Phaseolus vulgaris
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ABSTRACT:
PROVIDER: PRJNA279009 | ENA |
REPOSITORIES: ENA
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Project description:Dry bean (Phaseolus vulgaris L.) seeds are a rich source of dietary zinc, especially for people consuming plant-based diets. Within P. vulgaris there is at least two-fold variation in seed Zn concentration. Genetic studies have revealed seed Zn differences to be controlled by a single gene in two closely related navy bean genotypes, Albion and Voyager. In this study, these two genotypes were grown under controlled fertilization conditions and the Zn concentration of various plant parts were determined. The two genotypes had similar levels of Zn in their leaves and pods but Voyager had 52% more Zn in its seeds than Albion. RNA was sequence from developing pods of both genotypes. Transcriptome analysis of these genotypes identified 27,198 genes in the developing bean pods, representing 86% of the genes in the P. vulgaris genome (v 1.0 DOE-JGI and USDA-NIFA). Expression was detected in 18,438 genes. A relatively small number of genes (381) were differentially expressed between Albion and Voyager. Differentially expressed genes included three genes potentially involved in Zn transport, including zinc-regulated transporter, iron regulated transporter like (ZIP), zinc-induced facilitator (ZIF) and heavy metal associated (HMA) family genes. In addition 12,118 SNPs were identified between the two genotypes. Of the gene families related to Zn and/or Fe transport, eleven genes were found to contain SNPs between Albion and Voyager.
2015-03-24 | GSE67121 | GEO
Project description:Metabolomics of wild and domesticated varieties of common bean (Phaseolus vulgaris)
2022-05-13 | MSV000089468 | MassIVE
Project description:The goal of this study was to detemine the genes responsible of the pod indehiscence in Phaseolus vulgaris by comparing 4 accesions with total, middle and null dehiscence transcriptomes of three stages of pod develoment of Phaseolus vulgaris
2022-04-16 | GSE179985 | GEO
Project description:The pod is the main edible part of Phaseolus vulgaris L. (common bean). The commercial use of the pods is mainly affected by their color. Consumers seem to prefer golden pods. However, planters suffer economic losses because of pod color instability. The aim of the present study was to identify the gene responsible for the golden pod trait in the common bean. ‘A18-1’ (a golden bean line) and ‘Renaya’ (a green bean line) were chosen as the experimental materials. Genetic analysis indicated that a single recessive gene, pv-ye, controls the golden pod trait. A candidate region of 4.24-Mb was mapped to chromosome A02 using bulked-segregant analysis coupled to whole genome sequencing. In this region, linkage analysis in an F2 population localized the pv-ye gene to an interval of 182.9-kb between the simple sequence repeat markers SSR77 and SSR93. This region comprised 16 genes in this region, comprising 12 annotated genes from the P. vulgaris database, and 4 functionally unknown genes. Combined with transcriptome sequencing, we identified Phvul.002G006200 as the potential candidate gene for pv-ye. Sequencing of Phvul.002G006200 identified a single nucleotide polymorphism (SNP) in pv-ye. This SNP is located in the coding region and is responsible for substituting a glutamic acid with an glutamine at position 416 of the pv-ye protein (E416Q). A pair of primers covering the SNP was designed and the fragment was sequenced to screen 316 F2 plants with the ‘A18-1’ phenotype, based on the different site. Our findings showed that the among the 316 mapped individuals, the SNP cosegregated with the ‘A18-1’ phenotype. The findings presented here could form the basis to reveal the mechanism of the golden pod trait in the common bean at the molecular level.
2020-10-12 | GSE159374 | GEO
Project description:Comparative RNA-Seq study of expression in Phaseolus vulgaris nectaries
2018-04-10 | GSE112944 | GEO
Project description:Background: MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21 and no phasiRNAs have been identified for the legume model Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs of this organism and, particularly, new protagonists of the symbiotic nodulation events. Results: We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families. Degradome data allowed us to identify a total of 181 targets for these miRNAs. We reveal two regulatory networks involving conserved miRNAs, known to play crucial roles in the well-establishment of nodules, and novel miRNAs specific of the common bean suggesting a specific action of these sequences. In parallel, we identified 125 loci that potentially produce phased small RNAs and 47 of them present all the characteristics to be triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study. Conclusions: We provide here a set of new small RNAs, which contribute to the broader scene of the sRNAome of Phaseolus vulgaris. Thanks to the identification of the miRNA targets from degradome analysis and the construction of regulatory networks between the mature microRNAs, we draw up here the probable functional regulation associated with the sRNAome and particularly in N2-fixing symbiotic nodules. Degradome sequencing from Phaseolus vulgaris seedling
2015-09-01 | E-GEOD-67432 | biostudies-arrayexpress
Project description:Background: MiRNAs and phasiRNAs are negative regulators of gene expression. These small RNAs have been extensively studied in plant model species but only 10 mature microRNAs are present in miRBase version 21 and no phasiRNAs have been identified for the legume model Phaseolus vulgaris. Thanks to the recent availability of the first version of the common bean genome, degradome data and small RNA libraries, we are able to present here a catalog of the microRNAs and phasiRNAs of this organism and, particularly, new protagonists of the symbiotic nodulation events. Results: We identified a set of 185 mature miRNAs, including 121 previously unpublished sequences, encoded by 307 precursors and distributed in 98 families. Degradome data allowed us to identify a total of 181 targets for these miRNAs. We reveal two regulatory networks involving conserved miRNAs, known to play crucial roles in the well-establishment of nodules, and novel miRNAs specific of the common bean suggesting a specific action of these sequences. In parallel, we identified 125 loci that potentially produce phased small RNAs and 47 of them present all the characteristics to be triggered by a total of 31 miRNAs, including 14 new miRNAs identified in this study. Conclusions: We provide here a set of new small RNAs, which contribute to the broader scene of the sRNAome of Phaseolus vulgaris. Thanks to the identification of the miRNA targets from degradome analysis and the construction of regulatory networks between the mature microRNAs, we draw up here the probable functional regulation associated with the sRNAome and particularly in N2-fixing symbiotic nodules. Small RNA sequencing from 5 Phaseolus vulgaris tissues
2015-09-01 | E-GEOD-67409 | biostudies-arrayexpress
Project description:A Phaseolus vulgaris genome-wide analysis led to identify the small RNAs (sRNA) of this agronomical important legume. It revealed newly identified P. vulgaris-specific microRNAs (miRNAs) that could be involved in the regulation of the rhizobia-symbiotic process. Generally, novel miRNAs are difficult to identify and study because they are very lowly expressed in a tissue- or cell-specific manner. We aimed to analyze sRNAs from common bean root hairs (RH), a single-cell model, induced with pure Rhizobium etli-Nod factors (NF), a unique type of signal molecule. The sequence analysis of samples from NF-induced and control libraries led to identify 132 mature miRNAs, including 63 novel miRNAs and 1984 phasiRNAs. From these, six miRNAs were significantly differentially expressed during NF-induction, including one novel miRNA: miR-RH82. A parallel degradome analysis of the same samples revealed 29 targets potentially cleaved by novel miRNAs specifically in NF-induced RH samples, however these novel miRNAs were not differentially accumulated in this tissue. This study reveals Phaseolus vulgaris-specific novel miRNA candidates and their corresponding targets that meet all criteria to be involved in the regulation of the early nodulation events.
2017-05-01 | GSE81176 | GEO
Project description:Cytosine methylation is a base modification that is often used by genomes to store information that is stably inherited through mitotic cell divisions. Most cytosine DNA methylation is stable throughout different cell types or by exposure to different environmental conditions in plant genomes. Here, we profile the epigenomes of ~100 Phaseolus vulgaris lines to explore the extent of natural epigenomic variation. We also use these data to determine the extent to which DNA methylation variants are linked to genetic variations.
2018-05-11 | GSE114341 | GEO