梅花鹿鹿茸全长转录组测序及鹿茸产量相关基因的挖掘

doi:10.11843/j.issn.0366-6964.2024.12.020

摘要/Abstract

摘要：

旨在获得梅花鹿鹿茸组织全长转录本和结构信息，并进一步挖掘出影响梅花鹿鹿茸产量的功能基因。本研究采取饲养管理条件一致的6头2锯龄健康雄性东大梅花鹿，取其相同部位鹿茸组织。根据茸重将鹿茸分为高、低产两组，每组3个重复。利用PacBio Sequel平台以及Illumina平台分别对高、低产鹿茸混合样品进行全长转录组测序。结合高、低产两组二代测序技术，使用SUPPA、KOBOS-I、Cytoscape等工具对可变剪接、功能富集及Hub基因等预测分析。高、低产组测序分别获得有效插入片段36 074 385 bp和32 413 962 bp；转录因子注释显示高产组中bHLH家族转录本数量要高于TF_bZIP家族，低产组中则相反。高产鹿茸组共存在6 644个可变剪接事件，而低产鹿茸组则为7 626个可变剪接事件；经比对，COL1A1在多个融合基因中起主效作用；两组样品中共筛选出207个差异表达基因，KEGG富集显示差异表达基因主要集中在甲状旁腺激素的合成、分泌以及胆固醇代谢等通路；鉴定到11个Hub基因，分别是APOB、SH3GL2、SYT1、ANGPTL4、FGF21、CACNA1E、SERPINF2、CACNB4、KLK4、LRP2、KCNA1。本研究结果为进一步的功能基因鉴定工作和分子育种策略的发展提供了新的理论基础和研究路径。

关键词: 梅花鹿鹿茸, 全长转录组测序, 产茸性状, 功能基因, 差异分析

Abstract:

The study aimed to obtain the full-length transcript and structure information of the antler tissue of Sika deer, and to further mine the functional genes that affect the antler production of Sika deer. In this study, six two-sained healthy male Dongda Sika deer with the same feeding and management conditions were used to collect antler tissues from the same parts of the deer. According to the antler weight, the antler was divided into 2 groups of high and low production with 3 replicates per group. The whole length transcriptome of antler with high and low production were sequenced using PacBio Sequel platform and Illumina platform, respectively. Combined with the next generation sequencing technology of high and low yield groups, the alternative splicing, functional enrichment and Hub genes were predicted and analyzed by SUPPA, KOBOS-I and Cytoscape tools. The effective insertion fragments of 36 074 385 bp and 32 413 962 bp were obtained in the high and low yield groups, respectively. Transcription factor annotation showed that the number of bHLH family transcripts in the high yield group was higher than that of TF_bZIP family, but the opposite was observed in the low yield group. There were 6 644 alternative splicing events in the high production group and 7 626 alternative splicing events in the low production group. COL1A1 played a major role in multiple fusion genes. A total of 207 differentially expressed genes were screened out from the two groups of samples. KEGG enrichment showed that the differentially expressed genes were mainly concentrated in the synthesis and secretion of parathyroid hormone and cholesterol metabolism pathways. Eleven Hub genes were identified, including APOB, SH3GL2, SYT1, ANGPTL4, FGF21, CACNA1E, SERPINF2, CACNB4, KLK4, LRP2, KCNA1. This study provides a new theoretical basis and research path for further functional gene identification and the development of molecular breeding strategies.

Key words: sika deer antler, full-length transcriptome sequencing, anlter producing characters, functional gene, difference analysis

中图分类号:

S813.1

闵祥玉, 卫佳丽, 许彪, 刘汇涛, 郑军军, 王桂武. 梅花鹿鹿茸全长转录组测序及鹿茸产量相关基因的挖掘[J]. 畜牧兽医学报, 2024, 55(12): 5549-5566.

MIN Xiangyu, WEI Jiali, XU Biao, LIU Huitao, ZHENG Junjun, WANG Guiwu. Full-length Transcriptome Sequencing of Sika Deer Antler and Mining of Antler Yield-related Genes[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(12): 5549-5566.

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样品名称Sample name	H1	H2	H3	L1	L2	L3
单支重量Single weight	670	777	780	234	216	291

引物名称 Primer name	序列(5′→3′) Sequence	产物大小/bp Product length	退火温度/℃ Tm
APOB	F: GACTCCAGCCCTCAACTTCC	183	60
	R: GTGTTGCCGCCAGTATAGGA
CACNB4	F: CACAGCAACCACTCCACAGA	114	60
	R: CTGGAAGACAAGCGGTTCCT
FGF21	F: CAGCCATCTGAGAACCTGCT	105	60
	R: CTGGGGTCTGGGGTTTGAAG
ANGPTL4	F: CGGCCCAGCTCACAATATCA	134	60
	R: TTACAGTCCAGCCTCCGTCT
SERPINF2	F: ATGACACAGTGTTGCTTCTCCT	151	60
	R: AGTGGGTATGTGAGGGCTTG
SYT1	F: CTACGCCACCCATCACAAGT	102	60
	R: CAGAAGGGTACGTGTGGCTT
GAPDH	F: ATGTTTGTGATGGGCGTGAAC	265	60
	R: CCAGTAGAAGCAGGGATGATGTT

样品名称 Sample	注释到基因总数 Total genes	外显子跳跃 SE	外显子互斥 MX	内含子滞留 RI	5′端可变剪接 A5	3′端可变剪接 A3	起始外显子可变剪接 AF	终止外显子可变剪接 AL
HIGH	6 644	1 361	123	728	753	901	1 005	280
LIGHT	7 626	1 561	124	1 051	952	1 026	1 164	324

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