Insights into Conifer Giga-Genomes

Torre, Amanda R. De La; Birol, İnanç; Bousquet, Jean; Ingvarsson, Pär K.; Jansson, Stefan; Jones, Steven J.M.; Keeling, Christopher I.; Mackay, John; Nilsson, Ove; Ritland, Kermit; Street, Nathaniel R.; Yanchuk, Alvin D.; Zerbe, Philipp; Bohlmann, Jörg

doi:10.1104/pp.114.248708

Cited by 153 publications

(123 citation statements)

References 75 publications

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“…Conifers dominate approximately 39% of world forests and play an important role in forestry-dependent economics and global ecosystems (e.g., carbon capture, the diversity of native habitat, and erosion control/water quality) [1,2]. They comprise 69 genera, representing approximately 614 known species [3][4][5].…”

Section: Introductionmentioning

confidence: 99%

Assessing 62 Chinese Fir (Cunninghamia lanceolata) Breeding Parents in a 12-Year Grafted Clone Test

Zheng

Wang

et al. 2015

Forests

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Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is one of the major commercial conifer species in China. The present study concentrated on the assessment of growth, wood property traits, and strobili number in a 12-year grafted clone test of 62 Chinese fir breeding parents, aiming to describe the variation and correlations between these traits and to identify parent clones with the highest potential for future breeding. The results indicate that all of the growth (height, diameter at breast height, stem volume, crown-width) and wood property (wood basic density and hygroscopicity) traits varied significantly (p < 0.01) among clones, with coefficients of variation ranging from 7.6% to 30.6%. Furthermore, these traits consistently had a moderate to high (0.39-0.87) repeatability estimate (broad-sense heritability). Remarkable clonal differences were also observed for the production of male and female strobili. Phenotypic correlations among growth traits were strong (p < 0.01) and positive. Significantly negative correlations (p < 0.01 or 0.05) were found between wood basic density and growth (except for height) and hygroscopicity. The production of male and female strobili appeared to be significantly (p < 0.01) positively correlated with each other. A notable number of faster-growing parent clones were identified (n = 30); 11 of these had higher density wood with an average realized gain of 10.5% in diameter, and a 5.4% gain in wood basic density. When selection was made for growth and strobili, 10 faster-growing parent clones with medium to high production of female strobili were identified. OPEN ACCESSForests 2015, 6 3800

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Section: Introductionmentioning

confidence: 99%

Assessing 62 Chinese Fir (Cunninghamia lanceolata) Breeding Parents in a 12-Year Grafted Clone Test

Zheng

Wang

et al. 2015

Forests

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“…1). Given the different levels of gene space coverage of the various transcriptome data and the highly fragmented nature of conifer genome assemblies (De La Torre et al, 2014;Warren et al, 2015), the CYP720Bs found in the six different species almost certainly represent only subsets of the complete CYP720B subfamily in each of these species. Nonetheless, they provide a multispecies topography of this apparently gymnosperm-specific (or perhaps conifer-specific) group of P450s (Fig.…”

Section: Discovery Annotation and Phylogeny Of Cyp720bs In Six Diffmentioning

confidence: 99%

Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products

et al. 2016

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Cytochrome P450 enzymes of the CYP720B subfamily play a central role in the biosynthesis of diterpene resin acids (DRAs), which are a major component of the conifer oleoresin defense system. CYP720Bs exist in families of up to a dozen different members in conifer genomes and fall into four different clades (I-IV). Only two CYP720B members, loblolly pine (Pinus taeda) PtCYP720B1 and Sitka spruce (Picea sitchensis) PsCYP720B4, have been characterized previously. Both are multisubstrate and multifunctional clade III enzymes, which catalyze consecutive three-step oxidations in the conversion of diterpene olefins to DRAs. These reactions resemble the sequential diterpene oxidations affording ent-kaurenoic acid from ent-kaurene in gibberellin biosynthesis. Here, we functionally characterized the CYP720B clade I enzymes CYP720B2 and CYP720B12 in three different conifer species, Sitka spruce, lodgepole pine (Pinus contorta), and jack pine (Pinus banksiana), and compared their activities with those of the clade III enzymes CYP720B1 and CYP720B4 of the same species. Unlike the clade III enzymes, clade I enzymes were ultimately found not to be active with diterpene olefins but converted the recently discovered, unstable diterpene synthase product 13-hydroxy-8(14)-abietene. Through alternative routes, CYP720B enzymes of both clades produce some of the same profiles of conifer oleoresin DRAs (abietic acid, neoabietic acid, levopimaric acid, and palustric acid), while clade III enzymes also function in the formation of pimaric acid, isopimaric acid, and sandaracopimaric acid. These results highlight the modularity of the specialized (i.e. secondary) diterpene metabolism, which produces conifer defense metabolites through variable combinations of different diterpene synthase and CYP720B enzymes.

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“…(Nystedt et al, 2013), white spruce (P. glauca (Moench) Voss) (Birol et al, 2013) and loblolly pine (Pinus taeda L.) (Neale et al, 2014), have been sequenced for their giga-genomes. However, whole genome sequencing of a conifer population is still unaffordable because of its dramatic cost and analytical effort (Du et al, 2012;De La Torre et al, 2014). Thus, alternative strategies for large-scale SNP detection in conifer are highly required.…”

Section: Introductionmentioning

confidence: 99%

Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)

Shu

Zheng

2016

Dendrobiology

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Compared to angiosperms, conifers represent more complex genomes with larger giga-genome size. To detect large-scale single nucleotide polymorphisms (SNPs), whole genome sequencing of a conifer population is still unaffordable. In this work, we report the use of DNA specific-locus amplified fragment sequencing (SLAF-seq) for large-scale SNP detection in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook), an ecological and economic important conifer in China. SLAF libraries of 18 parent clones of a Chinese fir 2.5 generation seed orchard were sequenced and a total of 117,924 SLAFs were developed. We detected 147,376 SNPs from these SLAFs; 146,231 of them represented simple nucleotide change in A/G, C/T, A/C, A/T, C/G or G/T. The most frequent SNPs occurred in C/T (34.3%), while the majority of SNPs (68.2%) belonged to transition events (A/G and C/T). Notably, all the sequenced samples had high portion (78.2-80.9%) of common SNPs indicating that the Chinese fir genomes tended to change its nucleotides at common loci. 48,406 informative SNPs were then successfully utilized to genotype the tested samples (n = 18) followed by a phylogenetic tree to clarify their genetic relationship. Furthermore, a set of very high linkage disequilibrium (0.51-1.00) were identified from these informative SNPs. In brief, our work demonstrated that SLAF-seq is an alternative and cost-effectively high-throughput approach for large-scale SNP exploitation in Chinese fir. While the obtained SNPs offer useful marker resource for further genetic and genomic studies and will be helpful for Chinese fir breeding programs.

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Insights into Conifer Giga-Genomes

Cited by 153 publications

References 75 publications

Assessing 62 Chinese Fir (Cunninghamia lanceolata) Breeding Parents in a 12-Year Grafted Clone Test

Assessing 62 Chinese Fir (Cunninghamia lanceolata) Breeding Parents in a 12-Year Grafted Clone Test

Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products

Detection of SNPs based on DNA specific-locus amplified fragment sequencing in Chinese fir (Cunninghamia lanceolata (Lamb.) Hook)

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