Unified Genomic Chip: Advancing Genetic Improvement in Indian Dairy Animals

• he Unified Genomic Chip represents a significant advancement in the field of animal genomics, specifically tailored for the genomic profiling and genetic evaluation of Indian cattle breeds and buffaloes. 
• Developed by a consortium led by the Department of Animal Husbandry and Dairying (DAHD) under the Ministry of Animal Husbandry, Dairying and Fisheries, this innovative SNP chip serves as a robust tool for the genetic improvement of dairy animals.

Overview of the Unified Genomic Chip

Objective and Scope

• Genomic Profiling:
  • The chip is designed to enable comprehensive genomic profiling of indigenous cattle and buffalo breeds. 
  • By evaluating single nucleotide polymorphisms (SNPs) across the genome, the chip provides detailed insights into genetic diversity, trait associations, and overall breed potential.
• Genetic Enhancement:
  • Utilizing SNP data, the Unified Genomic Chip facilitates precision breeding by identifying superior genetic profiles. 
  • This targeted approach supports genetic improvement programs aimed at enhancing productivity and disease resistance in dairy animals.

Technical Specifics

• SNP Chip Technology:
  • As a single nucleotide polymorphism (SNP) chip, the device detects minute genetic variations at individual nucleotide positions. 
  • SNPs, the most common form of genetic variation, serve as reliable biomarkers for identifying trait-associated genes and tracing genetic lineages.
• Variants for Specific Species:
  • Gau Chip: Specifically optimized for cattle genomic analysis.
  • Mahish Chip: Tailored for buffalo genomic evaluation, addressing the unique genetic architecture of these animals.

Underlying Genomic Principles: Single Nucleotide Polymorphisms (SNPs)

Scientific Basis

• Definition and Role:
  • SNPs represent variations at a single nucleotide within the DNA sequence. 
  • For example, a specific nucleotide may vary between individuals—where a Guanine (G) is replaced by a Thymine (T) in certain cases.
• Biomarker Utility:
  • These genetic markers are extensively used to map genetic traits, identify susceptibility to diseases, and study population genetics. 
  • Their prevalence and stable inheritance patterns render SNPs invaluable for genomic selection and breeding strategies.

Genetic Inheritance

• Maternal Lineage Tracing:
  • In addition to nuclear genomic analyses, mitochondrial DNA (mtDNA) studies, which focus on maternally inherited traits, complement SNP data. 
  • This dual approach enhances the overall understanding of genetic lineage and breed development.

Integration with Reproductive Technologies: Sex-Sorted Semen

Sex-Sorted Semen Technology:

• This reproductive technology involves the sorting of semen based on sex chromosomes, ensuring that artificial insemination (AI) procedures yield predominantly female offspring. 
• In dairy farming, where female animals are preferred for milk production, this technology enhances herd productivity.

Technical Performance:

• With an accuracy exceeding 90%, sex-sorted semen technology optimizes the reproductive efficiency compared to conventional semen, which results in an approximately equal male-to-female ratio (50:50).

National Developments

• Indigenous Innovations:
  • The National Dairy Development Board (NDDB) has pioneered indigenous methods for sex-sorted semen in India, aligning reproductive technologies with advanced genomic tools such as the Unified Genomic Chip for integrated genetic improvement programs.

Strategic Initiatives and Technological Advancement in India

Regulatory and Institutional Support

• Amendment of Clinical Trial Rules (2019):
  • Recent regulatory amendments have facilitated the incorporation of advanced genomic tools including human and animal organ-on-chip models into clinical and genetic research frameworks.
• Genome India Project (GIP):
  • Initiated in 2020 by the Department of Biotechnology, the GIP aims to establish a comprehensive 10,000-genome database accessible to researchers worldwide, thereby enriching genetic resources for animal genomics.
• Indian Biological Data Centre (IBDC):
  • As the first national repository for life science data, the IBDC supports the integration and analysis of extensive genomic datasets, further strengthening research in livestock genetics.
• Phenome India Project:
  • Led by CSIR, this project is creating an expansive phenotypic database (phenome) that complements genomic data, enabling a deeper understanding of trait expression and genetic performance in dairy animals.