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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.

It is imperative to assess the maternal lineage in order to achieve a broad picture of evolution, phylogenetic and genetic biodiversity within and among different breeds of livestock. In recent past, there has been a considerable advancement in sequencing of complete mammalian mtDNA molecules and their analysis. Most of the studies have focused on the mitochondrial D-loop region, the most variable part of mtDNA due to increased substitution rate than in the rest of the mtDNA genome which serves as a better genetic marker to assess the diversity. Mitochondrial DNA (mtDNA) possesses several favorable characteristics, including large quantity in the cell, small genome size, haploid, maternal inheritance with extremely low probability of paternal leakage, higher mutation rate than nuclear DNA, and amenable to change mainly through mutation rather than recombination. All these features make mtDNA a useful and one of the most frequently used markers in molecular systematic and has been widely employed to address questions of genetic diversity, population structure and population evolution of animals including equines. Many native breeds of horses as well as ponies were assessed for their genetic diversity and ancestry on the basis of studies on mitochondrial DNA to address the questions of evolution along with breed development and conservation.