Genome-Wide Identification of NBS-Encoding Resistance Genes in Sunflower (Helianthus annuus L.)

Neupane, Surendra; Andersen, Ethan J.; Neupane, Achal; Nepal, Madhav P.

doi:10.3390/genes9080384

Cited by 40 publications

(30 citation statements)

References 97 publications

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“…Defining a complete set of NBS-LRR genes in a species is not only helpful for obtaining new insights into the evolution of this important gene family but also practical for the identification and utilization of functional R genes from the species and its close relatives (Meyers et al, 2003;Zhang et al, 2015). Genome-wide identification and evolutionary analysis has been performed in many angiosperms in the past 20 years (Bai et al, 2002;Meyers et al, 2003;Shao et al, 2016Shao et al, , 2019Zhang et al, 2016;Neupane et al, 2018a). Several evolutionary features have been documented, including frequent tandem duplication for gene expansion, cluster organization on the chromosome, rapid species-specific gene loss, and duplication (Meyers et al, 2003;Gu et al, 2015;Shao et al, 2016;Die et al, 2018;Song et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Evolutionary Analysis of NBS-LRR Genes From Dioscorea rotundata

et al. 2020

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Dioscorea rotundata is an important food crop that is mainly cultivated in subtropical regions of the world. D. rotundata is frequently infected by various pathogens during its lifespan, which results in a substantial economic loss in terms of yield and quality. The disease resistance gene (R gene) profile of D. rotundata is largely unknown, which has greatly hampered molecular study of disease resistance in this species. Nucleotidebinding site-leucine-rich repeat (NBS-LRR) genes are the largest group of plant R genes, and they play important roles in plant defense responses to various pathogens. In this study, 167 NBS-LRR genes were identified from the D. rotundata genome. Subsequently, one gene was assigned to the resistance to powdery mildew8 (RPW8)-NBS-LRR (RNL) subclass and the other 166 genes to the coiled coil (CC)-NBS-LRR (CNL) subclass. None of the Toll/interleukin-1 receptor (TIR)-NBS-LRR (TNL) genes were detected in the genome. Among them, 124 genes are located in 25 multigene clusters and 43 genes are singletons. Tandem duplication serves as the major force for the cluster arrangement of NBS-LRR genes. Segmental duplication was detected for 18 NBS-LRR genes, although no whole-genome duplication has been documented for the species. Phylogenetic analysis revealed that D. rotundata NBS-LRR genes share 15 ancestral lineages with Arabidopsis thaliana genes. The NBS-LRR gene number increased by more than a factor of 10 during D. rotundata evolution. A conservatively evolved ancestral lineage was identified from D. rotundata, which is orthologs to the Arabidopsis RPM1 gene. Transcriptome analysis for four different tissues of D. rotundata revealed a low expression of most NBS-LRR genes, with the tuber and leaf displaying a relatively high NBS-LRR gene expression than the stem and flower. Overall, this study provides a complete set of NBS-LRR genes for D. rotundata, which may serve as a fundamental resource for mining functional NBS-LRR genes against various pathogens.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Evolutionary Analysis of NBS-LRR Genes From Dioscorea rotundata

et al. 2020

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“…In spite of the availability of a reference genome for the species [22], there is still little knowledge about the abundance and distribution of the genes associated with disease resistance. According to Neupane et al [23], sunflower chromosome 13, followed by chromosomes 9, 4 and 2, contains the highest number of nucleotide Binding Site-Leucine-Rich Repeat (NBS-LRR) genes, which encode disease resistance proteins involved in plant defense .…”

Section: Introductionmentioning

confidence: 99%

Unveiling the genetic basis of Sclerotinia head rot resistance in sunflower

et al. 2020

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Background: Sclerotinia sclerotiorum is a necrotrophic fungus that causes Sclerotinia head rot (SHR) in sunflower, with epidemics leading to severe yield losses. In this work, we present an association mapping (AM) approach to investigate the genetic basis of natural resistance to SHR in cultivated sunflower, the fourth most widely grown oilseed crop in the world. Results: Our association mapping population (AMP), which comprises 135 inbred breeding lines (ILs), was genotyped using 27 candidate genes, a panel of 9 Simple Sequence Repeat (SSR) markers previously associated with SHR resistance via bi-parental mapping, and a set of 384 SNPs located in genes with molecular functions related to stress responses. Moreover, given the complexity of the trait, we evaluated four disease descriptors (i.e, disease incidence, disease severity, area under the disease progress curve for disease incidence, and incubation period). As a result, this work constitutes the most exhaustive AM study of disease resistance in sunflower performed to date. Mixed linear models accounting for population structure and kinship relatedness were used for the statistical analysis of phenotype-genotype associations, allowing the identification of 13 markers associated with disease reduction. The number of favourable alleles was negatively correlated to disease incidence, disease severity and area under the disease progress curve for disease incidence, whereas it was positevily correlated to the incubation period. Conclusions: Four of the markers identified here as associated with SHR resistance (HA1848, HaCOI_1, G33 and G34) validate previous research, while other four novel markers (SNP117, SNP136, SNP44, SNP128) were consistently associated with SHR resistance, emerging as promising candidates for marker-assisted breeding. From the germplasm point of view, the five ILs carrying the largest combination of resistance alleles provide a valuable resource for sunflower breeding programs worldwide.

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“…The H. annuus genome and annotation version 1.2 were downloaded from Phytozome [19]. The results were compared to information provided by the published automatic annotation of NBS-LRR genes [20]. This provides a complementary view on performance, as the genome was automatically annotated and NBS-LRR genes were identified based on protein sequences.…”

Section: Helianthus Annuusmentioning

confidence: 99%

NLGenomeSweeper: A Tool for Genome-Wide NBS-LRR Resistance Gene Identification

Toda

Rustenholz

Baud

et al. 2020

Genes

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Although there are a number of bioinformatic tools to identify plant nucleotide-binding leucine-rich repeat (NLR) disease resistance genes based on conserved protein sequences, only a few of these tools have attempted to identify disease resistance genes that have not been annotated in the genome. The overall goal of the NLGenomeSweeper pipeline is to annotate NLR disease resistance genes, including RPW8, in the genome assembly with high specificity and a focus on complete functional genes. This is based on the identification of the complete NB-ARC domain, the most conserved domain of NLR genes, using the BLAST suite. In this way, the tool has a high specificity for complete genes and relatively intact pseudogenes. The tool returns all candidate NLR gene locations as well as InterProScan ORF and domain annotations for manual curation of the gene structure.

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Genome-Wide Identification of NBS-Encoding Resistance Genes in Sunflower (Helianthus annuus L.)

Cited by 40 publications

References 97 publications

Genome-Wide Identification and Evolutionary Analysis of NBS-LRR Genes From Dioscorea rotundata

Genome-Wide Identification and Evolutionary Analysis of NBS-LRR Genes From Dioscorea rotundata

Unveiling the genetic basis of Sclerotinia head rot resistance in sunflower

NLGenomeSweeper: A Tool for Genome-Wide NBS-LRR Resistance Gene Identification

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