Development and Validation of Diagnostic KASP Markers for Brown Planthopper Resistance in Rice

Lakshmi, V G I and Sreedhar, M and JhansiLakshmi, V and Gireesh, C and Rathod, S and Bohar, R (2022) Development and Validation of Diagnostic KASP Markers for Brown Planthopper Resistance in Rice. Frontiers in Genetics (TSI), 13. pp. 1-17. ISSN 1664-8021

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Rice (Oryza sativa L.) is an important source of nutrition for the world’s burgeoning population that often faces yield loss due to infestation by the brown planthopper (BPH, Nilaparvata lugens (Stål)). The development of rice cultivars with BPH resistance is one of the crucial precedences in rice breeding programs. Recent progress in high-throughput SNP-based genotyping technology has made it possible to develop markers linked to the BPH more quickly than ever before. With this view, a genome-wide association study was undertaken for deriving marker-trait associations with BPH damage scores and SNPs from genotyping-by-sequencing data of 391 multi-parent advanced generation inter-cross (MAGIC) lines. A total of 23 significant SNPs involved in stress resistance pathways were selected from a general linear model along with 31 SNPs reported from a FarmCPU model in previous studies. Of these 54 SNPs, 20 were selected in such a way to cover 13 stress-related genes. Kompetitive allele-specific PCR (KASP) assays were designed for the 20 selected SNPs and were subsequently used in validating the genotypes that were identified, six SNPs, viz, snpOS00912, snpOS00915, snpOS00922, snpOS00923, snpOS00927, and snpOS00929 as efficient in distinguishing the genotypes into BPH-resistant and susceptible clusters. Bph17 and Bph32 genes that are highly effective against the biotype 4 of the BPH have been validated by gene specific SNPs with favorable alleles in M201, M272, M344, RathuHeenati, and RathuHeenati accession. These identified genotypes could be useful as donors for transferring BPH resistance into popular varieties with marker-assisted selection using these diagnostic SNPs. The resistant lines and the significant SNPs unearthed from our study can be useful in developing BPH-resistant varieties after validating them in biparental populations with the potential usefulness of SNPs as causal markers.

Item Type: Article
Divisions: Global Research Program - Accelerated Crop Improvement
Uncontrolled Keywords: rice, brown planthopper, SNP, GWAS, GBS, KASP
Subjects: Others > Rice
Others > Genetics and Genomics
Depositing User: Mr Nagaraju T
Date Deposited: 12 Jan 2024 05:44
Last Modified: 12 Jan 2024 05:44
Official URL:
Projects: High-Throughput Genotyping-HTPG
Funders: Bill and Melinda Gates Foundation
Acknowledgement: The authors are grateful to PJTSAU and ICAR-IIRR, Hyderabad, for providing experimental fields and glasshouse facilities. The authors acknowledge the Excellence in Breeding (EiB) platform through HTPG services for supporting the KASP genotyping at the Intertek-Agritech Laboratory,Hyderabad.
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