Preliminary assessment of COSII gene diversity in lulo and a relative species: Initial identification of genes potentially associated with domestication

Bedoya-Reina, Oscar C.; Barrero, Luz Stella

doi:10.1016/j.gene.2010.03.005

Cited by 5 publications

(3 citation statements)

References 66 publications

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“…Nonetheless, dominant RAM markers as well as codominant markers such as SSRs and COSII, conserved in related species as tomato have been used in genetic studies in Physalis (Bonilla et al, 2008; Morillo Paz et al, 2011; Wei et al, 2012). COSII markers represent a strong strategy to integrate diversity estimations over extended genetic distances and to map highly variable gene spots (Bedoya-Reina and Barrero, 2010). Besides, due to the fact they are derived from universal primers transferred among species, these are an economic alternative to other types of co-dominant markers such as SSRs (Enciso-Rodríguez et al, 2010).…”

Section: Discussionmentioning

confidence: 99%

“…We selected 327 COSII markers based on their distribution across the 12 linkage groups of the tomato genome, considering their orthologous nature in a broad range of Solanaceae family species (Fulton et al, 2002; Wu et al, 2006; Bedoya-Reina and Barrero, 2010). Furthermore, 33 COSII genes were selected, based on resistance to biotic factors related ontologies (i.e.…”

Section: Methodsmentioning

confidence: 99%

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Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers

et al. 2015

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The genus Physalis is common in the Americas and includes several economically important species, among them Physalis peruviana that produces appetizing edible fruits. We studied the genetic diversity and population structure of P. peruviana and characterized 47 accessions of this species along with 13 accessions of related taxa consisting of 222 individuals from the Colombian Corporation of Agricultural Research (CORPOICA) germplasm collection, using Conserved Orthologous Sequences (COSII) and Immunity Related Genes (IRGs). In addition, 642 Single Nucleotide Polymorphism (SNPs) markers were identified and used for the genetic diversity analysis. A total of 121 alleles were detected in 24 InDels loci ranging from 2 to 9 alleles per locus, with an average of 5.04 alleles per locus. The average number of alleles in the SNP markers was two. The observed heterozygosity for P. peruviana with InDel and SNP markers was higher (0.48 and 0.59) than the expected heterozygosity (0.30 and 0.41). Interestingly, the observed heterozygosity in related taxa (0.4 and 0.12) was lower than the expected heterozygosity (0.59 and 0.25). The coefficient of population differentiation FST was 0.143 (InDels) and 0.038 (SNPs), showing a relatively low level of genetic differentiation among P. peruviana and related taxa. Higher levels of genetic variation were instead observed within populations based on the AMOVA analysis. Population structure analysis supported the presence of two main groups and PCA analysis based on SNP markers revealed two distinct clusters in the P. peruviana accessions corresponding to their state of cultivation. In this study, we identified molecular markers useful to detect genetic variation in Physalis germplasm for assisting conservation and crossbreeding strategies.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers

et al. 2015

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“…Each read was processed with a variant call pipeline [53] that uses Phred/Phrap/Consed for base calling and assembly [54,55]. …”

Section: Methodsmentioning

confidence: 99%

Identification of Immunity Related Genes to Study the Physalis peruviana – Fusarium oxysporum Pathosystem

et al. 2013

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The Cape gooseberry ( Physalis peruviana L) is an Andean exotic fruit with high nutritional value and appealing medicinal properties. However, its cultivation faces important phytosanitary problems mainly due to pathogens like Fusarium oxysporum, Cercosporaphysalidis and Alternaria spp. Here we used the Cape gooseberry foliar transcriptome to search for proteins that encode conserved domains related to plant immunity including: NBS (Nucleotide Binding Site), CC (Coiled-Coil), TIR (Toll/Interleukin-1 Receptor). We identified 74 immunity related gene candidates in P . peruviana which have the typical resistance gene (R-gene) architecture, 17 Receptor like kinase (RLKs) candidates related to PAMP-Triggered Immunity (PTI), eight (TIR-NBS-LRR, or TNL) and nine (CC–NBS-LRR, or CNL) candidates related to Effector-Triggered Immunity (ETI) genes among others. These candidate genes were categorized by molecular function (98%), biological process (85%) and cellular component (79%) using gene ontology. Some of the most interesting predicted roles were those associated with binding and transferase activity. We designed 94 primers pairs from the 74 immunity-related genes (IRGs) to amplify the corresponding genomic regions on six genotypes that included resistant and susceptible materials. From these, we selected 17 single band amplicons and sequenced them in 14 F. oxysporum resistant and susceptible genotypes. Sequence polymorphisms were analyzed through preliminary candidate gene association, which allowed the detection of one SNP at the PpIRG-63 marker revealing a nonsynonymous mutation in the predicted LRR domain suggesting functional roles for resistance.

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Lulo (Solanum quitoense Lam.) reproductive physiology: A review

Ramírez¹,

Kallarackal

Davenport

2018

Scientia Horticulturae

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Preliminary assessment of COSII gene diversity in lulo and a relative species: Initial identification of genes potentially associated with domestication

Cited by 5 publications

References 66 publications

Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers

Genetic diversity and population structure in Physalis peruviana and related taxa based on InDels and SNPs derived from COSII and IRG markers

Identification of Immunity Related Genes to Study the Physalis peruviana – Fusarium oxysporum Pathosystem

Lulo (Solanum quitoense Lam.) reproductive physiology: A review

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