Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut
Cultivated peanut (Arachis hypogaea L.) forms root nodules to enable a symbiotic relationship with rhizobia for biological nitrogen fixation. To understand the genetic factors of peanut nodulation, it is fundamental to genetically map and clone the genes involved in nodulation. For genetic mapping,...
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Frontiers Media S.A.
2020-03-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2020.00222/full |
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| author | Ze Peng Zifan Zhao Josh Paul Clevenger Ye Chu Dev Paudel Peggy Ozias-Akins Jianping Wang Jianping Wang |
| author_facet | Ze Peng Zifan Zhao Josh Paul Clevenger Ye Chu Dev Paudel Peggy Ozias-Akins Jianping Wang Jianping Wang |
| author_sort | Ze Peng |
| collection | DOAJ |
| description | Cultivated peanut (Arachis hypogaea L.) forms root nodules to enable a symbiotic relationship with rhizobia for biological nitrogen fixation. To understand the genetic factors of peanut nodulation, it is fundamental to genetically map and clone the genes involved in nodulation. For genetic mapping, high throughput genotyping with a large number of polymorphic markers is critical. In this study, two sets of sister recombinant inbred lines (RILs), each containing a nodulating (Nod+) and non-nodulating (Nod-) line, and their Nod+ parental lines were extensively genotyped. Several next generation sequencing (NGS) methods including target enrichment sequencing (TES), RNA-sequencing (RNA-seq), genotyping by sequencing (GBS), and the 48K Axiom Arachis2 SNP array, and various analysis pipelines were applied to identify single nucleotide polymorphisms (SNP) among the two sets of RILs and their parents. TES revealed the largest number of homozygous SNPs (15,947) between the original parental lines, followed by the Axiom Arachis2 SNP array (1,887), RNA-seq (1,633), and GBS (312). Among the five SNP analysis pipelines applied, the alignment to A/B genome followed by HAPLOSWEEP revealed the largest number of homozygous SNPs and highest concordance rate (79%) with the array. A total of 222 and 1,200 homozygous SNPs were polymorphic between the Nod+ and Nod− sister RILs and between their parents, respectively. A graphical genotype map of the sister RILs was constructed with these SNPs, which demonstrated the candidate genomic regions harboring genes controlling nodulation across the whole genome. Results of this study mainly provide the pros and cons of NGS and SNP genotyping platforms for genetic mapping in peanut, and also provide potential genetic resources to narrow down the genomic regions controlling peanut nodulation, which would lay the foundation for gene cloning and improvement of nitrogen fixation in peanut. |
| first_indexed | 2024-12-14T22:08:19Z |
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| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-14T22:08:19Z |
| publishDate | 2020-03-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-ea86922acac14116bd8e5afdf0ae34822022-12-21T22:45:49ZengFrontiers Media S.A.Frontiers in Genetics1664-80212020-03-011110.3389/fgene.2020.00222521391Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated PeanutZe Peng0Zifan Zhao1Josh Paul Clevenger2Ye Chu3Dev Paudel4Peggy Ozias-Akins5Jianping Wang6Jianping Wang7Agronomy Department, University of Florida, Gainesville, FL, United StatesAgronomy Department, University of Florida, Gainesville, FL, United StatesCenter for Applied Genetic Technologies, University of Georgia, Athens, GA, United StatesGenetic and Genomics and Department of Horticulture, Institute of Plant Breeding, University of Georgia, Tifton, GeorgiaAgronomy Department, University of Florida, Gainesville, FL, United StatesGenetic and Genomics and Department of Horticulture, Institute of Plant Breeding, University of Georgia, Tifton, GeorgiaAgronomy Department, University of Florida, Gainesville, FL, United StatesGenetics Institute and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United StatesCultivated peanut (Arachis hypogaea L.) forms root nodules to enable a symbiotic relationship with rhizobia for biological nitrogen fixation. To understand the genetic factors of peanut nodulation, it is fundamental to genetically map and clone the genes involved in nodulation. For genetic mapping, high throughput genotyping with a large number of polymorphic markers is critical. In this study, two sets of sister recombinant inbred lines (RILs), each containing a nodulating (Nod+) and non-nodulating (Nod-) line, and their Nod+ parental lines were extensively genotyped. Several next generation sequencing (NGS) methods including target enrichment sequencing (TES), RNA-sequencing (RNA-seq), genotyping by sequencing (GBS), and the 48K Axiom Arachis2 SNP array, and various analysis pipelines were applied to identify single nucleotide polymorphisms (SNP) among the two sets of RILs and their parents. TES revealed the largest number of homozygous SNPs (15,947) between the original parental lines, followed by the Axiom Arachis2 SNP array (1,887), RNA-seq (1,633), and GBS (312). Among the five SNP analysis pipelines applied, the alignment to A/B genome followed by HAPLOSWEEP revealed the largest number of homozygous SNPs and highest concordance rate (79%) with the array. A total of 222 and 1,200 homozygous SNPs were polymorphic between the Nod+ and Nod− sister RILs and between their parents, respectively. A graphical genotype map of the sister RILs was constructed with these SNPs, which demonstrated the candidate genomic regions harboring genes controlling nodulation across the whole genome. Results of this study mainly provide the pros and cons of NGS and SNP genotyping platforms for genetic mapping in peanut, and also provide potential genetic resources to narrow down the genomic regions controlling peanut nodulation, which would lay the foundation for gene cloning and improvement of nitrogen fixation in peanut.https://www.frontiersin.org/article/10.3389/fgene.2020.00222/fullgenotyping by sequencingnodulationpeanutRNA sequencingsingle nucleotide polymorphismSNP array |
| spellingShingle | Ze Peng Zifan Zhao Josh Paul Clevenger Ye Chu Dev Paudel Peggy Ozias-Akins Jianping Wang Jianping Wang Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut Frontiers in Genetics genotyping by sequencing nodulation peanut RNA sequencing single nucleotide polymorphism SNP array |
| title | Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut |
| title_full | Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut |
| title_fullStr | Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut |
| title_full_unstemmed | Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut |
| title_short | Comparison of SNP Calling Pipelines and NGS Platforms to Predict the Genomic Regions Harboring Candidate Genes for Nodulation in Cultivated Peanut |
| title_sort | comparison of snp calling pipelines and ngs platforms to predict the genomic regions harboring candidate genes for nodulation in cultivated peanut |
| topic | genotyping by sequencing nodulation peanut RNA sequencing single nucleotide polymorphism SNP array |
| url | https://www.frontiersin.org/article/10.3389/fgene.2020.00222/full |
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