Chinese Indigenous Breeds Research Articles

Integrated analysis of muscle lncRNA and mRNA of Chinese indigenous breed Ningxiang pig in four developmental stages.

Meat and its derivatives serve as crucial sources of protein, vitamins, minerals, and other essential nutrients for humans. Pork stands as China's primary animal-derived food product consumed widely across diverse dietary structures; evaluating intramuscular fat content becomes pivotal in assessing its quality standards. Nonetheless, the intricate molecular mechanisms governing intramuscular fat deposition remain elusive. Our study utilized sequencing technology to scrutinize longitudinal development stages within Ningxiang pig's longest dorsal muscles aiming to unravel these underlying mechanisms. In three distinct comparisons (30d vs. 90d, 90d vs. 150d and 150d vs. 210d) there were 578, 1,000 and 3,238 differentially expressed mRNA, along with 16, 158 and 85 lncRNAs were identified. STEM analysis unveiled six enriched model profiles for lncRNAs while seven such profiles emerged for mRNAs; notably, multiple shared model profiles existed between both RNA types. Enriched analysis highlighted numerous genes from mRNA profile8 and lncRNA profile7 significantly associated with pathways linked to fat deposition. Weight Gene Co-Expression Network Analysis (WGCNA) revealed that differential expression modules (DMEs) & differential expression lncRNAs primarily clustered within cyan, dark slate blue and pale turquoise modules. Furthermore, target genes PKD2 (MSTRG21592.MTRSG8859 and MTRSG18175), COL5A1 (MTRSG9969 and MTRSG180) and SOX13 (MTRSG21592 and MTRSG9088) as core components all intricately tied into processes related to fat deposition. This study lays the groundwork for deeper exploration into the molecular mechanisms underlying LDM fat deposition traits, and it also presents candidate genes for future molecular marker-assisted breeding.

Chromosome-level genome assembly of Huai pig (Sus scrofa)

Although advances in long-read sequencing technology and genome assembly techniques have facilitated the study of genomes, little is known about the genomes of unique Chinese indigenous breeds, including the Huai pig. Huai pig is an ancient domestic pig breed and is well-documented for its redder meat color and high forage tolerance compared to European domestic pigs. In the present study, we sequenced and assembled the Huai pig genome using PacBio, Hi-C, and Illumina sequencing technologies. The final highly contiguous chromosome-level Huai pig genome spans 2.53 Gb with a scaffold N50 of 138.92 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score for the assembled genome was 95.33%. Remarkably, 23,389 protein-coding genes were annotated in the Huai-pig genome, along with 45.87% repetitive sequences. Overall, this study provided new foundational resources for future genetic research on Chinese domestic pigs.

A novel codominant plumage color pattern of white breast patches in WugangTong geese was controlled by EDNRB2

Two basic plumage color patterns are observed in adult geese: solid grey (G) or colorless white (W). However, a Chinese indigenous breed, the Wugangtong goose (WGT), continues to be subject to selective breeding efforts as it displays segregation of plumage colors, including G, W, and a novel color pattern designated Wb (G with white breast circles). The underlying genetic mechanisms responsible for the Wb phenotype are yet to be determined. The current study employed the population differentiation index (FST) to analyze 90 geese exhibiting diverse plumage colors, identifying the fifth intron of EDNRB2 as a particularly noteworthy region with the highest FST values. Sanger sequencing of the region surrounding the EDNRB2 gene identified a 14-bp insertion within exon 3 as the causal mutation. The heterozygosity of this 14-bp insertion and wild-type alleles was completely associated with the Wb phenotype, thereby substantiating the codominant nature of the G and W phenotypes. An inter-species corroborated this finding cross between the graylag (no 14-bp insertion) and the swan goose (homozygous for the 14-bp insertion) breeds, as hybrids from this cross exhibited the Wb phenotype. Transcriptomes from white breast patches and gray dorsal skins of 4 Wb geese were compared. A significant downregulation of genes involved in melanin synthesis and melanocyte development was observed, including EDRNB2 and MLANA. The downregulation of MLANA indicated that the mutated EDNRB2 resulted in melanocyte loss in specific body regions, as MLANA is a marker gene for melanocytes. The findings were corroborated by melanin staining using the Mansson-Fontana method, which revealed no melanin particles deposited in the white breast patches. In summary, the gray plumage color was codominant to the white color in WGT geese, and plumage color variations were controlled by EDNRB2. The findings of our study offer valuable and practical guidance for the purification of plumage colors among WGT, whether through traditional phenotype selection or molecular breeding methods.

Population structure and breed identification of Chinese indigenous sheep breeds using whole genome SNPs and InDels

BackgroundAccurate breed identification is essential for the conservation and sustainable use of indigenous farm animal genetic resources. In this study, we evaluated the phylogenetic relationships and genomic breed compositions of 13 sheep breeds using SNP and InDel data from whole genome sequencing. The breeds included 11 Chinese indigenous and 2 foreign commercial breeds. We compared different strategies for breed identification with respect to different marker types, i.e. SNPs, InDels, and a combination of SNPs and InDels (named SIs), different breed-informative marker detection methods, and different machine learning classification methods.ResultsUsing WGS-based SNPs and InDels, we revealed the phylogenetic relationships between 11 Chinese indigenous and two foreign sheep breeds and quantified their purities through estimated genomic breed compositions. We found that the optimal strategy for identifying these breeds was the combination of DFI_union for breed-informative marker detection, which integrated the methods of Delta, Pairwise Wright's FST, and Informativeness for Assignment (namely DFI) by merging the breed-informative markers derived from the three methods, and KSR for breed assignment, which integrated the methods of K-Nearest Neighbor, Support Vector Machine, and Random Forest (namely KSR) by intersecting their results. Using SI markers improved the identification accuracy compared to using SNPs or InDels alone. We achieved accuracies over 97.5% when using at least the 1000 most breed-informative (MBI) SI markers and even 100% when using 5000 SI markers.ConclusionsOur results provide not only an important foundation for conservation of these Chinese local sheep breeds, but also general approaches for breed identification of indigenous farm animal breeds.

Characterization of Flavor Compounds in Chinese Indigenous Sheep Breeds Using Gas Chromatography-Ion Mobility Spectrometry and Chemometrics.

This study analyzed the flavor compounds in the meat of four indigenous breeds of Chinese sheep through the use of gas chromatography-ion mobility spectrometry (GC-IMS). GC-IMS provided information on the characteristics and strength of 71 volatile flavor compounds (monomers and dimers), with aldehydes, alcohols and ketones being the most abundant in all types of sheep meat. The compounds with higher intensity peaks in the sheep meat were aldehydes (n-nonanal, octanal, heptanal, 3-methylbutanal, and hexanal), alcohols (1-octen-3-ol, hexanol, and pentanol), ketones (3-hydroxy-2-butanon, 2-butanone, and 2-propanone), esters (methyl benzoate), and thiazole (trimethylthiazole). The volatile flavor components in the meat of the different breeds of sheep obtained via GC-IMS were further differentiated using principal component analysis. In addition, orthogonal partial least squares discriminant analysis (OPLS-DA) and variable importance on projection (VIP) were used to determine the characteristic flavor compounds in the meats of different breeds of sheep, and 21 differentially volatile components were screened out based on having a VIP above 1. These results indicate that GC-IMS combined with multivariate analysis is a convenient and powerful method for characterizing and discriminating sheep meat.

Flaxseed promotes productive performance through regulating gut microbiome in ducks

BackgroundFlaxseed has been widely used in animal diets to increase the omega-3 polyunsaturated fatty acid content in animal products and promote overall animal health, but little known about its effects on the productive performance and the mictobita of gut of laying duck.Methods and resultsJinding duck, a Chinese indigenous breed, was used in the study. The corn-soybean basal diet supplemented with 0, 2%, 3% 4% and 5% flaxseed were provided to Control, 2% Fla, 3% Fla, 4% Fla and 5% Fla groups for 53 days, respectively. Compared with Control group, groups fed with flaxseed diets showed higher egg production, egg mass, ovary weight and more preovulatory follicles. The Docosahexaenoic Acid content of egg was extremely significantly elevated by flaxseed diets (P < 0.01), and the albumen height and haugh unit were elevated, especially in 4% Fla and/or 5% Fla group (P < 0.05). Groups 4% Fla and 5% Fla had highest ileal villus height, jejunal and ileal crypt depth. Moreover, Flaxseed diets significantly increased the levels of IgG and IgM in all Fla groups (P < 0.01), while increased IgA levels except for in 3% Fla group (P < 0.05). The results of 16s rDNA sequencing showed that flaxseed diet altered the microbial composition of gut and reduced the diversity and evenness of gut microbial communities except for 5% Fla. The correlation analysis identified Blautia, Butyricicoccus and Subdoligranulum positively associated with egg production. Genera Fourinierella, Fusobacterium and Intestinimonas positively associated with ovary weight, haught unit and album height. And Mucispirillum positively associated with haugh unit and album height.ConclusionThis study has suggested that flaxseed play a positive role in productive performance, the overall or intestinal health of laying ducks.

Exercise Volume Provides New Insight into the Effects of Housing Systems on Chicken Body Conformation, Carcass Traits, Meat Quality, and Serum Biochemical Parameters.

This study aims to investigate the dynamic changes in daily step counts under different housing systems and further explore the effects of housing system on the body conformation, carcass traits, meat quality, and serum biochemical parameters of a Chinese indigenous chicken breed. At 60 d of age, 300 Jiuyuan Black male chickens with similar body weights in each housing system were further raised until the age of 150 d. At 90, 120, and 150 d of age, in both cage-reared and free-range systems, the top 20 chickens with the highest step counts measured using pedometers and the bottom 20 chickens with the lowest step counts were designated as the cage high-steps group (CHS), the cage low-steps group (CLS), the free-range high-steps group (FHS), and the free-range low-steps group (FLS), respectively. The results show that, at any age stage, the average daily steps (ADS) and total steps (TS) of the FHS group are significantly higher than the other three groups (p < 0.05). The TS of almost all groups showed an overall downward trend as the age increased. Increased exercise volume results in reduced shank length (90 d), breast width (90 d), and keel length (150 d) (p < 0.05). Only birds at 90 d of age from the FHS and FLS groups exhibited lower live body weight, carcass weight, half-eviscerated weight, eviscerated weight, breast muscle weight, leg muscle weight, and percentage of eviscerated weight than the CLS group (p < 0.05). Birds from the FHS group showed the highest heart weight values but the lowest abdominal fat weight values among these four groups (p < 0.05). Both the breast and leg muscle samples from the FHS group displayed higher dry matter and shear force than those from the CHS and CLS groups (p < 0.05). The FHS group displayed the lowest intramuscular fat among the four groups (p < 0.05). The creatine kinase (CK) and lactate dehydrogenase (LDH) levels in chickens of all age stages were almost observed to rise with increased physical activity. In conclusion, free-range chickens with more exercise volume exhibited an elevated heart weight and reduced abdominal fat but showed negative effects on some body measurements and carcass traits. These results can provide a theoretical basis for the selection of different housing systems for Chinese indigenous chickens.

Integrated analyses of the intestinal microbiome and transcriptome in Ningxiang piglets

Ningxiang (NX) pig has been recognized as one of the most famous Chinese indigenous breeds due to its characteristics in stress resistance. However, intestinal microbial feature and gene profiling in NX piglets have not been studied. Here, we compared the intestinal microbiome and transcriptome between NX and Duroc × Landrace × Large white (DLY) piglets and found the high enrichment of several colonic Bacteroides, Prevotella and Clostridium species in NX piglets. Further functional analyses revealed their predominant function in methane, glycolysis and gluconeogenesis metabolism. Our mRNA-sequencing data unraveled the distinct colonic gene expression between these two breeds. In particular, we showed that the improved intestinal function in NX piglets may be determined by enhanced intestinal barrier gene expression and varied immune gene expression through modulating the composition of the gut microbes. Together, our study revealed the intestinal characteristics of NX piglets, providing their potential application in improving breeding strategies and developing dietary interventions.

Genetic diversity, demographic history, and selective signatures of Silkie chicken

BackgroundSilkie is a traditional Chinese chicken breed characterized by its unique combination of specialized morphological traits. While previous studies have focused on the genetic basis of these traits, the overall genomic characteristics of the Silkie breed remain largely unexplored. In this study, we employed whole genome resequencing data to examine the genetic diversity, selective signals and demographic history of the Silkie breed through comparative analyses with seven other Chinese indigenous breeds (IDGBs), a commercial breed, and the wild ancestor Red Jungle Fowl.ResultsIn total, 20.8 million high-quality single nucleotide polymorphisms and 86 large structural variations were obtained. We discovered that Silkie exhibits a relatively high level of inbreeding and is genetically distinct from other IDGBs. Furthermore, our analysis indicated that Silkie has experienced a stronger historical population bottleneck and has a smaller effective population size compared with other IDGBs. We identified 45 putatively selected genes that are enriched in the melanogenesis pathway, which probably is related to the feather color. Among these genes, LMBR1 and PDSS2 have been previously associated with the extra toe and the hookless feathers, respectively. Six of the selected genes (KITLG, GSK3B, SOBP, CTBP1, ELMO2, SNRPN) are known to be associated with neurodevelopment and mental diseases in human, and are possibly related to the distinct behavior of Silkie. We further identified structural variants in Silkie and found previously reported variants linked to hyperpigmentation (END3), muff and beard (HOXB8), and Rose-comb phenotype (MNR2). Additionally, we found a 0.61 Mb inversion overlapping with the GMDS gene, which was previously linked to neurodevelopmental defects in zebrafish and humans. This may also be related to the behavior distinctiveness of Silkie.ConclusionsOur study revealed that Silkie is genetically distinct and relatively highly inbred compared to other IDGB chicken populations, possibly attributed to more prolong population bottlenecks and selective breeding practice. These results enhance our understanding of how domestication and selective breeding have shaped the genome of Silkie. These findings contribute to the broader field of domestication and avian genomics, and have implications for the future conservation and breeding efforts.

Sheep litter size heredity basis using genome-wide selective analysis.

Sheep are important herbivorous domestic animal globally, and the Chinese indigenous sheep breed has a multitude of economically significant variations due to the diverse geographical and ecological conditions. In particular, certain native breeds exhibit a visible high litter size phenotype due to the selection pressure of natural and artificial for thousands of years, offering an ideal animal model for investigating sheep's fecundity. In this study, selective signal analysis was performed on public whole-genome sequencing data from 60 sheep across eight breeds to identify candidate genes related to litter size. Results revealed that a total of 34,065,017 single-nucleotide polymorphisms (SNPs) were identified from all sheep, and 65 candidate genes (CDGs) were pinpointed from the top 1% of interacted windows and SNPs between the pairwise fixation index (FST, >0.149543) and cross-population extended haplotype homozygosity (XP-EHH, >0.701551). A total of 41 CDGs (e.g. VRTN, EYA2 and MCPH1) were annotated to 576 GO terms, of which seven terms were directly linked to follicular and embryonic development (e.g. TBXT, BMPR1B, and BMP2). In addition, 73 KEGG pathways were enriched by 21 CDGs (e.g. ENTPD5, ABCD4 and RXFP2), mainly related to Hippo (TCF4, BMPR1B and BMP2), TGF-β (BMPR1B and BMP2), PI3K-Akt (ITGB4, IL4R and PPP2R5A) and Jak-STAT signalling pathways (IL20RA and IL4R). Notably, a series of CDGs was under strong selection in sheep with high litter size traits. These findings result could improve the comprehension of the genetic underpinnings of sheep litter size. Furthermore, it provides valuable CDGS for future molecular breeding.

Whole-genome selection signature differences between Chaohu and Ji'an red ducks.

Assessing the genetic structure of local varieties and understanding their genetic data are crucial for effective management and preservation. However, the genetic differences among local breeds require further explanation. To enhance our understanding of their population structure and genetic diversity, we conducted a genome-wide comparative study of Chaohu and Ji'an Red ducks using genome sequence and restriction site-associated DNA sequencing technology. Our analysis revealed a distinct genetic distinction between the two breeds, leading to divided groups. The phylogenetic tree for Chaohu duck displayed two branches, potentially indicating minimal impact from artificial selection. Additionally, our ROH (runs of homozygosity) analysis revealed that Chaohu ducks had a lower average inbreeding coefficient than Ji'an Red ducks. We identified several genomic regions with high genetic similarity in these indigenous duck breeds. By conducting a selective sweep analysis, we identified 574 candidate genes associated with muscle growth (BMP2, ITGA8, MYLK, and PTCH1), fat deposits (ELOVL1 and HACD2), and pigmentation (ASIP and LOC101797494). These results offer valuable insights for the further enhancement and conservation of Chinese indigenous duck breeds.

Integrated analysis of muscle transcriptome, miRNA, and proteome of Chinese indigenous breed Ningxiang pig in three developmental stages.

The Ningxiang pig, a distinguished local breed in China, is recognized for its good meat quality traits. This study examines the proteomics of Ningxiang pigs at three developmental stages and delves into the upstream transcriptomics of these proteomics. Such an analysis facilitates a deeper understanding of the molecular interplay between proteins and transcriptomes in the Ningxiang pig muscle, influencing muscle growth and development. In this research, we analyzed the muscles of Ningxiang pigs at three developmental stages: 30days in weaned piglets, 90days in nursery pigs, and 210days in late fattening pigs. There a total of 16 differentially co-expressed miRNAs (ssc-miRNA-1, ssc-miRNA-378, ssc-miRNA-143, ssc-miRNA-30e, etc.), 74 differentially co-expressed mRNA (PLIN3, CPT2, IGF2 and HSP90AB1, etc.) have been identified in the three stages. 572 differentially abundant proteins (DAPs) (APOC3, NDUFA2, HSPD1, ATP5E, PDHA1, etc.) were readily identified by comparing different time periods. According to the KEGG enrich pathway results that DAPs most enriched in growth and development pathways, immune mechanism pathways and maintaining functions of physical. Through short time-series expression miner (STEM) association analysis, a total of 571 negative miRNA-mRNA interaction pairs and 2 negative miRNA-mRNA-protein (Chr05_11955-Pig.17268.1-ATP5F1B, ssc-miR-194a-3p-Pig.15802.1-ACY1) interaction pairs were found. Our study provides a theoretical basis on molecular mechanism for the study of IMF deposition, muscle growth and immunity in Ningxiang pig breed.

Transcriptome analysis of adipose tissue and muscle of Laiwu and Duroc pigs

Fat content is an important trait in pig production. Adipose tissue and muscle are important sites for fat deposition and affect production efficiency and quality. To regulate the fat content in these tissues, we need to understand the mechanisms behind fat deposition. Laiwu pigs, a Chinese indigenous breed, have significantly higher fat content in both adipose tissue and muscle than commercial breeds such as Duroc. In this study, we analyzed the transcriptomes in adipose tissue and muscle of 21-d-old Laiwu and Duroc piglets. Results showed that there were 828 and 671 differentially expressed genes (DEG) in subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT), respectively. Functional enrichment analysis showed that these DEG were enriched in metabolic pathways, especially carbohydrate and lipid metabolism. Additionally, in the longissimus muscle (LM) and psoas muscle (PM), 312 and 335 DEG were identified, demonstrating enrichment in the cell cycle and metabolic pathways. The protein–protein interaction (PPI) networks of these DEG were analyzed and potential hub genes were identified, such as FBP1 and SCD in adipose tissues and RRM2 and GADL1 in muscles. Meanwhile, results showed that there were common DEG between adipose tissue and muscle, such as LDHB, THRSP, and DGAT2. These findings showed that there are significant differences in the transcriptomes of the adipose tissue and muscle between Laiwu and Duroc piglets (P < 0.05), especially in metabolic patterns. This insight serves to advance our comprehensive understanding of metabolic regulation in these tissues and provide targets for fat content regulation.

Study on the origin of the Baise horse based on whole-genome resequencing.

The Baise horse, an indigenous horse breed mainly distributed in the Baise region of Guangxi province in southwest China, has a long history as draft animal. However, there is a lack of research regarding the origin and ancestral composition of the Baise horse. In this study, whole-genome resequencing data from 236 horses of seven Chinese indigenous horse breeds, five foreign horse breeds, and four Przewalski's horses were used to investigate the relationships between the Baise horse and other horse breeds. The results showed that foreign horse breeds had no significant impact on the formation of the Baise horse. The two southwestern horse populations, the Debao pony and the Jinjiang horse, exhibit the closest genetic affinity with the Baise horse. This is consistent with their adjacent geographical distribution. Analysis of the migration route revealed a gene flow from the Chakouyi horse into the Baise horse. In summary, our results confirm that the formation of the Baise horse did not involve participation from foreign breeds. Geographical distance emerges as a crucial factor in determining the genetic relationships with the Baise horse. Gene flows of indigenous horse breeds along ancient routes of trade activities had played a role in the formation of the Baise horse.

Whole-genome resequencing of Chinese indigenous sheep provides insight into the genetic basis underlying climate adaptation

BackgroundChinese indigenous sheep are valuable resources with unique features and characteristics. They are distributed across regions with different climates in mainland China; however, few reports have analyzed the environmental adaptability of sheep based on their genome. We examined the variants and signatures of selection involved in adaptation to extreme humidity, altitude, and temperature conditions in 173 sheep genomes from 41 phenotypically and geographically representative Chinese indigenous sheep breeds to characterize the genetic basis underlying environmental adaptation in these populations.ResultsBased on the analysis of population structure, we inferred that Chinese indigenous sheep are divided into four groups: Kazakh (KAZ), Mongolian (MON), Tibetan (TIB), and Yunnan (YUN). We also detected a set of candidate genes that are relevant to adaptation to extreme environmental conditions, such as drought-prone regions (TBXT, TG, and HOXA1), high-altitude regions (DYSF, EPAS1, JAZF1, PDGFD, and NF1) and warm-temperature regions (TSHR, ABCD4, and TEX11). Among all these candidate genes, eight ABCD4, CNTN4, DOCK10, LOC105608545, LOC121816479, SEM3A, SVIL, and TSHR overlap between extreme environmental conditions. The TSHR gene shows a strong signature for positive selection in the warm-temperature group and harbors a single nucleotide polymorphism (SNP) missense mutation located between positions 90,600,001 and 90,650,001 on chromosome 7, which leads to a change in the protein structure of TSHR and influences its stability.ConclusionsAnalysis of the signatures of selection uncovered genes that are likely related to environmental adaptation and a SNP missense mutation in the TSHR gene that affects the protein structure and stability. It also provides information on the evolution of the phylogeographic structure of Chinese indigenous sheep populations. These results provide important genetic resources for future breeding studies and new perspectives on how animals can adapt to climate change.

Genome-wide association studies of egg production traits by whole genome sequencing of Laiwu Black chicken

Compared to high-yield commercial laying hens, Chinese indigenous chicken breeds have poor egg laying capacity due to the lack of intensive selection. However, as these breeds have not undergone systematic selection, it is possible that there is a greater abundance of genetic variations related to egg laying traits. In this study, we assessed 5 egg number (EN) traits at different stages of the egg-laying period: EN1 (from the first egg to 23 wk), EN2 (from 23 to 35 wk), EN3 (from 35 to 48 wk), EN4 (from the first egg to 35 wk), and EN5 (from the first egg to 48 wk). To investigate the molecular mechanisms underlying egg number traits in a Chinese local chicken breed, we conducted a genome-wide association study (GWAS) using data from whole-genome sequencing (WGS) of 399 Laiwu Black chickens. We obtained a total of 3.01 Tb of raw data with an average depth of 7.07 × per individual. A total of 86 genome-wide suggestive or significant single-nucleotide polymorphisms (SNP) contained within a set of 45 corresponding candidate genes were identified and found to be associated with stages EN1-EN5. The genes vitellogenin 2 (VTG2), lipase maturation factor 1 (LMF1), calcium voltage-gated channel auxiliary subunit alpha2delta 3 (CACNA2D3), poly(A) binding protein cytoplasmic 1 (PABPC1), programmed cell death 11 (PDCD11) and family with sequence similarity 213 member A (FAM213A) can be considered as the candidate genes associated with egg number traits, due to their reported association with animal reproduction traits. Noteworthy, results suggests that VTG2 and PDCD11 are not only involved in the regulation of EN3, but also in the regulation of EN5, implies that VTG2 and PDCD11 have a significant influence on egg production traits. Our study offers valuable genomic insights into the molecular genetic mechanisms that govern egg number traits in a Chinese indigenous egg-laying chicken breed. These findings have the potential to enhance the egg-laying performance of chickens.

Geographic distribution of a missense mutation in the KRT38 gene in Chinese indigenous cattle breeds

Context China has a vast area across many temperature zones and a variety of cattle breeds. These cattle resources are ideal models to research their adaptability to the environment. The KRT38 gene is an acidic protein, and its coding product can be used as a component of hair production. Aims The objective of this study was to investigate the diversity of the KRT38 gene in Chinese local cattle and the association of different genotypes with mean temperature, relative humidity and temperature humidity index. Methods A missense mutation g.41650738 A &gt; G in the KRT38 gene was screened from the database of bovine genomic variation (BGVD) and was genotyped in a total of 246 samples from 15 local cattle breeds in China by polymerase chain reaction amplification and sequencing. Finally, the correlation between the locus and the three climatic factors was analysed. Key results We successfully obtained the frequency of this single-nucelotide polymorphism in three groups of cattle in northern, central and southern China. The frequency of allele A gradually declined from north to south, whereas the frequency of allele G showed the opposite trend with a clear geographic distribution. Conclusions Our results indicate that KRT38 variation in Chinese indigenous cattle might be linked to heat tolerance. Implications Our analysis may assist in determining the importance of the variation as a genetic signal for heat tolerance in cattle reproduction and genetics.

Comparative Analysis of Intestinal Inflammation and Microbiota Dysbiosis of LPS-Challenged Piglets between Different Breeds.

Post-weaning diarrhea is common in piglets, causing huge economic losses worldwide. Associations between LPS challenge, intestinal inflammation, and microbiota have been reported in Duroc × Landrace × Yorkshire (DLY) crossbred pigs. However, the effects of LPS challenge in other breeds remain unclear. In the current study, we performed a comprehensive comparative analysis of the effects of LPS challenge on jejunal mucosal morphology, jejunal microbial composition, and serum indexes in two pig breeds: DLY and Heigai, an indigenous Chinese breed. The results showed that LPS caused considerable damage to the mucosal morphology, enhanced serum levels of inflammatory cytokines and the intestinal permeability index, and lowered the antioxidant capacity index. LPS challenge also changed the microbial composition and structure of the jejunum, significantly increased the abundances of Escherichia-Shigella in DLY pigs, and decreased those of Gemella and Saccharimonadales in Heigai pigs. Furthermore, LPS challenge triggered functional changes in energy metabolism and activities related to the stress response in the jejunal bacterial community, alleviating the inflammatory response in Heigai pigs. This study also revealed that Heigai pigs had a weaker immune response to LPS challenge than DLY pigs, and identified several genera related to the breed-specific phenotypes of Heigai pigs, including Gemella, Saccharimonadales, Clostridia_UCG_014, Terrisporobacter, and Dielma. Our collective findings uncovered differences between Heigai and DLY pigs in intestinal inflammation and microbiota dysbiosis induced by LPS challenge, providing a theoretical basis for unraveling the mechanism of intestinal inflammation in swine and proposing microbial candidates involved in the resistance to diarrhea in piglets.

Transcriptome and Weighted Gene Co-Expression Network Analysis for Feather Follicle Density in a Chinese Indigenous Breed.

Feather follicle density plays an important role in appealing to consumers' first impressions when making purchasing decisions. However, the molecular network that contributes to this trait remains largely unknown. The aim of this study was to perform transcriptome and weighted gene co-expression network analyses to determine the candidate genes relating to feather follicle density in Wannan male chickens. In total, five hundred one-day-old Wannan male chickens were kept in a conventional cage system. Feather follicle density was recorded for each bird at 12 weeks of age. At 12 weeks, fifteen skin tissue samples were selected for weighted gene co-expression network analysis, of which six skin tissue samples (three birds in the H group and three birds in the L group) were selected for transcriptome analysis. The results showed that, in total, 95 DEGs were identified, and 56 genes were upregulated and 39 genes were downregulated in the high-feather-follicle-density group when compared with the low-feather-follicle-density group. Thirteen co-expression gene modules were identified. The red module was highly significantly negatively correlated with feather follicle density (p < 0.01), with a significant negative correlation coefficient of -0.72. In total, 103 hub genes from the red module were screened. Upon comparing the 103 hub genes with differentially expressed genes (DEGs), it was observed that 13 genes were common to both sets, including MELK, GTSE1, CDK1, HMMR, and CENPE. From the red module, FOXM1, GTSE1, MELK, CDK1, ECT2, and NEK2 were selected as the most important genes. These genes were enriched in the DNA binding pathway, the heterocyclic compound binding pathway, the cell cycle pathway, and the oocyte meiosis pathway. This study suggests that FOXM1, GTSE1, MELK, CDK1, ECT2, and NEK2 may be involved in regulating the development of feather follicle density in Wannan male chickens. The results of this study reveal the genetic structure and molecular regulatory network of feather follicle density in Wannan male chickens, and provide a basis for further elucidating the genetic regulatory mechanism and identifying molecular markers with breeding value.

Integrated 4D Analysis of Intramuscular Fat Deposition: Quantitative Proteomic and Transcriptomic Studies in Wannanhua Pig Longissimus Dorsi Muscle.

Wannanhua (WH) is a pig breed indigenous to Anhui Province, China. This breed has a high intramuscular fat (IMF) content, making it an ideal model for investigating lipid deposition mechanisms in pigs. IMF content is one of the main indicators of meat quality in pigs and is regulated by multiple genes and metabolic pathways. Building upon our prior transcriptomic investigation, the present study focused on the longissimus dorsi muscle tissue of Wannanhua (WH) pigs in the rapid fat-deposition stages (120 and 240 days of age). Employing 4D label-free quantitative proteomic analysis, we identified 106 differentially expressed proteins (DEPs). Parallel reaction monitoring (PRM) technology was used to verify the DEPs, and the results showed that the 4D label-free results were reliable and valid. Functional enrichment and protein-protein interaction analyses showed that the DEPs were mainly involved in the skeletal-muscle-associated structural proteins, mitochondria, energy metabolism, and fatty acid metabolism. By integrating transcriptomic data, we identified seven candidate genes including ACADL, ACADM, ANKRD2, MYOZ2, TNNI1, UCHL1, and ART3 that play a regulatory role in fat deposition and muscle development. These findings establish a theoretical foundation for future analyses of lipid deposition traits, contributing to potential enhancements in pig meat quality during breeding and advancing the selection process for Chinese indigenous breeds.