ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, 132 001, India.
Equine Production Campus, ICAR-National Research Centre on Equines, Bikaner, Rajasthan, 334 001, India.
Funct Integr Genomics. 2024 Oct 23;24(6):195. doi: 10.1007/s10142-024-01482-0.
The unique horse and pony breeds of India are declining at an alarming rate. These horses have been integral to the Indian culture and customs for centuries and represent a valuable genetic resource. It is imperative to harness the potential of this equine genetic resource that urgently needs conservation. The study highlights the design and development of a high density SNP array, the Axiom_Ashwa to aid in the genetic analysis and conservation efforts for Indian horse and pony breeds. With 613,950 SNPs, this chip offers extensive genome coverage having an average inter-marker distance of 4 kb. The Axiom_Ashwa has been validated on a larger set of diverse indigenous samples as well as Thoroughbreds, demonstrating a high call rate of 99.4% and robustness for genotyping indigenous breeds. Linkage disequilibrium (LD) analysis showed higher average LD in Indian breeds compared to exotic breeds, suggesting a limited effective population size and recent bottlenecks. Phylogenetic and population stratification analyses using PCA and DAPC clearly distinguished horses, ponies and Thoroughbreds, confirming the efficacy of the Axiom_Ashwa chip. These findings underscore the urgent need for conservation efforts for Indian horse breeds, which have experienced significant drop in population size. The Axiom_Ashwa SNP chip offers advantages such as cost-effectiveness and high throughput, providing a more accurate genetic representation of Indian horses.
印度独特的马和小型马品种正以惊人的速度减少。这些马几个世纪以来一直是印度文化和习俗的组成部分，代表着宝贵的遗传资源。利用这一急需保护的马类遗传资源的潜力至关重要。本研究强调了设计和开发高密度 SNP 芯片 Axiom_Ashwa，以帮助进行印度马和小型马品种的遗传分析和保护工作。该芯片拥有 613,950 个 SNP，具有广泛的基因组覆盖度，平均标记间距离为 4kb。Axiom_Ashwa 已在更多不同的本地样本和纯种马中进行了验证，其基因分型本地品种的呼叫率高达 99.4%，稳健性强。连锁不平衡（LD）分析表明，与外来品种相比，印度品种的平均 LD 更高，这表明其有效种群规模有限且近期经历了瓶颈。使用 PCA 和 DAPC 进行的系统发育和群体分层分析清楚地区分了马、小马和纯种马，证实了 Axiom_Ashwa 芯片的有效性。这些发现强调了保护印度马品种的紧迫性，这些品种的种群规模已经大幅减少。Axiom_Ashwa SNP 芯片具有成本效益高和高通量等优势，能够更准确地代表印度马的遗传特征。
