Species-diagnostic markers in <Emphasis Type="Italic">Larix</Emphasis> spp. based on RAPDs and nuclear,cpDNA, and mtDNA gene sequences,and their phylogenetic implications |
| |
Authors: | Marie-Claude?Gros-Louis Jean?Bousquet Luc?E?Paques Email author" target="_blank">Nathalie?IsabelEmail author |
| |
Institution: | (1) Chaire de recherche du Canada en génomique forestière et environnementale and Centre de recherche en biologie forestière, Pavillon Charles-Eugène-Marchand, Université Laval, Ste-Foy, Québec, G1K 7P4, Canada;(2) Ressources naturelles Canada, Service canadien des forêts, Centre de foresterie des Laurentides, 1055 du P.E.P.S., P.O. Box 3800, Ste-Foy, Québec, G1V 4C7, Canada;(3) INRA, Station d'Amélioration des Arbres Forestiers, rue de la Pomme de Pin, Olivet, Cedex, 45160, France |
| |
Abstract: | Genetic markers from the nuclear, chloroplast, and mitochondrial genomes were developed to distinguish unambiguously among
four larch species Larix laricina (Du Roi) K. Koch, Larix decidua (Mill.), Larix kaempferi (Lamb.) Sarg., and Larix sibirica (Ledeb.)] used in intensive forestry in eastern North America. Nine random amplified polymorphic DNA (RAPD) fragments had
good diagnostic value, and 3 out of 12 nuclear genes were found to harbor fixed interspecific polymorphisms implicating a
total of 17 single nucleotide polymorphisms (SNPs) and 2 indels. The sequencing of five mtDNA introns (cox1-intron1, matR-intron1, nad1-intron b/c, nad3-intron1, and nad5-intron1) and four cpDNA regions (matK, trnL-intron, trnT–trnL and trnL–trnF intergenic spacers) resulted in the identification of 14 sites with fixed interspecific differences among the four species.
Including the ten Larix species, one polymorphic site per 47 nucleotide sites sampled was observed for nuclear genes, one per 283 sites for cpDNA,
and one per 374 sites for mtDNA. The phylogeny of the genus could be estimated from variation among the ten species detected
in two cpDNA intergenic regions and four mtDNA introns. There was congruence between cpDNA and mtDNA phylogenies with three
large groups delineated: the North American, North Eurasian, and South Asian taxa. The position of L. sibirica differed between organelle genomes. It was regrouped with South Asian species on the cpDNA tree, but with its North Eurasian
congenerics on the mtDNA tree. To simplify the detection of diagnostic DNA sequence polymorphisms among the four main Larix species, cleaved amplified polymorphic sequence (CAPS) assays were developed from the polymorphisms identified in the various
genomes. Seventeen primer–enzyme combinations were tested, and six were selected for their high level of informativeness.
These new species-specific diagnostic markers should be useful for the certification of larch breeding materials and hybrid
stocks used in intensive forestry in the northern hemisphere. |
| |
Keywords: | ESTP Hybrids Larix Genetic identity Genetic fingerprint cpDNA mtDNA Phylogeny RAPD |
本文献已被 SpringerLink 等数据库收录! |
|