Dataset Information

Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum).

ABSTRACT: BACKGROUND:Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield traits are poorly understood in garlic. RESULTS:In the present study, we carried out an association mapping for three yield traits of garlic bulbs: bulb weight (BW), diameter (BD), and the number of garlic cloves (CN), using the recently proposed transcriptome-referenced association study. In total 25, 2, and 30 single nucleotide polymorphisms (SNPs), were identified in the transcripts to be associated with BW, BD, and CN traits, respectively. Of the transcripts with associated SNPs, the expression of 17 of them showed a significant correlation with the corresponding traits in the population, suggesting their relation to bulbs yield traits. Six transcripts were long non-coding RNAs (lncRNAs), and the others encode proteins involved mainly in carbohydrate metabolism, transcription regulation, cytokinin activity, protein degradation, etc. In addition, expression quantitative trait locus (eQTL) and expression correlation analysis have revealed that seven CN-related transcripts displayed interrelation, constituting two potential pathways. CONCLUSION:This study provides novel insights into the genetic basis of the yield traits in garlic bulbs, and the identification of trait-associated SNPs/transcripts provides a basis for improving the bulb yield in garlic breeding.

SUBMITTER: Zhu S

PROVIDER: S-EPMC6698038 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum).

Zhu Siyuan S Chen Xiaojun X Liu Xia X Zhao Jian J Liu Touming T

BMC genomics 20190817 1

<h4>Background</h4>Garlic bulbs are abnormal expanding axillary buds that are rarely found among vascular plants. Bulb-yield is one of the valuable agronomic traits of garlic. However, due to the large genome size and a strictly asexual life cycle in the cultivars, the genetic basis of the yield traits are poorly understood in garlic.<h4>Results</h4>In the present study, we carried out an association mapping for three yield traits of garlic bulbs: bulb weight (BW), diameter (BD), and the number ...[more]

PMID: 31419936

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Project description:BackgroundGarlic is cultivated and consumed worldwide as a popular condiment and green vegetable with medicinal and neutraceutical properties. Garlic cultivars do not produce seeds, and therefore, this plant has not been the subject of either classical breeding or genetic studies. However, recent achievements in fertility restoration in a number of genotypes have led to flowering and seed production, thus enabling genetic studies and breeding in garlic.ResultsA transcriptome catalogue of fertile garlic was produced from multiplexed gene libraries, using RNA collected from various plant organs, including inflorescences and flowers. Over 32 million 250-bp paired-end reads were assembled into an extensive transcriptome of 240,000 contigs. An abundant transcriptome assembled separately from 102,000 highly expressed contigs was annotated and analyzed for gene ontology and metabolic pathways. Organ-specific analysis showed significant variation of gene expression between plant organs, with the highest number of specific reads in inflorescences and flowers. Analysis of the enriched biological processes and molecular functions revealed characteristic patterns for stress response, flower development and photosynthetic activity. Orthologues of key flowering genes were differentially expressed, not only in reproductive tissues, but also in leaves and bulbs, suggesting their role in flower-signal transduction and the bulbing process. More than 100 variants and isoforms of enzymes involved in organosulfur metabolism were differentially expressed and had organ-specific patterns. In addition to plant genes, viral RNA of at least four garlic viruses was detected, mostly in the roots and cloves, whereas only 1-4% of the reads were found in the foliage leaves.ConclusionsThe de novo transcriptome of fertile garlic represents a new resource for research and breeding of this important crop, as well as for the development of effective molecular markers for useful traits, including fertility and seed production, resistance to pests and neutraceutical characteristics.

Dataset Information

Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum).

Publications

Transcriptome-wide association study and eQTL analysis to assess the genetic basis of bulb-yield traits in garlic (Allium sativum).

Similar Datasets

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