Annotated genetic linkage maps of Pinus pinaster Ait. from a Central Spain population using microsatellite and gene based markers

Abstract

BackgroundPinus pinaster Ait. is a major resin producing species in Spain. Genetic linkage mapping can facilitate marker-assisted selection (MAS) through the identification of Quantitative Trait Loci and selection of allelic variants of interest in breeding populations. In this study, we report annotated genetic linkage maps for two individuals (C14 and C15) belonging to a breeding program aiming to increase resin production. We use different types of DNA markers, including last-generation molecular markers.ResultsWe obtained 13 and 14 linkage groups for C14 and C15 maps, respectively. A total of 211 and 215 markers were positioned on each map and estimated genome length was between 1,870 and 2,166 cM respectively, which represents near 65% of genome coverage. Comparative mapping with previously developed genetic linkage maps for P. pinaster based on about 60 common markers enabled aligning linkage groups to this reference map. The comparison of our annotated linkage maps and linkage maps reporting QTL information revealed 11 annotated SNPs in candidate genes that co-localized with previously reported QTLs for wood properties and water use efficiency.ConclusionsThis study provides genetic linkage maps from a Spanish population that shows high levels of genetic divergence with French populations from which segregating progenies have been previously mapped. These genetic maps will be of interest to construct a reliable consensus linkage map for the species. The importance of developing functional genetic linkage maps is highlighted, especially when working with breeding populations for its future application in MAS for traits of interest.

Genetic control of functional traits related to photosynthesis and water use efficiency in Pinus pinaster Ait. drought response: integration of genome annotation, allele association and QTL detection for candidate gene identification

“…Synteny and colinearity were highly conserved when compared with 654 common markers with previous studies [20, 81, 82]. Only three discrepancies were found that supposed just a 0.46% over all the common markers analyzed: Contig CT577280 was mapped in LG 7 and LG 4 in two of three obtained maps for P. pinaster in Chancerel et al [20] and it was suggested the existence of two paralogous genes for this sequence.…”

Resin tapping in Pinus pinaster: effects on growth and response function to climate

“…P. pinaster originated on, and is distributed throughout, the Iberian Peninsula, from where it spread along the mountain ranges (Gil 1991), becoming diversified in numerous populations with their own genetic characteristics (González-Martínez et al 2004;Sánchez-Gómez et al 2010;de Miguel et al 2012). The different responses to climate established for the center, the Mediterranean area and the Atlantic coast of the Iberian Peninsula (Bogino and Bravo 2008;Vieira et al 2009;Rozas et al 2009;Sánchez-Salguero et al 2010;CandelPérez et al 2012), also indicate marked differences with regard to adaptation to very diverse climate conditions, which should also be considered in ecological restoration, with seeds being selected from the regions of origin (Alia et al 1996).…”

Molecular Proxies for Climate Maladaptation in a Long-Lived Tree (Pinus pinasterAiton, Pinaceae)

“…To corroborate that historical and demographic processes were adequately accounted for, 12 nuclear microsatellites (SSRs) distributed in 8 of the 12 linkage groups of the species (Chancerel et al 2011;de-Miguel et al 2012) were genotyped following Santos-Del-Blanco et al (2012) and references therein. However, three of them (epi6, ctg275, NZPR544) were excluded from further analyses after detecting high frequencies of null alleles, which led to significant deviations from HardyWeinberg expectations in more than half of the populations (see Table S1).…”