BMC Genomics最新文献

Background: The WD40 proteins constitute a large regulatory family involved in a wide range of biological processes and stress responses. Advances in sequencing technologies have facilitated the identification of numerous WD40 proteins with diverse functions in many plant species. However, research on tree species remains limited. Populus yunnanensis is an economically and ecologically important tree species that faces salt stress in certain habitats. Therefore, studying WD40 proteins in P. yunnanensis is of particular significance for understanding its salt tolerance mechanisms.

Results: A variable number of WD40 proteins were identified across six poplar species, generally correlating with their genome sizes. In P. yunnanensis, 258 PyWD40s were identified, exhibiting considerable variation in amino acid number, and other physicochemical properties, suggesting potential functional diversity. The chromosomal distribution of these genes was uneven, indicative of gene family formation and replication events. High collinearity among members and low Ka/Ks values suggested strong sequence conservation and purifying selection. Notable similarities were also observed between the WD40 proteins of P. yunnanensis and A. thaliana. Structural analysis revealed that representative PyWD40s from the eight subfamilies could be modeled into three-dimensional structures rich in β-sheets. Variations in conserved domains and exon numbers contributed to sequence and functional divergence. Expression profiling under salt stress indicated that most PyWD40s were upregulated under both short-term and prolonged stress conditions, a finding validated by qRT-PCR for 14 selected genes. Protein-protein interaction network analysis demonstrated that PyWD40s interact with proteins involved in process such as signal transduction, and their co-expression under salt stress suggests a coordinated role in facilitating the stress response.

Conclusions: In summary, this study provides comprehensive insights into the roles of PyWD40 proteins in the salt stress response of P. yunnanensis. These findings contribute significantly to the understanding of stress tolerance mechanisms in this species and offer a valuable resource for future functional studies.

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.