A full saturated linkage map of Picea abies including AFLP, SSR, ESTP, 5S rDNA and morphological markers

Acheré, Virginie; Faivre-Rampant, Patricia; Jeandroz, Sylvain; Besnard, Guillaume; Markussen, T.; Aragonés, Ana Cristina Márquez; Fladung, Matthias; Ritter, Enrique; Favre, Jean-Michel

doi:10.1007/s00122-004-1587-y

Cited by 44 publications

(42 citation statements)

References 55 publications

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“…This in turn can be due to chance or to differences in the heterozygosity levels of the two trees. Colinearity is generally verified between the map in [1] and the inclusive map presented here [1], thus supporting map order and chromosome consistency for codominant markers. Since a subset of SSR markers is also shared between the present map and the one by [37], it was possible to check this further pair of maps for consistency.…”

Section: Discussionmentioning

confidence: 93%

“…Maps of species belonging to the genus Picea [4,20,37] typically do not show the expected number of linkage groups, corresponding to the haploid chromosome number (n =12), despite the fact that some [37] included a number of markers comparable with those mapped in Pinus species saturated maps [12,15,43], for which 12 linkage groups were identified (an exception is the map of [1], which is based on a different mapping strategy than the others). This is perhaps due to incomplete genome coverage that may be caused by nonrandom genomic distribution of marker types.…”

Section: Introductionmentioning

confidence: 96%

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Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (Picea abies karst)

Burelli

Cattonaro

Chagné

et al. 2005

Tree Genetics & Genomes

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Scotti, I., Burelli, A., Cattonaro, F., Chagne, D., Fuller, J., Hedley, P. E., Jansson, G., Lalanne, C., Madur, D., Neale, D., Plomion, C., Powell, W., Troggio, M., Morgante, M. (2005). Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (Picea abies karst).?Tree Genetics and Genomes, 1, (3), 93-102.In order to analyze the large-scale structure of the genome of Norway spruce (Picea abies Karst.), a pseudo-testcross genetic linkage map was built using markers of six different types, belonging to the low (amplified fragment length polymorphisms, simple sequence repeats) or high (sequence-specific amplified polymorphisms, inter-retrotransposon amplified polymorphisms) copy-number fraction of the genome, and including expressed region-derived markers (expressed sequence tag polymorphisms). Twenty seven and 23 linkage groups of at least four markers were obtained for the female and the male parent maps, respectively. A subset of these linkage groups coalesced into 13 bi-parental linkage groups through markers shared between the two maps. This map was used to investigate the frequency of each marker type over chromosomes and the distribution of marker types relative to each other, using autocorrelation techniques. Our results show that, while the composition of chromosomes is homogeneous, low- and high-copy-number markers tend to occupy separate regions of the linkage groups, and that expressed sequences are preferentially associated with microsatellites and separated from retrotransposons. These results indicate that the spatial structure of Norway spruce chromosomes is not homogeneous.Peer reviewe

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Section: Discussionmentioning

confidence: 93%

Section: Introductionmentioning

confidence: 96%

Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (Picea abies karst)

Burelli

Cattonaro

Chagné

et al. 2005

Tree Genetics & Genomes

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“…However, SSR markers may be very useful for the integration of the parental maps (Achere et al 2004). In the present study, two kinds of SSR markers, genomic SSR and cDNA-SSR, were used.…”

Section: Discussionmentioning

confidence: 99%

Construction of a framework map for Pinus koraiensis Sieb. et Zucc. using SRAP, SSR and ISSR markers

Chen

Feng

Sui

et al. 2010

Trees

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Genetic linkage maps are essential for molecular breeding program. The first genetic linkage map of Pinus koraiensis, using an F1 progeny of 94 individuals, was constructed in the present paper. One hundred and twenty-two molecular markers were mapped onto 11 linkage groups, 1 triple and 8 pairs at the linkage criteria LOD 4.0. Among these markers, there were 96 sequencerelated amplified polymorphism (SRAP) markers, 25 simple sequence repeat (SSR) markers, and 1 inter-simple sequence repeat (ISSR) marker. The consensus map gained covers 857.464 cM Kosambi (K) with an average marker spacing of 7.03 cM K. The presented map provides a basis and crucial information for future genomic studies of P. koraiensis, in particular for quantitative trait loci (QTL) mapping of economically important breeding target traits.

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“…Linkage maps with comparable or greater marker densities are available for only a few additional conifers-Cryptomeria japonica D. Don (Tani et al 2003), Picea abies (L.) Karst. (Acheré et al 2004), Pinus pinaster Ait. (Ritter et al 2002), and Pinus sylvestris L. (Komulainen et al 2003).…”

Section: Introductionmentioning

confidence: 99%

High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.)

Eckert

Pande

Ersoz

et al. 2008

Tree Genetics & Genomes

125

116

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The development and application of genomic tools to loblolly pine (Pinus taeda L.) offer promising insights into the organization and structure of conifer genomes. The application of a high-throughput genotyping assay across diverse forest tree species, however, is currently limited taxonomically. This is despite the ongoing development of genome-scale projects aiming at the construction of expressed sequence tag (EST) libraries and the resequencing of EST-derived unigenes for a diverse array of forest tree species. In this paper, we report on the application of Illumina's high-throughput GoldenGate™ SNP genotyping assay to a loblolly pine mapping population. Single nucleotide polymorphisms (SNPs) were identified through resequencing of previously identified wood quality, drought tolerance, and disease resistance candidate genes prior to genotyping. From that effort, a 384 multiplexed SNP assay was developed for high-throughput genotyping. Approximately 67% of the 384 SNPs queried converted into high-quality genotypes for the 48 progeny samples. Of those 257 successfully genotyped SNPs, 70 were segregating within the mapping population. A total of 27 candidate genes were subsequently mapped onto the existing loblolly pine consensus map, which consists of 12 linkage groups spanning a total map distance of 1,227.6 cM. The ability of SNPs to be mapped to the same position as fragment-based markers previously developed within the same candidate genes, as well as the pivotal role that SNPs currently play in the dissection of complex phenotypic traits, illustrate the usefulness of high-throughput SNP genotyping technologies to the continued development of pine genomics.

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A full saturated linkage map of Picea abies including AFLP, SSR, ESTP, 5S rDNA and morphological markers

Cited by 44 publications

References 55 publications

Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (Picea abies karst)

Analysis of the distribution of marker classes in a genetic linkage map: a case study in Norway spruce (Picea abies karst)

Construction of a framework map for Pinus koraiensis Sieb. et Zucc. using SRAP, SSR and ISSR markers

High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.)

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