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

20

---

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

Kenji Fujino Yoshihiro Kawahara Kanako O. Koyanagi Kenta Shirasawa

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.20089, (Released:2021-02-17)

被引用文献数

8

---

Understanding genetic diversity among local populations is a primary goal of modern crop breeding programs. Here, we demonstrated the genetic relationships of rice varieties in Hokkaido, Japan, one of the northern limits of rice cultivation around the world. Furthermore, artificial selection during rice breeding programs has been characterized using genome sequences. We utilized 8,565 single nucleotide polymorphisms and insertion/deletion markers distributed across the genome in genotype-by-sequencing for genetic diversity analyses. Phylogenetics, genetic population structure, and principal component analysis showed that a total of 110 varieties were classified into four distinct clusters according to different populations geographically and historically. Furthermore, the genome sequences of 19 rice varieties along with historic representations in Hokkaido, nucleotide diversity and FST values in each cluster revealed that artificial selection of elite phenotypes focused on chromosomal regions. These results clearly demonstrated the history of the selections on agronomic traits as genome sequences among current rice varieties from Hokkaido.

著者

Katsuhiko Sumitomo Kenta Shirasawa Sachiko N. Isobe Hideki Hirakawa Akiho Harata Masato Kawabe Masafumi Yagi Masaaki Osaka Miyuki Kunihisa Fumiya Taniguchi

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

pp.20063, (Released:2021-03-25)

被引用文献数

6

---

White rust caused by Puccinia horiana Henn. adversely affects chrysanthemum (Chrysanthemum morifolium Ramat.) production. The breeding of resistant varieties is effective in controlling the disease. Here we aimed to develop DNA markers for the strong resistance to P. horiana. We conducted a linkage analysis based on the genome-wide association study (GWAS) method. We employed a biparental population for the GWAS, wherein the single nucleotide polymorphism (SNP) allele frequency could be predicted. The population was derived from crosses between a strong resistant “Southern Pegasus” and a susceptible line. The GWAS used simplex and double-simplex SNP markers selected out of SNP candidates mined from ddRAD-Seq data of an F1 biparental population. These F1 individuals segregated in a 1:1 ratio of resistant to susceptible. Twenty-one simplex SNPs were significantly associated with P. horiana resistance in “Southern Pegasus” and generated one linkage group. These results show the presence of a single resistance gene in “Southern Pegasus”. We identified the nearest SNP marker located 2.2 cM from P. horiana resistance locus and demonstrated this SNP marker-resistance link using an independent population. This is the first report of an effective DNA marker linked to a gene for P. horiana resistance in chrysanthemum.

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

20

---

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

Kenji Nashima Makoto Takeuchi Chie Moromizato Yuta Omine Moriyuki Shoda Naoya Urasaki Kazuhiko Tarora Ayaka Irei Kenta Shirasawa Masahiko Yamada Miyuki Kunihisa Chikako Nishitani Toshiya Yamamoto

出版者

The Japanese Society for Horticultural Science

雑誌

The Horticulture Journal (ISSN:21890102)

巻号頁・発行日

pp.QH-063, (Released:2023-05-31)

---

The pineapple (Ananas comosus (L.) Merr.) is an economically important tropical fruit crop. In this study, we performed quantitative trait locus (QTL) analysis using 168 individuals of the F1 population of ‘Yugafu’ × ‘Yonekura’ for 15 traits: leaf color (L*, a*, b*), harvest day, crown number, slip number, stem shoot number, sucker number, fruit weight, fruit height, fruit diameter, fruit shell color, soluble solid content, acidity, and ascorbic acid content. The constructed single-nucleotide polymorphism (SNP)-based genetic linkage map consisted of a total genetic distance of 2,595 cM with 3,123 loci, including 22,330 SNPs across 25 chromosomes. QTL analysis detected 13 QTLs for 9 traits: leaf color a*, harvest day, fruit weight, fruit height, fruit diameter, fruit shell color, soluble solid content, acidity, and ascorbic acid content. The causative gene for each QTL was predicted with two genes identified as candidate genes. The AcCCD4 gene on Aco3.3C08 was the predicted causative gene for the shell color QTL, which negatively controls shell color by carotenoid degradation. The Myb domain protein-encoding gene on Aco3.3C02 was the predicted causative gene for shell color and leaf color a* QTL, which positively regulates anthocyanin accumulation. The QTL and gene information provided here contributes to future marker-assisted selection for fruit quality.

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

---

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

Masako Ichikawa Norio Kato Erika Toda Masakazu Kashihara Yuji Ishida Yukoh Hiei Sachiko N. Isobe Kenta Shirasawa Hideki Hirakawa Takashi Okamoto Toshihiko Komari

出版者

Japanese Society of Breeding

雑誌

Breeding Science (ISSN:13447610)

巻号頁・発行日

vol.73, no.3, pp.349-353, 2023 (Released:2023-07-27)

参考文献数

25

被引用文献数

1

---

Somaclonal variation was studied by whole-genome sequencing in rice plants (Oryza sativa L., ‘Nipponbare’) regenerated from the zygotes, mature embryos, and immature embryos of a single mother plant. The mother plant and its seed-propagated progeny were also sequenced. A total of 338 variants of the mother plant sequence were detected in the progeny, and mean values ranged from 9.0 of the seed-propagated plants to 37.4 of regenerants from mature embryos. The natural mutation rate of 1.2 × 10–8 calculated using the variants in the seed-propagated plants was consistent with the values reported previously. The ratio of single nucleotide variants (SNVs) among the variants in the seed-propagated plants was 91.1%, which is higher than 56.1% previously reported, and not significantly different from those in the regenerants. Overall, the ratio of transitions to transversions of SNVs was lower in the regenerants as shown previously. Plants regenerated from mature embryos had significantly more variants than different progeny types. Therefore, using zygotes and immature embryos can reduce somaclonal variation during the genetic manipulation of rice.

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)

---

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

---

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

10

---

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.