Association of the leptin gene with carcass characteristics in Nellore cattle

Genetic structure of some candidate genes of repeat breeder syndrome in Egyptian buffaloes

Background

This study aimed to explore the association between polymorphisms in three genes: leptin (LEP), leptin receptor (LEPR), and BMP4, and incidence of repeat breeding in Egyptian buffaloes.

Methods

DNA was extracted from 160 female buffaloes, involving 108 fertile and 52 repeat breeders. Genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Sequence analysis and alignment were performed by employing NCBI/BLAST/blastn suite, to identify SNPs among different patterns and alleles. We utilized PredictSNP software to predict the non-synonymous SNPs influences on protein function. Moreover, the conservation score of the amino acids within the target proteins was computed by ConSurf server.

Results

The genotyping results showed that LEP and BMP4 genes were monomorphic (CC, GG) in all tested fertile and repeat breeder buffaloes. Leptin gene sequencing showed a non-synonymous C73T SNP, replacing R to C at position 25 within the leptin polypeptide (position 4 in the mature form; R4C) which is a neutral mutation, not affecting function or structure of LEP protein. For LEPR, one synonymous SNP (T102C) and two non-synonymous SNPs (A106G and C146A), triggering V967A and G954C replacements, respectively in LEPR protein. Moreover, they are neutral mutations. Sequencing results of BMP4 showed HinfI restriction site indicate fixed GG genotype (CC genotype in the anti-sense strand) in all sequenced samples. No SNPs were observed within the amplified region.

Conclusion

Genotyping and sequencing results of the surveyed three genes revealed that there is no association between these genes mutations and the incidence of repeat breeding in Egyptian buffaloes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-022-00397-2.

Leptin gene contributes to beef marbling standard, meat brightness, meat firmness, and beef fat standard of the Kumamoto sub-breed of Japanese Brown cattle

The Kumamoto sub-breed of Japanese Brown cattle has unique characteristics, such as great growth rate, and their contribution as future breeding materials is expected. To develop a DNA marker for their breeding, we investigated the effects of Leptin gene, controlling energy homeostasis, on carcass traits of the Kumamoto sub-breed. Sequence comparison identified five single nucleotide polymorphisms (SNPs): four linked synonymous mutations and one nonsynonymous mutation. Statistical analysis revealed that c.239C > T (p.A80V) had significant effects on the traits related with quality grade: beef marbling standard (p = 0.0132), meat brightness (p = 0.0383), and meat firmness (p = 0.0115). The C allele showed favorable effects; these scores of the C/C cattle were significantly higher than those of the C/T cattle. On the other hand, the effect of c.399T > C was observed on meat firmness (p = 0.0172) and beef fat standards (BFS) (p = 0.0129). The C/C cattle showed higher values of these traits than the T/T cattle. Our data suggested that these SNPs in Leptin gene could be used as a DNA marker for breeding of the Kumamoto sub-breed.

Circulating leptin and its muscle gene expression in Nellore cattle with divergent feed efficiency

Background

Leptin has a strong relation to important traits in animal production, such as carcass composition, feed intake, and reproduction. It is mainly produced by adipose cells and acts predominantly in the hypothalamus. In this study, circulating leptin and its gene expression in muscle were evaluated in two groups of young Nellore bulls with divergent feed efficiency. Individual dry matter intake (DMI) and average daily gain (ADG) of 98 Nellore bulls were evaluated in feedlot for 70 d to determinate the residual feed intake (RFI) and select 20 animals for the high feed efficient (LRFI) and 20 for the low feed efficient (HRFI) groups. Blood samples were collected on d 56 and at slaughter (80 d) to determine circulating plasma leptin. Samples of Longissimus dorsi were taken at slaughter for leptin gene expression levels.

Results

DMI and RFI were different between groups and LRFI animals showed less back fat and rump fat thickness, as well as less pelvic and kidney fat weight. Circulating leptin increased over time in all animals. Plasma leptin was greater in LRFI on 56 d and at slaughter (P = 0.0049). Gene expression of leptin were greater in LRFI animals (P = 0.0022) in accordance with the plasma levels. The animals of the LRFI group were leaner, ate less, and had more circulating leptin and its gene expression.

Conclusion

These findings demonstrated that leptin plays its physiological role in young Nellore bulls, probably controlling food intake because feed efficient animals have more leptin and lower residual feed intake.

Comparative genome-wide methylation analysis of longissimus dorsi muscles between Japanese black (Wagyu) and Chinese Red Steppes cattle

DNA methylation is an important epigenetic mechanism involved in expression of genes in many biological processes including muscle growth and development. Its effects on economically important traits are evinced from reported significant differences in meat quality traits between Japanese black (Wagyu) and Chinese Red Steppes cattle, thus presenting a unique model for analyzing the effects of DNA methylation on these traits. In the present study, we performed whole genome DNA methylation analysis in the two breeds by whole genome bisulfite sequencing (WGBS). Overall, 23150 differentially methylated regions (DMRs) were identified which were located in 8596 genes enriched in 9922 GO terms, of which 1046 GO terms were significantly enriched (p<0.05) including lipid translocation (GO: 0034204) and lipid transport (GO: 0015914). KEGG analysis showed that the DMR related genes were distributed among 276 pathways. Correlation analysis found that 331 DMRs were negatively correlated with the expression levels of differentially expressed genes (DEGs) with 21 DMRs located in promoter regions. Our results identified novel candidate DMRs and DEGs correlated with meat quality traits, which will be valuable for future genomic and epigenomic studies of muscle development and for marker assisted selection of meat quality traits.

The novel SNPs of leptin gene and their associations with growth traits in Chinese Nanjiang Yellow goat

The leptin (LEP) gene encodes a protein that greatly affects the regulation of body weight, energy balance, and food intake in mammals. The objective of the present work was to identify genetic variants of the caprine LEP gene in 411 individuals from five Chinese goat breeds. Six novel single nucleotide polymorphisms (SNPs) (g.117T > C, g.1642G > A, g.2883G > A, g.3053T > C, g.3190G > A, and g.3314T > C) were detected using DNA sequencing. A chi-squared (χ(2)) test showed that all of the LEP SNPs were in Hardy-Weinberg equilibrium in the studied population (P > 0.05). Six common haplotypes were identified in the five goat populations, with frequencies ranging from 0.083 to 0.244. The r(2) linkage disequilibrium plot of the LEP SNPs indicated linkage disequilibrium only in the cultured breeds (NJ and JY). Statistical analysis revealed that all of the six SNPs of the LEP gene were associated with growth traits. The individuals with the GG genotype at g.1642G>A and g.3190G > A loci showed higher birth weight (2.38 ± 0.03, 2.43 ± 0.05) and weight at 2 months of age (10.59 ± 0.16, 10.71 ± 0.26) than the A-bearing genotypes (AA or GA, P < 0.05). Our findings indicate that polymorphisms of the caprine LEP gene might be important genetic factors influencing growth traits, and these genetic markers may be useful for future marker-assisted selection programs in goat breeding and production.