Scientia Agricultura Sinica ›› 2019, Vol. 52 ›› Issue (12): 2171-2182.doi: 10.3864/j.issn.0578-1752.2019.12.014

• FOOD SCIENCE AND ENGINEERING • Previous Articles     Next Articles

Transcriptome Analysis of Differentially Gene Expression Associated with Ovary Tissue During the Follicular Stage in Fuqing Goat and Nubian Black Goat

LI WenYang,LIU Yuan(),WU XianFeng,GAO ChengFang,HUANG QinLou()   

  1. Institute of animal husbandry and veterinary medicine, Fujian Academy of Agricultural Sciences, Fuzhou 350013
  • Received:2018-07-15 Accepted:2019-04-15 Online:2019-06-16 Published:2019-06-22
  • Contact: Yuan LIU,QinLou HUANG E-mail:seayuan521@163.com;hql202@126.com

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Abstract:

【Objective】The aim of this study was to analyze the differentially expressed genes of ovary tissue during follicular stage in Fuqing goat and Nubian black goat.【Method】Transcriptome sequencing of ovary tissue during the follicular stage in Fuqing goat and Nubian black goat were performed by using the Illumina HiSeq TM 2500 platform with 3 biological replicates per goat breed, and verified by quantitative real-time PCR (qRT-PCR). Differentially expressed genes (DEGs) were selected and enriched based on GO, COG and KEGG database. 【Result】A total of 46.68 Gb clean data were obtained in six samples. 149 DEGs were found between Fuqing goat and Nubian black goat, including 53 DEGs up-regulated genes and 96 DEGs down-regulated genes. According to published papers, the genes, including OVN, STAR and EGR1, were considered as candidate genes of fecundity in goats. 108, 30 and 91 DEGs were enriched by GO, COG and KEGG database, respectively. KEGG pathway analysis showed that DEGs annotated to 21 metabolic pathways, and 6 pathways were enriched significantly, such as autoimmune thyroid disease, and allograft rejection, and phagosome and viral myocarditis associated with reproduction traits in goat. 1506 new genes or transcripts were found by BLAST, including 25 DEGs between two breeds. Verified by qRT-PCR, the pattern of selected genes was consistent with the results of transcriptome sequencing, which showed the sequencing results were reliable. 【Conclusion】149 DEGs and 1506 new genes of ovary tissue during follicular stage in Fuqing goat and Nubian black goat were screened by transcriptonal analysis. DEGs between Fuqing goat and Nubian black goat, including OVN, STAR and EGR1, maybe play an important role in goat reproduction traits.

Key words: Fuqing goat, Nubian black goat, ovary tissue, follicular stage, transcriptome

Table 1

The qRT-PCR primers"

基因名称
Gene		 上游引物
Forward primer（5′-3′）		 下游引物
Reverse primer（5′-3′）		 产物长度
Product size（bp）
18S rRNA GTAACCCGTTGAACCCCATT CCATCCAATCGGTAGTAGCG 151
New-Gene 4708 CTCCAAATCGGGCAACACAG TCCACAGTAATAATCGGCCTCG 77
New-Gene 1125 ACAACAGTGTCAGCATCCGT TGTTGGAGTCCCGTTATGGC 136
CREB3L4 GGGCTCTTCGAAACAGCAGA AGTCCCAGCTCCAGGAAAGA 104
THSD7B AGTTACAAGGCGCATCACCA TTTCGGCATGATGCAGGACT 159
CRABP1 GTGCAGGAGCTTACCCACTT CGGGTCCAGTAGGTTTTGGG 93
CTHRC1 TTGGTGCTGGACTAGTGGAC ATGCGAGACACCGAATTCCA 100

Table 2

RNA-Seq and mapping to the reference genome"

样品
Sample		 总Reads
Total reads		 可定位的Reads
Mapped reads		 唯一定位Reads
Uniq mapped reads		 多点定位Reads
Multiple mapped reads
F-1 48567844 41489885/85.43% 39687502/81.72% 1802383/3.71%
F-2 49910620 42262711/84.68% 40565566/81.28% 1697145/3.40%
F-3 49890394 42216928/84.62% 40925490/82.03% 1791438/3.59%
N-4 53482074 46603840/87.14% 45110457/84.35% 1293383/2.42%
N-5 53379622 46077636/86.32% 44696951/83.73% 1380685/2.59%
N-6 53967784 46261607/85.72% 45017922/83.42% 1243685/2.30%

Fig. 1

Correlation heat map of gene expression level in 6 samples"

Fig. 2

Volcano plot of differentially expressed genesGreen dots are significantly down-regulated genes. Red dots are significantly up-regulated genes. Black dots are genes without differentially expression"

Fig. 3

GO annotation of DEGs 细胞过程Cellular process：1细胞部分 Cell part;2细胞 Cell;3细胞器 Organelle;4膜 Membrane;5膜部分 Membrane part;6细胞器部分Organelle part;7高分子复合物 Macromolecular complex;8胞外区Extracellular region;9膜包围内腔Membrane-enclosed lumen;10细胞外区域部分Extracellular region part;11细胞连接Cell junction;12细胞外基质Extracellular matrix;13突触Synapse;14突出部分Synapse part;15细胞外基质部分 Extracellular matrix part;16胶原三聚体Collagen trimer;17细胞核Nucleoid;18病毒体Virion;19病毒体部分Virion part"

Fig. 4

COG annotation classification statistics of DEGs"

Fig. 5

List of KEGG pathway for DEGs"

Fig. 6

Enriched scatter map of DEGs KEGG pathway"

Fig. 7

The number of different SNP/InDel effects of DEGs"

Fig. 8

Validation of sequencing results by qRT-PCR"

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