Development of a Genetic Map for Onion (Allium cepa L.) Using Reference-Free Genotyping-by-Sequencing and SNP Assays

Jo, Jinkwan; Purushotham, Preethi M.; Han, Koeun; Lee, Heung-Ryul; Nah, Gyoungju; Kang, Byoung−Cheorl

doi:10.3389/fpls.2017.01606

Cited by 43 publications

(39 citation statements)

References 39 publications

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“…NGS-based genotyping produces instead thousands of single nucleotide polymorphism which allow detecting loci involved in the resistance to pathogens narrowing down the regions underlying genes of interest. Reduced representation sequencing method for genotyping such GBS (genotyping by sequencing) or RADseq (restriction site-associated DNA sequencing) are paramount, allowing high throughput genome scans at relatively low cost [93,168,283]. These NGS technologies, therefore, can be used to generate diagnostic markers able to detect the allelic variation within resistance genes.…”

Section: Impact Of Genomics and Future Challenges In Plant Disease Rementioning

confidence: 99%

Overview of Biotic Stresses in Pepper (Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics

Parisi¹,

Alioto

Tripodi³

2020

IJMS

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Pepper (Capsicum spp.) is one of the major vegetable crops grown worldwide largely appreciated for its economic importance and nutritional value. This crop belongs to the large Solanaceae family, which, among more than 90 genera and 2500 species of flowering plants, includes commercially important vegetables such as tomato and eggplant. The genus includes over 30 species, five of which (C. annuum, C. frutescens, C. chinense, C. baccatum, and C. pubescens) are domesticated and mainly grown for consumption as food and for non-food purposes (e.g., cosmetics). The main challenges for vegetable crop improvement are linked to the sustainable development of agriculture, food security, the growing consumers’ demand for food. Furthermore, demographic trends and changes to climate require more efficient use of plant genetic resources in breeding programs. Increases in pepper consumption have been observed in the past 20 years, and for maintaining this trend, the development of new resistant and high yielding varieties is demanded. The range of pathogens afflicting peppers is very broad and includes fungi, viruses, bacteria, and insects. In this context, the large number of accessions of domesticated and wild species stored in the world seed banks represents a valuable resource for breeding in order to transfer traits related to resistance mechanisms to various biotic stresses. In the present review, we report comprehensive information on sources of resistance to a broad range of pathogens in pepper, revisiting the classical genetic studies and showing the contribution of genomics for the understanding of the molecular basis of resistance.

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Section: Impact Of Genomics and Future Challenges In Plant Disease Rementioning

confidence: 99%

Overview of Biotic Stresses in Pepper (Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics

Parisi¹,

Alioto

Tripodi³

2020

IJMS

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“…gDNA extraction and genotyping by sequencing DNA was extracted from the 'TH' RIL and GWAS populations using the CTAB method and diluted to 50 ng/lL with distilled water. GBS libraries of 'TH RIL' were generated by digestion with PstI/MseI using a SBG 100-Kit v2.0 (Keygene N.V., Wageningen, the Netherlands), while those of the GWAS population were constructed manually following digestion with PstI/MseI and EcoRI/MseI, according to a previously reported protocol (Jo et al, 2017;Truong et al, 2012). In either case, DNA was digested with the restriction enzymes and adapters were ligated to it.…”

Section: Evaluation Of Capsaicinoid Contentmentioning

confidence: 99%

QTLmapping andGWASreveal candidate genes controlling capsaicinoid content inCapsicum

Han

Lee

et al. 2018

Plant Biotechnology Journal

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126

102

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SummaryCapsaicinoids are unique compounds produced only in peppers (Capsicum spp.). Several studies using classical quantitative trait loci (QTLs) mapping and genomewide association studies (GWAS) have identified QTLs controlling capsaicinoid content in peppers; however, neither the QTLs common to each population nor the candidate genes underlying them have been identified due to the limitations of each approach used. Here, we performed QTL mapping and GWAS for capsaicinoid content in peppers using two recombinant inbred line (RIL) populations and one GWAS population. Whole‐genome resequencing and genotyping by sequencing (GBS) were used to construct high‐density single nucleotide polymorphism (SNP) maps. Five QTL regions on chromosomes 1, 2, 3, 4 and 10 were commonly identified in both RIL populations over multiple locations and years. Furthermore, a total of 109 610 SNPs derived from two GBS libraries were used to analyse the GWAS population consisting of 208 C. annuum‐clade accessions. A total of 69 QTL regions were identified from the GWAS, 10 of which were co‐located with the QTLs identified from the two biparental populations. Within these regions, we were able to identify five candidate genes known to be involved in capsaicinoid biosynthesis. Our results demonstrate that QTL mapping and GBS‐GWAS represent a powerful combined approach for the identification of loci controlling complex traits.

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“…DNA-based molecular markers have been extensively used to accelerate plant breeding programs through marker-assisted selection for improving germplasm efficiency, and to understand the molecular mechanisms underlying genetic traits. Numerous genetic markers, including simple sequence repeats (SSRs) [ 7 ], expressed sequence tag SSRs (EST SSRs) [ 8 ], Inter-simple sequence repeats (ISSRs) [ 9 ], amplified fragment length polymorphisms (AFLPs) [ 10 ], randomly amplified polymorphic DNA (RAPD) [ 11 ] and single nucleotide polymorphisms (SNPs) [ 12 ] have been developed and used to determine genetic diversity, construct genetic linkage maps, and conduct phylogenetic analyses of onion germplasm [ 13 ]. SNPs are considered to be the most reliable genetic markers, with advantages of flexibility, cost-effectiveness, rapid, and low error rate [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

“…To date, the most recently developed genotyping methods are genotyping by sequencing (GBS) [ 17 ] and restriction site-associated DNA sequencing (RAD-seq) These simple, techniques reduce the complexity of large and multifarious genomes for easier genome-wide SNP discovery, and have been used in several plant species including onion inbred lines [ 12 ], garlic [ 18 ], maize [ 19 ], barley and wheat [ 19 ], and soybean [ 20 ]. They are also cost-effective ways of performing high-throughput sequencing of large sample sets in a single experiment, and offer the possibility of detecting SNPs on a large scale, with or without reference genome sequence.…”

Section: Introductionmentioning

confidence: 99%

SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing

et al. 2018

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Onion (Allium cepa L.) is an economically important vegetable crop around the world. Genetic and genomic research into various onion accessions will provide insights into the onion genome to enhance breeding strategies and improve crops. However, the onion’s large genome size means that studies of molecular markers are limited in onion. This study aimed to discover high quality single nucleotide polymorphisms (SNPs) from 192 onion inbred lines relating to short-day cultivation in Korea. Paired-end (PE) double digested restriction site-associated DNA sequencing (ddRAD-seq) was used to discover SNPs in onion. A total of 538,973,706 reads (25.9 GB), with an average of 2,658,491 high-quality reads, were generated using ddRAD-seq. With stringent filtering, 1904 SNPs were discovered based on onion reference scaffolds. Further, population structure and genetic relationship studies suggested that two well-differentiated sub-populations exist in onion lines. SNP-associated flanking sequences were also compared with a public non-redundant database for gene ontology and pathway analysis. To our knowledge, this is the first report to identify high-quality SNPs in onion based on reference sequences using the ddRAD-seq platform. The SNP markers identified will be useful for breeders and the research community to deepen their understanding, enhance breeding programs, and support the management of onion genomic resources.

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Development of a Genetic Map for Onion (Allium cepa L.) Using Reference-Free Genotyping-by-Sequencing and SNP Assays

Cited by 43 publications

References 39 publications

Overview of Biotic Stresses in Pepper (Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics

Overview of Biotic Stresses in Pepper (Capsicum spp.): Sources of Genetic Resistance, Molecular Breeding and Genomics

QTLmapping andGWASreveal candidate genes controlling capsaicinoid content inCapsicum

SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing

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