Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

Zhu, Wei; Ouyang, Shuai; Iovene, Marina; O’Brien, Kimberly; Vuong, Hue; Jiang, Jiming; Buell, C. Robin

doi:10.1186/1471-2164-9-286

Cited by 38 publications

(28 citation statements)

References 65 publications

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“…The expected phenotypic mean values were calculated from the allele substitution effects as well as the bi-, tri-, and tetragenic interaction effects, which were calculated on the basis of the mixed-model described in materials and methods comprising both markers simultaneously. whole genome sequence of potato (Zhu et al 2008) (www.potatogenome.net) will facilitate further research on this topic.…”

Section: R3bmentioning

confidence: 99%

Single Nucleotide Polymorphisms in the Allene Oxide Synthase 2 Gene Are Associated With Field Resistance to Late Blight in Populations of Tetraploid Potato Cultivars

et al. 2009

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The oomycete Phytophthora infestans causes late blight, the most relevant disease of potato (Solanum tuberosum) worldwide. Field resistance to late blight is a complex trait. When potatoes are cultivated under long day conditions in temperate climates, this resistance is correlated with late plant maturity, an undesirable characteristic. Identification of natural gene variation underlying late blight resistance not compromised by late maturity will facilitate the selection of resistant cultivars and give new insight in the mechanisms controlling quantitative pathogen resistance. We tested 24 candidate loci for association with field resistance to late blight and plant maturity in a population of 184 tetraploid potato individuals. The individuals were genotyped for 230 single nucleotide polymorphisms (SNPs) and 166 microsatellite alleles. For association analysis we used a mixed model, taking into account population structure, kinship, allele substitution and interaction effects of the marker alleles at a locus with four allele doses. Nine SNPs were associated with maturity corrected resistance (P , 0.001), which collectively explained 50% of the genetic variance of this trait. A major association was found at the StAOS2 locus encoding allene oxide synthase 2, a key enzyme in the biosynthesis of jasmonates, plant hormones that function in defense signaling. This finding supports StAOS2 as being one of the factors controlling natural variation of pathogen resistance.

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Section: R3bmentioning

confidence: 99%

Single Nucleotide Polymorphisms in the Allene Oxide Synthase 2 Gene Are Associated With Field Resistance to Late Blight in Populations of Tetraploid Potato Cultivars

et al. 2009

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“…Whereas, comparative mapping among close species by BAC-FISH does not rely on mapping group and polymorphism, and the effective fragments are larger, then the homologous or rearrangement found were greater. Therefore, based on the physical comparative mapping by using FISH, chromosome rearrangement and collinearity between Arabidopsis and Brassica (Howell et al, 2005;Ziolkowski and Sadowski, 2002), tomato and potato Szinay et al, 2008;Zhu et al, 2008), Oryza genus and Sorghum genus (Hass-Jacobus et al, 2006) were revealed, which provided information of systematic development and evolution research. In the present study, the corresponding locations between D genome and D subgenome as well as within D genomes indicated a conserved collinearity relationship.…”

Section: Comparative Analysis Of Bacs In Different Cottonmentioning

confidence: 99%

Individual chromosome identification, chromosomal collinearity and genetic-physical integrated map in <i>Gossypium darwinii</i> and four D genome cotton species revealed by BAC-FISH

et al. 2012

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The study was conducted on the individual chromosome identification in Gossypium darwinii (A d ) were found switched. The SSR marker in the middle of linkage group 04 was corrected at nearby the end of chromosome 04 by FISH. The study will be helpful to establish a theoretical basis using the wild gene bank to exploit more genes aiming for cotton breeding and will provide powerful evidences both for the evolution of Gossypium and assembling the sequences of the obtained and as well the on-going whole genome sequencing projects of cotton.D

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“…Several molecular marker-based genetic linkage maps of diploid potato were developed (Bonierbale et al 1988;Gebhardt et al 1989Gebhardt et al , 1991Tanksley et al 1992;Jacobs et al 1995), including a 10,000-marker ultradense map that represents one of the densest genetic maps in any eukaryote (van Os et al 2006). Other resources for genomics research have also been developed, including expressed sequence tags (ESTs) (Ronning et al 2003;Flinn et al 2005), bacterial artificial chromosome (BAC) libraries Zhang et al 2003;Chen et al 2004), and BAC end sequences (Zhu et al 2008). An international potato genome sequencing consortium has been established recently (http:/ /potatogenome.net) that will make potato one of few major crop species whose genome will be sequenced using a BAC-by-BAC-based approach.…”

mentioning

confidence: 99%

Chromatin Structure and Physical Mapping of Chromosome 6 of Potato and Comparative Analyses With Tomato

et al. 2008

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Potato (Solanum tuberosum) has the densest genetic linkage map and one of the earliest established cytogenetic maps among all plant species. However, there has been limited effort to integrate these maps. Here, we report fluorescence in situ hybridization (FISH) mapping of 30 genetic marker-anchored bacterial artificial chromosome (BAC) clones on the pachytene chromosome 6 of potato. The FISH mapping results allowed us to define the genetic positions of the centromere and the pericentromeric heterochromatin and to relate chromatin structure to the distribution of recombination along the chromosome. A drastic reduction of recombination was associated with the pericentromeric heterochromatin that accounts for 28% of the physical length of the pachytene chromosome. The pachytene chromosomes 6 of potato and tomato (S. lycopersicum) share a similar morphology. However, distinct differences of heterochromatin distribution were observed between the two chromosomes. FISH mapping of several potato BACs on tomato pachytene chromosome 6 revealed an overall colinearity between the two chromosomes. A chromosome inversion was observed in the euchromatic region of the short arms. These results show that the potato and tomato genomes contain more chromosomal rearrangements than those reported previously on the basis of comparative genetic linkage mapping.

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Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition

Cited by 38 publications

References 65 publications

Single Nucleotide Polymorphisms in the Allene Oxide Synthase 2 Gene Are Associated With Field Resistance to Late Blight in Populations of Tetraploid Potato Cultivars

Single Nucleotide Polymorphisms in the Allene Oxide Synthase 2 Gene Are Associated With Field Resistance to Late Blight in Populations of Tetraploid Potato Cultivars

Individual chromosome identification, chromosomal collinearity and genetic-physical integrated map in <i>Gossypium darwinii</i> and four D genome cotton species revealed by BAC-FISH

Chromatin Structure and Physical Mapping of Chromosome 6 of Potato and Comparative Analyses With Tomato

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