▪ Abstract Meiotic chromosomes have been studied for many years, in part because of the fundamental life processes they represent, but also because meiosis involves the formation of homolog pairs, ...

Meiotic chromosomes: integrating structure and function.

Arabidopsis SGS2 and SGS3 Genes Are Required for Posttranscriptional Gene Silencing and Natural Virus Resistance

Molecular genetic markers have been developed into powerful tools to analyse genetic relationships and genetic diversity. As an extension to the variety of existing techniques using polymorphic DNA markers, the Random Amplified Polymorphic DNA (RAPD) technique may be used in molecular ecology to determine taxonomic identity, assess kinship relationships, analyse mixed genome samples, and create specific probes. Main advantages of the RAPD technology include (i) suitability for work on anonymous genomes, (ii) applicability to problems where only limited quantities of DNA are available, (iii) efficiency and low expense.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-294X.1992.tb00155.x

Applications of random amplified polymorphic DNA (RAPD) in molecular ecology

Publisher Summary Cucumber mosaic virus (CMV), the type member of the cucumovirus group, was first reported in 1916 as the causal agent of a disease of cucumber and muskmelon in Michigan and cucumber in New York. Since then, CMV has been found in most countries of the world, predominantly in the temperate zones, but increasingly more often in the tropical countries. CMV has the largest host range of any virus. The number of plant species identified as hosts for CMV has increased steadily over the past 60 years. The highlights of the more recent research include the following: (1) the complete nucleotide sequence of the genome of three strains of CMV has been determined, as well as nucleotide sequences of individual RNAs of eight other CMV strains, (2) the CMV replicase has been purified to homogeneity, and it functions in vitro to synthesize CMV RNA de novo , (3) infectious transcripts have been synthesized from full-length cDNA clones of the three strains of CMV, (4) these biologically active cDNAs are being used to map sequences involved in replication, movement, pathogenesis, resistance, and vector transmission. Biologically active cDNA clones of the satellite RNAs of CMV have been produced in seven laboratories and sequences involved in replication and pathogenicity have/are being identified, (5) finally, transgenic plants have been produced expressing either the CMV coat protein gene or satellite RNA sequences that show to protect such plants from infection by CMV. This chapter, while focusing on the more recent developments in CMV biology and biochemistry, also covers some of the same ground albeit in brief. The chapter presents a comprehensive review that can be used as a reference work for general virologists and plant pathologists, as well as those specializing in the molecular biology of CMV and/or other multicomponent plant viruses.

Cucumber Mosaic Virus

The development and maturation of fruits has received considerable scientific scrutiny because of both the uniqueness of such processes to the biology of plants and the importance of fruit as a significant component of the human diet. Molecular and genetic analysis of fruit development, and especially ripening of fleshy fruits, has resulted in significant gains in knowledge over recent years. Great strides have been made in the areas of ethylene biosynthesis and response, cell wall metabolism, and environmental factors, such as light, that impact ripening. Discoveries made in Arabidopsis in terms of general mechanisms for signal transduction, in addition to specific mechanisms of carpel development, have assisted discovery in more traditional models such as tomato. This review attempts to coalesce recent findings in the areas of fruit development and ripening.

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Molecular biology of fruit maturation and ripening.

A new DNA polymorphism assay was developed in 1990 that is based on the amplification by the polymerase chain reaction (PCR) of random DNA segments, using single primers of arbitrary nucleotide sequence. The amplified DNA fragments, referred to as RAPD markers, were shown to be highly useful in the construction of genetic maps (“RAPD mapping”). We have now adapted the RAPD assay to tomato. Using a set of 11 oligonucleotide decamer primers, each primer directed the amplification of a genome-specific “fingerprint” of DNA fragments. The potential of the original RAPD assay to generate polymorphic DNA markers with a given set of primers was further increased by combining two primers in a single PCR. By comparing “fingerprints” of L. esculentum, L. pennellii, and the L. esculentum chromosome 6 substitution line LA1641, which carries chromosome 6 from L. pennellii, three chromosome 6-specific RAPD markers could be directly identified among the set of amplified DNA fragments. Their chromosomal position on the classical genetic map of tomato was subsequently established by restriction fragment length polymorphism (RFLP) linkage analysis. One of the RAPD markers was found to be tightly linked to the nematode resistance gene Mi.

Isolation of molecular markers for tomato (L. esculentum) using random amplified polymorphic DNA (RAPD)

The contribution of introgressed regions derived from wild species to the genetic variation within the species of Lycopersicon esculentum was investigated by comparing the RFLP patterns of 2 introgression-free, obsolete cultivars ('Moneymaker' and 'Premier') and a modern cultivar ('Sonatine') that carries at least 5 introgressed resistance genes. In this analysis 195 mapped nuclear markers were used in combination with 6 restriction enzymes. Among the 1170 probe-enzyme combinations tested, only 3 showed a polymorphism between the 2 introgression-free cultivars. On the other hand 24 probe-enzyme combinations were found to exhibit polymorphisms between 'Moneymaker' and 'Sonatine'. These represented ten polymorphic loci distributed among 5 linkage groups on chromosomes 1, 3, 4, 6, and 9.On the assumption that most of the polymorphic loci corresponded to introgressed chromosome segments of wild species carrying resistance genes, linkages between these loci and the component resistance genes were examined by RFLP analysis of pairs of near-isogenic lines differing only for one particular resistance gene, and a variety of commercial cultivars having different resistance gene compositions. Two of the polymorphic linkage groups could thus be ascribed to resistance genes whose map positions were already known: Cf2 on chromosome 6 and Tm2a on chromosome 9, whereas another marker, TG301 on chromosome 1, could be assigned to the Cladosporium fulvum resistance gene Cf9 with a hitherto disputable map position. By linkage analysis of a segregating F2 population the genetic distance between the Cf9 gene and the marker TG301 was estimated at 5.5 ± 2.3 cM.

Mapping strategy for resistance genes in tomato based on RFLPs between cultivars: Cf9 (resistance to Cladosporium fulvum) on chromosome 1.

Summary
The superior regeneration capacity of Lycopersicon peruvianum was introduced into the cultivated tomato Lycopersicon esculentum by backcrossing hybrid material with the tomato genotype VF11. In segregating material derived from these backcrosses, the ability to regenerate shoots on root explants cultured on a zeatin-containing medium, was highly correlated with the ability to regenerate shoots on established callus cultures. The efficient shoot-regenerating root explant system permitted us to study the genetics of this trait and to locate the genes involved, using a set of morphological markers defining all 12 tomato chromosomes. Depending on the tomato genotype, mono, -di- or trigenic ratios were observed. It is concluded that a dominant L. peruvianum allele at a locus (Rg-1) near the middle of chromosome 3 determines efficient shoot regeneration on root explants in tomato in combination with dominant alleles at one or two other loci of either L. peruvianum or L. esculentum origin. The map location of the Rg-1 locus was refined further using a number of chromosome-3-specific RFLPs. The addition of new classical and RFLP linkage data to existing literature data and subsequent processing resulted in a revised and integrated map of tomato chromosome 3. From a morphological and physiological analysis of genotypes differing in Rg phenotype, it is concluded that the genetic component associated with regeneration determines the maintenance of morphogenetic competence and not the sensitivity to hormones.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.1993.tb00016.x

Characterization and mapping of a gene controlling shoot regeneration in tomato

As part of a map-based cloning strategy designed to isolate the root-knot nematode resistance gene Mi, tomato F2 populations were analyzed in order to identify recombination points close to this economically important gene. A total of 21 089 F2 progeny plants were screened using morphological markers. An additional 1887 F2 were screened using PCR-based flanking markers. Fine-structure mapping of recombinants with newly developed AFLP markers, and RFLP markers derived from physically mapped cosmid subclones, localized Mi to a genomic region of about 550 kb. The low frequency of recombinants indicated that recombination was generally suppressed in these crosses and that crossovers were restricted to particular regions. To circumvent this problem, a population of Lycopersicon peruvianum, the species from which Mi was originally introgressed, that was segregating for resistance was developed. Screening of this population with PCR, RFLP and AFLP markers identified several plants with crossovers near Mi. Recombination frequency was approximately eight-fold higher in the Mi region of the L. peruvianum cross. However, even within the wild species cross, recombination sites were not uniformly distributed in the region. By combining data from the L. esculentum and L. peruvianum recombinant analyses, it was possible to localize Mi to a region of the genome spanning less than 65 kb.

Genetic and physical localization of the root-knot nematode resistance locus Mi in tomato.

A dominant allele at the Mi locus on chromosome 6 of tomato (Lycopersicon esculentum Mill) confers resistance to three species of root-knot nematodes (Meloidogyne). The resistance, which is associated with a localized necrotic response, was originally introduced into tomato from the wild species Lycopersicon peruvianum. As a step towards the molecular cloning of Mi, we have identified closely linked DNA markers from both cDNA and genomic DNA libraries as restriction fragment length polymorphisms (RFLPs). DNA from tomato populations segregating for nematode resistance was analyzed to generate a high-resolution genetic map of this region. Additional information on gene order was obtained by comparing the size of the introgressed L. peruvianum chromosomal segment within a collection of nematode-resistant tomato lines. Among the four cDNA markers that are tightly linked to Mi, three are dominant, i.e. L. peruvianum-specific. One cDNA marker corresponds to a gene family comprising 20-30 members, one of which is diagnostic for all nematode-resistant genotypes tested. The presence of non-homologous sequences around the Mi gene may contribute to the suppression of recombination in this region of the genome in crosses heterozygous for Mi. The potential of 'walking' from closely linked markers to Mi is discussed.

https://onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-313X.1992.t01-8-00999.x

The root-knot nematode resistance gene (Mi) in tomato: construction of a molecular linkage map and identification of dominant cDNA markers in resistant genotypes.

P. Zabel

Papers

Isolation of molecular markers for tomato (L. esculentum) using random amplified polymorphic DNA (RAPD)

Mapping strategy for resistance genes in tomato based on RFLPs between cultivars: Cf9 (resistance to Cladosporium fulvum) on chromosome 1.

Characterization and mapping of a gene controlling shoot regeneration in tomato

Genetic and physical localization of the root-knot nematode resistance locus Mi in tomato.

The root-knot nematode resistance gene (Mi) in tomato: construction of a molecular linkage map and identification of dominant cDNA markers in resistant genotypes.