Comparative Genomic Analysis of Soybean Flowering Genes

Jung, Chol‐Hee; Wong, Chui Eng; Singh, Mohan B.; Bhalla, Prem L.

doi:10.1371/journal.pone.0038250

Cited by 101 publications

(117 citation statements)

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“…33,[36][37][38][39][40] These FT homologs of legumes are commonly classified into three clades, designated FTa, FTb, and FTc, according to phylogenetic analyses. Some of them have been demonstrated that they have an ability to promote flowering.…”

Section: )mentioning

confidence: 99%

Clock-Controlled and FLOWERING LOCUS T (FT)-Dependent Photoperiodic Pathway in Lotus japonicus I: Verification of the Flowering-Associated Function of an FT Homolog

Yamashino

Yamawaki

Hagui

et al. 2013

Bioscience, Biotechnology, and Biochemistry

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During the last decade, significant research progress in the study of Arabidopsis thaliana has been made in defining the molecular mechanism by which the plant circadian clock regulates flowering time in response to changes in photoperiod. It is generally accepted that the clock-controlled CONSTANS (CO)-FLOWERING LOCUS T (FT)-mediated external coincidence mechanism underlying the photoperiodic control of flowering time is conserved in higher plants, including A. thaliana and Oryza sativa. However, it is also assumed that the mechanism differs considerably in detail among species. Here we characterized the clock-controlled CO-FT pathway in Lotus japonicus (a model legume) in comparison with that of A. thaliana. L. japonicus has at least one FT orthologous gene (named LjFTa), which is induced specifically in long-days and complements the mutational lesion of the A. thaliana FT gene. However, it was speculated that this legume might lack the upstream positive regulator CO. By employing L. japonicus phyB mutant plants, we showed that the photoreceptor mutant displays a phenotype of early flowering due to enhanced expression of LjFTa, suggesting that LjFTa is invovled in the promotion of flowering in L. japonicus. These results are discussed in the context of current knowledge of the flowering in crop legumes such as soybean and garden pea.

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Section: )mentioning

confidence: 99%

Clock-Controlled and FLOWERING LOCUS T (FT)-Dependent Photoperiodic Pathway in Lotus japonicus I: Verification of the Flowering-Associated Function of an FT Homolog

Yamashino

Yamawaki

Hagui

et al. 2013

Bioscience, Biotechnology, and Biochemistry

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“…The first objective of this thesis, as described in Chapters 3-4, was achieved using bioinformatic approaches based on information available in the flowering literature of Arabidopsis and Soybean (Table 1.2), and also molecular biology techniques. The second objective of this thesis, also described in Chapters 3-4, was APETALA1 ( FLOWERING LOCUS T AT1G65480 (Kobayashi et al, 1999) Glyma16g26660 (Jung et al, 2012;Kim et al, 2012;Kong et al, 2010), Glyma16g04830…”

Section: Aim and Objectives Of Researchmentioning

confidence: 99%

“…Glyma08g47810 (Kim et al, 2012;Kong et al, 2010;Zhai et al, 2014) GIGANTEA (GI) AT1G22770 (Fowler et al, 1999) Glyma09g07240 (Jung et al, 2012) Glyma10g36600 (Kim et al, 2012;Watanabe et al, 2011) LEAFY ( Matsuzaki, H., Dong, S., Loi, H., Di, X., Liu, G., Hubbell, E., Law, J., Berntsen, T., Chadha, M., Hui, H., et al (2004). Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays.…”

Section: Aim and Objectives Of Researchmentioning

confidence: 99%

“…They were crucial to the regulation of photoperiodic flowering time and have been reported by a number of publications (Fowler et al, 1999;Kobayashi et al, 1999;Nelson et al, 2000;Briggs and Olney, 2001;Suarez-Lopez et al, 2001;Sawa et al, 2007;Jang et al, 2009;Zuo et al, 2011;Song et al, 2012). Sequences of the flowering genes in Soybean (Jung et al, 2012;Kim et al, 2012) were obtained from Phytozome v 9.1 database (Goodstein et al, 2012). Geneious Pro version 6 (http://www.geneious.com, ) was used to map Pongamia short reads libraries, genomic (SRA051251) and transcriptome (SRA046342.1) to the Soybean flowering genes, genomic and coding sequences (CDS), in which matching sequences within the short reads libraries were aligned with the sequence of reference genes.…”

Section: Mapping Of Reference Genes With Pongamia Databasesmentioning

confidence: 99%

“…As described in Section 2.2, Geneious Pro Version 6 software (http://www.geneious.com, ) was used to map short paired sequence reads libraries of Pongamia genomic and transcriptome to the PHY reference genes isolated from Soybean (Gm09g03990, Gm10g28170 and Gm20g22160) which were published in (Jung et al, 2012;Kim et al, 2012). Consensus sequences were generated from aligned Pongamia short paired reads during the mapping process and used to design primers in this study.…”

Section: Bioinformaticsmentioning

confidence: 99%

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Molecular characterisation of flowering genes in Pongamia Pinnata

Kamde¹

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Pongamia pinnata (Pongamia) is a multipurpose tree that has been used traditionally for medicine, green manure, insecticide, fuel and also a source of timber. It is an indigenous plant to the Indian subcontinent and Southeast Asia, and has been successfully introduced to Northern Australia, New Zealand and several other countries with humid tropical lowlands. Recently, Pongamia has attracted interest as one of the alternative feedstock for biodiesel productions due to its ability to produce seeds with high oil content. The fatty acid methyl ester (FAME) composition of Pongamia met the biodiesel specification standards of USA (ASTMD 6751), Germany (DIN 51606) and European Standard Organisation (EN 14214), and is considered as one of the most suitable sources of biodiesel. Despite the positive attributes described above, Pongamia is not a domesticated species and further research is required for the selection of elite cultivars with desirable traits optimal for large scale production of Pongamia oil. In addition, limited information is currently available regarding the flowering mechanism of Pongamia at the molecular level that could provide the platform for the development of oil-rich seeds.The aim of this thesis is to provide insight and increase the understanding of the genetic network that leads to flowering in Pongamia. Based on large phenotypic diversity of Pongamia, this information could subsequently be used to determine and select traits with unique flowering time that will allow a harvesting window, where harvesting process will not clash with flowering. The first objective of this project is to identify, isolate and characterise the candidate genes that regulate flowering time in Pongamia. This was achieved using molecular biology techniques and bioinformatic approaches based on the information available on flowering mechanisms of Arabidopsis and soybean in the literature. The second objective of this project is to determine the expression pattern of isolated genes during flowering onset. This was achieved through transcriptome methodologies such as RT-PCR and qRT-PCR. The third objective of this project is to investigate the genetic variety of Pongamia. This was achieved through Single Nucleotide Polymorphism (SNPs) analysis and its correlation with the late flowering phenotype of Pongamia.PpCOL-1 and PpPHYB are the two genes that were investigated in this thesis. The orthologue genes of PpCOL-1 and PpPHYB are involved in the flowering regulation of the annual plant Arabidopsis.Since Arabidopsis and Pongamia are both long day plants, it is postulated that these genes might play a role in the flowering time control in Pongamia. PpCOL-1 and PpPHYB were successfully isolated, characterised and compared to their respective orthologue genes in Arabidopsis, Soybean and Medicago. It was found that the amino acid residues within the domain regions in these genes iii are highly conserved in Pongamia. Interestingly, there were no significant differences in the expression patterns of PpCOL-1 and PpPHYB in...

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Overexpression of PIF4 affects plant morphology and accelerates reproductive phase transitions in soybean

Arya

Singh

Bhalla

2021

Food and Energy Security

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Phytochrome‐interacting factor 4 acts as a signalling hub for integrating multiple environmental cues like light and temperature. While the function of PIF4 in the model plant Arabidopsis has been studied, there is limited knowledge regarding the role of PIF4 in agronomically important legume crop soybean. Here, we employed a constitutive overexpression approach to functionally characterise a soybean PIF4 homolog, GmPIF4b in a determinate short‐day cultivar, Bragg. Multiple sequence alignment of seven soybean PIF4 homologs (GmPIF4a‐g) with Arabidopsis PIF4 revealed the presence of an active phytochrome‐binding (APB) domain in the N‐terminal region of six soybean PIF4 homologs. Cis‐elements related to plant hormone biosynthesis, stress response, meristem and endosperm gene expression were located in the promoter region of soybean PIF4s. Interestingly, transgenic soybean plants carrying 35s::GmPIF4b::polyA construct showed reduced plant height, reduced leaf surface area, decreased branching, early flowering and faster transition from full‐bloom flowering stage to full maturity stage without any decline in yield. Further, pod colour of transgenic soybean plants changed to dark brown, whereas wild‐type plants showed tan or light brown pod colour. Clear hilum was observed in seeds obtained from transgenic plants as opposed to the dark or black hilum of wild‐type seeds. Transcripts of soybean florigens GmFT2a and GmFT5a were also elevated in transgenic plants. Collectively, our results suggest that GmPIF4b overexpression could affect phenotypes related to plant morphology and reproductive stages in soybean, and can be used as a gene target for soybean improvement programmes to ensure future food security.

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Comparative Genomic Analysis of Soybean Flowering Genes

Cited by 101 publications

References 55 publications

Clock-Controlled and FLOWERING LOCUS T (FT)-Dependent Photoperiodic Pathway in Lotus japonicus I: Verification of the Flowering-Associated Function of an FT Homolog

Clock-Controlled and FLOWERING LOCUS T (FT)-Dependent Photoperiodic Pathway in Lotus japonicus I: Verification of the Flowering-Associated Function of an FT Homolog

Molecular characterisation of flowering genes in Pongamia Pinnata

Overexpression of PIF4 affects plant morphology and accelerates reproductive phase transitions in soybean

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