Transcriptomes reveal microRNAs and mRNAs in different photoperiods influencing cashmere growth in goat

PLOS ONE RESEARCH ARTICLE Transcriptomes reveal microRNAs and mRNAs in different photoperiods influencing cashmere growth in goat Bin Liu1☯, Ruoyang Zhao1,2,3☯, Tiecheng Wu1, Yuejun Ma1, Yulin Gao1, Yahan Wu1, Bayasihuliang Hao4,5, Jun Yin4*, Yurong Li ID1* a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 1 Institute of Animal Husbandry, Academy of Agriculture and Stockbreeding Sciences, Hohhot, Inner Mongolia, China, 2 Wenzhou Institute, University of Chinese Academy of Sciences, Oujiang Laboratory, Wenzhou, Wenzhou, China, 3 College of Life Science, University of Chinese Academy of Sciences, Beijing, China, 4 College of Life Science, Inner Mongolia Agricultural University, Hohhot, China, 5 Etuokeqianqi Arctic God Research Institute of Cashmere and Livestock, Erdos, China ☯ These authors contributed equally to this work. * (JY); (YL) Abstract OPEN ACCESS Citation: Liu B, Zhao R, Wu T, Ma Y, Gao Y, Wu Y, et al. (2023) Transcriptomes reveal microRNAs and mRNAs in different photoperiods influencing cashmere growth in goat. PLoS ONE 18(3): e0282772. https://doi.org/10.1371/journal. pone.0282772 Editor: Abdul Qadir Syed, Northwest University, UNITED STATES Received: April 25, 2022 Accepted: February 22, 2023 Published: March 17, 2023 Peer Review History: PLOS recognizes the benefits of transparency in the peer review process; therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. The editorial history of this article is available here: https://doi.org/10.1371/journal.pone.0282772 Copyright: © 2023 Liu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: All clean data and sequences are deposited at the National Center for Biotechnology Information (http://www.ncbi.nlm. nih.gov/) under a BioProject and SRA accession Cashmere goat has a typical characteristic in seasonal growth of cashmere. Studies have shown that one of the main factors affecting the cyclical growth of the cashmere is the photoperiod, however, its molecular mechanism remains unclear. Inner Mongolia Arbas cashmere goat was used to reveal the mRNA-microRNA regulatory mechanisms of cashmere growth in different photoperiod. Skin samples from cashmere goats under light control (short photoperiod) and normal conditions (long photoperiod) were collected. Sequencing was performed after RNA extraction. The differentially expressed miRNA and mRNA expression profiles were successfully constructed. We found 56 significantly differentially expressed known mRNAs (P<0.01) and 14 microRNAs (P<0.05). The association analysis of the microRNAs and mRNAs showed that two differentially expressed miRNAs might be targeted by six differentially expressed genes. Targeting relationships of these genes and miRNAs are revealed and verified. In all, the light control technology provides a new way to promote cashmere growth. Our results provide some references in the cashmere growth and development. Introduction The cashmere of goats is composed of two types of fibers: medullated and unmedullated fiber, which are called primary and secondary hair follicles [1]. Cashmere growth pattern is influenced by photoperiod with a strong seasonal variation. The cashmere growth (secondary hair follicle) starts at about summer solstice every year, when photoperiod changes from long to short [2]. When the duration of sunshine decreases, cashmere grows faster. Inner Mongolia Arbas cashmere goat is unique species resources with white cashmere, originated from ordos city, Alxa League and Bayan Nur city in Inner Mongolia, China. Cashmere, with good fiber length and plasticity, is famous in the world. Cashmere growth reaches a peak in November. PLOS ONE | https://doi.org/10.1371/journal.pone.0282772 March 17, 2023 1 / 12 PLOS ONE NO. PRJNA718356. The six BioSample accessions were SAMN18529823, SAMN18529824, SAMN18529825, SAMN18529826, SAMN18529827 and SAMN18529828 (https:// www.ncbi.nlm.nih.gov/sra/PRJNA718356). Funding: This research was supported by the National Natural Science Foundation of China in the form of grants to BL [31760653, 32161143026] and JY [31960126]; the Innovation Fund of Inner Mongolia Autonomous Region in the form of a grant to BL [2020CXJJM01]; the Inner Mongolia Autonomous Region Science and Technology Project in the form of a grant to BL [2020GG0095]; and the Inner Mongolia Cashmere Goat Science and Technology Major Project in the form of a grant to BL [2017]. There was no additional external funding received for this study. Competing interests: The authors have declared that no competing interests exist. Transcriptomes reveal short photoperiods influencing cashmere growth After the winter solstice, the sunlight changes from short to long. Cashmere growth gradually turns to slow until it stops growing, and begins to fall off in around April. The length and production of cashmere has significant differences in different photoperiod [3]. Previous studies suggest that photoperiod is one of the main factors affecting cashmere growth, and has an important influence on hair follicle and its cyclical rhythms [3]. Plenty of evidences have showed that photoperiod plays an important role in hair seasonal changes. The biological clock in skin is not only regulated by the neuroendocrine regulation of suprachiasmatic nucleus (SCN) circadian clocks. The skin itself which has inherent inner clock. In the process of early maturity of skin in mice, the circadian clock is also of great importance [4, 5]. In recent decades, researchers have developed a variety of methods by changing photoperiod or directly regulating hormone levels to increase cashmere [6–9]. Inner Mongolia in China, as one of the major areas of cashmere products, has excellent germplasm resource. Regulatory mechanism of induction of hair follicles is a very complicated process. Once conditions (such as region, photoperiod, climate, nutrition etc.) change, the cashmere quality will change. The molecular mechanism of the regulation of cashmere growth is still unrevealed. Inner Mongolia white cashmere goats, as project of this study, are divided in two groups (under light control technology and normal feeding condition). Skin samples are used for sequencing. The interaction network between the differentially expressed are build, the target relationships of these miRNAs and mRNAs are revealed, so as to explore why short photoperiod could promote cashmere growth. Materials and methods Animals and tissues Ethics statement. The Inner Mongolia white cashmere goats selected for this study were chosen from the Cashmere Goat Technology Demonstration Zone of Ordos City, Inner Mongolia, China. The animal experiments were approved by the Animal Care and Use Committee of the Ins (...truncated)