Study on the molecular mechanism of pod wall fiber formation using the bean pod fiber mutant (bfm) of Phaseolus vulgaris L.
Ontology highlight
ABSTRACT:
ORGANISM(S): Phaseolus vulgaris
PROVIDER: GSE327568 | GEO | 2026/05/11
REPOSITORIES: GEO
Similar Datasets
Project description:<p>The tender pod is the primary edible part of the snap bean (Phaseolus vulgaris L.), and the level of suture fiber content is one of the key factors affecting its edible quality. To elucidate the key regulatory mechanisms and metabolic basis underlying suture fiber formation in pods, this study employed the high-suture-fiber-content bean cultivar ‘P1171’ and the low-suture-fiber-content cultivar ‘P16192’. We conducted cytological observations, fiber content measurements, transcriptomic, and metabolomic analyses. Results indicate that increased pod suture fiber content in snap beans results from phloem fiber proliferation, and that crude fiber content is significantly correlated with cellulose content within the fiber fraction. Transcriptome and metabolome analyses indicated that starch and sucrose metabolism pathways, as well as secondary metabolite biosynthesis pathways, are closely linked to cellulose synthesis. Metabolites in these pathways—UDP-glucose, ethylene (ETH), jasmonic acid (JA), and flavonoids—showed significant correlations with the differentially expressed genes Phvul. 005G082800, Phvul. 003G268600, Phvul. 006G031700, Phvul. 008G213800, Phvul. 011G189200, Phvul. 011G189300, and Phvul. 001G083000. We therefore hypothesize that variations in the expression levels of these genes across different cultivars may lead to changes in related metabolites, ultimately resulting in differences in fiber synthesis. This study systematically investigated the molecular mechanisms underlying fiber synthesis in the suture tissue of snap beans through integrated transcriptomic and metabolomic analyses. This work lays a foundation for further exploration of the regulatory networks governing cellulose-related synthesis genes in plant fiber formation, offering potential avenues to improve crop quality, enhance snap bean traits, and advance breeding programs.</p>
2026-01-30 | MTBLS13805 | MetaboLights
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:P. syringae pv. phaseolicola is the causal agent of the halo blight disease of beans (Phaseolus vulgaris L). The disease attacks both foliage and pods of plant host. Many genes involve in pathogenicity and virulence are induced only in plant or in the presence of host components. In this work we investigated the effect of bean pod extract on the transcriptomic profile of the bacterium, when grown at low temperature in minimal medium with or without bean pod extract.
2009-03-03 | GSE14625 | GEO
Project description:P. syringae pv. phaseolicola is the causal agent of the halo blight disease of beans (Phaseolus vulgaris L). The disease attacks both foliage and pods of plant host. Many genes involve in pathogenicity and virulence are induced only in plant or in the presence of host components. In this work we investigated the effect of bean pod extract on the transcriptomic profile of the bacterium, when grown at low temperature in minimal medium with or without bean pod extract. Two RNA samples were compared, one prepared from cells grown in minimal medium M9 and the other from cells grown in minimal medium supplemented with bean pod extract.To control de biological variation that might interfere with data interpretation, a minimum of three biological replicates and two technical replicates (swap) were prepared.
2010-05-22 | E-GEOD-14625 | biostudies-arrayexpress
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:Pod size varies among soybean cultivars, but the mechanism is largely unknown. We investigated pod size differences between two cultivars. The larger pod of ‘Tachinagaha’ was due to longer cell proliferation activity than in the shorter pod of ‘Iyodaizu’. Pod size of soybean 9 (GmPSS9), a member of the heat shock protein 70 family, was detected in a major QTL (qPSS on Chr. 2) as a candidate gene for determining pod length by QTL and expression QTL analysis. Expression of GmPSS9 in pods was higher in ‘Tachinagaha’ than in ‘Iyodaizu’ and was highest in early pod development. The difference in expression resulted from an indel polymorphism, Tachinagaha-specific-1, which has a 5′-UTR Py-rich stretch motif that boosts transcription. Treatment with an HSP70 inhibitor reduced plant height, pod length, and pod cell number. Our results identify GmPSS9 as a target gene for pod length which regulates cell number during early pod development.
2021-04-01 | GSE136772 | GEO
Project description:To study the development of flowers and pods in Medicago truncatula, eight stages of flower and pod development (designated F1-F4 and P1-P4, respectively) were chosen for tissue harvesting. As a common reference, young but already fully developed leaves (corresponding to the third-distant node from the apices) from plants grown in the field were selected. For each stage of flower and pod development, two biological replicates were harvested, one from plants grown in the greenhouse and one from plants grown in the field.
2005-05-31 | E-MEXP-143 | biostudies-arrayexpress
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:Pod development transcriptomes of four Phaseolus vulgaris accesions
| PRJNA746142 | ENA
Project description:Upland cotton (Gossypium hirsutum L.) is one of the world’s most important fiber crops, accounting for more than 90% of all cotton production. While their wild progenitors have relatively short and coarse, often tan-colored fibers, modern cotton cultivars possess longer, finer, stronger, and whiter fiber. In this study, the wild and cultivated cottons (YU-3 and TM-1) selected show significant differences on fibers at 10 day post-anthesis (DPA), 20 DPA and mature stages at the physiological level. In order to explore the effects of domestication, reveal molecular mechanisms underlying these phenotypic differences and better inform our efforts to further enhance cotton fiber quality, an iTRAQ-facilitated proteomic methods were performed on developing fibers. There were 6990 proteins identified, among them 336 were defined as differentially expressed proteins (DEPs) between fibers of wild versus domesticated cotton. The down- or up-regulated proteins in wild cotton were involved in Phenylpropanoid biosynthesis, Zeatin biosynthesis, Fatty acid elongation and other processes. Association analysis between transcroptome and proteome showed positive correlations between transcripts and proteins at both 10 DPA and 20 DPA. The difference of proteomics had been verified at the mRNA level by qPCR, also at physiological and biochemical level by POD activity determination and ZA content estimation. This work corroborate the major pathways involved in cotton fiber development and demonstrate that POD activity and zeatin content have a great potential related to fiber elongation and thickening.
2017-08-28 | PXD006604 | Pride