토마토 marker-assisted background selection을 위한 SNP 마커 선발 데이터베이스
Genome-wide SNP Database for Marker-assisted Background Selection in Tomato
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참고문헌
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초록
Backcrossing is a plant breeding method most commonly used to incorporate one or a few genes into an adapted or elite variety. To facilitate MAB (marker-assisted backcrossing) in a practice breeding program, we developed a SNP database and a program for providing selected markers for background selection from genome-wide SNPs of seven tomato accessions downloaded from NCBI-SRA. We identified 410,074 SNPs among 21 parental combinations with data from seven transcriptomes and developed a SNP database. To select the optimized number of markers for background selection, we divided 12 chromosomes according to physical length and genetic length. Initially, each chromosome was equally divided into five blocks according to physical length, and three SNPs were positioned per block. Additionally, we applied the genetic distance from tomato-EXPEN 2000 map because the frequency of recombination can vary greatly among chromosomal regions. When considering genetic distance, each chromosome was divided into fifteen blocks unequally and one SNP was positioned per block. The program for background selection was designed to be simple and easy to use, and it is available at http://tgsol.seeders.co.kr/index.php/tg/mab. When the user selects the parental combination, the program provides selected markers with primer information. The value of this program for tomato breeding will further increase if more accession numbers are added to the database.
Abstract
Backcrossing is a plant breeding method most commonly used to incorporate one or a few genes into an adapted or elite variety. To facilitate MAB (marker-assisted backcrossing) in a practice breeding program, we developed a SNP database and a program for providing selected markers for background selection from genome-wide SNPs of seven tomato accessions downloaded from NCBI-SRA. We identified 410,074 SNPs among 21 parental combinations with data from seven transcriptomes and developed a SNP database. To select the optimized number of markers for background selection, we divided 12 chromosomes according to physical length and genetic length. Initially, each chromosome was equally divided into five blocks according to physical length, and three SNPs were positioned per block. Additionally, we applied the genetic distance from tomato-EXPEN 2000 map because the frequency of recombination can vary greatly among chromosomal regions. When considering genetic distance, each chromosome was divided into fifteen blocks unequally and one SNP was positioned per block. The program for background selection was designed to be simple and easy to use, and it is available at http://tgsol.seeders.co.kr/index.php/tg/mab. When the user selects the parental combination, the program provides selected markers with primer information. The value of this program for tomato breeding will further increase if more accession numbers are added to the database.
참고문헌 (32)
- 안송지, "멜론 및 참외 순도 검정을 위한 SNP 마커 개발 및 F1 종자 순도 검정", 한국육종학회지, 42(4), pp.397~406 (2010), 한국육종학회
- Bombarely A, "The Sol Genomics Network (solgenomics.net): growing tomatoes using perl", Nucleic Acids Res, 39, pp.D1149~D1155 (2011)
- Bowers JE, "Development of a 10,000 locus geneticmap of the sunflower genome basedon multiple crosses", G3, 2, pp.721~729 (2012)
- Chagné D, "Genome-wide SNP detection, validation, and development of an 8k SNP array for apple", PLOS ONE, 7, pp.e31745~ (2012)
- Collard BC, "Marker-assisted selection: an approach for precision plant breeding in the twenty-first century", Phil. Trans. R. Soc. B, 363, pp.557~572 (2008)
- Cox MP, "SolexaQA: at-aglance quality assessment of Illumina second-generation sequencing data", BMC Bioinformatics, 11, pp.485~ (2010)
- Cuesta-Marcos A, "Genome-wide SNPs and re-sequencing of growth habit and inflorescence genes in barley:implications for association mapping in germplasm arrays varying in size and structure", BMC Genomics, 11, pp.707~ (2010)
- Edwards D, "Plant genome sequencing: application for crop improvement", Plant Biotechnol. J, 8, pp.2~9 (2010)
- Foolad MR, "Genome mapping and molecular breeding of tomato", Internat. J. Plant Genomics, 2007, pp.1~52 (2007)
- Fulton TM, "Identification, analysis and utilization of a conserved orthologset (COS) markers for comparative genomics in higher plants", Plant Cell, 14, pp.1457~1467 (2002)
- Garg R, "De novo assembly of chickpea transcriptomeusing short reads for gene discovery and marker identification", DNA Research, 18, pp.53~63 (2011)
- Gupta PK, "Single nucleotide polymorphisms: A new paradigm for molecular marker technology and DNA polymorphism detection with emphasis on their use in plants", Current Science, 80, pp.524~535 (2001)
- Hamilton JP, "Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis", Plant Genome, 5, pp.17~29 (2012)
- Hyten DL, "High-throughput SNP discovery and assay development in common bean", BMC Genomics, 11, pp.475~ (2010)
- Ibitoye DO, "Marker-assisted-selection (MAS): A fast track to increase genetic gain in horticultural crop breeding", African J. Biotechnol, 9, pp.8889~8895 (2010)
- Jena KK, "Molecular markers and their use in marker-assisted selection in rice", Crop Science, 48, pp.1266~1276 (2008)
- Jiménez-Gómez JM, "Sequence diversity in three tomato species: SNPs, markers, and molecular evolution", BMC Plant Biology, 9, pp.85~ (2009)
- Jung JK, "Discovery of single nucleotide polymorphism in Capsicum and SNP markers for cultivar identification", Euphytica, 175, pp.91~107 (2010)
- King J, "Physical and genetic mapping in the grasses Loliumperenne and Festucapratensis", Genetics, 161, pp.315~324 (2002)
- Li H, "The sequence alignment", map format and SAMtools, 2009, pp.25, 2078~2079
- Neeraja CN, "A marker-assisted backcross approach for developing submergence-tolerant rice cultivars", Theor. Appl. Genet, 115, pp.767~776 (2007)
- Ness RW, "De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants", BMC Genomics, 12, pp.298~ (2011)
- "International tomato genome sequencing project" (2011)[URL]
- Shirasawa K, "SNP discovery and linkage map construction in cultivated tomato", DNA Research, 17, pp.381~391 (2010)
- Shirasawa K, "An interspecipic linkage map of SSR and intronic polymorphism markers in tomato", Theor. Appl. Genet, 121, pp.731~739 (2010)
- The Tomato Genome Consortium, "The tomato genome sequence provides insights into fleshy fruit evolution", Nature, 485, pp.635~641 (2012)
- Trapnell C, "TopHat: discovering splice junctions with RNA-Seq", Bioinformatics, 25, pp.1105~1111 (2009)
- Trebbi D, "High-throughput SNP discovery and genotyping in durum wheat (Triticum durum desf.)", Theor. Appl. Genet, 123, pp.555~569 (2011)
- Wu J, "Physical maps and recombination frequency of six rice chromosomes", Plant J, 36, pp.720~730 (2003)
- You FM, "BatchPrimer3: A high throughput web application for PCR and sequencing primer design", BMC Bioinformatics, 9, pp.253~ (2008)
- Xu Y, "Marker-assisted selection in plant breeding: from publications to practice", Crop Science, 48, pp.391~407 (2008)
- Xu X, "Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes", Nature Biotechnol, 30, pp.105~111 (2012)