The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation Sequencing
Mutagenesis in combination with Genotyping by Sequencing (GBS) is a powerful tool for introducing variation, studying gene function and identifying causal mutations underlying phenotypes of interest in crop plant genomes. About 400 million paired-end reads were obtained from 82 ethylmethane sulfonat...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2018-04-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/article/10.3389/fpls.2018.00524/full |
| _version_ | 1818609421015580672 |
|---|---|
| author | Fatemeh Maghuly Stephan Pabinger Julie Krainer Margit Laimer |
| author_facet | Fatemeh Maghuly Stephan Pabinger Julie Krainer Margit Laimer |
| author_sort | Fatemeh Maghuly |
| collection | DOAJ |
| description | Mutagenesis in combination with Genotyping by Sequencing (GBS) is a powerful tool for introducing variation, studying gene function and identifying causal mutations underlying phenotypes of interest in crop plant genomes. About 400 million paired-end reads were obtained from 82 ethylmethane sulfonate (EMS) induced mutants and 14 wild-type accessions of Jatropha curcas for the detection of Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletions (InDels) by two different approaches (nGBS and ddGBS) on an Illumina HiSeq 2000 sequencer. Using bioinformatics analyses, 1,452 induced SNPs and InDels were identified in coding regions, which were distributed across 995 genes. The predominantly observed mutations were G/C to A/T transitions (64%), while transversions were observed at a lower frequency (36%). Regarding the effect of mutations on gene function, 18% of the mutations were located in intergenic regions. In fact, mutants with the highest number of heterozygous SNPs were found in samples treated with 0.8% EMS for 3 h. Reconstruction of the metabolic pathways showed that in total 16 SNPs were located in six KEGG pathways by nGBS and two pathways by ddGBS. The most highly represented pathways were ether-lipid metabolism and glycerophospholipid metabolism, followed by starch and sucrose metabolism by nGBS and triterpenoid biosynthesis as well as steroid biosynthesis by ddGBS. Furthermore, high genome methylation was observed in J. curcas, which might help to understand the plasticity of the Jatropha genome in response to environmental factors. At last, the results showed that continuously vegetatively propagated tissue is a fast, efficient and accurate method to dissolve chimeras, especially for long-lived plants like J. curcas. Obtained data showed that allelic variations and in silico analyses of gene functions (gene function prediction), which control important traits, could be identified in mutant populations using nGBS and ddGBS. However, the handling of GBS data is more difficult and more challenging than the traditional TILLING strategy in mutated plants, since the Jatropha genome sequence is incomplete, which makes alignment and variant analysis of target sequence reads challenging to perform and interpret. Therefore, providing a complete Jatropha reference genome sequence with high quality should be a priority for any breeding program. |
| first_indexed | 2024-12-16T14:58:16Z |
| format | Article |
| id | doaj.art-0d4db431552c4776af4032a32b300f88 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-16T14:58:16Z |
| publishDate | 2018-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-0d4db431552c4776af4032a32b300f882022-12-21T22:27:21ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-04-01910.3389/fpls.2018.00524349845The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation SequencingFatemeh Maghuly0Stephan Pabinger1Julie Krainer2Margit Laimer3Plant Biotechnology Unit, Department of Biotechnology, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Vienna, AustriaMolecular Diagnostics, Center for Health & Bioresources, Austrian Institute of Technology, Vienna, AustriaMolecular Diagnostics, Center for Health & Bioresources, Austrian Institute of Technology, Vienna, AustriaPlant Biotechnology Unit, Department of Biotechnology, Vienna Institute of BioTechnology, University of Natural Resources and Life Sciences, Vienna, AustriaMutagenesis in combination with Genotyping by Sequencing (GBS) is a powerful tool for introducing variation, studying gene function and identifying causal mutations underlying phenotypes of interest in crop plant genomes. About 400 million paired-end reads were obtained from 82 ethylmethane sulfonate (EMS) induced mutants and 14 wild-type accessions of Jatropha curcas for the detection of Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletions (InDels) by two different approaches (nGBS and ddGBS) on an Illumina HiSeq 2000 sequencer. Using bioinformatics analyses, 1,452 induced SNPs and InDels were identified in coding regions, which were distributed across 995 genes. The predominantly observed mutations were G/C to A/T transitions (64%), while transversions were observed at a lower frequency (36%). Regarding the effect of mutations on gene function, 18% of the mutations were located in intergenic regions. In fact, mutants with the highest number of heterozygous SNPs were found in samples treated with 0.8% EMS for 3 h. Reconstruction of the metabolic pathways showed that in total 16 SNPs were located in six KEGG pathways by nGBS and two pathways by ddGBS. The most highly represented pathways were ether-lipid metabolism and glycerophospholipid metabolism, followed by starch and sucrose metabolism by nGBS and triterpenoid biosynthesis as well as steroid biosynthesis by ddGBS. Furthermore, high genome methylation was observed in J. curcas, which might help to understand the plasticity of the Jatropha genome in response to environmental factors. At last, the results showed that continuously vegetatively propagated tissue is a fast, efficient and accurate method to dissolve chimeras, especially for long-lived plants like J. curcas. Obtained data showed that allelic variations and in silico analyses of gene functions (gene function prediction), which control important traits, could be identified in mutant populations using nGBS and ddGBS. However, the handling of GBS data is more difficult and more challenging than the traditional TILLING strategy in mutated plants, since the Jatropha genome sequence is incomplete, which makes alignment and variant analysis of target sequence reads challenging to perform and interpret. Therefore, providing a complete Jatropha reference genome sequence with high quality should be a priority for any breeding program.http://journal.frontiersin.org/article/10.3389/fpls.2018.00524/fullchemical mutagenesisSNP callingcrop improvementbiofuelreverse genetic |
| spellingShingle | Fatemeh Maghuly Stephan Pabinger Julie Krainer Margit Laimer The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation Sequencing Frontiers in Plant Science chemical mutagenesis SNP calling crop improvement biofuel reverse genetic |
| title | The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation Sequencing |
| title_full | The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation Sequencing |
| title_fullStr | The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation Sequencing |
| title_full_unstemmed | The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation Sequencing |
| title_short | The Pattern and Distribution of Induced Mutations in J. curcas Using Reduced Representation Sequencing |
| title_sort | pattern and distribution of induced mutations in j curcas using reduced representation sequencing |
| topic | chemical mutagenesis SNP calling crop improvement biofuel reverse genetic |
| url | http://journal.frontiersin.org/article/10.3389/fpls.2018.00524/full |
| work_keys_str_mv | AT fatemehmaghuly thepatternanddistributionofinducedmutationsinjcurcasusingreducedrepresentationsequencing AT stephanpabinger thepatternanddistributionofinducedmutationsinjcurcasusingreducedrepresentationsequencing AT juliekrainer thepatternanddistributionofinducedmutationsinjcurcasusingreducedrepresentationsequencing AT margitlaimer thepatternanddistributionofinducedmutationsinjcurcasusingreducedrepresentationsequencing AT fatemehmaghuly patternanddistributionofinducedmutationsinjcurcasusingreducedrepresentationsequencing AT stephanpabinger patternanddistributionofinducedmutationsinjcurcasusingreducedrepresentationsequencing AT juliekrainer patternanddistributionofinducedmutationsinjcurcasusingreducedrepresentationsequencing AT margitlaimer patternanddistributionofinducedmutationsinjcurcasusingreducedrepresentationsequencing |