猪SLC39A基因家族鉴定及SNP位点与繁殖性状的关联分析

Identification of porcine SLC39A gene family and association analysis of its SNP loci with reproductive traits

  • 摘要: 【目的】开展猪SLC39A基因家族鉴定及SNP位点与繁殖性状的关联分析,为猪高繁殖力的遗传改良提供候选分子标记。【方法】使用生物信息学方法鉴定大白猪SLC39A基因家族成员并分析其理化性质。筛选SLC39A基因家族单核苷酸多态性(SNP)位点,并采用一般线性模型进行各SNP位点不同基因型与健仔数的关联分析。合成含有C和G等位基因的靶序列,构建至pGL3-basic双荧光素酶报告载体并转染至人胚胎肾细胞中,转染48 h后测定萤火虫荧光素酶和海肾荧光素酶活性。【结果】SLC39A基因家族蛋白相对分子质量介于9.37~94.20,理论等电点(pI)介于5.03~8.46,属于不稳定蛋白。SLC39A基因家族成员在染色体上均有多个编码蛋白的基因编码区,基因结构较复杂,共鉴定出7个保守基序(Motif),长度介于21~44个氨基酸,Motif-2、Motif-3和Motif-7的保守程度较高,Motif-2为所有SLC39A基因家族蛋白共有的保守基序。SLC39A基因家族成员不均匀地分布在10条染色体上。在大白猪基因组内共检测到1次片段复制事件,SLC39A5SLC39A10基因存在片段重复。系统发育树显示,猪与人、大鼠、牛、羊和猴的SLC39A1~SLC39A14蛋白亲缘关系较近,猴与人的SLC39A1~SLC39A14蛋白亲缘关系较近。大白猪SLC39A基因家族蛋白中SLC39A1、SLC39A2、SLC39A9和SLC39A11蛋白位于网络的核心位置,与其他蛋白表现出较强的互作关系。大白猪SLC39A基因家族共鉴定到13个符合哈迪—温伯格平衡的SNP位点,3个SNP位点与健仔数显著关联(P<0.05,下同)。SLC39A8基因rs344840408C>G的CC基因型个体的健仔数显著高于GG基因型个体。【结论】猪SLC39A基因家族在进化上较为保守,蛋白成员间存在紧密的互作网络,共同维持锌稳态。SLC39A基因家族部分成员的变异(SLC39A1基因rs319315931A>G、SLC39A8基因rs344840408C>G、SLC39A11基因rs338265001T>C)可能通过影响基因表达或锌转运功能而改变母猪健仔数。

     

    Abstract: 【Objective】To identify the porcine SLC39A gene family and conduct association analysis between SNP loci and reproductive traits, which could provide candidate molecular markers for the genetic improvement of high fertility in pigs.【Method】Bioinformatic method was used to identify members of the Large White pig SLC39A gene family and analyze their physicochemical properties. Single nucleotide polymorphism (SNP) loci in the SLC39A gene family were screened, and a general linear model was used to analyze the association between different genotypes at each SNP loci and the number of healthy piglets. Target sequences containing C and G alleles were synthesized, constructed into the pGL3-basic dual luciferase reporter vector, and stained into human embryonic kidney cells. The activities of firefly luci-ferase and renilla luciferase were measured 48 h after transfection.【Result】The SLC39A gene family protein had molecular weights ranging from 9.37 to 94.20 and theoretical isoelectric points ranging from 5.03 to 8.46, classifying them as unstable proteins. Each member of the SLC39A gene family possessed multiple gene coding regions encoding proteins on the chromosome, exhibiting a complex gene structure. Seven conserved motifs, ranging in length from 21 to 44 amino acids, were identified. Motif-2, Motif-3, and Motif-7 showed high levels of conservation, with Motif-2 being a conserved motif shared by all proteins of the SLC39A gene family. The SLC39A gene family members were unevenly distri-buted across the 10 chromosomes. One fragment duplication event was detected in Large White pig genome, with duplicate segments found in SLC39A5 and SLC39A10 genes. Phylogenetic tree analysis showed that proteins SLC39A1-SLC39A14 of pigs, humans, rats, cattle, sheep, and monkeys shared close relationships, while proteins of monkey SLC39A1-SLC39A14 were more closely related to human origins. Four proteins in Large White of monkey SLC39A gene family, SLC39A1, SLC39A2, SLC39A9, and SLC39A11, were located at the core of the network and exhibited strong interactions with other proteins. Thirteen SNP loci conforming to Hardy-Weinberg equilibrium were identified in the Large White pig SLC39A gene family, and three SNP loci were significantly associated with the number of healthy piglets (P<0.05, the same below). Individuals with the CC genotype (rs344840408C>G) of SLC39A8 gene had significantly more healthy piglets than those with the GG genotype.【Conclusion】The porcine SLC39A family is evolutionarily conserved, with a tight network of interactions among its protein members working together to maintain zinc homeostasis. Genetic variations in some members of the SLC39A gene family (SLC39A1 gene rs319315931A>G, SLC39A8 gene rs344840408C>G, SLC39A11 gene rs338265001T>C) may alter the number of healthy piglets in sows by affecting gene expression or zinc transport function.

     

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