Detection of candidate genes affecting milk production traits in sheep using whole-genome sequencing analysis

Revealing gene expression links between milk fat globules and mammary glands in rodents via transcriptomics

Currently, most studies on lactation-related traits and gene expression rely on invasive techniques to obtain mammary tissue. These methods are not only difficult to perform but also limit the availability of samples. Therefore, this study aimed to utilize whole transcriptome sequencing to investigate the gene expression profiles of Golden hamsters (Gh, n = 5) and Kunming mice (Km, n = 5). It compared the transcriptome expression between milk fat globules (MFG) and the mammary gland (MG), identified candidate genes and pathways associated with lactation traits, and assessed the potential of MFG as an effective alternative to MG. The data showed that a total of 21,360 genes were identified in the Gh group, with 66.5% of the mRNAs showing no differential expression between MG and MFG. In the Km group, a total of 44,248 genes were identified, with non-differentially expressed genes (NDEGs) accounting for 58.8%. Additionally, the majority of ncRNA data consisted of NDEGs. In both groups, approximately 80% of miRNA data were NDEGs. Notably, the proportion of NDEGs in circRNA data approached 100%. Enrichment analysis revealed that NDEGs from both groups were significantly enriched in several pathways, including the MAPK signaling pathway, PI3K-Akt signaling pathway, JAK-STAT signaling pathway, and prolactin signaling pathway, all of which are closely associated with lactation traits and the lactation process. Furthermore, we identified various ncRNAs that regulate the expression of target genes either directly or indirectly, thereby influencing the lactation process. This study validates MFG as a reliable substitute for MG, with potential applications in improving dairy science. By identifying key genes and pathways, it provides new insights for optimizing genetic selection and breeding strategies. It also supports the improvement of dairy animal management practices.

Associations Between Non-Steroidal and Steroidal Anti-Inflammatory Drug Use, Welfare, and Milk Production in Dairy Sheep: A Multivariate Study

This study examines the use of analgesic medications among sheep farmers, highlighting both their benefits and the significant gaps in their adoption. Our findings indicate that 26.7% of sheep farmers did not utilize any analgesics, a figure that contrasts sharply with high usage rates among swine (over 80%) and cattle (over 85%) farmers. The low utilization of NSAIDs and corticosteroids in sheep farming may be attributed to inadequate education and the lack of approved indications for these medications in Greece. Additionally, we found a positive correlation between farm size and the use of NSAIDs, with larger farms using more NSAIDs, especially flunixin. Furthermore, farms with higher NSAID use-typically the larger ones-tended to have higher milk yields, suggesting that enhanced management practices may contribute to improved outcomes. The results underscore the need for targeted educational initiatives to improve the use of analgesics in sheep farming and address welfare concerns. Overall, this research highlights the importance of addressing gaps in pain management practices in the sheep farming sector to promote better animal welfare. However, further studies with larger sample sizes are needed to expand our understanding of analgesic use and its implications for sheep welfare.

A systematic review of hypervirulent Klebsiella pneumoniae research: bibliometric and topic modeling perspectives

Background/objective

Hypervirulent Klebsiella pneumoniae (hvKP) is an emerging global health threat, exhibiting increased virulence and multidrug resistance compared to classic K. pneumoniae. Understanding the research landscape surrounding hvKP is crucial for developing effective control strategies. This study aimed to comprehensively analyze the global research trends in hvKP from 2013 to 2024 using bibliometric and topic modeling techniques.

Methods

Data from 1,014 articles on hvKP, retrieved from the Web of Science Core Collection, were analyzed using Bibliometrix, CiteSpace, and VOSviewer to assess publication trends, collaborations, geographical distribution, and keyword co-occurrence. Latent Dirichlet Allocation (LDA) topic modeling was employed to identify key research themes.

Results

The analysis revealed a steadily increasing volume of hvKP research, with China and the United States as major contributors. Four primary research themes emerged: high virulence phenotypes and mechanisms; drug resistance and treatment strategies; genetic and molecular mechanisms; and epidemiological and transmission characteristics. Research hotspots included virulence mechanisms, drug resistance, genomic detection approaches, and epidemiological features.

Conclusion

This bibliometric analysis provides a comprehensive overview of hvKP research, highlighting key trends and research gaps. The identified research hotspots inform future research directions and contribute to the development of effective strategies for combating hvKP infections. The increasing research volume underscores the urgent need for continued investigation into this significant public health threat.

Whole-Genome Resequencing in Sheep: Applications in Breeding, Evolution, and Conservation

Sheep (Ovis aries) were domesticated around 10,000 years ago and have since become an integral part of human agriculture, providing essential resources, such as wool, meat, and milk. Over the past century, advances in communication and agricultural productivity have driven the evolution of selective breeding practices, further enhancing the value of sheep in the global economy. Recently, the rapid development of whole-genome resequencing (WGR) technologies has significantly accelerated research in sheep molecular biology, facilitating the discovery of genetic underpinnings for critical traits. This review offers a comprehensive overview of the evolution of whole-genome resequencing and its application to sheep genetics. It explores the domestication and genetic origins of sheep, examines the genetic structure and differentiation of various sheep populations, and discusses the use of WGR in the development of genetic maps. In particular, the review highlights how WGR technology has advanced our understanding of key traits, such as wool production, lactation, reproductive performance, disease resistance, and environmental adaptability. The review also covers the use of WGR technology in the conservation and sustainable utilization of sheep genetic resources, offering valuable insights for future breeding programs aimed at enhancing the genetic diversity and resilience of sheep populations.

Genome-wide landscape of genetic diversity, runs of homozygosity, and runs of heterozygosity in five Alpine and Mediterranean goat breeds

BACKGROUND

Goat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection and adaptability to harsh environments. Understanding their adaptive traits can aid breeding programs target enhanced resilience and productivity, especially as we are facing important climate and agriculture challenges. To this aim the genomic architecture of 480 goats belonging to five breeds (i.e., Saanen [SAA], Camosciata delle Alpi [CAM], Murciano-Granadina [MUR], Maltese [MAL], Sarda [SAR]) reared in the Sardinia Island were genotyped and their genomic architecture evaluated to find molecular basis of adaptive traits. Inbreeding, runs of homozygosity (ROH) and runs of heterozygosity (ROHet) were identified. Finally, candidate genes in the ROH and ROHet regions were explored through a pathway analysis to assess their molecular role.

RESULTS

In total, we detected 10,341 ROH in the SAA genome, 11,063 ROH in the CAM genome, 12,250 ROH in the MUR genome, 8,939 ROH in the MAL genome, and 18,441 ROH in the SAR genome. Moreover, we identified 4,087 ROHet for SAA, 3,360 for CAM, 2,927 for MUR, 3,701 for MAL, and 3,576 for SAR, with SAR having the highest heterozygosity coefficient. Interestingly, when computing the inbreeding coefficient using homozygous segment (FROH), SAA showed the lowest value while MAL the highest one, suggesting the need to improve selecting strategies to preserve genetic diversity within the population. Among the most significant candidate genes, we identified several ones linked to different physiological functions, such as milk production (e.g., DGAT1, B4GALT1), immunity (GABARAP, GPS2) and adaptation to environment (e.g., GJA3, GJB2 and GJB6).

CONCLUSIONS

This study highlighted the genetic diversity within and among five goat breeds. The high levels of ROH identified in some breeds might indicate high levels of inbreeding and a lack in genetic variation, which might negatively impact the animal population. Conversely, high levels of ROHet might indicate regions of the genetic diversity, beneficial for breed health and resilience. Therefore, these findings could aid breeding programs in managing inbreeding and preserving genetic diversity.

A phenotypic journey into NT5DC proteins in cancer and other diseases

5'-nucleotidases are proteins involved in nucleotide metabolism by dephosphorylating nucleotide monophosphates. A group of four related proteins (NT5DC1-4) has been described and an increasing amount of corresponding data has been published over the last years. Here, we review the current scientific literature on NT5DC proteins, present data on the four proteins, and discuss their potential involvement in cancer and other diseases. It seems that these proteins can have a role in various brain-related diseases, and there is a compelling amount of results showing that in particular NT5DC2 can be considered a drug target in cancer. More work is needed to conclude whether these proteins are involved or not in the nucleotide metabolism and thus potentially in purinergic signaling.

Assessment of breeding nuclei contributions to the genetic diversity and population structure of the Cyprus Chios sheep

Cyprus, facing climate change and desertification, has Europe's second highest population growth. Halloumi cheese's Protected Designation of Origin status boosted goat and sheep milk demand. Optimizing primary sector production is key to balancing food production and environmental sustainability. The present study aims to explore the genetic diversity and population structure of Cyprus Chios sheep, as well as the impact of existing breeding nuclei on the breed's gene pool. Two breeding nuclei aiming to preserve genetic diversity and boost local milk production and four private farms were sampled. Genome-wide data using Illumina 50 K arrays were generated, analyzing over 1000 animals from six farms. At least three distinct genetic groups were identified, two of which are represented by the nuclei's distinct genetic profiles and a third was found in private farms. Calculated metrics indicate a negative correlation of gene flow with geographic distance in case of the Eastern nucleus. Presented results support recent, though limited inbreeding (mean FROH=0.046), compared to other commercial breeds. Estimated effective population size reveals a stabilizing trend to a relatively high number (Ne ~ 200) which indicates relatively high diversity that allows further genetic improvement. Revealed genomic diversity highlights the necessity of such exploration before effectively implementing genomic evaluation programs.

Whole genome resequencing-based analysis of plateau adaptation in Meiren yak (Bos grunniens)

The Meiren yak is an important genetic resource in Gansu Province, China. In this study, we aimed to explore the evolutionary history and population structure of the genetic resource of Meiren yak and to mine the characteristic genes of Meiren yak. We analysed a total of 93 yaks of eight yak breeds based on whole genome resequencing combined with population genomics and used θπ ratio and Fst method to screen the selected sites in the genome region. The results proved that Meiren yak can be used as a potential genetic resource in Gansu Province. The genes in Meiren yak with positive selection in selection signal analysis were subjected to the Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analyses, which indicated that the genes were related to the adaptability to high altitude and hypoxic environment. By analysing the genetic variation of Meiren yak at the genome-wide level, this study provided a theoretical basis for genetic improvement of Meiren yak and for the development of high-quality yak resources.

Host-microbe interaction-mediated resistance to DSS-induced inflammatory enteritis in sheep

BACKGROUND

The disease resistance phenotype is closely related to immunomodulatory function and immune tolerance and has far-reaching implications in animal husbandry and human health. Microbes play an important role in the initiation, prevention, and treatment of diseases, but the mechanisms of host-microbiota interactions in disease-resistant phenotypes are poorly understood. In this study, we hope to uncover and explain the role of microbes in intestinal diseases and their mechanisms of action to identify new potential treatments.

METHODS

First, we established the colitis model of DSS in two breeds of sheep and then collected the samples for multi-omics testing including metagenes, metabolome, and transcriptome. Next, we made the fecal bacteria liquid from the four groups of sheep feces collected from H-CON, H-DSS, E-CON, and E-DSS to transplant the fecal bacteria into mice. H-CON feces were transplanted into mice named HH group and H-DSS feces were transplanted into mice named HD group and Roseburia bacteria treatment named HDR groups. E-CON feces were transplanted into mice named EH group and E-DSS feces were transplanted into mice in the ED group and Roseburia bacteria treatment named EDR groups. After successful modeling, samples were taken for multi-omics testing. Finally, colitis mice in HD group and ED group were administrated with Roseburia bacteria, and the treatment effect was evaluated by H&E, PAS, immunohistochemistry, and other experimental methods.

RESULTS

The difference in disease resistance of sheep to DSS-induced colitis disease is mainly due to the increase in the abundance of Roseburia bacteria and the increase of bile acid secretion in the intestinal tract of Hu sheep in addition to the accumulation of potentially harmful bacteria in the intestine when the disease occurs, which makes the disease resistance of Hu sheep stronger under the same disease conditions. However, the enrichment of harmful microorganisms in East Friesian sheep activated the TNFα signalling pathway, which aggravated the intestinal injury, and then the treatment of FMT mice by culturing Roseburia bacteria found that Roseburia bacteria had a good curative effect on colitis.

CONCLUSION

Our study showed that in H-DSS-treated sheep, the intestinal barrier is stabilized with an increase in the abundance of beneficial microorganisms. Our data also suggest that Roseburia bacteria have a protective effect on the intestinal barrier of Hu sheep. Accumulating evidence suggests that host-microbiota interactions are associated with IBD disease progression. Video Abstract.

Whole Genome Scan Uncovers Candidate Genes Related to Milk Production Traits in Barka Cattle

In this study, our primary aim was to explore the genomic landscape of Barka cattle, a breed recognized for high milk production in a semi-arid environment, by focusing on genes with known roles in milk production traits. We employed genome-wide analysis and three selective sweep detection methods (ZFST, θπ ratio, and ZHp) to identify candidate genes associated with milk production and composition traits. Notably, ACAA1, P4HTM, and SLC4A4 were consistently identified by all methods. Functional annotation highlighted their roles in crucial biological processes such as fatty acid metabolism, mammary gland development, and milk protein synthesis. These findings contribute to understanding the genetic basis of milk production in Barka cattle, presenting opportunities for enhancing dairy cattle production in tropical climates. Further validation through genome-wide association studies and transcriptomic analyses is essential to fully exploit these candidate genes for selective breeding and genetic improvement in tropical dairy cattle.

Understanding Circular RNAs in Health, Welfare, and Productive Traits of Cattle, Goats, and Sheep

Circular RNAs (circRNAs) are unique noncoding RNA molecules, notable for their covalent closed-loop structures, which play a crucial role in regulating gene expression across a variety of biological processes. This review comprehensively synthesizes the existing knowledge of circRNAs in three key livestock species: Bos taurus (cattle), Ovis aries (sheep), and Capra hircus (goats). It focuses on their functional importance and emerging potential as biomarkers for disease detection, stress response, and overall physiological health. Specifically, it delves into the expression and functionality of circRNAs in these species, paying special attention to traits critical to livestock productivity such as milk production, meat quality, muscle development, wool production, immune responses, etc. We also address the current challenges faced in circRNA research, including the need for standardized methodologies and broader studies. By providing insights into the molecular mechanisms regulated by circRNAs, this review underscores their scientific and economic relevance in the livestock industry. The potential of circRNAs to improve animal health management and the quality of animal-derived products aligns with growing consumer concerns for animal welfare and sustainability. Thus, this paper aims to guide future research directions while supporting the development of innovative strategies in livestock management and breeding.

Pan-Omics in Sheep: Unveiling Genetic Landscapes

Multi-omics-integrated analysis, known as panomics, represents an advanced methodology that harnesses various high-throughput technologies encompassing genomics, epigenomics, transcriptomics, proteomics, and metabolomics. Sheep, playing a pivotal role in agricultural sectors due to their substantial economic importance, have witnessed remarkable advancements in genetic breeding through the amalgamation of multiomics analyses, particularly with the evolution of high-throughput technologies. This integrative approach has established a robust theoretical foundation, enabling a deeper understanding of sheep genetics and fostering improvements in breeding strategies. The comprehensive insights obtained through this approach shed light on diverse facets of sheep development, including growth, reproduction, disease resistance, and the quality of livestock products. This review primarily focuses on the application of principal omics analysis technologies in sheep, emphasizing correlation studies between multiomics data and specific traits such as meat quality, wool characteristics, and reproductive features. Additionally, this paper anticipates forthcoming trends and potential developments in this field.

Genomic signatures reveal selection in Chinese and European domesticated geese

The Swan goose and Greylag goose are species of geese native to East Asia and Europe, respectively, and are widely believed to be the ancestors of Chinese and European domesticated geese. The Yili goose (YL) and European domestic geese originated from the Greylag goose, but the history of domestication is unclear. In this study, we sequenced and analyzed the genome of the YL goose and the Hortobagy goose to combine with other previously sequenced goose populations for in-depth analysis. The population genetic variations in Stone geese, East Zhejiang White Geese, Taihu geese and Zi geese were also identified and compared. The results showed that admixture gene flow existed in the YL geese population, which was introgressed by Chinese geese, suggesting that gene flow events were frequent and widespread among domesticated geese. Further selected sweep analysis identified candidate genes and metabolic pathways that may be related to the differences in morphology. Several genes such as TGFBR3L, CMYA5, FOXD1, ARHGEF28 and SUCLG2 are associated with growth, reproduction and fertility traits. The results of this study will help to understand the genetic characteristics of domestic geese and the genes affecting important traits and provide a basis for the improved breed of domestic geese.

The implications of various gene variant combinations on breeding values for Awassi ewe milk production

Background and Aim

Milk production is an important factor to consider in selecting Awassi sheep. This trait is influenced by various genes that can be managed to boost production. The breeding values (BVs) for milk production in Jordan's Awassi sheep flocks have been established. This study determined how combined gene variants of BLG, PRL, CSN3, CSN1S1, and CSN2 affect the estimated BVs (EBVs) for milk production in Awassi sheep.

Materials and Methods

Milk and blood samples were collected from 391 Awassi sheep, which was then subjected to molecular analysis through sequencing in order to identify potential alleles and genotypes that could be linked to the EBVs of milk.

Results

The predicted BVs for milk were significantly influenced by PRL and CSN3 gene variants. Through performing the act of epistasis, the interactions of BLG with CSN3 and -CSN1S1 greatly impacted EBVs for milk production. Likewise, the three-way interaction among PRL, CSN3, and CSN1S1, as well as the combined effect of CSN3 with CSN1S1 and CNS1 significantly improved BVs for milk production. When the breeding selection program incorporates the polymorphisms of these genes, gains in milk production can be obtained.

Conclusion

Alleles within the examined genomic areas are crucial for evaluating BVs and maximizing genetic gain in milk production.

Comparative genomic analysis uncovers candidate genes related with milk production and adaptive traits in goat breeds

During the process of animal domestication, both natural and artificial selection cause variation in allele frequencies among populations. Identifying genomic areas of selection in domestic animals may aid in the detection of genomic areas linked to ecological and economic traits. We studied genomic variation in 140 worldwide goat individuals, including 75 Asian, 30 African and 35 European goats. We further carried out comparative population genomics to detect genomic regions under selection for adaptability to harsh conditions in local Asian ecotypes and also milk production traits in European commercial breeds. In addition, we estimated the genetic distances among 140 goat individuals. The results showed that among all studied goat groups, local breeds from West and South Asia emerged as an independent group. Our search for selection signatures in local goats from West and South Asia revealed candidate genes related to adaptation to hot climate (HSPB6, HSF4, VPS13A and NBEA genes) and immune response (IL7, IL5, IL23A and LRFN5) traits. Furthermore, selection signatures in European commercial goats involved several milk production related genes, such as VPS13C, NCAM2, TMPRSS15, CSN3 and ABCG2. The identified candidate genes could be the fundamental genetic resource for enhancement of goat production and environmental-adaptive traits, and as such they should be used in goat breeding programs to select more efficient breeds.

Freeze-dried powder of daylily bud improves bromocriptine-induced lactation disorder in rats via JAK2/STAT5 pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Milk deficiency is a prevalent problem in the world. Daylily (Hemerocallis citrina Borani), called the Chinese mother flower, is a traditional vegetable and is believed to possess a galactagogue effect in China. Flavonoids and phenols are considered as the active ingredients of daylily to promote lactation and improve depression.

AIM OF THE STUDY

The aim of this study was to investigate the prolactin effects of freeze-dried powder of flower buds of H. citrina Baroni in rat and its action mechanisms.

MATERIALS AND METHODS

The chemical constituents of flower buds of H. citrina Baroni treated by different drying techniques were analyzed by ultrahigh pressure liquid chromatography-mass spectrometry. Sprague-Dawley (SD) rat model induced by bromocriptine was used to evaluate the effect of freeze-dried powder of daylily buds on promoting lactation. Network pharmacology method, ELISA, qPCR, and Western blot were used to clarify the action mechanisms.

RESULTS

We detected 657 compounds in daylily buds. The relative contents of total flavonoids and phenols in freeze-dried samples were higher than those in dried ones. Bromocriptine, as a dopamine receptor agonist, can significantly inhibit prolactin in rats. Daylily buds can restore the levels of prolactin, progesterone and estradiol depressed by bromocriptine, effectively improve the milk production of the rat, and promote the repair of rat mammary gland tissue. We analyzed the relationship between the chemical components of daylily buds and the genes related to lactation with network pharmacology method, revealing that flavonoids and phenols may be the active components that promoted milk production via JAK2/STAT5 pathway, which was confirmed by the results of qPCR and Western blot. Daylily buds can increase the mRNA expression of PRLR, CSN2, LALBA and FASN and the protein expression of PRLR, JAK2 and STAT5.

CONCLUSION

Daylily buds can improve the insufficient lactation of rats induced by bromocriptine through PRLR/JAK2/STAT5 pathway, and the freeze-dried processing method may better retain the active components of flavonoids and phenols that promote milk in daylily.

The ovine HIAT1 gene: mRNA expression, InDel mutations, and growth trait associations

Background

The hippocampal abundant transcript 1 (HIAT1) gene, also known as major facilitator superfamily domain-containing 14A (MFSD14A), encodes for a transmembrane transporter protein and has been previously shown to be associated with milk production in buffalo and sheep breeds, as well as growth traits in chicken and goats. However, tissue level distribution of the ovine HIAT1 gene, as well as its effect on body morphometric traits in sheep, has yet to be studied.

Methods

The HIAT1 mRNA expression profile of Lanzhou fat-tailed (LFT) sheep was determined by quantitative real-time PCR (qPCR). A total of 1498 sheep of three indigenous Chinese sheep breeds were PCR-genotyped for polymorphisms of HIAT1 gene. Student's t-test was used to observe the association between the genotype and sheep morphometric traits.

Results

HIAT1 was widely expressed in all examined tissues, and was particularly abundant in the testis of male LFT sheep. Additionally, a 9-bp insertion mutation (rs1089950828) located within the 5'-upstream region of HIAT1 was investigated in Luxi black-headed (LXBH) sheep and Guiqian semi-fine wool (GSFW) sheep. The wildtype allele frequency 'D' was found to be more prevalent than that of the mutant allele 'I'. Furthermore, low genetic diversity was confirmed in all sampled sheep populations. Subsequent association analyses indicated an association between the 9-bp InDel mutation of interest and the morphometric traits of LXBH and GSFW sheep. Furthermore, yearling ewes with a heterozygous genotype (ID) demonstrated smaller body sizes, while yearling rams and adult ewes with the heterozygous genotype were found to have overall better growth performance.

Conclusion

These findings imply that functional InDel polymorphism (rs1089950828) has the potential to be utilized for marker-assisted selection (MAS) of growth traits in domestic Chinese sheep populations.