scholarly journals Natural variation in insect egg-induced cell death uncovers a role for L-type LECTIN RECEPTOR KINASE-I.1 in Arabidopsis

2020 ◽  
Author(s):  
Raphaël Groux ◽  
Caroline Gouhier-Darimont ◽  
Envel Kerdaffrec ◽  
Philippe Reymond
Keyword(s):  
Signaling Pathway ◽  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Pieris Brassicae ◽  
Receptor Kinase ◽  
Large White ◽  
Lectin Receptor ◽  
Genome Wide ◽  
A Genome ◽  
Close Homolog

AbstractIn Arabidopsis thaliana, a hypersensitive-like response (HR-like) is triggered underneath the eggs of the large white butterfly Pieris brassicae, and this response is dependent on salicylic acid (SA) accumulation and signaling. Previous reports indicate that the clade I L-type lectin receptor kinase LecRK-I.8 is involved in early steps of egg recognition. A genome-wide association study (GWAS) was used to better characterize the genetic structure of HR-like and discover loci that contribute to this response. We report here the identification of LecRK-I.1, a close homolog of LecRK-I.8, and show that two main haplotypes that explain part of the variation in HR-like segregate amongst natural Arabidopsis accessions. In addition, signatures of balancing selection at this locus suggest that it may be ecologically important. Disruption of LecRK-I.1 resulted in decreased HR-like and SA signaling, indicating that this protein is important for the observed responses. Furthermore, we provide evidence that LecRK-I.1 functions in the same signaling pathway as LecRK-I.8. Altogether, our results show that the response to eggs of P. brassicae is controlled by LecRKs that operate at various steps of the signaling pathway.

scholarly journals Population genetics of the coral Acropora millepora: Towards a genomic predictor of bleaching

2019 ◽  
Author(s):  
Zachary L. Fuller ◽  
Veronique J.L. Mocellin ◽  
Luke Morris ◽  
Neal Cantin ◽  
Jihanne Shepherd ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Genome Wide Association ◽  
Conservation Strategies ◽  
Genome Sequences ◽  
Acropora Millepora ◽  
Genome Wide ◽  
A Genome ◽  
In The Wild

AbstractAlthough reef-building corals are rapidly declining worldwide, responses to bleaching vary both within and among species. Because these inter-individual differences are partly heritable, they should in principle be predictable from genomic data. Towards that goal, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We then obtained whole genome sequences for 237 phenotyped samples collected at 12 reefs distributed along the Great Barrier Reef, among which we inferred very little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We further used 213 of the samples to conduct a genome-wide association study of visual bleaching score, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for the use of genomics-based approaches in conservation strategies.

A genome‐wide association study reveals additive and dominance effects on growth and fatness traits in large white pigs

2021 ◽  
Vol 52 (5) ◽  
pp. 749-753
Author(s):  
W. Yang ◽  
J. Wu ◽  
J. Yu ◽  
X. Zheng ◽  
H. Kang ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Large White ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-wide sexually antagonistic variants reveal longstanding constraints on sexual dimorphism in the fruitfly

2017 ◽  
Author(s):  
Filip Ruzicka ◽  
Mark S. Hill ◽  
Tanya M. Pennell ◽  
Ilona Flis ◽  
Fiona C. Ingleby ◽  
...  
Keyword(s):  
Sexual Dimorphism ◽  
Evolutionary Dynamics ◽  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Sexual Antagonism ◽  
Protein Coding ◽  
Genome Wide ◽  
Genomic Location ◽  
Classic Theory ◽  
A Genome

The evolution of sexual dimorphism is constrained by a shared genome, leading to ‘sexual antagonism’ where different alleles at given loci are favoured by selection in males and females. Despite its wide taxonomic incidence, we know little about the identity, genomic location and evolutionary dynamics of antagonistic genetic variants. To address these deficits, we use sex-specific fitness data from 202 fully sequenced hemiclonal D. melanogaster fly lines to perform a genome-wide association study of sexual antagonism. We identify ~230 chromosomal clusters of candidate antagonistic SNPs. In contradiction to classic theory, we find no clear evidence that the X chromosome is a hotspot for sexually antagonistic variation. Characterising antagonistic SNPs functionally, we find a large excess of missense variants but little enrichment in terms of gene function. We also assess the evolutionary persistence of antagonistic variants by examining extant polymorphism in wild D. melanogaster populations. Remarkably, antagonistic variants are associated with multiple signatures of balancing selection across the D. melanogaster distribution range, indicating widespread and evolutionarily persistent (>10,000 years) genomic constraints. Based on our results, we propose that antagonistic variation accumulates due to constraints on the resolution of sexual conflict over protein coding sequences, thus contributing to the long-term maintenance of heritable fitness variation.

scholarly journals A Genome-Wide Association Study in Large White and Landrace Pig Populations for Number Piglets Born Alive

PLoS ONE ◽  
2015 ◽  
Vol 10 (3) ◽  
pp. e0117468 ◽  
Author(s):  
Sarah Bergfelder-Drüing ◽  
Christine Grosse-Brinkhaus ◽  
Bianca Lind ◽  
Malena Erbe ◽  
Karl Schellander ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Large White ◽  
Genome Wide ◽  
A Genome ◽  
Landrace Pig

Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching

Science ◽  
2020 ◽  
Vol 369 (6501) ◽  
pp. eaba4674 ◽  
Author(s):  
Zachary L. Fuller ◽  
Veronique J. L. Mocellin ◽  
Luke A. Morris ◽  
Neal Cantin ◽  
Jihanne Shepherd ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Balancing Selection ◽  
Conservation Strategies ◽  
Genome Sequences ◽  
Acropora Millepora ◽  
Genome Wide ◽  
A Genome ◽  
Bleaching Response ◽  
In The Wild

Although reef-building corals are declining worldwide, responses to bleaching vary within and across species and are partly heritable. Toward predicting bleaching response from genomic data, we generated a chromosome-scale genome assembly for the coral Acropora millepora. We obtained whole-genome sequences for 237 phenotyped samples collected at 12 reefs along the Great Barrier Reef, among which we inferred little population structure. Scanning the genome for evidence of local adaptation, we detected signatures of long-term balancing selection in the heat-shock co-chaperone sacsin. We conducted a genome-wide association study of visual bleaching score for 213 samples, incorporating the polygenic score derived from it into a predictive model for bleaching in the wild. These results set the stage for genomics-based approaches in conservation strategies.

scholarly journals Genome-Wide Association Study Identifies Eight Novel Loci for Susceptibility of Scrub Typhus and Highlights Immune-Related Signaling Pathways in Its Pathogenesis

Cells ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 570
Author(s):  
Yong-Chan Kim ◽  
Soriul Kim ◽  
Hee-Kwon Kim ◽  
Yi Lee ◽  
Chol Shin ◽  
...  
Keyword(s):  
Association Study ◽  
Signaling Pathways ◽  
Signaling Pathway ◽  
Genome Wide Association Study ◽  
Scrub Typhus ◽  
Systemic Vasculitis ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
A Genome

Scrub typhus is a fatal zoonotic disease caused by Orientia tsutsugamushi. This disease is accompanied by systemic vasculitis, lymphadenopathy, headache, myalgia, and eschar. In recent studies, a novel strain that is resistant to current medical treatment was identified in Thailand. Thus, the development of new specific drugs for scrub typhus is needed. However, the exact molecular mechanism governing the progression of scrub typhus has not been fully elucidated. To understand disease-related genetic factors and mechanisms associated with the progression of scrub typhus, we performed a genome-wide association study (GWAS) in scrub typhus-infected patients and found a scrub typhus-related signaling pathway by molecular interaction search tool (MIST) and PANTHER. We identified eight potent scrub typhus-related single nucleotide polymorphisms (SNPs) located on the PRMT6, PLGLB2, DTWD2, BATF, JDP2, ONECUT1, WDR72, KLK, MAP3K7, and TGFBR2 genes using a GWAS. We also identified 224 genes by analyzing protein-protein interactions among candidate genes of scrub typhus and identified 15 signaling pathways associated with over 10 genes by classifying these genes according to signaling pathways. The signaling pathway with the largest number of associated genes was the gonadotropin-releasing hormone receptor pathway, followed by the TGF-beta signaling pathway and the apoptosis signaling pathway. To the best of our knowledge, this report describes the first GWAS in scrub typhus.

scholarly journals Genome-Wide Association Analysis Identified BMPR1A as a Novel Candidate Gene Affecting the Number of Thoracic Vertebrae in a Large White × Minzhu Intercross Pig Population

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2186
Author(s):  
Qian Liu ◽  
Jingwei Yue ◽  
Naiqi Niu ◽  
Xin Liu ◽  
Hua Yan ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Genome Wide Association Study ◽  
Splice Variants ◽  
Genome Wide Association ◽  
Thoracic Vertebrae ◽  
Phenotypic Variance ◽  
Nucleotide Polymorphisms ◽  
Large White ◽  
Genome Wide ◽  
A Genome

The number of vertebrae (NV), especially the number of thoracic vertebrae (NTV), varies among pig breeds. The NTV is controlled by vertebral segmentation and the number of somites during embryonic development. Although there is a high correlation between the NTV and NV, studies on a fixed NV have mainly considered the absolute numbers of thoracic vertebrae instead of vertebral segmentation. Therefore, this study aimed to discover variants associated with the NTV by considering the effect of the NV in pigs. The NTV and NV of 542 F2 individuals from a Large White × Minzhu pig crossbreed were recorded. All animals were genotyped for VRTN g.19034 A > C, LTBP2 c.4481A > C, and 37 missense or splice variants previously reported in a 951-kb interval on SSC7 and 147 single nucleotide polymorphisms (SNPs) on SSC14. To identify NTV-associated SNPs, we firstly performed a genome-wide association study (GWAS) using the Q + K (population structure + kinship matrix) model in TASSEL. With the NV as a covariate, the obtained data were used to identify the SNPs with the most significant genome-wide association with the NTV by performing a GWAS on a PorcineSNP60K Genotyping BeadChip. Finally, a conditional GWAS was performed by fixing this SNP. The GWAS showed that 31 SNPs on SSC7 have significant genome-wide associations with the NTV. No missense or splice variants were found to be associated with the NTV significantly. A linkage disequilibrium analysis suggested the existence of quantitative trait loci (QTL) in a 479-Kb region on SSC7, which contained a critical candidate gene FOS for the NTV in pigs. Subsequently, a conditional GWAS was performed by fixing M1GA0010658, the most significant of these SNPs. Two SNPs in BMPR1A were found to have significant genome-wide associations and a significant dominant effect. The leading SNP, S14_87859370, accounted for 3.86% of the phenotypic variance. Our study uncovered that regulation variants in FOS on SSC7 and in BMPR1A on SSC14 might play important roles in controlling the NTV, and thus these genetic factors may be harnessed for increasing the NTV in pigs.

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