)
[22] 王德前. 运用微卫星标记分析地方鸡亲缘关系[D]. 扬州: 扬州大学, 2003.
WANG D Q. The genetic relationship analysis among Chinese native chicken breeds by means of microsatellite[D]. Yangzhou: Yangzhou University, 2003. (in Chinese)
[23] 沈见成, 陈宽维, 王金玉, 等. 利用微卫星标记分析江苏三个地方鸡品种的遗传多样性[J]. 中国家禽, 2004, 26(6): 14-16.
SHEN J C, CHEN K W, WANG J Y, et al. Analysis of genetic diversity of three Jiangsu native chickens with microsatellite markers[J]. China Poultry, 2004, 26(6): 14-16. (in Chinese)
[24] 吴兆林, 高玉时, 童海兵. 鹿苑鸡微卫星和AFLP指纹分析[J]. 中国家禽, 2005, 9(1): 83-85. (in Chinese)
WU Z L, GAO Y S, TONG H B. Analysis of genetic variation of Luyuan chicken using microsatellite and AFLP fingerprintings[J]. China Poultry, 2005, 9(1): 83-85. (in Chinese)
[25] WRIGHT S. Evolution and the genetics of populations, Volume 4: variability within and among natural population[M]. Chicago: University of Chicago Press, 1978: 439-459.