Abstract
Limber pine (Pinus flexilis) is a keystone species of high-elevation forest ecosystems of western North America, but some parts of the geographic range have high infection and mortality from the non-native white pine blister rust caused byCronartium ribicola. Genetic maps can provide essential knowledge for understanding genetic disease resistance as well as local adaptation to changing climates. Exome-seq was performed to construct high-density genetic maps in two seed families. Composite maps positioned 9612 unigenes across 12 linkage groups (LGs). Syntenic analysis of genome structure revealed that the majority of orthologs were positional orthologous genes (POGs) with localization on homologousLGs among conifer species. Gene ontology (GO) enrichment analysis showed relatively fewer constraints forPOGs with putative roles in adaptation to environments and relatively more conservation forPOGs with roles in basic cell function and maintenance. The mapped genes included 639 nucleotide-binding site leucine-rich repeat genes (NBS-LRRs), 290 receptor-like protein kinase genes (RLKs), and 1014 genes with potential roles in the defense response and induced systemic resistance to attack by pathogens. Orthologous loci for resistance to rust pathogens were identified and were co-positioned with multiple members of theR gene family, revealing the evolutionary pressure acting upon them. This high-density genetic map provides a genomic resource and practical tool for breeding and genetic conservation programs, with applications in genome-wide association studies (GWASs), the characterization of functional genes underlying complex traits, and the sequencing and assembly of the full-length genomes of limber pine and relatedPinus species.
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Claims 8
Claim · model-written summary
Composite genetic maps of limber pine positioned 9612 unigenes across 12 linkage groups.
- Taxon
- Limber pine
Pinus flexilise0 - Material
- two seed familiese2
- Outcome
- unigenese1
- Value
- 9612e1
- Qualifier
- 12 linkage groupse1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Limber pine (Pinus flexilis) is a keystone species of high-elevation forest ecosystems”
e1“Composite maps positioned 9612 unigenes across 12 linkage groups (LGs)”
e2“Exome-seq was performed to construct high-density genetic maps in two seed families”
Claim · model-written summary
Most orthologs in limber pine were positional orthologous genes localized on homologous linkage groups among conifer species.
- Taxon
- Limber pinePinus flexilise0
- Gene
- positional orthologous genes (POGs)e3
- Outcome
- majority of orthologse3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Limber pine (Pinus flexilis) is a keystone species of high-elevation forest ecosystems”
e3“Syntenic analysis of genome structure revealed that the majority of orthologs were positional orthologous genes (POGs) with localization on homologousLGs among conifer species”
Claim · model-written summary
Gene ontology enrichment showed relatively fewer evolutionary constraints on POGs with putative roles in adaptation to environments in limber pine.
- Taxon
- Limber pinePinus flexilise0
- Gene
- POGse4
- Outcome
- constraintse4
- Direction
- fewere4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Limber pine (Pinus flexilis) is a keystone species of high-elevation forest ecosystems”
e4“Gene ontology (GO) enrichment analysis showed relatively fewer constraints forPOGs with putative roles in adaptation to environments”
Claim · model-written summary
Gene ontology enrichment showed relatively more conservation of POGs with roles in basic cell function and maintenance in limber pine.
- Taxon
- Limber pinePinus flexilise0
- Gene
- POGse5
- Outcome
- conservatione5
- Direction
- moree5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Limber pine (Pinus flexilis) is a keystone species of high-elevation forest ecosystems”
e5“relatively more conservation forPOGs with roles in basic cell function and maintenance”
Claim · model-written summary
The mapped genes included 639 NBS-LRR genes in limber pine.
- Taxon
- Limber pinePinus flexilise0
- Gene
- NBS-LRRse6
- Outcome
- mapped genese6
- Value
- 639e6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Limber pine (Pinus flexilis) is a keystone species of high-elevation forest ecosystems”
e6“The mapped genes included 639 nucleotide-binding site leucine-rich repeat genes (NBS-LRRs)”
Claim · model-written summary
The mapped genes included 290 receptor-like protein kinase genes (RLKs) in limber pine.
- Taxon
- Limber pinePinus flexilise0
- Gene
- RLKse7
- Outcome
- receptor-like protein kinase genese7
- Value
- 290e7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Limber pine (Pinus flexilis) is a keystone species of high-elevation forest ecosystems”
e7“290 receptor-like protein kinase genes (RLKs)”
Claim · model-written summary
The mapped genes included 1014 genes with potential roles in the defense response in limber pine.
- Taxon
- Limber pinePinus flexilise0
- Outcome
- genes with potential roles in the defense responsee1
- Value
- 1014e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Limber pine (Pinus flexilis) is a keystone species of high-elevation forest ecosystems”
e1“1014 genes with potential roles in the defense response and induced systemic resistance to attack by pathogens”
Claim · model-written summary
Orthologous loci for resistance to rust pathogens were identified in limber pine and co-positioned with multiple R gene family members.
- Taxon
- Limber pinePinus flexilise0
- Interactor
- rust pathogense1pathogen
- Outcome
- Orthologous loci for resistance to rust pathogense1
- Qualifier
- revealing the evolutionary pressure acting upon theme1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Limber pine (Pinus flexilis) is a keystone species of high-elevation forest ecosystems”
e1“Orthologous loci for resistance to rust pathogens were identified and were co-positioned with multiple members of theR gene family, revealing the evolutionary pressure acting upon them”