A genome‐wide SNP genotyping resource for tropical pine tree species

Jackson, Colin; Christie, Nanette; Reynolds, Sharon Melissa; Marais, Christopher; Tii-Kuzu, Yokateme; Caballero, Madison; Kampman, Tamanique; Visser, Erik A.; Naidoo, Sanushka; Kain, Dominic; Whetten, Ross; Isik, Fikret; Wegrzyn, Jill; Hodge, Gary R.; Acosta, Juan J.; Myburg, Alexander Andrew

doi:10.1111/1755-0998.13484

Cited by 12 publications

(10 citation statements)

References 70 publications

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“…More than 45% of SNPs are within the PHR category, which are considered the most informative markers. This highlights the benefit of prior evaluation of candidate SNPs on a screening array, similar to what has been reported by other conifer groups [27,42,43] where conversion rates have improved from 39% on the screening array to 96% on the genotyping array.…”

Section: Performance Of the Genotyping Arraysupporting

confidence: 79%

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Development and Validation of a 36K SNP Array for Radiata Pine (Pinus radiata D.Don)

Graham

Telfer

Frickey

et al. 2022

Forests

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Radiata pine (Pinus radiata D.Don) is one of the world’s most domesticated pines and a key economic species in New Zealand. Thus, the development of genomic resources for radiata pine has been a high priority for both research and commercial breeding. Leveraging off a previously developed exome capture panel, we tested the performance of 438,744 single nucleotide polymorphisms (SNPs) on a screening array (NZPRAD01) and then selected 36,285 SNPs for a final genotyping array (NZPRAD02). These SNPs aligned to 15,372 scaffolds from the Pinus taeda L. v. 1.01e assembly, and 20,039 contigs from the radiata pine transcriptome assembly. The genotyping array was tested on more than 8000 samples, including material from archival progenitors, current breeding trials, nursery material, clonal lines, and material from Australia. Our analyses indicate that the array is performing well, with sample call rates greater than 98% and a sample reproducibility of 99.9%. Genotyping in two linkage mapping families indicated that the SNPs are well distributed across the 12 linkage groups. Using genotypic data from this array, we were also able to differentiate representatives of the five recognized provenances of radiata pine, Año Nuevo, Monterey, Cambria, Cedros and Guadalupe. Furthermore, principal component analysis of genotyped trees revealed clear patterns of population structure, with the primary axis of variation driven by provenance ancestry and the secondary axis reflecting breeding activities. This represents the first commercial use of genomics in a radiata pine breeding program.

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Section: Performance Of the Genotyping Arraysupporting

confidence: 79%

“…As part of an international Conifer SNP Consortium (CSC) [27,[41][42][43], we have developed a 36K SNP array for radiata pine using the Axiom™ platform. Fixed array platforms are regarded as the gold standard for robust and reliable high throughput genotyping.…”

Section: Introductionmentioning

confidence: 99%

Development and Validation of a 36K SNP Array for Radiata Pine (Pinus radiata D.Don)

Graham

Telfer

Frickey

et al. 2022

Forests

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“…All non‐pine origin sequences and unannotated contigs were discarded to produce the final transcriptomes for P. oocarpa (Pioo_v1.0), P. greggii (Pigr_v1.0) and P. maximinoi (Pima_v1.0). Remaining protein sequences were additionally annotated using Mercator (Lohse et al, 2014) to allow visualisation of expression in MapMan v3.5.1R2 (Thimm et al, 2014), as well as GhostKOALA (Kanehisa et al, 2016) to predict Kyoto Encyclopaedia of Genes and Genomes (KEGG) orthology (KO) of proteins. Benchmarking Universal Single Copy Orthologs (BUSCO) v3.0.2 (Simão et al, 2015; Waterhouse et al, 2017), with the eukaryote ( n = 255), viridiplantae ( n = 425) and embryophyte ( n = 1,614) OrthoDB 10 databases, was used to determine the completeness and contiguity of assemblies.…”

Section: Methodsmentioning

confidence: 99%

Multispecies comparison of host responses to Fusarium circinatum challenge in tropical pines show consistency in resistance mechanisms

Visser

Kampmann

Wegrzyn

et al. 2023

Plant Cell & Environment

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Fusarium circinatum poses a threat to both commercial and natural pine forests. Large variation in host resistance exists between species, with many economically important species being susceptible. Development of resistant genotypes could be expedited and optimised by investigating the molecular mechanisms underlying host resistance and susceptibility as well as increasing the available genetic resources. RNA-seq data, from F. circinatum inoculated and mock-inoculated ca. 6-month-old shoot tissue at 3-and 7-days postinoculation, was generated for three commercially important tropical pines, Pinus oocarpa, Pinus maximinoi and Pinus greggii. De novo transcriptomes were assembled and used to investigate the NLR and PR gene content within available pine references. Host responses to F. circinatum challenge were investigated in P. oocarpa (resistant) and P. greggii (susceptible), in comparison to previously generated expression profiles from Pinus tecunumanii (resistant) and Pinus patula (susceptible).Expression results indicated crosstalk between induced salicylate, jasmonate and ethylene signalling is involved in host resistance and compromised in susceptible hosts. Additionally, higher constitutive expression of sulfur metabolism and flavonoid biosynthesis in resistant hosts suggest involvement of these metabolites in resistance.

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“…Phylogenetic reconstruction using a small number of genes is susceptible to random errors (Hedtke et al, 2006;Zhang et al, 2015). Transcriptomes and genomes are widely used in phylogenetic and evolutionary studies of plants (Jackson et al, 2022) and animals (Bi et al, 2021;Meyer et al, 2021). However, due to the giga-genome of pine trees, it is difficult to assemble genomes and use them to study evolution in Pinaceae.…”

Section: Introductionmentioning

confidence: 99%

Phylotranscriptomics and evolution of key genes for terpene biosynthesis in Pinaceae

Jiang

Du²,

Huang³

et al. 2023

Front. Plant Sci.

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Pinaceae is the largest family of conifers, dominating forest ecosystems and serving as the backbone of northern, temperate and mountain forests. The terpenoid metabolism of conifers is responsive to pests, diseases, and environmental stress. Determining the phylogeny and evolution of terpene synthase genes in Pinaceae may shed light on early adaptive evolution. We used different inference methods and datasets to reconstruct the Pinaceae phylogeny based on our assembled transcriptomes. We identified the final species tree of Pinaceae by comparing and summarizing different phylogenetic trees. The genes encoding terpene synthase (TPS) and cytochrome P450 proteins in Pinaceae showed a trend of expansion compared with those in Cycas. Gene family analysis revealed that the number of TPS genes decreased while the number of P450 genes increased in loblolly pine. Expression profiles showed that TPSs and P450s were mainly expressed in leaf buds and needles, which may be the result of long-term evolution to protect these two vulnerable tissues. Our research provides insights into the phylogeny and evolution of terpene synthase genes in Pinaceae and offers some useful references for the investigation of terpenoids in conifers.

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A genome‐wide SNP genotyping resource for tropical pine tree species

Cited by 12 publications

References 70 publications

Development and Validation of a 36K SNP Array for Radiata Pine (Pinus radiata D.Don)

Development and Validation of a 36K SNP Array for Radiata Pine (Pinus radiata D.Don)

Multispecies comparison of host responses to Fusarium circinatum challenge in tropical pines show consistency in resistance mechanisms

Phylotranscriptomics and evolution of key genes for terpene biosynthesis in Pinaceae

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