Identification and characterization of granule bound starch synthase I (GBSSI) gene of tartary buckwheat (Fagopyrum tataricum Gaertn.)

Wang, Xun; Feng, Bo; Xu, Zhibin; Sestili, Francesco; Zhao, Guo-Jun; Xiang, Chao; Lafiandra, D.; Wang, Tao

doi:10.1016/j.gene.2013.10.053

Cited by 24 publications

(18 citation statements)

References 46 publications

(49 reference statements)

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“…In the cladogram, a GBSS sequence, Fes sc0004292.1.g000004, clustered with a GBSS sequence from F. tataricum, which belongs to the same genus. GBSS of F. tataricum was confirmed to be expressed in the endosperm, 68 thus Fes sc0004292.1.g000004 is likely to be expressed in the endosperm too. If more than one GBSS is active within endosperms, the amylose content of buckwheat flour can be controlled by altering their copy number.…”

Section: Resultsmentioning

confidence: 92%

“…Of the 27,852 sequences identified, 238 sequences remained after the same filtering procedure as mentioned earlier and were subjected to phylogenetic analysis. Two GBSS sequences of Fagopyrum species, one from F. esculentum deposited at the EMBL/GENBANK/DDBJ (accession number: HW041459) and the other from F. tataricum (AHA36967.1), 68 were also included in the analyses. A NJ-tree based on the alignment was suggested to contain the following five known phylogenetic groups: SSI, SSII, SSIII, SSIV, and GBSS ( Supplementary Fig.…”

Section: Resultsmentioning

confidence: 99%

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Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes

Yasui

Hirakawa

Ueno

et al. 2016

DNA Res

123

139

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Buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is a nutritionally dense annual crop widely grown in temperate zones. To accelerate molecular breeding programmes of this important crop, we generated a draft assembly of the buckwheat genome using short reads obtained by next-generation sequencing (NGS), and constructed the Buckwheat Genome DataBase. After assembling short reads, we determined 387,594 scaffolds as the draft genome sequence (FES_r1.0). The total length of FES_r1.0 was 1,177,687,305 bp, and the N50 of the scaffolds was 25,109 bp. Gene prediction analysis revealed 286,768 coding sequences (CDSs; FES_r1.0_cds) including those related to transposable elements. The total length of FES_r1.0_cds was 212,917,911 bp, and the N50 was 1,101 bp. Of these, the functions of 35,816 CDSs excluding those for transposable elements were annotated by BLAST analysis. To demonstrate the utility of the database, we conducted several test analyses using BLAST and keyword searches. Furthermore, we used the draft genome as a reference sequence for NGS-based markers, and successfully identified novel candidate genes controlling heteromorphic self-incompatibility of buckwheat. The database and draft genome sequence provide a valuable resource that can be used in efforts to develop buckwheat cultivars with superior agronomic traits.

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Section: Resultsmentioning

confidence: 92%

Section: Resultsmentioning

confidence: 99%

Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes

Yasui

Hirakawa

Ueno

et al. 2016

DNA Res

123

139

View full text Add to dashboard Cite

show abstract

“…In buckwheat, starch account for over 70% of the seeds’ dry weight, thus lead its quality to be the main determinant of the quality of buckwheat seeds production 8 . However, the buckwheat starch biosynthesis genes remain largely unknown, except for two GBSS genes 54 , 55 . In our data, we identified 23 genes in starch biosynthesis which were differentially regulated during seed development of tartary buckwheat, including 3, 2, 5, 6, 2, 2, and 3 corresponding to the genes encoding SUS, UGPase, AGPase, GBSS, SS, BE, and DBE, respectively (Fig.…”

Section: Discussionmentioning

confidence: 99%

Global transcriptome analysis and identification of genes involved in nutrients accumulation during seed development of rice tartary buckwheat (Fagopyrum Tararicum)

Huang

Deng

Shi

et al. 2017

Sci Rep

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Tartary buckwheat seeds are rich in various nutrients, such as storage proteins, starch, and flavonoids. To get a good knowledge of the transcriptome dynamics and gene regulatory mechanism during the process of seed development and nutrients accumulation, we performed a comprehensive global transcriptome analysis using rice tartary buckwheat seeds at different development stages, namely pre-filling stage, filling stage, and mature stage. 24 819 expressed genes, including 108 specifically expressed genes, and 11 676 differentially expressed genes (DEGs) were identified. qRT-PCR analysis was performed on 34 DEGs to validate the transcriptome data, and a good consistence was obtained. Based on their expression patterns, the identified DEGs were classified to eight clusters, and the enriched GO items in each cluster were analyzed. In addition, 633 DEGs related to plant hormones were identified. Furthermore, genes in the biosynthesis pathway of nutrients accumulation were analyzed, including 10, 20, and 23 DEGs corresponding to the biosynthesis of seed storage proteins, flavonoids, and starch, respectively. This is the first transcriptome analysis during seed development of tartary buckwheat. It would provide us a comprehensive understanding of the complex transcriptome dynamics during seed development and gene regulatory mechanism of nutrients accumulation.

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“…Tartary buckwheat seeds and leaves are used mainly for human consumption and animal fodder, Electronic supplementary material The online version of this article (doi:10.1007/s11105-015-0907-5) contains supplementary material, which is available to authorized users. and contain proteins with high biological value, a balanced amino acid composition, starch, mineral compounds, bioflavonoid rutin, relatively high crude fiber and vitamins (B1, B2, B6) (Fabjan et al 2003;Lee et al 2013;Wang et al 2014). The seeds contain more rutin than common buckwheat, and tartary buckwheat has recently also attracted attention as a pharmaceutical plant.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Buckwheat Cultivars (Fagopyrum tartaricum Gaertn.) Assessed with SSR Markers Developed from Genome Survey Sequences

et al. 2015

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Tartary buckwheat is an important edible crop as well as medicinal plant in China. More and more research is being focused on this minor grain crop because of its medicinal functions, but there is a paucity of molecular markers for tartary buckwheat due to the lack of genomics. In this study, a genome survey was carried out in tartary buckwheat, from which SSR markers were developed for analysis of genetic diversity. The survey generated 21.9 Gb raw sequence reads which were assembled into 348.34 Mb genome sequences included 204,340 contigs. The genome size was estimated to be about 497 Mb based on K-mer analysis. In total, 24,505 SSR motifs were identified and characterised from this genomic survey sequence. Most of the SSR motifs were dinucleotide (67.14 %) and tri-nucleotide (26.05 %) repeats.AT/AT repeat motifs were the most abundant, accounting for 78.60 % of di-nucleotide repeat motifs. SSR fingerprinting of 64 accessions yielded 49.71 effective allele loci from a total of 63 with the 23 polymorphic SSR primer combinations. Analyses of the population genetic structure using SSR data strongly suggested that the 64 accessions of tartary buckwheat clustered into two separate subgroups. One group was mainly distributed in Nepal, Bhutan and the Yunnan-Guizhou Plateau regions of China; the other group was mainly derived from the Loess Plateau regions, Hunan and Hubei of China and USA. The cluster analysis of these accession's genetic similarity coefficient by UPMGA methods strongly supported the two subgroup interpretation. However accessions from Qinghai of China could be grouped into either of the two subgroups depending on which classification method was used. This region is at the intersection of the two geographical regions associated with the two subgroups. These results and information could be used to identify and utilize germplasm resources for improving tartary buckwheat breeding.

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Identification and characterization of granule bound starch synthase I (GBSSI) gene of tartary buckwheat (Fagopyrum tataricum Gaertn.)

Cited by 24 publications

References 46 publications

Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes

Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes

Global transcriptome analysis and identification of genes involved in nutrients accumulation during seed development of rice tartary buckwheat (Fagopyrum Tararicum)

Genetic Diversity of Buckwheat Cultivars (Fagopyrum tartaricum Gaertn.) Assessed with SSR Markers Developed from Genome Survey Sequences

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