Differentially Expressed Circular RNA Profile Signatures Identified in Prolificacy Trait of Yunshang Black Goat Ovary at Estrus Cycle

Abstract

CircRNAs acting as miRNA sponges play important roles in the growth process of animal individuals. The prolificacy trait of goats is involved in many pathways, however, the variation of circRNA expression profiles in the different phases of the estrus cycle at high and low fecundity groups is still unknown. Here, we analyzed the circRNA profiles of ovarian tissues among high and low fecundity groups in the follicular phase (HF vs LF), high and low fecundity groups in the luteal phase (HL vs LL), and high and low fecundity in the whole estrus cycle (HF vs HL and LF vs LL) using RNA-seq. A total of 283 (114 upregulated and 169 downregulated), 559 (299 upregulated and 260 downregulated), 449 (254 upregulated and 195 downregulated), and 314 (210 upregulated and 104 downregulated) differentially expressed (DE) circRNAs were screened in HF vs LF, HF vs HL, HL vs LL, and LF vs LL groups, respectively. Enrichment analysis suggested that the targeting of DE circRNAs was mainly enriched in oocyte meiosis, the GnRH signaling pathway, and estrogen signaling pathway. After integrating our previous study of miRNA-seq, there were 56 miRNAs that could target to 192 DE circRNAs, including the miR-133 family (including miR-133a-3p and miR-133b), miR-129-3p, and miR-21, which also had important influence on the prolificacy trait of goats. Then, 18 circRNAs with coding potential were obtained by four software predictions, and 9 circRNAs were validated by RT-qPCR. Together, circRNAs play a key role in the prolificacy trait and the transformation of the follicular phase to the luteal phase in the estrus cycle of goats.

Characterization of circular RNA profiles of oviduct reveal the potential mechanism in prolificacy trait of goat in the estrus cycle

“…Further analysis showed that the circRNAs identified were mainly generated by cyclization of gene exons (Zhang M. L. et al, 2018), in the sheep (Lv et al, 2020) and cattle (Liu et al, 2020), indicating similar origins of circRNAs in different species. In our present study, we found that the majority of circRNAs are less than 10,000 nt in length, which is consistent with the results of a previous study in goat ovary (Liu et al, 2022), but longer than circRNAs identified in goat endometrial (Li et al, 2022), indicating that the longer the sequence, the greater the corresponding increase in the difficulty of circRNA loop formation. Moreover, most of the identified circRNAs were Frontiers in Physiology frontiersin.org typically distributed on chromosomes 1-11, and the expression of circRNAs in the luteal phase was more abundant than that in the follicular phase of the oviduct, indicating that the functions of circRNAs in the oviduct are diverse.…”

“…The library fragments were purified, and cDNA fragments with different lengths (250–300 bp) were screened by the AMPure XP system (Beckman Coulter, Beverly, United States). After that, PCR amplification was performed by adding 3 μL USER enzyme (NEB, United States) and screening the cDNA for aptamer ligation at 37°C for 15°min, followed by 95°C for 5 min ( Liu et al, 2022 ). PCR was then performed with Phusion High–Fidelity DNA polymerase, Index (X), and primer universal PCR primers.…”

“…Liu et al analysed 2,331 DE circRNAs in goat uterine membranes (Liu X. R. et al, 2021). Similarly, previous studies have analysed circRNAs in goat ovaries (Liu et al, 2022) and pituitary glands (Liu Y. F. et al, 2021), and some DE circRNA as miRNA sponges were identified, which have the potential to regulate fertility in goats. Although circRNAs have been identified in different reproductive organs of goats, however, their biological role in the oviduct remains unclear.…”

Genetic Diversity and Selection Signatures in Jianchang Black Goats Revealed by Whole-Genome Sequencing Data

“…Furthermore, it is relatively simple to breed black goats by phenotypic selection because the black coat color is usually recessive compared with other coat colors (e.g., white and yellow/red) in goats. Another important reason is that black goats (e.g., YS) often have tender meat with a unique flavor [ 4 ].…”

“…To our knowledge, the JT goat (native to Jintang County and neighboring regions on the Chengdu Plain), which is known for its large body size, has been introduced to Huidong County to genetically improve the body size and growth rate of JC goats in recent years. Furthermore, the YS goat, a meat-producing breed that originated from crossing Chinese indigenous Yunling goats and Nubian goats [ 5 ], is also intriguing because of the desirable characteristics mentioned above [ 4 ]. Although historical records briefly describe that these breeds originated from different geographical locations, the genetic relationships between these breeds are not well understood.…”