Nucleotide diversity and linkage disequilibrium in Populus nigra cinnamyl alcohol dehydrogenase (CAD4) gene

Abstract

Cinnamyl alcohol dehydrogenase (CAD) is involved in the biosynthesis of lignin, a component of plant cell wall which negatively impacts paper pulp processing and biomass fermentation to ethanol. Transgenic poplars with depressed CAD activity show structural alterations of lignin. Natural CAD mutants have been identified in several plants; however, no natural CAD mutants have been identified in poplar. We surveyed the natural genetic variation in CAD4, a gene coding for CAD, in 360 poplar trees from Western Europe. We measured linkage disequilibrium (LD) between single-nucleotide polymorphisms (SNPs), performed neutrality tests and estimated diversity indexes, and investigated their dependence from sample size. We identified 45 SNPs, six of which caused an amino acid substitution. Our results suggest a short span of LD in Populus nigra CAD4 gene. We identified carriers of different nonsynonymous SNPs in CAD4; those subjects are candidate to be used in classical breeding programs to obtain carriers of different combinations of functional polymorphisms. We showed that use of small sample size might lead to biased estimates of LD, neutrality tests, and diversity indexes.

Single nucleotide polymorphisms in a cellulose synthase gene (PtoCesA3) are associated with growth and wood properties in Populus tomentosa

“…The comparison suggested that these candidate genes may have a similar pattern of genetic variance in the natural populations of P. tomentosa. Compared with other species within the genus Populus, the nucleotide diversity at the PtoCesA3 in our study was notably higher than that in P. trichocarpa (p T = 0.0018; Gilchrist et al 2006), P. tremula (p T = 0.0042; Ingvarsson et al 2008), P. balsamifera (p T = 0.0028, Olson et al 2010), and P. nigra (p T = 0.0012, Marroni et al 2011). The variation in nucleotide diversity detected among Populus species may be due to many factors, such as demographic history, differences in sampling or genetic background, recombination rate, gene conversion, or selection intensity (Olson et al 2010;Zhang et al 2011).…”

Allelic Variation in Cinnamyl Alcohol Dehydrogenase (LoCAD) Associated with Wood Properties of Larix olgensis

“…This result suggests the action of purifying selection on exonic regions is directly linked to the primary structure of the protein. Compared with previous reports on other genes detected in forest tree species, the nucleotide diversity (π was 0.00622) of L. olgensis was higher than that of CAD4 (π was 0.0012) in Populus nigra and nine different genes (π was 0.0018)in Populus trichocarpa [21,43], somewhat lower than that of PtoCesA7 (π was 0.0091) [44] and PtGA20Ox (π was 0.0099) [45], and similar to that of PtACT1 (π was 0.0079) [35] and PtCOBL4 (π was 0.0080) [46]. This suggested that a similar pattern of genetic variance exists in LoCAD, similar to the candidate genes in Populus.…”

“…The consensus sequence GD(X)9,10C(X)2C(X)2C(X)7C for binding the Zn-2 metal ion is preserved in LoCAD. In addition, 12 amino acids have been identified as substrate-binding residues in the bona fide CADs of various plant species [20,21,[37][38][39][40]. Among the CAD in L. olgensis, LoCAD contains nine of these 12 conserved residues.…”

“…Due to its important role in determining lignin content and composition, the involvement of CAD in lignin biosynthesis has been studied in several plant species, including dicot and monocot plants and coniferous species [8,[16][17][18][19][20][21][22][23]. The CAD genes belong to small multigene families.…”

Genome-wide association studies identified novel loci for non-high-density lipoprotein cholesterol and its postprandial lipemic response

“…The observed variations in LD measures (D′ → 1, r 2 → 0) may be explained by low MAF of the lead SNP (Marroni et al 2011; Muller 2004; Hedrick and Kumar 2001). We took advantage of the larger FamHS data, compared the unconditional model (rs3768725 only) against conditional model (rs3768725 and rs6544903) using a likelihood ratio test, and found support for partial dependence of rs3768725 on rs6544903 (χ 2 = 4.1, df = 1, p = 0.04; data not shown in Results).…”