1
|
Chen Y, Liu Y, Chu M. miRNA-mRNA analysis of sheep adrenal glands reveals the network regulating reproduction. BMC Genom Data 2022; 23:44. [PMID: 35710353 PMCID: PMC9205095 DOI: 10.1186/s12863-022-01060-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 05/16/2022] [Indexed: 11/29/2022] Open
Abstract
Background The adrenal gland participates in the process of sheep reproduction. MicroRNAs (miRNAs), endogenous small noncoding RNAs, regulate gene expression at the posttranscriptional level. However, the miRNA-mRNA network profile of adrenal glands relating to reproduction in sheep is still not well-studied. As sheep with FecBBB genotype show higher lambing number compare with the sheep with FecB++ genotype. This research aims to compare gene expression by small RNA-seq in adrenal tissues at follicular (F) and luteal (L) phases in FecBBB (MM) and FecB++ (ww) sheep. After analysis of gene expression, significant differentially expressed microRNAs (DEMs) and corresponding target genes were identified. Results A total of 180 miRNAs were found in this study, of which 19 DEMs were expressed in the four comparison groups (MM_F_A vs. MM_L_A, MM_F_A vs. ww_F_A, MM_L_A vs. ww_L_A, ww_F_A vs. ww_L_A). Subsequently, 354 target genes of 19 DEMs were predicted by integrated analysis. Cluster analysis was performed by K_means_cluster, and the expression patterns of these DEMs were separated into four subclusters. Functional analysis of target genes was performed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The results indicated that the target genes were involved mainly in the Notch signaling pathway, signal transduction, cell communication, innate immune response and amino acid metabolism. Specifically, the Notch signaling pathway, biosynthetic process and metabolic process of pyrimidine nucleotide and amino acid metabolism appear to play key regulatory roles in the sheep fertility trait. Furthermore, miRNA-mRNA interaction networks were constructed by differentially expressed genes combined with our previous study of transcriptome data. The results showed that several key genes, including TDRD3, ANAPC7, CCNL2, BRD2 and MUT, were related to the transformation from the follicular phase to the luteal phase. PLAC8L1, NFAT5, DDX24 and MBD1 were related to the high fecundity of small tail Han sheep. Conclusions In this study, the miRNA transcriptome profile was identified, and miRNA-mRNA interaction networks were constructed in adrenal gland tissue of small tail Han sheep, the interaction between miR-370-3p and its targets were considered to play a major role in the reproduction regulation process. The results enriched the number of known miRNAs in adrenal glands and provided novel ideas and further information to demonstrate posttranscriptional regulation mechanisms at follicular and luteal phases in different genotypes of small tail Han sheep. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01060-y.
Collapse
|
2
|
Li C, Zhang R, Zhang Z, Ren C, Wang X, He X, Mwacharo JM, Zhang X, Zhang J, Di R, Chu M. Expression characteristics of piRNAs in ovine luteal phase and follicular phase ovaries. Front Vet Sci 2022; 9:921868. [PMID: 36157184 PMCID: PMC9493120 DOI: 10.3389/fvets.2022.921868] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
PIWI-interacting RNAs (piRNAs), as a novel class of small non-coding RNAs that have been shown to be indispensable in germline integrity and stem cell development. However, the expressed characteristics and regulatory roles of piRNAs during different reproductive phases of animals remain unknown. In this study, we investigated the piRNAs expression profiles in ovaries of sheep during the luteal phase (LP) and follicular phase (FP) using the Solexa sequencing technique. A total of 85,219 and 1,27,156 piRNAs tags were identified in ovine ovaries across the two phases. Most expressed piRNAs start with uracil. piRNAs with a length of 24 nt or 27–29 nts accounted for the largest proportion. The obvious ping-pong signature appeared in the FP ovary. The piRNA clusters in the sheep ovary were unevenly distributed on the chromosomes, with high density on Chr 3 and 1. For genome distribution, piRNAs in sheep ovary were mainly derived from intron, CDS, and repeat sequence regions. Compared to the LP ovary, a greater number of expressed piRNA clusters were detected in the FP ovary. Simultaneously, we identified 271 differentially expressed (DE) piRNAs between LP and FP ovaries, with 96 piRNAs upregulated and 175 piRNAs downregulated, respectively. Functional enrichment analysis (GO and KEGG) indicated that their target genes were enriched in reproduction-related pathways including oocyte meiosis, PI3K-Akt, Wnt, and TGF-β signaling pathways. Together, our results highlighted the sequence and expression characteristics of the piRNAs in the sheep ovary, which will help us understand the roles of piRNAs in the ovine estrus cycle.
Collapse
Affiliation(s)
- Chunyan Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Rensen Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zijun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Chunhuan Ren
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Joram Mwashigadi Mwacharo
- Small Ruminant Genomics, International Center for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
- Institute of Animal and Veterinary Sciences, Animal and Veterinary Sciences, SRUC and Center for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | | | - Jinlong Zhang
- Tianjin Institute of Animal Sciences, Tianjin, China
| | - Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Ran Di
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Mingxing Chu
| |
Collapse
|
3
|
Cheng J, Zhang X, Xu D, Zhang D, Zhang Y, Song Q, Li X, Zhao Y, Zhao L, Li W, Wang J, Zhou B, Lin C, Yang X, Zhai R, Cui P, Zeng X, Huang Y, Ma Z, Liu J, Wang W. Relationship between rumen microbial differences and traits among Hu sheep, Tan sheep, and Dorper sheep. J Anim Sci 2022; 100:skac261. [PMID: 35953151 PMCID: PMC9492252 DOI: 10.1093/jas/skac261] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Rumen microbes play an important role in the growth and development of ruminants. Differences in variety will affect the rumen community structure. The three excellent sheep breeds were selected for this study (Hu sheep, Tan sheep, and Dorper sheep) have different uses and origins. The sheep were raised on the same diet to 180 d of age in a consistent environment. 16S rDNA V3 to V4 region sequencing was used to assess the rumen microbes of 180 individuals (60 per breed). There were differences in microbial diversity among different sheep breeds (P < 0.05). Principal coordinate analysis showed that the three varieties were separated, but also partially overlapped. Linear discriminant analysis effect size identified a total of 19 biomarkers in three breeds. Of these biomarkers, five in Hu sheep were significantly negatively correlated with average feed conversion rate (P < 0.05). Six biomarkers were identified in the rumen of Dorper sheep, among which Ruminococcus was significantly positively correlated with body weight at 80 d (P < 0.05). In Tan sheep, Rikenellaceae_RC9_gut_group was significantly positively correlated with meat fat, and significantly positively correlated with volatile fatty acids (VFAs), such as butyric acid and isobutyric acid (P < 0.05). The Rikenellaceae_RC9_gut_group may regulate Tan mutton fat deposition by affecting the concentration of VFAs. Functional prediction revealed enrichment differences of functional pathways among different sheep breeds were small. All were enriched in functions, such as fermentation and chemoheterotrophy. The results show that there are differences in the rumen microorganisms of the different sheep breeds, and that the microorganisms influence the host.
Collapse
Affiliation(s)
- Jiangbo Cheng
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Yukun Zhang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Qizhi Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yuan Zhao
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yongliang Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu 730020, China
| |
Collapse
|
4
|
Peng H, Hu M, Liu Z, Lai W, Shi L, Zhao Z, Ma H, Li Y, Yan S. Transcriptome Analysis of the Liver and Muscle Tissues of Dorper and Small-Tailed Han Sheep. Front Genet 2022; 13:868717. [PMID: 35480317 PMCID: PMC9035493 DOI: 10.3389/fgene.2022.868717] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/21/2022] [Indexed: 11/25/2022] Open
Abstract
It is well known that Dorper (DP) is a full-bodied, fast-growing and high dressing percentage breed, while the production performance of Small-tailed Han sheep (STH) is not so excellent, in contrast to DP. Therefore, in this study, a comparative transcriptomic analysis of liver and muscle tissues from DP and STH breeds was carried out to find differentially expressed genes (DEGs) that affect their growth and meat quality traits. The results showed that the total number of DEGs was 2,188 in the two tissues. There were 950, 160 up-regulated and 1,007, 71 down-regulated genes in the liver and muscle, respectively. Several DEGs such as TGFB1, TGFB3, FABP3, LPL may be associated with growth and development in DP. Also, several GO terms were found to be associated with muscle growth and development, such as developmental growth (GO:0048589), and myofibril (GO:0030016). Further validation of eight genes (6 up-regulated, and 2 down-regulated) was performed using quantitative RT-PCR. These findings will provide valuable information for studying growth and development as well as meat quality traits in sheep.
Collapse
Affiliation(s)
- Hongyang Peng
- College of Animal Science, Jilin University, Changchun, China
| | - Mingyue Hu
- College of Animal Science, Jilin University, Changchun, China
| | - Zhengxi Liu
- College of Animal Science, Jilin University, Changchun, China
| | - Weining Lai
- College of Animal Science, Jilin University, Changchun, China
| | - Lulu Shi
- College of Animal Science, Jilin University, Changchun, China
| | - Zhongli Zhao
- Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Huihai Ma
- Institute of Animal Husbandry and Veterinary, Jilin Academy of Agricultural Sciences, Gongzhuling, China
| | - Yumei Li
- College of Animal Science, Jilin University, Changchun, China
- *Correspondence: Yumei Li, ; Shouqing Yan,
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun, China
- *Correspondence: Yumei Li, ; Shouqing Yan,
| |
Collapse
|
5
|
Han Q, He X, Di R, Chu M. Comparison of expression patterns of six canonical clock genes of follicular phase and luteal phase in Small-tailed Han sheep. Arch Anim Breed 2021; 64:457-466. [PMID: 34746369 PMCID: PMC8567854 DOI: 10.5194/aab-64-457-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 08/30/2021] [Indexed: 12/24/2022] Open
Abstract
The circadian rhythm is a biological rhythm that is closely related to
the rhythmic expression of a series of clock genes. Results from several
studies have indicated that clock genes are associated with the estrous cycle in
female animals. Until now, the relationship between estrus cycle transition
and clock gene expression in reproductive-axis-related tissues has remained
unknown in Small-tailed Han (STH) sheep. This study was conducted to analyze
the expression patterns of six canonical clock genes (Clock, BMAL1, Per1, Per2, Cry1, and Cry2) in the follicle
phase and luteal phase of STH sheep. We found that all six genes were
expressed in the brain, cerebellum, hypothalamus, pituitary, ovary, uterus,
and oviduct in follicle and luteal phases. The results indicated that Clock expression
was significantly higher in the cerebellum, hypothalamus, and uterus of
the luteal phase than that of the follicle phase, whereas BMAL1 expression was
significantly higher in the hypothalamus of the luteal phase than that of
the follicle phase. Per1 expression was significantly higher in the brain,
cerebellum, hypothalamus, and pituitary of the luteal phase than that of the follicle
phase, and Per2 expression was significantly higher in the hypothalamus,
pituitary, and uterus of the luteal phase than that of the follicle phase. Cry1
expression was significantly higher in the brain, cerebellum, and
hypothalamus of the luteal phase than that of the follicle phase, whereas Cry2 expression
was significantly higher in the pituitary of the luteal phase than that of the
follicle phase. The clock gene expression in all tissues was different
between follicle and luteal phases, but all clock gene mRNA levels were
found to exhibit higher expression among seven tissues in the luteal
phase. Our results suggest that estrous cycles may be associated
with clock gene expression in the STH sheep. This is the first study to
systematically analyze the expression patterns of clock genes of different
estrous cycle in ewes, which could form a basis for further studies to
develop the relationship between clock genes and the estrous cycle.
Collapse
Affiliation(s)
- Qi Han
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Ran Di
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R. China
| |
Collapse
|
6
|
Li Z, He X, Zhang X, Zhang J, Guo X, Sun W, Chu M. Analysis of Expression Profiles of CircRNA and MiRNA in Oviduct during the Follicular and Luteal Phases of Sheep with Two Fecundity ( FecB Gene) Genotypes. Animals (Basel) 2021; 11:ani11102826. [PMID: 34679847 PMCID: PMC8532869 DOI: 10.3390/ani11102826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/09/2021] [Accepted: 09/20/2021] [Indexed: 12/11/2022] Open
Abstract
CircRNA and miRNA, as classes of non-coding RNA, have been found to play pivotal roles in sheep reproduction. There are many reports of circRNA and miRNA in the ovary and uterus, but few in the oviduct. In this study, RNA-Seq was performed to analyze the expression profile of circRNA and miRNA in the oviduct during the follicular phase and luteal phase of sheep with FecBBB and FecB++ genotypes. The results showed that a total of 3223 circRNAs and 148 miRNAs were identified. A total of 15 DE circRNAs and 40 DE miRNAs were found in the comparison between the follicular phase and luteal phase, and 1 DE circRNA and 18 DE miRNAs were found in the comparison between the FecBBB genotype and FecB++ genotype. GO and KEGG analyses showed that the host genes of DE circRNAs were mainly enriched in the Rap1 signaling pathway, PI3K-Akt signaling pathway and neuroactive ligand-receptor interactions. Novel_circ_0004065, novel_circ_0005109, novel_circ_0012086, novel_circ_0014274 and novel_circ_0001794 were found to be possibly involved in the oviductal reproduction process. GO and KEGG analyses showed that the target genes of DE miRNAs were mainly enriched in insulin secretion, the cAMP signaling pathway, the cGMP-PKG signaling pathway, the Rap1 signaling pathway and the TGF-β signaling pathway, and the target genes LPAR1, LPAR2, FGF18, TACR3, BMP6, SMAD4, INHBB, SKP1 and TGFBR2 were found to be associated with the reproductive process. Miranda software was used to identify 27 miRNAs that may bind to 13 DE circRNAs, including miR-22-3p (target to novel_circ_0004065), miR-127, miR-136 (target to novel_circ_0000417), miR-27a (target to novel_circ_0014274) and oar-miR-181a (target to novel_circ_ 0017815). The results of this study will help to elucidate the regulatory mechanisms of circRNAs and miRNAs in sheep reproduction. Our study, although not establishing direct causal relationships of the circRNA and miRNA changes, enriches the sheep circRNA and miRNA database and provides a basis for further studies on sheep reproduction.
Collapse
Affiliation(s)
- Zhifeng Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.L.); (X.H.)
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.L.); (X.H.)
| | - Xiaosheng Zhang
- Tianjin Institute of Animal Sciences, Tianjin 300381, China; (X.Z.); (J.Z.); (X.G.)
| | - Jinlong Zhang
- Tianjin Institute of Animal Sciences, Tianjin 300381, China; (X.Z.); (J.Z.); (X.G.)
| | - Xiaofei Guo
- Tianjin Institute of Animal Sciences, Tianjin 300381, China; (X.Z.); (J.Z.); (X.G.)
| | - Wei Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence: (W.S.); (M.C.); Tel.: +86-0514-8797-9213 (W.S.); +86-010-6281-9850 (M.C.)
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Z.L.); (X.H.)
- Correspondence: (W.S.); (M.C.); Tel.: +86-0514-8797-9213 (W.S.); +86-010-6281-9850 (M.C.)
| |
Collapse
|
7
|
Li C, He X, Zhang Z, Ren C, Chu M. Pineal gland transcriptomic profiling reveals the differential regulation of lncRNA and mRNA related to prolificacy in STH sheep with two FecB genotypes. BMC Genom Data 2021; 22:9. [PMID: 33602139 PMCID: PMC7893892 DOI: 10.1186/s12863-020-00957-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/16/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Long noncoding RNA (lncRNA) has been identified as important regulator in hypothalamic-pituitary-ovarian axis associated with sheep prolificacy. However, little is known of their expression pattern and potential roles in the pineal gland of sheep. Herein, RNA-Seq was used to detect transcriptome expression pattern in pineal gland between follicular phase (FP) and luteal phase (LP) in FecBBB (MM) and FecB++ (ww) STH sheep, respectively, and differentially expressed (DE) lncRNAs and mRNAs associated with reproduction were identified. RESULTS Overall, 135 DE lncRNAs and 1360 DE mRNAs in pineal gland between MM and ww sheep were screened. Wherein, 39 DE lncRNAs and 764 DE mRNAs were identified (FP vs LP) in MM sheep, 96 DE lncRNAs and 596 DE mRNAs were identified (FP vs LP) in ww sheep. Moreover, GO and KEGG enrichment analysis indicated that the targets of DE lncRNAs and DE mRNAs were annotated to multiple biological processes such as phototransduction, circadian rhythm, melanogenesis, GSH metabolism and steroid biosynthesis, which directly or indirectly participate in hormone activities to affect sheep reproductive performance. Additionally, co-expression of lncRNAs-mRNAs and the network construction were performed based on correlation analysis, DE lncRNAs can modulate target genes involved in related pathways to affect sheep fecundity. Specifically, XLOC_466330, XLOC_532771, XLOC_028449 targeting RRM2B and GSTK1, XLOC_391199 targeting STMN1, XLOC_503926 targeting RAG2, XLOC_187711 targeting DLG4 were included. CONCLUSION All of these differential lncRNAs and mRNAs expression profiles in pineal gland provide a novel resource for elucidating regulatory mechanism underlying STH sheep prolificacy.
Collapse
Affiliation(s)
- Chunyan Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zijun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Chunhuan Ren
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| |
Collapse
|
8
|
Xia Q, Wang X, Pan Z, Zhang R, Wei C, Chu M, Di R. Genetic diversity and phylogenetic relationship of nine sheep populations based on microsatellite markers. Arch Anim Breed 2021; 64:7-16. [PMID: 34084899 PMCID: PMC8160997 DOI: 10.5194/aab-64-7-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 11/02/2020] [Indexed: 11/11/2022] Open
Abstract
The objective of this study was to assess the genetic diversity and
phylogenetic relationship of nine sheep populations, including two famous
high prolific populations and seven popular mutton populations raised in
China. Overall, these sheep populations in this study exhibited a rich
genetic diversity. Both the expected heterozygosity and Nei's unbiased gene
diversity ranged from 0.64 to 0.75, with the lowest value found in Dorset sheep (DST) and
the highest in Hu sheep (HUS) and Ba Han sheep (BAS). The polymorphic information content (PIC) varied between 0.59 in DST and 0.71 in HUS and BAS. Specifically, for
individual breeds, the small-tail Han sheep (STH) and the four introduced populations did not
display the expected diversity; therefore more attention should be paid to
the maintenance of diversity during management of these populations. The
results of un-weighted pair-group method (UPGMA) phylogenetic tree and structure analysis indicated that the
nine investigated populations can be divided into two groups. Suffolk (SUF) and DST
were clustered in one group, and the other group can be further divided into
three clusters: German Mutton Merino (GMM)–BAS–Bamei Mutton sheep (BAM), HUS–STH and Du Han (DOS)–Dorper (DOP). This clustering result is
consistent with sheep breeding history. TreeMix analysis also hinted at the
possible gene flow from GMM to SUF. Together, an in-depth view of genetic
diversity and genetic relationship will have important implications for
breed-specific management.
Collapse
Affiliation(s)
- Qing Xia
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Zhangyuan Pan
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Rensen Zhang
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Caihong Wei
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Ran Di
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| |
Collapse
|
9
|
Xia Q, Li Q, Gan S, Guo X, Zhang X, Zhang J, Chu M. Exploring the roles of fecundity-related long non-coding RNAs and mRNAs in the adrenal glands of small-tailed Han Sheep. BMC Genet 2020; 21:39. [PMID: 32252625 PMCID: PMC7137433 DOI: 10.1186/s12863-020-00850-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2019] [Accepted: 03/30/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) can play important roles in uterine and ovarian functions. However, little researches have been done on the role of lncRNAs in the adrenal gland of sheep. Herein, RNA sequencing was used to compare and analyze gene expressions in adrenal tissues between follicular phases and luteal phases in FecBBB (MM) and FecB++ (WW) sheep, respectively, and differentially expressed lncRNAs and genes associated with reproduction were identified. RESULTS In MM sheep, 38 lncRNAs and 545 mRNAs were differentially expressed in the adrenal gland between the luteal and follicular phases; In WW sheep, 513 differentially expressed lncRNAs and 2481 mRNAs were identified. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that differentially expressed lncRNAs and their target genes are mainly involved in the circadian rhythm, the mitogen activated protein kinase, thyroid, ovarian steroidogenesis and transforming growth factor beta signaling pathways. Differentially expressed lncRNAs can regulate reproduction by modulating genes involved in these signaling pathways and biological processes. Specifically, XLOC_254761, XLOC_357966, 105,614,839 and XLOC_212877 targeting CREB1, PER3, SMAD1 and TGFBR2, respectively, appear to play key regulatory roles. CONCLUSION These results broaden our understanding of lncRNAs in adrenal gland of sheep and provide new insights into the molecular mechanisms underlying sheep reproduction.
Collapse
Affiliation(s)
- Qing Xia
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China
| | - Qiuling Li
- College of Life Sciences, Langfang Normal University, Langfang, 065000, P.R. China
| | - Shangquan Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, 832000, P. R. China
| | - Xiaofei Guo
- Tianjin Institute of Animal Sciences, Tianjin, 300381, P. R. China
| | - Xiaosheng Zhang
- Tianjin Institute of Animal Sciences, Tianjin, 300381, P. R. China
| | - Jinlong Zhang
- Tianjin Institute of Animal Sciences, Tianjin, 300381, P. R. China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics and Breeding and Reproduction of the Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, P. R. China.
| |
Collapse
|
10
|
La Y, Tang J, He X, Di R, Wang X, Liu Q, Zhang L, Zhang X, Zhang J, Hu W, Chu M. Identification and characterization of mRNAs and lncRNAs in the uterus of polytocous and monotocous Small Tail Han sheep ( Ovis aries). PeerJ 2019; 7:e6938. [PMID: 31198626 PMCID: PMC6535221 DOI: 10.7717/peerj.6938] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/09/2019] [Indexed: 12/15/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) regulate endometrial secretion and uterine volume. However, there is little research on the role of lncRNAs in the uterus of Small Tail Han sheep (FecB++). Herein, RNA-seq was used to comparatively analyze gene expression profiles of uterine tissue between polytocous and monotocous sheep (FecB++) in follicular and luteal phases. Methods To identify lncRNA and mRNA expressed in the uterus, the expression of lncRNA and mRNA in the uterus of Small Tail Han sheep (FecB++) from the polytocous group (n = 6) and the monotocous group (n = 6) using RNA-sequencing and real-time polymerase chain reaction (RT-PCR). Identification of differentially expressed lncRNAs and mRNAs were performed between the two groups and two phases . Gene ontology (GO) and pathway enrichment analyses were performed to analyze the biological functions and pathways for the differentially expressed mRNAs. LncRNA-mRNA co-expression network was constructed to further analyses the function of related genes. Results In the follicular phase, 473 lncRNAs and 166 mRNAs were differentially expressed in polytocous and monotocous sheep; in the luteal phase, 967 lncRNAs and 505 mRNAs were differentially expressed in polytocous and monotocous sheep. GO and KEGG enrichment analysis showed that the differentially expressed lncRNAs and their target genes are mainly involved in ovarian steroidogenesis, retinol metabolism, the oxytocin signaling pathway, steroid hormone biosynthesis, and the Foxo signaling pathway. Key lncRNAs may regulate reproduction by regulating genes involved in these signaling pathways and biological processes. Specifically, UGT1A1, LHB, TGFB1, TAB1, and RHOA, which are targeted by MSTRG.134747, MSTRG.82376, MSTRG.134749, MSTRG.134751, and MSTRG.134746, may play key regulatory roles. These results offer insight into molecular mechanisms underlying sheep prolificacy.
Collapse
Affiliation(s)
- Yongfu La
- Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Beijing, China.,Gansu Agricultural University, College of Animal Science and Technology, Lanzhou, China
| | - Jishun Tang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Beijing, China.,Anhui Academy of Agricultural Sciences, Institute of Animal Husbandry and Veterinary Medicine, Hefei, China
| | - Xiaoyun He
- Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Beijing, China
| | - Ran Di
- Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Beijing, China
| | - Xiangyu Wang
- Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Beijing, China
| | - Qiuyue Liu
- Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Beijing, China
| | - Liping Zhang
- Gansu Agricultural University, College of Animal Science and Technology, Lanzhou, China
| | | | - Jinlong Zhang
- Tianjin Institute of Animal Sciences, Tianjin, China
| | - Wenping Hu
- Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Beijing, China
| | - Mingxing Chu
- Chinese Academy of Agricultural Sciences, Key Laboratory of Animal Genetics and Breeding and Reproduction of Ministry of Agriculture, Institute of Animal Science, Beijing, China
| |
Collapse
|
11
|
Rigoglio NN, Matias GDSS, Miglino MA, Mess AM, Jacob JCF, Smith LC. Morphological characteristics of mule conceptuses during early development. Anim Reprod 2018; 15:1214-1222. [PMID: 34221135 PMCID: PMC8203116 DOI: 10.21451/1984-3143-ar2017-0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hybrids between species are often infertile and extremely rare among mammals. Mules, i.e.
crossing between the horse and the donkey, on the other hand are very common in agricultural
and leisure practices due to their enhanced post-natal physical characteristics that is
believed to occur for outbreeding or hybrid vigor. Since no reports are availableon the effects
of hybrid vigor during early development, this study focused on characterizing the intrauterine
development of mule conceptuses during critical embryo-to-fetus transition period. Nine
embryos and fetuses of early gestation, obtained after artificial insemination and transcervical
flushing, were evaluated by means of gross anatomy and histology and compared to data available
for the equine. We found that some events, such as C-shape turning, apearence of branchial
archs, limb and tail buds, formation of primary and secondary brain vesicles, heart compartmentalization,
and development of somites, occurred slightly earlier in the mule. Nonetheless, no major
differences were observed in other developmental features, suggesting similarities between
the mule and the horse development. In conclusion, these data suggest that the effect of hybrid
vigor is present during intrauterine development in the mule, at least with regard to its maternal
parent.
Collapse
Affiliation(s)
- Nathia Nathaly Rigoglio
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Brazil
| | | | - Maria Angelica Miglino
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Brazil
| | - Andrea Maria Mess
- Department of Surgery, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Brazil
| | - Julio Cesar Ferraz Jacob
- Department of Reproduction and Animal Evaluation, Federal Rural University of Rio de Janeiro, Seropedica, Rio de Janeiro, Brazil
| | - Lawrence Charles Smith
- Department of Veterinary Biomedicine, Centre de recherche en reproduction et fertilité, Faculty of Veterinary Medicine, University of Montreal, QC J2S 2M2, Saint-Hyacinthe, QC, Canada
| |
Collapse
|
12
|
Prediction of maize single cross hybrids using the total effects of associated markers approach assessed by cross-validation and regional trials. ScientificWorldJournal 2014; 2014:924348. [PMID: 25110752 PMCID: PMC4106173 DOI: 10.1155/2014/924348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/23/2014] [Accepted: 06/04/2014] [Indexed: 01/03/2023] Open
Abstract
The present study aimed to predict the performance of maize hybrids and assess whether the total effects of associated markers (TEAM) method can correctly predict hybrids using cross-validation and regional trials. The training was performed in 7 locations of Southern Brazil during the 2010/11 harvest. The regional assays were conducted in 6 different South Brazilian locations during the 2011/12 harvest. In the training trial, 51 lines from different backgrounds were used to create 58 single cross hybrids. Seventy-nine microsatellite markers were used to genotype these 51 lines. In the cross-validation method the predictive accuracy ranged from 0.10 to 0.96, depending on the sample size. Furthermore, the accuracy was 0.30 when the values of hybrids that were not used in the training population (119) were predicted for the regional assays. Regarding selective loss, the TEAM method correctly predicted 50% of the hybrids selected in the regional assays. There was also loss in only 33% of cases; that is, only 33% of the materials predicted to be good in training trial were considered to be bad in regional assays. Our results show that the predictive validation of different crop conditions is possible, and the cross-validation results strikingly represented the field performance.
Collapse
|
13
|
Amuzu-Aweh EN, Bijma P, Kinghorn BP, Vereijken A, Visscher J, van Arendonk JAM, Bovenhuis H. Prediction of heterosis using genome-wide SNP-marker data: application to egg production traits in white Leghorn crosses. Heredity (Edinb) 2013; 111:530-8. [PMID: 24105438 PMCID: PMC3833690 DOI: 10.1038/hdy.2013.77] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 06/20/2013] [Accepted: 07/01/2013] [Indexed: 01/26/2023] Open
Abstract
Prediction of heterosis has a long history with mixed success, partly due to low numbers of genetic markers and/or small data sets. We investigated the prediction of heterosis for egg number, egg weight and survival days in domestic white Leghorns, using ∼400 000 individuals from 47 crosses and allele frequencies on ∼53 000 genome-wide single nucleotide polymorphisms (SNPs). When heterosis is due to dominance, and dominance effects are independent of allele frequencies, heterosis is proportional to the squared difference in allele frequency (SDAF) between parental pure lines (not necessarily homozygous). Under these assumptions, a linear model including regression on SDAF partitions crossbred phenotypes into pure-line values and heterosis, even without pure-line phenotypes. We therefore used models where phenotypes of crossbreds were regressed on the SDAF between parental lines. Accuracy of prediction was determined using leave-one-out cross-validation. SDAF predicted heterosis for egg number and weight with an accuracy of ∼0.5, but did not predict heterosis for survival days. Heterosis predictions allowed preselection of pure lines before field-testing, saving ∼50% of field-testing cost with only 4% loss in heterosis. Accuracies from cross-validation were lower than from the model-fit, suggesting that accuracies previously reported in literature are overestimated. Cross-validation also indicated that dominance cannot fully explain heterosis. Nevertheless, the dominance model had considerable accuracy, clearly greater than that of a general/specific combining ability model. This work also showed that heterosis can be modelled even when pure-line phenotypes are unavailable. We concluded that SDAF is a useful predictor of heterosis in commercial layer breeding.
Collapse
Affiliation(s)
- E N Amuzu-Aweh
- Animal Breeding and Genomics Centre,
Wageningen University and Research Centre, Wageningen, The
Netherlands
- Department of Animal Breeding and Genetics,
Swedish University of Agricultural Sciences, Uppsala,
Sweden
| | - P Bijma
- Animal Breeding and Genomics Centre,
Wageningen University and Research Centre, Wageningen, The
Netherlands
| | - B P Kinghorn
- School of Environmental and Rural Science,
University of New England, Armidale, Australia
| | - A Vereijken
- Institut de Sélection Animale B.V.,
Hendrix Genetics, Boxmeer, The Netherlands
| | - J Visscher
- Institut de Sélection Animale B.V.,
Hendrix Genetics, Boxmeer, The Netherlands
| | - J AM van Arendonk
- Animal Breeding and Genomics Centre,
Wageningen University and Research Centre, Wageningen, The
Netherlands
| | - H Bovenhuis
- Animal Breeding and Genomics Centre,
Wageningen University and Research Centre, Wageningen, The
Netherlands
| |
Collapse
|
14
|
Investigation of individual heterozygosity correlated to growth traits in Tongshan Black-boned goat. Mol Biol Rep 2013; 40:6075-9. [DOI: 10.1007/s11033-013-2717-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 09/14/2013] [Indexed: 10/26/2022]
|