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Pradeepkumara N, Sharma PK, Munshi AD, Behera TK, Bhatia R, Kumari K, Singh J, Jaiswal S, Iquebal MA, Arora A, Rai A, Kumar D, Bhattacharya RC, Dey SS. Fruit transcriptional profiling of the contrasting genotypes for shelf life reveals the key candidate genes and molecular pathways regulating post-harvest biology in cucumber. Genomics 2022; 114:110273. [PMID: 35092817 DOI: 10.1016/j.ygeno.2022.110273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 02/07/2023]
Abstract
Cucumber fruits are perishable in nature and become unfit for market within 2-3 days of harvesting. A natural variant, DC-48 with exceptionally high shelf life was developed and used to dissect the genetic architecture and molecular mechanism for extended shelf life through RNA-seq for first time. A total of 1364 DEGs were identified and cell wall degradation, chlorophyll and ethylene metabolism related genes played key role. Polygalacturunase (PG), Expansin (EXP) and xyloglucan were down regulated determining fruit firmness and retention of fresh green colour was mainly attributed to the low expression level of the chlorophyll catalytic enzymes (CCEs). Gene regulatory networks revealed the hub genes and cross-talk associated with wide variety of the biological processes. Large number of SSRs (21524), SNPs (545173) and InDels (126252) identified will be instrumental in cucumber improvement. A web genomic resource, CsExSLDb developed will provide a platform for future investigation on cucumber post-harvest biology.
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Affiliation(s)
- N Pradeepkumara
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Parva Kumar Sharma
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - A D Munshi
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - T K Behera
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Reeta Bhatia
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Khushboo Kumari
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jogendra Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ajay Arora
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - R C Bhattacharya
- ICAR-National Institute of Plant Biotechnology, New Delhi, India
| | - S S Dey
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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Li G, Tang L, Yin Y, Zhang A, Yu Z, Yang E, Tang Z, Fu S, Yang Z. Molecular dissection of Secale africanum chromosome 6R afr in wheat enabled localization of genes for resistance to powdery mildew and stripe rust. BMC PLANT BIOLOGY 2020; 20:134. [PMID: 32234016 PMCID: PMC7106737 DOI: 10.1186/s12870-020-02351-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/23/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Introgression of chromatin from Secale species into common wheat has for decades been a successful strategy for controlling the wheat diseases. The wild Secale species, Secale africanum Stapf., is a valuable source for resistance to foliar disease of wheat. A wheat-S. africanum chromosome 6Rafr substitution line displayed resistance to both powdery mildew and stripe rust at the adult-plant stage. RESULTS Wheat-S. africanum chromosome 6Rafr deletion and translocation lines were produced and identified by sequential non-denaturing fluorescence in situ hybridization (ND-FISH) using multiple Oligo-based probes. Different ND-FISH patterns were observed between S. cereale 6R and S. africanum 6Rafr. With reference to the physical map of the draft genome sequence of rye inbred line Lo7, a comprehensive PCR marker analysis indicated that insertions and deletions had occurred by random exchange between chromosomes 6R and 6Rafr. A survey of the wheat- S. africanum 6Rafr lines for disease resistance indicated that a powdery mildew resistance gene(s) was present on the long arm of 6Rafr at FL0.85-1.00, and that a stripe rust resistance gene(s) was located in the terminal region of 6RafrS at FL0.95-1.00. The wheat-S. africanum 6Rafr introgression lines also displayed superior agronomic traits, indicating that the chromosome 6Rafr may have little linkage drag in the wheat background. CONCLUSIONS The combination of molecular and cytogenetic methods allowed to precisely identify the chromosome rearrangements in wheat- S. africanum 6Rafr substitution, deletion and translocation lines, and compare the structural difference between chromosomes 6R and 6Rafr. The wheat- S. africanum 6Rafr lines containing gene(s) for powdery mildew and stripe rust resistance could be used as novel germplasm for wheat breeding by chromosome engineering.
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Affiliation(s)
- Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, Sichuan, China
| | - Lingrong Tang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, Sichuan, China
| | - Yan Yin
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, Sichuan, China
| | - Ahui Zhang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, Sichuan, China
| | - Zhihui Yu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, Sichuan, China
| | - Ennian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Zongxiang Tang
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shulan Fu
- Province Key Laboratory of Plant Breeding and Genetics, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, Sichuan, China.
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Zhou Q, Wang A, Duan R, Yan J, Zhao G, Nevo E, Chen G. Comparative transcriptome profile of the leaf elongation zone of wild barley (Hordeum spontaneum) eibi1 mutant and its isogenic wild type. Genet Mol Biol 2017; 40:834-843. [PMID: 29064514 PMCID: PMC5738607 DOI: 10.1590/1678-4685-gmb-2016-0321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 08/13/2017] [Indexed: 11/21/2022] Open
Abstract
The naturally occurring wild barley mutant eibi1/hvabcg31
suffers from severe water loss due to the permeable leaf cuticle.
Eibi1/HvABCG31 encodes a full ATP-binding cassette (ABC)
transporter, HvABCG31, playing a role in cutin deposition in the elongation zone
of growing barley leaves. The eibi1 allele has pleiotropic
effects on the appearance of leaves, plant stature, fertility, spike and grain
size, and rate of germination. Comparative transcriptome profile of the leaf
elongation zone of the eibi1 mutant as well as its isogenic
wild type showed that various pathogenesis-related genes were up-regulated in
the eibi1 mutant. The known cuticle-related genes that we
analyzed did not show significant expression difference between the mutant and
wild type. These results suggest that the pleiotropic effects may be a
compensatory consequence of the activation of defense genes in the
eibi1 mutation. Furthermore, we were able to find the
mutation of the eibi1/hvabcg31 allele by comparing transcript
sequences, which indicated that the RNA-Seq is useful not only for researches on
general molecular mechanism but also for the identification of possible mutant
genes.
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Affiliation(s)
- Qin Zhou
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Aidong Wang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
| | - Ruijun Duan
- College of Eco-Environmental Engineering, Qinghai University, Xining, Qinghai, China
| | - Jun Yan
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, Sichuan. China
| | - Gang Zhao
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, Sichuan. China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa Israel
| | - Guoxiong Chen
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China
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Shitan N. Secondary metabolites in plants: transport and self-tolerance mechanisms. Biosci Biotechnol Biochem 2016; 80:1283-93. [DOI: 10.1080/09168451.2016.1151344] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
Plants produce a host of secondary metabolites with a wide range of biological activities, including potential toxicity to eukaryotic cells. Plants generally manage these compounds by transport to the apoplast or specific organelles such as the vacuole, or other self-tolerance mechanisms. For efficient production of such bioactive compounds in plants or microbes, transport and self-tolerance mechanisms should function cooperatively with the corresponding biosynthetic enzymes. Intensive studies have identified and characterized the proteins responsible for transport and self-tolerance. In particular, many transporters have been isolated and their physiological functions have been proposed. This review describes recent progress in studies of transport and self-tolerance and provides an updated inventory of transporters according to their substrates. Application of such knowledge to synthetic biology might enable efficient production of valuable secondary metabolites in the future.
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Affiliation(s)
- Nobukazu Shitan
- Laboratory of Natural Medicinal Chemistry, Kobe Pharmaceutical University, Kobe, Japan
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Holmes GD, Hall NE, Gendall AR, Boon PI, James EA. Using Transcriptomics to Identify Differential Gene Expression in Response to Salinity among Australian Phragmites australis Clones. FRONTIERS IN PLANT SCIENCE 2016; 7:432. [PMID: 27148279 PMCID: PMC4829608 DOI: 10.3389/fpls.2016.00432] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/21/2016] [Indexed: 05/22/2023]
Abstract
Common Reed (Phragmites australis) is a frequent component of inland and coastal wetlands in temperate zones worldwide. Ongoing environmental changes have resulted in the decline of this species in many areas and invasive expansion in others. In the Gippsland Lakes coastal waterway system in south-eastern Australia, increasing salinity is thought to have contributed to the loss of fringing P. australis reed beds leading to increased shoreline erosion. A major goal of restoration in this waterway is to address the effect of salinity by planting a genetically diverse range of salt-tolerant P. australis plants. This has prompted an interest in examining the variation in salinity tolerance among clones and the underlying basis of this variation. Transcriptomics is an approach for identifying variation in genes and their expression levels associated with the exposure of plants to environmental stressors. In this paper we present initial results of the first comparative culm transcriptome analysis of P. australis clones. After sampling plants from sites of varied surface water salinity across the Gippsland Lakes, replicates from three clones from highly saline sites (>18 g L(-1) TDS) and three from low salinity sites (<6 g L(-1)) were grown in containers irrigated with either fresh (<0.1 g L(-1)) or saline water (16 g L(-1)). An RNA-Seq protocol was used to generate sequence data from culm tissues from the 12 samples allowing an analysis of differential gene expression. Among the key findings, we identified several genes uniquely up- or down-regulated in clones from highly saline sites when irrigated with saline water relative to clones from low salinity sites. These included the higher relative expression levels of genes associated with photosynthesis and lignan biosynthesis indicative of a greater ability of these clones to maintain growth under saline conditions. Combined with growth data from a parallel study, our data suggests local adaptation of certain clones to salinity and provides a basis for more detailed studies.
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Affiliation(s)
| | - Nathan E. Hall
- La Trobe Institute for Molecular Science, La Trobe University, BundooraVIC, Australia
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, BundooraVIC, Australia
| | - Anthony R. Gendall
- Department of Animal, Plant and Soil Sciences, AgriBio, La Trobe University, BundooraVIC, Australia
| | - Paul I. Boon
- Institute for Sustainability and Innovation, Victoria University, Footscray ParkVIC, Australia
| | - Elizabeth A. James
- Royal Botanic Gardens Victoria, MelbourneVIC, Australia
- *Correspondence: Elizabeth A. James,
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Agarwal P, Parida SK, Mahto A, Das S, Mathew IE, Malik N, Tyagi AK. Expanding frontiers in plant transcriptomics in aid of functional genomics and molecular breeding. Biotechnol J 2014; 9:1480-92. [PMID: 25349922 DOI: 10.1002/biot.201400063] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 09/02/2014] [Accepted: 10/01/2014] [Indexed: 12/30/2022]
Abstract
The transcript pool of a plant part, under any given condition, is a collection of mRNAs that will pave the way for a biochemical reaction of the plant to stimuli. Over the past decades, transcriptome study has advanced from Northern blotting to RNA sequencing (RNA-seq), through other techniques, of which real-time quantitative polymerase chain reaction (PCR) and microarray are the most significant ones. The questions being addressed by such studies have also matured from a solitary process to expression atlas and marker-assisted genetic enhancement. Not only genes and their networks involved in various developmental processes of plant parts have been elucidated, but also stress tolerant genes have been highlighted. The transcriptome of a plant with altered expression of a target gene has given information about the downstream genes. Marker information has been used for breeding improved varieties. Fortunately, the data generated by transcriptome analysis has been made freely available for ample utilization and comparison. The review discusses this wide variety of transcriptome data being generated in plants, which includes developmental stages, abiotic and biotic stress, effect of altered gene expression, as well as comparative transcriptomics, with a special emphasis on microarray and RNA-seq. Such data can be used to determine the regulatory gene networks, which can subsequently be utilized for generating improved plant varieties.
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Affiliation(s)
- Pinky Agarwal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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Nevo E. Evolution in action: adaptation and incipient sympatric speciation with gene flow across life at “Evolution Canyon”, Israel. Isr J Ecol Evol 2014. [DOI: 10.1080/15659801.2014.986879] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Various major evolutionary problems are still open, controversial or unsettled. These include even the basic evolutionary processes of adaptation and speciation. The “Evolution Canyon” model is a microscale natural laboratory that can highlight some of the basic problems requiring clarification (Nevo list of “Evolution Canyon” publications at http://evolution.haifa.ac.il). This is especially true if an interdisciplinary approach is practiced including ecological functional genomics, transcriptomics, proteomics, metabolomics and phenomics. Here I overview and reanalyze the incipient sympatric adaptive ecological speciation of five model organisms at “Evolution Canyon”, across life: the soil bacterium, Bacillus simplex; wild barley, the progenitor of cultivated barley, Hordeum spontaneum; the tiny beetle Oryzaephilus surinamensis; the cosmopolitan fruit-fly, Drosophila melanogaster, and the Africa-originated spiny mouse, Acomys cahirinus. All five models of organisms display evolution in action of microclimatic adaptation and incipient sympatric adaptive ecological speciation on the tropical and temperate abutting slopes, separated on average by only 250 meters. Some distant species converge in their micro-climatic adaptations to the hot and dry “African”, south-facing slope (SFS or AS) and to the cool and humid “European”, north-facing slope (NSF or ES). Natural selection overrules ongoing inter-slope gene-flow between the free interbreeding populations within and between slopes, and leads to adaptive incipient sympatric ecological speciation on the dramatically opposite abutting xeric savannoid and mesic forested slopes.
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