Development and validation of the Axiom-MaruPri SNP chip for genetic analyses of domesticated old world camelids

Development and validation of a high-density SNP chip tailored for genomic analysis in Indian backyard chickens

1. Indian backyard chicken breeds are well adapted to local climatic conditions and possess distinct genetic characteristics, necessitating a dedicated SNP chip to address their unique genetic diversity, breed identification and conservation needs. In this study, a high-density SNP chip, Axiom_Kukkut was developed with SNP markers derived from genomes of 16 indigenous chicken breeds, Red Jungle Fowl and White Leghorn.2. A total of 622,376 markers and an inter-marker distance of 1.9 kb, the Axiom_Kukkut provided a denser marker distribution compared to existing arrays. The chip was validated by genotyping a set of samples from diverse Indian chicken breeds. All the SNPs were used for validation. An average call rate of 99.92% and 91.28%, as high resolution polymorphic markers, demonstrated the high precision of the designed array.3. Population stratification analysis revealed high genetic diversity and distinct linkage disequilibrium patterns among various breeds. Multivariate principal component analysis confirmed the genetic distinctiveness of Red Jungle Fowl and Uttara, suggesting low genetic diversity due to geographic isolation or specific breeding practices.4. The customised SNP chip allows a multitude of possibilities, including applications in genome-wide association analysis, identification of selection signatures, population genetics and breed improvement programmes for Indian chicken. Continued refinement will expand its utility to include exotic and commercial breeds as well, enhancing its overall applicability across a wider range of chicken populations.

Review on camel genetic diversity: ecological and economic perspectives

Camels, known as the "Ship of the Desert," play a vital role in the ecosystems and economies of arid and semi-arid regions. They provide meat, milk, transportation, and other essential services, and their resilience to harsh environments makes them invaluable. Despite their similarities, camel breeds exhibit notable differences in size, color, and structure, with over 40 million camels worldwide. This number is projected to increase, underscoring their growing significance. Economically, camels are crucial for food production, tourism, and trade, with camel racing being particularly significant in Arab countries. Their unique physiological traits, such as low disease susceptibility and efficient water conservation, further enhance their value. Camel products, especially meat and milk, offer substantial nutritional and therapeutic benefits, contributing to their high demand. Genetic diversity studies have advanced our understanding of camels' adaptation to extreme environments. Functional genomics and whole-genome sequencing have identified genes responsible for these adaptations, aiding breeding programs and conservation efforts. High-throughput sequencing has revealed genetic markers linked to traits like milk production and disease resistance. The development of SNP chips has revolutionized genetic studies by providing a cost-effective alternative to whole-genome sequencing. These tools facilitate large-scale genotyping, essential for conserving genetic diversity and improving breeding strategies. To prevent the depletion of camel genetic diversity, it is crucial to streamline in situ and ex situ conservation efforts to maintain their ecological and economic value. A comprehensive approach to camel conservation and genetic preservation, involving advanced genomic technologies, reproductive biotechniques, and sustainable management practices, will ensure their continued contribution to human societies.

Advancing equine genomics: the development of a high density Axiom_Ashwa SNP chip for Indian horses and ponies

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.