Special Issue "Genetics, Genomics, Transcriptomics, Proteomics, Health and Product Quality of Small Ruminants"

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Small Ruminants".

Deadline for manuscript submissions: 31 March 2021.

Special Issue Editors

Dr. Emilia Bagnicka
Website
Guest Editor
Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzebiec, Poland
Interests: dairy cattle; dairy goats; quantitative genetics; molecular genetics; genomics; epigenomics
Dr. Aldona Kawęcka
Website
Guest Editor
National Research Institute of Animal Production, 1, Krakowska Street, 32-083 Balice near Krakow, Poland
Interests: native sheep; goats; genetic resources; biodiversity; molecular genetics; traditional product quality

Special Issue Information

Sheep and goat breeds are important farm animals that are bred worldwide for meat, milk, wool and skins. Moreover, small ruminants are very important in active protection of valuable natural habitats and management wastelands. Modern tools such as genomics, which allows for improving important functional traits, open new perspectives for small ruminant breeding programs. This field of molecular and theoretical biology makes the assessment of the genetic diversity of sheep and goat breeds possible. SNP microarrays are a new generation of molecular genetic tools that have been applied in population biodiversity analysis; studies of sheep and goat diseases, including mastitis, foot rot and internal parasites; and research into lamb/kid survival and ewe/doe longevity. However, the basic studies in genomic, transcriptomic and proteomic areas are still limited for small ruminants as compared to other farm species. Moreover, studying epigenomic phenomena in small ruminants could help to explain part of the genetic–environmental interaction influencing the phenotypes of these species.

We invite original research papers and review articles on genetic, genomic, transcriptomic, proteomic and epigenomic research regarding sheep and goats; the implementation of genomic selection for production of sheep and goats; the identification of functional traits to improve animal welfare; the conservation of genetic diversity; advances in genetics for animal health monitoring; and research on genetic variability of traits related to milking ability of dairy sheep and goats and the composition and cheese making ability of small ruminants’ milk.

Dr. Emilia Bagnicka
Dr. Aldona Kawęcka
Guest Editors

Manuscript Submission Information

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Keywords

  • small ruminants
  • genetic diversity
  • genetic parameters
  • genomics
  • transcriptomics
  • proteomics
  • epigenomics
  • health
  • product quality

Published Papers (5 papers)

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Research

Open AccessArticle
Exploring the Rumen and Cecum Microbial Community from Fetus to Adulthood in Goat
Animals 2020, 10(9), 1639; https://doi.org/10.3390/ani10091639 - 11 Sep 2020
Abstract
The present study aimed to investigate the colonization process of epithelial bacteria attached to the rumen and intestinal tract tissue during the development of goats after birth. However, this process from fetus to adulthood was very limited. In goats, the rumen and cecum [...] Read more.
The present study aimed to investigate the colonization process of epithelial bacteria attached to the rumen and intestinal tract tissue during the development of goats after birth. However, this process from fetus to adulthood was very limited. In goats, the rumen and cecum are two important fermentation organs, and it is important to study the acquisition and development of the neonatal microbiome, as well as the difference between these two organs. To characterize the microbial establishment and dynamic changes in the rumen and cecum from fetus to adulthood, we performed 16S rRNA gene sequencing for 106 samples from 47 individuals of nine pregnant mother–fetus pairs and 16 kids from birth up to 6 months. The diversity, structure and composition of the microbial communities were distinct between the rumen and cecum after birth, while they were similar in the fetal period. The study showed a rapid loss and influx of microbes at birth, followed by slight selection after drinking colostrum, and then a strong selection after weaning, suggesting that the establishment and dynamic fluctuations of the gut microbiome undergoes three distinct phases of microbiome progression in life: a conserved phase (during late pregnancy in the fetus), a transitional phase (newborn until weaning), and a stable phase (from weaning to adulthood). The results supported the view that microbes exist in the fetus, and revealed the establishment and dynamic fluctuations of the gut microbiome from fetus to adulthood in goats. Full article
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Open AccessArticle
Using RNA-Seq to Identify Reference Genes of the Transition from Brown to White Adipose Tissue in Goats
Animals 2020, 10(9), 1626; https://doi.org/10.3390/ani10091626 - 10 Sep 2020
Abstract
Brown adipose tissues have unique non-shivering thermogenesis functions, can be found in newborn ruminate animals, and then are gradually replaced by white adipose tissues in adulthood. For the purpose of exploring the intrinsic mechanism underlying the conversion process from brown (BAT) to white [...] Read more.
Brown adipose tissues have unique non-shivering thermogenesis functions, can be found in newborn ruminate animals, and then are gradually replaced by white adipose tissues in adulthood. For the purpose of exploring the intrinsic mechanism underlying the conversion process from brown (BAT) to white adipose tissue (WAT), it is necessary to utilize Quantitative PCR (qPCR) to study gene expression profiling. In this study, we identified reference genes that were consistently expressed during the transformation from goat BAT to WAT using RNA-seq data. Then, twelve genes were evaluated as candidate reference genes for qPCR in goat perirenal adipose tissue using three tools (geNorm, Normfinder, and BestKeeper). In addition, the selected reference genes were used to normalize the gene expression of PGC-1α and GPAT4. It was found that traditional reference genes, such as GAPDH, RPLP0, HPRT1, and PPIA were not suitable for target gene normalization. In contrast, CTNNB, PFDN5, and EIF3M, selected from RNA sequencing data, showed the least variation and were recommended as the best reference genes during the transformation from BAT to WAT. Full article
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Open AccessArticle
Selection Signatures Analysis Reveals Genes Associated with High-Altitude Adaptation in Tibetan Goats from Nagqu, Tibet
Animals 2020, 10(9), 1599; https://doi.org/10.3390/ani10091599 - 08 Sep 2020
Cited by 1
Abstract
Tibetan goat is an ancient breed, which inhabits the adverse conditions of the plateaus in China. To investigate the role of selection in shaping its genomes, we genotyped Tibetan goats (Nagqu Prefecture, above 4500 m) and three lowland populations (Xinjiang goats, Taihang goats [...] Read more.
Tibetan goat is an ancient breed, which inhabits the adverse conditions of the plateaus in China. To investigate the role of selection in shaping its genomes, we genotyped Tibetan goats (Nagqu Prefecture, above 4500 m) and three lowland populations (Xinjiang goats, Taihang goats and Huanghuai goats). The result of PCA, neighbor-joining (N-J) tree and model-based clustering showed that the genetic structure between the Tibetan goat and the three lowland populations has significant difference. As demonstrated by the di statistic, we found that some genes were related to the high-altitude adaptation of Tibetan goats. Functional analysis revealed that these genes were enriched in the VEGF (vascular endothelial growth factor) signaling pathway and melanoma, suggesting that nine genes (FGF2, EGFR, AKT1, PTEN, MITF, ENPEP, SIRT6, KDR, and CDC42) might have important roles in the high-altitude adaptation of Nagqu Tibetan goats. We also found that the LEPR gene was under the strongest selection (di value = 16.70), and it could induce upregulation of the hypoxic ventilatory response. In addition, five genes (LEPR, LDB1, EGFR, NOX4 and FGF2) with high di values were analyzed using q-PCR. Among them, we found that LEPR, LDB1 and FGF2 exhibited higher expression in the lungs of the Tibetan goats; LEPR, EGFR and LDB1 exhibited higher expression in the hearts of the Huanghuai goat. Our results suggest that LEPR, LDB1, EGFR and FGF2 genes may be related to the high-altitude adaptation of the goats. These findings improve our understanding of the selection of the high-altitude adaptability of the Nagqu Tibetan goats and provide new theoretical knowledge for the conservation and utilization of germplasm resources. Full article
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Open AccessArticle
Cultivation of Hair Matrix Cells from Cashmere Goat Skins and Exemplified Applications
Animals 2020, 10(8), 1400; https://doi.org/10.3390/ani10081400 - 12 Aug 2020
Abstract
A functional interpretation of filtered candidates and predicted regulatory pathways related to cashmere growth from sequencing trials needs available cell models, especially for hair matrix cells (HMCs), whose continual proliferation and differentiation result in rapid hair growth. To fulfill such goals, we herein [...] Read more.
A functional interpretation of filtered candidates and predicted regulatory pathways related to cashmere growth from sequencing trials needs available cell models, especially for hair matrix cells (HMCs), whose continual proliferation and differentiation result in rapid hair growth. To fulfill such goals, we herein obtained primary goat HMCs via a microdissection-based method; optimized the selection of the culture medium and coating substances for better cell maintenance; and exemplified their usefulness through examining the effects of calcium and all-trans retinoic acid (ATRA) on cells using immunoblotting, flow cytometry, and other techniques. As a result, we successfully acquired primary and passaged goat HMCs with typical keratinocyte morphology. Calcium-free RPMI (Roswell Park Memorial Institute) 1640 and MEM (minimum Eagle’s medium) outperformed normal DMEM/F12 (Dulbecco’s modified Eagle’s medium/Nutrient Mixture F-12) on long-term cell maintenance, whereas serum-free media K-SFM and EpiLife failed to support cell growth. HMCs differed molecularly and morphologically from their neighbor dermal papilla cells on expressions of feature genes, such as HOXC13, and on characteristic keratinocyte-like appearances versus fibroblast shapes, respectively. Higher calcium concentrations significantly stimulated the expression of the genes (e.g., KRT1 and IVL) involved in keratinocyte differentiation and, promoted cell proliferation. Moreover, 10−5 M ATRA obviously boosted goat HMC expansions and changed their cell cycle distributions compared to the controls. Our study shines a light on researches exploring the mechanisms underlying the growth of cashmere. Full article
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Open AccessArticle
Association between Single Nucleotide Polymorphisms in SIRT1 and SIRT2 Loci and Growth in Tibetan Sheep
Animals 2020, 10(8), 1362; https://doi.org/10.3390/ani10081362 - 06 Aug 2020
Abstract
Silent information regulator 1 and 2 (SIRT1, 2) were NAD+-dependent histone or non-histone deacetylase, which emerged as key metabolic sensors in several tissues of mammals. In the present study, the search for polymorphisms within the ovine SIRT1 and SIRT2 loci as [...] Read more.
Silent information regulator 1 and 2 (SIRT1, 2) were NAD+-dependent histone or non-histone deacetylase, which emerged as key metabolic sensors in several tissues of mammals. In the present study, the search for polymorphisms within the ovine SIRT1 and SIRT2 loci as well as association analyses between SNPs and growth-related traits were performed in Tibetan sheep. To determine the expression pattern of SIRT1 and SIRT2 genes in Tibetan sheep, the quantitative real-time polymerase chain reaction (qPCR) analysis revealed that those two genes were widely expressed in diverse tissues. Expression of SIRT1 was less in abomasum of lamb, whereas it was greater in duodenum within adult stage. In the case of SIRT2, the greatest expression was observed in reticulum (lamb) and in muscle (adult), whereas the least expression was in liver for lamb and in kidney for adult animals. The association analysis demonstrated that g.3148 C > T polymorphism of SIRT1 affected heart girth (p = 0.002). The g.8074 T > A SNP of SIRT2 had a significant correlation with body weight (p = 0.011) and body length (p = 0.008). These findings suggested that the SIRT1 and SIRT2 polymorphism was involved in growth-related traits in Tibetan sheep, which may be considered to be genetic markers for improving the growth traits of Tibetan sheep. Full article
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