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

【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.