Genomic Insights into the Origin of a Thermotolerant Tomato Line and Identification of Candidate Genes for Heat Stress
Climate change represents the main problem for agricultural crops, and the constitution of heat-tolerant genotypes is an important breeder’s strategy to reduce yield losses. The aim of the present study was to investigate the whole genome of a heat-tolerant tomato genotype (E42), in order to identif...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-02-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/3/535 |
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| author | Salvatore Graci Valentino Ruggieri Silvana Francesca Maria Manuela Rigano Amalia Barone |
| author_facet | Salvatore Graci Valentino Ruggieri Silvana Francesca Maria Manuela Rigano Amalia Barone |
| author_sort | Salvatore Graci |
| collection | DOAJ |
| description | Climate change represents the main problem for agricultural crops, and the constitution of heat-tolerant genotypes is an important breeder’s strategy to reduce yield losses. The aim of the present study was to investigate the whole genome of a heat-tolerant tomato genotype (E42), in order to identify candidate genes involved in its response to high temperature. E42 presented a high variability for chromosomes 1, 4, 7 and 12, and phylogenetic analysis highlighted its relationship with the wild <i>S. pimpinellifolium</i> species. Variants with high (18) and moderate (139) impact on protein function were retrieved from two lists of genes related to heat tolerance and reproduction. This analysis permitted us to prioritize a subset of 35 candidate gene mapping in polymorphic regions, some colocalizing in QTLs controlling flowering in tomato. Among these genes, we identified 23 HSPs, one HSF, six involved in flowering and five in pollen activity. Interestingly, one gene coded for a flowering locus T1 and mapping on chromosome 11 resides in a QTL region controlling flowering and also showed 100% identity with an <i>S. pimpinellifolium</i> allele. This study provides useful information on both the E42 genetic background and heat stress response, and further studies will be conducted to validate these genes. |
| first_indexed | 2024-03-11T06:29:49Z |
| format | Article |
| id | doaj.art-2bc9b6edb9f5464a8af6bc17df0ae99e |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T06:29:49Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-2bc9b6edb9f5464a8af6bc17df0ae99e2023-11-17T11:15:56ZengMDPI AGGenes2073-44252023-02-0114353510.3390/genes14030535Genomic Insights into the Origin of a Thermotolerant Tomato Line and Identification of Candidate Genes for Heat StressSalvatore Graci0Valentino Ruggieri1Silvana Francesca2Maria Manuela Rigano3Amalia Barone4Department of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Naples, ItalyBiomeets Consulting, Carrer d’Àlaba, 61, 08005 Barcelona, SpainDepartment of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Naples, ItalyDepartment of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Naples, ItalyDepartment of Agricultural Sciences, University of Naples Federico II, Portici, 80055 Naples, ItalyClimate change represents the main problem for agricultural crops, and the constitution of heat-tolerant genotypes is an important breeder’s strategy to reduce yield losses. The aim of the present study was to investigate the whole genome of a heat-tolerant tomato genotype (E42), in order to identify candidate genes involved in its response to high temperature. E42 presented a high variability for chromosomes 1, 4, 7 and 12, and phylogenetic analysis highlighted its relationship with the wild <i>S. pimpinellifolium</i> species. Variants with high (18) and moderate (139) impact on protein function were retrieved from two lists of genes related to heat tolerance and reproduction. This analysis permitted us to prioritize a subset of 35 candidate gene mapping in polymorphic regions, some colocalizing in QTLs controlling flowering in tomato. Among these genes, we identified 23 HSPs, one HSF, six involved in flowering and five in pollen activity. Interestingly, one gene coded for a flowering locus T1 and mapping on chromosome 11 resides in a QTL region controlling flowering and also showed 100% identity with an <i>S. pimpinellifolium</i> allele. This study provides useful information on both the E42 genetic background and heat stress response, and further studies will be conducted to validate these genes.https://www.mdpi.com/2073-4425/14/3/535high temperatureswhole-genome resequencingSNPsInDelswild species introgressions<i>Solanum pimpinellifolium</i> |
| spellingShingle | Salvatore Graci Valentino Ruggieri Silvana Francesca Maria Manuela Rigano Amalia Barone Genomic Insights into the Origin of a Thermotolerant Tomato Line and Identification of Candidate Genes for Heat Stress Genes high temperatures whole-genome resequencing SNPs InDels wild species introgressions <i>Solanum pimpinellifolium</i> |
| title | Genomic Insights into the Origin of a Thermotolerant Tomato Line and Identification of Candidate Genes for Heat Stress |
| title_full | Genomic Insights into the Origin of a Thermotolerant Tomato Line and Identification of Candidate Genes for Heat Stress |
| title_fullStr | Genomic Insights into the Origin of a Thermotolerant Tomato Line and Identification of Candidate Genes for Heat Stress |
| title_full_unstemmed | Genomic Insights into the Origin of a Thermotolerant Tomato Line and Identification of Candidate Genes for Heat Stress |
| title_short | Genomic Insights into the Origin of a Thermotolerant Tomato Line and Identification of Candidate Genes for Heat Stress |
| title_sort | genomic insights into the origin of a thermotolerant tomato line and identification of candidate genes for heat stress |
| topic | high temperatures whole-genome resequencing SNPs InDels wild species introgressions <i>Solanum pimpinellifolium</i> |
| url | https://www.mdpi.com/2073-4425/14/3/535 |
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