Role of SLC11A1 gene in disease resistance

Thomas, Naicy; Joseph, Siju

doi:10.2298/bah1201099t

Cited by 10 publications

(4 citation statements)

References 27 publications

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“…This is a highly conserved gene across mammals and is associated with resistance and susceptibility to various intracellular pathogens in humans as well as in livestock species (Blackwell et al. 2001; Thomas and Joseph 2012). Previous studies have shown that microsatellite alleles localized in the 3′ UTR of the SLC11A1 are involved in macrophage function and resistance to Brucella abortus infections in both cattle and buffalo (Kumar et al.…”

Section: Resultsmentioning

confidence: 99%

Systematic profiling of short tandem repeats in the cattle genome

Haasl

Sun

et al. 2016

Genome Biol Evol

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Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2–6 base pair motifs in many mammalian genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in dairy cattle. We observed significant STRs overlap with functional genes and quantitative trait loci (QTL). We performed evolutionary and population genetic analyses using over 20,000 common dinucleotide STRs. Besides corroborating the well-established positive correlation between allele size and variance in allele size, these analyses also identified dozens of outlier STRs based on two anomalous relationships that counter expected characteristics of neutral evolution. And one STR locus overlaps with a significant region of a summary statistic designed to detect STR-related selection. Additionally, our results showed that only 57.1% of STRs located within SNP-based linkage disequilibrium (LD) blocks whereas the other 42.9% were out of blocks. Therefore, a substantial number of STRs are not tagged by SNPs in the cattle genome, likely due to STR's distinct mutation mechanism and elevated polymorphism. This study provides the foundation for future STR-based studies of cattle genome evolution and selection.

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Section: Resultsmentioning

confidence: 99%

Systematic profiling of short tandem repeats in the cattle genome

Haasl

Sun

et al. 2016

Genome Biol Evol

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“…The role of Slc11a1 is very important due to its association with resistance and susceptibility to various intracellular pathogens in humans as well as in livestock species (Thomas & Joseph, ). Sequence analysis of Slc11a1 gene from different bovine and bubaline breeds has been carried out to determine polymorphisms on this gene.…”

Section: Discussionmentioning

confidence: 99%

Molecular comparison of Slc11a1 and Slc11a2 genes of swamp‐ and riverine‐type water buffaloes

Padiernos

Mingala

2016

Int J Immunogenetics

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Solute-linked carrier 11a and 11a2 (Slc) have been associated with disease resistance and/or susceptibility across animal species. These genes have an important mechanism in the regulation against intracellular infection. This study analysed the genetic characteristic of Slc 11a and 11a2 in swamp-type and riverine-type water buffaloes to understand their immunological distinction. Characterization of Slc11a1 and Slc11a2 genes from swamp- and riverine-type water buffaloes was carried out by molecular cloning, sequencing and phylogenetic analysis. The cloned cDNA of Slc11a1 and Slc11a2 contained an open reading frame of 1647 and 1723 nucleotides, encoding 549 and 574 amino acids, respectively. Nucleotide sequence homology of both Slc11a1 and Slc11a2 had 99% in swamp and riverine type, which gives almost identical polypeptide. However, Slc11a1 and Slc11a2 have substitutions of 5 and 1 amino acid residues, correspondingly. These substitutions suggest as a potential gene markers for resistance and/or susceptibility to intracellular infection. Furthermore, phylogenetic analysis confirmed the degree of relationship between the bubaline species and justifies the distinctness of each breed by the bootstrap value generated.

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“…This is a highly conserved gene across mammals and is associated with resistance and susceptibility to various intracellular pathogens in humans as well as in livestock species (Blackwell et al 2001;Thomas and Joseph 2012). Previous studies have shown that microsatellite alleles localized in the 3 0 UTR of the SLC11A1 are involved in macrophage function and resistance to Brucella abortus infections in both cattle and buffalo (Kumar et al 2005;Borriello et al 2006;Capparelli et al 2007;Ganguly et al 2008;Martinez et al 2008;Kumar et al 2011).…”

Section: Strs Overlap With Genesmentioning

confidence: 99%

0309 Systematic profiling of short tandem repeats in the cattle genome

Liu

Haasl

et al. 2016

Journal of Animal Science

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Short tandem repeats (STRs), or microsatellites, are genetic variants with repetitive 2-6 base pair motifs in many mammalian genomes. Using high-throughput sequencing and experimental validations, we systematically profiled STRs in five Holsteins. We identified a total of 60,106 microsatellites and generated the first high-resolution STR map, representing a substantial pool of polymorphism in dairy cattle. We observed significant STRs overlap with functional genes and quantitative trait loci (QTL). We performed evolutionary and population genetic analyses using over 20,000 common dinucleotide STRs. Besides corroborating the well-established positive correlation between allele size and variance in allele size, these analyses also identified dozens of outlier STRs based on two anomalous relationships that counter expected characteristics of neutral evolution. And one STR locus overlaps with a significant region of a summary statistic designed to detect STR-related selection. Additionally, our results showed that only 57.1% of STRs located within SNP-based linkage disequilibrium (LD) blocks whereas the other 42.9% were out of blocks. Therefore, a substantial number of STRs are not tagged by SNPs in the cattle genome, likely due to STR's distinct mutation mechanism and elevated polymorphism. This study provides the foundation for future STR-based studies of cattle genome evolution and selection.

show abstract

Role of SLC11A1 gene in disease resistance

Cited by 10 publications

References 27 publications

Systematic profiling of short tandem repeats in the cattle genome

Systematic profiling of short tandem repeats in the cattle genome

Molecular comparison of Slc11a1 and Slc11a2 genes of swamp‐ and riverine‐type water buffaloes

0309 Systematic profiling of short tandem repeats in the cattle genome

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