Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. IV. Cold-hardiness QTL verification and candidate gene mapping

Wheeler, Nicholas C.; Jermstad, K. D.; Krutovsky, Konstantin V.; Aitken, Sally N.; Howe, Glenn T.; Krakowski, Jodie; Neale, David B.

doi:10.1007/s11032-004-3978-9

Cited by 55 publications

(49 citation statements)

References 40 publications

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“…Revealing the genetics of wood and growth traits in forest trees initially proceeded through mapping quantitative trait loci (QTL) (Groover et al 1994;Bradshaw and Stettler 1995;Grattapaglia et al 1996;Plomion et al 1996;Sewell et al 2000;Wheeler et al 2005;Ukrainetz et al 2008). Major QTL were identified and reported to explain up to a total of $25% of the naturally occurring variation depending on the species and the trait (Kirst et al 2004).…”

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confidence: 99%

Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression

et al. 2011

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Marker-assisted selection holds promise for highly influencing tree breeding, especially for wood traits, by considerably reducing breeding cycles and increasing selection accuracy. In this study, we used a candidate gene approach to test for associations between 944 single-nucleotide polymorphism markers from 549 candidate genes and 25 wood quality traits in white spruce. A mixed-linear model approach, including a weak but nonsignificant population structure, was implemented for each marker-trait combination. Relatedness among individuals was controlled using a kinship matrix estimated either from the known half-sib structure or from the markers. Both additive and dominance effect models were tested. Between 8 and 21 single-nucleotide polymorphisms (SNPs) were found to be significantly associated (P # 0.01) with each of earlywood, latewood, or total wood traits. After controlling for multiple testing (Q # 0.10), 13 SNPs were still significant across as many genes belonging to different families, each accounting for between 3 and 5% of the phenotypic variance in 10 wood characters. Transcript accumulation was determined for genes containing SNPs associated with these traits. Significantly different transcript levels (P # 0.05) were found among the SNP genotypes of a 1-aminocyclopropane-1-carboxylate oxidase, a b-tonoplast intrinsic protein, and a long-chain acyl-CoA synthetase 9. These results should contribute toward the development of efficient marker-assisted selection in an economically important tree species.

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Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression

et al. 2011

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“…Quantitative trait loci (QTL) mapping studies have allowed us to begin dissecting these complex traits (Jermstad et al 2001a(Jermstad et al , b, 2003Wheeler et al 2005;Carlson et al 2007). Several genomic regions responsible for genetic control of growth rhythm and cold hardiness traits were found, but QTL mapping does not reveal which individual genes are responsible for these effects.…”

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Estimation of population structure in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] using allozyme and microsatellite markers

Krutovsky

Clair

Saich

et al. 2009

Tree Genetics & Genomes

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Characterizing population structure using neutral markers is an important first step in association genetic studies in order to avoid false associations between phenotypes and genotypes that may arise from nonselective demographic factors. Population structure was studied in a wide sample of ∼1,300 coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] trees from Washington and Oregon. This sample is being used for association mapping between cold hardiness and phenology phenotypes and single-nucleotide polymorphisms in adaptive-trait candidate genes. All trees were genotyped for 25 allozyme and six simple sequence repeat (SSR) markers using individual megagametophytes. Population structure analysis was done separately for allozyme and SSR markers, as well as for both datasets combined.

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“…Fall frosts can damage actively elongating shoots in the autumn and adversely affect growth the following spring. Therefore, fall and spring cold hardiness are important adaptive traits in Douglas fir that show high genetic variation in common garden studies and vary among populations from environmentally diverse locations (reviewed in Wheeler et al 2005).…”

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confidence: 99%

“…Quantitative trait loci (QTL) mapping studies have confirmed these observations and have allowed us to begin dissecting these complex traits ( Jermstad et al 2001a( Jermstad et al ,b, 2003Wheeler et al 2005). Several genomic regions responsible for genetic control of growth rhythm and coldhardiness traits were found, but QTL mapping does not reveal which individual genes are responsible for these effects.…”

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confidence: 99%

Nucleotide Diversity and Linkage Disequilibrium in Cold-Hardiness- and Wood Quality-Related Candidate Genes in Douglas Fir

2005

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Nuclear sequence variation and linkage disequilibrium (LD) were studied in 15 cold-hardiness-and 3 wood quality-related candidate genes in Douglas fir [Pseudotsuga menziesii (Mirb.) Franco]. This set of genes was selected on the basis of its function in other plants and collocation with cold-hardiness-related quantitative trait loci (QTL). The single-nucleotide polymorphism (SNP) discovery panel represented 24 different trees from six regions in Washington and Oregon plus parents of a segregating population used in the QTL study. The frequency of SNPs was one SNP per 46 bp across coding and noncoding regions on average. Haplotype and nucleotide diversities were also moderately high with H d ¼ 0.827 6 0.043 and p ¼ 0.00655 6 0.00082 on average, respectively. The nonsynonymous (replacement) nucleotide substitutions were almost five times less frequent than synonymous ones and substitutions in noncoding regions. LD decayed relatively slowly but steadily within genes. Haploblock analysis was used to define haplotype tag SNPs (htSNPs). These data will help to select SNPs for association mapping, which is already in progress.

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Mapping of quantitative trait loci controlling adaptive traits in coastal Douglas-fir. IV. Cold-hardiness QTL verification and candidate gene mapping

Cited by 55 publications

References 40 publications

Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression

Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression

Estimation of population structure in coastal Douglas-fir [Pseudotsuga menziesii (Mirb.) Franco var. menziesii] using allozyme and microsatellite markers

Nucleotide Diversity and Linkage Disequilibrium in Cold-Hardiness- and Wood Quality-Related Candidate Genes in Douglas Fir

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