Estimates of genomic heritability and genome-wide association study for fatty acids profile in Santa Inês sheep.

BACKGROUND: Despite the health concerns and nutritional importance of fatty acids, there is a relative paucity of studies in the literature that report genetic or genomic parameters, especially in the case of sheep populations. To investigate the genetic architecture of fatty acid composition of sheep, we conducted genome-wide association studies (GWAS) and estimated genomic heritabilities for fatty acid profile in Longissimus dorsi muscle of 216 male sheep. RESULTS: Genomic heritability estimates for fatty acid content ranged from 0.25 to 0.46, indicating that substantial genetic variation exists for the evaluated traits. Therefore, it is possible to alter fatty acid profiles through selection. Twenty-seven genomic regions of 10 adjacent SNPs associated with fatty acids composition were identified on chromosomes 1, 2, 3, 5, 8, 12, 14, 15, 16, 17, and 18, each explaining ≥0.30% of the additive genetic variance. Twenty-three genes supporting the understanding of genetic mechanisms of fat composition in sheep were identified in these regions, such as DGAT2, TRHDE, TPH2, ME1, C6, C7, UBE3D, PARP14, and MRPS30. CONCLUSIONS: Estimates of genomic heritabilities and elucidating important genomic regions can contribute to a better understanding of the genetic control of fatty acid deposition and improve the selection strategies to enhance meat quality and health attributes.

A single nucleotide polymorphism in NEUROD1 is associated with production traits in Nelore beef cattle.

Feed efficiency and carcass characteristics are late-measured traits. The detection of molecular markers associated with them can help breeding programs to select animals early in life, and to predict breeding values with high accuracy. The objective of this study was to identify polymorphisms in the functional and positional candidate gene NEUROD1 (neurogenic differentiation 1), and investigate their associations with production traits in reference families of Nelore cattle. A total of 585 steers were used, from 34 sires chosen to represent the variability of this breed. By sequencing 14 animals with extreme residual feed intake (RFI) values, seven single nucleotide polymorphisms (SNPs) in NEUROD1 were identified. The investigation of marker effects on the target traits RFI, backfat thickness (BFT), ribeye area (REA), average body weight (ABW), and metabolic body weight (MBW) was performed with a mixed model using the restricted maximum likelihood method. SNP1062, which changes cytosine for guanine, had no significant association with RFI or REA. However, we found an additive effect on ABW (P ≤ 0.05) and MBW (P ≤ 0.05), with an estimated allele substitution effect of -1.59 and -0.93 kg0.75, respectively. A dominant effect of this SNP for BFT was also found (P ≤ 0.010). Our results are the first that identify NEUROD1 as a candidate that affects BFT, ABW, and MBW. Once confirmed, the inclusion of this SNP in dense panels may improve the accuracy of genomic selection for these traits in Nelore beef cattle as this SNP is not currently represented on SNP chips.

Feed efficiency indexes and their relationships with carcass, non-carcass and meat quality traits in Nellore steers.

Five hundred and seventy-five Nellore steers were evaluated for residual feed intake and residual feed intake and gain and their relationships between carcass, non-carcass and meat quality traits. RFI was measured by the difference between observed and predicted dry matter intake and RIG was obtained by the sum of -1*RFI and residual gain. Efficient and inefficient animals were classified adopting ±0.5 standard deviations from RFI and RIG mean. A mixed model was used including RFI or RIG and contemporary group as fixed effects, initial age as covariate and sire and experimental period as random effects, testing the significance of the regression slope for each evaluated trait. RIG was positively related to longissimus muscle area. Efficient-RFI animals had lower liver and internal fat proportions compared to inefficient-RFI animals. Efficient-RFI and efficient-RIG animals had 11.8% and 11.2% lower extracted intramuscular fat, compared to inefficient-RFI and inefficient-RIG animals, respectively. Efficient-RFI animals had tougher meat compared to inefficient-RFI animals.

Estimation of taurindicine hybridization of American Zebu cattle in Brazil.

Our objective was to estimate Bos primigenius taurus introgression in American Zebu cattle. One hundred and four American Zebu (Nellore) cattle were submitted to mtDNA, microsatellite and satellite analysis. Twenty-three alleles were detected in microsatellite analysis, averaging 4.6 ± 1.82/locus. Variance component comparisons of microsatellite allele sizes allowed the construction of two clusters separating taurus and indicus. No significant variation was observed when indicus and taurus mtDNA were compared. Three possible genotypes of 1711b satellite DNA were identified. All European animals showed the same restriction pattern, suggesting a Zebu-specific restriction pattern. The frequencies of B. primigenius indicus-specific microsatellite alleles and 1711b satellite DNA restriction patterns lead to an estimate of 14% taurine contribution in purebred Nellore.

Influence of the halothane gene (HAL) on pork quality in two commercial crossbreeds.

We evaluated the effect of the halothane (HAL) gene on the quality of pork in domestic pigs. Half-carcasses from two different commercial pig (Sus domestica) crossbreeds were analyzed, 46 of which were homozygous dominant (HAL(NN)) and 69 of which were heterozygous (HAL(Nn)) for the halothane gene. The measures included backfat thickness, lean meat percentage, carcass weight, pH 24 h after slaughtering, color, and drip loss; DNA was extracted from the haunch muscle. Swine with the HAL(Nn) genotype had less backfat thickness and higher lean meat percentages than swine with the HAL(NN) genotype. Yet, swine with the HAL(Nn) genotype had lower quality meat than those with the HAL(NN) swine. The pH at 24 h was lower in HAL(Nn) swine. The meat color was paler in HAL(Nn) animals, the drip loss was greater in those animals bearing the n allele, and the amount of intramuscular fat was not related to the halothane genotype. We conclude that bearers of the recessive allele of the halothane gene produce more meat, but with quality parameters that are inferior to those sought by consumers and industry.

Influence of Chinese breeds on pork quality of commercial pig lines.

We compared carcass and meat quality of pigs from the same sire line and two different dam lines, one that included Chinese breeds and one that did not. Line A consisted of 1/4 Landrace, 1/2 Large White, 1/8 Chinese breeds (Meishan, Fengjing, Jiaxing), and 1/8 Large White, Duroc and Pietrain, and line B consisted of 1/2 Large White and 1/2 Pietrain. The animals (N = 144) were slaughtered at a live weight of 108 kg. Backfat thickness, percentage of lean meat, pH 24 h after slaughter, meat color, percentage of drip loss, and percentage of intramuscular fat were measured and compared using analysis of variance in a completely randomized design; the BioEstat 5.0 test was applied for the comparison of means at a significance level of 5% for all analyses. Backfat was significantly lower for line A (12.78 mm) than for line B (15.90 mm). The pH measured 24 h after slaughter was significantly lower in line A (5.68) compared to line B (5.84). Percent lean meat was significantly higher for line A (61.21%) compared to line B (59.72%). Percentage drip loss was significantly higher in line A (2.73%) than in line B (2.23%). Percentage intramuscular fat and meat color were not significantly different between the lines. The inclusion of Chinese breeds produced a higher percentage of lean meat and reduced fat thickness, along with increased heterosis, which are important characteristics for breeding programs.

PIT1 gene polymorphism in Pietrain and Large White pigs after divergent selection.

We examined the polymorphisms in the PIT1 gene of 103 pigs and compared their frequencies in the maternal and paternal lineages of the Pietrain and Large White breeds, which have undergone divergent selection for over 30 years. DNA samples extracted from the blood of these animals were amplified by PCR and genotyped by RFLP, using the restriction enzyme RsaI. The data were analyzed with the chi-square test. We found that 57.3% of the animals were genotype AB, among which 26.2% were of the Large White paternal lineage, 18.5% the Pietrain paternal lineage and 12.6% the Pietrain maternal lineage. The AA genotype appeared in 20.4%, of which 7.8% were Large White, 4.8% the Pietrain paternal lineage and 7.8% the Pietrain maternal lineage. BB was observed in 22.3% (6.8% were of the Large White paternal lineage, 9.7% of the Pietrain paternal lineage and 5.8% of the Pietrain maternal lineage). The allele frequencies were 49.0% A and 51.0% B allele. When we examined the Pietrain maternal and paternal lineages, we found that the PIT1 gene had been fixed in the paternal lineage, suggesting that the B allele is associated with low body fat and improved muscle development when compared to the maternal lineage. However, no significant differences were found between the Pietrain and Large White paternal lineages.

Obese gene polymorphism in Pietrain and Large White pigs after a divergent selection.

The aim of the present study was to identify polymorphisms in the leptin gene of 112 pigs and compare the maternal and paternal lineage of Pietrain and Large White breeds that underwent a divergent selection for over 30 years. DNA samples extracted from the blood of these animals were amplified by polymerase chain reaction and genotyped by restriction fragment length polymorphism using the restriction enzyme HinfI. The data were statistically analyzed by the chi-square test. The results showed that 87.5% of the animals were genotype TT, where 31.25% were Large White paternal lineage, 31.25% were Pietrain paternal lineage and 25% were Pietrain maternal lineage. The TC genotype appeared in 12.5%, where 10% were Large White, 0.5% were Pietrain paternal lineage and 2% were of the same maternal lineage breed; CC was not observed. As for the allele frequency, 93.75% of the T and 6.25% of the C allele were found. In Pietrain maternal and paternal lineages, it could not be determined that the Obese gene had been fixed in the maternal lineage. However, in the Pietrain and Large White paternal lineages there was a statistically significant difference, suggesting that the C allele is associated with growth and daily weight gain and that the low frequency of C in the Pietrain lineage is related to low rate of body fat, a typical feature of this breed.