Localization of jointless-2 gene in the centromeric region of tomato chromosome 12 based on high resolution genetic and physical mapping

Budiman, Muhammad A.; Chang, Song Bin; Lee, S.; Yang, Tae Jin; Zhang, H. B.; Jong, Hans de; Wing, Rod A.

doi:10.1007/s00122-003-1429-3

Cited by 59 publications

(55 citation statements)

References 28 publications

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“…This approach assumes that tight linkage between a molecular locus and a gene locus indicates close physical proximity. While this can be true in some cases, we and others have shown that the validity of this assumption differs along the length of tomato pachytene chromosomes (Zhong et al 1999;Budiman et al 2004). The RN-cM map can help overcome this limitation by defining the relation between map distances and physical distances on pachytene chromosomes so that more accurate estimates of the physical distance between two loci can be made.…”

Section: Discussionmentioning

confidence: 99%

“…This is because the frequency of crossing over along the length of chromosomes is not uniform, and as a result loci that are physically far apart on chromosomes can be nearby on linkage maps and vice versa (Sturtevant and Beadle 1939;Khush and Rick 1968;Sherman and Stack 1995;Zhong et al 1999;Islam-Faridi et al 2002;Budiman et al 2004). Such discrepancies are impediments to applying linkage maps to guide genome sequence assembly or for gene discovery by chromosome walking (Budiman et al 2004).…”

Section: W Hile Linkage Maps Accurately Describe Genementioning

confidence: 99%

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Predicting and Testing Physical Locations of Genetically Mapped Loci on Tomato Pachytene Chromosome1

Chang¹,

Anderson

Sherman

et al. 2007

Genetics

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Predicting the chromosomal location of mapped markers has been difficult because linkage maps do not reveal differences in crossover frequencies along the physical structure of chromosomes. Here we combine a physical crossover map based on the distribution of recombination nodules (RNs) on Solanum lycopersicum (tomato) synaptonemal complex 1 with a molecular genetic linkage map from the interspecific hybrid S. lycopersicum 3 S. pennellii to predict the physical locations of 17 mapped loci on tomato pachytene chromosome 1. Except for one marker located in heterochromatin, the predicted locations agree well with the observed locations determined by fluorescence in situ hybridization. One advantage of this approach is that once the RN distribution has been determined, the chromosomal location of any mapped locus (current or future) can be predicted with a high level of confidence.

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Section: Discussionmentioning

confidence: 99%

Section: W Hile Linkage Maps Accurately Describe Genementioning

confidence: 99%

Predicting and Testing Physical Locations of Genetically Mapped Loci on Tomato Pachytene Chromosome1

Chang¹,

Anderson

Sherman

et al. 2007

Genetics

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“…VFNT Cherry (LA1221, 2n=2Â=24) was used in all our FISH experiments. For the spread preparations of mitotic root tip and meiotic pachytene complements we followed the protocols of Zhong et al (1996) and Budiman et al (2004).…”

Section: Methodsmentioning

confidence: 99%

“…However, recent DNA sequence analyses of centromeres and flanking pericentromeres in various plants (e.g. Budiman et al 2004, Copenhaver et al 1999, Nagaki et al 2004) demonstrated that transcribed genes exist in these regions. The repeat fraction of the tomato genome can be divided into tandem repeat families like the 45S and 5S rDNAs, the [TTTAGGG] telomere repeat, and several speciesspecific repeats that are abundant in the centromeres, telomeres and other heterochromatic regions, and other dispersed repeats such as retrotransposons and transposable elements that occur both in heterochromatin and in euchromatin.…”

Section: Introductionmentioning

confidence: 99%

FISH mapping and molecular organization of the major repetitive sequences of tomato

et al. 2008

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This paper presents a bird_s-eye view of the major repeats and chromatin types of tomato. Using fluorescence insitu hybridization (FISH) with Cot-1, Cot-10 and Cot-100 DNA as probes we mapped repetitive sequences of different complexity on pachytene complements. Cot-100 was found to cover all heterochromatin regions, and could be used to identify repeat-rich clones in BAC filter hybridization. Next we established the chromosomal locations of the tandem and dispersed repeats with respect to euchromatin, nucleolar organizer regions (NORs), heterochromatin, and centromeres. The tomato genomic repeats TGRII and TGRIII appeared to be major components of the pericentromeres, whereas the newly discovered TGRIV repeat was found mainly in the structural centromeres. The highly methylated NOR of chromosome 2 is rich in [GACA] 4 , a microsatellite that also forms part of the pericentromeres, together with [GA] 8 , [GATA] 4 and Ty1-copia. Based on the morphology of pachytene chromosomes and the distribution of repeats studied so far, we now propose six different chromatin classes for tomato: (1) euchromatin, (2) chromomeres, (3) distal heterochromatin and interstitial heterochromatic knobs, (4) pericentromere heterochromatin, (5) functional centromere heterochromatin and (6)

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“…In comparison, maize pachytene chromosomes differ little in width between heterochromatic and euchromatic regions, and the DNA in pericentric heterochromatin is only 1.4 times as dense as that in euchromatin. Second, the pericentric heterochromatin of tomato contains a large proportion of retrotransposons and repeated sequences but also contains most of the single-copy sequences, including some genes (Peterson et al 1998;Budiman et al 2004;Chang 2004;Guyot et al 2005). Indeed, the majority (77%) of the tomato genome is located in heterochromatin.…”

Section: Chromosomal Structurementioning

confidence: 99%

Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes

Anderson

Lai²,

Stack³

et al. 2005

Genome Res.

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Examining the relationships among DNA sequence, meiotic recombination, and chromosome structure at a genome-wide scale has been difficult because only a few markers connect genetic linkage maps with physical maps. Here, we have positioned 1195 genetically mapped expressed sequence tag (EST) markers onto the 10 pachytene chromosomes of maize by using a newly developed resource, the RN-cM map. The RN-cM map charts the distribution of crossing over in the form of recombination nodules (RNs) along synaptonemal complexes (SCs, pachytene chromosomes) and allows genetic cM distances to be converted into physical micrometer distances on chromosomes. When this conversion is made, most of the EST markers used in the study are located distally on the chromosomes in euchromatin. ESTs are significantly clustered on chromosomes, even when only euchromatic chromosomal segments are considered. Gene density and recombination rate (as measured by EST and RN frequencies, respectively) are strongly correlated. However, crossover frequencies for telomeric intervals are much higher than was expected from their EST frequencies. For pachytene chromosomes, EST density is about fourfold higher in euchromatin compared with heterochromatin, while DNA density is 1.4 times higher in heterochromatin than in euchromatin. Based on DNA density values and the fraction of pachytene chromosome length that is euchromatic, we estimate that ∼1500 Mbp of the maize genome is in euchromatin. This overview of the organization of the maize genome will be useful in examining genome and chromosome evolution in plants.[Supplemental material is available online at www.genome.org.]Maize (Zea mays ssp. mays) is both a genetic model and an economically important crop. Further progress exploiting maize as a model and a crop will be greatly aided by obtaining its complete genome sequence. However, the maize genome is large (2365 Mb vs. the 450-Mb rice genome) (Rayburn et al. 1993;Messing et al. 2004) and consists of ∼60%-80% repetitive sequence (Flavell et al. 1974;Hake and Walbot 1980;Messing et al. 2004). Both of these features make sequencing and assembling the entire maize genome difficult. Methods that concentrate on sequencing the gene space promise to provide important information on genetically active regions of the maize genome (Palmer et al. 2003;Whitelaw et al. 2003;Yuan et al. 2003) but, by their very nature, will not elucidate large-scale genome organization.To date, several strategies have been used to provide insights into maize genome organization. These include the use of highdensity genetic linkage maps (Davis et al. 1999;Cone et al. 2002;Sharopova et al. 2002), methylation filtration and high C o t selection to sequence the gene space (Palmer et al. 2003;Whitelaw et al. 2003;Yuan et al. 2003), and DNA contigs constructed from overlapping BACs (Coe et al. 2002;Cone et al. 2002). Many of these BAC contigs have been anchored by genetic markers to a commonly used linkage map (IBM2 Neighbors; http:// www.maizegdb.org) and are useful both for estimatin...

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Localization of jointless-2 gene in the centromeric region of tomato chromosome 12 based on high resolution genetic and physical mapping

Cited by 59 publications

References 28 publications

Predicting and Testing Physical Locations of Genetically Mapped Loci on Tomato Pachytene Chromosome1

Predicting and Testing Physical Locations of Genetically Mapped Loci on Tomato Pachytene Chromosome1

FISH mapping and molecular organization of the major repetitive sequences of tomato

Uneven distribution of expressed sequence tag loci on maize pachytene chromosomes

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