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Genetic linkage maps of Populus nigra L. including AFLPs, SSRs, SNPs, and sex trait

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Abstract

Black poplar (Populus nigra L.) is a tree of ecological and economic interest. A better knowledge of P. nigra genome is needed for an effective protection and use of its genetic resources. The main objective of this study is the construction of a highly informative genetic map of P. nigra species including genes of adaptive and economic interest. Two genotypes originated from contrasted natural Italian populations were crossed to generate a F1 mapping pedigree of 165 individuals. Amplification fragment length polymorphism (AFLP), simple sequence repeat (SSR), and single nucleotide polymorphism (SNP) markers were used to genotype 92 F1 individuals, and the pseudo-test-cross strategy was applied for linkage analysis. The female parent map included 368 markers (274 AFLPs, 91 SSRs, and 3 SNPs) and spanned 2,104 cM with 20 linkage groups, and the male parent map, including 317 markers (205 AFLPs, 106 SSRs, 5 SNPs, and sex trait), spanned 2,453 cM with 23 main linkage groups. The sex, as morphological trait, was mapped on the linkage group XIX of the male parent map. The generated maps are among the most informative in SSRs when compared to the Populus maps published so far and allow a complete alignment with the 19 haploid chromosomes of Populus sequence genome. These genetic maps provide informative tools for a better understanding of P. nigra genome structure and genetic improvement of this ecologically and economically important European tree species.

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Acknowledgment

The authors thank G. Zaina and M. Morgante for providing the sequence of the SNPs and A. G. Fara for the laboratory analysis of the SNP markers. This work was supported by grants from the European Project QLK5-CT-2002-00953 (POPYOMICS).

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Correspondence to M. Sabatti.

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Communicated by W. Boerjan

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ESM S1

AFLP primer combination code with selective nucleotides at the 3’ end of the E (EcoRI) primer (2 nucleotides) and the M (MseI) primer (3 nucleotides) respectively. (DOC 47 Kb)

ESM S2

Marker description of each linkage group of the female (♀) and male (♂)map. The number of total markers mapped (N i ), the number of each sort of markers (AFLP, SSR, SNP, sex trait (S)), framework markers, and distorted markers (p ≤ 0.05) are presented. The number (∑N.j ) of significant (α ≤ 0.05) clustered and dispersed markers with the proportion (L i %) of the corresponding region relative to the linkage group length (L i ) are also reported (see “Materials and methods” and Electronic Supplementary Materials S3 for details). (DOC 63 Kb)

ESM S3

Significant clustered and dispersed region on each linkage group in the female and male map. (DOC 82 Kb)

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Gaudet, M., Jorge, V., Paolucci, I. et al. Genetic linkage maps of Populus nigra L. including AFLPs, SSRs, SNPs, and sex trait. Tree Genetics & Genomes 4, 25–36 (2008). https://doi.org/10.1007/s11295-007-0085-1

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