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Yepuri V, Jalali S, Kancharla N, Reddy VB, Arockiasamy S. Development of genome wide transposable elements based repeat junction markers in Jatropha (Jatropha curcas L.). Mol Biol Rep 2020; 47:5091-5099. [PMID: 32562173 DOI: 10.1007/s11033-020-05579-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 06/10/2020] [Indexed: 11/29/2022]
Abstract
Jatropha curcas is a potential biodiesel crop and a highly adaptable species to various agro-climatic conditions. In this study, we have utilized transposable elements' (TE) repeat junctions (RJs) which are an important constituent of the genome, used to form a genome-wide molecular marker platform owing to its use in genomic studies of plants. We screened our previously generated Jatropha hybrid genome assembly of size 265 Mbp using RJPrimers pipeline software and identified a total of 1274 TE junctions. For the predicted RJs, we designed 2868 polymerase chain reaction (PCR) based RJ markers (RJMs) flanking the junction regions. In addition to marker design, the identified RJs were utilized to detect 225,517 TEs across the genome. The different types of transposable repeat elements mainly were scattered into Retro, LTR, Copia and Gypsy categories. The efficacy of the designed markers was tested by utilizing a subset of RJMs selected randomly. We have validated 96 randomly selected RJ primers in a group of 32 J. curcas genotypes and more than 90% of the markers effectively intensified as amplicons. Of these, 10 primers were shown to be polymorphic in estimating genetic diversity among the 32 Jatropha lines. UPGMA cluster analysis revealed the formation of two clusters such as A and B exhibiting 85.5% and 87% similarity coefficient respectively. The various RJMs identified in this study could be utilized as a significant asset in Jatropha functional genomics including genome determination, mapping and marker-assisted selection.
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Affiliation(s)
- Vijay Yepuri
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India
| | - Saakshi Jalali
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India
| | - Nagesh Kancharla
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India
| | - V B Reddy
- AgriGenome Labs Private Limited, Hyderabad, 500078, India
| | - S Arockiasamy
- Agronomy Division, Reliance Technology Group, Reliance Industries Limited, Navi Mumbai, Maharashtra, 400701, India.
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Souza RCD, Marques DDA, de Carvalho Filho MM, Oliveira ARDS, Siqueira WJ, Benko-Iseppon AM, Brasileiro-Vidal AC. Genome composition and pollen viability of Jatropha (Euphorbiaceae) interspecific hybrids by Genomic In Situ Hybridization (GISH). Genet Mol Biol 2020; 42:e20190112. [PMID: 32059051 PMCID: PMC7198012 DOI: 10.1590/1678-4685-gmb-2019-0112] [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: 04/05/2019] [Accepted: 11/10/2019] [Indexed: 11/24/2022] Open
Abstract
Interspecific hybridization is required for the development of Jatropha
curcas L. improved cultivars, due to its narrow genetic basis. The
present study aimed to analyze the parental genomic composition of F1
and BC1F1 generations derived from interspecific crosses
(J. curcas/J. integerrima and J. curcas/J.
multifida) by GISH (Genomic In Situ
Hybridization), and the meiotic index and pollen viability of F1
hybrids. In F1 cells from both hybrids, 11 chromosomes of each
parental was observed, as expected, but chromosome rearrangement events could be
detected using rDNA chromosome markers, suggesting unbalanced cells. In the
BC1F1, both hybrids had 22 chromosomes, suggesting
that only n = 11 gametes were viable in the next generation.
However, GISH allowed the identification of three and two alien chromosomes in
J. curcas//J. integerrima and J. curcas//J.
multifida BC1F1 hybrids, respectively,
suggesting a preferential transmission of J. curcas chromosomes
for both hybrids. Pollen viability in F1 hybrids derived from
J. curcas/J. integerrima crosses were higher (82-83%) than
those found for J. curcas/J. multifida (68%), showing
post-meiotic problems in these last hybrids, with dyads, triads, polyads, and
micronuclei as post-meiosis results. The here presented cytogenetic
characterization of interspecific hybrids and their backcross progenies can
contribute to the selection of the best genotypes for future assisted breeding
of J. curcas.
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Affiliation(s)
- Rosilda Cintra de Souza
- Universidade Federal de Pernambuco, Departamento de Genética, Recife, PE, Brazil.,Universidade Federal Rural de Pernambuco, Departamento de Agronomia, Recife, Pernambuco, Brazil
| | | | | | | | | | | | - Ana Christina Brasileiro-Vidal
- Universidade Federal de Pernambuco, Departamento de Genética, Recife, PE, Brazil.,Universidade Federal Rural de Pernambuco, Departamento de Agronomia, Recife, Pernambuco, Brazil
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Zhao Y, Kong H, Guo Y, Zou Z. Light-harvesting chlorophyll a/b-binding protein-coding genes in jatropha and the comparison with castor, cassava and arabidopsis. PeerJ 2020; 8:e8465. [PMID: 32025382 PMCID: PMC6993755 DOI: 10.7717/peerj.8465] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 12/27/2019] [Indexed: 12/27/2022] Open
Abstract
The Lhc (light-harvesting chlorophyll a/b-binding protein) superfamily represents a class of antennae proteins that play indispensable roles in capture of solar energy as well as photoprotection under stress conditions. Despite their importance, little information has been available beyond model plants. In this study, we presents a first genome-wide analysis of Lhc superfamily genes in jatropha (Jatropha curcas L., Euphorbiaceae), an oil-bearing plant for biodiesel purpose. A total of 27 members were identified from the jatropha genome, which were shown to distribute over nine out of the 11 chromosomes. The superfamily number is comparable to 28 present in castor (Ricinus communis, Euphorbiaceae), but relatively less than 35 in cassava (Manihot esculenta, Euphorbiaceae) and 34 in arabidopsis (Arabidopsis thaliana) that experienced one or two recent whole-genome duplications (WGDs), respectively. In contrast to a high number of paralogs present in cassava and arabidopsis, few duplicates were found in jatropha as observed in castor, corresponding to no recent WGD occurred in these two species. Nevertheless, 26 orthologous groups representing four defined families were found in jatropha, and nearly one-to-one orthologous relationship was observed between jatropha and castor. By contrast, a novel group named SEP6 was shown to have been lost in arabidopsis. Global transcriptome profiling revealed a predominant expression pattern of most JcLhc superfamily genes in green tissues, reflecting their key roles in photosynthesis. Moreover, their expression profiles upon hormones, drought, and salt stresses were also investigated. These findings not only improve our knowledge on species-specific evolution of the Lhc supergene family, but also provide valuable information for further studies in jatropha.
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Affiliation(s)
- Yongguo Zhao
- Guangdong University of Petrochemical Technology, Maoming, China.,Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, China
| | - Hua Kong
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, China
| | - Yunling Guo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, China
| | - Zhi Zou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture and Rural Affairs, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science, Haikou, China
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Vandepitte K, Valdés-Rodríquez OA, Sánchez-Sánchez O, De Kort H, Martinez-Herrera J, García-Pérez E, De Meyer T, Pérez-Vázquez A, Muys B, Honnay O. High SNP diversity in the non-toxic indigenous Jatropha curcas germplasm widens the potential of this upcoming major biofuel crop species. ANNALS OF BOTANY 2019; 124:645-652. [PMID: 30715120 PMCID: PMC6821362 DOI: 10.1093/aob/mcz008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 01/08/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS Jatropha curcas (jatropha) is an oil crop cultivated in (sub)tropical regions around the world, and holds great promise as a renewable energy source. However, efforts to fully commercialize jatropha are currently hampered by the lack of genetic diversity in the extant breeding germplasm, and by the toxicity of its seeds meaning that its seed cake cannot be used as a protein source in animal feed, among other constraints. In Mexico, the species' native range, there are jatropha plants whose seeds are used to prepare traditional meals. This non-toxic jatropha 'type' is considered to harbour low genetic variation due to a presumed domestication bottleneck and therefore to be of limited breeding value; yet, very little is known regarding its origin and genetic diversity. METHODS Using genotyping-by-sequencing (GBS), we extensively genotyped both indigenous toxic and non-toxic jatropha collected along roads and home gardens throughout southern Mexico. KEY RESULTS Single nucleotide polymorphism diversity in non-toxic jatropha is relatively high, particularly in northern Veracruz state, the probable origin of this germplasm. Genetic differences between toxic and non-toxic indigenous genotypes are overall quite small. A a genome-wide association study supported a genomic region (on LG 8, scaffold NW_012130064), probably involved in the suppression of seed toxicity. CONCLUSIONS Conservation actions are urgently needed to preserve this non-toxic indigenous, relatively wild germplasm, having potential as a fuel feedstock, animal feed and food source among other uses. More generally, this work demonstrates the value of conservation genomic research on the indigenous gene pool of economically important plant species.
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Affiliation(s)
- K Vandepitte
- Plant Conservation and Population Biology, Biology Department, KU Leuven, Leuven, Belgium
| | | | - O Sánchez-Sánchez
- Centro de Investigaciones Tropicales, Universidad Veracruzana, Xalapa, Ver. México
| | - H De Kort
- Plant Conservation and Population Biology, Biology Department, KU Leuven, Leuven, Belgium
| | | | - E García-Pérez
- Colegio de Postgraduados, Campus Veracruz, Veracruz, México
| | - T De Meyer
- Laboratory for Bioinformatics and Computational Genomics, Mathematical Modelling, Statistics & Bioinformatics Department, Ghent University, Ghent, Belgium
| | | | - B Muys
- Division of Forest, Nature and Landscape, KU Leuven, Leuven, Belgium
| | - O Honnay
- Plant Conservation and Population Biology, Biology Department, KU Leuven, Leuven, Belgium
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Govender N, Senan S, Mohamed-Hussein ZA, Wickneswari R. A gene co-expression network model identifies yield-related vicinity networks in Jatropha curcas shoot system. Sci Rep 2018; 8:9211. [PMID: 29907786 PMCID: PMC6003958 DOI: 10.1038/s41598-018-27493-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/04/2018] [Indexed: 11/18/2022] Open
Abstract
The plant shoot system consists of reproductive organs such as inflorescences, buds and fruits, and the vegetative leaves and stems. In this study, the reproductive part of the Jatropha curcas shoot system, which includes the aerial shoots, shoots bearing the inflorescence and inflorescence were investigated in regard to gene-to-gene interactions underpinning yield-related biological processes. An RNA-seq based sequencing of shoot tissues performed on an Illumina HiSeq. 2500 platform generated 18 transcriptomes. Using the reference genome-based mapping approach, a total of 64 361 genes was identified in all samples and the data was annotated against the non-redundant database by the BLAST2GO Pro. Suite. After removing the outlier genes and samples, a total of 12 734 genes across 17 samples were subjected to gene co-expression network construction using petal, an R library. A gene co-expression network model built with scale-free and small-world properties extracted four vicinity networks (VNs) with putative involvement in yield-related biological processes as follow; heat stress tolerance, floral and shoot meristem differentiation, biosynthesis of chlorophyll molecules and laticifers, cell wall metabolism and epigenetic regulations. Our VNs revealed putative key players that could be adapted in breeding strategies for J. curcas shoot system improvements.
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Affiliation(s)
- Nisha Govender
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
- Center for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
| | - Siju Senan
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Zeti-Azura Mohamed-Hussein
- Center for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Ratnam Wickneswari
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
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