Genomic predictions can accelerate selection for resistance against Piscirickettsia salmonis in Atlantic salmon (Salmo salar)

BMC Genomics, Journal Year: 2017, Volume and Issue: 18(1)

Published: Jan. 31, 2017

Salmon Rickettsial Syndrome (SRS) caused by Piscirickettsia salmonis is a major disease affecting the Chilean salmon industry. Genomic selection (GS) method wherein genome-wide markers and phenotype information of full-sibs are used to predict genomic EBV (GEBV) candidates expected have increased accuracy response over traditional pedigree based Best Linear Unbiased Prediction (PBLUP). Widely GS methods such as BLUP (GBLUP), SNPBLUP, Bayes C Bayesian Lasso may perform differently with respect GEBV prediction. Our aim was compare accuracy, in terms reliability genome-enabled prediction, from different PBLUP for resistance SRS an Atlantic breeding program. Number days death (DAYS), binary survival status (STATUS) phenotypes, 50 K SNP array genotypes were obtained 2601 smolts challenged P. salmonis. The at densities without compared using five-fold cross validation scheme. Heritability estimated significantly higher than PBLUP. Pearson's correlation between predicted models ranged 0.79 0.91 0.79–0.95 DAYS STATUS, respectively. relative increase STATUS 8 25% 27–30%, All outperformed all marker densities. showed superior even lowest density 3 500 SNP, 20 close maximal both traits little improvement These results indicate that predictions can accelerate genetic progress implementation this approach will contribute control Chile. We recommend GBLUP routine evaluation because computationally faster very similar other methods. use lower or combination low imputation strategy help reduce genotyping costs compromising gain reliability.

Language: Английский

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Towards a comprehensive picture of C-to-U RNA editing sites in angiosperm mitochondria

Plant Molecular Biology, Journal Year: 2018, Volume and Issue: 97(3), P. 215 - 231

Published: May 14, 2018

Language: Английский

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Genome-wide characterization and expression analyses of superoxide dismutase (SOD) genes in Gossypium hirsutum

BMC Genomics, Journal Year: 2017, Volume and Issue: 18(1)

Published: May 12, 2017

Superoxide dismutases (SODs) are a key antioxidant enzyme family, which have been implicated in protecting plants against the toxic effects of reactive oxygen species. Despite current studies shown that gene family involved plant growth and developmental processes biotic abiotic stress responses, little is known about its functional role upland cotton. In present study, we comprehensively analyzed characteristics SOD cotton (Gossypium hirsutum). Based on their conserved motifs, 18 GhSOD genes were identified phylogenetically classified into five subgroups corroborated classifications based gene-structure patterns subcellular localizations. The sequences distributed at different densities across 12 26 chromosomes. domains, evolution cis-acting elements promoter regions miRNA-mediated posttranscriptional regulation predicted analyzed. addition, expression pattern tested tissues/organs stages, stresses abscisic acid, indicated possessed temporal spatial specificity may play important roles species scavenging caused by various This study describes first genome-wide analysis results will help establish foundation for further cloning verification during leading to crop improvement.

Language: Английский

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Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters

BMC Genomics, Journal Year: 2017, Volume and Issue: 18(1)

Published: Aug. 29, 2017

The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions genome sequence were highly fragmented, causing errors in prediction protein-coding genes preventing analysis repetitive sequences architecture. Here, we re-sequenced using single-molecule real-time (SMRT) sequencing technology and, combination with optical map data, this provided a gapless assembly all twelve chromosomes except for ribosomal DNA repeat cluster on chromosome 7. more accurate gene annotation made possible by new revealed large repertoire secondary metabolism (SM) key (89) putative biosynthetic pathways (77 SM clusters). two mini-chromosomes differed from ten core being repeat- AT-rich gene-poor but significantly enriched encoding secreted effector proteins. Transposable elements (TEs) found to occupy 7% length. Certain TE families showed statistically significant association transcriptionally active at particular stages fungal development. All 24 subtelomeres contain one three highly-conserved which, providing sites homologous recombination, probably instrumental four segmental duplications. C. provides access repeat-rich regions that previously poorly assembled, notably subtelomeres, allowed complete repertoire. It also insights into potential role TEs evolution host adaptation asexual pathogen.

Language: Английский

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The utility of transcriptomics in fish conservation

Journal of Experimental Biology, Journal Year: 2018, Volume and Issue: 221(2)

Published: Jan. 15, 2018

ABSTRACT There is growing recognition of the need to understand mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) environmental change support conservation management sensitive and economically important species. Here, we discuss how functional genomics can be used in biology provide a cellular-level understanding responses conditions. In particular, integration transcriptomics with physiological ecological research increasingly playing an role identifying thresholds predictive compensatory detrimental outcomes, transforming way study issues biology. Notably, technological advances RNA sequencing, transcriptome-wide approaches now applied species where no prior genomic sequence information available develop species-specific tools investigate sublethal impacts that contribute population declines over generations undermine prospects for long-term success. examine use as means determining stressors key examples concern fishes highlight added value data identification response pathways. Finally, gaps between core science policy frameworks identified through transcriptomic evaluations evidence more readily by resource managers.

Language: Английский

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