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Liquid-phase sequence capture and targeted re-sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway
Tomato ( Solanum lycopersicum L.) plants are characterized by having a variety of fruit colours that reflect the composition and accumulation of diverse carotenoids in the berries. Carotenoids are extensively studied for their health-promoting effects and this explains the great attention these pigm...
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| Published in: | Scientific reports 2017-07, Vol.7 (1), p.5616-13, Article 5616 |
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| creator | Terracciano, Irma Cantarella, Concita Fasano, Carlo Cardi, Teodoro Mennella, Giuseppe D’Agostino, Nunzio |
| description | Tomato (
Solanum lycopersicum
L.) plants are characterized by having a variety of fruit colours that reflect the composition and accumulation of diverse carotenoids in the berries. Carotenoids are extensively studied for their health-promoting effects and this explains the great attention these pigments received by breeders and researchers worldwide. In this work we applied Agilent’s SureSelect liquid-phase sequence capture and Illumina targeted re-sequencing of 34 tomato genes belonging to the methylerythritol phosphate (MEP) carotenoid pathway on a panel of 48 genotypes which differ for carotenoid content calculated as the sum of β-carotene,
cis
- and
trans
-lycopene. We targeted 230 kb of genomic regions including all exons and regulatory regions and observed ~40% of on-target capture. We found ample genetic variation among all the genotypes under study and generated an extensive catalog of SNPs/InDels located in both genic and regulatory regions. SNPs/InDels were also classified based on genomic location and putative biological effect. With our work we contributed to the identification of allelic variations possibly underpinning a key agronomic trait in tomato. Results from this study can be exploited for the promotion of novel studies on tomato bio-fortification as well as of breeding programs related to carotenoid accumulation in fruits. |
| doi_str_mv | 10.1038/s41598-017-06120-3 |
| format | article |
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Solanum lycopersicum
L.) plants are characterized by having a variety of fruit colours that reflect the composition and accumulation of diverse carotenoids in the berries. Carotenoids are extensively studied for their health-promoting effects and this explains the great attention these pigments received by breeders and researchers worldwide. In this work we applied Agilent’s SureSelect liquid-phase sequence capture and Illumina targeted re-sequencing of 34 tomato genes belonging to the methylerythritol phosphate (MEP) carotenoid pathway on a panel of 48 genotypes which differ for carotenoid content calculated as the sum of β-carotene,
cis
- and
trans
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Solanum lycopersicum
L.) plants are characterized by having a variety of fruit colours that reflect the composition and accumulation of diverse carotenoids in the berries. Carotenoids are extensively studied for their health-promoting effects and this explains the great attention these pigments received by breeders and researchers worldwide. In this work we applied Agilent’s SureSelect liquid-phase sequence capture and Illumina targeted re-sequencing of 34 tomato genes belonging to the methylerythritol phosphate (MEP) carotenoid pathway on a panel of 48 genotypes which differ for carotenoid content calculated as the sum of β-carotene,
cis
- and
trans
-lycopene. We targeted 230 kb of genomic regions including all exons and regulatory regions and observed ~40% of on-target capture. We found ample genetic variation among all the genotypes under study and generated an extensive catalog of SNPs/InDels located in both genic and regulatory regions. SNPs/InDels were also classified based on genomic location and putative biological effect. With our work we contributed to the identification of allelic variations possibly underpinning a key agronomic trait in tomato. 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Terracciano, Irma</au><au>Cantarella, Concita</au><au>Fasano, Carlo</au><au>Cardi, Teodoro</au><au>Mennella, Giuseppe</au><au>D’Agostino, Nunzio</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Liquid-phase sequence capture and targeted re-sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2017-07-17</date><risdate>2017</risdate><volume>7</volume><issue>1</issue><spage>5616</spage><epage>13</epage><pages>5616-13</pages><artnum>5616</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Tomato (
Solanum lycopersicum
L.) plants are characterized by having a variety of fruit colours that reflect the composition and accumulation of diverse carotenoids in the berries. Carotenoids are extensively studied for their health-promoting effects and this explains the great attention these pigments received by breeders and researchers worldwide. In this work we applied Agilent’s SureSelect liquid-phase sequence capture and Illumina targeted re-sequencing of 34 tomato genes belonging to the methylerythritol phosphate (MEP) carotenoid pathway on a panel of 48 genotypes which differ for carotenoid content calculated as the sum of β-carotene,
cis
- and
trans
-lycopene. We targeted 230 kb of genomic regions including all exons and regulatory regions and observed ~40% of on-target capture. We found ample genetic variation among all the genotypes under study and generated an extensive catalog of SNPs/InDels located in both genic and regulatory regions. SNPs/InDels were also classified based on genomic location and putative biological effect. With our work we contributed to the identification of allelic variations possibly underpinning a key agronomic trait in tomato. Results from this study can be exploited for the promotion of novel studies on tomato bio-fortification as well as of breeding programs related to carotenoid accumulation in fruits.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>28717173</pmid><doi>10.1038/s41598-017-06120-3</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0001-9840-3817</orcidid><orcidid>https://orcid.org/0000-0002-6368-1398</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Publicly Available Content Database; PubMed Central; Free Full-Text Journals in Chemistry; Springer Nature - nature.com Journals - Fully Open Access |
| subjects | 45/41 631/449/2491 631/449/711 Biological effects Carotenoids Carotenoids - biosynthesis Exons Fruits Genetic diversity Genetic Variation Genotype Genotypes Health promotion Humanities and Social Sciences INDEL Mutation Lycopene Metabolic Networks and Pathways multidisciplinary Pigments Plant breeding Plant Proteins - genetics Polymorphism, Single Nucleotide Regulatory Elements, Transcriptional Regulatory sequences Science Science (multidisciplinary) Sequence Analysis, DNA - methods Single-nucleotide polymorphism Solanum lycopersicum Solanum lycopersicum - genetics Studies Tomatoes β-Carotene |
| title | Liquid-phase sequence capture and targeted re-sequencing revealed novel polymorphisms in tomato genes belonging to the MEP carotenoid pathway |
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