2,913
Views
10
CrossRef citations to date
0
Altmetric
Research Article

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

ORCID Icon & ORCID Icon
Pages 1-9 | Received 01 Oct 2019, Accepted 02 Dec 2019, Published online: 10 Dec 2019

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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Morgante M, Hanafey M, Powell W. Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet. 2002;30(2):194–200.
  • Victoria FC, Da Maia LC, De Oliveira AC. In silico comparative analysis of SSR markers in plants. BMC Plant Biol. 2011;11(1):15.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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
  • 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
  • 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.
  • 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
  • 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
  • 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.
  • 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.
  • 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.
  • 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.
  • Ma ZG, Kong XP, Liu LJ, et al. The unique origin of orange carrot cultivars in China. Euphytica 2016;212(1):37–49.
  • 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.
  • 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.
  • 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
  • Parsons J, Matthews W, Iorizzo M, et al. Meloidogyne incognita nematode resistance QTL in carrot. Mol Breed 2015;35:114.
  • 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.
  • 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
  • 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.
  • Wang X, Wang L. GMATA: An integrated software package for genome-scale SSR mining, marker development and viewing. Front Plant Sci. 2016;7:1350
  • Schuler GD. Sequence mapping by electronic PCR. Genome Res. 1997;7(5):541–550.
  • Doyle JJ, Doyle JL. Isolation of plant DNA from fresh tissue. Focus 1990;12:13–15.
  • 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.
  • Nei M. Analysis of gene diversity in subdivided populations. PNAS 1973;70(12):3321–3323.
  • 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.
  • 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.
  • 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.
  • Gu T, Tan S, Gou X, et al. Avoidance of long mononucleotide repeats in codon pair usage. Genetics 2010;186(3):1077–1084.