Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

Shirasawa, Kenta; Isobe, Sachiko; Tabata, Satoshi; Hirakawa, Hideki

doi:10.1270/jsbbs.64.264

Cited by 27 publications

(18 citation statements)

References 45 publications

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“…MITEs are inserted mainly in the gene-rich regions and can affect gene expression (44). In peanut, due to the availability of genome sequence information, several TE markers commonly known as Arachis hypogaea transposable element (AhTE) have been identified and are made available in a database at Kazusa Peanut Database (45). AhTE markers have shown greater potential to differentiate the genotypes in groundnut (42,43,46).…”

Section: Introductionmentioning

confidence: 99%

Profiling of Nutraceuticals and Proximates in Peanut Genotypes Differing for Seed Coat Color and Seed Size

et al. 2020

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A total of 60 genotypes of peanut comprising 46 genotypes selected from ICRISAT mini core collection and 14 elite cultivars with differing kernel color and size were used to profile the nutritional parameters such as proximates (moisture, fat, ash, crude protein, crude fiber, carbohydrate content) and nutraceuticals (total polyphenol content and total antioxidant activity). The genotypes showed varied kernel color ranging from white to purple. Kernel skin color was quantified using colorimetry, and the color parameters were expressed as CIELAB color parameters. In total, nine morphological traits, six yield related traits, eight nutritional traits and eleven color parameters were observed across 60 genotypes. The sixty genotypes were grouped into ten clusters based on the color strength. Among them, Cluster-III with dark red seeds had the maximum fat content and total polyphenol content (TPC). Cluster-VI with light pink colored seeds had high antioxidant activity (AOA) and Cluster-X with white colored seeds had highest moisture and crude protein content. Color strength (K/S) was found to be positively correlated with TPC. Another color parameter, redness/greenness (a *) was found to be positively correlated with AOA. However, seed size was positively correlated with the crude protein content, but not with any other nutritional traits under study. The population studies based on the genotypic data indicated two distinct groups pertaining to botanical types of peanut. The marker-trait association (MTA) using single marker analysis indicated 75 major MTAs for most of the nutritional traits except for moisture content. The markers associated with nutritional parameters and other important yield related traits can further be utilized for genomics-assisted breeding for nutrient-rich peanuts.

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Section: Introductionmentioning

confidence: 99%

Profiling of Nutraceuticals and Proximates in Peanut Genotypes Differing for Seed Coat Color and Seed Size

et al. 2020

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“…Table 2 provides a partial list of deployed or planned breedingrelevant technology and tools currently in use. The Kazusa marker database [150] features genomics and genetics information for 10 plant species, whereas SolGenomics is a portal for several solanaceous plant species [130]. These and other breeders' toolboxes such as Soybase and MaizeGDB can serve as a starting point for comparative analysis of orphan crops with limited genomic resources.…”

Section: Breeding Data Managementmentioning

confidence: 99%

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

Gedil¹,

Ferguson²,

Girma³

et al. 2016

Next Generation Sequencing - Advances, Applications and Challenges

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The persistent challenge of insufficient food, unbalanced nutrition, and deteriorating natural resources in the most vulnerable nations, characterized by fast population growth, calls for utilization of innovative technologies to curb constraints of crop production. Enhancing genetic gain by using a multipronged approach that combines conventional and genomic technologies for the development of stress-tolerant varieties with high yield and nutritional quality is necessary. The advent of nextgeneration sequencing (NGS) technologies holds the potential to dramatically impact the crop improvement process. NGS enables whole-genome sequencing (WGS) and re-sequencing, transcriptome sequencing, metagenomics, as well as high-throughput genotyping, which can be applied for genome selection (GS). It can also be applied to diversity analysis, genetic and epigenetic characterization of germplasm and pathogen detection, identification, and elimination. High-throughput phenotyping, integrated data management, and decision support tools form the necessary supporting environment for effective utilization of genome sequence information. It is important that these opportunities for mainstreaming innovative breeding strategies, enabled by cutting-edge "Omics" technologies, are seized in Africa; however, several constraints must be addressed before the benefit of NGS can be fully realized. African breeding programs must have access to high-throughput genotyping facilities, capacity in the application of genome selection and marker-assisted breeding must be built and supported by capacity in genomic analysis and bioinformatics. This chapter demonstrates how interventions with NGS-enabled innovative strategies can be applied to increase genetic gain with insights from the Consortium of International

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“…Information on genetic diversity and relationships within and among crop species and their wild relatives is essential for the efficient utilization of plant genetic resource collections (Shirasawa et al, 2014). Moreover, the availability of this genetic diversity is a pre-requisite for any breeding of the crop improvement programs.…”

Section: Molecular Markers and Genetic Diversity Studiesmentioning

confidence: 99%

Molecular markers and their application for DNA fingerprinting and genetic diversity studies in Coffea species Marka molekuler dan penerapannya untuk studi sidik jari DNA dan keragaman genetik pada spesies Coffea

Priyono¹,

Putranto²

2016

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AbstrakStrategi klasik yang meliputi perbandingan anatomi, fisiologi dan sitogenetika telah banyak diterapkan untuk mengidentifikasi karakter tertentu serta untuk menentukan keragaman dan hubungan antar dan intra spesies. Namun, saat ini penanda molekuler telah melengkapi strategi sebelumnya dengan sangat cepat. Berbagai jenis penanda molekuler digunakan untuk menilai tingkat polimorfisme DNA. Penanda molekuler ini diklasifikasikan sebagai penanda berbasis hibridisasi dan berbasis Polymerase Chain Reaction (PCR). Dalam beberapa tahun terakhir, sistem penanda DNA yang berbeda seperti Restriction Fragment Length Polymorphisms (RFLPs), Random Amplied Polymorphic DNAs (RAPDs), Amplified Fragment Length Polymorphisms (AFLPs), Simple Sequence Repeats (SSRs) yang juga disebut Mikrosatelit, Single Nucleotide Polymorphims (SNPs) dan lain-lain telah dikembangkan dan diterapkan pada berbagai spesies tanaman. Penanda molekuler ini dapat digunakan untuk sidik jari DNA dan studi keragaman genetik. Sidik jari berdasarkan DNA telah banyak digunakan dalam ilmu forensik, juga memiliki berbagai aplikasi dalam pemuliaan tanaman. Tulisan ini memberikan overview tentang berbagai penanda molekuler dan aplikasinya untuk sidik jari dan kajian keragaman genetik tanaman berdasarkan DNA pada berbagai spesies tanaman, dan secara khusus pada Coffea sp.AbstractConventional strategies including comparative anatomy, physiology and cytogenetics were applied to identify the certain character as well as to determine inter- and intra-species diversity and relationships. However, more recently molecular markers have very rapidly complemented the previous strategies. Various types of molecular markers are used to assess DNA polymorphism. They are classified as hybridization-based markers and polymerase chain reaction (PCR) based markers. In recent years, different DNA marker systems such as Restriction Fragment Length Polymorphisms (RFLPs), Random Amplied Polymorphic DNAs (RAPDs), Amplified Fragment Length Polymorphisms (AFLPs), Simple Sequence Repeats (SSRs) which also called as microsatellites, Single Nucleotide Polymorphims (SNPs) and others have been developed and applied to a range of plant species. These molecular markers can be used for DNA fingerprinting and genetic diversity study. DNA fingerprinting has been widely used in forensic science, but is has also a variety of application in plant breeding. This paper provides an overview about various molecular markers and their application for DNA plant fingerprinting and genetic diversity, especially in Coffea sp.

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Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

Cited by 27 publications

References 45 publications

Profiling of Nutraceuticals and Proximates in Peanut Genotypes Differing for Seed Coat Color and Seed Size

Profiling of Nutraceuticals and Proximates in Peanut Genotypes Differing for Seed Coat Color and Seed Size

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

Molecular markers and their application for DNA fingerprinting and genetic diversity studies in Coffea species Marka molekuler dan penerapannya untuk studi sidik jari DNA dan keragaman genetik pada spesies Coffea

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