Nucleotide variation in genes involved in wood formation in two pine species

Abstract

Summary• Nucleotide diversity in eight genes related to wood formation was investigated in two pine species, Pinus pinaster and P. radiata .• The nucleotide diversity patterns observed and their properties were compared between the two species according to the specific characteristics of the samples analysed.• A lower diversity was observed in P. radiata compared with P. pinaster . In particular, for two genes ( Pp1 , a glycin-rich protein homolog and CesA3 , a cellulose synthase) the magnitude of the reduction of diversity potentially indicates the action of nonneutral factors. For both, particular patterns of nucleotide diversity were observed in P. pinaster (high genetic differentiation for Pp1 and close to zero differentiation associated with positive Tajima's D -value for CesA3). In addition, KORRIGAN , a gene involved in cellulose-hemicellulose assembly, demonstrated a negative Tajima's D -value in P. radiata accompanied by a high genetic differentiation in P. pinaster .• The consistency of the results obtained at the nucleotide level, together with the physiological roles of the genes analysed, indicate their potential susceptibility to artificial and/or natural selection.

Contrasting relationships between the diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks

“…Interestingly, the overall diversity was of similar magnitude in their study (p ¼ 6.93 Â 10 À3 ) as in ours Diversity of candidate genes for bud burst in oaks J Derory et al (p ¼ 6.15 Â 10 À3 ). These figures are lower than those previously reported on Populus tremula (11.1 Â 10 À3 ) (Ingvarsson, 2005), but higher than in pine species, Pinus taeda (3.98 Â 10 À3 ) (Brown et al, 2004), Pinus pinaster (2.41 Â 10 À3 in Pot et al (2005); 5.51 Â 10 À3 in Eveno et al (2008)) or Pinus sylvestris (1.4 Â 10 À3 ) (Dvornyk et al, 2002) or other conifers (Gonzalez-Martinez et al, 2006;. Larger diversity in broadleaves than in conifers is also observed when comparative analysis is conducted at the level of silent polymorphism: the level of diversity in oaks (p silent ¼ 11.2 Â 10 À3 ) is higher than in earlier reports on pines (p silent ¼ 7.7 Â 10 À3 in P. sylvestris, Wachowiak et al (2009); p silent ¼ 8.6 Â 10 À3 in P. pinaster, Eveno et al (2008)).…”

Contrasting relations between diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks

“…Interestingly, the overall diversity was of similar magnitude in their study (p ¼ 6.93 Â 10 À3 ) than in ours (p ¼ 6.15 Â 10 À3 ). These figures are lower than those previously reported on Populus tremula (11.1 Â 10 À3 ) (Ingvarsson, 2005), but higher than in pine species, Pinus taeda (3.98 Â 10 À3 ) (Brown et al, 2004), Pinus pinaster (2.41 Â 10 À3 in Pot et al, 2005;5.51 Â 10 À3 in Eveno et al, 2008) or Pinus sylvestris (1.4 Â 10 À3 ) (Dvornyk et al, 2002), or other conifers (Gonzalez-Martinez et al, 2006;. Larger diversity in broadleaves than in conifers is also observed when the comparative analysis is conducted at the level of silent polymorphism: the level of diversity in oaks (p silent ¼ 11.2 Â 10 À3 ) is higher than earlier reports in pines (p silent ¼ 7.7 Â 10 À3 in P. sylvestris, Wachowiak et al, 2009; p silent ¼ 8.6 Â 10 À3 in P. pinaster, Eveno et al, 2008) Although the number of genes is still low, our results confirm earlier findings obtained with other marker systems, suggesting that oak is highly variable species (Kremer and Petit, 1993;Mariette et al, 2002).…”

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

“…As recommended in other studies, genes with a low level of polymorphism were excluded to adequately evaluate LD at the single gene level (Tenaillon et al, 2001;Wachowiak et al, 2009). Genes exhibiting a minimum of 15 pairwise site comparisons were kept (Pot et al, 2005). After applying this cutoff, 67 genes were retained for single gene analysis, which aimed at evaluating the relationship between LD and other parameters at the gene level, including nucleotide diversity, recombination, gene function and selection.…”

“…In other conifer species less displaced during the Holocene, the excess of negative Tajima's D values is not the rule. In P. pinaster populations from the Mediterranean regions and from the European Atlantic coast, and in P. taeda populations from the southeastern range of its natural distribution (in Atlantic Coastal Plain, central Florida, northern Florida, Marion County and Gulf Coast provenances), such a general skew towards negative D or H values was not observed (Pot et al, 2005;González-Martínez et al, 2006b). This trend could be an indication that these populations were less severely affected by Pleistocene glaciations and the ensuing recolonization process than boreal species.…”

“…Moreover, recombination rates observed in conifer genomes are different from those of other plant species: they are significantly lower in conifer trees (gymnosperms) than in angiosperm species, both at the genome and at the gene levels (Jaramillo-Correa et al, 2010). Studies of small gene sets have shown low-to-moderate levels of nucleotide diversity and LD decaying within gene limits in several conifer species (Brown et al, 2004;Neale and Savolainen, 2004;Pot et al, 2005;Heuertz et al, 2006;González-Martínez et al, 2006b;Pyhäjärvi et al, 2007;Wachowiak et al, 2009;Li et al, 2010;Namroud et al, 2010). Higher LD was found in Douglas fir genes with a half-decay of LD over 1 kb, on average (Eckert et al, 2009a).…”