Differential Expression Analysis of Hypothalamus During Estrous Cycle in Xinjiang Goats with Different Fertility Levels

doi:10.11924/j.issn.1000-6850.casb2025-0479

Abstract

Abstract:

The study aims to explore differentially expressed genes related to reproductive traits in Xinjiang goats and screen out key genes associated with goat reproduction. In this study, transcriptome sequencing analysis was used to compare the transcriptomes of hypothalamic tissues between Xinjiang goats with different fecundity during the follicular phase and luteal phase, aiming to screen key reproduction-related genes in the hypothalamus of Xinjiang goats with high and low fecundity during these two phases. In the differential expression analysis of the hypothalamus during the follicular phase, a total of 680 differentially expressed genes were identified in the XJLSX vs XJLDX group (high-fecundity ewes vs low-fecundity ewes in the follicular phase), among which 210 were up-regulated and 470 were down-regulated. GO and KEGG functional analyses of these differentially expressed genes revealed 9 GO Terms containing 16 differentially expressed genes and 8 KEGG pathways containing 23 differentially expressed genes that were related to goat reproductive traits. Combined with protein-protein interaction network analysis of differentially expressed genes and relevant literature, 6 differentially expressed genes, namely NPR1, KITLG, GABRAI, CRHR2, ADCYAP1, IGF2BP3, were screened out as potential key genes affecting the reproductive traits of Xinjiang goats. In the differential expression analysis of the hypothalamus during the luteal phase, a total of 656 differentially expressed genes were found in the XJHSX vs XJHDX group (high-fecundity ewes vs low-fecundity ewes in the luteal phase), with 178 up-regulated and 478 down-regulated. GO and KEGG functional analyses showed that 7 GO Terms, involving 9 differentially expressed genes, were associated with oocyte growth and differentiation, follicular development, and reproductive hormones; 6 KEGG signaling pathways, containing 10 differentially expressed genes, were related to goat reproductive traits. Through integration with protein-protein interaction network analysis and literature review, 5 differentially expressed genes (WT1, IGF1, ESR1, NR5A1, MET) were identified as potential key genes influencing the reproductive traits of Xinjiang goats. This study screened out key genes related to goat reproduction, which provided a theoretical basis and molecular markers for breeding new high-fecundity and multi-fetal strains of Xinjiang goats.

Key words: Xinjiang goats, reproductive traits, differential analysis, transcriptome

QUAN Kaili, ZHENG Wenxin, LV Xuefeng, XING Weiting, LIU Jianxin. Differential Expression Analysis of Hypothalamus During Estrous Cycle in Xinjiang Goats with Different Fertility Levels[J]. Chinese Agricultural Science Bulletin, 2025, 41(21): 64-75.

Figures/Tables 18

References 25

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基因序号	引物名称	序列(5'to3')	退火温度/℃
内参	β-actin -F	AGAGCAAGAGAGGCATCC	60
内参	β-actin -R	TCGTTGTAGAAGGTGTGGT	60
1	LCN2-F	CCTGTCCTTCCCATCTTC	62
1	LCN2-R	GGTTGTAGTCGGTGTTCA	62
2	GABRA6-F	GCCATCCAACCATCTCAT	62
2	GABRA6-R	TCCAACCAGTCCATCCTA	62
3	MZT1-F	AAGGCAGTGTTGGTGAAG	64
3	MZT1-R	GTGAAGGAGAGAGGTAGGG	64
4	HDC-F	CACTGGATGACTGCTTCTC	62
4	HDC-R	ACTGCCTTCTTCTTGTTCTG	62
5	HOXB8-F	CCCTTCTTTCCTTCCTTCCT	64
5	HOXB8-R	GCCACCCTTTCTCCACTA	64
6	RBM20-F	CCATAGACCAGAAGGACAA	64
6	RBM20-F	GTGACTTGAGGCTGATTTC	64
7	PRLH-F	GGGACAGGAAAGGAAGGG	64
7	PRLH-R	CTACCCGCAAAGGAGGAT	64
8	C1QL4-F	GTGGGTTGTCCTGTTCTC	62
8	C1QL4-R	TGGCGTAGTCGTAGTTCT	62

基因序号	引物名称	序列(5'to3')	退火温度/℃
内参	β-actin -F	AGAGCAAGAGAGGCATCC	60
内参	β-actin -R	TCGTTGTAGAAGGTGTGGT	60
1	LCN2-F	CCTGTCCTTCCCATCTTC	62
1	LCN2-R	GGTTGTAGTCGGTGTTCA	62
2	GABRA6-F	GCCATCCAACCATCTCAT	62
2	GABRA6-R	TCCAACCAGTCCATCCTA	62
3	MZT1-F	AAGGCAGTGTTGGTGAAG	64
3	MZT1-R	GTGAAGGAGAGAGGTAGGG	64
4	HDC-F	CACTGGATGACTGCTTCTC	62
4	HDC-R	ACTGCCTTCTTCTTGTTCTG	62
5	HOXB8-F	CCCTTCTTTCCTTCCTTCCT	64
5	HOXB8-R	GCCACCCTTTCTCCACTA	64
6	RBM20-F	CCATAGACCAGAAGGACAA	64
6	RBM20-F	GTGACTTGAGGCTGATTTC	64
7	PRLH-F	GGGACAGGAAAGGAAGGG	64
7	PRLH-R	CTACCCGCAAAGGAGGAT	64
8	C1QL4-F	GTGGGTTGTCCTGTTCTC	62
8	C1QL4-R	TGGCGTAGTCGTAGTTCT	62

Sample	Total clean reads	Total mapped	Unique mapped
XJLDX1	47276504	45123174(95.45%)	39143856(82.80%)
XJLDX2	42431284	40504918(95.46%)	35932632(84.68%)
XJLDX3	49212048	46839434(95.18%)	41636410(84.61%)
XJLDX4	55745388	52907728(94.91%)	47257544(84.77%)
XJLDX5	59122378	55947972(94.63%)	49351868(83.47%)
XJLSX1	48549506	46020270(94.79%)	41730226(85.95%)
XJLSX2	49063618	46640442(95.06%)	41215282(84.00%)
XJLSX3	43502708	40818808(93.83%)	33404466(76.79%)
XJLSX4	45717086	43325070(94.77%)	38179254(83.51%)
XJLSX5	45604984	43198960(94.72%)	36765638(80.62%)
XJHDX1	50686348	48298968(95.29%)	40612706(80.13%)
XJHDX2	46425840	44063820(94.91%)	37186408(80.10%)
XJHDX3	59957406	57053158(95.16%)	50638298(84.46%)
XJHSX1	73071842	69436812(95.03%)	61802134(84.58%)
XJHSX2	86668774	82282118(94.94%)	70766570(81.65%)
XJHSX3	61951726	58485872(94.41%)	51276738(82.77%)

Sample	Total clean reads	Total mapped	Unique mapped
XJLDX1	47276504	45123174(95.45%)	39143856(82.80%)
XJLDX2	42431284	40504918(95.46%)	35932632(84.68%)
XJLDX3	49212048	46839434(95.18%)	41636410(84.61%)
XJLDX4	55745388	52907728(94.91%)	47257544(84.77%)
XJLDX5	59122378	55947972(94.63%)	49351868(83.47%)
XJLSX1	48549506	46020270(94.79%)	41730226(85.95%)
XJLSX2	49063618	46640442(95.06%)	41215282(84.00%)
XJLSX3	43502708	40818808(93.83%)	33404466(76.79%)
XJLSX4	45717086	43325070(94.77%)	38179254(83.51%)
XJLSX5	45604984	43198960(94.72%)	36765638(80.62%)
XJHDX1	50686348	48298968(95.29%)	40612706(80.13%)
XJHDX2	46425840	44063820(94.91%)	37186408(80.10%)
XJHDX3	59957406	57053158(95.16%)	50638298(84.46%)
XJHSX1	73071842	69436812(95.03%)	61802134(84.58%)
XJHSX2	86668774	82282118(94.94%)	70766570(81.65%)
XJHSX3	61951726	58485872(94.41%)	51276738(82.77%)

GO条目	基因数目	基因名
biological regulation	7	PRLR、IGF2BP3、KITLG、GABRA1、HTR1D、NPR1、SLC9A1
system development	8	FGF5、TNNI3、PRLR、KITLG、GABRA1、SLC9A1、GDNF、GCG
hormone activity	1	FSHβ
extra cellular region	1	FSHβ
multicellular organismal process	8	NPR1、PRLR、KITLG、GABRA1、SSTR5、CRHR2、SLC9A1、ADCYAP1
membrane	6	KITLG、NPR1、PRLR、CRHR2、GABRA1、HTR1D
transferase activity	1	AANAT
receptor ligand activity	1	FGF1
regulation of phosphate metabolic process	2	PRLR、KITLG