Indian Journal of Animal Research
SCOPUSWeb of Science
  • Year: 2026
  • Volume: 60
  • Issue: 8

Genetic Diversity Analysis of Kachchhi-Sindhi Horses and Repercussions for Conservation in India

  • Author:
  • Bhavya Maggo1, Sonali1, Yash Pal2, Varij Nayan2, Shiv Kumar Giri3, Tarun Kumar Bhattacharya1, Bhupendra Nath Tripathi1, Anuradha Bhardwaj1,*
  • Total Page Count: 10
  • Page Number: 1368 to 1377

1ICAR-National Research Centre on Equines, Hisar-125 001, Haryana, India

2ICAR-Central Institute for Research on Buffaloes, Hisar-125 001, Haryana, India

3Maharaja Agrasen University, Baddi, Solan-174 103, Himachal Pradesh, India

*Corresponding Author: Anuradha Bhardwaj, ICAR-National Research Centre on Equines, Hisar-125 001, Haryana, India, Email: dranu.biotech@gmail.com

Abstract

The Kachchhi-Sindhi horse is a native Indian breed, mainly found in the Gujarat and Rajasthan regions of India, with an estimated population of about 4,000 horses. A comprehensive genetic assessment to understand the genetic diversity and population structure of this breed is essential for conservation strategies and for maintaining the health and vitality of the breed.

To determine the genetic diversity and population structure of the Kachchhi-Sindhi breed, we genotyped 50 unrelated, healthy adult horses using 30 microsatellite DNA loci. The genetic data were analyzed to calculate the number of alleles, observed and expected heterozygosity and the inbreeding coefficient (FIS). We also tested for Hardy-Weinberg equilibrium deviations and marker neutrality. We used Structure analysis to assess the admixture within the breed. Besides, population structure analysis was done with principal coordinates analysis (PCoA). Alongside mode shift tests, as well as Sign, Standardized differences and Wilcoxon sign rank tests, were made for assessing signs of a potential population bottleneck recently.

Our study disclosed substantial genetic diversity in the Kachchhi-Sindhi breed. Key genetic parameters averaged an average number of alleles of 10.10±3.18, with an effective number of alleles of 5.15±1.88 and observed heterozygosity of 0.90±0.11, indicating significant genetic variation in the population. The inbreeding coefficient (FIS) was very low at -0.17±0.19, indicating limited inbreeding. While 14 of the 30 microsatellites showed deviations from Hardy-Weinberg equilibrium, most markers were considered neutral, with only four showing non-neutral behaviour, according to the Ewens-Watterson neutrality test. Population analysis by PCoA revealed a single large but fragmented population of Kachchhi-Sindhi horses. Further tests, such as the mode-shift test and M ratio value, showed no evidence of a recent bottleneck in the breed. These are crucial for guiding future breeding and conservation efforts for the Kachchhi-Sindhi breed.

Keywords

Conservation, Genetic diversity, Indian native horse, Marker, Sindhi