Mapping Fusiform Rust Resistance Genes within a Complex Mating Design of Loblolly Pine

Quesada, Tania; Resende, Marcio F. R.; Muñoz, Patricio; Wegrzyn, Jill L.; Neale, David B.; Kirst, Matias; Peter, Gary F.; Gezan, Salvador A.; Nelson, C. Dana; Davis, John M.

doi:10.3390/f5020347

Cited by 25 publications

(27 citation statements)

References 36 publications

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“…In cases where resistance is associated with single genes, such as the major QTL Fr1 conferring resistance to Cronartium quercuum in Pinus (Wilcox et al, 1996;Kuhlman et al, 1997), genetic effects may be large and detection can be relatively uncomplicated (Quesada et al, 2010;Neale et al, 2014;Quesada et al, 2014). In contrast, quantitative disease resistance, e.g.…”

Section: Discussionmentioning

confidence: 99%

Different alleles of a gene encoding leucoanthocyanidin reductase (PaLAR3) influence resistance against the fungus Heterobasidion parviporum in Picea abies

et al. 2016

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Despite the fact that fungal diseases are a growing menace for conifers in modern silviculture, only a very limited number of molecular markers for pathogen resistance have been validated in conifer species. A previous genetic study indicated that the resistance of Norway spruce (Picea abies) to Heterobasidion annosum s.l., a pathogenic basidiomycete species complex, is linked to a quantitative trait loci that associates with differences in fungal growth in sapwood (FGS) that includes a gene, PaLAR3, which encodes a leucoanthocyanidin reductase. In this study, gene sequences showed the presence of two PaLAR3 allelic lineages in P. abies. Higher resistance was associated with the novel allele, which was found in low frequency in the four P. abies populations that we studied. Norway spruce plants carrying at least one copy of the novel allele showed a significant reduction in FGS after inoculation with Heterobasidion parviporum compared to their half-siblings carrying no copies, indicating dominance of this allele. The amount of (+) catechin, the enzymatic product of PaLAR3, was significantly higher in bark of trees homozygous for the novel allele. Although we observed that the in vitro activities of the enzymes encoded by the two alleles were similar, we could show that allele-specific transcript levels were significantly higher for the novel allele, indicating that regulation of gene expression is responsible for the observed effects in resistance, possibly caused by differences in cis-acting elements that we observe in the promoter region of the two alleles.

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Section: Discussionmentioning

confidence: 99%

Different alleles of a gene encoding leucoanthocyanidin reductase (PaLAR3) influence resistance against the fungus Heterobasidion parviporum in Picea abies

et al. 2016

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“…Application of consensus maps with syntenic markers localized P. lambertiana Cr1 on the Pinus consensus LG2 [ 16 ], the same LG where P. taeda Fr1 for resistance to fusiform rust pathogen Cronartium quercuum sp . fusiforme ( Cqf ) was localized [ 27 , 39 ]. P. monticola Cr2 was localized on Pinus consensus LG1 (Liu et al unpublished data).…”

Section: Discussionmentioning

confidence: 99%

Genetic mapping of Pinus flexilis major gene (Cr4) for resistance to white pine blister rust using transcriptome-based SNP genotyping

et al. 2016

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BackgroundLinkage of DNA markers with phenotypic traits provides essential information to dissect clustered genes with potential phenotypic contributions in a target genome region. Pinus flexilis E. James (limber pine) is a keystone five-needle pine species in mountain-top ecosystems of North America. White pine blister rust (WPBR), caused by a non-native fungal pathogen Cronartium ribicola (J.C. Fisch.), has resulted in mortality in this conifer species and is still spreading through the distribution. The objective of this research was to develop P. flexilis transcriptome-wide single nucleotide polymorphism (SNP) markers using RNA-seq analysis for genetic mapping of the major gene (Cr4) that confers complete resistance to C. ribicola.ResultsNeedle tissues of one resistant and two susceptible seedling families were subjected to RNA-seq analysis. In silico SNP markers were uncovered by mapping the RNA-seq reads back to the de novo assembled transcriptomes. A total of 110,573 in silico SNPs and 2,870 indels were identified with an average of 3.7 SNPs per Kb. These SNPs were distributed in 17,041 unigenes. Of these polymorphic P. flexilis unigenes, 6,584 were highly conserved as compared to the genome sequence of P. taeda L (loblolly pine). High-throughput genotyping arrays were designed and were used to search for Cr4-linked genic SNPs in megagametophyte populations of four maternal trees by haploid-segregation analysis. A total of 32 SNP markers in 25 genes were localized on the Cr4 linkage group (LG). Syntenic relationships of this Cr4-LG map with the model conifer species P. taeda anchored Cr4 on Pinus consensus LG8, indicating that R genes against C. ribicola have evolved independently in different five-needle pines. Functional genes close to Cr4 were annotated and their potential roles in Cr4-mediated resistance were further discussed.ConclusionsWe demonstrated a very effective, low-cost strategy for developing a SNP genetic map of a phenotypic trait of interest. SNP discovery through transcriptome comparison was integrated with high-throughput genotyping of a small set of in silico SNPs. This strategy may be applied to mapping any trait in non-model plant species that have complex genomes. Whole transcriptome sequencing provides a powerful tool for SNP discovery in conifers and other species with complex genomes, for which sequencing and annotation of complex genomes is still challenging. The genic SNP map for the consensus Cr4-LG may help future molecular breeding efforts by enabling both Cr4 positional characterization and selection of this gene against WPBR.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3079-2) contains supplementary material, which is available to authorized users.

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“…Further refinements of genome assembly of forest trees coupled with increasing marker density and improved genetic maps should enable breeders to identify resistance genes in the near future. For example, in loblolly pine, the top five SNP markers explained about 30% of the variance in gall score caused by the fusiform rust fungus (Quesada et al, 2014). Isik (2014) developed a strategy to use genomic selection in loblolly pine for a proof of concept breeding plan in the southern USA.…”

Section: Summary Of Empirical Studiesmentioning

confidence: 99%

Acceleration of Forest and Fruit Tree Domestication by Genomic Selection

Isik¹,

Kumar²,

Martínez-García³

et al. 2015

Advances in Botanical Research

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Mapping Fusiform Rust Resistance Genes within a Complex Mating Design of Loblolly Pine

Cited by 25 publications

References 36 publications

Different alleles of a gene encoding leucoanthocyanidin reductase (PaLAR3) influence resistance against the fungus Heterobasidion parviporum in Picea abies

Different alleles of a gene encoding leucoanthocyanidin reductase (PaLAR3) influence resistance against the fungus Heterobasidion parviporum in Picea abies

Genetic mapping of Pinus flexilis major gene (Cr4) for resistance to white pine blister rust using transcriptome-based SNP genotyping

Acceleration of Forest and Fruit Tree Domestication by Genomic Selection

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