Recognition and fine genetic mapping of the golden pod gene (pv-ye) from the common bean (Phaseolus vulgaris L.)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA668634 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12808329_1.fastq.gz | Fastqsanger.gz | |||
| SRR12808329_2.fastq.gz | Fastqsanger.gz | |||
| SRR12808330_1.fastq.gz | Fastqsanger.gz | |||
| SRR12808330_2.fastq.gz | Fastqsanger.gz | |||
| SRR12808331_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 36 |
Similar Datasets
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: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: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:Pod development transcriptomes of four Phaseolus vulgaris accesions
| PRJNA746142 | ENA
Project description:To reveal genetic factors or pathways involved in the pod degreening, we performed transcriptome and metabolome analyses using a yellow pod cultivar of the common bean "golden hook" ecotype and its green pod mutants yielded via gamma radiation. Transcriptional profiling showed that expression levels of red chlorophyll catabolite reductase (RCCR, Phvul.008G280300) involved in chlorophyll degradation was strongly enhanced at an early stage (2 cm long) in wild type but not in green pod mutants. The expression levels of genes involved in cellulose synthesis was inhibited by the pod degreening. Metabolomic profiling showed that the content of most flavonoid, flavones, and isoflavonoid was decreased during pod development, but the content of afzelechin, taxifolin, dihydrokaempferol, and cyanidin 3-O-rutinoside was remarkably increased in both wild type and green pod mutant. This study revealed that the pod degreening of the golden hook resulting from chlorophyll degradation could trigger changes in cellulose and flavonoids biosynthesis pathway, offering this cultivar a special color appearance and good flavor.
| S-EPMC7573562 | biostudies-literature
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:Pod maturation of common bean relies upon complex gene expression changes, which in turn are crucial for seed formation and dispersal. Hence, dissecting the transcriptional regulation of pod maturation would be of great significance for breeding programs. In this study, a comprehensive characterization of expression changes has been performed in two common bean cultivars (ancient and modern) by analyzing the transcriptomes of five developmental pod stages, from fruit setting to maturation. RNA-seq analysis allowed for the identification of key genes shared by both accessions, which in turn were homologous to known Arabidopsis maturation genes and furthermore showed a similar expression pattern along the maturation process. Gene- expression changes suggested a role in promoting an accelerated breakdown of photosynthetic and ribosomal machinery associated with chlorophyll degradation and early activation of alpha-linolenic acid metabolism. A further study of transcription factors and their DNA binding sites revealed three candidate genes whose functions may play a dominant role in regulating pod maturation. Altogether, this research identifies the first maturation gene set reported in common bean so far and contributes to a better understanding of the dynamic mechanisms of pod maturation, providing potentially useful information for genomic-assisted breeding of common bean yield and pod quality attributes.
| S-EPMC7238275 | biostudies-literature
Project description:Pod dehiscence is an important agronomic trait. Pod dehiscence would cause huge yield losses before soybean maturity. Although some of soybean pod dehiscence associated genes have been identified, the underlying mechanism of pod dehiscence is still not comprehensively explained. In this study, we have identified differentially expressed genes (DEGs) between shattering-resistant and shattering-susceptible soybean accessions based on transcriptome analyses of 10 soybean accessions. Long non-coding RNAs (lncRNAs) that may be involved in soybean pod dehiscence were also identified, and we constructed co-expression networks between mRNAs and lncRNAs. RNA sequencing results were further verified by real-time PCR. Furthermore, DEGs were screened through analyzing positions of soybean pod dehiscence quantitative trait locus (QTLs) and phenotypes of soybean pod dehiscence for achieving pod-dehiscence candidate genes.
2019-07-22 | GSE130010 | GEO
Project description:Pod quality and yield traits in snap bean (Phaseolus vulgaris L.) influence consumer preferences, crop adoption by farmers, and the ability of the product to be commercially competitive locally and globally. The objective of the study was to identify the quantitative trait loci (QTL) for pod quality and yield traits in a snap × dry bean recombinant inbred line (RIL) population. A total of 184 F6 RILs derived from a cross between Vanilla (snap bean) and MCM5001 (dry bean) were grown in three field sites in Kenya and one greenhouse environment in Davis, CA, USA. They were genotyped at 5,951 single nucleotide polymorphisms (SNPs), and composite interval mapping was conducted to identify QTL for 16 pod quality and yield traits, including pod wall fiber, pod string, pod size, and harvest metrics. A combined total of 44 QTL were identified in field and greenhouse trials. The QTL for pod quality were identified on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, and Pv07, and for pod yield were identified on Pv08. Co-localization of QTL was observed for pod quality and yield traits. Some identified QTL overlapped with previously mapped QTL for pod quality and yield traits, with several others identified as novel. The identified QTL can be used in future marker-assisted selection in snap bean.
| S-EPMC11345156 | biostudies-literature