RESUMEN
BACKGROUND: Several resistance traits, including the I2 resistance against tomato fusarium wilt, were mapped to the long arm of chromosome 11 of Solanum. However, the structure and evolution of this locus remain poorly understood. RESULTS: Comparative analysis showed that the structure and evolutionary patterns of the I2 locus vary considerably between potato and tomato. The I2 homologues from different Solanaceae species usually do not have orthologous relationship, due to duplication, deletion and frequent sequence exchanges. At least 154 sequence exchanges were detected among 76 tomato I2 homologues, but sequence exchanges between I2 homologues in potato is less frequent. Previous study showed that I2 homologues in potato were targeted by miR482. However, our data showed that I2 homologues in tomato were targeted by miR6024 rather than miR482. Furthermore, miR6024 triggers phasiRNAs from I2 homologues in tomato. Sequence analysis showed that miR6024 was originated after the divergence of Solanaceae. We hypothesized that miR6024 and miR482 might have facilitated the expansion of the I2 family in Solanaceae species, since they can minimize their potential toxic effects by down-regulating their expression. CONCLUSIONS: The I2 locus represents a most divergent resistance gene cluster in Solanum. Its high divergence was partly due to frequent sequence exchanges between homologues. We propose that the successful expansion of I2 homologues in Solanum was at least partially attributed to miRNA mediated regulation.
Asunto(s)
Evolución Molecular , Genes de Plantas , MicroARNs/genética , Interferencia de ARN , Solanum/genética , Secuencia de Bases , Sitios de Unión , Mapeo Cromosómico , Cromosomas de las Plantas , Eliminación de Gen , Duplicación de Gen , Regulación de la Expresión Génica de las Plantas , Haplotipos , Solanum lycopersicum/genética , MicroARNs/química , Datos de Secuencia Molecular , Fenotipo , Filogenia , Sitios de Carácter Cuantitativo , ARN Mensajero/química , ARN Mensajero/genética , ARN Mensajero/metabolismo , Solanum tuberosum/genéticaRESUMEN
Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.
Asunto(s)
Genoma de Planta/genética , Genómica , Solanum tuberosum/genética , Evolución Molecular , Duplicación de Gen , Regulación de la Expresión Génica de las Plantas , Genes de Plantas/genética , Variación Genética , Haplotipos/genética , Heterocigoto , Homocigoto , Inmunidad Innata , Endogamia , Anotación de Secuencia Molecular , Datos de Secuencia Molecular , Enfermedades de las Plantas/genética , Ploidias , Solanum tuberosum/fisiologíaRESUMEN
Massive resistance (R) gene stacking is considered to be one of the most promising approaches to provide durable resistance to potato late blight for both conventional and genetically modified breeding strategies. The R3 complex locus on chromosome XI in potato is an example of natural R gene stacking, because it contains two closely linked R genes (R3a and R3b) with distinct resistance specificities to Phytophthora infestans. Here, we report about the positional cloning of R3b. Both transient and stable transformations of susceptible tobacco and potato plants showed that R3b conferred full resistance to incompatible P. infestans isolates. R3b encodes a coiled-coil nucleotide-binding site leucine-rich repeat protein and exhibits 82% nucleotide identity with R3a located in the same R3 cluster. The R3b gene specifically recognizes Avr3b, a newly identified avirulence factor from P. infestans. R3b does not recognize Avr3a, the corresponding avirulence gene for R3a, showing that, despite their high sequence similarity, R3b and R3a have clearly distinct recognition specificities. In addition to the Rpi-mcd1/Rpi-blb3 locus on chromosome IV, the R3 locus on chromosome XI is the second example of an R-gene cluster with multiple genes recognizing different races of P. infestans.
Asunto(s)
Genes de Plantas , Phytophthora infestans/patogenicidad , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/microbiología , Solanum tuberosum/genética , Solanum tuberosum/microbiología , Agrobacterium tumefaciens/genética , Secuencia de Bases , Mapeo Cromosómico , Cromosomas de las Plantas/genética , Clonación Molecular , ADN de Plantas/genética , Prueba de Complementación Genética , Interacciones Huésped-Patógeno/genética , Familia de Multigenes , Filogenia , Enfermedades de las Plantas/prevención & control , Hojas de la Planta/microbiología , Plantas Modificadas Genéticamente , Nicotiana/genética , Nicotiana/microbiología , Transformación Genética , VirulenciaRESUMEN
Cultivated and wild potatoes contain a major disease-resistance cluster on the short arm of chromosome V, including the R1 resistance (R) gene against potato late blight. To explore the functional and evolutionary significance of clustering in the generation of novel disease-resistance genes, we constructed three approximately 1 Mb physical maps in the R1 gene region, one for each of the three genomes (haplotypes) of allohexaploid Solanum demissum, the wild potato progenitor of the R1 locus. Totals of 691, 919 and 559 kb were sequenced for each haplotype, and three distinct resistance-gene families were identified, one homologous to the potato R1 gene and two others homologous to either the Prf or the Bs4 R-gene of tomato. The regions with R1 homologues are highly divergent among the three haplotypes, in contrast to the conserved flanking non-resistance gene regions. The R1 locus shows dramatic variation in overall length and R1 homologue number among the three haplotypes. Sequence comparisons of the R1 homologues show that they form three distinct clades in a distance tree. Frequent sequence exchanges were detected among R1 homologues within each clade, but not among those in different clades. These frequent sequence exchanges homogenized the intron sequences of homologues within each clade, but did not homogenize the coding sequences. Our results suggest that the R1 homologues represent three independent groups of fast-evolving type I resistance genes, characterized by chimeric structures resulting from frequent sequence exchanges among group members. Such genes were first identified among clustered RGC2 genes in lettuce, where they were distinguished from slow-evolving type II R-genes. Our findings at the R1 locus in S. demissum may indicate that a common or similar mechanism underlies the previously reported differentiation of type I and type II R-genes and the differentiation of type I R-genes into distinct groups, identified here.
Asunto(s)
Evolución Molecular , Genes de Plantas/genética , Variación Genética/genética , Haplotipos , Familia de Multigenes/genética , Enfermedades de las Plantas/genética , Solanum/genética , Cromosomas Artificiales Bacterianos/genética , Clonación Molecular , Secuencia Conservada/genética , Intrones/genética , Datos de Secuencia Molecular , Filogenia , Proteínas de Plantas/genética , Solanum/metabolismo , SolventesRESUMEN
Comparative genomics provides a tool to utilize the exponentially increasing sequence information from model plants to clone agronomically important genes from less studied crop species. Plant disease resistance (R) loci frequently lack synteny between related species of cereals and crucifers but appear to be positionally well conserved in the Solanaceae. In this report, we adopted a local RGA approach using genomic information from the model Solanaceous plant tomato to isolate R3a, a potato gene that confers race-specific resistance to the late blight pathogen Phytophthora infestans. R3a is a member of the R3 complex locus on chromosome 11. Comparative analyses of the R3 complex locus with the corresponding I2 complex locus in tomato suggest that this is an ancient locus involved in plant innate immunity against oomycete and fungal pathogens. However, the R3 complex locus has evolved after divergence from tomato and the locus has experienced a significant expansion in potato without disruption of the flanking colinearity. This expansion has resulted in an increase in the number of R genes and in functional diversification, which has probably been driven by the co-evolutionary history between P. infestans and its host potato. Constitutive expression was observed for the R3a gene, as well as some of its paralogues whose functions remain unknown.
Asunto(s)
Expresión Génica/fisiología , Genómica , Proteínas de Plantas/metabolismo , Solanum tuberosum/genética , Solanum tuberosum/metabolismo , Secuencia de Aminoácidos , Evolución Molecular , Marcadores Genéticos , Inmunidad Innata/genética , Solanum lycopersicum/genética , Solanum lycopersicum/metabolismo , Datos de Secuencia Molecular , Phytophthora/fisiología , Enfermedades de las Plantas/microbiología , Hojas de la Planta/microbiología , Proteínas de Plantas/genética , Homología de Secuencia de AminoácidoRESUMEN
Late blight, caused by the oomycete pathogen Phytophthora infestans, is the most devastating potato disease in the world. Control of late blight in the United States and other developed countries relies extensively on fungicide application. We previously demonstrated that the wild diploid potato species Solanum bulbocastanum is highly resistant to all known races of P. infestans. Potato germplasm derived from S. bulbocastanum has shown durable and effective resistance in the field. Here we report the cloning of the major resistance gene RB in S. bulbocastanum by using a map-based approach in combination with a long-range (LR)-PCR strategy. A cluster of four resistance genes of the CC-NBS-LRR (coiled coil-nucleotide binding site-Leu-rich repeat) class was found within the genetically mapped RB region. Transgenic plants containing a LR-PCR product of one of these four genes displayed broad spectrum late blight resistance. The cloned RB gene provides a new resource for developing late blight-resistant potato varieties. Our results also demonstrate that LR-PCR is a valuable approach to isolate genes that cannot be maintained in the bacterial artificial chromosome system.