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Core set construction and association analysis of Pinus massoniana from Guangdong province in southern China using SLAF-seq. Sci Rep 2019; 9:13157. [PMID: 31511632 PMCID: PMC6739479 DOI: 10.1038/s41598-019-49737-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 08/31/2019] [Indexed: 12/31/2022] Open
Abstract
Germplasm resource collection and utilization are important in forestry species breeding. High-through sequencing technologies have been playing increasing roles in forestry breeding. In this study, specific-locus amplified fragment sequencing (SLAF-seq) was employed to analyze 149 masson pine (Pinus massoniana) accessions collected from Guangdong in China. A large number of 471,660 SNPs in the total collection were identified from 599,164 polymorphic SLAF tags. Population structure analysis showed that 149 masson pines could not be obviously divided into subpopulations. Two core sets, containing 29 masson pine accessions for increasing resin and wood yield respectively, were obtained from the total collection. Phenotypic analyses of five traits showed abundant variations, 25 suggestive and 9 significant SNPs were associated with the resin-yielding capacity (RYC') and volume of wood (VW) using EMMAX and FaST-LMM; 22 suggestive and 11 significant SNPs were associated with RYC' and VW using mrMLM and FASTmrMLM. Moreover, a large number of associated SNPs were detected in trait HT, DBH, RW and RYC using mrMLM, FASTmrMLM, FASTmrEMMA and ISIS EM-BLASSO. The core germplasm sets would be a valuable resource for masson pine improvement and breeding. In addition, the associated SNP markers would be meaningful for masson pine resource selection.
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Serin EAR, Snoek LB, Nijveen H, Willems LAJ, Jiménez-Gómez JM, Hilhorst HWM, Ligterink W. Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population. Front Genet 2017; 8:201. [PMID: 29259624 PMCID: PMC5723289 DOI: 10.3389/fgene.2017.00201] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/21/2017] [Indexed: 12/17/2022] Open
Abstract
High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binning method, 1059 bin-markers were identified, physically anchored on the genome. The total length of the RNA-seq genetic map spans 471.70 centimorgans (cM) with an average marker distance of 0.45 cM and a maximum marker distance of 4.81 cM. This high resolution genotyping revealed new recombination breakpoints in the population. To highlight the advantages of such high-density map, we compared it to two publicly available genetic maps for the same population, comprising 69 PCR-based markers and 497 gene expression markers derived from microarray data, respectively. In this study, we show that SNP markers can effectively be derived from RNA-seq data. The new RNA-seq map closes many existing gaps in marker coverage, saturating the previously available genetic maps. Quantitative trait locus (QTL) analysis for published phenotypes using the available genetic maps showed increased QTL mapping resolution and reduced QTL confidence interval using the RNA-seq map. The new high-density map is a valuable resource that facilitates the identification of candidate genes and map-based cloning approaches.
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Affiliation(s)
- Elise A R Serin
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | - L B Snoek
- Laboratory of Nematology, Wageningen University, Wageningen, Netherlands.,Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | - Harm Nijveen
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands.,Laboratory of Bioinformatics, Wageningen University, Wageningen, Netherlands
| | - Leo A J Willems
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | - Jose M Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany.,Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Versailles Cedex, France
| | - Henk W M Hilhorst
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
| | - Wilco Ligterink
- Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, Netherlands
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Hunt AG. A rapid, simple, and inexpensive method for the preparation of strand-specific RNA-Seq libraries. Methods Mol Biol 2015; 1255:195-207. [PMID: 25487215 DOI: 10.1007/978-1-4939-2175-1_17] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
High-throughput sequencing of short cDNA tags, or RNA-Seq, has become a staple of genome-wide gene expression studies in plants. RNA-Seq libraries necessarily contain tags that correspond to the mRNA-poly(A) junction, or polyadenylation site, and thus may be mined for data that can help study alternative polyadenylation. This report presents a simple, rapid, and inexpensive method for preparing strand-specific RNA-Seq libraries from varying quantities of total RNA.
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Affiliation(s)
- Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, 301A Plant Science Building, 1405 Veterans Drive, Lexington, KY, 40546-0312, USA,
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Schneeberger K. Using next-generation sequencing to isolate mutant genes from forward genetic screens. Nat Rev Genet 2014; 15:662-76. [PMID: 25139187 DOI: 10.1038/nrg3745] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The long-lasting success of forward genetic screens relies on the simple molecular basis of the characterized phenotypes, which are typically caused by mutations in single genes. Mapping the location of causal mutations using genetic crosses has traditionally been a complex, multistep procedure, but next-generation sequencing now allows the rapid identification of causal mutations at single-nucleotide resolution even in complex genetic backgrounds. Recent advances of this mapping-by-sequencing approach include methods that are independent of reference genome sequences, genetic crosses and any kind of linkage information, which make forward genetics amenable for species that have not been considered for forward genetic screens so far.
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Affiliation(s)
- Korbinian Schneeberger
- Genome Plasticity and Computational Genetics, Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
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Fang C, Li W, Li G, Wang Z, Zhou Z, Ma Y, Shen Y, Li C, Wu Y, Zhu B, Yang W, Tian Z. Cloning of Ln gene through combined approach of map-based cloning and association study in soybean. J Genet Genomics 2013; 40:93-6. [PMID: 23439408 DOI: 10.1016/j.jgg.2013.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 01/15/2013] [Accepted: 01/15/2013] [Indexed: 11/16/2022]
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Fernie AR. Grand Challenges in Plant Systems Biology: Closing the Circle(s). FRONTIERS IN PLANT SCIENCE 2012; 3:35. [PMID: 22639645 PMCID: PMC3355630 DOI: 10.3389/fpls.2012.00035] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 02/07/2012] [Indexed: 05/24/2023]
Affiliation(s)
- Alisdair R. Fernie
- Department of Molecular Physiology, Max-Planck-Institute of Molecular Plant PhysiologyPotsdam, Germany
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Fernie AR. Editorial overview - computational approaches in aid of advancing understanding in plant physiology. FRONTIERS IN PLANT SCIENCE 2011; 2:78. [PMID: 22639611 PMCID: PMC3355588 DOI: 10.3389/fpls.2011.00078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Accepted: 10/26/2011] [Indexed: 06/01/2023]
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