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

Abstract

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.

CLC Number:

S831.2

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.

0
/ / Recommend

Add to citation manager EndNote|Reference Manager|ProCite|BibTeX|RefWorks

URL: https://www.xmsyxb.com/EN/10.11843/j.issn.0366-6964.2017.05.005

https://www.xmsyxb.com/EN/Y2017/V48/I5/818

References

[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.

Conservation Status Evaluation of Two Luyuan Chicken Populations Based on RAD-seq Simplified Genome Sequencing Technology

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	TANG Xinxin, ZHENG Jumei, LUO Na, YING Fan, ZHU Dan, LI Sen, LIU Dawei, AN Bingxing, WEN Jie, ZHAO Guiping, LI Hegang. Genetic Mechanism of Broiler Leg Disease Based on Genome-Wide Association Analysis [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 99-109.
[2]	XU Xiaojing, DONG Ruiling, WEI Limin, ZHAO Shaomeng, ZHAO Guiping, ZHANG Minhong, FENG Jinghai. Study on Growth Model of Wenchang Chickens [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 4952-4961.
[3]	QI Lina, LU Xuelin, YANG Kaixuan, ZHOU Jin, LI Xianyu, LIU Ke, ZHANG Wengang, GU Xin, ZHANG Weijian. Analysis of Genetic Diversity and Genetic Structure of New Pudong Chicken Based on SNP Chips [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 4962-4971.
[4]	WANG Yanxing, ZHANG Yushi, JI Haigang, LIU Yang, NIU Yufang, HAN Ruili, LIU Xiaojun, TIAN Yadong, KANG Xiangtao, LI Zhuanjian. Establishment and Analysis of the Chicken Skeletal Satellite Cell Line [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 4972-4981.
[5]	FAN Chenyu, SHAN Yanju, ZHANG Ming, JI Gaige, JU Xiaojun, TU Yunjie, HE Xi, SHU Jingting, LIU Yifan, ZHANG Haihan. Genome-wide Association Study of Body Weight and Meat Quality Traits in Lihua Mahuang Chickens [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(12): 4982-4992.
[6]	CHEN Cheng, QIAO Xibo, SUN Yi, KANG Li, JIANG Yunliang. Study on the Polymorphism and Genetic Effect of the -868 Locus of FSHR Gene on Egg Laying Traits in Langya Chickens [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4560-4568.
[7]	JIN Sihua, JIA Fumin, HE Peili, JIA Yuqing, SHUI Fei, LIU Xuling, LIU Xing, WANG Xin, XU Man, GENG Zhaoyu. Effect of IHH Gene Overexpression on Proliferation and Differentiation of Chicken Primary Chondrocytes [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4569-4576.
[8]	CHEN Xuejiao, LIU Huijie, ZANG Lei, FENG Jing, PENG Da, ZHANG Hao. Transcriptome Data from Chicken Embryo Heart Tissue Identified Key Genes for Altitude Hypoxia Adaptation in Xueyu White Chickens [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4154-4163.
[9]	ZHANG Yinliang, YUE Qiaoxian, HUANG Chenxuan, CHEN Hui, WANG Dehe, ZHOU Rongyan. Construction of Tibia Transcript Profile of Laying Hens at the Early and Late Laying Stages and Analysis of Genes Related to Bone Metabolism [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4164-4173.
[10]	ZHENG Gang, LIAN Ling. Research Progress of Key Regulatory Gene DMRT1 in Chicken Sex Determination and Differentiation [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(8): 3152-3163.
[11]	BAI Lu, WANG Mengjie, MA Xiaochun, HE Zhengxiao, TAN Xiaodong, LIU Jie, ZHAO Guiping, WEN Jie, LIU Ranran. A Method for Quickly Mining the Characteristic SNP Markers Set of Chicken [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(8): 3252-3261.
[12]	CHEN Chun, KANG Zhaofeng, WEI Yue, LI Guanhong, WU Yanping, XIE Jinfang. Correlation of Wnt3a Gene Polymorphism with Skin Follicle Traits in Chongren Partridge Chicken [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2810-2823.
[13]	LIU Hang, WANG Huanhuan, GE Ying, ZHANG Lei, ZHANG Weiwu, WEI Yinghui, LI Qinghai, FAN Jinghui, ZHANG Xuedong. Screening of Candidate Genes of Skin Color of Black-Bone Chicken Based on Transcriptome and Proteome [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2320-2329.
[14]	WANG Hui, XU Mengyuan, LIU Lingkang, ZHENG Xibang, LI Gonghe, WU Wende. PhiC31 Integrase Triggers Site-specific Cassette Exchange in Chicken Fibroblast Cells through Electroporation [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2330-2342.
[15]	WANG Zheng, GUO Wenjie, CHENG Jin, YUAN Yitong, LUO Rong, XUE Yi, ZHANG Lihuan, ZHU Zhiwei, LI Huifeng. Association Study of Polymorphism in the Regulatory Region of Nutrient Transport-related Genes and Feed Conversion Ratio in Yellow-feather Broiler [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2343-2352.