Comparative physical mapping reveals features of microsynteny between Glycine max, Medicago truncatula, and Arabidopsis thaliana

To gain insight into genomic relationships between soybean (Glycine max) and Medicago truncatula, eight groups of bacterial artificial chromosome (BAC) contigs, together spanning 2.60 million base pairs (Mb) in G. max and 1.56 Mb in M. truncatula, were compared through high-resolution physical mapping combined with sequence and hybridization analysis of low-copy BAC ends. Cross-hybridization among G. max and M. truncatula contigs uncovered microsynteny in six of the contig groups and extensive microsynteny in three. Between G. max homoeologous (within genome duplicate) contigs, 85% of coding and 75% of noncoding sequences were conserved at the level of cross-hybridization. By contrast, only 29% of sequences were conserved between G. max and M. truncatula, and some kilobase-scale rearrangements were also observed. Detailed restriction maps were constructed for 11 contigs from the three highly microsyntenic groups, and these maps suggested that sequence order was highly conserved between G. max duplicates and generally conserved between G. max and M. truncatula. One instance of homoeologous BAC contigs in M. truncatula was also observed and examined in detail. A sequence similarity search against the Arabidopsis thaliana genome sequence identified up to three microsyntenic regions in A. thaliana for each of two of the legume BAC contig groups. Together, these results confirm previous predictions of one recent genome-wide duplication in G. max and suggest that M. truncatula also experienced ancient large-scale genome duplications.Key words: Glycine max, Medicago truncatula, Arabidopsis thaliana, conserved microsynteny, genome duplication.

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Genetic and Physical Mapping of the RPP13 Locus, in Arabidopsis, Responsible for Specific Recognition of Several Peronospora parasitica (Downy Mildew) Isolates

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.1999.12.9.792 ◽

1999 ◽

Vol 12 (9) ◽

pp. 792-802 ◽

Cited By ~ 28

Author(s):

Peter Bittner-Eddy ◽

Canan Can ◽

Nick Gunn ◽

Matthieu Pinel ◽

Mahmut Tör ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Bacterial Artificial Chromosome ◽

Downy Mildew ◽

Physical Mapping ◽

Single Gene ◽

Artificial Chromosome ◽

Chromosome 3 ◽

Peronospora Parasitica ◽

Bac Contig ◽

Recognition Capability

Fifteen isolates of the biotrophic oomycete Peronospora parasitica (downy mildew) were obtained from a population of Arabidopsis thaliana plants that established naturally in a garden the previous year. They exhibited phenotypic variation in a set of 12 Arabidopsis accessions that suggested that the parasite population consisted of at least six pathotypes. One isolate, Maks9, elicited an interaction phenotype of flecking necrosis and no sporulation (FN) in the Arabidopsis accession Nd-1, and more extensive pitting necrosis with no sporulation (PN) in the accession Ws-2. RPP13 was designated as the locus for a single dominant resistance gene associated with the resistance in Nd-1 and mapped to an interval of approximately 60 kb on a bacterial artificial chromosome (BAC) contig on the lower arm of chromosome 3. This locus is approximately 6 cM telomeric to RPP1, which was previously described as the locus for the PN interaction with five Peronospora isolates, including resistance to Maks9 in Ws-2. New Peronospora isolates were obtained from four other geographically distinct populations of P. parasitica. Four isolates were characterized that elicited an FN phenotype in Nd-1 and mapped resistance to the RPP13 locus. This suggests that the RPP13 locus contains either a single gene capable of multiple isolate recognition or a group of tightly linked genes. Further analysis suggests that the RPP11 gene in the accession Rld-0 may be allelic to RPP13 but results in a different recognition capability.

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An integrated physical, genetic and cytogenetic map around the sunn locus of Medicago truncatula

Genome ◽

10.1139/g03-019 ◽

2003 ◽

Vol 46 (4) ◽

pp. 665-672 ◽

Cited By ~ 19

Author(s):

E Schnabel ◽

O Kulikova ◽

R V Penmetsa ◽

T Bisseling ◽

D R Cook ◽

...

Keyword(s):

Genetic Distance ◽

Medicago Truncatula ◽

Genetic Map ◽

Sinorhizobium Meliloti ◽

Chromosome Region ◽

Single Gene ◽

Artificial Chromosome ◽

Cytogenetic Map ◽

Bac Contig ◽

Group 4

The sunn mutation of Medicago truncatula is a single-gene mutation that confers a novel supernodulation phenotype in response to inoculation with Sinorhizobium meliloti. We took advantage of the publicly available codominant PCR markers, the high-density genetic map, and a linked cytogenetic map to define the physical and genetic region containing sunn. We determined that sunn is located at the bottom of linkage group 4, where a fine-structure genetic map was used to place the locus within a ~400-kb contig of bacterial artificial chromosome (BAC) clones. Genetic analyses of the sunn contig, as well as of a second, closely linked BAC contig designated NUM1, indicate that the physical to genetic distance within this chromosome region is in the range of 1000 1100 kb·cM1. The ratio of genetic to cytogenetic distance determined across the entire region is 0.3 cM·μm1. These estimates are in good agreement with the empirically determined value of ~300 kb·μm1 measured for the NUM1 contig. The assignment of sunn to a defined physical interval should provide a basis for sequencing and ultimately cloning the responsible gene.Key words: FISH, physical to genetic distance, Medicago truncatula, map-based cloning.

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Fractionation of Synteny in a Genomic Region Containing Tandemly Duplicated Genes across Glycine max, Medicago truncatula, and Arabidopsis thaliana

Journal of Heredity ◽

10.1093/jhered/esn010 ◽

2008 ◽

Vol 99 (4) ◽

pp. 390-395 ◽

Cited By ~ 21

Author(s):

J. A. Schlueter ◽

B. E. Scheffler ◽

S. Jackson ◽

R. C. Shoemaker

Keyword(s):

Arabidopsis Thaliana ◽

Glycine Max ◽

Medicago Truncatula ◽

Genomic Region ◽

Duplicated Genes

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Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana

Theoretical and Applied Genetics ◽

10.1007/s00122-002-1183-y ◽

2003 ◽

Vol 106 (7) ◽

pp. 1256-1265 ◽

Cited By ~ 44

Author(s):

H. H. Yan ◽

J. Mudge ◽

D.-J. Kim ◽

D. Larsen ◽

R. C. Shoemaker ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Glycine Max ◽

Medicago Truncatula

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Comparative Fluorescence in Situ Hybridization Mapping of a 431-kb Arabidopsis thaliana Bacterial Artificial Chromosome Contig Reveals the Role of Chromosomal Duplications in the Expansion of the Brassica rapa Genome

Genetics ◽

10.1093/genetics/156.2.833 ◽

2000 ◽

Vol 156 (2) ◽

pp. 833-838 ◽

Cited By ~ 7

Author(s):

Scott A Jackson ◽

Zhukuan Cheng ◽

Ming Li Wang ◽

Howard M Goodman ◽

Jiming Jiang

Keyword(s):

Arabidopsis Thaliana ◽

In Situ Hybridization ◽

Fluorescence In Situ Hybridization ◽

Brassica Rapa ◽

Physical Mapping ◽

Large Scale ◽

Repetitive Sequences ◽

Comparative Genome ◽

Artificial Chromosomes

Abstract Comparative genome studies are important contributors to our understanding of genome evolution. Most comparative genome studies in plants have been based on genetic mapping of homologous DNA loci in different genomes. Large-scale comparative physical mapping has been hindered by the lack of efficient and affordable techniques. We report here the adaptation of fluorescence in situ hybridization (FISH) techniques for comparative physical mapping between Arabidopsis thaliana and Brassica rapa. A set of six bacterial artificial chromosomes (BACs) representing a 431-kb contiguous region of chromosome 2 of A. thaliana was mapped on both chromosomes and DNA fibers of B. rapa. This DNA fragment has a single location in the A. thaliana genome, but hybridized to four to six B. rapa chromosomes, indicating multiple duplications in the B. rapa genome. The sizes of the fiber-FISH signals from the same BACs were not longer in B. rapa than those in A. thaliana, suggesting that this genomic region is duplicated but not expanded in the B. rapa genome. The comparative fiber-FISH mapping results support that chromosomal duplications, rather than regional expansion due to accumulation of repetitive sequences in the intergenic regions, played the major role in the evolution of the B. rapa genome.

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Comparative Genomics of Glycine max, Medicago truncatula, Other Legumes, and Arabidopsis thaliana

Legume Crop Genomics ◽

10.1201/9781439822265.ch9 ◽

2004 ◽

Author(s):

Nevin Dale Young

Keyword(s):

Arabidopsis Thaliana ◽

Glycine Max ◽

Comparative Genomics ◽

Medicago Truncatula

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Comparative genomic analysis of sequences sampled from a small region on soybean (Glycine max) molecular linkage group G

Genome ◽

10.1139/g02-027 ◽

2002 ◽

Vol 45 (4) ◽

pp. 634-645 ◽

Cited By ~ 25

Author(s):

Dawn Foster-Hartnett ◽

Joann Mudge ◽

Dana Larsen ◽

Dariush Danesh ◽

Huihuang Yan ◽

...

Keyword(s):

Glycine Max ◽

Linkage Group ◽

Large Scale ◽

Repetitive Sequences ◽

Comparative Genomic ◽

Sequence Comparisons ◽

Cross Hybridization ◽

Molecular Linkage Group ◽

Artificial Chromosomes ◽

Bac Clones

Eight DNA markers spanning an interval of approximately 10 centimorgans (cM) on soybean (Glycine max) molecular linkage group G (MLG-G) were used to identify bacterial artificial chromosome (BAC) clones. Twenty-eight BAC clones in eight distinct contiguous groups (contigs) were isolated from this genome region, along with 59 BAC clones on 17 contigs homoeologous to those on MLG-G. BAC clones in four of the MLG-G contigs were also digested to produce subclones and detailed physical maps. All of the BAC-ends were sequenced, as were the subclones, to estimate proportions in different sequence categories, compare similarities among homoeologs, and explore microsynteny with Arabidopsis. Homoeologous BAC contigs were enriched in repetitive sequences compared with those on MLG-G or the soybean genome as a whole. Fingerprint and cross-hybridization comparisons between MLG-G and homoeologous contigs revealed cases of highly similar physical organization between soybean duplicates, as did DNA sequence comparisons. Twenty-seven out of 78 total sequences on soybean MLG-G showed significant similarity to Arabidopsis. The homologs mapped to six compact genome segments in Arabidopsis, with the longest containing seven homologs spanning two million base pairs. These results extend previous observations of large-scale duplication and selective gene loss in Arabidopsis, suggesting that networks of conserved synteny between Arabidopsis and other angiosperm families can stretch over long physical distances.Key words: Arabidopsis thaliana, bacterial artificial chromosomes, Glycine max, microsynteny.

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