High-throughput genotyping in onion reveals structure of genetic diversity and informative SNPs useful for molecular breeding

Villano, Clizia; Esposito, Salvatore; Carucci, Francesca; Iorizzo, Massimo; Frusciante, Luigi; Carputo, Domenico

doi:10.1007/s11032-018-0912-0

Cited by 24 publications

(24 citation statements)

References 54 publications

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“…Although the authors used SNP markers to assess the genetic diversity of a wider onion collection, the genotyping was not able to discriminate "Acquaviva" from "Tropea" and "Montoro" onions. Probably, this discrepancy is due to the low mean PIC value found (0.292), suggesting a modest general informativeness of the loci under analysis as claimed by [29]. Furthermore, in order to investigate the presence of sub-structure in their Italian cluster, it would have been better to analyze the Italian genotypes separately from the rest of the collection.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, based on the results obtained, the ARO landrace can be considered clearly distinct at the genetic level from the TRO and MCO landraces. In a recent study, [29] assessed the genetic diversity of several Italian onion landraces including "Acquaviva," "Tropea," and "Montoro." Although the authors used SNP markers to assess the genetic diversity of a wider onion collection, the genotyping was not able to discriminate "Acquaviva" from "Tropea" and "Montoro" onions.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, sulphur-based fertilization, agronomic practices, type of soil, climatic conditions, and the genotype of cultivars or landraces can influence the bulb quality by conferring peculiar organoleptic and nutritional values [23][24][25][26][27]. In Italy, despite the wide onion germplasm availability, only a few onion varieties are often subjected to scientific studies and properly characterized [28,29].…”

Section: Introductionmentioning

confidence: 99%

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Assessment of Genetic Diversity of the “Acquaviva Red Onion” (Allium cepa L.) Apulian Landrace

Ricciardi

Mazzeo

Marcotrigiano

et al. 2020

Plants

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Onion (Allium cepa L.) is the second most important vegetable crop worldwide and is widely appreciated for its health benefits. Despite its significant economic importance and its value as functional food, onion has been poorly investigated with respect to its genetic diversity. Herein, we surveyed the genetic variation in the “Acquaviva red onion” (ARO), a landrace with a century-old history of cultivation in a small town in the province of Bari (Apulia, Southern of Italy). A set of 11 microsatellite markers were used to explore the genetic variation in a germplasm collection consisting of 13 ARO populations and three common commercial types. Analyses of genetic structure with parametric and non-parametric methods highlighted that the ARO represents a well-defined gene pool, clearly distinct from the Tropea and Montoro landraces with which it is often mistaken. In order to provide a description of bulbs, usually used for fresh consumption, soluble solid content and pungency were evaluated, showing higher sweetness in the ARO with respect to the two above mentioned landraces. Overall, the present study is useful for the future valorization of the ARO, which could be promoted through quality labels which could contribute to limit commercial frauds and improve the income of smallholders.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Assessment of Genetic Diversity of the “Acquaviva Red Onion” (Allium cepa L.) Apulian Landrace

Ricciardi

Mazzeo

Marcotrigiano

et al. 2020

Plants

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“…SNPs are the most abundant genetic variations in most plant species, and the exploitation of SNP markers in single-copy regions is considerably easier than use of the other DNA markers [14][15][16].…”

Section: Introductionmentioning

confidence: 99%

“…Several studies have also reported the development and application of SNP/InDel markers in tea plant genetic studies. For instance, 16 expressed sequence tag (EST)-SNP based CAPS markers were developed and applied for tea plant cultivar identification [23]. A set of SNPs from EST databases was identified and verified [24].…”

Section: Introductionmentioning

confidence: 99%

Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research

Liu

Tong

et al. 2019

Preprint

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Background: Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) are the major genetic variations and are distributed extensively across the whole plant genome. However, few studies of these variations have been conducted in the long-lived perennial tea plant. Results: In this study, we investigated the genome-wide genetic variations between Camellia sinensis var. sinensis ‘Shuchazao’ and Camellia sinensis var. assamica ‘Yunkang 10’, identified 7,511,731 SNPs and 255,218 InDels based on their whole genome sequences, and we subsequently analyzed their distinct types and distribution patterns. A total of 48 InDel markers that yielded polymorphic and unambiguous fragments were developed when screening six tea cultivars. These markers were further deployed on forty-six tea cultivars for transferability and genetic diversity analysis, exhibiting information with an average 4.02 of the number of alleles (Na) and 0.457 of polymorphism information content (PIC). The dendrogram showed that the phylogenetic relationships among these tea cultivars are highly consistent with their genetic backgrounds or original places. Interestingly, we observed that the catechin/caffeine contents between ‘Shuchazao’ and ‘Yunkang 10’ were significantly different, and a large number of SNPs/InDels were identified within catechin/caffeine biosynthesis-related genes. Conclusion: The identified genome-wide genetic variations and newly-developed InDel markers will provide a valuable resource for tea plant genetic and genomic studies, especially the SNPs/InDels within catechin/caffeine biosynthesis-related genes, which may serve as pivotal candidates for elucidating the molecular mechanism governing catechin/caffeine biosynthesis.

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Practical Workflow from High-Throughput Genotyping to Genomic Estimated Breeding Values (GEBVs)

Contaldi¹,

Cappetta

Esposito³

2020

Methods in Molecular Biology

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High-throughput genotyping in onion reveals structure of genetic diversity and informative SNPs useful for molecular breeding

Cited by 24 publications

References 54 publications

Assessment of Genetic Diversity of the “Acquaviva Red Onion” (Allium cepa L.) Apulian Landrace

Assessment of Genetic Diversity of the “Acquaviva Red Onion” (Allium cepa L.) Apulian Landrace

Characterization of genome-wide genetic variations between two varieties of tea plant (Camellia sinensis) and development of InDel markers for genetic research

Practical Workflow from High-Throughput Genotyping to Genomic Estimated Breeding Values (GEBVs)

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