Comparative analysis of ovarian transcriptomes between prolific and non‐prolific goat breeds via high‐throughput sequencing

Zi, Xiang-Dong; Lu, Jin-You; Zhou, Haihong; Ma, Li; Xia, Wei; Xr, Xiong; Dl, Lan; Wu, Xiaosheng

doi:10.1111/rda.13111

Cited by 11 publications

(4 citation statements)

References 32 publications

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“…2e, f). Approximately 37% of the DEgenes in the Uni-S vs Mul-S group and 41% in the Uni-L vs Mul-L group were reported to be associated with mammalian reproduction, such as TNFAIP6, MMP9, INSL3, LEPR, 3BHSD, LHCGR, ARL4C, CD36, CYP11A1, AMDHD1, SPOCK2, AMDHD1, MFAP5, CCL21, PTGFR, and SERPINA5 [23,[47][48][49][50][51][52][53][54][55][56][57][58][59][60]. Of these genes, TNFAIP6, CYP11A1, CD36, PTGFR, and SER-PINA5 were found to be associated with the ovulation rate.…”

Section: Discussionmentioning

confidence: 99%

“…However, little is known about goat follicles. In goat, previous studies have identified the key genes involved in the regulation of ovulation rate and kidding rate by transcriptome analysis of goat ovaries, as well as the signaling pathways that affect ovulation and fertility [1,4,[23][24][25][26][27][28][29]. Studies on litter size of goats have shown that PDGFRB, MARCH1, KDM6A, CSN1S1, SIRT3, KITLG, GHR, ATBF1, INHA, GNRH1, and GDF9 might be candidate genes for goat reproductive traits [26,[30][31][32][33][34][35][36][37][38][39].…”

Section: Introductionmentioning

confidence: 99%

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Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase

Zou

Zhao

et al. 2020

BMC Genomics

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Background: Fertility is an important economic trait in the production of meat goat, and follicular development plays an important role in fertility. Although many mRNAs and microRNAs (miRNAs) have been found to play critical roles in ovarian biological processes, the interaction between mRNAs and miRNAs in follicular development is not yet completely understood. In addition, less attention has been given to the study of single follicle (dominant or atretic follicle) in goats. This study aimed to identify mRNAs, miRNAs, and signaling pathways as well as their interaction networks in the ovarian follicles (large follicles and small follicles) of uniparous and multiple Chuanzhong black goats at estrus phase using RNAsequencing (RNA-seq) technique. Results: The results showed that there was a significant difference in the number of large follicles between uniparous and multiple goats (P < 0.05), but no difference in the number of small follicles was observed (P > 0.05). For the small follicles of uniparous and multiple goats at estrus phase, 289 differentially expressed mRNAs (DEmRNAs) and 16 DEmiRNAs were identified; and for the large follicles, 195 DEmRNAs and 7 DEmiRNAs were identified. The functional enrichment analysis showed that DE genes in small follicles were significantly enriched in ovarian steroidogenesis and steroid hormone biosynthesis, while in large follicles were significantly enriched in ABC transporters and steroid hormone biosynthesis. The results of quantitative real-time polymerase chain reaction were consistent with those of RNA-seq. Analysis of the mRNA-miRNA interaction network suggested that CD36 (miR-122, miR-200a, miR-141), TNFAIP6 (miR-141, miR-200a, miR-182), CYP11A1 (miR-122), SERPINA5 (miR-1, miR-206, miR-133a-3p, miR-133b), and PTGFR (miR-182, miR-122) might be related to fertility, but requires further research on follicular somatic cells. Conclusions: This study was used for the first time to reveal the DEmRNAs and DEmiRNAs as well as their interaction in the follicles of uniparous and multiple goats at estrus phase using RNA-seq technology. Our findings provide new clues to uncover the molecular mechanisms and signaling networks of goat reproduction that could be potentially used to increase ovulation rate and kidding rate in goat.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase

Zou

Zhao

et al. 2020

BMC Genomics

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“…RNA-Seq methods have been broadly utilized to determine DEGs or gene expression patterns, new transcripts, AS events and SNPS, and have empowered studies examining porcine [24,25], cattle [26,27] and mouse [28,29] testicular development. In goats, the profiles of ovarian [30,31], uterine [32,33] and testicular [34,35] tissues under different conditions were recently compared by RNA-Seq. However, limited data on testicular development in goats were available.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic Analysis of the Developing Testis and Spermatogenesis in Qianbei Ma Goats

Zou,

Chen,

Tian

et al. 2023

Genes

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Reproductive competence in male mammals depends on testicular function. Testicular development and spermatogenesis in goats involve highly complex physiological processes. In this study, six testes were, respectively, obtained from each age group, immature (1 month), sexually mature (6 months) and physically mature (12 months old) Qianbei Ma goats. RNA-Seq was performed to assess testicular mRNA expression in Qianbei Ma goats at different developmental stages. Totally, 18 libraries were constructed to screen genes and pathways involved in testis development and spermatogenesis. Totally, 9724 upregulated and 4153 downregulated DEGs were found between immature (I) and sexually mature (S) samples; 7 upregulated and 3 downregulated DEGs were found between sexually mature (S) and physically mature (P) samples, and about 4% of the DEGs underwent alternative splicing events between I and S. Select genes were assessed by qRT-PCR, corroborating RNA-Seq findings. The detected genes have key roles in multiple developmental stages of goat testicular development and spermatogenesis. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to determine differentially expressed genes (DEGs). GO analysis revealed DEGs between S and P contributed to “reproduction process”, “channel activity” and “cell periphery part” between I and S, and in “ion transport process”, “channel activity” and “transporter complex part”. KEGG analysis suggested the involvement of “glycerolipid metabolism”, “steroid hormone biosynthesis” and “MAPK signaling pathway” in testis development and spermatogenesis. Genes including IGF1, TGFB1, TGFBR1 and EGFR may control the development of the testis from immature to sexually mature, which might be important candidate genes for the development of goat testis. The current study provides novel insights into goat testicular development and spermatogenesis.

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“…The high throughput sequencing approach is the most effective method for exploring of genetic resources. For goats, Zi et al identified 407 DEGs between prolific and non-prolific goat breeds and 171,829 versus 140,529 putative SNPs in Tibetan goats and Jintang black goats, respectively [ 31 ]. Yang et al explored hair follicle development-related microRNAs in cashmere goats at various fetal periods and found oar-let-7 and oar-miR-200 families in 55 days and 66 days of pregnancy samples had been notably up-regulated relative to those in 45 days of pregnancy samples [ 32 ].…”

Section: Discussionmentioning

confidence: 99%

Integrated analysis of lncRNA and gene expression in longissimus dorsi muscle at two developmental stages of Hainan black goats

He²,

Xia³

et al. 2022

PLoS ONE

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It is deemed that meat quality of kids’ is better than that of adults’ for Hainan black goat. Generally, meat quality is affected by many indicators, such as intramuscular fat (IMF) content, muscle fiber diameter and shear force. It is indicated that long non-coding RNAs (lncRNAs) play essential roles in meat quality of goats. However, it is unclear whether and how lncRNAs and genes play their roles in meat quality of Hainan Black goats. Here, we firstly compared the meat quality between two-month-old kids (kids) and adult goats (adults). Then, the lncRNA-seq and RNA-seq data were integrated and analyzed to explore the potential functions of lncRNAs and genes. The results showed that adults’ IMF content and muscle fiber diameter were extremely significantly higher than that of kids (P<0.01). For the sequenced data, average 84,970,398, and 83,691,250 clean reads were obtained respectively for Kids and adults, among which ~96% were mapped to the reference genome of goats. Through analyzing, 18,242 goat annotated genes, 1,429 goat annotated lncRNAs and 2,967 novel lncRNAs were obtained. Analysis of differential expression genes (DEGs) and lncRNAs (DELs) showed that 328 DEGs and 98 DELs existed between kids and adults. Furthermore, functional enrichment analysis revealed that a number of DEGs and DELs were mainly associated with IMF. Primarily, DGAT2 expressed higher in adults than that in kids and CPT1A expressed higher in kids than that in adults. Both of them were overlapped by DEGs and targets of DELs, suggesting the two DEGs and the DELs targeted by the two DEGs might be the potential regulators of goat IMF deposition. Taken together, our results provide basic support for further understanding the function and mechanism of lncRNAs and genes in meat quality of Hainan black goats.

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Comparative analysis of ovarian transcriptomes between prolific and non‐prolific goat breeds via high‐throughput sequencing

Cited by 11 publications

References 32 publications

Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase

Comprehensive analysis of mRNAs and miRNAs in the ovarian follicles of uniparous and multiple goats at estrus phase

Transcriptomic Analysis of the Developing Testis and Spermatogenesis in Qianbei Ma Goats

Integrated analysis of lncRNA and gene expression in longissimus dorsi muscle at two developmental stages of Hainan black goats

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