BMC Genomics最新文献

Background: The rising demand for high-quality pork among consumers has driven interest in genetic improvement strategies. Crossbreeding is well known to influence carcass performance and meat quality; however, the molecular mechanisms underlying these effects are still poorly understood. In this study, the F1 generation of the Songlei Crossbred Pig (SL) was developed through crossing the Songliao Black Pig (male) (SS) and the Leixiang Pig (female) (LL). We integrated the transcriptomes and metabolomes of the longissimus dorsi (LD) muscle of SS and SL under identical conditions to identify key mechanisms regulating the quality of crossbred meat.

Results: Compared with those of SS, the slaughter weight, carcass weight, and dressing percentage of SL were significantly lower, but the backfat thickness was greater; however, meat quality traits, including intramuscular fat (IMF), colour, and pH_24h, were significantly greater, and the pressure loss and shear force were lower in SL. Transcriptome and metabolome analyses revealed a total of 616 differentially expressed genes (DEGs) and 681 significantly differentially expressed metabolites (DEMs) in the LD muscles of SS and SL. Protein-protein interaction (PPI) network analysis revealed key FASN, ADIPOQ, IGF1R and SREBF1 genes that regulate fat metabolism. Furthermore, multiomics joint analysis identified 99 common KEGG pathways, among which the first four pathways were related to fat metabolism, including the AMPK signalling pathway, PPAR signalling pathway, and the regulation of lipolysis in adipocytes and insulin resistance. Gene and metabolite association analysis revealed that the expression of alpha-dimorphecolic acid metabolites was strongly correlated with that of the adipose metabolism-related genes IRS1 and ANGPTL4.

Conclusions: The meat quality of SL was better than that of their male parents, but not the carcass traits were not. Additionally, several critical genes and pathways related to lipid metabolism were identified. These findings provide new insights into how meat quality can be improved by hybridization.

Background: Runs of homozygosity (ROH) occurrence in animal genomes may result from a high level of relatedness within the population or from positive selection. ROH investigation enables the assessment of the degree of individual autozygosity at the genome-wide level, providing insights into genetic background and development history of a population. In this context, the main objectives of this study were to: 1) develop a method based on permutation tests for detecting single nucleotide polymorphisms (SNP) significantly included in ROH genomic regions of Italian Holstein bulls; 2) identify candidate genes close to the SNP frequently positioned within ROH; 3) investigate the effects of genetic selection on ROH distribution and ROH islands; and 4) assess potential associations between ROH and economically important traits in Italian Holstein cattle. We used high-density SNP data of 3,009 Italian Holstein bulls for identifying ROH regions. The threshold for declaring a SNP as significantly included in a ROH region was obtained by randomly shuffling SNP within animals for each chromosome. The chromosome-wide threshold was the 99th percentile of the distribution of the number of times a SNP was included in a ROH segment (SNP_ROH) for a specific chromosome. To investigate the influence of ROH on relevant traits, a genome-wide association study testing the presence/absence of specific ROH and a mixed model to quantify the effect of ROH-based inbreeding were carried out.

Results: The top 24,905 significant SNP were distributed on ten chromosomes, in genomic regions known to harbor genes involved in milk traits. One region on BTA20 exhibited an interesting pattern of SNP_ROH occurrence across animals grouped according to the year of birth, underlining an intense selection pressure in this genomic region. The analyses on the relationship between ROH and pseudo-phenotypes for various traits showed a significant influence of inbreeding on milk and protein yields, and a fertility aggregate index, with the presence/absence of 14 ROH regions having a significant effect on different traits (milk, fat, and protein yields; fat percentage; and somatic cell score).

Conclusions: The application of permutation to a high-density (HD) SNP chip data enabled the identification of genomic regions with high levels of homozygosity in Italian Holstein bulls and revealed associations between ROH occurrence and economically important traits in the studied population.

Background: Class Ⅲ peroxidases (PODs) are widely involved in multiple physiological processes, including lignin biosynthesis and stress responses. However, there are no reports on the identification and function of POD family in Hippophae rhamnoides subsp. sinensis Rousi.

Results: In this study, we identified 71 non-redundant HrPODs. Based on phylogenetic analysis, these genes were classified into 7 subgroups. Then, we analyzed the conserved domains of HrPODs proteins and found that they contain highly conserved domain. We also investigated their expression patterns in three developmental stages of sea buckthorn fruit, and the results showed that most of them were highly expressed in early stage. The GO and KEGG functional enrichment analysis showed that they widely involved in oxidative stress response and phenylpropanoid biosynthesis, respectively. According to the Pearson correlation analysis of HrPODs expression with lignin content and peroxidase activity, we further screened five HrPODs that may be involved in fruit texture quality by regulating lignin biosynthesis during fruit development. Sea buckthorn is usually distributed in arid areas with higher salt and alkaline content, and our findings showed that the different degrees of drought, salt, or alkali treatment can also affect the expression of these genes and lignin content during the germination stage. These results will help us better investigate the role of HrPODs in lignin biosynthesis to provide certain theoretical foundation in ideal berry breeding and broad spectrum stress resistance in cultivated sea buckthorn.

Conclusion: In this study, the findings not only provide us with a comprehensive identification and analysis of HrPODs from a bioinformatics perspective, but also preliminary intimation that the POD family may be tightly associated with fruit texture quality and abiotic stress response. These results will help us better investigate the role of HrPODs in lingin biosynthesis, enrich the theoretical research on the formation of sea buckthorn texture quality and understand the roles of HrPODs in abiotic stress resistance in cultivated sea buckthorn.