Comparative Genomic Annotation Gap Analysis: Feed-Efficiency Candidate Genes in Cattle vs. Water Buffalo (Bubalus bubalis)

Abstract

Genomic selection tools for feed efficiency have been extensively developed and validated in high-input cattle breeds, but it is unclear whether the same candidate genes are equally well characterized in water buffalo (Bubalus bubalis), the dominant dairy species across Pakistani smallholder systems. This note reports a small-scale, self-directed annotation audit of five feed-efficiency candidate genes (APOA2, TLR4, TMEM40, PHOX2A, KDELC2/POGLUT3), drawn from published cattle GWAS literature, comparing their annotation status in Bos taurus versus Bubalus bubalis using the NCBI Gene database. Four of the five genes exist in the buffalo reference genome only as computationally predicted models with no dedicated functional studies; only TLR4 has been experimentally validated in buffalo. This gap is discussed in the context of feed efficiency's dual relevance to productivity and enteric methane output, and its implications for applying cattle-derived genomic selection tools to buffalo breeding programmes.