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Transcriptome-referenced association study of clove shape traits in garlic.

ABSTRACT: Genome-wide association studies are a powerful approach for identifying genes related to complex traits in organisms, but are limited by the requirement for a reference genome sequence of the species under study. To circumvent this problem, we propose a transcriptome-referenced association study (TRAS) that utilizes a transcriptome generated by single-molecule long-read sequencing as a reference sequence to score population variation at both transcript sequence and expression levels. Candidate transcripts are identified when both scores are associated with a trait and their potential interactions are ascertained by expression quantitative trait loci analysis. Applying this method to characterize garlic clove shape traits in 102 landraces, we identified 22 candidate transcripts, most of which showed extensive interactions. Eight transcripts were long non-coding RNAs (lncRNAs), and the others were proteins involved mainly in carbohydrate metabolism, protein degradation, etc. TRAS, as an efficient tool for association study independent of a reference genome, extends the applicability of association studies to a broad range of species.

SUBMITTER: Chen X

PROVIDER: S-EPMC6289775 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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Transcriptome-referenced association study of clove shape traits in garlic.

Chen Xiaojun X Liu Xia X Zhu Siyuan S Tang Shouwei S Mei Shiyong S Chen Jing J Li Shan S Liu Mengdi M Gu Yuejiao Y Dai Qiuzhong Q Liu Touming T

DNA research : an international journal for rapid publication of reports on genes and genomes 20181201 6

Genome-wide association studies are a powerful approach for identifying genes related to complex traits in organisms, but are limited by the requirement for a reference genome sequence of the species under study. To circumvent this problem, we propose a transcriptome-referenced association study (TRAS) that utilizes a transcriptome generated by single-molecule long-read sequencing as a reference sequence to score population variation at both transcript sequence and expression levels. Candidate t ...[more]

PMID: 30084885

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Project description:BackgroundThe increase in demand and consumption of single clove garlic or 'Solo garlic' (Allium sativum) has resulted in an increase in research on its therapeutic properties. The present study aims to evaluate the antioxidant activities, oxidant-scavenging efficiency and preventive effects of SCG (single clove garlic) and MCG (multi clove garlic) on CCl4-induced acute hepatotoxicity in male rabbits.MethodsFor this purpose, rabbits were orally administered with 3 ml of CCl4 /kg of body weight, followed by 0.8 g of MCG or SCG/kg twice a week for three successive weeks. Oxidative hepatotoxicity was then assessed.ResultsSCG extracts exhibited higher antioxidant capacity than the MCG extract. Scavenging ability of SCG showed significant (p < 0.05) elevation against 2,2-diphenyl-1-picrylhydrazyl (DPPH) and superoxide radicals in comparison to MCG. In addition, total phenolic content of SCG was significantly elevated (p < 0.001), thereby suggesting that the composition of garlic storage constituents varies with the number of cloves present. CCl4-induced hepatotoxicity demonstrated histological changes including severe damage in the structure of liver tissues which correlated well to oxidative stress levels. Simultaneously, administration of SCG resulted in a significant reduction of serum alkaline phosphatase (ALP), aspartate aminotransferase (AST), alanine aminotransferase (ALT), and total bilirubin (TB) levels in addition to improvement in some histological parameters. Low levels of lipid peroxidation (malondialdehyde, MDA) (p < 0.001), along with a huge reduction in peroxidase (POx) (p < 0.001) revealed protection against oxidative toxicity in the liver homogenate. Higher levels of catalase (CAT) (p < 0.001) and superoxide dismutase (SOD) (p < 0.05) when compared to the MCG test (TM) group indicates that removal of H2O2 is based on CAT activity in SCG test (TS) group rather than the POx activity demonstrated in the former group.ConclusionThe present study indicates that SCG possesses more protective ability than MCG against CCl4-induced liver injury and might be an effective alternative medicine against acute oxidative liver toxicity.

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Transcriptome-referenced association study of clove shape traits in garlic.

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Transcriptome-referenced association study of clove shape traits in garlic.

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