Ketosis is a common metabolic disorder in the early lactation of dairy cows. It is typically diagnosed by measuring the concentration of β-hydroxybutyrate (BHB) in the blood. This study aimed to estimate the genetic parameters of blood BHB and conducted a genome-wide association study (GWAS) based on the estimated breeding value. Phenotypic data were collected from December 2019 to August 2023, comprising blood BHB concentrations in 45,617 Holstein cows during the three weeks post-calving across seven dairy farms. Genotypic data were obtained using the Neogen Geneseek Genomic Profiler (GGP) Bovine 100 K SNP Chip and GGP Bovine SNP50 v3 (Illumina Inc., San Diego, CA, USA) for genotyping. The estimated heritability and repeatability values for blood BHB levels were 0.167 and 0.175, respectively. The GWAS result detected a total of ten genome-wide significant associations with blood BHB. Significant SNPs were distributed in Bos taurus autosomes (BTA) 2, 6, 9, 11, 13, and 23, with 48 annotated candidate genes. These potential genes included those associated with insulin regulation, such as INSIG2, and those linked to fatty acid metabolism, such as HADHB, HADHA, and PANK2. Enrichment analysis of the candidate genes for blood BHB revealed the molecular functions and biological processes involved in fatty acid and lipid metabolism in dairy cattle. The identification of novel genomic regions in this study contributes to the characterization of key genes and pathways that elucidate susceptibility to ketosis in dairy cattle.

Gestation length (GL) is a critical indicator of reproductive performance in sows and is closely associated with other reproductive traits, such as total number born (TNB) and number born alive (NBA). Despite its importance, the genetic mechanisms underlying GL and its impact on reproductive traits remain poorly understood. In this study, we investigated the relationship between GL and reproductive traits using 7013 farrowing records and conducted an imputed whole-genome sequence-based genome-wide association study (GWAS) for GL in first-parity sows, involving 3005 French Large White sows. Our findings revealed that the heritability of GL ranged from 0.22 to 0.26. Both excessively short and long GLs were associated with negative impacts on TNB, NBA, and other reproductive traits. A total of 64 SNPs exceeded the significance threshold, leading to the identification of two novel quantitative trait loci (QTLs) on chromosome 5 (QTL-1: 15.29–15.39 Mb and QTL-2: 12.86–12.94 Mb) and three promising candidate genes: TROAP, RFX4, and ADCY6. Gene ontology and KEGG pathway enrichment analyses revealed that these candidate genes are enriched in key biological processes, including ovarian steroidogenesis, the GnRH signaling pathway, and the regulation of cAMP biosynthesis, all of which are crucial for gestation and pregnancy maintenance. These findings improve our understanding of the genetic architecture of GL in sows and offer valuable genetic markers for enhancing reproductive efficiency in breeding programs.

Intestinal probiotics significantly regulate the growth performance of their host, with their composition being influenced by various factors. While many studies have explored how gut microbiota composition affects growth traits such as body weight and BMI, the research on probiotics influenced by host genetic factors, and their subsequent impact on host growth performance, remains limited. To address this research gap, we collected fecal and tissue samples, as well as phenotypic data, from 193 Yunong black pigs at 280 days of age. We then sequenced and genotyped all 193 subjects using the 50K SNP BeadChip, yielding a comprehensive dataset for genetic and microbiome analyses. We then employed microbiome-wide association studies (MWAS), a meta-analysis, and microbiome-wide genetic association studies (MGWASs) to examine the relationship between host genetics, gut microbiota, and growth performance. Four key microbial taxa, namely Coprococcus, Blautia, Ruminococcaceae, and RF16, were identified as being significantly associated with body weight and BMI. The MGWAS analysis revealed that both Coprococcus and Ruminococcaceae were significantly associated with host genomic variations. A total of four important single nucleotide polymorphisms (SNPs) were mapped to two chromosomal regions, corresponding to three candidate genes. Among them, the candidate genes INPP4B, SCOC, and PABPC4L were identified as being related to the abundance of key microbes. This study provides new insights into the joint contributions of host genetics and probiotics to host growth traits, offering theoretical guidance and data support for the development of efficient and targeted breeding strategies.

Resilience usually refers to the ability of an animal to be minimally affected by disturbance or to quickly return to its pre-disturbance state. Pigs with strong resilience usually have better production performance and higher tolerance to common diseases. This study utilized feed intake records collected by a Feed Intake Recording Equipment from three pig breeds (Duroc: 823; Landrace: 582; and Yorkshire: 2032). Six resilience traits were constructed using the root mean square error (RMSE) of daily feed intake and feeding duration, cumulative feed intake, and cumulative feeding duration derived from ordinary least squares (OLS) regression, along with quantile regression (QR) estimates of daily feed intake and feeding duration. The correlations between these resilience traits and production traits were subsequently estimated. Single-trait genome-wide association studies (GWASs) were performed using imputed resequencing data to identify key genomic regions and candidate genes associated with resilience traits. The estimated heritability ranged from 0.103 to 0.267 for resilience traits and 0.293 to 0.560 for production traits. Moderate genetic correlations were observed among the resilience traits, while moderate to high genetic correlations were found between resilience traits and production traits. In particular, the traits RMSE_FI, RMSE_CFI, QR_FI, and QR_FD exhibited significant moderate to high correlations with most production traits. A genome-wide association study (GWAS) based on imputed whole-genome sequencing data was conducted to identify genomic regions associated with resilience traits in pigs. Using single-trait mixed linear models, 188 SNPs were identified and annotated to 44 candidate genes. Several of these genes (CD74, CSF1R, and HTR4) are involved in host immune responses and signal transduction pathways. These findings contribute to a better understanding of the genetic mechanisms underlying resilience in pigs and provide insights for enhancing genomic selection in pig breeding.

Background: Labour dystocia (LAD) in sows is a common reproductive disorder that reduces piglet survival rates and increases the number of stillbirths, causing substantial economic losses to pig farms. However, the genetic basis of LAD remains elusive. Herein, we performed a single-breed genome-wide association study (GWAS) for LAD using imputed whole-genome sequence data from 3263 sows (487 Landrace and 2776 Yorkshire). Results: In this study, analysis of the reproductive traits showed that the total number of piglets born and the number of piglets born alive were 1.43–2.85 and 1.60–2.94 higher, respectively, in sows with natural labour than in those with LAD. We identified 250 and 12 SNPs associated with LAD in primiparous and multiparous sows, respectively. Furthermore, in primiparous Yorkshire sows, two major QTL were fine-mapped to a 498.44 kb interval (23.18–23.68 Mb) on SSC2 and a 779.85 kb interval (43.34–44.12 Mb) on SSC9. Further analysis revealed that the two significant SNPs (2_23340612 and 9_44119733) within these QTL regions were located within regulatory regions across multiple pig breeds and tissues. The potentially regulatory SNP (2_23340612) is located within the binding sites of 27 transcription factors, that are primarily involved in oxytocin signalling, muscle contraction, and the development of female genitalia and embryo. The other potentially regulatory SNP (9_44119733) is located within the binding sites of eight transcription factors, among which three transcription factors (ZNF274, HMGA1, and CTCF) are predicted to interact with six candidate genes ( APOA1 , APOC3 , APOA4 , APOA5 , BUD13 , and ZPR1 ). Finally, eight promising candidate genes ( APOA1 , APOC3 , APOA4 , APOA5 , BUD13 , ZPR1 , ACAN , and HAPLN3 ) were identified to be associated with LAD. Functional enrichment analysis indicated that the candidate genes were enriched in pathways related to lipid metabolism, extracellular matrix organization, cell adhesion and response to estrogen. Conclusions: The LAD is a prominent reproductive disorder trait that negatively impacts the reproductive efficiency of sows. This study identified potentially regulatory SNPs (2_23340612 and 9_44119733) and eight promising genes ( APOA1 , APOC3 , APOA4 , APOA5 , BUD13 , ZPR1 , ACAN , HAPLN3 ) associated with LAD. To our knowledge, this is the first whole-genome-sequence-based GWAS with large-scale reproductive data to identify genetic markers and candidate genes of LAD of sows.