Dataset Information

Detection and replication of QTL underlying resistance to gastrointestinal nematodes in adult sheep using the ovine 50K SNP array.

ABSTRACT: Persistence of gastrointestinal nematode (GIN) infection and the related control methods have major impacts on the sheep industry worldwide. Based on the information generated with the Illumina OvineSNP50 BeadChip (50 K chip), this study aims at confirming quantitative trait loci (QTL) that were previously identified by microsatellite-based genome scans and identifying new QTL and allelic variants that are associated with indicator traits of parasite resistance in adult sheep. We used a commercial half-sib population of 518 Spanish Churra ewes with available data for fecal egg counts (FEC) and serum levels of immunoglobulin A (IgA) to perform different genome scan QTL mapping analyses based on classical linkage analysis (LA), a combined linkage disequilibrium and linkage analysis (LDLA) and a genome-wide association study (GWAS).For the FEC and IgA traits, we detected a total of three 5 % chromosome-wise significant QTL by LA and 63 significant regions by LDLA, of which 13 reached the 5 % genome-wise significance level. The GWAS also revealed 10 significant SNPs associated with IgAt, although no significant associations were found for LFEC. Some of the significant QTL for LFEC that were detected by LA and LDLA on OAR6 overlapped with a highly significant QTL that was previously detected in a different half-sib population of Churra sheep. In addition, several new QTL and SNP associations were identified, some of which show correspondence with effects that were reported for different populations of young sheep. Other significant associations that did not coincide with previously reported associations could be related to the specific immune response of adult animals.Our results replicate a FEC-related QTL located on OAR6 that was previously reported in Churra sheep and provide support for future research on the identification of the allelic variant that underlies this QTL. The small proportion of genetic variance explained by the detected QTL and the large number of functional candidate genes identified here are consistent with the hypothesis that GIN resistance/susceptibility is a complex trait that is not determined by individual genes acting alone but rather by complex multi-gene interactions. Future studies that combine genomic variation analysis and functional genomic information may help elucidate the biology of GIN disease resistance in sheep.

SUBMITTER: Atlija M

PROVIDER: S-EPMC4719203 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Detection and replication of QTL underlying resistance to gastrointestinal nematodes in adult sheep using the ovine 50K SNP array.

Atlija Marina M Arranz Juan-Jose JJ Martinez-Valladares María M Gutiérrez-Gil Beatriz B

Genetics, selection, evolution : GSE 20160120

<h4>Background</h4>Persistence of gastrointestinal nematode (GIN) infection and the related control methods have major impacts on the sheep industry worldwide. Based on the information generated with the Illumina OvineSNP50 BeadChip (50 K chip), this study aims at confirming quantitative trait loci (QTL) that were previously identified by microsatellite-based genome scans and identifying new QTL and allelic variants that are associated with indicator traits of parasite resistance in adult sheep. ...[more]

PMID: 26791855

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Project description:BACKGROUND: In recent years, genome-wide association studies have successfully uncovered single-nucleotide polymorphisms (SNPs) associated with complex traits such as diseases and quantitative phenotypes. These variations account for a small proportion of heritability. With the development of high throughput techniques, abundant submicroscopic structural variations have been found in organisms, of which the main variations are copy number variations (CNVs). Therefore, CNVs are increasingly recognized as an important and abundant source of genetic variation and phenotypic diversity. RESULTS: Analyses of CNVs in the genomes of three sheep breeds were performed using the Ovine SNP50 BeadChip array. A total of 238 CNV regions (CNVRs) were identified, including 219 losses, 13 gains, and six with both events (losses and gains), which cover 60.35 Mb of the sheep genomic sequence and correspond to 2.27% of the autosomal genome sequence. The length of the CNVRs on autosomes range from 13.66 kb to 1.30 Mb with a mean size of 253.57 kb, and 75 CNVRs events had a frequency > 3%. Among these CNVRs, 47 CNVRs identified by the PennCNV overlapped with the CNVpartition. Functional analysis indicated that most genes in the CNVRs were significantly enriched for involvement in the environmental response. Furthermore, 10 CNVRs were selected for validation and 6 CNVRs were further experimentally confirmed by qPCR. In addition, there were 57 CNVRs overlapped in our new dataset and other published ruminant CNV studies. CONCLUSIONS: In this study, we firstly constructed a sheep CNV map based on the Ovine SNP50 array. Our results demonstrated the differences of two detection tools and integration of multiple algorithms can enhance the detection of sheep genomic structure variations. Furthermore, our findings would be of help for understanding the sheep genome and provide preliminary foundation for carrying out the CNVs association studies with economically important phenotypes of sheep in the future.

Project description:Detection of coding/functional SNPs that change the biological function of a gene may lead to identification of putative causative alleles within QTL regions and discovery of genetic markers with large effects on phenotypes. This study has two-fold objectives, first to develop, and validate a 50K transcribed gene SNP-chip using RNA-Seq data. To achieve this objective, two bioinformatics pipelines, GATK and SAMtools, were used to identify ~21K transcribed SNPs with allelic imbalances associated with important aquaculture production traits including body weight, muscle yield, muscle fat content, shear force, and whiteness in addition to resistance/susceptibility to bacterial cold-water disease (BCWD). SNPs ere identified from pooled RNA-Seq data collected from ~620 fish, representing 98 families from growth- and 54 families from BCWD-selected lines with divergent phenotypes. In addition, ~29K transcribed SNPs without allelic-imbalances were strategically added to build a 50K Affymetrix SNP-chip. SNPs selected included two SNPs per gene from 14K genes and ~5K non-synonymous SNPs. The SNP-chip was used to genotype 1728 fish. The average SNP calling-rate for samples passing quality control (QC; 1,641 fish) was ? 98.5%. The second objective of this study was to test the feasibility of using the new SNP-chip in GWA (Genome-wide association) analysis to identify QTL explaining muscle yield variance. GWA study on 878 fish (representing 197 families from 2 consecutive generations) with muscle yield phenotypes and genotyped for 35K polymorphic markers (passing QC) identified several QTL regions explaining together up to 28.40% of the additive genetic variance for muscle yield in this rainbow trout population. The most significant QTLs were on chromosomes 14 and 16 with 12.71 and 10.49% of the genetic variance, respectively. Many of the annotated genes in the QTL regions were previously reported as important regulators of muscle development and cell signaling. No major QTLs were identified in a previous GWA study using a 57K genomic SNP chip on the same fish population. These results indicate improved detection power of the transcribed gene SNP-chip in the target trait and population, allowing identification of large-effect QTLs for important traits in rainbow trout.

Dataset Information

Detection and replication of QTL underlying resistance to gastrointestinal nematodes in adult sheep using the ovine 50K SNP array.

Publications

Detection and replication of QTL underlying resistance to gastrointestinal nematodes in adult sheep using the ovine 50K SNP array.

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