• Bovine Genome Sequencing Consortium Publication: The draft sequence and analysis of the domestic cattle (Bos taurus) genome was published in the journal Science in April 2009 (Vol. 324, Issue 5926, pp. 522–528) by the Bovine Genome Sequencing and Analysis Consortium.
• Key Findings:
• Sequenced the genome of a Hereford cow named L1 Dominette 01449.
• Genome size of $\sim 2.87$ billion base pairs with at least 22,000 protein-coding genes.
• Revealed evolutionary changes in immune and lactation genes, laying the foundation for modern genomic selection in dairy and beef cattle.

Correct option: (4) 2009

• Recommended DNA Markers for Animal Genetic Diversity: Joint recommendations by FAO and ISAG (International Society for Animal Genetics) for evaluating livestock biodiversity, genetic distance, and breed structure:
• Microsatellites / STRs (C): Highly polymorphic, codominant, abundant across the genome, and standardized internationally for pedigree verification and diversity panels.
• Single Nucleotide Polymorphisms - SNPs (B): High-density, biallelic codominant markers with high throughput and automated genotyping arrays (e.g., 50K and 770K bovine chips).
• Other Markers:
• RFLP (A) and Minisatellites (D) were legacy early-generation markers now largely superseded due to lower throughput and technical complexity.

Correct option: (1) (B) and (C) only.

• RNA-Seq (RNA Sequencing): High-throughput next-generation sequencing of cDNA fragments used to quantify the entire cellular transcriptome.
• Differential Gene Expression:
• RNA-seq provides absolute digital counts of transcripts per million (TPM) or FPKM across biological samples.
• Directly identifies differentially expressed genes (DEGs), alternative splicing isoforms, and novel transcripts between diseased vs. healthy or heat-stressed vs. normal livestock tissues.
• Other Techniques:
• GWAS: Identifies genomic loci associated with phenotypic traits in DNA, not transcript expression levels.
• Whole Genome Sequencing: Decodes entire genomic DNA sequence.
• Metagenomics: Sequences microbial community genomes in an environmental sample (e.g., rumen microbiome).

Correct option: (2) RNA seq