Small Ruminant Genetics and Breeding

A topical collection in Animals (ISSN 2076-2615). This collection belongs to the section "Small Ruminants".

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Guest Editor
Research Institute of Animal Science, ELGO ‘DIMITRA’, General Directorate of Agricultural Research, Paralimni Giannitsa, 58100 Pella, Greece
Interests: animal genetics; aquaculture and fisheries genetics; quantitative genetics; population and conservation genetics; molecular genetics
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Small ruminants, such as sheep (Ovis aries) and goats (Capra hircus), were among the first animals to be domesticated, with historical evidence linking them to Western Asia approximately 9000–12,000 years ago. Domesticated sheep and goats provided early humans with a supply of fiber, pelt, meat, and milk. Owing to their small stature and versatility, small ruminants have become steadily important in the global rural economy, especially in the arid and semi-arid regions. Furthermore, the demand for meat and milk in developing countries is constantly increasing, and a sustainable increase in small ruminant production would therefore be desirable in order to meet the demands of the human population on livestock populations and their products.

Genetic improvement can substantially promote the efficiency of animal production, by increasing the performance of small ruminant flocks or populations over time with the use of genetically superior animals. A prerequisite is to select the most desirable breed or breed combination, and to define the breeding objectives.

Over the last two decades, advances in DNA technology have dramatically increased the efficiency and the affordability of gaining genome information, leading to the development of fast, cost-effective, and more accurate methods for the implementation of breeding programs.

For this Special Issue, original research manuscripts covering all aspects of small ruminant genetics, such as population genetics, breed investigation and characterization, quantitative genetics, QTL and marker assisted selection, genomic selection, gene polymorphisms, and genome-wide association studies, are welcome.

Dr. Dimitrios Loukovitis
Guest Editor

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Keywords

  • small ruminant
  • genetic improvement
  • population genetics
  • QTL
  • genomic selection
  • molecular markers

Published Papers (21 papers)

2024

Jump to: 2023, 2022, 2021, 2020

12 pages, 2418 KiB  
Article
The Role of BMP7 in the Proliferation of Hu Sheep Dermal Papilla Cells Is Influenced by DNA Methylation
by Xiaoyang Lv, Mingliang He, Shanhe Wang, Wenxin Zheng, Hanlin Zhou, Joram M. Mwacharo and Wei Sun
Animals 2024, 14(11), 1699; https://doi.org/10.3390/ani14111699 - 5 Jun 2024
Viewed by 688
Abstract
Previous studies have shown that the BMP7 gene is differentially expressed in Hu sheep lamb skin of different pattern types, and its expression level is significantly correlated with hair follicle indices of different pattern types, but the molecular mechanism of the differential expression [...] Read more.
Previous studies have shown that the BMP7 gene is differentially expressed in Hu sheep lamb skin of different pattern types, and its expression level is significantly correlated with hair follicle indices of different pattern types, but the molecular mechanism of the differential expression of the BMP7 gene remains unclear. This study investigated the effect of DNA methylation on the transcriptional expression of BMP7. Firstly, we found that the mRNA expression of the BMP7 gene and the activity of the core promoter of the BMP7 gene were upregulated after 5-Aza-Deoxycytidine-induced demethylation treatment using qRT-PCR and double luciferase reporter assay. Then, we found that the proliferation of Hu sheep DPCs in vitro was promoted after 5-Aza-Deoxycytidine-induced demethylation treatment through qRT-PCR, CCK-8, and EdU assay, and that the overexpression of DNMT1 in DPCs induced the opposite effect. In addition, the results of the cell cycle assay reveal that the percentage of cells in the S phase was increased after 5-Aza-Deoxycytidine-induced demethylation treatment, and that the percentage of cells in the S phase was decreased after overexpression of DNMT1 in DPCs. This study indicated that the differential expression of the BMP7 gene in different patterns of Hu sheep lamb skin may be regulated by DNA methylation modification. In addition, DNA methylation can regulate the proliferation and cell cycle of DPCs in Hu sheep. Full article
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13 pages, 1319 KiB  
Article
Reproductive Activity of Socorro Island Merino Ewes and Their Crosses with Pelibuey under Heat Stress Conditions
by Arturo César García-Casillas, Omar Francisco Prado-Rebolledo, María Isabel Carrillo-Díaz, José Luis Zepeda-Batista, Carlos Eduardo Barajas-Saucedo and Juan Augusto Hernández-Rivera
Animals 2024, 14(10), 1405; https://doi.org/10.3390/ani14101405 - 8 May 2024
Viewed by 856
Abstract
An experiment was carried out to evaluate the effect of spring and autumn seasons on the reproductive activity of Merino Socorro Island ewes and their crosses with Pelibuey under heat stress (HS) conditions in the tropics. All ewes (n = [...] Read more.
An experiment was carried out to evaluate the effect of spring and autumn seasons on the reproductive activity of Merino Socorro Island ewes and their crosses with Pelibuey under heat stress (HS) conditions in the tropics. All ewes (n = 80) were randomly assigned to one of two breeds during the first and second periods, respectively: (1) Twenty Socorro Island Merino ewes (SIM) and (2) 20 Pelibuey Crossbred ewes (PBC). Animals were fed the same diet and given water ad libitum. All statistical analyses were performed using SAS statistical software 9.12 procedures. In both seasons, a mean of more than 80 U of maximum THI was obtained, while in spring and autumn, the minimum THI exceeded 30 and 40 U, respectively. All animals were in oestrus and ovulated in both seasons. The frequency of animals in spring during the first 48 h of oestrus expression was greater (p < 0.05) than 48–55 h but similar (p > 0.05) than 55–65 h; in autumn during the first 48 h and 48–55 h were similar (p > 0.05), but different (p < 0.05) than 55–65 h. The duration of oestrus expression was longer in the spring than in the autumn (p < 0.05). The frequency of animals was higher (p < 0.05) in SIM than in PBC ewes during the first oestrus cycle (1–17 d) and was also higher (p < 0.05) in PBC than in SIM ewes during the second oestrus cycle (18–35 d). The SIM ewes produced more (p < 0.05) progesterone (P4) than the PBC ewes. During the sampling days of the oestrus cycle, more P4 was created in autumn than in spring (p < 0.05). Both breeds showed severe HS. In the future, ewes treated under assisted reproductive programs in the tropics may improve reproductive efficiency. Full article
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13 pages, 2820 KiB  
Article
SP1 and KROX20 Regulate the Proliferation of Dermal Papilla Cells and Target the CUX1 Gene
by Xiaoyang Lv, Mingliang He, Hui Zhou, Shanhe Wang, Xiukai Cao, Zehu Yuan, Tesfaye Getachew, Yutao Li and Wei Sun
Animals 2024, 14(3), 429; https://doi.org/10.3390/ani14030429 - 29 Jan 2024
Viewed by 1236
Abstract
Previous studies have demonstrated that CUX1 could contribute to the proliferation of DPCs in vitro, but the upstream transcriptional regulatory mechanisms of CUX1 remain largely unknown. This study aimed to investigate the upstream transcriptional regulators of CUX1 to enhance our comprehension of the [...] Read more.
Previous studies have demonstrated that CUX1 could contribute to the proliferation of DPCs in vitro, but the upstream transcriptional regulatory mechanisms of CUX1 remain largely unknown. This study aimed to investigate the upstream transcriptional regulators of CUX1 to enhance our comprehension of the mechanism of action of the CUX1 gene in ovine DPCs. Initially, the JASPAR (2024) software was used to predict the upstream target transcription factors for the CUX1 gene. Subsequently, through RT-qPCR and a double luciferase reporter assay, the interaction between SP1, KROX20, and CUX1 was established, respectively. The results indicated that SP1 and KROX20 were two highly reliable upstream transcription regulators for the CUX1 gene. Additionally, we found that SP1 promoted the proliferation of DPCs by overexpressing SP1 in DPCs, and KROX20 inhibited the proliferation of DPCs by overexpressing KROX20 in DPCs. These findings are also consistent with the transcriptional regulation of CUX1 by SP1 and KROX20, respectively. This study suggests that the effect of DPC proliferation in vitro by CUX1 may regulated by the transcription factors SP1 and KROX20. Full article
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17 pages, 1812 KiB  
Article
Transcriptomic Analysis Reveals Differentially Expressed Circular RNAs Associated with Fecundity in the Sheep Hypothalamus with Different FecB Genotypes
by Yu He, Si Chen, Xiaofei Guo, Xiaoyun He, Ran Di, Xiaosheng Zhang, Jinlong Zhang, Xiangyu Wang and Mingxing Chu
Animals 2024, 14(2), 198; https://doi.org/10.3390/ani14020198 - 7 Jan 2024
Viewed by 1324
Abstract
Circular RNAs (circRNAs) are a specific type of noncoding RNA, and some have defined roles in cellular and biological processes. However, little is known about the role of circRNAs in follicular development in sheep with FecB (fecundity Booroola) mutations. Here, the expression profiles [...] Read more.
Circular RNAs (circRNAs) are a specific type of noncoding RNA, and some have defined roles in cellular and biological processes. However, little is known about the role of circRNAs in follicular development in sheep with FecB (fecundity Booroola) mutations. Here, the expression profiles of circRNAs were investigated using RNA sequencing (RNA-seq) in the follicular phase (F) and the luteal phase (L) of FecB mutant homozygous (BB) and wild-type (WW) Small Tail Han sheep. A total of 38,979 circRNAs were identified, and 314, 343, 336, and 296 of them were differentially expressed (DE) between BB_F and BB_L, WW_F and WW_L, BB_F and WW_F, and BB_L and WW_L, respectively. The length, type, and chromosome distribution of the circRNAs and the expression characteristic between the circRNAs and their host genes in the sheep hypothalamus were ascertained. Enrichment analysis showed that the host genes of DE circRNAs in the follicular and luteal phases were annotated to MAPK, gap junctions, progesterone-mediated oocyte maturation, oocyte meiosis, and other hormone-related signaling pathways, and the different FecB genotypes were annotated to the gap junctions, circadian entrainment, MAPK, and other hormone-related signaling pathways. The competing endogenous RNA network prediction revealed that the 129 target miRNAs might be bound to 336 DE circRNAs. oar_circ_0000523 and oar_circ_0028984, which were specifically expressed during the follicular phase in the BB genotype sheep, probably acted as miRNA sponges involved in the regulation of LH synthesis and secretion. This study reveals the expression profiles and characterization of circRNAs at two phases of follicular development considering different FecB genotypes, thereby providing an improved understanding of the roles of circRNAs in the sheep hypothalamus and their involvement in follicular development and ovulation. Full article
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2023

Jump to: 2024, 2022, 2021, 2020

17 pages, 6672 KiB  
Article
NCAPG Regulates Myogenesis in Sheep, and SNPs Located in Its Putative Promoter Region Are Associated with Growth and Development Traits
by Zehu Yuan, Ling Ge, Pengwei Su, Yifei Gu, Weihao Chen, Xiukai Cao, Shanhe Wang, Xiaoyang Lv, Tesfaye Getachew, Joram M. Mwacharo, Aynalem Haile and Wei Sun
Animals 2023, 13(20), 3173; https://doi.org/10.3390/ani13203173 - 11 Oct 2023
Cited by 2 | Viewed by 1256
Abstract
Previously, NCAPG was identified as a candidate gene associated with sheep growth traits. This study aimed to investigate the direct role of NCAPG in regulating myogenesis in embryonic myoblast cells and to investigate the association between single-nucleotide polymorphisms (SNPs) in its promoter region [...] Read more.
Previously, NCAPG was identified as a candidate gene associated with sheep growth traits. This study aimed to investigate the direct role of NCAPG in regulating myogenesis in embryonic myoblast cells and to investigate the association between single-nucleotide polymorphisms (SNPs) in its promoter region and sheep growth traits. The function of NCAPG in myoblast proliferation and differentiation was detected after small interfering RNAs (siRNAs) knocked down the expression of NCAPG. Cell proliferation was detected using CCK-8 assay, EdU proliferation assay, and flow cytometry cell cycle analysis. Cell differentiation was detected via cell immunofluorescence and the quantification of myogenic regulatory factors (MRFs). SNPs in the promoter region were detected using Sanger sequencing and genotyped using the improved multiplex ligation detection reaction (iMLDR®) technique. As a result, a notable decrease (p < 0.01) in the percentage of EdU-positive cells in the siRNA-694-treated group was observed. A significant decrease (p < 0.01) in cell viability after treatment with siRNA-694 for 48 h and 72 h was detected using the CCK-8 method. The quantity of S-phase cells in the siRNA-694 treatment group was significantly decreased (p < 0.01). After interfering with NCAPG in myoblasts during induced differentiation, the relative expression levels of MRFs were markedly (p < 0.05 or p < 0.01) reduced compared with the control group on days 5–7. The myoblast differentiation in the siRNA-694 treatment group was obviously suppressed compared with the control group. SNP1, SNP2, SNP3, and SNP4 were significantly (p < 0.05) associated with all traits except body weight measured at birth and one month of age. SNP5 was significantly (p < 0.05) associated with body weight, body height, and body length in six-month-old sheep. In conclusion, interfering with NCAPG can inhibit the proliferation and differentiation of ovine embryonic myoblasts. SNPs in its promoter region can serve as potential useful markers for selecting sheep growth traits. Full article
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20 pages, 9438 KiB  
Article
Whole-Genome Resequencing Reveals Selection Signal Related to Sheep Wool Fineness
by Wentao Zhang, Meilin Jin, Taotao Li, Zengkui Lu, Huihua Wang, Zehu Yuan and Caihong Wei
Animals 2023, 13(18), 2944; https://doi.org/10.3390/ani13182944 - 16 Sep 2023
Cited by 6 | Viewed by 1934
Abstract
Wool fineness affects the quality of wool, and some studies have identified about forty candidate genes that affect sheep wool fineness, but these genes often reveal only a certain proportion of the variation in wool thickness. We further explore additional genes associated with [...] Read more.
Wool fineness affects the quality of wool, and some studies have identified about forty candidate genes that affect sheep wool fineness, but these genes often reveal only a certain proportion of the variation in wool thickness. We further explore additional genes associated with the fineness of sheep wool. Whole-genome resequencing of eight sheep breeds was performed to reveal selection signals associated with wool fineness, including four coarse wool and four fine/semi-fine wool sheep breeds. Multiple methods to reveal selection signals (Fst and θπ Ratio and XP-EHH) were applied for sheep wool fineness traits. In total, 269 and 319 genes were annotated in the fine wool (F vs. C) group and the coarse wool (C vs. F) group, such as LGR4, PIK3CA, and SEMA3C and NFIB, OPHN1, and THADA. In F vs. C, 269 genes were enriched in 15 significant GO Terms (p < 0.05) and 38 significant KEGG Pathways (p < 0.05), such as protein localization to plasma membrane (GO: 0072659) and Inositol phosphate metabolism (oas 00562). In C vs. F, 319 genes were enriched in 21 GO Terms (p < 0.05) and 16 KEGG Pathways (p < 0.05), such as negative regulation of focal adhesion assembly (GO: 0051895) and Axon guidance (oas 04360). Our study has uncovered genomic information pertaining to significant traits in sheep and has identified valuable candidate genes. This will pave the way for subsequent investigations into related traits. Full article
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20 pages, 4892 KiB  
Article
Comparative Transcriptomics Identify Key Pituitary Circular RNAs That Participate in Sheep (Ovis aries) Reproduction
by Jianqi Yang, Jishun Tang, Xiaoyun He, Ran Di, Xiaosheng Zhang, Jinlong Zhang, Xiaofei Guo, Mingxing Chu and Wenping Hu
Animals 2023, 13(17), 2711; https://doi.org/10.3390/ani13172711 - 25 Aug 2023
Cited by 1 | Viewed by 1175
Abstract
CircRNAs have been found to play key roles in many biological processes and have diverse biological functions. There have been studies on circRNAs in sheep pituitary, and some important circRNAs have been found. But there are still few studies on circRNAs in sheep [...] Read more.
CircRNAs have been found to play key roles in many biological processes and have diverse biological functions. There have been studies on circRNAs in sheep pituitary, and some important circRNAs have been found. But there are still few studies on circRNAs in sheep pituitary with different fecundity. In this study, we obtained the circRNAs expression profiles in the pituitary of FecB ++ genotype Small Tail Han sheep with different fecundity and estrous phases. A total of 34,878 circRNAs were identified in 12 pituitary samples, 300 differentially expressed circRNAs (DE circRNAs) (down: 104; up: 196) were identified in polytocous sheep in the follicular phase (PF) and monotocous sheep in the follicular phase (MF) (PF vs. MF), and 347 DE circRNAs (down: 162; up: 185) were identified in polytocous sheep in the luteal phase (PL) and monotocous sheep in the luteal phase (ML) (PL vs. ML). Cortisol synthesis and secretion pathway (follicular phase) and estrogen signaling pathway (luteal phase) were obtained by functional enrichment analysis of circRNAs source genes. Competing endogenous RNA (ceRNA) network analysis of key DE circRNAs revealed that oar-circ-0022776 (source gene ITPR2, follicular phase) targeted oar-miR-432, oar-circ-0009003 (source gene ITPR1, luteal phase) and oar-circ-0003113 (source gene PLCB1, luteal phase) targeted oar-miR-370-3p. We also explored the coding ability of DE circRNAs. In conclusion, our study shows that changes in the pituitary circRNAs may be related to the response of the pituitary to steroid hormones and regulate the reproductive process of sheep by affecting the pituitary function. Results of this study provide some new information for understanding the functions of circRNAs and the fecundity of FecB ++ genotype sheep. Full article
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11 pages, 1729 KiB  
Article
Goat Pleomorphic Adenoma Gene 1 (PLAG1): mRNA Expression, CNV Detection and Associations with Growth Traits
by Qian Wang, Zhenyu Wei, Haijing Zhu, Chuanying Pan, Zhanerke Akhatayeva, Xiaoyue Song and Xianyong Lan
Animals 2023, 13(12), 2023; https://doi.org/10.3390/ani13122023 - 18 Jun 2023
Cited by 4 | Viewed by 1397
Abstract
The pleomorphic adenoma gene 1 (PLAG1) gene, as the major gene responsible for growth, plays a vital role in myogenesis. Meanwhile, the relationship between copy number variation (CNV) of this gene and growth traits in goats remains unclear. Therefore, this study [...] Read more.
The pleomorphic adenoma gene 1 (PLAG1) gene, as the major gene responsible for growth, plays a vital role in myogenesis. Meanwhile, the relationship between copy number variation (CNV) of this gene and growth traits in goats remains unclear. Therefore, this study investigated four aspects: bioinformatics analysis, mRNA expression (n = 6), CNV detection (n = 224), and association analysis. The findings indicated that the gene had a large number of conserved motifs, and the gene expression level was higher in fetal goats than in adult goats. Three CNV loci were selected from the database, among which CNV1 was located in the bidirectional promoter region and was associated with goat growth traits. CNV analysis showed that CNV2 and CNV3 of the PLAG1 gene were associated with growth traits such as body weight, heart girth, height at hip cross, and hip width (p < 0.05), with CNV1 loss genotype being the superior genotype, and CNV2 and CNV3 median and gain genotypes of being superior genotypes. This finding further confirms that the PLAG1 gene is the dominant gene for growth traits, which will serve as theoretical guidance for goat breeding. Full article
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18 pages, 5883 KiB  
Article
Effect of CXCL17 on Subcutaneous Preadipocytes Proliferation in Goats
by Guangyu Lu, Xiaotong Ma, Fei Wang, Dingshuang Chen, Yaqiu Lin, Youli Wang, Wei Liu and Yanyan Li
Animals 2023, 13(11), 1757; https://doi.org/10.3390/ani13111757 - 25 May 2023
Cited by 1 | Viewed by 1586
Abstract
The presence or absence of subcutaneous adipose accumulation will affect the energy storage, insulation resistance and metabolism of animals. Proliferation and differentiation of preadipocytes play a significant role in lipid deposition. The objective of this study was to clone the goat CXCL17 gene [...] Read more.
The presence or absence of subcutaneous adipose accumulation will affect the energy storage, insulation resistance and metabolism of animals. Proliferation and differentiation of preadipocytes play a significant role in lipid deposition. The objective of this study was to clone the goat CXCL17 gene and investigate its potential functions on goat subcutaneous preadipocytes’ proliferation by gaining or losing function in vitro. The goat CXCL17 gene was cloned by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and bioinformatics analysis was performed. The expression of the CXCL17 gene in the different goat tissues and adipocytes at different differentiation stages was detected by real-time fluorescence quantitative PCR (qPCR). The results showed that the cloned sequence of goat CXCL17 gene is 728 bp and the CDS region is 357 bp, encoding 118 amino acids. CXCL17 protein is located in nucleus, cytoplasm, mitochondria and extracellular matrix. Tissue-expression profiles revealed that CXCL17 expressed in all of the examined tissues. In visceral tissues, the highest expression level was found in lung (p < 0.01); in muscle tissues, the highest CXCL17 expression level was found in the longissimus dorsi (p < 0.01) and in adipose tissues, the highest expression level was found in subcutaneous adipose (p <0.01). Compared with those cells before differentiation, CXCL17 expression levels upregulated at 48 h (p < 0.01), 72 h (p < 0.01), 120 h (p < 0.01) and downregulated at 96 h (p < 0.01). Furthermore, the results of crystal violet staining and semi-quantitative assay showed that transfection with 1 μg CXCL17 expression plasmid reduced the cell numbers in vitro. Meanwhile, the expression of CCND1 was significantly decreased. A similar consequence happened after interfering with CXCL17 expression. However, plasmid transfected with 2 μg pEGFPN1-CXCL17 increased the number of cells in vitro. These results suggest that CXCL17 is involved in the proliferation of goat subcutaneous preadipocytes. Full article
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2022

Jump to: 2024, 2023, 2021, 2020

11 pages, 753 KiB  
Article
An Origanum majorana Leaf Diet Influences Myogenin Gene Expression, Performance, and Carcass Characteristics in Lambs
by Seyed Mohammad Hadi Safaei, Mohammad Dadpasand, Mohammadreza Mohammadabadi, Hadi Atashi, Ruslana Stavetska, Nataliia Klopenko and Oleksandr Kalashnyk
Animals 2023, 13(1), 14; https://doi.org/10.3390/ani13010014 - 20 Dec 2022
Cited by 48 | Viewed by 2057
Abstract
Myogenin is a protein in the myogenic regulatory factor family that plays an important role in determining carcass and meat traits and is vital for the growth and development of livestock muscles. The objective of this study was to determine the impact of [...] Read more.
Myogenin is a protein in the myogenic regulatory factor family that plays an important role in determining carcass and meat traits and is vital for the growth and development of livestock muscles. The objective of this study was to determine the impact of Origanum majorana leaf (MOL) on the myogenin gene expression of lambs. Twenty-four male Kermani lambs were used in a completely randomized design using two experimental groups (0% Origanum majorana L. = MOL0 and 4% Origanum majorana L. = MOL4). Final weight, average daily gain, hot and cold carcass weight, feed conversion ratio, empty body weight, hot and cold dressing percentage, the weight of the shoulder, loin, leg, and lean meat, and the lean/bone ratio were measured. A standard kit was used for extracting total RNA from the loin, leg, and shoulder muscles of the lambs’ tissues. The cDNA was synthesized, a real-time PCR was performed, and the obtained data were analyzed. The results of this study showed that the effect of MOL4 on dry matter intake is not significant. The MOL4 diet increased final weight by 8.22%, average daily gain by 28.57%, hot carcass weight by 11.38%, cold carcass weight by 13.43%, feed conversion ratio by 31.03%, empty body weight by 9.38%, hot dressing percentage by 2.92%, cold dressing percentage by 3.75%, shoulder weight by 56.70%, loin weight by 8.98%, leg weight by 10.90%, lean meat weight by 14.62%, and the lean/bone ratio by 2.85% (p < 0.05) compared to the MOL0. Along with adding MOL4 in the lambs’ diets, in comparison with MOL0, there was higher expression of myogenin in the loin (3.5 times), leg (3.9 times), and shoulder (3.6 times) muscles of the lambs. Due to the fact that adding Origanum majorana to the diet of the lambs enhanced the expression of the myogenin gene in the loin, leg, and shoulder muscles and increased parameters related to growth, it can be used to improve the parameters related to growth and to increase myogenin gene expression in the muscle of lambs. Full article
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14 pages, 1334 KiB  
Article
Genetic Diversity of Montenegrin Local Sheep Breeds Based on Microsatellite Markers
by Milan Marković, Dušica Radonjić, Minja Zorc, Milena Đokić and Božidarka Marković
Animals 2022, 12(21), 3029; https://doi.org/10.3390/ani12213029 - 3 Nov 2022
Cited by 3 | Viewed by 2575
Abstract
The Montenegrin sheep population mostly consists of local breeds and their crossbreeds that are very valuable from their genome preservation point of view. The aim of this study was the investigation of the genetic diversity of seven Montenegrin sheep breeds (Jezeropivska—JP, Sora—SOR, Zetska [...] Read more.
The Montenegrin sheep population mostly consists of local breeds and their crossbreeds that are very valuable from their genome preservation point of view. The aim of this study was the investigation of the genetic diversity of seven Montenegrin sheep breeds (Jezeropivska—JP, Sora—SOR, Zetska zuja—ZZ, Bardoka—BAR, Sjenička—SJ, Ljaba—Lj, and Piperska zuja—PIP) using 18 microsatellite sets of markers. The genotyping was done for 291 samples from seven populations using the multiplex amplification of sequences with polymerase chain reaction (PCR). The parameters of genetic diversity were estimated using several software tools. In total, 243 alleles were found, with a range of 6 to 25 by locus. The mean observed heterozygosity (Ho), polymorphism information content (PIC), and Fis values (fixation index) per marker were 0.728, 0.781, and −0.007, respectively. The mean number of alleles per breed varied from 4.889 in ZZ to 10.056 in JP. The highest Ho was estimated for JP (0.763) and the lowest for ZZ (0.640). The genetic structure showed close relations between SOR and JP, and both of them with SJ, while ZZ, LJ, and PIP were more distanced. This study provides useful indicators for the development of further in-depth studies and the creation of appropriate conservation programs. Full article
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13 pages, 1518 KiB  
Article
Using Pedigree and Genomic Data toward Better Management of Inbreeding in Italian Dairy Sheep and Goat Breeds
by Matteo Cortellari, Alessio Negro, Arianna Bionda, Silverio Grande, Alberto Cesarani, Antonello Carta, Nicola Macciotta, Stefano Biffani and Paola Crepaldi
Animals 2022, 12(20), 2828; https://doi.org/10.3390/ani12202828 - 18 Oct 2022
Cited by 9 | Viewed by 2794
Abstract
The inbreeding coefficient is an important parameter for livestock management. Small ruminant breeders and associations mainly rely on pedigree information, but genomic tools are gaining relevance, overcoming possible pedigree inconsistencies. This study investigates the relationship between pedigree-based and genomic inbreeding in two goat [...] Read more.
The inbreeding coefficient is an important parameter for livestock management. Small ruminant breeders and associations mainly rely on pedigree information, but genomic tools are gaining relevance, overcoming possible pedigree inconsistencies. This study investigates the relationship between pedigree-based and genomic inbreeding in two goat and four sheep dairy breeds. Pedigree and genomic data (medium-density SNPchip) were obtained for 3107 goats and 2511 sheep. We estimated pedigree depth (number of fully traced generations, FullGen) and inbreeding (FPED), as well as two genomic inbreeding indexes, using runs of the homozygosity (FROH) and genomic relationship matrix (FGRM). The correlation between the inbreeding coefficients was assessed. A linear regression model (LRM) was fitted for estimating FPED from FROH. After quality control on genomic data, we retained 5085 animals. Mean inbreeding values were low, with higher FROH than FPED and FGRM. Breed differences can partially depend on different managements. The correlation between FPED and FROH was the highest and directly related to pedigree depth. The best LRM was chosen for FullGen ≥4 and ≥6 for goats and sheep, respectively; after excluding animals with extreme residuals, a new refined regression equation was calculated. Since massive genotyping is not affordable to small ruminant breeders, it is important to understand the distinction and relationship between differently calculated inbreeding coefficients, also in view of the introduction of genomic enhanced breeding values. Our study highlights the importance of accurate pedigree information and, especially if not obtainable, of calculating genomic-based inbreeding coefficients. A better estimation of animals’ relatedness contributes to improve animal breeding and conservation. Full article
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10 pages, 261 KiB  
Communication
Stepwise Method and Factor Scoring in Multiple Regression Analysis of Cashmere Production in Liaoning Cashmere Goats
by Yang Meng, Boqi Zhang, Zhiyun Qin, Yang Chen, Xuesong Shan, Limin Sun and Huaizhi Jiang
Animals 2022, 12(15), 1886; https://doi.org/10.3390/ani12151886 - 23 Jul 2022
Cited by 4 | Viewed by 1761
Abstract
Liaoning cashmere goat is a well-known local cashmere goat breed in China and even in the world. It is famous for producing cashmere with superior quality and high yield. Cashmere yield, body measurements, and body weight are the primary indicators of cashmere goat [...] Read more.
Liaoning cashmere goat is a well-known local cashmere goat breed in China and even in the world. It is famous for producing cashmere with superior quality and high yield. Cashmere yield, body measurements, and body weight are the primary indicators of cashmere goat breeding, but the correlation between them is not yet clear. Therefore, this study investigated the relationship between certain body measurements, body weight, and cashmere yield in Liaoning cashmere goats using stepwise and factor score analyses in a multiple regression analysis. For this purpose, the body measurements (body slanting length (BSL), body height (BH), chest circumference (CC), pipe circumference (PC), chest depth (CD), chest width (CW), hip breadth (HB), body weight (BW) and cashmere yield (CY)) of 200 (2-year-old) Liaoning cashmere goats were collected. Stepwise analysis of the results showed that body weight had the greatest direct effect on cashmere yield, followed by hip breadth, while chest circumference mainly affected cashmere yield indirectly. The results of factor score analysis showed that the independent variable can be represented by two factors, which explained 49.596% and 12.095% of the total variance, respectively. The factor scores used in the regression analysis explained 75.8% of the total variance in Liaoning cashmere yield. The above studies show that the growth traits of Liaoning cashmere goats are closely related to the cashmere yield. Growth traits should be considered important factors in breed selection, germplasm identification, and rearing. Full article
14 pages, 4148 KiB  
Article
Analysis of the Genetic Diversity and Population Structure of Four Senegalese Sheep Breeds Using Medium-Density Single-Nucleotide Polymorphisms
by Ayao Missohou, Basse Kaboré, Laurence Flori, Simplice Bosco Ayssiwede, Jean-Luc Hornick, Marianne Raes and Jean-François Cabaraux
Animals 2022, 12(12), 1512; https://doi.org/10.3390/ani12121512 - 10 Jun 2022
Cited by 3 | Viewed by 2768
Abstract
In Senegal, sheep breeds have adapted to their environment and play a key socio-economic role. This study aimed to explore the genetic diversity and structure of four Senegalese sheep breeds (Peul-peul, Djallonke, Touabire, and Ladoum) and their relationships with global sheep breeds. To [...] Read more.
In Senegal, sheep breeds have adapted to their environment and play a key socio-economic role. This study aimed to explore the genetic diversity and structure of four Senegalese sheep breeds (Peul-peul, Djallonke, Touabire, and Ladoum) and their relationships with global sheep breeds. To that end, forty-seven sheep were genotyped using the OvineSNP50 BeadChip, and these genotypic data were analysed with those of 73 sheep breeds representative of worldwide ovine diversity (2729 animals). The average observed heterozygosity (Ho) ranged from 0.293 in Djallonke sheep to 0.339 in Touabire sheep. The estimated Fis values were low, ranging from 0.019 for Ladoum to 0.034 for Peul-peul sheep. The estimated Fst values were low (0.003–0.044) among the trypanosusceptible breeds (Peul-peul, Touabire, and Ladoum) but high between the previous breeds and the trypanotolerant Djallonke breed (0.075–0.116), indicating better genetic conservation of the Djallonke sheep. A principal component analysis revealed clustering of the Senegalese sheep breeds according to their geographic distribution. However, owing to genetic improvement practices, the introgression of Touabire sheep blood seems to have reshaped the genetic landscape of the trypanosusceptible sheep breeds in Senegal. The Senegalese sheep breeds showed lower genetic diversity than their presumed ancestral sheep breeds of the Middle East. They also presented some relatedness with Caribbean sheep breeds, which reveals their contribution to the global genetic diversity and to the development of Caribbean sheep breeds. Full article
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2021

Jump to: 2024, 2023, 2022, 2020

10 pages, 2479 KiB  
Article
Variations in HIF-1α Contributed to High Altitude Hypoxia Adaptation via Affected Oxygen Metabolism in Tibetan Sheep
by Pengfei Zhao, Zhaohua He, Qiming Xi, Hongxian Sun, Yuzhu Luo, Jiqing Wang, Xiu Liu, Zhidong Zhao and Shaobin Li
Animals 2022, 12(1), 58; https://doi.org/10.3390/ani12010058 - 28 Dec 2021
Cited by 5 | Viewed by 2833
Abstract
The Tibetan sheep is an indigenous species of the Tibetan plateau and has been well adapted to high-altitude hypoxia. In comparison to lowland sheep breeds, the blood gas indicators have changed and the HIFs signaling pathway is activated in Tibetan sheep. These phenotypic [...] Read more.
The Tibetan sheep is an indigenous species of the Tibetan plateau and has been well adapted to high-altitude hypoxia. In comparison to lowland sheep breeds, the blood gas indicators have changed and the HIFs signaling pathway is activated in Tibetan sheep. These phenotypic and genetic alterations in Tibetan sheep are thought to be an important basis for adaptation to high-altitude hypoxia and variation in genes encoding the subunits that make up HIFs, such as HIF-1α can affect blood gas indicators. In this study, exons 9, 10, 12 of the HIF-1α gene were sequenced to find variations and 3 SNPs were detected, and these 3 SNPs were genotyped by KASP in 341 Hu sheep and 391 Tibetan sheep. In addition, 197 Hu sheep, 160 Tibetan sheep and 12 Gansu alpine merino sheep were used for blood gas indicators analysis. The results showed significant differences between the blood gas indicators of high-altitude breeds (Tibetan sheep and Gansu alpine merino sheep) and low-altitude breeds (Hu sheep), implying that the differences in blood gas indicators are mainly caused by differences in altitude. The haplotype combinations H2H3 and H1H3 were more frequent in the Tibetan sheep population, H2H3 increases O2 carrying capacity by increasing hematocrit and hemoglobin concentrations; H1H3 makes O2 dissociate more readily from oxyhemoglobin by decreasing partial pressure of oxygen and oxygen saturation. These results suggest that variants at the HIF-1α promote the ability of oxygen utilization in Tibetan sheep, which may underpin the survival and reproduction of Tibetan sheep on the Tibetan plateau. Full article
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16 pages, 2291 KiB  
Article
Rumen Fermentation—Microbiota—Host Gene Expression Interactions to Reveal the Adaptability of Tibetan Sheep in Different Periods
by Weibing Lv, Xiu Liu, Yuzhu Sha, Hao Shi, Hong Wei, Yuzhu Luo, Jiqing Wang, Shaobin Li, Jiang Hu, Xinyu Guo and Xiaoning Pu
Animals 2021, 11(12), 3529; https://doi.org/10.3390/ani11123529 - 10 Dec 2021
Cited by 10 | Viewed by 3654
Abstract
As an important ruminant on the Qinghai-Tibet Plateau, Tibetan sheep can maintain their population reproduction rate in the harsh high-altitude environment of low temperature and low oxygen, which relies on their special plateau adaptations mechanism that they have formed for a long time. [...] Read more.
As an important ruminant on the Qinghai-Tibet Plateau, Tibetan sheep can maintain their population reproduction rate in the harsh high-altitude environment of low temperature and low oxygen, which relies on their special plateau adaptations mechanism that they have formed for a long time. Microbiomes (known as “second genomes”) are closely related to the nutrient absorption, adaptability, and health of the host. In this study, rumen fermentation characteristics, the microbiota, and rumen epithelial gene expression of Tibetan sheep in various months were analyzed. The results show that the rumen fermentation characteristics of Tibetan sheep differed in different months. The total SCFAs (short-chain fatty acids), acetate, propionate, and butyrate concentrations were highest in October and lowest in June. The CL (cellulase) activity was highest in February, while the ACX (acid xylanase) activity was highest in April. In addition, the diversity and abundance of rumen microbes differed in different months. Bacteroidetes (53.4%) and Firmicutes (27.4%) were the dominant phyla. Prevotella_1 and Rikenellaceae_RC9_gut_group were the dominant genera. The abundance of Prevotella_1 was highest in June (27.8%) and lowest in December (17.8%). In addition, the expression of CLAUDIN4 (Claudin-4) and ZO1 (Zonula occludens 1) was significantly higher in April than in August and December, while the expression of SGLT1 (Sodium glucose linked transporter 1) was highest in August. Correlation analysis showed that there were interactions among rumen fermentation characteristics, the microbiota, and host gene expression, mainly by adjusting the amino acid metabolism pathway and energy metabolism pathway to improve energy utilization. At the same time, we adjusted the balance of the rumen “core microbiota” to promote the development of rumen and maintain the homeostasis of rumen environment, which makes Tibetan sheep better able to adapt to the harsh environment in different periods of the Qinghai-Tibet Plateau. Full article
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16 pages, 4792 KiB  
Article
MicroRNA-200b Regulates the Proliferation and Differentiation of Ovine Preadipocytes by Targeting p27 and KLF9
by Xiayang Jin, Jiqing Wang, Jiang Hu, Xiu Liu, Shaobin Li, Yujie Lu, Huimin Zhen, Mingna Li, Zhidong Zhao and Yuzhu Luo
Animals 2021, 11(8), 2417; https://doi.org/10.3390/ani11082417 - 17 Aug 2021
Cited by 11 | Viewed by 2996
Abstract
MicroRNAs (miRNAs) are crucial regulatory molecules in lipid deposition and metabolism. However, the effect of miR-200b on the regulation of proliferation and adipogenesis of ovine preadipocytes is unknown in the sheep (Ovis aries). In this study, the expression profiles of miR-200b [...] Read more.
MicroRNAs (miRNAs) are crucial regulatory molecules in lipid deposition and metabolism. However, the effect of miR-200b on the regulation of proliferation and adipogenesis of ovine preadipocytes is unknown in the sheep (Ovis aries). In this study, the expression profiles of miR-200b were investigated in the seven tissues of Tibetan ewes and differentiated preadipocytes. The effect of miR-200b, as well as its target genes p27 and KLF9, on the proliferation of ovine preadipocytes and adipogenesis was also investigated, using cell viability analysis, EdU staining, Oil Red O staining and reverse transcription-quantitative PCR (RT-qRCR). The miR-200b was expressed in all the tissues investigated, and it was highly expressed in lung, liver, subcutaneous adipose and spleen tissues. The expression of miR-200b continuously decreased when the differentiation of ovine preadipocytes initiated. The miR-200b mimic dramatically accelerated the proliferation but inhibited differentiation of ovine preadipocytes. The miR-200b inhibitor resulted in an opposite effect on the proliferation and differentiation of ovine preadipocytes. The dual luciferase reporter assay results showed that miR-200b mimic significantly decreased the luciferase activity of p27 and KLF9 in HEK293 cells transfected with wild-type dual luciferase reporter vectors. This suggests that p27 and KLF9 are the target genes of miR-200b. In over-expressed-p27 preadipocytes, the number of EdU-labeled preadipocytes and the expression levels of proliferation marker genes CDK2, CDK4, CCND1 and PCNA significantly decreased. In addition, the transfection of over-expressed-KLF9 vector into adipocytes remarkably increased the accumulation of lipid droplets and the expression levels of differentiation marker genes aP2, PPARγ, LPL and GLUT4. These results suggest that miR-200b accelerated the proliferation but inhibited the adipogenic differentiation of ovine preadipocytes by targeting p27 and KLF9, respectively. Full article
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14 pages, 939 KiB  
Article
Polymorphisms of Codons 110, 146, 211 and 222 at the Goat PRNP Locus and Their Association with Scrapie in Greece
by Athanasios I. Gelasakis, Evridiki Boukouvala, Maria Babetsa, Efstathios Katharopoulos, Vayia Palaska, Dimitra Papakostaki, Nektarios D. Giadinis, Dimitrios Loukovitis, Jan P. M. Langeveld and Loukia V. Ekateriniadou
Animals 2021, 11(8), 2340; https://doi.org/10.3390/ani11082340 - 8 Aug 2021
Cited by 5 | Viewed by 3415
Abstract
Scrapie is considered an endemic disease in both sheep and goats in Greece. However, contrary to sheep, in goats more than one prion protein (PrP) polymorphism has been recognized as a candidate for resistance breeding against the disease. For an impression, candidates which [...] Read more.
Scrapie is considered an endemic disease in both sheep and goats in Greece. However, contrary to sheep, in goats more than one prion protein (PrP) polymorphism has been recognized as a candidate for resistance breeding against the disease. For an impression, candidates which are circulating, (i) brain samples (n = 525) from scrapie-affected (n = 282) and non-affected (n = 243) animals within the national surveillance program, and (ii) individual blood samples (n = 1708) from affected (n = 241) and non-affected (n = 1467) herds, in a large part of mainland Greece and its islands, were collected and assayed. A dedicated Taqman method was used to test for amino acid polymorphisms 110T/P, 146N/S/D, 211R/Q, and 222Q/K. Highly prevalent genotypes were 110TT, 146NN, 211RR, and 222QQ. The frequencies of polymorphisms in blood and negative brain samples for codons 110P, 211Q, and 222K were 4.0%, 3.0%, and 1.9%, respectively, while 146D (0.7%) was present only on Karpathos island. Codon 110P was exclusively found in scrapie-negative brains, and homozygous 110P/P in two scrapie-negative goats. It is concluded that breeding programs in Karpathos could focus on codon 146D, while in other regions carriers of the 110P and 222K allele should be sought. Case-control and challenge studies are now necessary to elucidate the most efficient breeding strategies. Full article
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10 pages, 1534 KiB  
Article
Placental Characteristics Classification of Various Native Turkish Sheep Breeds
by Uğur Şen, Hasan Önder, Emre Şirin, Selçuk Özyürek, Dariusz Piwczynski, Magdalena Kolenda and Sezen Ocak Yetişgin
Animals 2021, 11(4), 930; https://doi.org/10.3390/ani11040930 - 25 Mar 2021
Cited by 6 | Viewed by 2383
Abstract
The aim of this study was to classify placental characteristics of Akkaraman, Morkaraman, Karayaka, Awassi, Malya, and Bafra sheep breeds using the hierarchical clustering method. In total, 240 individual data records were used as experimental material. Placental characteristics such as total cotyledon surface [...] Read more.
The aim of this study was to classify placental characteristics of Akkaraman, Morkaraman, Karayaka, Awassi, Malya, and Bafra sheep breeds using the hierarchical clustering method. In total, 240 individual data records were used as experimental material. Placental characteristics such as total cotyledon surface area, small and large cotyledon length, small cotyledon depth, etc. were used as explanatory variables to classify the breeds’ characteristics. Hierarchical clustering was used with the nearest neighbour method with Euclidean distance in order to classify the sheep breeds’ variations. As a result, six breeds were separated into three clusters: the first cluster consisted of Bafra, Karayaka, and Awassi breeds; the second consisted of Akkaraman and Malya breeds; and the third cluster included only the Morkaraman breed. Bafra and Karayaka were pointed as the nearest breeds, with a similarity of 98.7% in terms of placental characteristics. The similarity rate of the Akkaraman and Malya breeds was at a level of 97.5%, whereas it was 96.8% for Bafra, Karayaka, and Awassi breeds. The similarity of Akkaraman, Karayaka, Awassi, Malya, and Bafra sheep breeds was estimated as 95.7%. The overall similarity was found to be at a level of 93.2% among sheep breeds. The outcomes of the study might be useful as a selection tool for reproductivity and can be used to select the breed to be reared. Full article
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2020

Jump to: 2024, 2023, 2022, 2021

15 pages, 440 KiB  
Article
The LEPR Gene Is Associated with Reproductive Seasonality Traits in Rasa Aragonesa Sheep
by Kenza Lakhssassi, Malena Serrano, Belén Lahoz, María Pilar Sarto, Laura Pilar Iguácel, José Folch, José Luis Alabart and Jorge Hugo Calvo
Animals 2020, 10(12), 2448; https://doi.org/10.3390/ani10122448 - 21 Dec 2020
Cited by 9 | Viewed by 2891
Abstract
The aim of this study was to characterize and identify causative polymorphisms in the leptin receptor (LEPR) gene responsible for the seasonal variation of reproductive traits in sheep. Three reproductive seasonality traits were studied: the total days of anoestrous (TDA), the [...] Read more.
The aim of this study was to characterize and identify causative polymorphisms in the leptin receptor (LEPR) gene responsible for the seasonal variation of reproductive traits in sheep. Three reproductive seasonality traits were studied: the total days of anoestrous (TDA), the progesterone cycling months (P4CM) and the oestrous cycling months (OCM). In total, 18 SNPs were detected in 33 ewes with extreme values for TDA and OCM. Six SNPs were non-synonymous substitutions and two of them were predicted in silico as deleterious: rs596133197 and rs403578195. These polymorphisms were then validated in 239 ewes. The SNP rs403578195, located in exon 8 and leading to a change of alanine to glycine (Ala284Gly) in the extracellular domain of the protein, was associated with the OCM trait, being the G allele associated with a decrease of 12 percent of the OCM trait. Haplotype analyses also suggested the involvement of other non-synonymous SNP located in exon 20 (rs405459906). This SNP also produces an amino acid change (Lys1069Glu) in the intracellular domain of the protein and segregates independently of rs403578195. These results confirm for the first time the role of the LEPR gene in sheep reproductive seasonality. Full article
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13 pages, 1268 KiB  
Article
Genetic Signatures of Selection for Cashmere Traits in Chinese Goats
by Meilin Jin, Jian Lu, Xiaojuan Fei, Zengkui Lu, Kai Quan, Yongbin Liu, Mingxing Chu, Ran Di, Huihua Wang and Caihong Wei
Animals 2020, 10(10), 1905; https://doi.org/10.3390/ani10101905 - 18 Oct 2020
Cited by 27 | Viewed by 3584
Abstract
Inner Mongolia and Liaoning cashmere goats in China are well-known for their cashmere quality and yield. Thus, they are great models for identifying genomic regions associated with cashmere traits. Herein, 53 Inner Mongolia cashmere goats, Liaoning cashmere goats and Huanghuai goats were genotyped, [...] Read more.
Inner Mongolia and Liaoning cashmere goats in China are well-known for their cashmere quality and yield. Thus, they are great models for identifying genomic regions associated with cashmere traits. Herein, 53 Inner Mongolia cashmere goats, Liaoning cashmere goats and Huanghuai goats were genotyped, and 53,347 single-nucleotide polymorphisms (SNPs) were produced using the Illumina Caprine 50K SNP chip. Additionally, we identified some positively selected SNPs by analyzing Fst and XP-EHH. The top 5% of SNPs had selection signatures. After gene annotation, 222 and 173 candidate genes were identified in Inner Mongolia and Liaoning cashmere goats, respectively. Several genes were related to hair follicle development, such as TRPS1, WDR74, LRRC14, SPTLC3, IGF1R, PADI2, FOXP1, WNT10A and CSN3. Gene enrichment analysis of these cashmere trait-associated genes related 67 enriched signaling pathways that mainly participate in hair follicle development and stem cell pluripotency regulation. Furthermore, we identified 20 overlapping genes that were selected in both cashmere goat breeds. Among these overlapping genes, WNT10A and CSN3, which are associated with hair follicle development, are potentially involved in cashmere production. These findings may improve molecular breeding of cashmere goats in the future. Full article
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