scholarly journals Association analysis and functional annotation of imputed sequence data within genomic regions influencing resistance to gastro-intestinal parasites detected by an LDLA approach in a nucleus flock of Sarda dairy sheep

2022 ◽  
Vol 54 (1) ◽  
Author(s):  
Sara Casu ◽  
Mario Graziano Usai ◽  
Tiziana Sechi ◽  
Sotero L. Salaris ◽  
Sabrina Miari ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Candidate Genes ◽  
Association Analysis ◽  
Functional Annotation ◽  
Sequence Data ◽  
Ovis Aries ◽  
Differentially Expressed ◽  
Phenotypic Variance ◽  
Major Health Problem ◽  
Functional Variants

Abstract Background Gastroinestinal nematodes (GIN) are one of the major health problem in grazing sheep. Although genetic variability of the resistance to GIN has been documented, traditional selection is hampered by the difficulty of recording phenotypes, usually fecal egg count (FEC). To identify causative mutations or markers in linkage disequilibrium (LD) to be used for selection, the detection of quantitative trait loci (QTL) for FEC based on linkage disequilibrium-linkage analysis (LDLA) was performed on 4097 ewes (from 181 sires) all genotyped with the OvineSNP50 Beadchip. Identified QTL regions (QTLR) were imputed from whole-genome sequences of 56 target animals of the population. An association analysis and a functional annotation of imputed polymorphisms in the identified QTLR were performed to pinpoint functional variants with potential impact on candidate genes identified from ontological classification or differentially expressed in previous studies. Results After clustering close significant locations, ten QTLR were defined on nine Ovis aries chromosomes (OAR) by LDLA. The ratio between the ANOVA estimators of the QTL variance and the total phenotypic variance ranged from 0.0087 to 0.0176. QTL on OAR4, 12, 19, and 20 were the most significant. The combination of association analysis and functional annotation of sequence data did not highlight any putative causative mutations. None of the most significant SNPs showed a functional effect on genes’ transcript. However, in the most significant QTLR, we identified genes that contained polymorphisms with a high or moderate impact, were differentially expressed in previous studies, contributed to enrich the most represented GO process (regulation of immune system process, defense response). Among these, the most likely candidate genes were: TNFRSF1B and SELE on OAR12, IL5RA on OAR19, IL17A, IL17F, TRIM26, TRIM38, TNFRSF21, LOC101118999, VEGFA, and TNF on OAR20. Conclusions This study performed on a large experimental population provides a list of candidate genes and polymorphisms which could be used in further validation studies. The expected advancements in the quality of the annotation of the ovine genome and the use of experimental designs based on sequence data and phenotypes from multiple breeds that show different LD extents and gametic phases may help to identify causative mutations.

scholarly journals Transcriptional profiling of Ovis aries identifies Ovar-DQA1 allele frequency differences between nematode-resistant and susceptible selection lines

2007 ◽  
Vol 30 (3) ◽  
pp. 253-261 ◽  
Author(s):  
Orla M. Keane ◽  
Ken G. Dodds ◽  
Allan M. Crawford ◽  
John C. McEwan
Keyword(s):  
Linkage Disequilibrium ◽  
Null Allele ◽  
Intestinal Parasites ◽  
Transcriptional Profiling ◽  
Radical Scavenging ◽  
Gastrointestinal Nematodes ◽  
Ovis Aries ◽  
Differentially Expressed ◽  
Null Alleles ◽  
Transcription Profiles

Gastrointestinal nematodes are a major cause of disease in grazing livestock; however, individual animals differ in their response to infection. To identify genes whose expression correlates with resistance status, transcriptional profiling of resistant and susceptible sheep was undertaken. Transcription profiles were taken at three time points during the growth of lambs. The number of genes differentially expressed increased as animals were exposed to longer nematode challenge. Almost 300 genes, with a variety of functions, were differentially expressed overall, although genes more highly expressed in resistant animals typically had major histocompatibility complex (MHC) II, free radical scavenging or smooth muscle-specific functions. The Ovar-DQA1 gene was 8.4-fold more highly expressed in resistant animals. This was due in part to a higher frequency of DQA1 null alleles in susceptible animals. The null allele of DQA1 was also associated with susceptibility in a separate selection flock, presenting the hypothesis that failure to present parasite antigens to immune cells led to nematode susceptibility. To test this hypothesis, commercial rams from three breeds were genotyped for the null allele of DQA1. The homozygous null allele was associated with susceptibility in only one of the three breeds tested indicating that the null allele does not cause susceptibility to intestinal parasites per se but is probably in linkage disequilibrium with additional polymorphisms in the MHC region. A combination of these polymorphisms may contribute to susceptibility in some populations. The extent of linkage disequilibrium between polymorphisms may vary from breed to breed or population to population.

scholarly journals A targeted genotyping approach to enhance the identification of variants for lactation persistency in dairy cows

2019 ◽  
Vol 97 (10) ◽  
pp. 4066-4075
Author(s):  
Duy Ngoc Do ◽  
Nathalie Bissonnette ◽  
Pierre Lacasse ◽  
Filippo Miglior ◽  
Xin Zhao ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Mixed Model ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Genetic Selection ◽  
Phenotypic Variance ◽  
Potential Candidate ◽  
Nucleotide Polymorphisms ◽  
Functional Variants ◽  
Selection For

Abstract Lactation persistency (LP), defined as the ability of a cow to maintain milk production at a high level after milk peak, is an important phenotype for the dairy industry. In this study, we used a targeted genotyping approach to scan for potentially functional single nucleotide polymorphisms (SNPs) within 57 potential candidate genes derived from our previous genome wide association study on LP and from the literature. A total of 175,490 SNPs were annotated within 10-kb flanking regions of the selected candidate genes. After applying several filtering steps, a total of 105 SNPs were retained for genotyping using target genotyping arrays. SNP association analyses were performed in 1,231 Holstein cows with 69 polymorphic SNPs using the univariate liner mixed model with polygenic effects using DMU package. Six SNPs including rs43770847, rs208794152, and rs208332214 in ADRM1; rs209443540 in C5orf34; rs378943586 in DDX11; and rs385640152 in GHR were suggestively significantly associated with LP based on additive effects and associations with 4 of them (rs43770847, rs208794152, rs208332214, and rs209443540) were based on dominance effects at P < 0.05. However, none of the associations remained significant at false discovery rate adjusted P (FDR) < 0.05. The additive variances explained by each suggestively significantly associated SNP ranged from 0.15% (rs43770847 in ADRM1) to 5.69% (rs209443540 in C5orf34), suggesting that these SNPs might be used in genetic selection for enhanced LP. The percentage of phenotypic variance explained by dominance effect ranged from 0.24% to 1.35% which suggests that genetic selection for enhanced LP might be more efficient by inclusion of dominance effects. Overall, this study identified several potentially functional variants that might be useful for selection programs for higher LP. Finally, a combination of identification of potentially functional variants followed by targeted genotyping and association analysis is a cost-effective approach for increasing the power of genetic association studies.

scholarly journals Three quantitative trait loci explain more than 60% of phenotypic variation for chill coma recovery time in Drosophila ananassae

2019 ◽  
Author(s):  
Annabella Königer ◽  
Saad Arif ◽  
Sonja Grath
Keyword(s):  
Candidate Genes ◽  
Cold Tolerance ◽  
Quantitative Trait ◽  
Recovery Time ◽  
Differentially Expressed ◽  
Drosophila Ananassae ◽  
Phenotypic Variance ◽  
Climatic Fluctuations ◽  
Standard Interval ◽  
Chill Coma

AbstractEctothermic species such as insects are particularly vulnerable to climatic fluctuations. Nevertheless, many insects that evolved and diversified in the tropics have successfully colonized temperate regions all over the globe. To shed light on the genetic basis of cold tolerance in such species, we conducted a quantitative trait locus (QTL) mapping experiment for chill coma recovery time (CCRT) in Drosophila ananassae, a cosmopolitan species that has expanded its range from tropical to temperate regions.We created a mapping population of recombinant inbred advanced intercross lines (RIAILs) from two founder strains with diverging CCRT phenotypes. The RIAILs were phenotyped for their CCRT and, together with the founder strains, genotyped for polymorphic markers with double-digest restriction site-associated DNA (ddRAD) sequencing. Using a hierarchical mapping approach that combined standard interval mapping and a multiple-QTL model, we mapped three QTL which altogether explained 64% of the phenotypic variance. For two of the identified QTL, we found evidence of epistasis. To narrow down the list of cold tolerance candidate genes, we cross-referenced the QTL intervals with genes that we previously identified as differentially expressed in response to cold in D. ananassae, and with thermotolerance candidate genes of D. melanogaster. Among the 58 differentially expressed genes that were contained within the QTL, GF15058 showed a significant interaction of the CCRT phenotype and gene expression. Further, we identified the orthologs of four D. melanogaster thermotolerance candidate genes, MtnA, klarsicht, CG5246 (D.ana/GF17132) and CG10383 (D.ana/GF14829) as candidates for cold tolerance in D. ananassae.

scholarly journals Identification of genomic regions and candidate genes of functional importance for gastrointestinal parasite resistance traits in Djallonké sheep of Burkina Faso

2019 ◽  
Vol 62 (1) ◽  
pp. 313-323
Author(s):  
Isabel Álvarez ◽  
Iván Fernández ◽  
Albert Soudré ◽  
Amadou Traoré ◽  
Lucía Pérez-Pardal ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Candidate Genes ◽  
Genetic Basis ◽  
Ovis Aries ◽  
Enrichment Score ◽  
Phenotypic Variance ◽  
Potential Candidate ◽  
Parasite Resistance ◽  
Functional Importance ◽  
Resistance Traits

Abstract. A total of 184 Djallonké lambs from Burkina Faso with phenotypes for packed-cell volume (PCV), log-transformed fecal egg count (lnFEC), and FAffa MAlan CHArt (FAMACHA©) eye scores were typed with the OvineSNP50 BeadChip of Illumina to contribute to the knowledge of the genetic basis of gastrointestinal (GIN) parasite resistance in sheep. Association analysis identified a total of 22 single-nucleotide polymorphisms (SNPs) related with PCV (6 SNPs), lnFEC (7), and FAMACHA scores (9) distributed among 14 Ovis aries chromosomes (OAR). The identified SNPs accounted for 18.76 % of the phenotypic variance for PCV, 21.24 % for lnFEC, and 34.38 % for FAMACHA scores. Analyses pointed out the importance of OAR2 for PCV, OAR3 for FAMACHA scores, and OAR6 for lnFEC. The 125 kb regions surrounding the identified SNPs overlapped with seven previously reported quantitative trait loci (QTLs) for the traits analyzed in the current work. The only chromosome harboring markers associated with the three traits studied was OAR2. In agreement with the literature, two different chromosomal areas on OAR2 can play a major role in the traits studied. Gene-annotation enrichment analysis allowed us to identify a total of 34 potential candidate genes for PCV (6 genes), lnFEC (4), and FAMACHA scores (24). Annotation analysis allowed us to identify one functional term cluster with a significant enrichment score (1.302). The cluster included five genes (TRIB3, CDK4, CSNK2A1, MARK1, and SPATA5) involved in immunity-related and cell-proliferation processes. Furthermore, this research suggests that the MBL2 gene can underlie a previously reported QTL for immunoglobulin A levels on OAR22 and confirms the importance of genes involved in growth and size (such as the ADAMTS17 gene on OAR18) for GIN resistance traits. Since association studies for the ascertainment of the genetic basis of GIN resistance may be affected by genotype–environment interactions, obtaining information from local sheep populations managed in harsh environments contributes to the identification of novel genomic areas of functional importance for GIN resistance for that trait.

scholarly journals PSI-40 Two mitochondrial lineages revealed in North American yak

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 477-477
Author(s):  
Leah K Treffer ◽  
Edward S Rice ◽  
Anna M Fuller ◽  
Samuel Cutler ◽  
Jessica L Petersen
Keyword(s):  
Sequence Data ◽  
Haplotype Network ◽  
Ovis Aries ◽  
Similar Species ◽  
Nucleotide Polymorphisms ◽  
Mt Dna ◽  
Protein Coding ◽  
Sister Clade ◽  
Mtdna Sequence ◽  
The Impact

Abstract Domestic yak (Bos grunniens) are bovids native to the Asian Qinghai-Tibetan Plateau. Studies of Asian yak have revealed that introgression with domestic cattle has contributed to the evolution of the species. When imported to North America (NA), some hybridization with B. taurus did occur. The objective of this study was to use mitochondrial (mt) DNA sequence data to better understand the mtDNA origin of NA yak and their relationship to Asian yak and related species. The complete mtDNA sequence of 14 individuals (12 NA yak, 1 Tibetan yak, 1 Tibetan B. indicus) was generated and compared with sequences of similar species from GeneBank (B. indicus, B. grunniens (Chinese), B. taurus, B. gaurus, B. primigenius, B. frontalis, Bison bison, and Ovis aries). Individuals were aligned to the B. grunniens reference genome (ARS_UNL_BGru_maternal_1.0), which was also included in the analyses. The mtDNA genes were annotated using the ARS-UCD1.2 cattle sequence as a reference. Ten unique NA yak haplotypes were identified, which a haplotype network separated into two clusters. Variation among the NA haplotypes included 93 nonsynonymous single nucleotide polymorphisms. A maximum likelihood tree including all taxa was made using IQtree after the data were partitioned into twenty-two subgroups using PartitionFinder2. Notably, six NA yak haplotypes formed a clade with B. indicus; the other four haplotypes grouped with B. grunniens and fell as a sister clade to bison, gaur and gayal. These data demonstrate two mitochondrial origins of NA yak with genetic variation in protein coding genes. Although these data suggest yak introgression with B. indicus, it appears to date prior to importation into NA. In addition to contributing to our understanding of the species history, these results suggest the two major mtDNA haplotypes in NA yak may functionally differ. Characterization of the impact of these differences on cellular function is currently underway.

scholarly journals High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gehendra Bhattarai ◽  
Wei Yang ◽  
Ainong Shi ◽  
Chunda Feng ◽  
Braham Dhillon ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Downy Mildew ◽  
Association Analysis ◽  
Spinacia Oleracea ◽  
Genotyping By Sequencing ◽  
Significant Snps ◽  
Snp Markers ◽  
Resistance Locus ◽  
Downy Mildew Resistance ◽  
Mildew Resistance

Abstract Background Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new P. effusa races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with P. effusa race 16 in an environment-controlled facility; disease response was recorded and genotyped using genotyping by sequencing (GBS). The main objective of this study was to identify resistance-associated single nucleotide polymorphism (SNP) markers from the cultivar Whale against the P. effusa race 16. Results Association analysis conducted using GBS markers identified six significant SNPs (S3_658,306, S3_692697, S3_1050601, S3_1227787, S3_1227802, S3_1231197). The downy mildew resistance locus from cultivar Whale was mapped to a 0.57 Mb region on chromosome 3, including four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo12821) within 2.69–11.28 Kb of the peak SNP. Conclusions Genomewide association analysis approach was used to map the P. effusa race 16 resistance loci and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select resistant lines.

scholarly journals Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 457-467 ◽  
Author(s):  
Z W Luo ◽  
S H Tao ◽  
Z-B Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Allele Frequency ◽  
Random Mating ◽  
Natural Populations ◽  
Polymorphic Marker ◽  
Marker Locus ◽  
Model Parameters ◽  
Phenotypic Variance ◽  
Wide Range ◽  
Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

scholarly journals Genome-Wide Association Study Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 718
Author(s):  
Bingxin Meng ◽  
Tao Wang ◽  
Yi Luo ◽  
Deze Xu ◽  
Lanzhi Li ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Association Analysis ◽  
Genome Wide Association Study ◽  
Flag Leaf ◽  
Genome Wide Association ◽  
Lodging Resistance ◽  
Leaf Type ◽  
Stem Strength ◽  
Genome Wide

Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through “gene-based association analysis, haplotype analysis, and functional annotation”, the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR.

scholarly journals PSVII-37 Late-Breaking Abstract: CNV analysis of indigenous sheep reveals genes linked to disease resistance and adaptation

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 339-339
Author(s):  
Annelin Molotsi
Keyword(s):  
Candidate Genes ◽  
Copy Number ◽  
Structural Changes ◽  
Gene Annotation ◽  
Smallholder Farmers ◽  
Copy Number Variations ◽  
Ovis Aries ◽  
Matrix Composition ◽  
Low Input ◽  
Gene Group

Abstract Smallholder farmers often make use of low-input systems, suggesting that robust and adaptable individuals are needed in these systems that have good production and reproduction in these low-input systems. One of the reasons certain individuals may be more adaptable or have higher production outputs could be due to the presence of advantageous mutations or genetic structural variants. Genetic variants, namely copy number variations (CNVs), are structural changes to the DNA and are larger than a single nucleotide. In this study, 47 sheep were investigated for the presence of CNVs. A total of 206 CNVs passed quality control. These CNVs were compared to the NCBI RefSeq Ovis aries: Oar_v4.0 to identify candidate genes located within or overlapping the copy number variations identified. Gene annotation analysis was carried out on the identified candidate genes. Gene annotation assigned the candidate genes to two gene groups. The first gene group were protein coding genes responsible for interferons that are the natural defences individuals have against viral and bacterial infection. The second gene group was found to be responsible for a variety of biological functions including transport, metabolic precursors, neurogenesis, signalling as well as bone and cartilage matrix composition along with a number of other important functions. This indicates that CNVs could have various effects on important biological process which could possibly influence an individual’s survival or even production and reproduction. This highlights the need for CNV studies to determine the influence of these CNVs and how they can be utilised in breeding programmes to improve adaptation and production outputs.

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