High-throughput simple sequence repeat (SSR) mining saturates the carrot (Daucus carota L.) genome with chromosome-anchored markers

References

• Iorizzo M, Senalik DA, Grzebelus D, et al. De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity. BMC Genomics.2011;12(1):389.
   PubMed Web of Science ®Google Scholar
• Cavagnaro PF, Chung SM, Manin S, et al. Microsatellite isolation and marker development in carrot—genomic distribution, linkage mapping, genetic diversity analysis and marker transferability across Apiaceae. BMC Genomics.2011;12(1):386.
   PubMed Web of Science ®Google Scholar
• Cavagnaro PF, Chung SM, Szklarczyk M, et al. Characterization of a deep-coverage carrot (Daucus carota L.) BAC library and initial analysis of BAC-end sequences. Mol Genet Genomics. 2009;281(3):273–288.
   PubMed Web of Science ®Google Scholar
• Iorizzo M, Ellison S, Senalik D, et al. A high quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nat Genet. 2016;48(6):657–666.
   PubMed Web of Science ®Google Scholar
• Baranski R, Allender C, Klimek-Chodacka M. Towards better tasting and more nutritious carrots: Carotenoid and sugar content variations in carrot genetic resources. Food Res Int.2012;47(2):182–187.
   Web of Science ®Google Scholar
• Akhtar S, Rauf A, Imran M, et al. Black carrot (Daucus carota L.), dietary and health promoting perspectives of its polyphenols: A review. Trends Food Sci Technol. 2017;66:36–47.
   Web of Science ®Google Scholar
• Simon PW. Domestication, historical development, and modern breeding of carrot. In: Janick J, editor. Plant breeding reviews. Vol. 19. New York: Wiley; 2000. p. 157–185.
   Google Scholar
• Wang F, Wang GL, Hou XL, et al. The genome sequence of ‘Kurodagosun’, a major carrot variety in Japan and China, reveals insights into biological research and carrot breeding. Mol Genet Genomics. 2018;293(4):861–871.
   PubMed Web of Science ®Google Scholar
• Morgante M, Hanafey M, Powell W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet. 2002;30(2):194–200.
   PubMed Web of Science ®Google Scholar
• Victoria FC, Da Maia LC, De Oliveira AC. In silico comparative analysis of SSR markers in plants. BMC Plant Biol. 2011;11(1):15.
   PubMed Web of Science ®Google Scholar
• Boccacci P, Beltramo C, Sandoval Prando MA, et al. In silico mining, characterization and cross-species transferability of EST-SSR markers for European hazelnut (Corylus avellana L.). Mol Breed 2015;35:21.
   Web of Science ®Google Scholar
• Zhang XF, Sun HH, Xu Y, et al. Development of a large number of SSR and InDel markers and construction of a high-density genetic map on a RIL population of pepper (Capsicum annuum L.). Mol Breed 2016;36:92.
   Web of Science ®Google Scholar
• Agarwal G, Sabbavarapu MM, Singh VK, et al. Identification of a non-redundant set of 202 in silico SSR markers and applicability of a select set in chickpea (Cicer arietinum L.). Euphytica 2015;205(2):381–394.
   Web of Science ®Google Scholar
• Liu J, Qu J, Hu K, et al. Development of genomewide simple sequence repeat fingerprints and highly polymorphic markers in cucumbers based on next-generation sequence data. Plant Breed. 2015;134(5):605–611.
   Web of Science ®Google Scholar
• Bhattarai G, Mehlenbacher SA. In silico development and characterization of tri-nucleotide simple sequence repeat markers in hazelnut (Corylus avellana L.). PLoS ONE. 2017;12(5):e0178061.
   PubMed Web of Science ®Google Scholar
• Cavagnaro PF, Senalik DA, Yang L, et al. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics.2010;11(1):569.
   PubMed Web of Science ®Google Scholar
• Han B, Wang C, Tang Z, et al. Genome-wide analysis of microsatellite markers based on sequenced database in Chinese spring wheat (Triticum aestivum L.). PLoS ONE. 2015;10(11):e0141540.
   PubMed Web of Science ®Google Scholar
• Parida SK, Verma M, Yadav SK, et al. Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource. Front Plant Sci. 2015;6:645
   PubMed Web of Science ®Google Scholar
• Dettori MT, Micali S, Giovinazzi J, et al. Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species . Springerplus. 2015;4:337
   PubMedGoogle Scholar
• Zhu H, Guo L, Song P, et al. Development of genome-wide SSR markers in melon with their cross-species transferability analysis and utilization in genetic diversity study. Mol Breed 2016;36:153.
   Web of Science ®Google Scholar
• Cui J, Cheng J, Nong D, et al. Genome-wide analysis of simple sequence repeats in bitter gourd (Momordica charantia). Front Plant Sci. 2017;8:1103
   PubMed Web of Science ®Google Scholar
• Dossa K, Yu J, Liao B, et al. Development of highly informative genome-wide single sequence repeat markers for breeding applications in sesame and construction of a web resource: SisatBase. Front Plant Sci. 2017;8:1470
   PubMed Web of Science ®Google Scholar
• Wang X, Yang S, Chen Y, et al. Comparative genome-wide characterization leading to simple sequence repeat marker development for Nicotiana. BMC Genomics.2018;19(1):500.
   PubMed Web of Science ®Google Scholar
• Xia X, Luan LL, Qin G, et al. Genome-wide analysis of SSR and ILP markers in trees: diversity profiling, alternate distribution, and applications in duplication. Sci Rep. 2017;7(1):17902.
   PubMed Web of Science ®Google Scholar
• Baranski R, Maksylewicz-Kaul A, Nothnagel T, et al. Genetic diversity of carrot (Daucus carota L.) cultivars revealed by analysis of SSR loci. Genet Resour Crop Evol. 2012;59(2):163–170.
   Web of Science ®Google Scholar
• Ipek A, Turkmen O, Fidan S, et al. Genetic variation within the purple carrot population grown in Ereğli district in Turkey. Turk J Agric For 2016;40:570–576.
   Web of Science ®Google Scholar
• Ma ZG, Kong XP, Liu LJ, et al. The unique origin of orange carrot cultivars in China. Euphytica 2016;212(1):37–49.
   Web of Science ®Google Scholar
• Mandel J, Ramsey AJ, Iorizzo M, et al. Patterns of gene flow between crop and wild carrot, Daucus carota (Apiaceae) in the United States. PLoS ONE. 2016;11(9):e0161971.
   PubMed Web of Science ®Google Scholar
• Yildiz M, Willis DK, Cavagnaro PF, et al. Expression and mapping of anthocyanin biosynthesis genes in carrot. Theor Appl Genet. 2013;126(7):1689–1702.
   PubMed Web of Science ®Google Scholar
• Budahn H, Barański R, Grzebelus D, et al. Mapping genes governing flower architecture and pollen development in a double mutant population of carrot. Front Plant Sci. 2014;5:504
   PubMed Web of Science ®Google Scholar
• Parsons J, Matthews W, Iorizzo M, et al. Meloidogyne incognita nematode resistance QTL in carrot. Mol Breed 2015;35:114.
   Web of Science ®Google Scholar
• Iorizzo M, Senalik DA, Ellison SL, et al. Genetic Structure and domestication of carrot (Daucus carota subsp. sativus) (Apiaceae). Am J Bot.2013;100(5):930–938.
   PubMed Web of Science ®Google Scholar
• Stelmach K, Macko Podgorni A, Machaj G, et al. Miniature inverted repeat transposable element insertions provide a source of intron length polymorphism markers in the carrot (Daucus carota L.). Front Plant Sci. 2017;8:725
   PubMed Web of Science ®Google Scholar
• Grzebelus D, Iorizzo M, Senalik D, et al. Diversity, genetic mapping, and signatures of domestication in the carrot (Daucus carota L.) genome, as revealed by Diversity Arrays Technology (DArT) markers. Mol Breeding. 2014;33(3):625–637.
   PubMed Web of Science ®Google Scholar
• Wang X, Wang L. GMATA: An integrated software package for genome-scale SSR mining, marker development and viewing. Front Plant Sci. 2016;7:1350
   PubMed Web of Science ®Google Scholar
• Schuler GD. Sequence mapping by electronic PCR. Genome Res. 1997;7(5):541–550.
   PubMed Web of Science ®Google Scholar
• Doyle JJ, Doyle JL. Isolation of plant DNA from fresh tissue. Focus 1990;12:13–15.
   Google Scholar
• Botstein D, White RL, Skolnick M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 1980;32(3):314–331.
   PubMed Web of Science ®Google Scholar
• Nei M. Analysis of gene diversity in subdivided populations. PNAS 1973;70(12):3321–3323.
   PubMed Web of Science ®Google Scholar
• Sonah H, Deshmukh RK, Sharma A, et al. Genomewide distribution and organization of microsatellites in plants: An insight into marker development in Brachypodium. PLoS ONE.2011;6(6):e21298.
   PubMed Web of Science ®Google Scholar
• Uncu AO, Gultekin V, Allmer J, et al. Genomic simple sequence repeat markers reveal patterns of genetic relatedness and diversity in sesame. The Plant Genome. 2015;8(2):0.
   Web of Science ®Google Scholar
• Cheng J, Zhao Z, Li B, et al. A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum. Sci Rep. 2016;6(1):18919.
   PubMed Web of Science ®Google Scholar
• Gu T, Tan S, Gou X, et al. Avoidance of long mononucleotide repeats in codon pair usage. Genetics 2010;186(3):1077–1084.
   PubMed Web of Science ®Google Scholar