Solanaceae genomics: Current status of tomato (&lt;i&gt;Solanum lycopersicum&lt;/i&gt;) genome sequencing and its application to pepper (&lt;i&gt;Capsicum&lt;/i&gt; spp.) genome research

Lee, Sanghyeob; Jo, Sung Hwan; Choi, Doil

doi:10.5511/plantbiotechnology.24.11

Cited by 4 publications

(2 citation statements)

References 42 publications

(18 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Sequence editing for consensus contig formation was carried out using the Sequencher 4.1.5 (Gene codes Corp., Ann Arbor, USA). The tomato BAC sequences were generated by the same method as part of the International Tomato Sequencing Project of Korea [ 20 ].…”

Section: Methodsmentioning

confidence: 99%

Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

Park

Kwon

et al. 2011

BMC Genomics

Self Cite

View full text Add to dashboard Cite

BackgroundAmong the Solanaceae plants, the pepper genome is three times larger than that of tomato. Although the gene repertoire and gene order of both species are well conserved, the cause of the genome-size difference is not known. To determine the causes for the expansion of pepper euchromatic regions, we compared the pepper genome to that of tomato.ResultsFor sequence-level analysis, we generated 35.6 Mb of pepper genomic sequences from euchromatin enriched 1,245 pepper BAC clones. The comparative analysis of orthologous gene-rich regions between both species revealed insertion of transposons exclusively in the pepper sequences, maintaining the gene order and content. The most common type of the transposon found was the LTR retrotransposon. Phylogenetic comparison of the LTR retrotransposons revealed that two groups of Ty3/Gypsy-like elements (Tat and Athila) were overly accumulated in the pepper genome. The FISH analysis of the pepper Tat elements showed a random distribution in heterochromatic and euchromatic regions, whereas the tomato Tat elements showed heterochromatin-preferential accumulation.ConclusionsCompared to tomato pepper euchromatin doubled its size by differential accumulation of a specific group of Ty3/Gypsy-like elements. Our results could provide an insight on the mechanism of genome evolution in the Solanaceae family.

show abstract

Section: Methodsmentioning

confidence: 99%

Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

Park

Kwon

et al. 2011

BMC Genomics

Self Cite

View full text Add to dashboard Cite

show abstract

“…It is one of the worldwide favorite ingredients when cooking food since its domestication in South and Central America about 6,000 years ago (Perry et al, 2007). Pepper's consumption is increasing worldwide, and the vegetable is an important source of vitamins and essential nutrients (Lee et al, 2007). Moreover, medical usage of pepper is also developed to alleviate the pain and long-term inflammation (Ben Chaim et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

SNP Marker Integration and QTL Analysis of 12 Agronomic and Morphological Traits in F8RILs of Pepper (Capsicum annuum L.)

Kwon

Yoon

et al. 2012

Molecules and Cells

View full text Add to dashboard Cite

Red pepper, Capsicum annuum L., has been attracting geneticists' and breeders' attention as one of the important agronomic crops. This study was to integrate 41 SNP markers newly developed from comparative transcriptomes into a previous linkage map, and map 12 agronomic and morphological traits into the integrated map. A total of 39 markers found precise position and were assigned to 13 linkage groups (LGs) as well as the unassigned LGe, leading to total 458 molecular markers present in this genetic map. Linkage mapping was supported by the physical mapping to tomato and potato genomes using BLAST retrieving, revealing at least two-thirds of the markers mapped to the corresponding LGs. A sum of 23 quantitative trait loci from 11 traits was detected using the composite interval mapping algorithm. A consistent interval between a035_1 and a170_1 on LG5 was detected as a main-effect locus among the resistance QTLs to Phytophthora capsici at high-, intermediate- and low-level tests, and interactions between the QTLs for high-level resistance test were found. Considering the epistatic effect, those QTLs could explain up to 98.25% of the phenotype variations of resistance. Moreover, 17 QTLs for another eight traits were found to locate on LG3, 4, and 12 mostly with varying phenotypic contribution. Furthermore, the locus for corolla color was mapped to LG10 as a marker. The integrated map and the QTLs identified would be helpful for current genetics research and crop breeding, especially in the Solanaceae family.

show abstract

Genome analysis and genetic enhancement of tomato

Gupta

Mathur

Solanke

et al. 2009

Critical Reviews in Biotechnology

View full text Add to dashboard Cite

The Solanaceae is an important family of vegetable crops, ornamentals and medicinal plants. Tomato has served as a model member of this family largely because of its enriched cytogenetic, genetic, as well as physical, maps. Mapping has helped in cloning several genes of importance such as Pto, responsible for resistance against bacterial speck disease, Mi-1.2 for resistance against nematodes, and fw2.2 QTL for fruit weight. A high-throughput genome-sequencing program has been initiated by an international consortium of 10 countries. Since heterochromatin has been found to be concentrated near centromeres, the consortium is focusing on sequencing only the gene-rich euchromatic region. Genomes of the members of Solanaceae show a significant degree of synteny, suggesting that the tomato genome sequence would help in the cloning of genes for important traits from other Solanaceae members as well. ESTs from a large number of cDNA libraries have been sequenced, and microarray chips, in conjunction with wide array of ripening mutants, have contributed immensely to the understanding of the fruit-ripening phenomenon. Work on the analysis of the tomato proteome has also been initiated. Transgenic tomato plants with improved abiotic stress tolerance, disease resistance and insect resistance, have been developed. Attempts have also been made to develop tomato as a bioreactor for various pharmaceutical proteins. However, control of fruit quality and ripening remains an active and challenging area of research. Such efforts should pave the way to improve not only tomato, but also other solanaceous crops.

show abstract

Solanaceae genomics: Current status of tomato (<i>Solanum lycopersicum</i>) genome sequencing and its application to pepper (<i>Capsicum</i> spp.) genome research

Cited by 4 publications

References 42 publications

Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

Comparative analysis of pepper and tomato reveals euchromatin expansion of pepper genome caused by differential accumulation of Ty3/Gypsy-like elements

SNP Marker Integration and QTL Analysis of 12 Agronomic and Morphological Traits in F8RILs of Pepper (Capsicum annuum L.)

Genome analysis and genetic enhancement of tomato

Contact Info

Product

Resources

About