著者

Kenta Shirasawa Daijiro Harada Hideki Hirakawa Sachiko Isobe Chittaranjan Kole

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.20146, (Released:2021-04-06)

被引用文献数

19

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Genome sequence analysis in higher plants began with the whole-genome sequencing of Arabidopsis thaliana. Owing to the great advances in sequencing technologies, also known as next-generation sequencing (NGS) technologies, genomes of more than 300 plant species have been sequenced to date. Long-read sequencing technologies, together with sequence scaffolding methods, have enabled the synthesis of chromosome-level de novo genome sequence assemblies, which has further allowed comparative analysis of the structural features of multiple plant genomes, thus elucidating the evolutionary history of plants. However, the quality of the assembled chromosome-level sequences varies among plant species. In this review, we summarize the status of chromosome-level assemblies of 114 plant species, with genome sizes ranging from 125 Mb to 16.9 Gb. While the average genome coverage of the assembled sequences reached up to 88.7%, the average coverage of chromosome-level pseudomolecules was 72.9%. Thus, further improvements in sequencing technologies and scaffolding, and data analysis methods, are required to establish gap-free telomere-to-telomere genome sequence assemblies. With the forthcoming new technologies, we are going to enter into a new genomics era where pan-genomics and the >1,000 or >1 million genomes’ project will be routine in higher plants.

著者

Kenta Shirasawa Daijiro Harada Hideki Hirakawa Sachiko Isobe Chittaranjan Kole

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

vol.71, no.2, pp.117-124, 2021 (Released:2021-05-20)

参考文献数

44

被引用文献数

19

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Genome sequence analysis in higher plants began with the whole-genome sequencing of Arabidopsis thaliana. Owing to the great advances in sequencing technologies, also known as next-generation sequencing (NGS) technologies, genomes of more than 400 plant species have been sequenced to date. Long-read sequencing technologies, together with sequence scaffolding methods, have enabled the synthesis of chromosome-level de novo genome sequence assemblies, which has further allowed comparative analysis of the structural features of multiple plant genomes, thus elucidating the evolutionary history of plants. However, the quality of the assembled chromosome-level sequences varies among plant species. In this review, we summarize the status of chromosome-level assemblies of 114 plant species, with genome sizes ranging from 125 Mb to 16.9 Gb. While the average genome coverage of the assembled sequences reached up to 89.1%, the average coverage of chromosome-level pseudomolecules was 73.3%. Thus, further improvements in sequencing technologies and scaffolding, and data analysis methods, are required to establish gap-free telomere-to-telomere genome sequence assemblies. With the forthcoming new technologies, we are going to enter into a new genomics era where pan-genomics and the >1,000 or >1 million genomes’ project will be routine in higher plants.

著者

Taeko Shibaya Chika Kuroda Shinobu Nakayama Chiharu Minami Akiko Obara Takayoshi Fujii Sachiko Isobe

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.20120, (Released:2021-03-30)

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In carrot (Daucus carota L), the taproot colors orange, yellow and white are determined mostly by the Y, Y2, and Or loci. One of the most severe issues in carrot seed production is contamination by wild white carrot. To evaluate the contamination ratio, easily detectable DNA markers for white carrot are desired. To develop PCR-based DNA markers for the Y2 locus, we have re-sequenced two orange-colored carrot cultivars at our company (Fujii Seed, Japan), as well as six white- and one light-orange-colored carrots that contaminated our seed products. Within the candidate region previously reported for the Y2 locus, only one DNA marker, Y2_7, clearly distinguished white carrots from orange ones in the re-sequenced samples. The Y2_7 marker was further examined in 12 of the most popular hybrid orange cultivars in Japan, as well as ‘Nantes’ and ‘Chantenay Red Cored 2’. The Y2_7 marker showed that all of the orange cultivars examined had the orange allele except for ‘Beta-441’. False white was detected in the orange-colored ‘Beta-441’. The Y2_7 marker detected white root carrot contamination in an old open-pollinated Japanese cultivar, ‘Nakamura Senkou Futo’. This marker would be a useful tool in a carrot seed quality control for some cultivars.

著者

Sachiko Isobe Kenta Shirasawa Hideki Hirakawa

出版者

The Japanese Society for Horticultural Science

雑誌

The Horticulture Journal (ISSN:21890102)

巻号頁・発行日

vol.89, no.2, pp.108-114, 2020 (Released:2020-04-06)

参考文献数

37

被引用文献数

3

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Next generation sequencing (NGS) is one of the most impactful technologies to appear in the 21st century, and has already brought important changes to agriculture, especially in the field of breeding. Construction of a reference genome is key to the advancement of genomic studies, and therefore, de novo whole genome assembly has been performed in various plants, including strawberry. Strawberry (Fragaria × ananassa) is an allo-octoploid species (2n = 8x = 56), which has four discriminable subgenomes. Because of its complex genome structure, de novo whole genome assembly in strawberry has been considered a difficult challenge. However, recent advances of NGS technologies have allowed the construction of chromosome-scale de novo whole genome assembly. In this manuscript, we review the recent advances in de novo whole genome sequencing in strawberry and other Fragaria species. The genome structure and domestication history in strawberry is one of the largest questions in genetic and genomic studies in strawberry. Therefore, the domestication history in strawberry is also be reviewed based on comparisons of genes and genome sequences across Fragaria species.

著者

Takuya Wada Yuji Noguchi Sachiko Isobe Miyuki Kunihisa Takayuki Sueyoshi Katsumi Shimomura

出版者

一般社団法人 園芸学会

雑誌

The Horticulture Journal (ISSN:21890102)

巻号頁・発行日

pp.MI-142, (Released:2017-01-14)

被引用文献数

11

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A strawberry core collection was established based on simple sequence repeat and cleavage amplified polymorphic sequence marker polymorphisms in 119 strawberry cultivars using the “PowerCore” program. The core collection consisted of 19 cultivars. The correlation coefficients for the diversity index were significant between the core collection cultivars and all cultivars. Allele frequencies of each marker allele were not significantly different between the core collection cultivars and all cultivars according to Fisher’s exact test. Cluster analysis indicated that the selected core collection cultivars evenly distributed throughout the multiple clusters and principle component analysis clearly showed major principle components of core collection cultivars distributed widely among those of all cultivars. Furthermore, core collection cultivars tended to harbor minor alleles. These results demonstrated that the core collection cultivars were suitably selected in terms of reflecting the genetic diversity of all strawberry cultivars.

著者

Naoki Yokotani Yoshinori Hasegawa Yusuke Kouzai Hideki Hirakawa Sachiko Isobe

出版者

Japanese Society for Plant Biotechnology

雑誌

Plant Biotechnology (ISSN:13424580)

巻号頁・発行日

vol.40, no.4, pp.273-282, 2023-12-25 (Released:2023-12-25)

参考文献数

51

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Salicylic acid (SA) is known to be involved in the immunity against Clavibacter michiganensis ssp. michiganensis (Cmm) that causes bacterial canker in tomato. To identify the candidate genes associated with SA-inducible Cmm resistance, transcriptome analysis was conducted via RNA sequencing in tomato plants treated with SA. SA treatment upregulated various defense-associated genes, such as PR and GST genes, in tomato cotyledons. A comparison of SA- and Cmm-responsive genes revealed that both SA treatment and Cmm infection commonly upregulated a large number of genes. Gene Ontology (GO) analysis indicated that the GO terms associated with plant immunity were over-represented in both SA- and Cmm-induced genes. The genes commonly downregulated by both SA treatment and Cmm infection were associated with the cell cycle and may be involved in growth and immunity trade-off through cell division. After SA treatment, several proteins that were predicted to play a role in immune signaling, such as resistance gene analogs, Ca2+ sensors, and WRKY transcription factors, were transcriptionally upregulated. The W-box element, which was targeted by WRKYs, was over-represented in the promoter regions of genes upregulated by both SA treatment and Cmm infection, supporting the speculation that WRKYs are important for the SA-mediated immunity against Cmm. Prediction of protein–protein interactions suggested that genes encoding receptor-like kinases and EF-hand proteins play an important role in immune signaling. Thus, various candidate genes involved in SA-inducible Cmm resistance were identified.

著者

Takuya Wada Hiyori Monden Sachiko Isobe Kenta Shirasawa Takayuki Sueyoshi Chiharu Hirata Miyuki Mori Shiro Nagamatsu Yoshiki Tanaka

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.20151, (Released:2021-08-20)

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Male sterility is one of the reproductive isolation systems in plants and quite useful for F1 seed production. We previously identified three independent quantitative trait loci (QTLs) for male sterility of cultivated strawberry, Here, we identified the specific subgenomes in which these QTLs are located by QTL-seq approach. QTLs qMS4.1, qMS4.2, and qMS4.3 were mapped separately in subgenomes Fvb4-4, Fvb4-3, and Fvb4-1, respectively, in ‘Camarosa’ genome assembly v. 1.0.a1. Candidate regions of qMS4.1 and qMS4.3 were clearly detected around 12–26 Mb in Fvb4-4 and 12–14 Mb in Fvb4-1, respectively; those of qMS4.2 were fragmented in Fvb4-3, which suggests that some scaffolds were incorrectly assembled in Fvb4-3. qMS4.3 was mapped to chr4X1 of ‘Reikou’ genome assembly r2.3, and qMS4.1 and qMS4.2 were both mapped to chr4Av, which indicates that differentiation of the subgenomes in which both QTLs are located was insufficient in ‘Reikou’ r2.3. Although ‘Camarosa’ genome assembly v. 1.0.a1 is an unphased map, which merges homologous chromosomes into one sequence, ‘Reikou’ genome assembly r2.3 is a phased map, which separates homologous chromosomes. QTL mapping to different reference genomes clearly showed the specific features of each reference genome, and that using different kinds of reference map could accelerate fine mapping and map-based cloning of certain genes of cultivated strawberry.

著者

Emdadul Haque Eiji Yamamoto Kenta Shirasawa Hiroaki Tabuchi Ung-Han Yoon Sachiko Isobe Masaru Tanaka

出版者

Japanese Society for Root Research

雑誌

Plant Root (ISSN:18816754)

巻号頁・発行日

vol.14, pp.11-21, 2020 (Released:2020-10-09)

参考文献数

31

被引用文献数

6

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Genetic studies on the purple-fleshed sweetpotato (Ipomoea batatas L.), which is rich in anthocyanin (AN) in the storage root, were performed by polyploid GWAS based on the allele dosage probability using 59,675 SNPs obtained from 94 F1 progenies between the cultivars 'Konaishin' (which has a high yield but no AN) and 'Akemurasaki' (which has a high AN content but low to moderate yield). The distribution of relative AN content was highly biased, with 60% of clones showing a low to undetectable level (A530 < 0.5). Fifty-nine SNPs from six signals on homologous groups (HGs) 3, 5 (one major and one smaller signal), 7, 13, and 15 were strongly associated with the relative AN content. Twelve SNPs from the major signal and one from the smaller signal of HG 5 were further detected by QTL analysis. In a database search of the AN biosynthesis gene, transcription factors IbMYB1 and IbWD40 and AN structural genes IbF3H and IbDFR were located on HG 5, suggesting that an SNP marker or markers from HG 5 might be tightly linked to candidate gene(s) homologous to one of these transcription factors and AN structural genes as a major factor in determining AN accumulation in the storage roots. These results would enhance our understanding of the underlying genetic basis of AN accumulation in the storage roots of sweetpotatoes, and the SNP markers found here, especially 13 SNPs from HG 5, would be a potential platform for future marker-assisted selection for breeding high-AN sweetpotato varieties.

著者

Emdadul Haque Hiroaki Tabuchi Yuki Monden Keisuke Suematsu Kenta Shirasawa Sachiko Isobe Masaru Tanaka

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.19099, (Released:2020-05-19)

被引用文献数

7

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While sweetpotato (Ipomoea batatas L.) improvement has generally been done by field-based selection, molecular genetic studies on traits of interest, i.e., molecular markers are needed for enhancing the breeding program of this world’s 7th most important crop, as such markers facilitate marker-assisted selection. Here, we performed a combined approach of QTLs analyses and GWAS of storage root β-carotene content (BC), dry-matter (DM) and starch content (SC) using the genetic linkage maps constructed with 5,952 and 5,640 SNPs obtained from F1 progenies between cultivars ‘J-Red’ and ‘Choshu’. BC was negatively correlated with DM (r = –0.45) and SC (r = –0.51), while DM was positively correlated with SC (r = 0.94). In both parental maps, a total of five, two and five QTL regions on linkage groups 7 and 8 were associated with BC, DM and SC, respectively. In GWAS of BC, one strong signal (P = 1.04 × 10–9) was observed on linkage group 8, which co-located with one of the above QTL regions. The SNPs markers found here, particularly for β-carotene, would be useful base resources for future marker-assisted selection program with this trait.