International Journal of
Genetics and Molecular Biology

  • Abbreviation: Int. J. Genet. Mol. Biol.
  • Language: English
  • ISSN: 2006-9863
  • DOI: 10.5897/IJGMB
  • Start Year: 2009
  • Published Articles: 115

Full Length Research Paper

De novo assembly and characterization of transcriptome and microsatellite marker development for Taro (Colocasia esculenta (L.) Schott.)

Li Wang
  • Li Wang
  • Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
  • Google Scholar
Jianmei Yin
  • Jianmei Yin
  • Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
  • Google Scholar
Peitong Zhang
  • Peitong Zhang
  • Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
  • Google Scholar
Xiaoyong Han
  • Xiaoyong Han
  • Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
  • Google Scholar
Wenqi Guo
  • Wenqi Guo
  • Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
  • Google Scholar
Chunhong Li
  • Chunhong Li
  • Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.
  • Google Scholar


  •  Received: 19 July 2017
  •  Accepted: 30 October 2017
  •  Published: 31 December 2017

References

Ahmed I, Matthews PJ, Biggs PJ, Naeem M, Mclenachan PA, Lockhart PJ (2013). Identification of chloroplast genome loci suitable for high-resolution phylogeographic studies of Colocasia esculenta (L.) Schott (Araceae) and closely related taxa. Mol. Ecol. Resour. 13(5):929-937.
Crossref

 

Chaïr H, Traore RE, Duval MF, Rivallan R, Mukherjee A, Aboagye LM, Van Rensburg WJ, Andrianavalona V, De Pinheiro Carvalho MAA, Saborio F, Prana MS, Komolong B, Lawac F, Lebot V (2016). Genetic diversification and dispersal of taro (Colocasia esculenta (l.) schott). PloS One 11(6):e0157712.
Crossref

 
 

Chen X, Li J, Xiao S, Liu X (2016). De novo assembly and characterization of foot transcriptome and microsatellite marker development for Paphia textile. Gene 576:537-543.
Crossref

 
 

Cloutier S, Niu Z, Datla R, Duguid S (2009). Development and analysis of EST-SSRs for flax (Linum usitatissimum L.). Theor. Appl. Genet. 119:53-63.
Crossref

 
 

Dai HJ, Zhang YM, Sun XQ, Xue JY, Li MM, Cao MX, Shen XL, Hang YY (2016). Two-step identification of taro (Colocasia esculenta cv. Xinmaoyu) using specific psbE-petL and simple sequence repeat-sequence characterized amplified regions (SSR-SCAR) markers. Genet. Mol. Res. 15(3):gmr.15038108.

 
 

Das A, Das AB (2014). Karyotype analysis of ten draught resistant cultivars of Indian taro - Colocasia esculenta cv. antiquorom Schott. Nucleus (India) 57(2):113-120.
Crossref

 
 

Das AB, Das A, Pradhan C, Naskar SK (2015). Genotypic variations of ten Indian cultivars of Colocasia esculenta var. antiquorom Schott. evident by chromosomal and RAPD markers. Caryologia 68(1):44-54.
Crossref

 
 

Doungous O, Kalendar R, Adiobo A, Schulman AH (2015). Retrotransposon molecular markers resolve cocoyam (Xanthosoma sagittifolium) and taro (Colocasia esculenta) by type and variety. Euphytica 206(2):541-554.
Crossref

 
 

Edwards D, Batley J, Snowdon RJ (2013). Accessing complex crop genomes with next-generation sequencing. Theor. Appl. Genet. 126:1-11.
Crossref

 
 

Ellegren H (2014). Genome sequencing and population genomics in non-model organisms. Trends Ecol. Evol. 29:51-63.
Crossref

 
 

Fu N, Wang Q, Shen HL (2013). De novo assembly, gene annotation and marker development using Illumina paired-end transcriptome sequences in celery (Apium graveolens L.). PloS One 8:e57686.
Crossref

 
 

Hause RJ, Pritchard CC, Shendure J, Salipante SJ (2016). Classification and characterization of microsatellite instability across 18 cancer types. Nat. Med. 11:1342-1350.
Crossref

 
 

He J, Zhao X, Laroche A, Lu ZX, Liu H, Li Z (2014). Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci. 5:484.
Crossref

 
 

Hunt HV, Moots HM, Matthews PJ (2013). Genetic data confirms field evidence for natural breeding in a wild taro population (Colocasia esculenta) in northern Queensland, Australia. Genet. Resour. Crop Evol. 60:1695-1707.
Crossref

 
 

Liu HB, You YN, Zheng XF, Diao Y, Huang XF, Hu ZY (2015). Deep sequencing of the Colocasia esculenta transcriptome revealed candidate genes for major metabolic pathways of starch synthesis. S. Afr. J. Bot. 97:101-106.
Crossref

 
 

Liu K, Muse SV (2005). PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128-2129.
Crossref

 
 

Mathithumilan B, Kadam NN, Biradar J, Reddy SH, Ankaiah M, Narayanan MJ, Makarla U, Khurana P, Sreeman SM (2013). Development and characterization of microsatellite markers for Morus spp. and assessment of their transferability to other closely related species. BMC Plant Biol. 13:194.
Crossref

 
 

Namiki T, Hachiya T, Tanaka H, Sakakibara Y (2012). MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. Nucleic Acids Res. 40:e155.
Crossref

 
 

Nath VS, Sankar MSA, Hegde VM, Jeeva ML, Misra RS, Veena SS, Raj M (2014). Analysis of genetic diversity in Phytophthora colocasiae causing leaf blight of taro (Colocasia esculenta) using AFLP and RAPD markers. Ann. Microbiol. 64(1):185-197.
Crossref

 
 

Nguluta M, Adebola P, Pillay M (2016). Genetic diversity analysis in South African taro (Colocasia esculenta) accessions using molecular tools. Int. J. Genet. Mol. Biol. 8:18-24.
Crossref

 
 

Oliveira LSS, Harrington TC, Ferreira MA, Freitas RG, Alfenas AC (2017). Populations of Ceratocystis fimbriata on Colocasia esculenta and other hosts in the Mata Atlântica region in Brazil. Plant Pathol.

 
 

Ramanatha RV, Matthews PJ, Eyzaguirre PB, Hunter D (2010). The global diversity of taro: ethnobotany and conservation. Biodiversity International, Rome. Available at: 

View.

 
 

Shete S, Tiwari H, Elston RC (2000). On estimating the heterozygosity and polymorphism information content value. Theor. Popul. Biol. 57:265-271.
Crossref

 
 

Soulard L, Letourmy P, Cao TV, Lawac F, Chaïr H, Lebot V (2016). Evaluation of vegetative growth, yield and quality related traits in taro (Colocasia esculenta [L.] schott). Crop Sci. 56(3):976-989.
Crossref

 
 

Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L (2013). Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat. Biotechnol. 31:46-53.
Crossref

 
 

Vandenbroucke H, Mournet P, Vignes H, Chaïr H, Malapa R, Duval MF, Lebot V (2016). Somaclonal variants of taro (Colocasia esculenta Schott) and yam (Dioscorea alata L.) are incorporated into farmers' varietal portfolios in Vanuatu. Genet. Resour. Crop Evol. 63(3):495-511.
Crossref

 
 

Waples RK, Larson WA, Waples RS (2016). Estimating contemporary effective population size in non-model species using linkage disequilibrium across thousands of loci. Heredity 117:233-240.
Crossref

 
 

Yeh FC, Yang R, Boyle TJ, Ye Z, Xiyan JM (2000). PopGene32, Microsoft Windows-based freewarefor population genetic analysis, version 1.32. Molecular Biology Biotechnology Center, University of Alberta, Edmonton, Alberta, Canada.

 
 

You YN, Liu DC, Liu HB, Zheng XF, Diao Y, Huang XF, Hu ZY (2015). Development and characterisation of EST-SSR markers by transcriptome sequencing in taro (Colocasia esculenta (L.) Schoot). Mol. Breed. 35:134.
Crossref