AlliumMap-A comparative genomics resource for cultivated Allium vegetables

McCallum, John; Baldwin, Samantha; Shigyo, Masayoshi; Deng, Yanbo; Heusden, Sjaak van; Pither-Joyce, Meeghan; Kenel, Fernand

doi:10.1186/1471-2164-13-168

Cited by 43 publications

(23 citation statements)

References 37 publications

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“…The major genetic loci conditioning red bulb colour ( R ) and fructan content ( Frc ) were located on this map by QTL analysis on chromosomes 7 and 8 respectively, as expected [42-44]. This resource is useful across onion germplasm since the anchor markers used here have been tested in other mapping populations, allowing the linkage maps to be aligned for comparative mapping using the CMap tool [45] provided at http://alliumgenetics.org[41]. The map was then used as a reference to select a subset of genotypes for bin mapping [46,47] to facilitate rapid marker screening and targeted map development.…”

Section: Resultsmentioning

confidence: 96%

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A Toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)

et al. 2012

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BackgroundAlthough modern sequencing technologies permit the ready detection of numerous DNA sequence variants in any organisms, converting such information to PCR-based genetic markers is hampered by a lack of simple, scalable tools. Onion is an example of an under-researched crop with a complex, heterozygous genome where genome-based research has previously been hindered by limited sequence resources and genetic markers.ResultsWe report the development of generic tools for large-scale web-based PCR-based marker design in the Galaxy bioinformatics framework, and their application for development of next-generation genetics resources in a wide cross of bulb onion (Allium cepa L.). Transcriptome sequence resources were developed for the homozygous doubled-haploid bulb onion line ‘CUDH2150’ and the genetically distant Indian landrace ‘Nasik Red’, using 454™ sequencing of normalised cDNA libraries of leaf and shoot. Read mapping of ‘Nasik Red’ reads onto ‘CUDH2150’ assemblies revealed 16836 indel and SNP polymorphisms that were mined for portable PCR-based marker development. Tools for detection of restriction polymorphisms and primer set design were developed in BioPython and adapted for use in the Galaxy workflow environment, enabling large-scale and targeted assay design. Using PCR-based markers designed with these tools, a framework genetic linkage map of over 800cM spanning all chromosomes was developed in a subset of 93 F2 progeny from a very large F2 family developed from the ‘Nasik Red’ x ‘CUDH2150’ inter-cross. The utility of tools and genetic resources developed was tested by designing markers to transcription factor-like polymorphic sequences. Bin mapping these markers using a subset of 10 progeny confirmed the ability to place markers within 10 cM bins, enabling increased efficiency in marker assignment and targeted map refinement. The major genetic loci conditioning red bulb colour (R) and fructan content (Frc) were located on this map by QTL analysis.ConclusionsThe generic tools developed for the Galaxy environment enable rapid development of sets of PCR assays targeting sequence variants identified from Illumina and 454 sequence data. They enable non-specialist users to validate and exploit large volumes of next-generation sequence data using basic equipment.

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Section: Resultsmentioning

confidence: 96%

“…The overall map length was 808 cM. The map and underlying data can also be accessed at alliumgenetics.org [41]. The markers appeared to show both some overlap at particular positions, which may indicate redundancy or gene clusters but were also spread across the genome with an average spacing between markers of 7.5 cM.…”

Section: Resultsmentioning

confidence: 99%

A Toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)

et al. 2012

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“…However, the rapid advance in sequencing methodologies and bioinformatics tools means most genome sequencing projects now use shotgun gDNA sequencing or reduced representation sequencing (depending upon the size and complexity of genome) rather than sequencing BACs (Feuillet et al. ). A pilot genome sequencing project employing BAC and whole‐genome shotgun sequencing revealed that onion has one of the lowest gene densities found in plants (1 gene per 168 Kb), and that simple shotgun gDNA sequencing approaches would not be suitable due to large genome size and huge amount of repetitive sequences (Jakse et al.…”

Section: Genomic Resources In Onionmentioning

confidence: 99%

“…An online genomic database has been developed for the Allium genus called Allium Map https://allium.scinet.org.nz/ which consists of genomic data and genetic maps of economically important Allium species (McCallum et al. ). Recently, an onion transcriptome database (http://onion.riceblast.snu.ac.kr/) was created which contains a transcriptome assembly and gene annotations.…”

Section: Genomic Resources In Onionmentioning

confidence: 99%

Enhancing onion breeding using molecular tools

et al. 2015

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Bulb onion (Allium cepa L.) is an ancient crop that is thought to have originated in Central Asia and has been cultivated for over 5000 years. Classical genetic and plant breeding approaches have been used to improve onion yield, quality, and resistance against biotic and abiotic stresses. However, its biennial life cycle, cross-pollinated nature and high inbreeding depression have proved challenging for the characterization and breeding of improved traits. New technologies, notably next-generation sequencing, are providing researchers with the genomic resources and approaches to overcome these challenges. Using these genomic technologies, molecular markers are being rapidly developed and utilized for germplasm analysis and mapping in onion. These new tools and knowledge are allowing the integration of molecular and conventional breeding to speed up onion improvement programmes. In this review, we outline recent progress in onion genomics and molecular genetics and prospects for enhancing onion yield and quality in the future.

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“…Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as transfer RNA (tRNA) or small nuclear RNA (snRNA) genes, the product is a functional RNA [156][157][158][159][160][161][162]. In onion, the physiology of the bulb beginning was precisely defined by Mettananda and Fordham [163]; photoperiodic conditions mark bulb beginning, similar to the photoperiodic switch of flowering in other species [20,164].…”

Section: Gene Expression and Bulb Enlargementmentioning

confidence: 99%

Mechanism of Allium Crops Bulb Enlargement in Response to Photoperiod: A Review

Atif

Ahanger

Amin

et al. 2020

IJMS

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The photoperiod marks a varied set of behaviors in plants, including bulbing. Bulbing is controlled by inner signals, which can be stimulated or subdued by the ecological environment. It had been broadly stated that phytohormones control the plant development, and they are considered to play a significant part in the bulb formation. The past decade has witnessed significant progress in understanding and advancement about the photoperiodic initiation of bulbing in plants. A noticeable query is to what degree the mechanisms discovered in bulb crops are also shared by other species and what other qualities are also dependent on photoperiod. The FLOWERING LOCUS T (FT) protein has a role in flowering; however, the FT genes were afterward reported to play further functions in other biological developments (e.g., bulbing). This is predominantly applicable in photoperiodic regulation, where the FT genes seem to have experienced significant development at the practical level and play a novel part in the switch of bulb formation in Alliums. The neofunctionalization of FT homologs in the photoperiodic environments detects these proteins as a new class of primary signaling mechanisms that control the growth and organogenesis in these agronomic-related species. In the present review, we report the underlying mechanisms regulating the photoperiodic-mediated bulb enlargement in Allium species. Therefore, the present review aims to systematically review the published literature on the bulbing mechanism of Allium crops in response to photoperiod. We also provide evidence showing that the bulbing transitions are controlled by phytohormones signaling and FT-like paralogues that respond to independent environmental cues (photoperiod), and we also show that an autorelay mechanism involving FT modulates the expression of the bulbing-control gene. Although a large number of studies have been conducted, several limitations and research gaps have been identified that need to be addressed in future studies.

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AlliumMap-A comparative genomics resource for cultivated Allium vegetables

Cited by 43 publications

References 37 publications

A Toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)

A Toolkit for bulk PCR-based marker design from next-generation sequence data: application for development of a framework linkage map in bulb onion (Allium cepa L.)

Enhancing onion breeding using molecular tools

Mechanism of Allium Crops Bulb Enlargement in Response to Photoperiod: A Review

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