NLR diversity and candidate fusiform rust resistance genes in loblolly pine

Ence, Daniel; Smith, Katherine E.; Fan, Shenghua; Gomide Neves, Leandro; Paul, Robin; Wegrzyn, Jill; Peter, Gary F.; Kirst, Matias; Brawner, Jeremy; Nelson, C. Dana; Davis, John M.

doi:10.1093/g3journal/jkab421

NLR diversity and candidate fusiform rust resistance genes in loblolly pine

Journal Article · Mon Dec 13 00:00:00 EST 2021 · G3

DOI:https://doi.org/10.1093/g3journal/jkab421· OSTI ID:1904366

Ence, Daniel ^[1]; Smith, Katherine E. ^[2]; Fan, Shenghua ^[3]; Gomide Neves, Leandro ^[4]; Paul, Robin ^[5]; ^[5]; Peter, Gary F. ^[6]; Kirst, Matias ^[6]; Brawner, Jeremy ^[6]; Nelson, C. Dana ^[7]; Davis, John M. ^[6]

Univ. of Florida, Gainesville, FL (United States); OSTI
Univ. of Florida, Gainesville, FL (United States); USDA Forest Service, Saucier, MS (United States). Southern Institute of Forest Genetics
Univ. of Kentucky, Lexington, KY (United States)
Rapid Genomics, Gainesville, FL (United States)
Univ. of Connecticut, Storrs, CT (United States)
Univ. of Florida, Gainesville, FL (United States)
USDA Forest Service, Saucier, MS (United States). Southern Institute of Forest Genetics; USDA Forest Service, Lexington, KY (United States). Southern Research Station, Forest Health Research and Education Center

Resistance to fusiform rust disease in loblolly pine (Pinus taeda) is a classic gene-for-gene system. Early resistance gene mapping in the P. taeda family 10-5 identified RAPD markers for a major fusiform rust resistance gene, Fr1. More recently, single nucleotide polymorphism (SNP) markers associated with resistance were mapped to a full-length gene model in the loblolly pine genome encoding for a nucleotide-binding site leucine-rich repeat (NLR) protein. NLR genes are one of the most abundant gene families in plant genomes and are involved in effector-triggered immunity. Inter- and intraspecies studies of NLR gene diversity and expression have resulted in improved disease resistance. To characterize NLR gene diversity and discover potential resistance genes, we assembled de novo transcriptomes from 92 loblolly genotypes from across the natural range of the species. In these transcriptomes, we identified novel NLR transcripts that are not present in the loblolly pine reference genome and found significant geographic diversity of NLR genes providing evidence of gene family evolution. We designed capture probes for these NLRs to identify and map SNPs that stably cosegregate with resistance to the SC20-21 isolate of Cronartium quercuum f.sp. fusiforme (Cqf) in half-sib progeny of the 10-5 family. We identified 10 SNPs and 2 quantitative trait loci associated with resistance to SC20-21 Cqf. The geographic diversity of NLR genes provides evidence of NLR gene family evolution in loblolly pine. The SNPs associated with rust resistance provide a resource to enhance breeding and deployment of resistant pine seedlings.

View Accepted Manuscript (DOE)

Research Organization:: Univ. of Florida, Gainesville, FL (United States)

Sponsoring Organization:: USDA; USDOE Office of Science (SC)

Grant/Contract Number:: SC0019099

OSTI ID:: 1904366

Journal Information:: G3, Journal Name: G3 Journal Issue: 2 Vol. 12; ISSN 2160-1836

Publisher:: Genetics Society of AmericaCopyright Statement

Country of Publication:: United States

Language:: English

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Fr genes
NLR
Pinus taeda
RNAseq
fusiform rust
pan-NLRome
resistance genes
sequence-capture

NLR diversity and candidate fusiform rust resistance genes in loblolly pine

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References (83)

Cited By (1)

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