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

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Relation http://oar.icrisat.org/12358/
https://www.frontiersin.org/articles/10.3389/fgene.2022.914131/full
https://doi.org/10.3389/fgene.2022.914131
 
Title Development and Validation of Diagnostic KASP Markers for Brown Planthopper Resistance in Rice
 
Creator Lakshmi, V G I
Sreedhar, M
JhansiLakshmi, V
Gireesh, C
Rathod, S
Bohar, R
 
Subject Rice
Genetics and Genomics
 
Description 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.
 
Publisher Frontiers Media
 
Date 2022-07-08
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights cc_attribution
 
Identifier http://oar.icrisat.org/12358/1/Frontiers%20in%20Genetics_13_1-17_2022.pdf
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