Development and Validation of KASP Markers for <i>Stv-bi</i>, a Rice Stripe Virus Resistance Gene in Rice (<i>Oryza sativa</i> L.)

Kang, Ju-Won; Lee, Sais-Beul; Lee, Ji Yun; Kwon, Young-In; Lee, So-Myeong; Kabange, Nkulu Rolly; Shin, Dongjin; Cha, Jin-Gyeong; Park, Dong-Soo; Ko, Jong-Min; Lee, Jonghee

doi:10.9787/pbb.2020.8.2.196

Cited by 7 publications

(3 citation statements)

References 10 publications

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“…SNPs converted to KASP markers can be genotyped in small labs using fluorescent resonance energy transfer (FRET)-capable plate readers and qPCR machines. SNP markers have been successfully converted to KASP markers and used for various applications in different crops, including the faba bean [ 33 ], mung bean [ 34 ], pea [ 35 ], peanut [ 36 ], rice [ 37 , 38 ], rye [ 39 ], sorghum [ 40 ], and wheat [ 41 , 42 , 43 ].…”

Section: Introductionmentioning

confidence: 99%

New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses

Tsehay

Ortíz

Johansson

et al. 2020

Genes

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The development and use of genomic resources are essential for understanding the population genetics of crops for their efficient conservation and enhancement. Noug (Guizotia abyssinica) is an economically important oilseed crop in Ethiopia and India. The present study sought to develop new DNA markers for this crop. Transcriptome sequencing was conducted on two genotypes and 628 transcript sequences containing 959 single nucleotide polymorphisms (SNPs) were developed. A competitive allele-specific PCR (KASP) assay was developed for the SNPs and used for genotyping of 24 accessions. A total of 554 loci were successfully genotyped across the accessions, and 202 polymorphic loci were used for population genetics analyses. Polymorphism information content (PIC) of the loci varied from 0.01 to 0.37 with a mean of 0.24, and about 49% of the loci showed significant deviation from the Hardy-Weinberg equilibrium. The mean expected heterozygosity was 0.27 suggesting moderately high genetic variation within accessions. Low but significant differentiation existed among accessions (FST = 0.045, p < 0.0001). Landrace populations from isolated areas may have useful mutations and should be conserved and used in breeding this crop. The genomic resources developed in this study were shown to be useful for population genetics research and can also be used in, e.g., association genetics.

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Section: Introductionmentioning

confidence: 99%

New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses

Tsehay

Ortíz

Johansson

et al. 2020

Genes

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“…최근 형광물질을 활용한 single-nucleotide polymorphism(SNP) 기반 TaqMan probe 및 Kompetitive allele-specific PCR(KASP)기술 등의 방법으로 단일염기다형성 유전자형 분석(SNP genotyping assay)을 손 쉽게 할 수 있는 분자표지 기술이 개발되어 활용되고 있다. TaqMan probe에 의한 SNP genotyping assay 분석법은 원하는 염 기서열 구간의 SNP를 Real-time PCR을 이용하여 유전변이, 생물종 식별 및 작물 육종시 우수라인 선발 등의 분석에 활용되고 있다 (Tan et al, 2017;Broccanello et al, 2018;Ayalew et al, 2019;Kang et al, 2020;Shin et al, 2020) japonica and Z. sinica hybrid, Jeju, Korea; H-C) 종자로부터 확보한 잔디이며, ITS 기반 CAPS 마커 및 ITS 기반 TaqMan SNP genotyping assay 분석법에 의한 분자생물학적 분류를 위해서 대조구로 사용되었다(Table 1). 대조구인 종자는 소독 및 파종 후 MS (Murashige and Skoog, 1962) 기본 배지에 배양되었으며, 각 잔디 잎은 DNA 추출 재료로 사용되었다.…”

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“…Table 1). (Tan et al, 2017;Broccanello et al, 2018;Ayalew et al, 2019;Kang et al, 2020;Shin et al, 2020). (Hong and Yeam, 1985;Yang et al, 1995;Choi et al, 1997;Bae et al, 2010;Lee et al, 2013;Yang et al, 2021aYang et al, , 2021b 3).…”

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confidence: 99%

Comparative Analysis between the ITS TaqMan SNP Genotyping Assay and CAPS for the Rapid Molecular Identification of Zoysia japonica and Zoysia sinica, Related Hybrid Lines, and the Habitat Distribution of Each Species

Yang,

Jeong,

Kim

et al. 2023

HST

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Horticultural Science and Technology 한국에 자생하는 들잔디와 갯잔디, 교잡종의 신속한 식별을 위한 ITS TaqMan SNP genotyping assay와 CAPS의 비교 분석 및 각 종의 서식환경별 분포 this study produced results more rapidly compared to the ITS-based CAPS marker analysis method. The habitat distributions of each of the molecularly identified zoysiagrass plants investigated in this study were also assessed. The Z. japonica plants were mainly distributed in mountainous national parks and oreum areas as well as inland and coastal areas. The Z. sinica plants were distributed along the coast and on rocks and stones frequently submerged in seawater. The Z. japonica and Z. sinica hybrid plants were distributed more in the inland, coastal, and island areas than in the mountainous national parks and oreum areas. Findings related to the leaf blade width as a main external morphological classification characteristic of the molecularly identified 450 zoysiagrass plants are described below. The leaf blade width ranged from 4 to 5 mm for the Z. japonica plants, from 2 to 4 mm for the Z. sinica plants, and from 3 to 4 mm for the Z. japonica and Z. sinica hybrid plants. Additionally, some Z. japonica and Z. sinica plants and Z. japonica and Z. sinica hybrid plants with leaf blade widths of 2 to 3, 4 to 5, and from 2 to 3 and 4 to 5 mm, respectively, were also present. Because the ranges of the leaf blade width of each species overlapped, it was difficult to identify the hybrid lines using this metric. The feasibility of the developed molecular identification method for these three species of zoysiagrasses was confirmed in this study.

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KASP mapping of QTLs for yield components using a RIL population in Basmati rice (Oryza sativa L.)

et al. 2023

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Super Basmati is an elite variety with extra-long grains and superior quality but its yield is severely affected by water stress. Recombinant inbred lines (RILs) developed from the cross of Super Basmati and IR55419-04 (a coarse grained variety with high yield potential) were used to identify and map yield-related quantitative trait loci (QTLs) under normal field conditions. Genotypes for 244 KASP markers were obtained from 188 F9 RILs and a linkage map constructed of 1369.4 cM, with average marker interval of 10.5 cM. Eleven agronomic traits were phenotyped in RILs and parents. Composite interval mapping and inclusive composite interval mapping model identified 21 common QTLs related to nine agronomic traits; of the QTLs identified, twelve mapped at novel positions. LOD scores ranged from 2.51 for number of filled grains (qFG1.1) to 16.8 for plant height (qPH1.1). Four major effect QTLs could explain 20% of variation related for plant height, hundred-grain weight and grain width. Alleles from IR55419-04 improved grain filling, grain weight and grain width, while alleles from Super Basmati contributed to longer grains, panicles and flag leaves. Putative candidate genes were identified for 18 yield-related QTLs. These results validate the use of KASP genotyping for QTL mapping of yield-related traits in a bi-parental segregating population. SNPs in the QTLs identified in this study can be used in marker assisted selection for yield components to improve Basmati rice.

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Development and Validation of KASP Markers for Stv-bi, a Rice Stripe Virus Resistance Gene in Rice (Oryza sativa L.)

Cited by 7 publications

References 10 publications

New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses

New Transcriptome-Based SNP Markers for Noug (Guizotia abyssinica) and Their Conversion to KASP Markers for Population Genetics Analyses

Comparative Analysis between the ITS TaqMan SNP Genotyping Assay and CAPS for the Rapid Molecular Identification of Zoysia japonica and Zoysia sinica, Related Hybrid Lines, and the Habitat Distribution of Each Species

KASP mapping of QTLs for yield components using a RIL population in Basmati rice (Oryza sativa L.)

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