Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice

Lee, Chaewon; Cheon, Kyeong-Seong; Shin, Yu Su; Oh, Hyoja; Jeong, Young‐Min; Jang, Hoon; Park, Yong-Chan; Kim, Kyung-Yun; Cho, Hang-Chul; Won, Yong-Jae; Baek, Jeongho; Cha, Young-Soon; Kim, Song-Lim; Kim, Kyung-Hwan; Ji, Hyeonso

doi:10.3390/genes13050794

Cited by 11 publications

(5 citation statements)

References 41 publications

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“…The development of an efficient, robust and high-throughput SNP genotyping platform is greatly significant as it plays a pivotal role in crop genetics and breeding. Lee et al [20] studied the development and applications of a target capture-sequencing SNPgenotyping platform in rice. This platform was used in the diversity analysis of 50 rice varieties.…”

Section: Molecular Breeding Based On Snp Markersmentioning

confidence: 99%

Genetic Research and Plant Breeding

Kang

Cho

2022

Genes

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Section: Molecular Breeding Based On Snp Markersmentioning

confidence: 99%

Genetic Research and Plant Breeding

Kang

Cho

2022

Genes

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“…Single nucleotide polymorphism (SNP) markers are one of the molecular markers recently developed rapidly and simultaneously with advances in genome sequencing technology using next-generation sequencing (NGS). SNP markers show one base at a specific location between rice accessions which can then be used for various kinds of genetic analysis [8], [9]. Morales et al [10] reported that an SNP array containing 7,098 markers had been developed from the Cornell-IR LD Rice Array (C7AIR).…”

Section: Introductionmentioning

confidence: 99%

Application of SNP Markers to Identify Genetic Variation on Mutant Lines of Adan-Krayan, Special Local Rice from North Kalimantan

Prasetiyono,

Hidayatun,

Tasliah

et al. 2024

Int. J. Adv. Sci. Eng. Inf. Technol.

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Adan rice, a local rice from the Krayan highland of North Kalimantan is marked by its fine taste that consumers like. However, this rice can only be planted once a year due to its long lifespan. Efforts have been made to develop a short-lived version of Adan, to enable it to be planted twice a year. Adan Kelabit was initially exposed to gamma radiation, which produced several mutants. Field selection identified eight mutants with shorter lifespans than the Adan. In this study, these eight mutants were observed further. SNP markers were carried out to confirm the occurrence of mutations, while observations of agronomic characters and grain quality were carried out to determine the most promising lines. The molecular study showed mutations found in all chromosomes of the mutants and differentiated them from the original Adan, with the similarity level ranging from 0.746 to 0.843. However, this closeness is not correlated to the dosage of the gamma rays applied. The majority of the mutants have shorter plant height and higher yield potential. On average, the mutant is 11.5% shorter on heading date, 22.69% higher on tiller number, 27.14% higher on grain weight, and 26.64% higher on other parameters of yield potential. Apart from the shorter heading date, each mutant has its superiorities. The A25 and A28 mutant lines have much higher yield potential while maintaining the same level of amylose content as the Adan rice. These two mutants can be considered for further development or dissemination for farmer adoption.

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“…GBTS chips are adaptable, compatible with various sequencing platforms, efficient, and offer a simpler analysis process. Their application extends across various crops, such as maize ( Guo et al., 2021 ), soybean ( Liu et al., 2020 ; Yang et al., 2023 ), cotton ( Si et al., 2022 ), rice ( Lee et al., 2022 ), wheat ( Xiang et al., 2023 ), barley ( Nie et al., 2022 ), peanuts ( Lu et al., 2023 ), tomato ( Li et al., 2022 ), and pepper ( Miao et al., 2023 ), and genetic research areas, facilitating effective germplasm assessment, breeding material selection, and genotypic analysis ( Liu et al., 2020 ; Guo et al., 2021 ; Lee et al., 2022 ; Si et al., 2022 ; Xiang et al., 2023 ; Yang et al., 2023 ).…”

Section: Introductionmentioning

confidence: 99%

Development of a 45K pepper GBTS liquid-phase gene chip and its application in genome-wide association studies

Li,

Jia,

et al. 2024

Front. Plant Sci.

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IntroductionPepper (Capsicum spp.) is a vegetable that is cultivated globally and has undergone extensive domestication, leading to a significant diversification in its agronomic traits. With the advancement of genomics in pepper and the reduction in sequencing costs, the high-throughput detection of single nucleotide polymorphisms (SNPs) and small insertions-deletions (indels) has become increasingly critical for analyzing pepper germplasms and improving breeding programs. As a result, there is a pressing need for a cost-effective, high-throughput, and versatile technique suitable for both foreground and background selection in pepper breeding.MethodsIn the present study, Python-based web scraping scripts were utilized to systematically extract data from published literatures and relevant sequence databases focusing on pepper genomes. Subsequent to data extraction, SNPs and indels were meticulously identified and filtered. This process culminated in the delineation of core polymorphic sites, which were instrumental in the development of specific probes. Following this, comprehensive phenotypic and genotypic analyses were conducted on a diverse collection of 420 pepper germplasms. Concurrently, a genome-wide association study (GWAS) was conducted to elucidate the genetic determinants of helical fruit shape in peppers.ResultsIn this study, a 45K pepper Genotyping-By-Target-Sequencing (GBTS) liquid-phase gene chip was developed on the GenoBaits platform. This chip is composed of 45,389 probes, of which 42,535 are derived from core polymorphic sites (CPS) in the background genetic landscape, while 2,854 are associated with foreground agronomic traits, spanning across 43 traits. The CPS probes are spaced at an average interval of 68 Kb. We have assessed the performance of this chip on 420 pepper germplasms, with successful capture of target DNA fragments by 45,387 probes. Furthermore, the probe capture ratio surpassed 70% in 410 of the 420 germplasms tested. Using this chip, we have efficiently genotyped 273 germplasms for spiciness levels and elucidated the genetic relationships among 410 pepper germplasms. Our results allowed for precise clustering of sister lines and C. chinense germplasms. In addition, through a GWAS for helical fruit shape, we identified three quantitative trait loci (QTLs): heli2.1, heli11.1, and heli11.2. Within the heli11.1 QTL, a gene encoding the tubulin alpha chain was identified, suggesting its potential role in the helical growth pattern of pepper fruits.DiscussionIn summary, the 45K pepper GBTS liquid-phase gene chip offers robust detection of polymorphic sites and is a promising tool for advancing research into pepper germplasm and the breeding of new pepper varieties.

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Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice

Cited by 11 publications

References 41 publications

Genetic Research and Plant Breeding

Genetic Research and Plant Breeding

Application of SNP Markers to Identify Genetic Variation on Mutant Lines of Adan-Krayan, Special Local Rice from North Kalimantan

Development of a 45K pepper GBTS liquid-phase gene chip and its application in genome-wide association studies

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