Microsatellite marker-based estimation of the genetic diversity of cattle in Chongqing 

DOI: DOI: 10.18805/ijar.B-887    | Article Id: B-887 | Page : 1543-1547
Citation :- Microsatellite marker-based estimation of the genetic diversity of cattle in Chongqing.Indian Journal Of Animal Research.2018.(52):1543-1547
Weiwei Ni, An Jiang, Jian Zhang, Guangxin E and Yongfu Huang h67738337@swu.edu.cn
Address : College of Animal Science and Technology, Chongqing Key Laboratory of Forage and Herbivore, Chongqing Engineering Research Centre for Herbivores Resource Protection and Utilization, Southwest University, Chongqing-400 716, China.
Submitted Date : 17-12-2017
Accepted Date : 5-05-2018

Abstract

Cattle are the main source of meat in Chongqing. This study investigated the genetic diversity of cattle native to Chongqing and 4 introduced breeds. A total of 96 individuals from 5 breeds were genotyped using six microsatellite markers. Five markers were highly polymorphic within the breed populations, and one marker had moderate levels of polymorphism. Heterozygosity ranged from 0.5379±0.0434 in Simmental to 0.6667±0.0559 in Charolais. The heterozygosity deficit was significant in all populations analyzed compared with the expected level of heterozygosity. In addition, two microsatellite markers (TGLA53 and OarFCB20) deviated from Hardy-Weinberg equilibrium across populations (except in cattle native to Chongqing). The mean number of alleles ranged from 6.00±2.37 in Angus to 7.17±2.14 in Droughtmaster across six markers. The coefficient of inbreeding ranged from 0.0017 in Simmental and Droughtmaster to 0.0367 in Angus. Pairwise difference analyses revealed that Simmental and Droughtmaster were the most differentiated (FST= 0.06861) from each other, whereas cattle native to Chongqing and Charolais were the least differentiated (FST= 0.00557). In summary, this study showed that cattle native to Chongqing and 4 introduced breeds were genetically well protected in Chongqing, and information from this study would be helpful for guiding hybridization and genetic improvements in the future.

Keywords

Cattle Genetic diversity Microsatellites.

References

  1. Acosta AC, Uffo O, Sanz A, Ronda R, Osta R, Rodellar C, Martin-Burriel I, Zaragoza P. (2013).Genetic diversity and differentiation of five Cuban cattle breeds using 30 microsatellite loci. J Anim Breed Genet. 130(1) : 79-86. 
  2. Animal Genetic Resources in Chongqing Edit group.(Ed). (2013). Animal genetic resources in Chongqing. CHONGQING AGRICULTURAL    PRESS, Chongqing.84p.
  3. Brasil BS, Coelho EG, Drummond MG, Oliveira DA. (2013). Genetic diversity and differentiation of exotic and American commercial cattle breeds raised in Brazil. Genet Mol Res. 18;(4):5516-26.
  4. Botstein D, White RL, Skolnick M, Davis RW. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hun Genet. 32:314-331.
  5. Dadi H, Tibbo M, Takahashi Y, Nomura K, Hanada H, Amano T. (2008). Microsatellite analysis reveals high genetic diversity but low genetic structure in Ethiopian indigenous cattle populations. Anim Genet. 39(4): 425-31.
  6. Di Lorenzo P, Lancioni H, Ceccobelli S, Colli L, Cardinali I, Karsli T, Capodiferro MR, Sahin E, et al. (2018). Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin. PLoS One. 20:(2):e0192567.
  7. E GX, Zhong T, Ma YH, Gao HJ, He JN, Liu N, Zhao YJ, Zhang JH, Huang YF. (2016). Conservation genetics in Chinese sheep: diversity of fourteen indigenous sheep (Ovis aries) using microsatellite markers. Ecol Evol. 6(3): 810-7.
  8. Edea Z, Bhuiyan MS, Dessie T, Rothschild MF, Dadi H, Kim KS. (2015). Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds. Animal. ;9(2):218-26. 
  9. Earl, Dent A. and vonHoldt, Bridgett M. (2012). STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources . 4 (2): 359-361 doi: 10.1007/s12686-011-    9548-7.
  10. Excoffier, L., H. E. L. (2010). Lischer. Arlequin 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. .10: 564–567.
  11. Falush D, Stephens M, Pritchard JK. Pritchard. (2003). Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics. 164(4):1567-87.
  12. Felsenstein, J. (1993). PHYLIP-phylogenetic inference package, version 3.5c.University of Washington, Seattle.
  13. Goudet, J. (1995). STAT (Version 1.2): A computer program to Calculate F-Statistic. J. Hered. .86: 485–486.
  14. Han Xu, Wang Zhigang, Liu Chousheng, Zhang Guixiang, Song Weitao, Zhang Zifu. (2008). Geneitc Diversity of Microsatellite DNA of Cattle Breeds in Guangdong, Guangxi, Yunnan, Guizhou and Sichuan Reglons. BIOTECHNOLOGY BULLETIN.. (z1), p.251-257.
  15. Jakobsson M. and Rosenberg NA. (2007). CLUMPP: a cluster matching and permutation program for deal with label switching and multimodality in analysis of population structure. Bioinformatics. 23: 1801–6.
  16. Kalinowski ST, Taper ML, Marshall TC. (2007). Revising how the computer program CERVUS accommodates genotyping errorincreases success in paternity assignment. Molecular Ecology. v.16, p.1099–1006.
  17. Li RL, Zhang GX, Wang ZG, Wang H, Han X, Wang DL, Wang JH. (2007). Analysis of the genetic structure of 12 Chinese and foreign cattle breeds using DNA microsatellite markers. Yi Chuan. Dec. 29(12): 1463-70.
  18. Li Xiangyang. (2005). Study on Polymorphisms of Red Steppe Cattle by Microsatellite DNA. Jilin University.
  19. Mateus JC, Eding H, Penedo MC, Rangel-Figueiredo MT. (2004). Contributions of Portuguese cattle breeds to genetic diversity using marker-estimated kinships. Anim Genet. 35(4): 305-13.
  20. Maudet, C., Luikart, G., Taberlet, P. (2002). Genetic diversity and assignment tests among seven French cattle breeds based on microsatellite DNA analysis. J Anim Sci. 80(4): 942-50.
  21. Nishimaki T, Ibi T, Tanabe Y, Miyazaki Y, Kobayashi N, Matsuhashi T, Akiyama T, Yoshida E, Imai K, et al. (2013). The assessment of genetic diversity within and among the eight subpopulations of Japanese Black cattle using 52 microsatellite markers. Anim Sci J. 84(8): 85-91.
  22. Piccoli ML, Braccini Neto J, Brito FV, Campos LT, Bértoli CD, Campos GS, Cobuci JA, McManus CM, Barcellos JO, Gama LT. (2014). Origins and genetic diversity of British cattle breeds in Brazil assessed by pedigree analyses. J Anim Sci. 92(5):1920-30.
  23. Raymond, M., Rousset F. (1995). GENEPOP (Version 1.2): population genetics software for exact tests and ecumenicism. Heredity .86: 248–249.
  24. Rosenberg, N. A. (2004). Distruct: a program for the graphical display of population structure. online library. Molecular Ecology Notes.
  25. Saitou, N. and Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol.Biol. Evol., .4: 406–425.
  26. Shah TM, Patel JS, Bhong CD, Doiphode A, Umrikar UD, Parmar SS, Rank DN, Solanki JV, Joshi CG. (2013). Evaluation of genetic diversity and population structure of West-Central Indian cattle breeds. Anim Genet. 44(4):442-5.
  27. Sharma A, Lee SH, Lim D, Chai HH, Choi BH, Cho Y. (2016). A genome-wide assessment of genetic diversity and population structure of Korean native cattle breeds. BMC Genet. 17(1): 139.
  28. Slatkin, M. (1995). A measure of population subdivision based on microsatellite allele frequencies. Genetics . 139: 457–462.
  29. Suh S, Kim YS, Cho CY, Byun MJ, Choi SB, Ko YG, Lee CW, Jung KS, Bae KH, Kim JH. (2014). Assessment of Genetic Diversity, Relationships and Structure among Korean Native Cattle Breeds Using Microsatellite Markers. Asian-Australas J Anim Sci. 27(11): 1548-53.
  30. Wang Xiaojin, Huo Shendong, Chen Shien, Long Ling, Gao Xudong, Ye Yongli, He Xinrui. (2015). The Analysis of Genetic Diversity of Microsatellite Loci in ‘Zaosheng Cattle’. Chinese Agricultural Science Bulletin.. 31(2): 1-7.
  31. Yang Hongwen, Han Yong, Liu Jing, Xiao Lihua, Su Chaozhi. (2016). Analysis of the Genetic Diversity of 4 Guizhou Cattle Breeds Using DNA Microsatellite Markers. Guizhou Journal Of Animal Husbandry & Veterinary Medicine. 40(5): 5-9.
  32. Yongfa Luo, Zhigang Wang, Jiaqi Li, Guixiang Zhang, Yaosheng Chen, Yong Liang, Fuqing Yu, Weitao Song, Zifu Zhang. (2006). Genetic variation and genetic relationship among 13 Chinese and introduced cattle breeds using microsatellite DNA markers. Biodiversity Science. 14 (6): 498-507.
  33. Zhang Nana. (2010). Study on the genetic polymorphisms of eleven microsatellites and exon of BMP15 in Two Goat Breeds. Henan University of Science and Technology.p2-7.
  34. Zhong T, Han JL, Guo J, Zhao QJ, Fu BL, Pu YB, He XH, Jeon JT, Guan WJ, Ma YH. (2011). Tracing genetic differentiation of Chinese Mongolian sheep using microsatellites. Anim. Genet. 42:563–565.
  35. ZUO Fu-yuan, WANG Ling, LIU Chang-lin. (2010). Correlation between genetic distance and heterosis of cattle. Chinese Journal Of Animal Science. 46(11): 1-4. 

Global Footprints