Biology subjects

Karki, H. S.

Publications and source records attributed to Karki, H. S..

6 recordsLinked to original sources

bioRxiv2026

High-Resolution Melting (HRM) Assay for Molecular Detection of Calonectria ilicicola in Soybean

Calonectria ilicicola, an emerging and economically important soilborne pathogen in the U.S. Midwest, causes red crown rot (RCR) disease of soybean. It is essential to have an early and accurate detection method for effective management of RCR, since disease symptoms are nearly identical to those of other soybean diseases. In this study, we developed and validated a high resolution melting (HRM) assay targeting the translation elongation factor 1&alpha (TEF-1&alpha) gene for the specific detection of C. ilicicola. The assay was evaluated using a specificity panel of 78 DNA samples, including 67 fungal and oomycete DNA samples and 11 soybean host-DNA samples, as well as DNA from 56 field-collected symptomatic and asymptomatic soybean tissues. The HRM assay generated distinct melting profiles and, where applicable, absence or delayed amplification that reliably differentiated C. ilicicola from non target fungi and oomycetes. Additionally, the marker distinguished three haplotypes among C. ilicicola isolates, consistent with nucleotide polymorphisms in the TEF-1&alpha target region. The assay demonstrated strong quantitative performance, exhibiting high linearity (R^2= 0.9992) and acceptable amplification efficiency (94.05%) across a broad DNA concentration range. In field samples, HRM based detection aligned with disease status, accurately identifying C. ilicicola in symptomatic plants and no detection in asymptomatic tissues. Overall, this HRM assay provides a rapid, sensitive, and reliable diagnostic tool for routine molecular detection of C. ilicicola.

pathology↗

bioRxiv2025

Diverse haplotypes at a complex Solanum americanum locus confer resistance to Phytophthora infestans and P. capsici

Plants encounter diverse pathogens and have evolved a two-layered innate immune system to detect pathogen molecules and activate defense mechanisms that restrict infection. Most cloned plant Resistance (R) genes encode NLR immune receptors. NLR genes are often found in clusters of paralogs with sequence and copy number variation; whether these NLR clusters evolve in response to single or multiple pathogens has been unclear. We report here the isolation of a Phytophthora capsici resistance gene, Rpc2, along with a novel P. infestans resistance gene, Rpi-amr5, from two Solanum americanum accessions. These orthologous genes reside in the Rpi-amr1 cluster, which has previously been associated with resistance to P. infestans. By screening RXLR effector libraries of P. infestans and P. capsici, we identified multiple effectors recognized by both NLRs. Our findings highlight the complexity of NLR clusters and evolution driven by interactions with multiple pathogens. This work will underpin efforts to elevate resistance against Phytophthora pathogens and enhances our understanding of NLR evolution.

plant biology↗

bioRxiv2023

A KASP Marker for the Potato Late Blight Resistance Gene RB/Rpi-blb1

The disease late blight is a threat to potato production worldwide, making genetic resistance an important target for breeding. The resistance gene RB/Rpi-blb1 is effective against most strains of the causal pathogen, Phytophthora infestans. Until now, potato breeders have utilized a Sequence Characterized Amplified Region (SCAR) marker to screen for RB. Our objective was to design and validate a Kompetitive Allele Specific PCR (KASP) marker, which has advantages for high-throughput screening. First, the accuracy of the SCAR marker was confirmed in two segregating tetraploid populations. Then, using whole genome sequencing data for two RB-positive segregants and a diverse set of 23 RB-negative varieties, a SNP in the 5 untranslated (UTR) region was identified as unique to RB. The KASP marker based on this SNP, which had 100% accuracy in the cultivated diversity panel, was used to generate diploid breeding lines containing RB. The KASP marker is publicly available for others to utilize.

genetics↗

bioRxiv2021

Rpi-amr3 confers resistance to multiple Phytophthora species by recognizing a conserved RXLR effector

Diverse pathogens from the genus Phytophthora cause disease and reduce yields in many crop plants. Although many Resistance to Phytophthora infestans (Rpi) genes effective against potato late blight have been cloned, few have been cloned against other Phytophthora species. Most Rpi genes encode nucleotide-binding domain, leucine-rich repeat-containing (NLR) proteins, that recognize RXLR effectors. However, whether NLR proteins can recognize RXLR effectors from multiple different Phytophthora pathogens has rarely been investigated. Here, we report the effector AVRamr3 from P. infestans that is recognized by Rpi-amr3 from S. americanum. We show here that AVRamr3 is broadly conserved in many different Phytophthora species, and that recognition of AVRamr3 homologs enables resistance against multiple Phytophthora pathogens, including P. parasitica and P. palmivora. Our findings suggest a novel path to identifying R genes against important plant pathogens.

plant biology↗

bioRxiv2020

Characterization of a late blight resistance gene homologous to R2 in potato variety Payette Russet

Breeding for late blight resistance has traditionally relied on phenotypic selection, but as the number of characterized resistance (R) genes has grown, so have the possibilities for genotypic selection. One challenge for breeding russet varieties is the lack of information about the genetic basis of resistance in this germplasm group. Based on observations of strong resistance by Payette Russet to genotype US-23 of the late blight pathogen Phytophthora infestans in inoculated experiments, we deduced the variety must contain at least one major R gene. To identify the gene(s), 79 F1 progeny were screened using a detached leaf assay and classified as resistant vs. susceptible. Linkage mapping using markers from the potato SNP array revealed a single resistant haplotype on the short arm of chromosome group 4, which coincides with the R2/Rpi-abpt/Rpi-blb3 locus. PCR amplification and sequencing of the gene in Payette revealed it is homologous to R2, and transient expression experiments in Nicotiana benthamiana confirmed its recognition of the Avr2 effector. Sequencing of a small diversity panel revealed a SNP unique to resistant haplotypes at the R2 locus, which was converted to a KASP marker that showed perfect prediction accuracy in the F1 population and diversity panel. Although many genotypes of P. infestans are virulent against R2, even when defeated this gene may be valuable as one component of a multi-genic approach to quantitative resistance.

genetics↗

bioRxiv2020

A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector

Late blight caused by Phytophthora infestans greatly constrains potato production. Many Resistance (R) genes were cloned from wild Solanum species and/or introduced into potato cultivars by breeding. However, individual R genes have been overcome by P. infestans evolution; durable resistance remains elusive. We positionally cloned a new R gene, Rpi-amr1, from Solanum americanum, that encodes an NRC helper-dependent CC-NLR protein. Rpi-amr1 confers resistance in potato to all 19 P. infestans isolates tested. Using association genomics and long-read RenSeq, we defined eight additional Rpi-amr1 alleles from different S. americanum and related species. Despite only [~]90% identity between Rpi-amr1 proteins, all confer late blight resistance but differentially recognize Avramr1 orthologs and paralogs. We propose that Rpi-amr1 gene family diversity facilitates detection of diverse paralogs and alleles of the recognized effector, enabling broad-spectrum and durable resistance against P. infestans.

plant biology↗