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| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 黃永芬 | zh_TW |
| dc.contributor.advisor | Yung-Fen Huang | en |
| dc.contributor.author | 王群山 | zh_TW |
| dc.contributor.author | Chun-San Wang | en |
| dc.date.accessioned | 2025-02-19T16:20:56Z | - |
| dc.date.available | 2025-02-20 | - |
| dc.date.copyright | 2025-02-19 | - |
| dc.date.issued | 2024 | - |
| dc.date.submitted | 2025-02-05 | - |
| dc.identifier.citation | Aamir M, Karmakar P, Singh VK, et al (2021) A novel insight into transcriptional and epigenetic regulation underlying sex expression and flower development in melon (Cucumis melo L.). Physiologia Plantarum 173:1729–1764. https://doi.org/10.1111/ppl.13357
Aballay MM, Aguirre NC, Filippi CV, et al (2021) Fine-tuning the performance of ddRAD-seq in the peach genome. Sci Rep 11:6298. https://doi.org/10.1038/s41598-021-85815-0 Argyris JM, Ruiz-Herrera A, Madriz-Masis P, et al (2015) Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly. BMC Genomics 16:4. https://doi.org/10.1186/s12864-014-1196-3 Baird NA, Etter PD, Atwood TS, et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376. https://doi.org/10.1371/journal.pone.0003376 Bellundagi A, Ramya KT, Krishna H, et al (2022) Marker-assisted backcross breeding for heat tolerance in bread wheat (Triticum aestivum L.). Front Genet 13:1056783. https://doi.org/10.3389/fgene.2022.1056783 Beraldo-Hoischen P, Gomez-Guillamon ML, Lopez-Sese AI, et al (2012) QTL associated with one recessive gene for powdery mildew resistance in the melon genotype TGR-1551. Cucurbitaceae 2012: Proceedings of the Xth Eucarpia meeting on genetics and breeding of cucurbitaceae Branham SE, Kousik C, Mandal MK, Wechter WP (2021) Quantitative trait loci mapping of resistance to powdery mildew race 1 in a recombinant inbred line population of melon. Plant Dis 105:3809–3815. https://doi.org/10.1094/PDIS-12-20-2643-RE Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890. https://doi.org/10.1093/bioinformatics/btg112 Campos-Martin R, Schmickler S, Goel M, et al (2023) Reliable genotyping of recombinant genomes using a robust hidden Markov model. Plant Physiology 192:821–836. https://doi.org/10.1093/plphys/kiad191 Cao Y, Diao Q, Chen Y, et al (2021) Development of KASP markers and identification of a QTL underlying powdery mildew resistance in melon (Cucumis melo L.) by bulked segregant analysis and RNA-Seq. Front Plant Sci 11:593207. https://doi.org/10.3389/fpls.2020.593207 Castanera R, Ruggieri V, Pujol M, et al (2020) An improved melon reference genome with single-molecule sequencing uncovers a recent burst of transposable elements with potential impact on genes. Front Plant Sci 10:. https://doi.org/10.3389/fpls.2019.01815 Chafin TK, Martin BT, Mussmann SM, et al (2018) FRAGMATIC: in silico locus prediction and its utility in optimizing ddRADseq projects. Conservation Genetics Resources 10:325–328. https://doi.org/10.1007/s12686-017-0814-1 Chandrasekharan N, Ramanathan N, Pukalenthy B, et al (2022) Development of β-carotene, lysine, and tryptophan-rich maize (Zea mays) inbreds through marker-assisted gene pyramiding. Sci Rep 12:8551. https://doi.org/10.1038/s41598-022-11585-y Christiansen H, Heindler FM, Hellemans B, et al (2021) Facilitating population genomics of non-model organisms through optimized experimental design for reduced representation sequencing. BMC Genomics 22:625. https://doi.org/10.1186/s12864-021-07917-3 Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971 Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences 363:557–572. https://doi.org/10.1098/rstb.2007.2170 Cui H, Fan C, Ding Z, et al (2022) CmPMRl and CmPMrs are responsible for resistance to powdery mildew caused by Podosphaera xanthii race 1 in Melon. Theor Appl Genet. https://doi.org/10.1007/s00122-021-04025-4 Davey JW, Hohenlohe PA, Etter PD, et al (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics 12:499–510. https://doi.org/10.1038/nrg3012 DePristo MA, Banks E, Poplin R, et al (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics 43:491–498. https://doi.org/10.1038/ng.806 Egel DS, Adkins ST, Wintermantel WM, et al (2022) Diseases of cucumbers, melons, pumpkins, squash, and watermelons. In: Elmer WH, McGrath M, McGovern RJ (eds) Handbook of vegetable and herb diseases. Springer International Publishing, Cham, pp 1–105 Elshire RJ, Glaubitz JC, Sun Q, et al (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379. https://doi.org/10.1371/journal.pone.0019379 FAOSTAT (2022) Crops and livestock products. https://www.fao.org/faostat/en/#data/QCL. Accessed 16 Apr 2024 Fazza AC, Dallagnol LJ, Fazza AC, et al (2013) Mapping of resistance genes to races 1, 3 and 5 of Podosphaera xanthii in melon PI 414723. Crop Breed Appl Biotechnol 13:349–355. https://doi.org/10.1590/S1984-70332013000400005 Fragoso CA, Heffelfinger C, Zhao H, Dellaporta SL (2016) Imputing Genotypes in Biallelic Populations from Low-Coverage Sequence Data. Genetics 202:487–495. https://doi.org/10.1534/genetics.115.182071 Frisch M (2004) Breeding strategies: optimum design of marker-assisted backcross programs. In: Molecular marker systems in plant breeding and crop improvement. Springer, pp 319–334 Frisch M, Bohn M, Melchinger AE (1999a) Minimum sample size and optimal positioning of flanking markers in marker-assisted backcrossing for transfer of a target gene. Crop Sci 39:967–975 Frisch M, Bohn M, Melchinger AE (1999b) Comparison of selection strategies for marker-assisted backcrossing of a gene. Crop Sci 39:1295–1301 Fu Y-B, Peterson GW, Dong Y (2016) Increasing Genome Sampling and Improving SNP Genotyping for Genotyping-by-Sequencing with new Combinations of Restriction Enzymes. G3: Genes, Genomes, Genetics g3.115.025775. https://doi.org/10.1534/g3.115.025775 Fukino N, Ohara T, Monforte AJ, et al (2008) Identification of QTLs for resistance to powdery mildew and SSR markers diagnostic for powdery mildew resistance genes in melon (Cucumis melo L.). Theor Appl Genet 118:165–175. https://doi.org/10.1007/s00122-008-0885-1 Furuta T, Yamamoto T, Ashikari M (2023) GBScleanR: robust genotyping error correction using a hidden Markov model with error pattern recognition. Genetics 224:iyad055. https://doi.org/10.1093/genetics/iyad055 Gao J, Gileta AF, Bimschleger HV, et al (2019) Adapting genotyping-by-sequencing and variant calling for heterogeneous stock rats. bioRxiv 523043. https://doi.org/10.1101/523043 Garcia-Mas J, Benjak A, Sanseverino W, et al (2012) The genome of melon (Cucumis melo L.). Proc Natl Acad Sci U S A 109:11872–11877. https://doi.org/10.1073/pnas.1205415109 Gonda I, Ashrafi H, Lyon DA, et al (2019) Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection. The Plant Genome 12:0. https://doi.org/10.3835/plantgenome2018.02.0010 Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity 69:315–324 Hamblin MT, Rabbi IY (2014) The Effects of Restriction-Enzyme Choice on Properties of Genotyping-by-Sequencing Libraries: A Study in Cassava (Manihot esculenta). Crop Science 54:2603. https://doi.org/10.2135/cropsci2014.02.0160 Haonan C, Zhuo D, Chao F, et al (2020) Genetic mapping and nucleotide diversity of two powdery mildew resistance loci in melon (Cucumis melo). Phytopathology® 110:1970–1979. https://doi.org/10.1094/PHYTO-03-20-0078-R Heffelfinger C, Fragoso CA, Moreno MA, et al (2014) Flexible and scalable genotyping-by-sequencing strategies for population studies. BMC genomics 15:979 Hoffberg SL, Kieran TJ, Catchen JM, et al (2016) RAD cap: sequence capture of dual‐digest RAD seq libraries with identifiable duplicates and reduced missing data. Molecular Ecology Resources 16:1264–1278. https://doi.org/10.1111/1755-0998.12566 Huang JH, Wang YH (2007) The races of Podosphaera xanthii causing melon powdery mildew in Taiwan. J Taiwan Agric Res 56:307–315 Huang JH, Wang YH, Lo CT (2002) Development of leaf-disk method for screening melon varieties resistant to Sphaerotheca fuliginea race 1. J Agric Res China 51:49–56. https://doi.org/10.29951/JARC.200212.0005 Jiang G-L (2015) Molecular Marker-Assisted Breeding: A Plant Breeder’s Review. In: Al-Khayri JM, Jain SM, Johnson DV (eds) Advances in Plant Breeding Strategies: Breeding, Biotechnology and Molecular Tools. Springer International Publishing, Cham, pp 431–472 Jobes DV, Hurley DL, Thien LB (1995) Plant DNA isolation: A method to efficiently remove polyphenolics, polysaccharides, and RNA. Taxon 44:379–386. https://doi.org/10.2307/1223408 Kim HT, Park JI, Robin AHK, et al (2016) Identification of a new race and development of DNA markers associated with powdery mildew in melon. Plant Breeding and Biotechnology 4:225–233. https://doi.org/10.9787/PBB.2016.4.2.225 Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nature Methods 9:357–359. https://doi.org/10.1038/nmeth.1923 Lawrence M, Huber W, Pagès H, et al (2013) Software for Computing and Annotating Genomic Ranges. PLOS Comput Biol 9:e1003118. https://doi.org/10.1371/journal.pcbi.1003118 Lepais O, Weir JT (2014) SimRAD: an R package for simulation-based prediction of the number of loci expected in RADseq and similar genotyping by sequencing approaches. Mol Ecol Resour 1314–1312. https://doi.org/10.1111/1755-0998.12273 Li B, Zhao Y, Zhu Q, et al (2017) Mapping of powdery mildew resistance genes in melon (Cucumis melo L.) by bulked segregant analysis. Scientia Horticulturae 220:160–167. https://doi.org/10.1016/j.scienta.2017.04.001 Li H, Handsaker B, Wysoker A, et al (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079. https://doi.org/10.1093/bioinformatics/btp352 Li L-L, Huang S, Hou J, et al (2020) Construction of a high-density genetic map for melon using ddRAD-Seq technology from a population derived from flexuosus and reticulatus botanical groups. Scientia Horticulturae 272:109531. https://doi.org/10.1016/j.scienta.2020.109531 López-Martín M, Pérez-de-Castro A, Picó B, Gómez-Guillamón ML (2022) Advanced genetic studies on powdery mildew resistance in TGR-1551. IJMS 23:12553. https://doi.org/10.3390/ijms232012553 Lorieux M, Gkanogiannis A, Fragoso C, Rami J-F (2019) NOISYmputer: genotype imputation in bi-parental populations for noisy low-coverage next-generation sequencing data. bioRxiv. https://doi.org/10.1101/658237 Lübberstedt T, Beavis W, Bhattacharyya M, et al (2023) Molecular Plant Breeding. Iowa State University Digital Press Lübberstedt T, Varshney RK (eds) (2013) Diagnostics in Plant Breeding. Springer Netherlands, Dordrecht Manichaikul A, Moon JY, Sen Ś, et al (2009) A model selection approach for the identification of quantitative trait loci in experimental crosses, allowing epistasis. Genetics 181:1077–1086. https://doi.org/10.1534/genetics.108.094565 Marè C, Zampieri E, Cavallaro V, et al (2023) Marker-assisted introgression of the salinity tolerance locus Saltol in temperate Japonica Rice. Rice 16:2. https://doi.org/10.1186/s12284-023-00619-2 McCreight JD (2006) Melon-powdery mildew interactions reveal variation in melon cultigens and Podosphaera xanthii races 1 and 2. J Amer Soc Hort Sci 131:59–65 McKenna A, Hanna M, Banks E, et al (2010) The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20:1297–1303. https://doi.org/10.1101/gr.107524.110 Metzker ML (2010) Sequencing technologies — the next generation. Nat Rev Genet 11:31–46. https://doi.org/10.1038/nrg2626 Miao C, Fang J, Li D, et al (2018) Genotype-Corrector: improved genotype calls for genetic mapping in F2 and RIL populations. Scientific Reports 8:. https://doi.org/10.1038/s41598-018-28294-0 Mora-Márquez F, García-Olivares V, Emerson BC, López de Heredia U (2017) ddradseqtools: a software package for in silico simulation and testing of double-digest RADseq experiments. Molecular Ecology Resources 17:230–246. https://doi.org/10.1111/1755-0998.12550 Morgan M, Pagès H, Obenchain V, Hayden N (2024) Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import. R package version 2.22.0, https://bioconductor.org/packages/Rsamtools. Neeraja CN, Maghirang-Rodriguez R, Pamplona A, et al (2007) A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet 115:767–776. https://doi.org/10.1007/s00122-007-0607-0 Ning X, Wang X, Gao X, et al (2014) Inheritances and location of powdery mildew resistance gene in melon Edisto47. Euphytica 195:345–353. https://doi.org/10.1007/s10681-013-1000-5 Nishimura K, Kokaji H, Motoki K, et al (2024) Degenerate oligonucleotide primer MIG‐seq: an effective PCR‐based method for high‐throughput genotyping. The Plant Journal 118:2296–2317. https://doi.org/10.1111/tpj.16708 Pagès H, Aboyoun P, Gentleman R, DebRoy S (2024) Biostrings: Efficient manipulation of biological strings. R package version 2.74.0, https://bioconductor.org/packages/Biostrings. Pagès H, Kakopo AK (2024) BSgenomeForge: Forge your own BSgenome data package. R package version 1.6.0, https://bioconductor.org/packages/BSgenomeForge Perchepied L, Bardin M, Dogimont C, Pitrat M (2005) Relationship between loci conferring downy mildew and powdery mildew resistance in melon assessed by quantitative trait loci mapping. Phytopathology 95:556–565. https://doi.org/10.1094/PHYTO-95-0556 Pértille F, Guerrero-Bosagna C, Silva VH da, et al (2016) High-throughput and Cost-effective Chicken Genotyping Using Next-Generation Sequencing. Scientific Reports 6:. https://doi.org/10.1038/srep26929 Peterson BK, Weber JN, Kay EH, et al (2012) Double Digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7:e37135. https://doi.org/10.1371/journal.pone.0037135 Pitrat M (2016) Melon genetic resources: Phenotypic diversity and horticultural taxonomy. In: Genetics and Genomics of Cucurbitaceae. Springer, Cham, pp 25–60 Poland JA, Brown PJ, Sorrells ME, Jannink J-L (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7:e32253. https://doi.org/10.1371/journal.pone.0032253 R Core Team (2023) R: A language and environment for statistical computing. R foundation for statistical computing, Vienna, Austria. https://www.r-project.org/ Rodríguez-Moreno L, González VM, Benjak A, et al (2011) Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin. BMC Genomics 12:424. https://doi.org/10.1186/1471-2164-12-424 Ruggieri V, Alexiou KG, Morata J, et al (2018) An improved assembly and annotation of the melon ( Cucumis melo L.) reference genome. Scientific Reports 8:8088. https://doi.org/10.1038/s41598-018-26416-2 Scheben A, Batley J, Edwards D (2017) Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. Plant Biotechnol J 15:149–161. https://doi.org/10.1111/pbi.12645 Schubert M, Lindgreen S, Orlando L (2016) AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes 9:. https://doi.org/10.1186/s13104-016-1900-2 Semagn K, Babu R, Hearne S, Olsen M (2014) Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement. Mol Breeding 33:1–14. https://doi.org/10.1007/s11032-013-9917-x Shirasawa K, Hirakawa H, Isobe S (2016) Analytical workflow of double-digest restriction site-associated DNA sequencing based on empirical and in silico optimization in tomato. DNA Research 23:145–153. https://doi.org/10.1093/dnares/dsw004 Siberchicot A, Bessy A, Guéguen L, Marais GA (2017) MareyMap online: a user-friendly web application and database service for estimating recombination rates using physical and genetic maps. Genome Biology and Evolution 9:2506–2509. https://doi.org/10.1093/gbe/evx178 Sim S-C, Durstewitz G, Plieske J, et al (2012) Development of a Large SNP Genotyping Array and Generation of High-Density Genetic Maps in Tomato. PLoS ONE 7:e40563. https://doi.org/10.1371/journal.pone.0040563 Singh J, Sharma S, Kaur A, et al (2021) Marker-assisted pyramiding of lycopene-ε-cyclase, β-carotene hydroxylase1 and opaque2 genes for development of biofortified maize hybrids. Sci Rep 11:12642. https://doi.org/10.1038/s41598-021-92010-8 Sinn BT, Simon SJ, Santee MV, et al (2022) ISSRseq: An extensible method for reduced representation sequencing. Methods Ecol Evol 13:668–681. https://doi.org/10.1111/2041-210X.13784 Teixeira APM, Barreto FA da S, Camargo LEA (2008) An AFLP marker linked to the Pm-1 gene that confers resistance to Podosphaera xanthii race 1 in Cucumis melo. Genetics and Molecular Biology 31:547–550. https://doi.org/10.1590/S1415-47572008000300023 Thermo Fisher Scientific (2024) Custom TaqMan® assay design tool. https://www.thermofisher.com/order/custom-genomic-products/tools/genotyping/. Accessed 29 May 2024 Van der Auwera GA, Carneiro MO, Hartl C, et al (2013) From fastq data to high-confidence variant calls: The genome analysis toolkit best practices pipeline. In: Current Protocols in Bioinformatics. John Wiley & Sons, Inc., p 11.10.1-11.10.33 Wang J, Li L, Qi H, et al (2016a) RestrictionDigest: A powerful Perl module for simulating genomic restriction digests. Electronic Journal of Biotechnology 21:36–42. https://doi.org/10.1016/j.ejbt.2016.02.003 Wang X, Li G, Gao X, et al (2011) Powdery mildew resistance gene Pm-AN located in a segregation distortion region of melon LGV. Euphytica 180:421–428. https://doi.org/10.1007/s10681-011-0406-1 Wang YH (2016) Mapping quantitative trait loci for fruit traits and powdery mildew resistance in melon (Cucumis melo L.). Doctoral Dissertation, National Taiwan University Wang YH, Wu DH, Huang JinH, et al (2016b) Mapping quantitative trait loci for fruit traits and powdery mildew resistance in melon (Cucumis melo). Bot Stud 57:19. https://doi.org/10.1186/s40529-016-0130-1 Xu L, He Y, Tang L, et al (2022) Genetics, Genomics, and Breeding in Melon. Agronomy 12:2891. https://doi.org/10.3390/agronomy12112891 Xu Yunbi (2010) Molecular plant breeding. CABI, Cambridge, MA Yuste-Lisbona FJ, Capel C, Gómez-Guillamón ML, et al (2011a) Codominant PCR-based markers and candidate genes for powdery mildew resistance in melon (Cucumis melo L.). Theor Appl Genet 122:747–758. https://doi.org/10.1007/s00122-010-1483-6 Yuste-Lisbona FJ, Capel C, Sarria E, et al (2011b) Genetic linkage map of melon (Cucumis melo L.) and localization of a major QTL for powdery mildew resistance. Mol Breeding 27:181–192. https://doi.org/10.1007/s11032-010-9421-5 Yuste‐Lisbona FJ, López‐Sesé AI, Gómez‐Guillamón ML (2010) Inheritance of resistance to races 1, 2 and 5 of powdery mildew in the melon TGR-1551. Plant Breeding 129:72–75. https://doi.org/10.1111/j.1439-0523.2009.01655.x Zhang C, Ren Y, Guo S, et al (2013) Application of comparative genomics in developing markers tightly linked to the Pm-2F gene for powdery mildew resistance in melon (Cucumis melo L.). Euphytica 190:157–168. https://doi.org/10.1007/s10681-012-0828-4 Zhang T, Cui H, Luan F, et al (2023) A recessive gene Cmpmr2F confers powdery mildew resistance in melon (Cucumis melo L.). Theor Appl Genet 136:4. https://doi.org/10.1007/s00122-023-04269-2 Zhang Y, Yang Z, Ma H, et al (2021) Pyramiding of fusarium head blight resistance quantitative trait loci, Fhb1, Fhb4, and Fhb5, in modern Chinese wheat cultivars. Front Plant Sci 12:694023. https://doi.org/10.3389/fpls.2021.694023 | - |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/96522 | - |
| dc.description.abstract | 分子標誌為遺傳研究與作物育種之重要工具。隨著次世代定序的發展，開發高通量分子標誌並進行基因型分型已成為作物遺傳育種研究的常用方法，但針對目標物種發展適合的最佳化流程仍為挑戰。為此，本研究奠基於次世代定序，優化雙限制酶切位點標定法 (double digest restricted associated DNA sequencing, ddRADseq) 之分子標誌開發與基因型分型，並以甜瓜抗白粉病之遺傳分析與育成抗病近同源系作為方法驗證。我們以電腦模擬限制酶於甜瓜基因體之切位並以小規模實驗評估限制酶組合。之後分別以PstI和XbaI作為稀有切位限制酶與常見切位限制酶TaqαI組合並加入SphI與MseI排除序列，應用於單一F2分離族群以建立高通量分子標誌基因型資料校正法及建立高密度連鎖圖譜之最佳化流程。基於此最佳化流程，以三個F2族群（A6、B2和C4）定位甜瓜抗白粉病的數量性狀位基因座 (quantitative trait loci, QTL)。分別在A6族群中偵測到位於第2條染色體的qPM2，在B2族群中偵測到位於第5條染色體的qPM5.B2與在C4族群中偵測到第5與第12條染色體上的qPM5.C4與qPM12。其後，針對第2、5和12條染色體上的QTL開發一系列TaqMan分子標誌用於分子標誌輔助回交育種之前景選拔與重組選拔，並結合ddRADseq評估輪迴親基因體恢復率進行背景選拔。選用A6與C4族群的抗病親作為供給親，並分別與帶有綠色及橙色果肉的優良親本作為輪迴親進行分子標誌輔助回交增進優良甜瓜親本的白粉病抗病性。經過二到三個回交世代後，成功將單一抗病QTL導入優良輪迴親的遺傳背景中，最終在綠色和橙色果肉的輪迴親遺傳背景中分別獲得6個帶有白粉病抗病QTL的近同源系。從分子標誌開發完成到抗病近同源系的育成僅花費三年半的時間，顯示基於次世代定序的高通量基因分型技術可以有效與作物育種結合，提升作物分子育種的效率。 | zh_TW |
| dc.description.abstract | Molecular markers are important tools for genetic studies and crop breeding. With the development of next-generation sequencing, high-throughput genotyping has become a common tool for crop breeding. However, optimizing the genotyping process for each target crop is still challenging. Therefore, this study aimed to optimize the double digest restriction-site associated DNA sequencing (ddRADseq) genotyping platform and implement the optimized procedure in melon as a proof-of-concept. The framework consists of the identification of the genetic architecture of powdery mildew resistance in melon and the development of the powdery mildew resistance near-isogenic lines. We applied in silico digestion and empirical tests to evaluate candidate enzyme combinations in melon. Two candidate enzyme combinations were further applied to an F2 population, which were PstI-TaqαI-SphI and XbaI-TaqαI-MseI, for optimization of a high-throughput genotyping data error correction and linkage map construction. Based on the optimized procedure, quantitative trait locus (QTL) mapping of melon powdery mildew resistance was applied to three F2 populations, A6, B2, and C4. QTL were identified on chromosomes 2, 5, and 12, which were qPM2 in A6, qPM5.B2 in B2 and qPM5.C4, and qPM12 in C4. A series of TaqMan assays targeting QTL were developed and validated for foreground and recombinant selection, complemented with the ddRADseq genotyping system to evaluate the recurrent parent genome recovery. Three marker-assisted backcrossing (MABC) programs using resistant donor parents from A6 and C4 crossed with elite susceptible recurrent parents with green and orange fruit flesh were implemented. After two to three cycles of MABC, individual QTL was successfully introgressed into elite genetic backgrounds, giving six powdery mildew resistance near-isogenic lines in each green- and orange-flesh background. In three and a half years, we have achieved from marker development to the production of isogenic lines. This study demonstrated the power of high-throughput genotyping and its efficient implementation in molecular breeding. | en |
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| dc.description.tableofcontents | 口試委員審定書 i
誌謝 ii 摘要 iii Abstract iv Table of Contents vi List of Tables ix List of Figures xi 1. Introduction 1 1.1. Genetic markers in plant breeding 1 1.1.1. Conventional genetic markers 1 1.1.2. NGS-based high-throughput molecular markers 2 1.1.3. Applications of molecular markers to plant genetic analysis and breeding 5 1.2. Melon (Cucumis melo L.) 7 1.2.1. Overview of melon 7 1.2.2. Powdery mildew, a major disease for melon production 7 1.3. Objective of the study 9 2. Optimization of ddRADseq in melon 11 2.1. In silico analysis and empirical small-scale experiment for enzyme combination identification 11 2.1.1. Materials and Methods 11 2.1.1.1. In silico digestion 11 2.1.1.2. DNA extraction and ddRAD library preparation 12 2.1.1.3. Bioinformatic analysis 13 2.1.2. Results 14 2.1.2.1. In silico digestion 14 2.1.2.2. Empirical tests based on in silico recommendation 16 2.1.3. Discussion 19 2.2. Compare two enzyme combinations in an F2 population and improve the genotype quality for linkage map construction 20 2.2.1. Materials and Methods 20 2.2.1.1. The empirical test of the third restriction enzyme in three-enzyme ddRADseq 20 2.2.1.2. Plant materials 21 2.2.1.3. DNA extraction and modified ddRAD library preparation 21 2.2.1.4. The bioinformatics analysis 21 2.2.1.5. Improve the genotype quality through genotype filtering or correction 23 2.2.2. Results 23 2.2.2.1. Evaluation of the third restriction enzymes for sequence exclusion 23 2.2.2.2. Test of PstI-TaqαI-SphI and XbaI-TaqαI-MseI in an F2 population 24 2.2.2.3. Construction of high-density linkage maps 25 2.2.2.4. Genotype correction efficiently improved marker quality 26 2.2.3. Discussion 27 3. Application of optimized ddRADseq in melon 29 3.1. Identify Powdery mildew resistance QTL in three F2 populations 29 3.1.1. Materials and Methods 29 3.1.1.1. Three F2 populations for QTL mapping 29 3.1.1.2. powdery mildew evaluation 30 3.1.1.3. ddRAD library preparation for genotyping in F2 populations 30 3.1.1.4. Bioinformatic analysis workflow for SNP calling 31 3.1.1.5. Linkage map construction and QTL mapping 32 3.1.2. Results 33 3.1.2.1. The DI of powdery mildew in three F2 populations 33 3.1.2.2. powdery mildew resistance QTL 33 3.1.3. Discussion 34 3.2. MABC for powdery mildew resistance of elite inbred lines 36 3.2.1. Materials and Methods 36 3.2.1.1. The recurrent parents for MABC 36 3.2.1.2. Conversion between physical and genetic distances 36 3.2.1.3. TaqMan assay development for MABC 36 3.2.1.4. MABC for powdery mildew resistance introgression 37 3.2.2. Results 38 3.2.2.1. TaqMan assays for MABC 38 3.2.2.2. MABC process for developing powdery mildew resistance NILs carrying qPM2 38 3.2.2.3. MABC process for developing powdery mildew resistance NILs carrying qPM5 39 3.2.2.4. MABC process for developing powdery mildew resistance NILs carrying qPM12 40 3.2.3. Discussion 41 4. Conclusion 42 References 43 Supplementary Tables 95 Supplementary Figures 116 | - |
| dc.language.iso | en | - |
| dc.title | 開發最佳雙限制酶切位點標定法及其於甜瓜育種之應用 | zh_TW |
| dc.title | Developing optimal ddRADseq techniques and its application in melon breeding | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 113-1 | - |
| dc.description.degree | 博士 | - |
| dc.contributor.oralexamcommittee | 李承叡;許富鈞;陳凱儀;王毓華 | zh_TW |
| dc.contributor.oralexamcommittee | Cheng- Ruei Lee;Fu-Chiun Hsu;Kai-Yi Cheng;Yu-Hua Wang | en |
| dc.subject.keyword | 雙限制酶切位標定法,基因型校正,分子標誌輔助回交,甜瓜 (Cucumis melo L.),白粉病 (Podosphaera xanthii),數量性狀基因座定位,TaqMan分子標誌, | zh_TW |
| dc.subject.keyword | double digest restriction-site associated DNA sequencing (ddRADseq),genotype correction,marker-assisted backcrossing (MABC),melon (Cucumis melo L.),powdery mildew (Podosphaera xanthii),quantitative trait loci (QTL),TaqMan, | en |
| dc.relation.page | 121 | - |
| dc.identifier.doi | 10.6342/NTU202500264 | - |
| dc.rights.note | 同意授權(全球公開) | - |
| dc.date.accepted | 2025-02-06 | - |
| dc.contributor.author-college | 生物資源暨農學院 | - |
| dc.contributor.author-dept | 農藝學系 | - |
| dc.date.embargo-lift | 2025-02-20 | - |
| 顯示於系所單位： | 農藝學系 | |
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