Background: The Meishan pig, native to China, is renowned for its superior reproductive capabilities, including a high ovulation rate, substantial uterine capacity, and an impressively high rate of embryo implantation. The endometrium plays a pivotal role in facilitating embryo implantation and sustaining pregnancy. It is regulated by ovarian hormones and uterine prostaglandins and undergoes a complex series of coordinated processes across the estrous cycle, including proliferation, differentiation, shedding, and regeneration. A detailed examination of the intricate sow endometrial gene expression patterns during this cycle can yield valuable insights into creating ideal conditions for successful embryo implantation and early embryonic development. To gain a comprehensive understanding of the Meishan pig endometrial biological functions across the estrous cycle, we specifically used uterine tissues in the proliferative and secretory phases for single-cell transcriptomic sequencing. Results: The comprehensive transcriptional profile of uterine cells was elucidated throughout the estrous cycle in Meishan pigs. We identified 7 distinct cell types within the primary cell categories, with 4 subpopulations specifically discerned among the endometrial epithelial cells. Considerable variability was observed in the types and quantities of epithelial cell subpopulations spanning the proliferative and secretory phases of the estrous cycle. Significantly, SOX9-expressing epithelial cells were characterised as potential endometrial epithelial stem cells in Meishan pigs. NURP1 and HES1were identified as potential marker genes for these stem cells. Pseudotime analysis indicated that these SOX9-expressing epithelial cells can differentiate into glandular epithelial (GE) or luminal epithelial (LE) cells. We also observed that SOX9-expressing epithelial cells may differentiate into ciliated epithelial (CE) cells. There was a marked increase in the number of GE and CE cells during the secretory phase compared to the proliferative phase. GE cells are vital for processes such as glycolysis, amino acid biosynthesis, and N-glycan biosynthesis, all of which are crucial for supplying essential nutrients required for embryo implantation and early stages of embryonic development. Conclusions: We reveal the integrated transcriptional profile of uterine cells in sexually mature Meishan pigs and delineate the gene expression patterns within the uterine horns throughout the estrous cycle. These findings provide potential new diagnostic indicators for determining the estrous cycle in sows.

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.

实验旨在基于前期从二花脸猪群体鉴别到的猪8号染色体上影响产仔数性状的数量性状基因座(Quantitative trait loci,QTL),通过增加群体的数量(二花脸猪和梅山猪)以及分子标记的密度(1个SNP/14.5 kb),利用单标记关联分析和合并群体的荟萃分析精细定位猪8号染色体影响产仔数的QTL,并挖掘QTL区域内候选基因.结果表明,基于二花脸猪群体的单标记关联分析,将影响经产胎次(2～7胎)产活仔数(Number born alive,NBA)的QTL分别精细定位至33818121～34324224 bp;基于梅山猪群体的单标记关联分析,将影响经产胎次(2～7胎)NBA的QTL分别精细定位至33884473～34156584 bp;基于二花脸猪群体和梅山猪群体荟萃分析,将影响经产胎次(2～7胎)NBA的QTL精细定位到33934355～34094188 bp;最后将关联分析和荟萃分析重叠,将影响猪经产胎次(2～7胎)NBA的QTL精细定位到33934355～34094188 bp;并且在QTL区间内发现UCHL1为关键位置功能候选基因.综上,本研究通过增加群体和标记密度成功在猪8号染色体上精细定位影响产仔数的QTL,并在QTL精细定位区间内发现UCHL1基因为影响猪产仔数的候选基因.

Chinese indigenous pig breeds in the Taihu Lake (TL) region of Eastern China are well documented by their exceptional prolificacy. There are seven breeds in this region including Meishan (MS), Erhualian (EHL), Jiaxing Black (JXB), Fengjing (FJ), Shawutou (SWT), Mi (MI), and Hongdenglong (HDL). At present, these breeds are facing a great threat of population decline, inbreeding depression and lineage admixture since Western commercial pigs have dominated in Chinese pig industry. To provide better conservation strategies and identify candidate genes under selection for these breeds, we explored genome-wide single nucleotide polymorphism (SNP) markers to uncover genetic variability and relatedness, population structure, historical admixture and genomic signature of selection of 440 pigs representing the most comprehensive lineages of these breeds in TL region in a context of 1228 pigs from 45 Eurasian breeds. We showed that these breeds were more closely related to each other as compared to other Eurasian breeds, defining one of the main ancestral lineages of Chinese indigenous pigs. These breeds can be divided into two subgroups, one including JXB and FJ, and the other comprising of EHL, MI, HDL, MS, and SWT. In addition, HDL was highly inbred whereas EHL and MS had more abundant genetic diversity owing to their multiple conservation populations. Moreover, we identified a list of candidate genes under selection for body size and prolificacy. Our results would benefit the conservation of these valuable breeds and improve our understanding of the genetic mechanisms of body size and fecundity in pigs.

Eastern and Southern Chinese pigs have been imported to Western countries to improve economic traits including fertility in Western pig breeds by intensive selecting Chinese advantage genes. It was reported that the selected Asian-derived non-synonymous mutations including rs339939442 (G > T) in the aryl hydrocarbon receptor (AHR) gene could increase litter size in multiple European commercial lines. The objective of this study is to identify whether rs339939442 in the AHR gene is polymorphic and has an influence on the litter size in 10 pig populations including five Chinese indigenous breeds, one cultivated breed, one lean-type breed, two North American lean-type breeds, and one European lean-type breed. We found that rs339939442 had polymorphism in all 10 populations, whereas rs339939442 was associated with litter size only in French Yorkshire (FRA-Y) and Chinese cultivated Suhuai (SH) pigs containing approximately 75% British Yorkshire pigs ancestry. Our results indicated that rs339939442 in the AHR gene was a potential marker to improve litter size in European commercial lines and the pigs containing ancestries of European commercial lines, whereas this locus maybe not a causal mutation affecting the litter size but only in linkage disequilibrium with the causal mutation for litter size.

The vertnin (VRTN) gene g.20311_20312ins291 was reported as an important variant related to the number of ribs (RIB), and the ins/ins genotype was advantageous for improving RIB of Western pigs. The purpose of this study was to determine whether the VRTN gene g.20311_20312ins291 influences RIB, carcass traits, and body size traits, including cannon bone circumference (CBC) in Chinese Suhuai pigs. We found that the VRTN gene g.20311_20312ins291 was polymorphic in Suhuai fattening pigs and gilts. The polymorphism of g.20311_20312ins291 was significantly associated with RIB and CDL in Suhuai fattening pigs (p < 0.01), whereas this variant had no influence on carcass weight (CWT). There was a tendency of association between this variant and carcass straight length (CSL) in Suhuai fattening pigs (p = 0.06). The polymorphism of g.20311_20312ins291 was also significantly associated with CBC in Suhuai gilts (p = 0.04). Furthermore, CBC was positively genetically correlated with body length (0.22, p < 0.01) and body weight (0.15, p < 0.01). Our results indicated that the VRTN gene g.20311_20312ins291 could be used as a potential marker for improving RIB, CDL, and CBC in Suhuai pigs.

[目的]本文旨在通过研究猪ESR、FSHβ和AHR基因多态性对二花脸群体产仔数的影响,鉴别出影响二花脸猪产仔数变异的关键基因。[方法]对303头二花脸猪进行ESR基因g.14418786、FSHβ基因g.30398474 3 0398475ins292（292 bp大片段插入）、AHR基因g.86550830位点分型（Sscrofa11.1）,用Excel 2003软件进行基因多态性分布的分析和卡方检验,并利用SAS 9.2软件混合模型对ESR、FSHβ、AHR基因及其合并基因型与产仔数进行关联性分析。[结果]ESR基因g.14418786、FSHβ基因g.30398474 3 0398475ins292以及AHR基因g.86550830位点在二花脸群体中均具有多态性,且3个基因的不同等位基因频率差异很大,ESR基因g.14418786位点A、B等位基因频率分别为0.173和0.827,FSHβ基因g.30398474 3 0398475ins292位点A、B等位基因频率分别为0.889和0.111,而AHR基因g.86550830位点G、T等位基因频率分别为0.889和0.111。ESR基因g.14418786位点的AA、AB和BB基因型频率分别为0.050、0.248和0.703,FSHβ基因g.30398474 3 0398475ins292的AA、AB和BB基因型频率分别为0.808、0.162和0.030,AHR基因g.86550830位点的GG、GT和TT基因型频率则为0.792、0.194和0.013。ESR基因g.14418786与FSHβ基因g.30398474 3 0398475ins292位点显著偏离哈代-温伯格平衡（P＜0.05）,而AHR基因g.86550830位点符合哈代-温伯格平衡（P＞0.05）。关联性分析未发现ESR、FSHβ、AHR基因以及3个基因的合并基因型显著影响二花脸猪的产仔数（P＞0.05）。[结论]本试验未能证明ESR、FSHβ和AHR基因是影响二花脸猪产仔数的主效基因,二花脸猪产仔数变异可能受其他基因影响。