Genetic variation in promoter region of the bovine LAP3 gene associated with estimated breeding values of milk production traits and clinical mastitis in dairy cattle

Abstract

The purpose of this study was to identify genetic variants in the promoter and 5’UTR regions of bovine leucine amino peptidase three (LAP3) gene and analysed their associations with estimated breeding values (EBVs) of milk production traits and clinical mastitis in Sahiwal and Karan Fries cattle. Eleven SNPs were identified within the region under study of the LAP3 gene, including seven promoter variants (rs717156555: C>G, rs720373055: T>C, rs715189731: A>G, rs516876447: A>G, rs461857269: C>T, rs136548163: C>T, and rs720349928: G>A) and four 5’UTR variants (rs717884982: C>T, rs722359733: C>T, rs481631804: C>T and rs462932574: T>G). Out of them, 10 SNPs variants were found in both Sahiwal and Karan Fries cattle, with one SNP variant (rs481631804: C>T) being unique to Karan Fries cattle. Seven of these identified SNPs were chosen for association analyses. Individual SNP based association analysis revealed that two SNPs (rs720373055: T>C and rs720349928: G>A) were significantly associated with EBVs of lactation milk yield (LMY), 305-day milk yield (305dMY), and one significant association of SNP rs722359733: C>T with lactation length (LL) was observed. Haplotype based association analysis indicated that diplotypes are significantly associated with EBVs of LMY, 305dMY, and LL, individuals with H1H3 (CTACGCT/GCGTACG) being linked to higher lactation performance than other diplotypes. Further logistic regression analysis revealed that, animals with diplotype H1H3 was less susceptible to the incidence of clinical mastitis than other cows, as the odds ratio for the non-incidence of clinical mastitis was found to be low. Altogether, variations in the LAP3 gene promoter could be used as a genetic marker, most notably diplotype H1H3, may greatly benefit the simultaneous improvement of mastitis resistance and milk yield traits in dairy cattle. Moreover, bioinformatics analysis predicted that the SNPs rs720373055: T>C, rs715189731:A>G and rs720349928: G>A is located in the core promoter region and in TFBs, play key role in regulation of studied phenotypes.

Genetic variation in bovine LAP3 and SIRT1 genes associated with fertility traits in dairy cattle

“…All identified SNPs, along with their genotypic and allelic frequencies were described in our previous study [ 12 – 14 ]. In this analysis, we investigated the associations between ten SNPs in LAP3 and one SNP in SIRT1 and fertility traits in dairy cattle (Table 1 ).…”

“…Moreover, exploring genetic variants associated with fertility traits through a candidate gene approach contributes to unravelling the genetic basis of fertility in dairy cattle. Our previous studies in dairy cattle unveiled SNP variants in LAP3 and SIRT1 genes that affected the estimated breeding value of milk production traits and clinical mastitis in Sahiwal and Karan Fries dairy cattle [ 12 – 14 ]. This study sought to determine whether the polymorphisms in the LAP3 and SIRT1 genes, previously identified for milk production traits [ 12 – 14 ], were associated with fertility traits in dairy cattle.…”

“…The quality and quantity of DNA was assessed by agarose gel-electrophoresis and spectrophotometer. The sets of PCR primers used to amplify the targeted regions of LAP3 and SIRT1 genes, PCR amplification protocols and SNP genotyping methods were similar to those described in our previous work [ 12 – 14 ]. The genotype data obtained from 125 Sahiwal and 138 Karan Fries cows were used for single marker analysis.…”

“…In this context, researchers are actively working to pinpoint potential candidate genes and / or causal variants known to be associated with fertility traits in cattle [ 8 – 11 ]. In the last few years, several studies have explored the genetic variations of bovine leucine amino peptidase three (LAP3) and silent information regulator one (SIRT1) genes associated with milk production and health related traits in dairy cattle [ 12 – 16 ].…”

“…Consequently, LAPs and LAP related aminopeptidases may exert a variety of functions and have significant impacts on cellular and physiological activities. Moreover, substantial studies on cattle have reported numerous promising mutations in the LAP3 gene that explain genetic variations in traits such as milk production, somatic cell score, and clinical mastitis in dairy cattle [ 12 – 16 ], as well as birth weight in sheep [ 19 ]. LAP3 has also been identified as a candidate gene affecting the weight of the longissimus dorsi muscle in Huaxi cattle [ 20 ], milk traits [ 21 ] and direct calving ease [ 22 ] in cattle.…”