Establishment and Characterization of SV40 T-Antigen Immortalized Porcine Muscle Satellite Cell.

Muscle satellite cells (MuSCs) are crucial for muscle development and regeneration. The primary pig MuSCs (pMuSCs) is an ideal in vitro cell model for studying the pig's muscle development and differentiation. However, the long-term in vitro culture of pMuSCs results in the gradual loss of their stemness, thereby limiting their application. To address this conundrum and maintain the normal function of pMuSCs during in vitro passaging, we generated an immortalized pMuSCs (SV40 T-pMuSCs) by stably expressing SV40 T-antigen (SV40 T) using a lentiviral-based vector system. The SV40 T-pMuSCs can be stably sub-cultured for over 40 generations in vitro. An evaluation of SV40 T-pMuSCs was conducted through immunofluorescence staining, quantitative real-time PCR, EdU assay, and SA-ß-gal activity. Their proliferation capacity was similar to that of primary pMuSCs at passage 1, and while their differentiation potential was slightly decreased. SiRNA-mediated interference of SV40 T-antigen expression restored the differentiation capability of SV40 T-pMuSCs. Taken together, our results provide a valuable tool for studying pig skeletal muscle development and differentiation.

Genome-wide association study identified five quantitative trait loci and two candidate genes for digestive traits in Suhuai pigs.

This work aimed to identify markers and candidate genes underlying porcine digestive traits. In total, 331 pigs were genotyped by 80 K Chip data or 50 K Chip data. For apparent neutral detergent fiber digestibility, a total of 19 and 21 candidate single nucleotide polymorphisms (SNP) were respectively identified using a genome-wide efficient mixed-model association algorithm and linkage-disequilibrium adjusted kinship. Among them, three quantitative trait locus (QTL) regions were identified. For apparent acid detergent fiber digestibility, a total of 16 and 17 SNPs were identified by these two methods, respectively. Of these, three QTL regions were also identified. Moreover, two candidate genes (MST1 and LATS1), which are functionally related to intestinal homeostasis and health, were detected near these significant SNPs. Taken together, our results could provide a basis for deeper research on digestive traits in pigs.

Unravelling novel and pleiotropic genes for cannon bone circumference and bone mineral density in Yorkshire pigs.

Leg weakness is a prevalent health condition in pig farms. The augmentation of cannon bone circumference and bone mineral density can effectively improve limb strength in pigs and alleviate leg weakness. This study measured forelimb cannon bone circumference (fCBC) and rear limb cannon bone circumference (rCBC) using an inelastic tapeline and rear limb metatarsal area bone mineral density (raBMD) using a dual-energy X-ray absorptiometry bone density scanner. The samples of Yorkshire castrated boars were genotyped using a 50K single-nucleotide polymorphism (SNP) array. The SNP-chip data were imputed to the level of whole-genome sequencing data (iWGS). This study used iWGS data to perform genome-wide association studies and identified novel significant SNPs associated with fCBC on SSC6, SSC12, and SSC13, rCBC on SSC12 and SSC14, and raBMD on SSC7. Based on the high phenotypic and genetic correlations between CBC and raBMD, multi-trait meta-analysis was performed to identify pleiotropic SNPs. A significant potential pleiotropic quantitative trait locus (QTL) regulating both CBC and raBMD was identified on SSC15. Bayes fine mapping was used to establish the confidence intervals for these novel QTLs with the most refined confidence interval narrowed down to 56 kb (15.11 to 15.17 Mb on SSC12 for fCBC). Furthermore, the confidence interval for the potential pleiotropic QTL on SSC15 in the meta-analysis was narrowed down to 7.45 kb (137.55 to137.56 Mb on SSC15). Based on the biological functions of genes, the following genes were identified as novel regulatory candidates for different phenotypes: DDX42, MYSM1, FTSJ3, and MECOM for fCBC; SMURF2, and STC1 for rCBC; RGMA for raBMD. Additionally, RAMP1, which was determined to be located 23.68 kb upstream of the confidence interval of the QTL on SSC15 in the meta-analysis, was identified as a potential pleiotropic candidate gene regulating both CBC and raBMD. These findings offered valuable insights for identifying pathogenic genes and elucidating the genetic mechanisms underlying CBC and BMD.

Leg weakness, a highly prevalent health condition in pig breeding farms, adversely affects the lifespan of breeding pigs. The augmentation of cannon bone circumference (CBC) and bone mineral density (BMD), which are objective measures of limb strength in pigs, can effectively alleviate leg weakness. To identify candidate genes regulating CBC and BMD in pigs, this study performed single-trait genome-wide association studies and multi-trait meta-analysis on all individuals with phenotype data. Additionally, the confidence intervals of quantitative trait locus (QTL) were determined using Bayesian methods. Four CBC-associated QTLs and one BMD-associated QTL were identified. Additionally, one potential pleiotropic QTL associated with both CBC and rear limb metatarsal area BMD (raBMD) was identified. This study demonstrated that DDX42, MYSM1, FTSJ3, and MECOM were candidate genes regulating forelimb CBC, while SMURF2 and STC1 were candidate genes regulating rear limb CBC. Additionally, RGMA was demonstrated to regulate raBMD, while RAMP1 was identified as a potential pleiotropic gene regulating both CBC and raBMD. The findings of this study provide valuable insights into the genetic mechanisms underlying limb growth and bone mineral accumulation.

Genome-wide association analysis revealed new QTL and candidate genes affecting the teat number in Dutch Large White pigs.

Teat number (TNUM) is an important reproductive trait of sows, which affects the weaning survival rate of piglets. In this study, 1166 Dutch Large White pigs with TNUM phenotype were used as the research object. These pigs were genotyped by 50K SNP chip and the chip data were further imputed to the resequencing level. The estimated heritabilities of left teat number (LTN), right teat number (RTN) and total teat number (TTN) were 0.21, 0.19 and 0.3, respectively. Based on chip data, significant SNPs for RTN on SSC2, SSC5, SSC9 and SSC13 were identified using genome-wide association analysis (GWAS). Significant SNPs for TTN were identified on SSC2, SSC5 and SSC7. Based on imputed data, the GWAS identified a significant SNP (rs329158522) for LTN on SSC17, two significant SNPs (rs342855242 and rs80813115) for RTN on SSC2 and SSC9, and two significant SNPs (rs327003548 and rs326943811) for TTN on SSC5 and SSC6. Among them, four novel QTL were discovered. The Bayesian fine-mapping method was used to fine map the QTL identified in the GWAS of the imputed data, and the confidence intervals of QTL affecting LTN (SSC17: 45.22-46.20 Mb), RTN (SSC9: 122.18-122.80 Mb) and TTN (SSC5: 14.01-15.91 Mb, SSC6: 120.06-121.25 Mb) were detected. A total of 52 candidate genes were obtained. Furthermore, we identified five candidate genes, WNT10B, AQP5, FMNL3, NUAK1 and CKAP4, for the first time, which involved in breast development and other related functions by gene annotation. Overall, this study provides new molecular markers for the breeding of teat number in pigs.

Single-Cell RNA Sequencing Reveals the Cellular Landscape of Longissimus Dorsi in a Newborn Suhuai Pig.

The introduction of single-cell RNA sequencing (scRNA-seq) technology has spurred additional advancements in analyzing the cellular composition of tissues. The longissimus dorsi (LD) in pigs serves as the primary skeletal muscle for studying meat quality in the pig industry. However, the single-cell profile of porcine LD is still in its infancy stage. In this study, we profiled the transcriptomes of 16,018 cells in the LD of a newborn Suhuai pig at single-cell resolution. Subsequently, we constructed a cellular atlas of the LD, identifying 11 distinct cell populations, including endothelial cells (24.39%), myotubes (18.82%), fibro-adipogenic progenitors (FAPs, 18.11%), satellite cells (16.74%), myoblasts (3.99%), myocytes (5.74%), Schwann cells (3.81%), smooth muscle cells (3.22%), dendritic cells (2.99%), pericytes (1.86%), and neutrophils (0.33%). CellChat was employed to deduce the cell-cell interactions by evaluating the gene expression of receptor-ligand pairs across different cell types. The results show that FAPs and pericytes are the primary signal contributors in LD. In addition, we delineated the developmental trajectory of myogenic cells and examined alterations in the expression of various marker genes and molecular events throughout various stages of differentiation. Moreover, we found that FAPs can be divided into three subclusters (NR2F2-FAPs, LPL-FAPs, and TNMD-FAPs) according to their biological functions, suggesting that the FAPs could be associated with the differentiation of tendon cell. Taken together, we constructed the cellular atlas and cell communication network in LD of a newborn Suhuai pig, and analyzed the developmental trajectory of myogenic cells and the heterogeneity of FAPs subpopulation cells. This enhances our comprehension of the molecular features involved in skeletal muscle development and the meat quality control in pigs.

Introgression of pigs in Taihu Lake region possibly contributed to the improvement of fertility in Danish Large White pigs.

BACKGROUND: Eurasian pigs have undergone lineage admixture throughout history. It has been confirmed that the genes of indigenous pig breeds in China have been introduced into Western commercial pigs, providing genetic materials for breeding Western pigs. Pigs in Taihu Lake region (TL), such as the Meishan pig and Erhualian pig, serve as typical representatives of indigenous pig breeds in China due to their high reproductive performances. These pigs have also been imported into European countries in 1970 and 1980 s. They have played a positive role in improving the reproductive performances in European commercial pigs such as French Large White pigs (FLW). However, it is currently unclear if the lineage of TL pigs have been introgressed into the Danish Large White pigs (DLW), which are also known for their high reproductive performances in European pigs. To systematically identify genomic regions in which TL pigs have introgressed into DLW pigs and their physiological functions, we collected the re-sequencing data from 304 Eurasian pigs, to identify shared haplotypes between DLW and TL pigs. RESULTS: The findings revealed the presence of introgressed genomic regions from TL pigs in the genome of DLW pigs indeed. The genes annotated within these regions were found to be mainly enriched in neurodevelopmental pathways. Furthermore, we found that the 115 kb region located in SSC16 exhibited highly shared haplotypes between TL and DLW pigs. The major haplotype of TL pigs in this region could significantly improve reproductive performances in various pig populations. Around this genomic region, NDUFS4 gene was highly expressed and showed differential expression in multiple reproductive tissues between extremely high and low farrowing Erhualian pigs. This suggested that NDUFS4 gene could be an important candidate causal gene responsible for affecting the reproductive performances of DLW pigs. CONCLUSIONS: Our study has furthered our knowledge of the pattern of introgression from TL into DLW pigs and the potential effects on the fertility of DLW pigs.

Effects of Varying Levels of Wheat Bran Dietary Fiber on Growth Performance, Fiber Digestibility and Gut Microbiota in Erhualian and Large White Pigs.

To evaluate the tolerance of a high-fiber diet in Erhualian pigs (Er-HL), the present investigation systematically investigated the ramifications of varying wheat bran fiber levels, specified as total dietary fiber (TDF) values of 14.07%, 16.32%, 17.99%, and 18.85%, on growth performance, fiber digestibility and gut microbiota in Er-HL, large Large White pigs (L-LW, the same physiological stage as the Er-HL) and small Large White pigs (S-LW, the same body weight as the Er-HL). Our results revealed that fiber levels exerted no discernable impact on growth performance (average daily feed intake (ADFI), and average daily gain (ADG)) of Er-HL (p > 0.05). Conversely, L-LW exhibited a decrease in ADFI and ADG with increasing fiber levels (p < 0.05). Notably, the apparent total tract digestibility (ATTD) of various fiber components, including neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose, TDF and insoluble dietary fiber (IDF), in Er-HL were significantly higher than those in S-LW and L-LW irrespective of diets (p < 0.05). The ATTD of cellulose and hemicellulose in Er-HL significantly decreased with increasing fiber levels (p < 0.05), yet remained statistically indifferent when comparing the 7%-wheat-bran-replaced diet (7% WRB, TDF 16.32%) to the basal diet (TDF 14.07%) (p > 0.05). The cecal microbiota of Er-HL had higher richness estimators (Chao1 and ACE) than those of S-LW and L-LW irrespective of diets (p < 0.01). Breed serves as a pivotal determinant in shaping swine gut microbiota. Thirteen genera were selected as the key bacteria related to high fiber digestibility of Er-HL. Further functional examination of these key genera elucidated an enrichment of pathways pertinent to carbohydrate metabolism in Er-HL samples compared with S-LW and L-LW samples. In summary, Er-HL exhibited high-fiber tolerance both in terms of growth performance and fiber digestibility compared with Large White pigs. Specifically, the ATTD of NDF, ADF, hemicellulose, IDF and TDF were significantly higher in Er-HL compared with L-LW and S-LW, irrespective of diets. Fiber level exerted no discernable impact on growth performance (ADFI, ADG) and the ATTD of fiber (NDF, ADF, IDF and TDF) in Er-HL. The optimum fiber level of the Er-HL was identified as 7% WRB (TDF 16.32%). Thirteen genera were ascertained to significantly contribute to high fiber digestibility of Er-HL, correlating with an enhancement of carbohydrate metabolism pathways.

The selected genes NR6A1, RSAD2-CMPK2, and COL3A1 contribute to body size variation in Meishan pigs through different patterns.

The high-fertility Meishan pig is currently categorized into medium sized (MMS) and small sized (SMS) based on body size. To identify causal genes responsible for the variation in body size within the two categories, we sequenced individuals representing the entire consanguinity of the existing Meishan pig. This enabled us to conduct genome selective signal analysis. Our findings revealed the genomes of MMS and SMS are stratified, with selective sweep regions formed by differential genomic intervals between the two categories enriched in multiple pig body size related quantitative trait loci (QTLs). Furthermore, the missense mutation c.575T > C of candidate causal gene NR6A1, accounting for the variation in lumbar vertebrae number in pigs, was positively selected in MMS only, leading to an increase in body length of MMS at 6 months of age. To precisely identify causal genes accounting for body size variation through multi-omics, we collected femoral cartilage and liver transcription data from MMS and SMS respectively, and re-sequencing data from pig breeds exhibiting varying body sizes. We found that two selected regions where the RSAD2-CMPK2 and COL3A1 genes are located, respectively, showed different haplotypes in pig breeds of varying body size, and was associated with body or carcass length in hybridized Suhuai pig. Additionally, the above three hub genes, were significantly greater expressed in SMS femoral cartilage and liver tissues compared to MMS. These three genes could strengthen the pathways related to bone resorption and metabolism in SMS, potentially hindering bone and skeletal development and resulting in a smaller body size in SMS. These findings provide valuable insights into the genetic mechanism of body size variation in Meishan pig population.

The existing well-known Meishan pig population has been categorized into medium sized (MMS), and small sized (SMS) based on body size, which is a result of artificial selection. MMS is relatively large in all body size traits, but otherwise have highly similar appearance and performance traits. To effectively identify the candidate selected genes that contribute to the body size variation in Meishan pigs, this study collected individuals from all lineages of MMS and SMS for re-sequencing. Additionally, femoral cartilage and liver transcription data were collected from MMS and SMS, respectively, and re-sequencing data from pig breeds exhibiting varying body sizes were also analyzed. Through multi-omics analysis, it was discovered that the missense mutation c.575T > C in the candidate causal gene NR6A1 was positively selected in MMS only, leading to an increase in the body length of MMS at 6 months of age. Moreover, the selected genes RSAD2-CMPK2 and COL3A1 were found to be significantly greater expressed in SMS femoral cartilage and liver tissues compared with MMS. These genes could potentially strengthen bone resorption and metabolism-related pathways in SMS. These findings contribute to a better understanding of the genetic mechanisms underlying body size variation in Meishan pigs and Chinese indigenous pigs.

Low dose of zearalenone inhibited the proliferation of porcine prospermatogonia and transformed the physiology through cytokine-cytokine receptor interaction.

Zearalenone (ZEA) is a prevalent mycotoxin functions as an endocrine disrupter to the reproductive systems of farm animals, especially in pigs. To evaluate the effect and the underlying molecular changes that occurred when the porcine germline stem cells were exposed to ZEA, prospermatogonia (ProSGs) were enriched and treated with a gradient concentration (0-10 µM) of ZEA for 2-8 days. Our results showed that the ZEA treatment inhibited the proliferation of ProSGs in a dose-dependent manner with a critical concentration at 1 µM. Transcriptome analysis revealed that the differentially expressed genes mainly concentrated on the molecular function of positive regulation of response to stimulus, and the most enriching pathway is cytokine-cytokine receptor interaction. ZEA exposure decreased a buck of cytokine/chemokine expression involved in the inflammatory response and stem cells maintenance/self-renewal, moreover, some energy expenditure and anti-apoptosis genes were also down-regulated, while the up-regulated genes were mainly connected with the innate immunity. These data demonstrate that ZEA induces multiply cellular damage and may eventually do harm to the health and fertility of animals.

Advances in omics research on peanut response to biotic stresses.

Peanut growth, development, and eventual production are constrained by biotic and abiotic stresses resulting in serious economic losses. To understand the response and tolerance mechanism of peanut to biotic and abiotic stresses, high-throughput Omics approaches have been applied in peanut research. Integrated Omics approaches are essential for elucidating the temporal and spatial changes that occur in peanut facing different stresses. The integration of functional genomics with other Omics highlights the relationships between peanut genomes and phenotypes under specific stress conditions. In this review, we focus on research on peanut biotic stresses. Here we review the primary types of biotic stresses that threaten sustainable peanut production, the multi-Omics technologies for peanut research and breeding, and the recent advances in various peanut Omics under biotic stresses, including genomics, transcriptomics, proteomics, metabolomics, miRNAomics, epigenomics and phenomics, for identification of biotic stress-related genes, proteins, metabolites and their networks as well as the development of potential traits. We also discuss the challenges, opportunities, and future directions for peanut Omics under biotic stresses, aiming sustainable food production. The Omics knowledge is instrumental for improving peanut tolerance to cope with various biotic stresses and for meeting the food demands of the exponentially growing global population.

Genome-wide association study reveals new QTL and functional candidate genes for the number of ribs and carcass length in pigs.

The number of ribs (NR) and carcass length (CL) are important economic traits in pig breeding programs. Pigs with a higher NR and longer CL produce greater pork yields. In the present study, Suhuai pigs with NR and CL phenotypes were genotyped using the Neogen® GGP Porcine 80 K SNP array to identify the QTL affecting NR and CL and dissect the candidate genes for the two traits. The SNP-chip data was imputed to the whole-genome sequence (iWGS) to increase the probability of identifying causal variants. Through genome-wide association studies (GWAS) based on both chip and iWGS data, significant SNPs were detected on Sus scrofa chromosome (SSC) 1, SSC4 and SSC7 for NR and on SSC5, SSC16 and SSC17 for CL. Moreover, two SNPs (H3GA0022644 and WU_10.2_7_103460706) on SSC7 detected in chip-based GWAS were significantly associated with both NR and CL. Through Bayes fine mapping, one reported QTL for NR on SSC7 and two reported QTL for CL on SSC17 were verified, and two new QTL (SSC1: 14.05-15.84 Mb and SSC4: 64.83-66.59 Mb) affecting NR and two new QTL (SSC5: 58.31-59.84 Mb and SSC16: 22.98-23.43 Mb) affecting CL were detected. According to the biological functions of genes, MTHFD1L on SSC1 and SULF1 on SSC4 are novel functional candidate genes for NR, and EMP1 on SSC5 and EGFLAM on SSC16 are novel functional candidate genes for CL. Overall, our findings provide a basis for identifying new causal genes and mutations affecting NR and CL.

Chromatin Accessibility and Transcriptional Landscape during Inhibition of Salmonella enterica by Lactobacillus reuteri in IPEC-J2 Cells.

Lactobacillus reuteri is a probiotic with bacteriostatic effects, which can effectively inhibit the activity of pathogens. However, the molecular mechanism underlying the inhibition of pathogens by L. reuteri in intestinal cells remains unclear. Using the porcine intestinal cell line IPEC-J2 as a model, we combined RNA-seq and ATAC-seq methods to delineate the porcine genome-wide changes in biological processes and chromatin accessibility in IPEC-J2 cells stimulated by Salmonella enterica BNCC186354, as well as L. reuteri ATCC 53608. Overall, we found that many porcine transcripts were altered after S. enterica BNCC186354 treatment, while L. reuteri ATCC 53608 treatment partially restored this alteration, such as salmonella infection and PI3K/AKT and MAPK pathways. Combined analysis of these two datasets revealed that 26 genes with similar trends overlapped between gene expression and chromatin accessibility. In addition, we identified potential host functional transcription factors (TFs), such as GATA1, TAL1, TBP, RUNX1, Gmeb1, Gfi1b, RARA, and RXRG, in IPEC-J2 cells that might play a critical role and are targeted by L. reuteri ATCC 53608. Moreover, we verified that PI3K/AKT, MAPK, and apoptosis pathways are potentially regulated by S. enterica BNCC186354 but restored by L. reuteri ATCC 53608. The PI3K/AKT pathway was activated by L. reuteri ATCC 53608, thereby potentially inhibiting S. enterica BNCC186354 infection. In conclusion, our data provide new insights into the expression pattern of functional genes and the epigenetic alterations in IPEC-J2 cells underlying the bacteriostatic action of L. reuteri ATCC 53608.

Combining genome-wide association study based on low-coverage whole genome sequencing and transcriptome analysis to reveal the key candidate genes affecting meat color in pigs.

Meat color is an attractive trait that influences consumers' purchase decisions at the point of sale. To decipher the genetic basis of meat color traits, we performed a genome-wide association study based on low-coverage whole-genome sequencing. In total, 669 (Pietrain × Duroc) × (Landrace × Yorkshire) pigs were genotyped using low-coverage whole-genome sequencing. Single nucleotide polymorphism (SNP) calling and genotype imputation were performed using the BaseVar + STITCH channel. Six individuals with an average depth of 12.05× whole-genome resequencing were randomly selected to assess the accuracy of imputation. Heritability evaluation and genome-wide association study for meat color traits were conducted. Functional enrichment analysis of the candidate genes from genome-wide association study and integration analysis with our previous transcriptome data were conducted. The imputation accuracy parameters, allele frequency R2 , concordance rate, and dosage R2 were 0.959, 0.952, and 0.933, respectively. The heritability values of a*45 min , b*45 min , L*45 min , C*, and H0 were 0.19, 0.11, 0.06, 0.16, and 0.26, respectively. In total, 3884 significant SNPs and 15 QTL, corresponding to 382 genes, were associated with meat color traits. Functional enrichment analysis revealed that 10 genes were the potential candidates for regulating meat color. Moreover, integration analysis revealed that DMRT2, EFNA5, FGF10, and COL11A2 were the most promising candidates affecting meat color. In summary, this study provides new insights into the molecular basis of meat color traits, and provides a new theoretical basis for the molecular breeding of meat color traits in pigs.

Three-dimensional porous high boron-nitrogen-doped carbon for the ultrasensitive electrochemical detection of trace heavy metals in food samples.

Exposure to even trace amounts of Cd(II) and Pb(II) in food can have serious effects on the human body. Therefore, the development of novel electrochemical sensors that can accurately detect the different toxicity levels of heavy metal ions in food is of great significance. Based on the principle of green chemistry, we propose a new type of boron and nitrogen co-doped carbon (BCN) material derived from a metal-organic framework material and study its synthesis, characterization, and heavy-metal ion detection ability. Under the optimum conditions, the BCN-modified glassy carbon electrode was studied using square-wave anodic stripping voltammetry, which showed good electrochemical responses to Cd(II) and Pb(II), with sensitivities as low as 0.459 and 0.509 µA/µM cm2, respectively. The sensor was successfully used to detect Cd(II) and Pb(II) in Beta vulgaris var. cicla L samples, which is consistent with the results obtained using inductively coupled plasma-mass spectrometry. It also has a strong selectivity for complex samples. This study provides a novel approach for the detection of heavy metal ions in food and greatly expands the application of heteroatom-doped metal-free carbon materials in detection platforms.

A plant-unique protein BLISTER coordinates with core retromer to modulate endosomal sorting of plasma membrane and vacuolar proteins.

The retromer is a heteromeric protein complex that localizes to endosomal membranes and drives the formation of endosomal tubules that recycle membrane protein cargoes. In plants, the retromer plays essential and canonical functions in regulating the transport of vacuolar storage proteins and the recycle of endocytosed plasma membrane proteins (PM); however, the mechanisms underlying the regulation of assembly, protein stability, and membrane recruitment of the plant retromer complex remain to be elucidated. In this study, we identify a plant-unique endosomal regulator termed BLISTER (BLI), which colocalizes and associates with the retromer complex by interacting with the retromer core subunits VPS35 and VPS29. Depletion of BLI perturbs the assembly and membrane recruitment of the retromer core VPS26-VPS35-VPS29 trimer. Consequently, depletion of BLI disrupts retromer-regulated endosomal trafficking function, including transport of soluble vacuolar proteins and recycling of endocytosed PIN-FORMED (PIN) proteins from the endosomes back to the PM. Moreover, genetic analysis in Arabidopsis thaliana mutants reveals BLI and core retromer interact genetically in the regulation of endosomal trafficking. Taken together, we identified BLI as a plant-specific endosomal regulator, which functions in retromer pathway to modulate the recycling of endocytosed PM proteins and the trafficking of soluble vacuolar cargoes.

SUMO E3 ligase AtMMS21-dependent SUMOylation of AUXIN/INDOLE-3-ACETIC ACID 17 regulates auxin signaling.

Changes in plant auxin levels can be perceived and converted into cellular responses by auxin signal transduction. AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins are auxin transcriptional inhibitors that play important roles in regulating auxin signal transduction. The stability of Aux/IAA proteins is important for transcription initiation and downstream auxin-related gene expression. Here, we report that the Aux/IAA protein IAA17 interacts with the small ubiquitin-related modifier (SUMO) E3 ligase METHYL METHANESULFONATE-SENSITIVE 21 (AtMMS21) in Arabidopsis (Arabidopsis thaliana). AtMMS21 regulated the SUMOylation of IAA17 at the K41 site. Notably, root length was suppressed in plants overexpressing IAA17, whereas the roots of K41-mutated IAA17 transgenic plants were not significantly different from wild-type roots. Biochemical data indicated that K41-mutated IAA17 or IAA17 in the AtMMS21 knockout mutant was more likely to be degraded compared with nonmutated IAA17 in wild-type plants. In conclusion, our data revealed a role for SUMOylation in the maintenance of IAA17 protein stability, which contributes to improving our understanding of the mechanisms of auxin signaling.

Increased Proportion of Fiber-Degrading Microbes and Enhanced Cecum Development Jointly Promote Host To Digest Appropriate High-Fiber Diets.

Previous study found that appropriate high-fiber diet (containing 19.10% total dietary fiber [TDF], treatment II) did not reduce apparent fiber digestibility of Chinese Suhuai finishing pigs and increased the yield of short-chain fatty acids (SCFAs), but too high-fiber diet (containing 24.11% TDF, treatment IV) significantly reduced apparent fiber digestibility compared with normal diet (containing 16.70% TDF, control group). However, characteristics of microbiota at the species level and histological structure in pigs with the ability to digest appropriate high-fiber diets were still unknown. This study conducted comparative analysis of cecal physiology and microbial populations colonizing cecal mucosa. The results showed intestinal development indexes including cecum length, densities of cecal goblet cells, and renewal of cecal epithelial cells in treatment II and IV had better performance than those in the control. Paludibacter jiangxiensis, Coprobacter fastidiosus, Bacteroides coprocola CAG:162, Bacteroides barnesiae, and Parabacteroides merdae enriched in treatment II expressed large number of glycoside hydrolase (GH)-encoding genes and had the largest number of GH families. In addition, pathogenic bacteria (Shigella sonnei, Mannheimia haemolytica, and Helicobacter felis) were enriched in treatment IV. Correlation analysis revealed that the intestinal development index positively correlated with the relative abundance of cecal mucosal microbiota and the amount of digested fiber. These results indicated that increased proportions of fiber-degrading microbes and enhanced intestinal development jointly promote the host to digest an appropriate high-fiber diet. However, although too-high fiber levels in diet could maintain the adaptive development of cecal epithelium, the proportions of pathogenic bacteria increased, which might lead to a decrease of fiber digestion in pigs. IMPORTANCE Although studies about the effects of dietary fiber on fiber digestion and intestinal microbiota of pigs were widely in progress, few studies have been conducted on the dynamic response of intestinal microbiota to dietary fiber levels, and the characteristics of intestinal microbiota and intestinal epithelial development adapted to high-fiber diet s were still unclear. Appropriate high fiber promoted the thickness of large intestine wall, increased the density of cecal goblet cells, and promoted the renewal of cecal epithelial cells. In addition, appropriate high fiber improves the microbial abundance with fiber-digesting potential. However, excessive dietary fiber caused an increase in the abundance of pathogenic bacteria. These results indicated that an increased proportion of fiber-degrading microbes and enhanced intestinal development jointly promote host to digest appropriate high-fiber diets. However, although too-high fiber levels in diet could maintain the adaptive development of cecal epithelium, the proportions of pathogenic bacteria increased, which might lead to a decrease of fiber digestion in pigs. Our data provided a theoretical basis for rational and efficient utilization of unconventional feed resources in pig production.

Genome-wide association study and genomic prediction for intramuscular fat content in Suhuai pigs using imputed whole-genome sequencing data.

Integrating the single-nucleotide polymorphisms (SNPs) significantly affecting target traits from imputed whole-genome sequencing (iWGS) data into the genomic prediction (GP) model is an economic, efficient, and feasible strategy to improve prediction accuracy. The objective was to dissect the genetic architecture of intramuscular fat content (IFC) by genome wide association studies (GWAS) and to investigate the accuracy of GP based on pedigree-based BLUP (PBLUP) model, genomic best linear unbiased prediction (GBLUP) models and Bayesian mixture (BayesMix) models under different strategies. A total of 482 Suhuai pigs were genotyped using an 80 K SNP chip. Furthermore, 30 key samples were selected for resequencing and were used as a reference panel to impute the 80 K chip data to the WGS dataset. The 80 K data and iWGS data were used to perform GWAS and test GP accuracies under different scenarios. GWAS results revealed that there were four major regions affecting IFC. Two important functional candidate genes were found in the two most significant regions, including protein kinase C epsilon (PRKCE) and myosin light chain 2 (MYL2). The results of the predictions showed that the PBLUP model had the lowest reliability (0.096 ± 0.032). The reliability (0.229 ± 0.035) was improved by replacing pedigree information with 80 K chip data. Compared with using 80 K SNPs alone, pruning iWGS SNPs with the R-squared cutoff of linkage disequilibrium (0.55) led to a slight improvement (0.006), adding significant iWGS SNPs led to an improvement of reliability by 0.050 when using a one-component GBLUP, a further increase of 0.033 when using a two-component GBLUP model. For BayesMix models, compared with using 80 K SNPs alone, adding additional significant iWGS SNPs into one- or two-component BayesMix models led to improvements of reliabilities for IFC by 0.040 and 0.089, respectively. Our results may facilitate further identification of causal genes for IFC and may be beneficial for the improvement of IFC in pig breeding programs.