Selection signatures in Gir and Holstein cattle.

Area of Science:

• Genomics
• Animal Breeding
• Population Genetics

Background:

• Selection signatures on genomes indicate adaptive and economically important traits.
• Intensive selection in dairy cattle, like Holstein, can reduce genetic diversity, impacting breeding programs.
• Gir cattle are vital for milk production in tropical regions and have undergone selection since 1985.

Purpose of the Study:

• Assess genetic diversity in Holstein (HOL), Indian Gir (GIR_IN), and Brazilian Dairy Gir (GIR_BR) cattle.
• Characterize selection signatures within these cattle populations.
• Identify genes under selection related to economically important traits.

Main Methods:

• Evaluated genetic diversity using nucleotide diversity, variant density, minor allele frequency, heterozygosity, and inbreeding coefficient.
• Identified selection signatures using Tajima's D, integrated haplotype score (iHS), fixation index, and cross-population extended haplotype homozygosity tests on autosomes and the X chromosome.
• Analyzed specific genes including DNAJC18, FSHR, HELB, HMGA2, PLAG1, GAB3, and PTEN.

Main Results:

• Holstein cattle populations exhibited lower genetic diversity compared to Indian and Brazilian Gir cattle.
• Greater genetic diversity was observed in both GIR_IN and GIR_BR populations.
• Identified selection signatures pinpointed genes associated with growth, reproduction, mastitis, milk production, heat tolerance, health, and adaptation.

Conclusions:

• Holstein cattle show reduced genetic diversity due to intensive selection.
• Gir cattle populations maintain higher genetic diversity, crucial for tropical adaptation and milk production.
• Identified genes under selection provide insights into the genetic basis of economically important traits in dairy cattle.