Assessment of genetic diversity and phylogenetic relationship of Limousin herds in Hungary using microsatellite markers
2
조회
0
다운로드
1
인용
0
참고문헌
키워드
초록
Objective: This study was conducted to investigate basic information on genetic structure and characteristics of Limousin population in Hungary. Obtained results will be taken into consideration when adopting the new breeding strategy by the Association of Hungarian Limousin and Blonde d'Aquitaine Breeders (AHLBB). Methods: Genetic diversity and phylogenetic relationship of 3,443 Limousin cattle from 16 different herds were investigated by performing genotyping using 18 microsatellite markers. Amplified DNA was genotyped using an automated genetic analyzer. Results: Mean of effective alleles (ne) of the populations was 3.77. Population C had the lowest number of effective alleles (3.01) and the lowest inbreeding coefficient (FIS) value (–0.15). Principal component analysis of estimated genetic distance (FST) values (p<0.000) revealed two herds (C and E) distinct from the majority of other Limousin herds. The pairwise FST values of population C compared to the others (0.066 to 0.120) fell into the range of moderate genetic distance: 0.050 to 0.150, while population E displayed also moderate genetic distance (FST values in range 0.052 to 0.064) but only to six populations (G, H, J, L, N, and P). FST(C-E) was 0.148, all other pairs -excluding C and E herds- displayed low genetic distance (FST<0.049). Population D, F, I, J, K, L, N, O, and P carried private alleles, which alleles belonged to 1.1% of the individuals. Most probable number of clusters (K) were 2 and 7 determined by Structure and BAPS software. Conclusion: This study showed useful genetic diversity and phylogenetic relationship data that can be utilized for the development of a new breeding strategy by AHLBB. The results presented could also contribute to the proper selection of animals for further whole genome scan studies of Limousins.
Abstract
Objective: This study was conducted to investigate basic information on genetic structure and characteristics of Limousin population in Hungary. Obtained results will be taken into consideration when adopting the new breeding strategy by the Association of Hungarian Limousin and Blonde d'Aquitaine Breeders (AHLBB). Methods: Genetic diversity and phylogenetic relationship of 3,443 Limousin cattle from 16 different herds were investigated by performing genotyping using 18 microsatellite markers. Amplified DNA was genotyped using an automated genetic analyzer. Results: Mean of effective alleles (ne) of the populations was 3.77. Population C had the lowest number of effective alleles (3.01) and the lowest inbreeding coefficient (FIS) value (–0.15). Principal component analysis of estimated genetic distance (FST) values (p<0.000) revealed two herds (C and E) distinct from the majority of other Limousin herds. The pairwise FST values of population C compared to the others (0.066 to 0.120) fell into the range of moderate genetic distance: 0.050 to 0.150, while population E displayed also moderate genetic distance (FST values in range 0.052 to 0.064) but only to six populations (G, H, J, L, N, and P). FST(C-E) was 0.148, all other pairs -excluding C and E herds- displayed low genetic distance (FST<0.049). Population D, F, I, J, K, L, N, O, and P carried private alleles, which alleles belonged to 1.1% of the individuals. Most probable number of clusters (K) were 2 and 7 determined by Structure and BAPS software. Conclusion: This study showed useful genetic diversity and phylogenetic relationship data that can be utilized for the development of a new breeding strategy by AHLBB. The results presented could also contribute to the proper selection of animals for further whole genome scan studies of Limousins.
참고문헌 (25)
- (2016)[URL]
- (2004)[URL]
- (2018)[URL]
- (2018)[URL]
- Bhargava A, "Mutational dynamics of microsatellites", Mol Biotechnol, 44, pp.250~266 (2010)
- Guichoux E, "Current trends in microsatellite genotyping", Mol Ecol Resour, 11, pp.591~611 (2011)
- Mao Y, "Genetic structure and differentiation of three chinese indigenous cattle populations", Biochem Genet, 45, pp.195~209 (2007)
- Mahgoub O, "Disclosing the origin and diversity of Omani cattle", Anim Genet, 44, pp.336~339 (2013)
- 서주희, "Assessment of genetic diversity and phylogenetic relationships of Korean native chicken breeds using microsatellite markers", Animal Bioscience, 30(10), pp.1365~1371 (2017), 아세아·태평양축산학회[DOI]
- Zsolnai A, "Comparison of different Hungarian grey herds as based on microsatellite analysis", Anim Sci Pap Rep, 32, pp.121~130 (2014)
- Amigues Y, "Genetic characterization of the Blonde d’Aquitaine cattle breed using microsatellite markers and relationship with three other French cattle populations", J Anim Breed Genet, 128, pp.201~208 (2011)
- Radko A, "Analysis of microsatellite DNA polymorphism in Limousin cattle", Ann Anim Sci, 8, pp.225~232 (2008)
- (2003)[URL]
- Rousset F, "Genepop’007: a complete reimplementation of the Genepop software for Windows and Linux", Mol Ecol Resour, 8, pp.103~106 (2008)
- Goudet J, "FSTAT (Version 1.2): A computer program to calculate F-statistics", J Hered, 86, pp.485~486 (1995)
- Excoffier L, "Arlequin ver. 3.0: An integrated software package for population genetics data analysis", Evol Bioinform Online, 1, pp.47~50 (2005)
- Van Oosterhout C, "Microchecker : software for identifying and correcting genotyping errors in microsatellite data", Mol Ecol Notes, 4, pp.535~538 (2004)
- Peakall R, "Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research", Mol Ecol Notes, 6, pp.288~295 (2006)
- Evanno G, "Detecting the number of clusters of individuals using the software structure : a simulation study", Mol Ecol, 14, pp.2611~2620 (2005)
- Corander J, "Bayesian analysis of genetic differentiation between populations", Genetics, 163, pp.367~374 (2003)
- Takezaki N, "Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface", Mol Biol Evol, 27, pp.747~752 (2010)
- Piry S, "GeneClass2 : A software for genetic assignment and first-generation migrant detection", J Hered, 95, pp.536~539 (2004)
- Rannala B, "Detecting immigration by using multilocus genotypes", Proc Natl Acad Sci USA, 94, pp.9197~9221 (1997)
- Paetkau D, "Direct, real-time estimation of migration rate using assignment methods : a simulation-based exploration of accuracy and power", Mol Ecol, 13, pp.55~65 (2004)
- Hartl DL, "Principles of population genetics", pp.118~119 (1997), Sinauer Associates, Inc