海南黑山羊GDF9基因nsSNP功能性预测及与产羔数的关联分析

doi:10.16431/j.cnki.1671-7236.2025.05.021

摘要/Abstract

摘要： 【目的】探究海南黑山羊产羔性状的分子遗传信息以及生长分化因子9(growth differentiation factor 9，GDF9)基因多态性与产羔数间的相关性，以期为山羊多胎育种提供有用的分子标记。【方法】以海南黑山羊为研究对象，采集222只山羊的血液样本进行GDF9基因非同义单核苷酸多态性(non-synonymous single nucleotide polymorphism，nsSNP)筛选。采用SnaPshot方法进行基因分型，利用SPSS 19.0软件中一般线性模型对GDF9基因多态位点与海南黑山羊产羔数进行关联分析，并对nsSNP位点进行生物信息学分析。【结果】GDF9基因共检测到15个变异位点，其中错义突变位点7个：T755C、G1264T、G2296A、G2335A、C2730T、G2773A、C3330T；同义突变位点6个：G888A、T951G、A972C、T2631C、A2871C、G3101A；插入位点2个：3101G3102和3140T3141。755 bp处发生的T→C突变导致蛋氨酸(Met)变为苏氨酸(Thr)；1 264 bp处发生的G→T突变导致丙氨酸(Ala)变为丝氨酸(Ser)；2 296和2 335 bp处发生的G→A突变导致缬氨酸(Val)变为异亮氨酸(IIe)；2 730 bp处发生的C→T突变导致亮氨酸(Leu)变为苯丙氨酸(Phe)；2 773 bp处发生的G→A突变导致丙氨酸(Ala)变为苏氨酸(Thr)；3 330 bp处发生的C→T突变导致脯氨酸(Pro)变为亮氨酸(Leu)；而在3 101～3 102、3 140～3 141 bp处G与T的插入使得氨基酸完全改变。海南黑山羊T755C位点TT和CC基因型个体的平均产羔数显著高于TC基因型(P＜0.05)，G2335A和G2773A位点AA基因型个体的平均产羔数均显著高于GG和GA基因型(P＜0.05)，C2730T位点TT基因型个体的平均产羔数显著高于CC和CT基因型(P＜0.05)。nsSNP功能性预测及高级结构分析结果显示，T755C→M252T、C2730T→L912F、G2335A→V780I、G2296A→V767I、G2773A→A926T 5个nsSNPs位点均属于有害突变，其中，T755C→M252T、C2730T→L912F位点的mRNA二级结构和蛋白三级结构变化较大，可能对蛋白功能有较大影响。【结论】本研究预测到海南黑山羊GDF9基因的5个有害突变位点，结合与产羔数的关联分析和蛋白功能预测，推测T755C→M252T、C2730T→L912F 2个位点可作为海南黑山羊多胎性状选育的分子标记，为山羊多胎分子标记辅助育种提供了参考依据。

关键词: 海南黑山羊; GDF9基因; nsSNP; 产羔数; 生物信息学

Abstract: 【Objective】 This study was aimed to investigate the molecular genetic information of litter traits in Hainan Black goats and the correlation between polymorphism of growth differentiation factor 9 (GDF9) gene and litter size,in order to provide useful molecular markers for prolific breeding in goats.【Method】 Using Hainan Black goats as the research object,blood samples were collected from 222 goats for non-synonymous single nucleotide polymorphism (nsSNP) screening of GDF9 gene.Genotyping was performed using SnaPshot method,and the association analysis between GDF9 gene polymorphism and litter size in Hainan Black goats using the General Linear Model of SPSS 19.0 software,and the bioinformatics analysis was carried out on nsSNP.【Result】 A total of 15 variant sites were detected in GDF9 gene,including 7 missense mutations (T755C,G1264T,G2296A,G2335A,C2730T,G277A and C3330T),6 synonymous mutations (G888A,T951G,A972C,T631C,A2871C and G3101A),and 2 insertion sites (3101G312 and 3140T3141).The T→C mutation at 755 bp caused a mutation from methionine (Met) to threonine (Thr),the G→T mutation at 1 264 bp caused a mutation from alanine (Ala) to serine (Ser),the G→A mutation at 2 296 and 2 335 bp caused a mutation from valine (Val) to isoleucine (IIe),the C→T mutation at 2 730 bp caused a mutation from leucine (Leu) to phenylalanine (Phe),the G→A mutation at 2 773 bp caused a mutation from alanine (Ala) to threonine (Thr),and the C→T mutation at 3 330 bp caused a mutation from proline (Pro) to leucine (Leu).The insertion of G and T at 3 101-3 102 and 3 140-3 141 bp completely altered the amino acids.The average litter size of TT and CC genotypes in T755C of Hainan Black goats was significantly higher than that of TC genotype (P＜0.05).The average litter size of AA genotype in G2335A and G2773A was significantly higher than that of GG and GA genotypes (P＜0.05).The average litter size of TT genotype in C2730T was significantly higher than that of CC and CT genotypes (P＜0.05).The results of nsSNP functional prediction and advanced structure analysis showed that 5 nsSNPs of T755C→M252T,C2730T→L912F,G2335A→V780I,G2296A→V767I,and G2773A→A926T were deleterious,with significant changes in the mRNA secondary structure and protein tertiary structure at T755C→M252T and C2730T→L912F,which were predicted to have a greater effect on protein function.【Conclusion】 This study screened out 5 deleterious mutation sites of GDF9 gene in Hainan Black goats.Based on the correlation analysis with litter size and protein function prediction,it was speculated that T755C→M252T and C2730T→L912F could be used as molecular markers for the breeding of prolific trait in Hainan Black goats,providing a reference for molecular-assisted breeding in goats.

Key words: Hainan Black goats; GDF9 gene; nsSNP; litter size; bioinformatics

中图分类号:

S813.3

管凇, 施力光, 林雨, 蒋剑箫, 武洪志, 彭维祺. 海南黑山羊GDF9基因nsSNP功能性预测及与产羔数的关联分析[J]. 中国畜牧兽医, 2025, 52(5): 2166-2176.

GUAN Song, SHI Liguang, LIN Yu, JIANG Jianxiao, WU Hongzhi, PENG Weiqi. Functional Prediction of GDF9 Gene nsSNP and Its Correlation Analysis with Litter Size in Hainan Black Goats[J]. China Animal Husbandry and Veterinary Medicine, 2025, 52(5): 2166-2176.

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