Journal ArticleDOI
Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement
TLDR
An overview of the different aspects of the KASP genotyping platform is provided, its application in crop improvement, and a comparison with the chip-based Illumina GoldenGate platform is compared.Abstract:
Single nucleotide polymorphism (SNP) data can be obtained using one of the numerous uniplex or multiplex SNP genotyping platforms that combine a variety of chemistries, detection methods, and reaction formats. Kompetitive Allele Specific PCR (KASP) is one of the uniplex SNP genotyping platforms, and has evolved to be a global benchmark technology. However, there are no publications relating either to the technology itself or to its application in crop improvement programs. In this review, we provide an overview of the different aspects of the KASP genotyping platform, discuss its application in crop improvement, and compare it with the chip-based Illumina GoldenGate platform. The International Maize and Wheat Improvement Center routinely uses KASP, generating in excess of a million data points annually for crop improvement purposes. We found that (1) 81 % of the SNPs used in a custom-designed GoldenGate assay were transferable to KASP; (2) using KASP, negative controls (no template) consistently clustered together and rarely produced signals exceeding the threshold values for allele calling, in contrast to the situation observed using GoldenGate assays; (3) KASP’s average genotyping error in positive control DNA samples was 0.7–1.6 %, which is lower than that observed using GoldenGate (2.0–2.4 %); (4) KASP genotyping costs for marker-assisted recurrent selection were 7.9–46.1 % cheaper than those of the BeadXpress and GoldenGate platforms; and (5) KASP offers cost-effective and scalable flexibility in applications that require small to moderate numbers of markers, such as quality control analysis, quantitative trait loci (QTL) mapping in bi-parental populations, marker-assisted recurrent selection, marker-assisted backcrossing, and QTL fine mapping.read more
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Journal ArticleDOI
Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives
Awais Rasheed,Yuanfeng Hao,Xianchun Xia,Awais Khan,Yunbi Xu,Yunbi Xu,Rajeev K. Varshney,Zhonghu He,Zhonghu He +8 more
TL;DR: It is proposed that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops.
Journal ArticleDOI
High-Throughput SNP Genotyping to Accelerate Crop Improvement
TL;DR: The range of options available to modern breeders for integrating SNP markers into their programs, whether by outsourcing to service providers or setting up in-house genotyping facilities are discussed, and an example of SNP deployment for rice research and breeding is provided as demonstrated by the Genotyping Services Lab at the International Rice Research Institute.
Journal ArticleDOI
Development and validation of KASP assays for genes underpinning key economic traits in bread wheat.
Awais Rasheed,Awais Rasheed,Weie Wen,Fengmei Gao,Shengnan Zhai,Hui Jin,Jindong Liu,Qi Guo,Yingjun Zhang,Susanne Dreisigacker,Xianchun Xia,Zhonghu He,Zhonghu He +12 more
TL;DR: This is the first report on high-throughput screening of a large number of functional genes in a major crop and offers a robust and reliable molecular marker toolkit that can contribute towards maximizing genetic gains in wheat breeding programs.
Journal ArticleDOI
Genetic Gains in Grain Yield Through Genomic Selection in Eight Bi-parental Maize Populations under Drought Stress
Yoseph Beyene,Kassa Semagn,Stephen Mugo,Amsal Tarekegne,Raman Babu,Barbara Meisel,Pierre Sehabiague,Dan Makumbi,Cosmos Magorokosho,Sylvester O. Oikeh,John Gakunga,Mateo Vargas,Michael Olsen,Boddupalli M. Prasanna,Marianne Bänziger,José Crossa +15 more
TL;DR: It is demonstrated that genomic selection is more effective than pedigree-based conventional phenotypic selection for increasing genetic gains in grain yield under drought stress in tropical maize.
Journal ArticleDOI
Single Nucleotide Polymorphism-based Genetic Diversity in the Reference Set of Peanut (Arachis spp.) by Developing and Applying Cost-Effective Kompetitive Allele Specific Polymerase Chain Reaction Genotyping Assays
Pawan Khera,Hari D. Upadhyaya,Manish K. Pandey,Manish Roorkiwal,Manda Sriswathi,Pasupuleti Janila,Yufang Guo,Michael R. McKain,Ervin D. Nagy,Steven J. Knapp,Jim Leebens-Mack,Joann A. Conner,Peggy Ozias-Akins,Rajeev K. Varshney,Rajeev K. Varshney +14 more
TL;DR: These validated and highly informative GKAMs may be useful for genetics and breeding applications in Arachis species and are screened on 280 diverse genotypes of the reference set for estimating diversity features and elucidating genetic relationships.
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