Allele Specific Expression (ASE) analysis between Bos Taurus and Bos Indicus cows using RNA-Seq data at SNP level and...

Area of Science:

• Genomics and Bioinformatics
• Animal Genetics
• Transcriptomics

Background:

• Understanding genetic variation between cattle subspecies is crucial for breeding and conservation.
• Allele Specific Expression (ASE) analysis provides insights into gene regulation and functional genomics.
• Bos taurus (e.g., Holstein) and Bos indicus (e.g., Cholistani) represent distinct cattle lineages with potential genetic differences.

Purpose of the Study:

• To perform allele specific expression analysis in two major cattle subspecies: Bos taurus (Holstein) and Bos indicus (Cholistani).
• To identify and quantify single nucleotide polymorphisms (SNPs) and their expression patterns at both SNP and gene levels.
• To compare the genetic variations and ASE profiles between Holstein and Cholistani cattle populations.

Main Methods:

• RNA-Sequencing (RNA-Seq) data from whole blood samples of Holstein and Cholistani cows were utilized.
• Reads were quality controlled using FASTQC and Trimmomatic, then mapped to the bovine reference genome using TopHat2.
• Single nucleotide polymorphisms (SNPs) were discovered using Samtools, and Allele Specific Expression (ASE) was analyzed via Chi-square test.

Main Results:

• A substantial number of SNPs were identified: 50,183 in Holstein and 137,954 in Cholistani cattle, with 15,308 common SNPs.
• Significant proportions of identified SNPs were classified as ASE-SNPs: 20% (10,158) in Holstein and 23% (31,523) in Cholistani.
• Among 41 differentially expressed genes, 31 ASE-SNPs were detected, with a higher number in Cholistani (26) compared to Holstein (5) cows.

Conclusions:

• The study successfully identified and characterized allele specific expression patterns in two distinct cattle subspecies.
• Significant differences in ASE-SNP prevalence and distribution were observed between Holstein (Bos taurus) and Cholistani (Bos indicus) breeds.
• These findings contribute to understanding the genetic and regulatory divergence between major cattle lineages.