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.
The hard-to-cook defect in common beans is dictated by the ability to achieve cell separation during cooking. Hydrolysis of pectin methyl-esters by the pectin methyl-esterase (PME) enzyme influences cell separation. However, the contributions of the PME enzyme and the cell wall to the hard-to-cook defect have not been studied using molecular tools. We compared relevant molecular processes in fast- and slow-cooking bean varieties to understand the mechanisms underpinning the hard-to-cook defect. A PME spectrophotometric assay showed minor differences in enzyme activity between varieties. Meanwhile, a PME HMMER search in the P. vulgaris genome unveiled 113 genes encoding PMEs and PME inhibitors (PMEIs). Through RNA sequencing, we compared the gene expression of the PME-related genes in both varieties during seed development. A PME (Phvul010g080300) and PMEI gene (Phvul005g007600) showed the highest expression in the fast- and slow-cooking beans, respectively. We further identified 2132 differentially expressed genes (DEGs). Genes encoding cell-wall-related enzymes, mainly glycosylphosphatidylinositol mannosyltransferase, xyloglucan O-acetyltransferase, pectinesterase, and callose synthase, ranked among the top DEGs, indicating novel relations to the hard-to-cook defect. Gene ontology mapping revealed hydrolase activity and protein phosphorylation as functional categories with the most abundant upregulated DEGs in the slow-cooking bean. Additionally, the cell periphery contained 8% of the DEGs upregulated in the slow-cooking bean. This study provides new insights into the role of pectin methyl-esterase-related genes and novel cell wall processes in the occurrence of the hard-to-cook defect.
Stored grains of common bean (Phaseolus vulgaris L.) develop the hard‐to‐cook trait (HTC), which is manifested in a prolonged cooking time, thereby imposing time and energy constraints. The objective of this study was to determine variation in cooking time among common bean genotypes and to identify single nucleotide polymorphism (SNP) markers associated with cooking time.Seeds of 222 common bean accessions sourced from Kenyan institutions were multiplied in the Jomo Kenyatta University of Agriculture and Technology (JKUAT) field in 2019. The freshly harvested seeds and those stored at 35°C and 50% red haricot (RH) for 4 months for accelerated aging were soaked in distilled water for 16 h and evaluated for cooking time using the finger‐pressing method. The accessions were also genotyped to determine variation in SNP markers using Diversity Arrays Technology Sequencing (DArTseq). Genome‐wide association study (GWAS) analysis was conducted to identify SNPs significantly associated with cooking time.The study revealed significant differences (p ≤ 0.05) within and between fresh and aged bean accessions. Fresh seeds had a lower cooking time with a mean of 40.8 min and ranged from 28.1 to 72.2 min, whereas aged seeds had a higher average cooking time of 54.1 min and ranged from 32.1 to 96.3 min. GWAS identified a region in Chromosome 10 to be significantly (p ≤ 0.05) associated with the cooking time of aged seeds. Consequently, two potential candidate genes Phvul.010G038000 and Phvul.010G038100 were revealed. The characterized common bean accessions and the identified SNP markers can be utilized in breeding programs to improve the cooking quality of the common bean.
Researchers in bio-sciences are increasingly harnessing technology to improve processes that were traditionally pegged on pen-and-paper and highly manual. The pen-and-paper approach is used mainly to record and capture data from experiment sites. This method is typically slow and prone to errors. Also, bio-science research activities are often undertaken in remote and distributed locations. Timeliness and quality of data collected are essential. The manual method is slow to collect quality data and relay it in a timely manner. Capturing data manually and relaying it in real time is a daunting task. The data collected has to be associated to respective specimens (objects or plants). In this paper, we seek to improve specimen labelling and data collection guided by the following questions; (1) How can data collection in bio-science research be improved? (2) How can specimen labelling be improved in bio-science research activities? We present WebLog, an application that we prototyped to aid researchers generate specimen labels and collect data from experiment sites. We use the application to convert the object (specimen) identifiers into quick response (QR) codes and use them to label the specimens. Once a specimen label is successfully scanned, the application automatically invokes the data entry form. The collected data is immediately sent to the server in electronic form for analysis.
DHDPS is a key enzyme in the aspartate-derived lysine biosynthesis pathway and an evident object of study for biofortification strategies in plants. DHDPS isoforms with novel regulatory properties in Medicago truncatula were demonstrated earlier and hypothesized to be involved in abiotic and biotic stress responses. Here, we present a phylogenetic analysis of the DHPDS gene family in land plants which establishes the existence of a legume-specific class of DHDPS, termed DHDPS B-type, distinguishable from the DHDPS A-type commonly present in all land plants. The G. max genome comprises two A-type DHDPS genes (Gm.DHDPS-A1; Glyma.09G268200, Gm.DHDPS-A2; Glyma.18G221700) and one B-type (Gm.DHDPS-B; Glyma.03G022300). To further investigate the expression pattern of the G. max DHDPS isozymes in different plant tissues and under various stress conditions, 461 RNA-seq experiments were exploited and re-analyzed covering two expression atlases, 13 abiotic and 5 biotic stress studies. Gm.DHDPS-B is seen almost exclusively expressed in roots and nodules in addition to old cotyledons or senescent leaves while both DHDPS A-types are expressed constitutively in all tissues analyzed with the highest expression in mature seeds. Furthermore, Gm.DHDPS-B expression is significantly upregulated in some but not all stress responses including salt stress, flooding, ethylene or infection with Phytophthora sojae and coincides with downregulation of DHDPS A-types. In conclusion, we demonstrate the potential of an in-depth RNA-seq re-analysis for the guidance of future experiments and to expand on current knowledge.
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