Genetic Characterization of Myf5 and POU1F1 Genes in Different Egyptian Local Rabbit Breeds and Their Association with Growth Traits

Genetic characterization and its association with quantitative traits in local breeds are important tools for the genetic improvement and sustainable management of animal genetic resources. Myogenic regulatory factor 5 (MYf5) and POU class 1 homeobox 1 (POU1F1) are candidate genes which play important roles in growth and development of mammals. The present study aims to detect the genetic diversity of the MYf5 and POU1F1 genes in four local Egyptian rabbit breeds and their association with growth traits, using PCR-restriction enzyme (PCR-RFLP), PCR-single-strand conformational polymorphism (PCR-SSCP), and direct sequencing techniques. The results showed that MYF5 exon 1 was observed with two genotypes in Baladi Black (BB), Gabali (GB) and New Zealand White (NZW) breeds while APRI-line (APRI) presented one genotype. The genetic diversity of Myf5 exon 2 between breeds showed two genotypes in APRI compared to three in NZW and four genotypes in BB and GB breeds. The genetic diversity of the POU1F1 gene (intron 5 and partial cds) in different rabbit breeds was two genotypes in NZW and three genotypes in BB, GB, and APRI breeds with different frequencies for each genotype. Based on the statistically significant difference between genes genotypes and growth weight, the results suggested that the genotypes of Myf5 exon 2 (1 and 2) of the BB breed, Myf5 exon 2 genotype 2 of the APRI breed, and genotype 1 of Myf5 exon 1 and genotype 1 of POU1F1 of the NZW breed compared to genotypes for each gene can be considered candidate molecular markers associated with the improvement of growth traits in these breeds.

Genetic assessment of litter size, body weight, carcass traits and gene expression profiles in exotic and indigenous rabbit breeds: a study on New Zealand White, Californian, and Gabali rabbits in Egypt

Rabbits are essential for commercial meat production due to their efficient growth and productivity, breeds like New Zealand White (NZW), Californian (CAL), and Gabali (GAB) rabbits offer unique genetic traits in litter, growth, and carcass traits. This study aimed to evaluate heritability (h2), genetic and phenotypic correlations (rg and rp) for litter size, body weight and carcass traits across California (CAL), New Zealand white (NZW) and Gabali (GA) rabbits. Along with exploring gene expression profiles of TBC1D1, NPY, AGRP, POMC, Leptin, GH, GHR, IGF-1, CAA, GPR, ACC, CPT1, FAS, and CART in the brain, liver, and meat tissues of different rabbit breeds. The breed genotype had a significant impact on litter size (LS), litter weight (LW), body weight at 12 weeks (BW12), and daily weight gain (DWG) traits. NZW rabbits displayed superior performance in terms of litter size and litter weight, while CAL rabbits recorded the highest values for BW12 and DWG. Heritability estimates (h2) were generally low for litter size (ranging from 0.05 to 0.12) and medium for body weight (ranging from 0.16 to 0.31). Both genetic (rg) and phenotypic (rp) correlations for litter size were positive and moderate (ranging from 0.08 to 0.48), while correlations for body weight ranged from 0.21 to 0.58. Additionally, CAL rabbits exhibited higher carcass traits compared to NZW and GA rabbits. In terms of breed-specific gene expression patterns, New Zealand White (NZW) rabbits displayed the highest expression levels of key genes related to energy metabolism (TBC1D1), appetite regulation (NPY, AGRP, POMC), nutrient transport (CAA), and G protein-coupled receptors (GPR) in both brain and liver tissues. Californian (CAL) rabbits exhibited superior gene expression of the ACC gene in brain tissue and GH, GHR, and IGF-1 genes in brain and meat tissues. Gabali (GAB) rabbits demonstrated the highest expression levels of TBC1D1, NPY, AGRP, GPR, and ACC genes in meat tissues. These breed-specific gene expression differences, combined with genetic evaluation efforts, have the potential to enhance reproductive and productive performance in rabbits, offering valuable insights for rabbit breeding programs and genetic selection.

Candidate genes associated with reproductive traits in rabbits

In the era of scientific advances and genetic progress, opportunities in the livestock sector are constantly growing. The application of molecular-based methods and approaches in farm animal breeding would accelerate and improve the expected results. The current work aims to comprehensively review the most important causative mutations in candidate genes that affect prolificacy traits in rabbits. Rabbits are a source of excellent-tasting meat that is high in protein and low in fat. Their early maturity and intensive growth are highly valued all over the world. However, improving reproductive traits and prolificacy in rabbits could be very tricky with traditional selection. Therefore, traditional breeding programs need new methods based on contemporary discoveries in molecular biology and genetics because of the complexity of the selection process. The study and implementation of genetic markers related to production in rabbits will help to create populations with specific productive traits that will produce the desired results in an extremely short time. Many studies worldwide showed an association between different genes and productive traits in rabbits. The study of these polymorphisms and their effects could be useful for molecular-oriented breeding, particularly marker-assisted selection programs in rabbit breeding.

Genetic analysis of post-weaning growth traits in a simple crossbreeding experiment between Gabali and Hyplus line rabbits

A simple crossbreeding experiment between Gabali (G) bucks and Hyplus (H) does was performed to estimate crossbreeding effects for post-weaning growth traits (body weight at 5 (BW5), 7 (BW7), 9 (BW9), 11 (BW11), and 13 (BW13) weeks of age and daily weight gains (DG) during (DG5-7), (DG7-9), (DG9-11), (DG11-13) and (DG5-13), weeks of age). Estimates of heritability were mostly low or moderate for growth traits and ranged from 0.12 to 0.35 for body weights and 0.05 to 0.66 for daily weight gains. The percentages of direct additive genetic effects on body weights favored (p ≤ 0.01) the Gabali breed by 22.1, 31.2, 32.8, 31.1, and 25.2% at 5, 7, 9, 11, and 13 weeks and by 35.4, 38.1, 21.9, 3.7, and 27% for DG5-7, DG7-9, DG9-11, DG11-13, and DG5-13, respectively. The percentages of maternal effects ranged from 22 to 34.8% for body weights and ranged from 4.7 to 43.4% for daily weight gains. The percentages of direct heterosis were significantly positive by 11, 19.1, 20.3, 19.7, and 16.5% for body weights at 5, 7, 9, 11, and 13 weeks and by 25.6, 27.2, 17.3, 3.5, and 17.9% for DG5-7, DG7-9, DG9-11, DG11-13, and DG5-13, respectively. These results suggest that the Gabali breed could be used as a sire-group and the Hyplus line could be used as a dam-group to create new high growth rabbit lines in Egypt.

Association of insulin receptor substrate 1 (IRS-1) gene polymorphism with growth and litter-related traits in NMER rabbits

This study investigated the associations between the c.189G > T polymorphism of the insulin receptor substrate-1 (IRS-1) gene and the growth and litter size-related traits in the Native rabbit in Middle Egypt (NMER). One hundred sixty-two NMER rabbits were genotyped by RFLP-PCR using Sau3AI restriction enzyme and the associations of the reported genotypes with body weights at 5th, 6th, 8th, 10th, and 12th week old, body gain, and daily gain plus, the litter size-related traits were determined. Additionally, the genotypic and allelic frequencies, the effective (Ne) and observed (NA) numbers of alleles, observed (Ho) and expected (He) heterozygosity, Hardy-Weinberg equilibrium (HWE), and the decrease in heterozygosity because of inbreeding (FIS) were calculated. Three genotypes; GG, GT, and TT with 0.65, 0.33, and 0.02 frequencies, respectively which fit HWE were reported. These genotypes displayed a marked low FIS value. Significant associations of the genotypes with the body weights, and gains, except at the 5th week old determined with superiority of the GT genotype compared with the other genotypes. All reported litter size-related traits significantly varied among different genotypes. In summary, the c.189G > T SNP of the IRS-1 gene is an effective genetic marker to improve growth performance and litter size traits of the NMER rabbits.

Influence of polymorphisms in candidate genes on carcass and meat quality traits in rabbits

Candidate gene is a powerful approach to study gene-trait association and offers valuable information for genetic improvement using marker-assisted selection. The current work aimed to study the polymorphisms of four single nucleotide polymorphism (SNPs) at located growth hormone (GH), insulin-like growth factor-II (IGF-II), fat mass and obesity-associated (FTO), and insulin receptor substrate-1 (IRS-1) genes, and their association with the carcass, and meat quality traits in rabbits. The SNPs were genotyped using RFLP-PCR in New Zealand White and local Baladi rabbits. The results revealed that the heterozygous genotype was the most frequent in all cases, except for the FTO SNP in LB rabbits. There was a significant effect for GH genotypes on meat lightness after slaughter and hind-part weight. While, IGF-II mutation significantly affected slaughter, hot carcass, commercial carcass, and hind-part weights. The FTO SNP was associated with cooking loss and intramuscular fat weight, and the IRS-1 SNP was significantly associated with drip loss and intramuscular fat. Specific-breed effects were obtained for IGF-II SNP on cooking loss, and for the intramuscular fat. Although the results suggested that these mutations are useful candidate genes for selection, more research for detecting more variants associated with carcass and meat quality traits in rabbits are recommended.

Association analysis of nucleotide polymorphisms in growth hormone (GH) and its receptor (GHR) with body weight in Californian rabbits

The objective of the present study was to evaluate the influence of the genotypes of two single nucleotide polymorphisms (SNPs) – c.78C>T located in the growth hormone gene (GH) and c.106C>G in the growth hormone receptor gene (GHR) on individual body weight (IBW) during the growing period at 35, 70 and 90 d of age on a total of 107 weaned Californian breed rabbits. The restriction fragments obtained revealed that 74.8% of the rabbits carrying c.78C>T SNP and 52.3% of the rabbits carrying c.106C>G SNP were heterozygous, which indicated a moderate level of genetic diversity in this Californian population. Association analysis based on a single-gene approach revealed that c.78C>T polymorphism in the GH gene had a significant effect (P<0.05) on the weight at 70 and 90 d of age. The highest IBW (2530.4±66.6 g) was observed in rabbits carrying the c.78C>T TT genotype, and detected individuals were significantly affected by the dominance effect. Significant differences were observed between individuals with homozygous c.106C>G CC genotype and those with heterozygous CG genotype. The highest IBW (2462.0±198.3 g) was observed in rabbits carrying the c.106C>G CC genotype and detected individuals were significantly affected by the additive effect. A total of nine combined genotypes of c.78C>T and c.106C>G SNPs was found in the study, of which only four major groups (CT/CC, CC/CG, CT/CG, and CT/GG) were concerned in the diplotype analysis. Significant differences were observed between individuals with CT/CC and CC/CG genotype combinations, and between those with the CC/CG and CT/GG diplotypes. However, the highest IBW at 90 d of age (2447.2±213.8 g) was observed in rabbits carrying the CT/CC genotype combinations. The highest coefficient of determination found for individual body weight at 90 d of age (R2=10.8%) indicated a high effect of genotype combinations. In conclusion, the results obtained suggested that c.78C>T of GH gene and c.106C>G of GHR gene could be useful candidate genes to improve growth performance in Californian rabbits with potential application in rabbit breeding programmes.