Mamta Chauhan

Genetic diversity and bottleneck studies in the Marwari horse breed

Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (± s.e.) allelic diversity was 5.9 (± 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (±s.e.) effective number of alleles (3.3 ± 1.27), observed heterozygosity (0.5306 ± 0.22), expected Levene’s heterozygosity (0.6612 ± 0.15), expected Nei’s heterozygosity (0.6535 ± 0.14), and polymorphism information content (0.6120 ± 0.03). Low values of Wright’s fixation index, FIS (0.2433 ± 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal ‘L’ shaped distribution of mode-shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significantM ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers.

Genetic characterization of Indian Spiti horses

India has a rich biodiversity of equines in the form of six distinct indigenous horse (Equus caballus) breeds, namely Kathiawari, Marwari, Spiti, Zanskari, Bhutia and Manipuri, in addition to indigenous donkeys and wild asses (Yadav et al. 2001). These horse breeds are well adapted to different agroclimatic regions and possess certain unique characteristics. Spiti horses are slow moving, sure-footed, and are found mainly in the hilly areas of the Himalayan range, mostly in the districts of Lahaul-Spiti and Kinnaur in the state of Himachal Pradesh, India. Spiti horses not only thrive under such harsh conditions but are also used as pack animals. Unfortunately, the population numbers of this breed are decreasing at an alarming rate and it is thought to be close to extinction. Consequently, there is an urgent need to characterize this valuable breed to set priorities for its conservation. Molecular characterization is an essential prerequisite to developing an effective and meaningful conservation programme for Spiti horses. Several DNA-based technologies have been developed in the last decade to type polymorphic loci, including random amplified polymorphic DNA (RAPD), restriction fragment length polymorphism (RFLP), variable number of tandem repeats (VNTRs), single-strand conformational polymorphism (SSCP), and methods that make use of polymorphisms of short tandem repeats called microsatellites. Among the array of molecular markers, microsatellites are considered especially suitable for biodiversity evaluation, owing to their codominant inheritance, high heterozygosity, ease and reliability of scoring, ubiquitous presence throughout the genome, and high degree of polymorphism (Takezaki and Nei 1996). The aim of the present work was to assess genetic variation in the Spiti breed of Indian horses, using 25 microsatellite markers that had been observed in earlier studies to be polymorphic in exotic breeds of horses (Ellegren et al. 1992; van Haeringen et al. 1994, 1998; Ewen and Matthews 1995; Eggleston-Stott et al. 1996, 1997; Meyer et al. 1997; Swinburne et al. 1997, 2000; Coogle and Bailey 1998; Lindgren et al. 1999; Kakoi et al. 1999).

Microsatellite markers based genetic diversity and bottleneck studies in Zanskari pony

Genetic diversity in Zanskari pony breed was evaluated at 48 microsatellite loci using fifty adult, healthy and unrelated animals. Allele frequency data was used to detect genetic diversity and bottleneck. The estimated average number of alleles (±s.e.) was 8.5208±2.5010 with a total of 409 alleles. A high level of genetic diversity within this breed was observed in terms of number of alleles, observed heterozygosity (0.6763±0.1704), expected Levens heterozygosity (0.7724±0.795), expected Neis heterozygosity (0.7644±0.0787) and polymorphism information content (>0.5). In-breeding coefficient (F(is)) was 0.115±0.0209, suggesting moderately high in-breeding in Zanskari breed. Although analysis of bottleneck revealed no bottleneck in recent past but population of Zanskari ponies has decreased drastically and only a few thousand pure-bred animals are left. The information is useful for proposing effective population management strategies for future.

Genetic Diversity and Structure Analysis of Donkey Population Clusters in Different Indian Agro-climatic Regions

This study conducted with a panel of 24 polymorphic microsatellites revealed high number of alleles and heterozygosity in all the Indian donkey clusters available in different agro-climatic regions. All the markers are highly polymorphic as reflected from high allele number and heterozygosity, thus suitable for genotyping studies. Genetic diversity within each donkey population as well as between populations of different regions was also quite high indicating no extinction threat to population. The genetic differentiation suggested that 89.59% genetic variation corresponds to difference among individuals and 10.41% is attributed to differences among population clusters. However conservation and preservations of donkeys is important as their overall population is decreasing rapidly in country. Even the 24 microsatellites utilized for individual assignment did not reveal 100% assignment of donkeys to their clustered population. Breed relationship analysis revealed closeness among Leh and Bihar donkeys which seems to be unique as geographically these populations are at distant places and mixing of these donkeys cluster is not feasible. Closeness of donkey population from Haryana, Rajasthan, Gujarat and Baramati regions may be due to sharing of common breeding tract and movement of donkeys in these agro-climatic regions with their owners during harsh and odd environmental conditions for their survival. Population structure analysis revealed that donkey population from seven regions can be divided in two main clusters: first cluster having donkey population from Bihar and leh while second cluster included donkeys from Gujarat, Rajasthan, Spiti. Population from Baramati and Haryana had more than 50% individual population as admixed while Spiti donkeys had no admixed individuals. The current study aimed to provide insight into the genetic relationships and diversity between various indigenous donkey populations will offer a valuable reference for rational strategies in breed assignment to local non-descript donkeys, donkey conservation and breeding programs.

Phenotypic Clustering of Indian Donkey Population Belonging to Six Agro-Climatic Regions

Donkeys support rural livelihoods and low-income farmer’s family by providing economy at minimal maintenance cost. In India, donkeys constitute about 28% of total equine population but these are non-descript local donkeys without any breed characterization. This study describes phenotypic diversity among different donkey populations available in various agro-climatic regions in India including Gujarat, Rajasthan, Maharashtra, J&K, Haryana, Bihar and Himachal Pradesh for their phenotypic clustering as a distinct breed(s) by considering each population as a separate cluster. Biometric indices of seven local donkey populations were recorded and compared to French Poitou donkey breed which revealed that average body length of donkeys from Spiti, Gujarat, Rajasthan, Baramati, Bihar, Haryana and Leh areas was 97.09, 101.18, 97.60, 103.68, 96.31, 109 & 95.76 cm, respectively, while Poitou donkeys had significantly higher length (138.79 cm) than indigenous donkey populations. Further height at wither revealed that except leh donkey population, the rest of the donkeys prevalent throughout different agro-climatic regions met a “small standard’ pattern. Donkey populations from Leh were fitted in ‘Miniature’ donkey pattern. All local donkeys were well adapted to their agroclimatic environment and ecology as they were totally dependent upon the grass cover and roughages available within their reach for meeting their nutritional requirement. Coat colour varied across different regions. Black and brown colours were prevalent in donkeys from cold desert regions including Leh and Spiti region. Face length of donkeys from Spiti, Gujarat and Baramati were at par with each other while donkeys from Leh had smallest face length. Cluster analysis based on biometric indices revealed that exotic Poitou donkeys is an out-group as it formed a distinct cluster while Indigenous donkeys belonging to various agro-climatic zones were grouped in three clusters namely, C1-miniature or near miniature donkeys (Leh, Spiti and Bihar regions), C2- small standard ones including donkeys from Rajasthan and Gujarat while cluster C3 having donkeys from Baramati and Haryana region. Poitou cluster was phenotypically different from Cluster 1 as Eucledean cluster distance was maximum with donkeys of this cluster, followed by cluster 2 and cluster 3. This information will be useful for breed classification of these local non-descript donkeys.

Assessment of demographic bottleneck in Indian horse and endangered pony breeds

Bottleneck study of any continuously decreasing population is important and crucial issue in its conservation strategies including the analysis of simulated and real populations (Williamson-Natesan 2005; Busch et al. 2007). A bottleneck in a population can increase the rate of inbreeding, loss of genetic variation, fixation of deleterious alleles, thereby reducing evolutionary potential of animals to adapt to new selective pressures, such as climatic change or shift in available resources and increasing the probability of population extinction (Frankham 1995). The genetic changes caused by a bottleneck in a population’s effective size can lower the possibility of population’s persistence (Vrijenhoek 1994; Newman and Pilson 1997). Various endangered or threatened 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 show quantifiable lower levels of genetic diversity (Waldman et al. 1998) which also necessitates the assessment of bottlenecks with molecular marker for their conservation and evolutionary genetics. India is bestowed with a rich biodiversity of equids in the form of two horses (Marwari and Kathiawari) and four endangered pony breeds (Bhutia, Spiti, Manipuri and Zanskari) besides indigenous donkeys and wild asses (Gupta et al. 2012a,b; 2014). Overall population of these breeds, specially endangered pony breeds has declined in most of the pockets in their home tracts (less than 1000) which is due to their decreased utility and increased modernization of transport system even in hilly and difficult terrains (Gupta et al. 2012a, b). It is expected that bottleneck might have taken