Identification of functional candidate variants and genes for feed efficiency in Holstein and Jersey cattle breeds using RNA-sequencing

摘要

The identification of functional genetic variants andassociated candidate genes linked to feed efficiency mayhelp improve selection for feed efficiency in dairy cattle,providing economic and environmental benefits for thedairy industry. This study used RNA-sequencing dataobtained from liver tissue from 9 Holstein cows [n = 5low residual feed intake (RFI), n = 4 high RFI] and 10Jersey cows (n = 5 low RFI, n = 5 high RFI), whichwere selected from a single population of 200 animals.Using RNA-sequencing, 3 analyses were performed toidentify: (1) variants within low or high RFI Holsteincattle; (2) variants within low or high RFI Jersey cattle;and (3) variants within low or high RFI groups, whichare common across both Holstein and Jersey cattlebreeds. From each analysis, all variants were filtered formoderate, modifier, or high functional effect, and colocalizedquantitative trait loci (QTL) classes, enrichedbiological processes, and co-localized genes related tothese variants, were identified. The overlapping of theresulting genes co-localized with functional SNP fromeach analysis in both breeds for low or high RFI groupswere compared. For the first two analyses, the totalnumber of candidate genes associated with moderate,modifier, or high functional effect variants fixedwithin low or high RFI groups were 2,810 and 3,390for Holstein and Jersey breeds, respectively. The majorQTL classes co-localized with these variants includedmilk and reproduction QTL for the Holstein breed, andmilk, production, and reproduction QTL for the Jerseybreed. For the third analysis, the common variantsacross both Holstein and Jersey breeds, uniquely fixedwithin low or high RFI groups were identified, revealinga total of 86,209 and 111,126 functional variantsin low and high RFI groups, respectively. Across all3 analyses for low and high RFI cattle, 12 and 31 colocalizedgenes were overlapping, respectively. Amongthe overlapping genes across breeds, 9 were commonlydetected in both the low and high RFI groups (INSRR,CSK, DYNC1H1, GAB1, KAT2B, RXRA, SHC1,TRRAP, PIK3CB), which are known to play a key rolein the regulation of biological processes that have highmetabolic demand and are related to cell growth andregeneration, metabolism, and immune function. Thegenes identified and their associated functional variantsmay serve as candidate genetic markers and can beimplemented into breeding programs to help improvethe selection for feed efficiency in dairy cattle.