FABP4gene has a very large effect on feed efficiency in lactating Israeli Holstein cows

Abstract

Improving feed efficiency (FE) is a major goal for the livestock industry. Previously, we have identified 48 SNP markers distributed over 32 genes significantly associated with residual feed intake (RFI) in Israeli Holstein male calves, the most significant of which are located in the bovine FABP4 gene. In the present study, we tested associations of eight of the FABP4 markers with RFI and feed conversion ratio (FCR), along with milk composition and feeding behavioral traits, in 114 lactating Israeli Holstein cows. Large allele effects were found, along with large contributions of FABP4 markers to the phenotypic variation [mean contribution of all significant markers ( P < 0.05), 15.4 and 12.0% for RFI and FCR, respectively] and genotypic variation [means of all significant markers ( P < 0.05), 75.7 and 32.4% in RFI and FCR, respectively]. However, the association of all significant FABP4 markers with FE and milk content traits was found in opposite directions, such that improved FE was accompanied by decreased milk content. Hence, before inclusion in breeding programs, the gain in FE must be economically balanced with the loss in milk contents. On the other hand, these findings imply that in any current improvement program concentrated on milk traits alone, without taking into account the effect on FE, the progress in milk composition is probably accompanied by deterioration of FE. These results, if confirmed in other populations and breeds, set FABP4 as a prime candidate in any marker-assisted selection program targeting FE as a whole and RFI in particular.

Re-Evaluation of Genotyping Methodologies in Cattle: The Proficiency of Imputation

“…Equipped with an individual feeding system, the experimental dairy farm of ARO has been monitoring the RFI of lactating cows [ 12 ]. To further validate the findings of a QTL for RFI on BTA14 that have been based on a sample of 114 cows [ 12 ], we enlarged this sample to 192 cows all genotyped with the Illumina BovineHD BeadChip (777K SNPs). We also performed whole genome sequencing (WGS) for 19 Israeli Holstein sires, representing major lineages of the Israeli herd [ 20 ] with no RFI evaluations.…”

“…The indication that FABP4 has a large effect on RFI mostly relies on the fourth and fifth SNPs ( FABP4_4 and FABP4_5 ) of 10 SNPs detected in gene FABP4 , of which FABP4_4 is capable of encoding a conservative substitution of hydrophobic amino acids [ 12 ] ( Table 1 ). To infer unavailable genotypes for these SNPs in the enlarged test sample of cows and re-evaluate previous results, we examined an additional 15 SNPs within a short interval (~35 Kbp) of this gene locus ( Table 2 ).…”

“…To investigate why the predicted effect of FABP4 locus on RFI differs between studies, we compared the imputed genotypes to those previously recorded for the sample of 114 cows using the HRM and TaqMan methods [ 12 ]. Imputed genotypes were identical for the tightly linked FABP4_4 and FABP4_5 SNPs that are only 3387 bp apart.…”

“…A total of 192 Israeli Holstein multiparous dairy cows from the Agricultural Research Organization (ARO) dairy herd (Rishon-LeTsiyon, Israel) were used in the present study of which 114 cows were used in previous studies [ 12 ]. The RFI values were evaluated as previously described [ 12 ]. Briefly, the cows were healthy, multiparous, high yielding (35 kg/day), and 60–180 days in milking.…”

“…Thoroughly reviewing this approach, Lashmar et al [ 10 ] listed 14 imputation software programs commonly used in animal genetics research [ 10 ]. Of these, in the current work, we used Findhap.f90 and PLINK to compare and re-evaluate genotyping data of RFI studies indicating that BTA14 fatty-acid-binding protein 4 ( FABP4 ) has a large effect on this trait [ 11 , 12 ]. We demonstrate the superiority of genotyping by imputation over the TaqMan, HRM, and even Sanger sequencing methods concluding that the relevance of the FABP4 gene to RFI is smaller than has been previously estimated [ 11 , 12 ], compared to an additional gene candidate on BTA14.…”