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Assessment of Demographic Bottleneck in Indian Horse and Endangered Pony Breeds

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Assessment of Demographic Bottleneck in Indian Horse and Endangered Pony Breeds c Indian Academy of Sciences ONLINE RESOURCES Assessment of demographic bottleneck in Indian horse and endangered pony breeds A. K. GUPTA1∗, MAMTA CHAUHAN1, ANURADHA BHARDWAJ1 and R. K. VIJH2 1National Research Centre on Equines, Sirsa Road, Hisar 125 001, India 2National Bureau of Animal Genetic Resource, Karnal 132 001, India [Gupta A. K., Chauhan M., Bhardwaj A. and Vijh R. K. 2015 Assessment of demographic bottleneck in Indian horse and endangered pony breeds. J. Genet. 94, e56–e62. Online only: http://www.ias.ac.in/jgenet/OnlineResources/94/e56.pdf] Introduction place in some of the endangered pony breeds. Therefore it is important to identify bottlenecked populations for con- Bottleneck study of any continuously decreasing popula- servation of breed(s) as conservation of any breed is very tion is important and crucial issue in its conservation strate- important because the loss of animal species or subspecies gies including the analysis of simulated and real populations may represent a social or economic loss to human pop- (Williamson-Natesan 2005;Buschet al. 2007). A bottle- ulation, especially in developing countries. Further, India neck in a population can increase the rate of inbreeding, loss being a signatory to the State of the World Animal Genetic of genetic variation, fixation of deleterious alleles, thereby Resources (SoWAnGR) needs to characterize, document and reducing evolutionary potential of animals to adapt to new conserve these indigenous breeds. DNA-based molecular selective pressures, such as climatic change or shift in avail- genetics methods, which provide a powerful tool for infer- able resources and increasing the probability of population ring the demographic history of a population namely multi- extinction (Frankham 1995). The genetic changes caused locus genotypes from microsatellite were used along with by a bottleneck in a population’s effective size can lower three single-sample methods, namely heterozygosity excess, the possibility of population’s persistence (Vrijenhoek 1994; mode shift and M-ratio tests for assessing the presence of Newman and Pilson 1997). Various endangered or threatened bottlenecks in the Indian breeds. populations have been reported to have low levels of genetic variations (Vrijenhoek 1994; Gibbs et al. 1998). However, all the populations that have been reduced in size did not Material and methods show quantifiable lower levels of genetic diversity (Waldman et al. 1998) which also necessitates the assessment of bot- Breeds and blood samples tlenecks with molecular marker for their conservation and Genetically unrelated, adult, healthy animals (n = 284) evolutionary genetics. of all the six indigenous registered horse (Marwari and India is bestowed with a rich biodiversity of equids in Kathiawari) and pony breeds (Spiti, Zanskari, Manipuri and the form of two horses (Marwari and Kathiawari) and Bhutia) selected in different geographic locations in India four endangered pony breeds (Bhutia, Spiti, Manipuri and were chosen for evaluating bottleneck in these populations. Zanskari) besides indigenous donkeys and wild asses (Gupta Fifty horses/ponies of each breed except Bhutia (34) and et al. 2012a,b; 2014). Overall population of these breeds, Spiti (16) breeds were selected based on their phenotypic specially endangered pony breeds has declined in most of the characteristics. All these animals were selected from dif- pockets in their home tracts (less than 1000) which is due to ferent and somewhat isolated pockets in their home tracts. their decreased utility and increased modernization of trans- Thirty-four Indian Thoroughbred horses were also included port system even in hilly and difficult terrains (Gupta et al. in the study as an out-group. Blood samples (5–8 mL) were 2012a, b). It is expected that bottleneck might have taken collected from jugular vein using EDTA (0.5 mM, pH 8.0) coated tubes. Genomic DNA was isolated from blood using ∗ For correspondence. E-mail: [email protected]. standard procedure of digestion with proteinase K, separation Keywords. bottleneck; Indian equine breeds; mutation-drift equilibrium; mode shift indicator. Journal of Genetics Vol. 94, Online Resources e56 A. K. Gupta et al. with phenol : chloroform : isoamyl alcohol and precipitation the third method to further confirm the problem of bot- with ethanol (Sambrook et al. 1989). tlenecks by applying the m_p_val.exe program (Garza and Williamson 2001). Molecular techniques Results A panel of 48 microsatellite markers that were used previ- ously for assessing genetic diversity among different indige- Data on overall range and mean values for observed num- nous horse breeds were followed (Gupta et al. 2014). The ber of alleles (Na), expected alleles (Ne), heterozygosity, electropherograms drawn through Gene Scan were used to both observed and expected (Ho and He) along with poly- detect DNA fragment sizing details using Gene Mapper soft- morphic information content (PIC) in each breed indicated ware, ver. 3.0 (Applied Biosystems, Foster City, USA). Numbers high genetic diversity among these breeds (table 1)andall of alleles at each locus were recorded for all the microsatel- the microsatellite used were polymorphic in nature. Further, lites which amplified correctly in different multiplexes. some of microsatellites, namely ASB002, UM011, TKY333, HMS004, TKY321, AHT004, TKY337, LEX033, TKY312, COR007, HTG010, AHT016, TKY287 and LEX073 had Statistical analysis allele number more than 10 along with high heterozygosity Software PopGene (Kimura and Crow 1964) was used to cal- in most of the breeds. To characterize bottleneck in different culate allele number, allele frequency, expected and observed equine populations along with Thoroughbred horse, the heterozygosity (data on these parameters can be provided power of three statistical tests: sign, standard and Wilcoxon by author upon request). The bottleneck in the populations tests for mutation–drift equilibrium studies were used along was studied by estimating the heterozygosity excess using with mode-shift indicator test and M-ratio measurements. software BOTTLENECK accessible at http://www.ensam. inra.fr/URLB. Three tests: sign, standardized differences and Mutation–drift equilibrium Wilcoxon sign-rank tests under three models of microsatel- lite evolution: IAM, SMM and TPM were used to compute In IAM model of microsatellite evolution, observed numbers the distribution of gene diversity expected from the observed of loci with heterozygotic excess were significantly higher number of alleles, given sample size under the assumption than expected number of loci in all the breeds (table 2). of mutation–drift equilibrium (Cornuet and Luikart 1996). The probability values revealed that all the seven popula- IAM and SMM represent the extremes of how new alle- tions are not in mutation–drift equilibrium (P<0.05). The les were introduced in the population. TPM has been pro- TPM model revealed that excess heterozygotes to be sig- posed as an intermediate model that provides a more realistic nificant only in sign test of Manipuri, Zanskari and Bhutia picture of how some DNA sequences evolve (Di Rienzo et al. breeds depicting deviation from mutation–drift equilibrium. 1994). A qualitative descriptor of allele frequency distribu- However, probability values under sign test revealed that all tion, mode shift indicator which discriminates bottlenecked populations except Zanskari breed were in mutation–drift populations from stable populations was also used (Luikart equilibrium as these values were not significant (P > 0.05) et al. 1998). M-ratio measurements were also carried out as and hence null hypothesis was accepted in favour of Table 1. Various measure of genetic variability among different individual horse and pony breeds. Breed Parameter Na Ne Ho He PIC Kathiawari Range 3.0–14.0 1.76–6.99 0.12–0.98 0.44–0.87 0.37–0.833 Mean 7.90±0.41 3.88±0.20 0.67±0.03 0.70±0.02 0.662±0.0179 Marwari Range 5.0–20.0 1.54–10.73 0.26–0.94 0.35–0.92 0.34–0.87 Mean 10.06±0.36 5.04±0.23 0.67±0.02 0.76±0.02 0.727±0.0166 Manipuri Range 3.0–14.0 2.04–9.58 0.29–1.00 0.52–0.91 0.41–0.85 Mean 8.42±0.42 4.63±0.22 0.72±0.02 0.76±0.01 0.708±0.0131 Spiti Range 3.0–10.0 1.68–7.42 0.21–1.00 0.42–0.89 0.37–0.85 Mean 5.52±0.42 3.46±0.31 0.67±0.06 0.67±0.03 0.626±0.0189 Thoroughbred Range 3.0–12.0 1.14–7.32 0.21–1.00 0.30–0.88 0.27–0.84 Mean 6.27±0.35 3.62±0.25 0.66±0.04 0.68±0.02 0.632±0.0212 Zanskari Range 3.0–15.0 2.14–9.22 0.32–0.98 0.54–0.90 0.43–0.85 Mean 8.52±0.35 4.68±0.20 0.68±0.02 0.76±0.01 0.772±0.0136 Bhutia Range 3.0–16.0 2.11–10.47 0.29–1.00 0.54–0.92 0.51–0.85 Mean 8.70±0.46 4.89±0.31 0.71±0.04 0.77±0.02 0.704±0.0134 Na, observed number of alleles; Ne, expected number of alleles; Ho, observed heterozygosity; He, expected heterozygosity; PIC, polymorphic information content. Journal of Genetics Vol. 94, Online Resources e57 Table 2. Test for null hypothesis in six Indian horse and pony breeds along with English Thoroughbred horses. IAM TPM SMM Breed/model Test/model OHE EHE OHE EHE OHE EHE Bottlenecks assessment in Indian horse and pony breeds Manipuri Sign test: number of loci with heterozygosity excess (probability) 44 28.47 (0.00000)∗∗∗ 34 28.52 (0.06977) NS 22 28.38 (0.4320)NS Standard difference test: Ti values (probability) 5.786 (0.00000)*** 1.994 (0.02305)* −5.377 (0.00000)*** Journal of Genetics Wilcoxon rank test: (probability of heterozygosity excess) 0.00000*** 0.00450* 0.06376NS Zanskari Sign test: number of loci with heterozygosity excess 46 28.46 (0.00000)* 40 28.50 (0.00033)* 16 28.21 (0.00033)* Standard difference test: Ti values (probability) 6.178 (0.00000)* 2.745 (0.00302)* −4.167 (0.00002)* Wilcoxon rank test: (probability of heterozygosity excess) 0.00000*** 0.00006*** 0.00073*** Spiti Sign test: number of loci with heterozygosity excess (probability) 39 28.02 (0.00067)*** 32 28.46 (0.18644)NS 22 28.70 (0.03506)* Standard difference test: Ti values (probability) 4.032 (0.00003)*** 1.401 (0.08063)NS −2.242 (0.01248)* NS Vol.
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