Pangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus).
Helianthus
/ genetics
Ascomycota
/ genetics
Disease Resistance
/ genetics
Plant Diseases
/ microbiology
Phylogeny
Plant Proteins
/ genetics
Transcription Factors
/ genetics
Genome, Plant
Multigene Family
/ genetics
Genes, Plant
/ genetics
Polymorphism, Single Nucleotide
/ genetics
Haplotypes
/ genetics
NAC gene family
Basal stalk rot resistance
Pangenome characterization
Sclerotinia head rot resistance
Sunflower
Journal
BMC genomic data
ISSN: 2730-6844
Titre abrégé: BMC Genom Data
Pays: England
ID NLM: 101775394
Informations de publication
Date de publication:
01 May 2024
01 May 2024
Historique:
received:
07
01
2024
accepted:
22
04
2024
medline:
2
5
2024
pubmed:
2
5
2024
entrez:
1
5
2024
Statut:
epublish
Résumé
Sunflower (Helianthus annuus) is one of the most important economic crops in oilseed production worldwide. The different cultivars exhibit variability in their resistance genes. The NAC transcription factor (TF) family plays diverse roles in plant development and stress responses. With the completion of the H. annuus genome sequence, the entire complement of genes coding for NACs has been identified. However, the reference genome of a single individual cannot cover all the genetic information of the species. Considering only a single reference genome to study gene families will miss many meaningful genes. A pangenome-wide survey and characterization of the NAC genes in sunflower species were conducted. In total, 139 HaNAC genes are identified, of which 114 are core and 25 are variable. Phylogenetic analysis of sunflower NAC proteins categorizes these proteins into 16 subgroups. 138 HaNACs are randomly distributed on 17 chromosomes. SNP-based haplotype analysis shows haplotype diversity of the HaNAC genes in wild accessions is richer than in landraces and modern cultivars. Ten HaNAC genes in the basal stalk rot (BSR) resistance quantitative trait loci (QTL) are found. A total of 26 HaNAC genes are differentially expressed in response to Sclerotinia head rot (SHR). A total of 137 HaNAC genes are annotated in Gene Ontology (GO) and are classified into 24 functional groups. GO functional enrichment analysis reveals that HaNAC genes are involved in various functions of the biological process. We identified NAC genes in H. annuus (HaNAC) on a pangenome-wide scale and analyzed S. sclerotiorum resistance-related NACs. This study provided a theoretical basis for further genomic improvement targeting resistance-related NAC genes in sunflowers.
Sections du résumé
BACKGROUND
BACKGROUND
Sunflower (Helianthus annuus) is one of the most important economic crops in oilseed production worldwide. The different cultivars exhibit variability in their resistance genes. The NAC transcription factor (TF) family plays diverse roles in plant development and stress responses. With the completion of the H. annuus genome sequence, the entire complement of genes coding for NACs has been identified. However, the reference genome of a single individual cannot cover all the genetic information of the species.
RESULTS
RESULTS
Considering only a single reference genome to study gene families will miss many meaningful genes. A pangenome-wide survey and characterization of the NAC genes in sunflower species were conducted. In total, 139 HaNAC genes are identified, of which 114 are core and 25 are variable. Phylogenetic analysis of sunflower NAC proteins categorizes these proteins into 16 subgroups. 138 HaNACs are randomly distributed on 17 chromosomes. SNP-based haplotype analysis shows haplotype diversity of the HaNAC genes in wild accessions is richer than in landraces and modern cultivars. Ten HaNAC genes in the basal stalk rot (BSR) resistance quantitative trait loci (QTL) are found. A total of 26 HaNAC genes are differentially expressed in response to Sclerotinia head rot (SHR). A total of 137 HaNAC genes are annotated in Gene Ontology (GO) and are classified into 24 functional groups. GO functional enrichment analysis reveals that HaNAC genes are involved in various functions of the biological process.
CONCLUSIONS
CONCLUSIONS
We identified NAC genes in H. annuus (HaNAC) on a pangenome-wide scale and analyzed S. sclerotiorum resistance-related NACs. This study provided a theoretical basis for further genomic improvement targeting resistance-related NAC genes in sunflowers.
Identifiants
pubmed: 38693490
doi: 10.1186/s12863-024-01227-9
pii: 10.1186/s12863-024-01227-9
doi:
Substances chimiques
Plant Proteins
0
Transcription Factors
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
39Subventions
Organisme : National Natural Science Foundation of China
ID : 32160642 and 32060598
Organisme : National Natural Science Foundation of China
ID : 32160642 and 32060598
Organisme : National Natural Science Foundation of China
ID : 32160642 and 32060598
Organisme : National Natural Science Foundation of China
ID : 32160642 and 32060598
Organisme : National Natural Science Foundation of China
ID : 32160642 and 32060598
Organisme : Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region
ID : NMGIRT2320
Organisme : Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region
ID : NMGIRT2320
Organisme : Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region
ID : NMGIRT2320
Organisme : Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region
ID : NMGIRT2320
Organisme : Program for Innovative Research Team in Universities of Inner Mongolia Autonomous Region
ID : NMGIRT2320
Informations de copyright
© 2024. The Author(s).
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