A Comparison of Phenylpropanoid Pathway Gene Families in Common Bean. Focus on P450 and C4H Genes

Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.

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Annotation, phylogeny and expression analysis of the nuclear factor Y gene families in common bean (Phaseolus vulgaris)

Frontiers in Plant Science ◽

10.3389/fpls.2014.00761 ◽

2015 ◽

Vol 5 ◽

Cited By ~ 5

Author(s):

Carolina RÃpodas ◽

MÃ©lisse Castaingts ◽

JoaquÃn ClÃºa ◽

Flavio Blanco ◽

MarÃa Eugenia Zanetti

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Expression Analysis ◽

Gene Families ◽

Nuclear Factor ◽

Nuclear Factor Y

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Phenylpropanoid Pathway Engineering: An Emerging Approach towards Plant Defense

Pathogens ◽

10.3390/pathogens9040312 ◽

2020 ◽

Vol 9 (4) ◽

pp. 312 ◽

Cited By ~ 11

Author(s):

Vivek Yadav ◽

Zhongyuan Wang ◽

Chunhua Wei ◽

Aduragbemi Amo ◽

Bilal Ahmed ◽

...

Keyword(s):

Cell Wall ◽

Plant Defense ◽

Plant Cell Wall ◽

Shikimate Pathway ◽

Gene Families ◽

Phenylpropanoid Pathway ◽

Pathway Engineering ◽

Multiple Gene ◽

Regulator Genes ◽

Microbial Attack

Pathogens hitting the plant cell wall is the first impetus that triggers the phenylpropanoid pathway for plant defense. The phenylpropanoid pathway bifurcates into the production of an enormous array of compounds based on the few intermediates of the shikimate pathway in response to cell wall breaches by pathogens. The whole metabolomic pathway is a complex network regulated by multiple gene families and it exhibits refined regulatory mechanisms at the transcriptional, post-transcriptional, and post-translational levels. The pathway genes are involved in the production of anti-microbial compounds as well as signaling molecules. The engineering in the metabolic pathway has led to a new plant defense system of which various mechanisms have been proposed including salicylic acid and antimicrobial mediated compounds. In recent years, some key players like phenylalanine ammonia lyases (PALs) from the phenylpropanoid pathway are proposed to have broad spectrum disease resistance (BSR) without yield penalties. Now we have more evidence than ever, yet little understanding about the pathway-based genes that orchestrate rapid, coordinated induction of phenylpropanoid defenses in response to microbial attack. It is not astonishing that mutants of pathway regulator genes can show conflicting results. Therefore, precise engineering of the pathway is an interesting strategy to aim at profitably tailored plants. Here, this review portrays the current progress and challenges for phenylpropanoid pathway-based resistance from the current prospective to provide a deeper understanding.

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Plant Defense Genes Associated with Quantitative Resistance to Potato Late Blight in Solanum phureja × Dihaploid S. tuberosum Hybrids

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi.2002.15.6.587 ◽

2002 ◽

Vol 15 (6) ◽

pp. 587-597 ◽

Cited By ~ 65

Author(s):

Friederike Trognitz ◽

Patricia Manosalva ◽

Rene Gysin ◽

David Niño-Liu ◽

Reinhard Simon ◽

...

Keyword(s):

Late Blight ◽

Plant Defense ◽

Permutation Test ◽

Quantitative Resistance ◽

Late Blight Resistance ◽

Gene Families ◽

Phenylpropanoid Pathway ◽

Defense Genes ◽

Plant Defense Genes ◽

Hybridization Probes

Markers corresponding to 27 plant defense genes were tested for linkage disequilibrium with quantitative resistance to late blight in a diploid potato population that had been used for mapping quantitative trait loci (QTLs) for late blight resistance. Markers were detected by using (i) hybridization probes for plant defense genes, (ii) primer pairs amplifying conserved domains of resistance (R) genes, (iii) primers for defense genes and genes encoding transcriptional regulatory factors, and (iv) primers allowing amplification of sequences flanking plant defense genes by the ligation-mediated polymerase chain reaction. Markers were initially screened by using the most resistant and susceptible individuals of the population, and those markers showing different allele frequencies between the two groups were mapped. Among the 308 segregating bands detected, 24 loci (8%) corresponding to six defense gene families were associated with resistance at χ2 ≥ 13, the threshold established using the permutation test at P = 0.05. Loci corresponding to genes related to the phenylpropanoid pathway (phenylalanine ammonium lyase [PAL], chalcone isomerase [CHI], and chalcone synthase [CHS]), loci related to WRKY regulatory genes, and other defense genes (osmotin and a Phytophthora infestans-induced cytochrome P450) were significantly associated with quantitative disease resistance. A subset of markers was tested on the mapping population of 94 individuals. Ten defense-related markers were clustered at a QTL on chromosome III, and three defense-related markers were located at a broad QTL on chromosome XII. The association of candidate genes with QTLs is a step toward understanding the molecular basis of quantitative resistance to an important plant disease.

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CLE peptide-encoding gene families in Medicago truncatula and Lotus japonicus, compared with those of soybean, common bean and Arabidopsis

Scientific Reports ◽

10.1038/s41598-017-09296-w ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 22

Author(s):

April H. Hastwell ◽

Thomas C. de Bang ◽

Peter M. Gresshoff ◽

Brett J. Ferguson

Keyword(s):

Common Bean ◽

Medicago Truncatula ◽

Lotus Japonicus ◽

Gene Families ◽

Cle Peptide ◽

Encoding Gene

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Comparative bioinformatic analysis of genes expressed in common bean (Phaseolus vulgaris L.) seedlings

Genome ◽

10.1139/g05-010 ◽

2005 ◽

Vol 48 (3) ◽

pp. 562-570 ◽

Cited By ~ 31

Author(s):

Maeli Melotto ◽

Claudia B Monteiro-Vitorello ◽

Adriano G Bruschi ◽

Luis E.A Camargo

Keyword(s):

Phaseolus Vulgaris ◽

Common Bean ◽

Expressed Sequence Tag ◽

Gene Families ◽

Bioinformatic Analysis ◽

Colletotrichum Lindemuthianum ◽

Cdna Libraries ◽

Nucleotide Polymorphisms ◽

Phaseolus Vulgaris L ◽

Single Nucleotide

To rapidly and cost-effectively generate gene expression data, we developed an annotated unigene database of common bean (Phaseolus vulgaris L.). In this study, 3 cDNA libraries were constructed from the bean breeding line SEL1308, 1 from young leaf and 2 from seedlings inoculated or not inoculated with the fungal pathogen Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara, which causes anthracnose in common bean. To this date, 5255 single-pass sequences have been included in the database after selection based on sequence quality. These ESTs were trimmed and clustered using the computer programs Phred and CAP3 to form a unigene collection of 3126 unique sequences. Within clusters, 318 single nucleotide polymorphisms (SNPs) and 68 insertions–deletions (indels) were found, indicating the presence of paralogous gene families in our database. Each unigene sequence was analyzed for possible function using their similarity to known genes represented in the GenBank database and classified into 14 categories. Only 314 unigenes showed significant similarities to Phaseolus genomic sequences and P. vulgaris ESTs, which indicates that 90% (2818 unigenes) of our database represent newly discovered common bean genes. In addition, 12% (387 unigenes) were shown to be specific to common bean. This study represents a first step towards the discovery of novel genes in beans and a valuable source of molecular markers for expressed gene tagging and mapping.Key words: expressed sequence tag (EST), Colletotrichum lindemuthianum, Phaseolus vulgaris, simple sequence repeat (SSR), single nucleotide polymorphism (SNP).

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Orchestration of the stilbene synthase gene family and their regulators by subgroup 2 MYB genes

10.1101/2020.12.31.424746 ◽

2021 ◽

Author(s):

Luis Orduña ◽

Miaomiao Li ◽

David Navarro-Payá ◽

Chen Zhang ◽

Živa Ramšak ◽

...

Keyword(s):

Transcription Factors ◽

Dna Sequences ◽

Transcriptional Control ◽

Affinity Purification ◽

Methodological Approach ◽

Gene Families ◽

Phenylpropanoid Pathway ◽

Interesting Case ◽

High Confidence

1AbstractThe control of plant specialised metabolism is exerted by transcription factors and co-regulators acting on cis-regulatory DNA sequences of pathway-structural genes, determining when, where, and how metabolites are accumulated. A particularly interesting case for studying the transcriptional control of metabolism is represented by stilbenoids, produced within the phenylpropanoid pathway, as their ability to inhibit infection by coronaviruses MERS-CoV and SARS-CoV has been recently demonstrated in vitro. Integrative omic studies in grapevine (Vitis vinifera L.), including gene co-expression networks, have previously highlighted several transcription factors (TFs) from different gene families as potential modulators of stilbenoid accumulation, offering an ideal framework for gene function characterisation using genome-wide approaches. In the context of non-model plant species, DNA affinity purification sequencing (DAP-Seq) results a novel and potentially powerful tool for the analysis of novel uncharacterised regulators, however, it has not yet been applied in fruit crops. Accordingly, we tested as a proof-of-concept the binding of two previously characterised R2R3-MYB TFs to their known targets of the stilbene pathway, MYB14 and MYB15, obtaining 5,222 and 4,502 binding events assigned to 4,038 and 3,645 genes for each TF, respectively. Bound genes (putative targets) were overlapped with aggregated gene centred co-expression networks resulting in shared and exclusive High Confidence Targets (HCTs) suggesting a high, but not complete, redundancy. Our results show that in addition to the previously known but few STS targets, these regulators bind to almost half of the complete STS family in addition to other phenylpropanoid- and stilbenoid-related genes. We also suggest they are potentially involved in other processes such as the circadian rhythm or the synthesis of biotin. We searched the activated transcriptomes of transiently MYB15-overexpressing grapevine plants and observed a large activation of its high confidence targets, validating our methodological approach. Our results also show that MYB15 seems to play a role in regulating other stilbenoid-related TFs such as WRKY03.

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