Kompetitive Allele-Specific PCR (KASP): An Efficient High-Throughput Genotyping Platform and Its Applications in Crop Variety Development

Rahman, Mijanur; Hasan, Masud; Rahman, Jamilur

doi:10.1007/978-981-99-1612-2_2

Molecular Marker Techniques 2023

DOI: 10.1007/978-981-99-1612-2_2

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Kompetitive Allele-Specific PCR (KASP): An Efficient High-Throughput Genotyping Platform and Its Applications in Crop Variety Development

Mijanur Rahman

Masud Hasan

Jamilur Rahman

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2024

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Cited by 4 publications

(1 citation statement)

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“…PCR-RFLP (Chuang et al, 2008) and high-throughput genotyping methods, i.e. Taqman technology (Wang et al, 2006), DNA microarray (Shen et al, 2005), MALDI-TOF mass spectrometry (Griffin & Smith, 2000), pyrosequencing (Ahmadian et al, 2006) and kompetitive allele specific PCR (KASP) (Rahman et al, 2023;Zhang et al, 2020). These high-throughput genotyping methods are expensive (Syvänen, 2005) and thus not feasible for routine diagnostics of small number of samples.…”

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confidence: 99%

Multiplex fluorescent amplification‐refractory mutation system PCR method for the detection of 10 genetic defects in Holstein cattle and its comparison with the KASP genotyping assay

Khan,

Dai,

et al. 2024

Animal Genetics

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The common deleterious genetic defects in Holstein cattle include haplotypes 1–6 (HH1–HH6), haplotypes for cholesterol deficiency (HCD), bovine leukocyte adhesion deficiency (BLAD), complex vertebral malformation (CVM) and brachyspina syndrome (BS). Recessive inheritance patterns of these genetic defects permit the carriers to function normally, but homozygous recessive genotypes cause embryo loss or neonatal death. Therefore, rapid detection of the carriers is essential to manage these genetic defects. This study was conducted to develop a single‐tube multiplex fluorescent amplification–refractory mutation system (mf‐ARMS) PCR method for efficient genotyping of these 10 genetic defects and to compare its efficiency with the kompetitive allele specific PCR (KASP) genotyping assay. The mf‐ARMS PCR method introduced 10 sets of tri‐primers optimized with additional mismatches in the 3′ end of wild and mutant‐specific primers, size differentiation between wild and mutant‐specific primers, fluorescent labeling of universal primers, adjustment of annealing temperatures and optimization of primer concentrations. The genotyping of 484 Holstein cows resulted in 16.12% carriers with at least one genetic defect, while no homozygous recessive genotype was detected. This study found carrier frequencies ranging from 0.0% (HH6) to 3.72% (HH3) for individual defects. The mf‐ARMS PCR method demonstrated improved detection, time and cost efficiency compared with the KASP method for these defects. Therefore, the application of mf‐ARMS PCR for genotyping Holstein cattle is anticipated to decrease the frequency of lethal alleles and limit the transmission of these genetic defects.

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confidence: 99%

Multiplex fluorescent amplification‐refractory mutation system PCR method for the detection of 10 genetic defects in Holstein cattle and its comparison with the KASP genotyping assay

Khan,

Dai,

et al. 2024

Animal Genetics

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Genetic mapping and QTL analysis of multigenic resistance to powdery mildew (Podosphaera macularis) in hop (Humulus lupulus L.)

Henning,

Wiseman,

Gent

et al. 2024

Crop Science

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Hop powdery mildew (PM) (Podosphaera macularis) causes substantial losses if left uncontrolled. Most resistant hop cultivars possess qualitative resistance based on R‐genes. One cultivar, Comet, has uncharacterized resistance that may be polygenic. This study focused on identifying genomic regions controlling PM resistance in Comet and ascertaining putative genetic mechanisms behind such resistance. A cross between Comet and susceptible male, USDA 64035M, was made. Offspring were screened for resistance under greenhouse conditions and genotyped using genotyping‐by‐sequencing. Genome‐wide analysis using mixed linear model analysis along with quantitative trait locus (QTL) analysis using either composite interval mapping or stepwise regression analyses was performed to identify QTLs. All analyses identified a region on chromosome 6 covering positions 308–314 Mb on the physical map. Analysis of the putative genes within this region identified 140 genes with 27 plant resistance‐like genes found in nine clusters. Six sulfur‐rich protein genes with homology to patatins, thionins, and agglutinins were identified in two clusters. Two glucan‐endo‐1,3‐beta‐glucosidase genes were identified bordering different R‐gene clusters. Finally, putative upregulators of transcription and stress‐response genes were identified. The 10 most highly associated single‐nucleotide polymorphisms for PM resistance were subsequently developed as KASP markers. The combination of R‐gene clusters, sulfur‐rich proteins, endo‐1,3‐beta‐glucosidase genes, and stress‐response genes may be responsible for resistance to PM in the cultivar Comet.

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KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance

Dipta,

Sood,

Mangal

et al. 2024

Mol Biol Rep

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Kompetitive Allele-Specific PCR (KASP): An Efficient High-Throughput Genotyping Platform and Its Applications in Crop Variety Development

Cited by 4 publications

References 108 publications

Multiplex fluorescent amplification‐refractory mutation system PCR method for the detection of 10 genetic defects in Holstein cattle and its comparison with the KASP genotyping assay

Multiplex fluorescent amplification‐refractory mutation system PCR method for the detection of 10 genetic defects in Holstein cattle and its comparison with the KASP genotyping assay

Genetic mapping and QTL analysis of multigenic resistance to powdery mildew (Podosphaera macularis) in hop (Humulus lupulus L.)

KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance

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