African Journal of
Agricultural Research

  • Abbreviation: Afr. J. Agric. Res.
  • Language: English
  • ISSN: 1991-637X
  • DOI: 10.5897/AJAR
  • Start Year: 2006
  • Published Articles: 6865

Full Length Research Paper

In silico identification of putative expressed sequence tag (EST)-simple sequence repeats (SSRs) markers of resistance to Meloidogyne spp. in common bean

Lucas Donizetti Vieira
  • Lucas Donizetti Vieira
  • Department of Genetics and Molecular Biology, Universidade Federal de Goiás, Goiânia, Brazil.
  • Google Scholar
Juliana Oliveira da Silva
  • Juliana Oliveira da Silva
  • Department of Agronomy, IF Goiano, Urutaí, Goiás, Brazil.
  • Google Scholar
Caio César de Oliveira Pereira
  • Caio César de Oliveira Pereira
  • Department of Agronomy, IF Goiano, Urutaí, Goiás, Brazil.
  • Google Scholar
Solange Aline de Carvalho
  • Solange Aline de Carvalho
  • Department of Biology, IF Goiano, Urutaí, Goiás, Brazil.
  • Google Scholar
Ricardo Diogenes Dias Silveira
  • Ricardo Diogenes Dias Silveira
  • Department of Biology, IF Goiano, Urutaí, Goiás, Brazil.
  • Google Scholar
Guilherme Malafaia
  • Guilherme Malafaia
  • Department of Biology, IF Goiano, Urutaí, Goiás, Brazil.
  • Google Scholar
Ivandilson Pessoa Pinto de Menezes
  • Ivandilson Pessoa Pinto de Menezes
  • Department of Biology, IF Goiano, Urutaí, Goiás, Brazil.
  • Google Scholar


  •  Received: 10 April 2016
  •  Accepted: 16 May 2016
  •  Published: 09 June 2016

References

Alzate-Marin AL, Cervigni GD, Moreira MA, Barros EG (2005). Seleção assistida por marcadores moleculares visando ao desenvolvimento de plantas resistentes a doenças, com ênfase em feijoeiro e soja. Fitopatol. Bras. 30(4):333-342.
Crossref

 

Andersen JR, Lübberstedt T (2003). Functional markers in plants. Trends Plant. Sci. 8(11):554-560.
Crossref

 
 

Bernard HR (2011). Research methods in anthropology: Qualitative and quantitative approaches. Rowman Altamira.

 
 

Boccacci P, Beltramo C, Prando MS,Lembo A, Sartor C, Mehlenbacher S, Botta R, Marinoni DT (2015). In silico mining, characterization and cross-species transferability of EST-SSR markers for European hazelnut (Corylus avellana L.). Mol. Breed. 35(1):1-14.
Crossref

 
 

Bornet B, Branchard M (2001). Nonanchored inter simple sequence repeat (ISSR) markers: reproducible and specific tools for genome fingerprinting. Plant Mol. Biol. Rep. 19(3):209-215.
Crossref

 
 

Broughton WJ, Hernandez G, Blair M, Beebe S, Gepts P, Vanderleyden J (2003). Beans (Phaseolus spp.)–model food legumes. Plant Soil 252(1):55-128.
Crossref

 
 

Burle ML, Fonseca JR, Kami JA, Gepts P (2010). Microsatellite diversity and genetic structure among common bean (Phaseolus vulgaris L.) landraces in Brazil, a secondary center of diversity. Theor. Appl. Genet. 121(5):801-813.
Crossref

 
 

Buso G,Amaral Z, Brondani R, Ferreira M (2006). Microsatellite markers for the common bean Phaseolus vulgaris. Mol. Ecol. Notes 6(1):252-254.
Crossref

 
 

Cardoso PC, Veiga MM, Menezes IPP; Valdisser PAMR, Borba TC, Melo LC, Del Peloso MJ, Brondani C, Vianello RP (2013). Molecular characterization of high performance inbred lines of Brazilian common beans. Genet. Mol. Res. 12(4):5467-5484.
Crossref

 
 

Cardoso PC, Brondani C, Menezes IPP,Valdisser PAMR, Borba TC, Del Peloso MJ,Vianello RP (2014). Discrimination of common bean cultivars using multiplexed microsatellite markers. Genet. Mol. Res. 13(1):1964-1978.
Crossref

 
 

Carneiro RG, Ferraz S, Regazzi AJ (1992). Estudo de mecanismo de resistência a Meloidogyne incognita raça 3 em variedades de feijoeiro. Nematol. Bras. 16(1/2):41-52.

 
 

Concibido VC, Diers BW, Arelli PR (2004). A decade of QTL mapping for cyst nematode resistance in soybean. Crop Sci. 44(4):1121-1131.
Crossref

 
 

Conesa A, Götz S, García-Gómez JM, Terol J, Talón M, Robles M (2005). Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21(18):3674-3676.
Crossref

 
 

Ellegren H (2004). Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 5(6):435-445.
Crossref

 
 

Gupta S, Shukla R, Roy S, Sen N, Sharma A (2010). In silico SSR and FDM analysis through EST sequences in Ocimum basilicum. Plant Omics 3(4): 121-128.

 
 

Hong JH, Kwon YS, Mishra RK, Kim DH (2015). Construction of EST-SSR databases for effective cultivar identification and their applicability to complement for Lettuce (Lactuca sativa L.) Distinctness Test. Am. J. Plant Sci. 6(01):113.
Crossref

 
 

Kaliswamy P, Vellingiri S, Nathan B, Selvaraj S (2015). Microsatellite analysis in the genome of Acanthaceae: An in silico approach. Pharmacogn. Mag. 11(41):152-156.
Crossref

 
 

Kaur S, Panesar PS, Bera MB, Kaur V (2015). Simple sequence repeat markers in genetic divergence and marker-assisted selection of rice cultivars: A review. Crit. Rev. Food. Sci. Nutr. 55(1):41-49.
Crossref

 
 

Lavin M, Herendeen PS, Wojciechowski MF (2005). Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the Tertiary. Syst. Biol. 54(4):575-594.
Crossref

 
 

Li OJ, Chen XM, Xia PX, Pei ZY, Wang Y, Lan QK, Zhang RW (2015a). EST-SSR marker-based assay for purity identification of melon "Green Angle". Adv. Appl. Biotechnol. 333:637-642.
Crossref

 
 

Li X, Hu X, Hu T, Li G, Ru Z, Zhang L, Lang Y (2015b). Identification of a novel wheat-Thinopyrum ponticumaddition line revealed with cytology, SSR, EST-SSR, EST-STS and PLUG markers. Cereal Res. Commun. 43(4):1-10.
Crossref

 
 

Li YC, Korol AB, Fahima T, Beiles A, Nevo E (2002). Microsatellites: genomic distribution, putative functions and mutational mechanisms: a review. Mol. Ecol. 11(12):2453-2465.
Crossref

 
 

Luro FL, Costantino G, Terol J, Argou X, Allario T, Wincker P, Talon M, Ollitrault P, Morillon R (2008). Transferability of the EST-SSRs developed on Nules clementine (Citrus clementina Hort ex Tan) to other Citrus species and their effectiveness for genetic mapping. BMC Genome 9:1-13.
Crossref

 
 

Luzzi B, Boerma H, Hussey R (1994). A gene for resistance to the southern root-knot nematode in soybean. J. Hered. 85(6):484-486.

 
 

Maia LC, Palmieri DA, Souza VQ, Kopp MM, Carvalho FIF, Oliveira AC (2008). SSR Locator: Tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int. J. Plant. Genome 1-9
Crossref

 
 

Metzgar D, Liu L, Hansen C, Dybvig K, Wills C (2002). Domain-level differences in microsatellite distribution and content result from different relative rates of insertion and deletion mutations. Genome Res.12(3):408-413.
Crossref

 
 

Müller BS, Pappas GJ Jr, Valdisser PA, Coelho GR, Menezes IP, Abreu AG, Borba TC, Sakamoto T, Brondani C, Barros EG (2015). An Operational SNP Panel Integrated to SSR Marker for the Assessment of Genetic Diversity and Population Structure of the Common Bean. Plant Mol. Biol. Rep. 33(6):1697-1711.
Crossref

 
 

Müller BS, Sakamoto T, Menezes IPP, Prado GS, Martins WS, Brondani C, Barros EG, Vianello RP (2014). Analysis of BAC-end sequences in common bean (Phaseolus vulgaris L.) towards the development and characterization of long motifs SSRs. Plant Mol. Biol. 86(45):455-470.
Crossref

 
 

Oliveira EJ, Pádua JG, Zucchi MI, Vencovsky R, Vieira MLC (2006). Origin, evolution and genome distribution of microsatellites. Genet. Mol. Biol. 29(2):294-307.
Crossref

 
 

Pandey M, Sharma J (2012). Efficiency of microsatellite isolation from orchids via next generation sequencing.

 
 

Pham AT, Mcnally K, Abdel-Haleem H, Boerma HR, Li Z (2013). Fine mapping and identification of candidate genes controlling the resistance to southern root-knot nematode in PI 96354. Theor. Appl. Genet. 126(7):1825-1838.
Crossref

 
 

Rozen S, Skaletsky H (2000). Primer3 on the WWW for general users and for biologist programmers. Meth. Mol. Biol. 132:365-386.

 
 

Saha MC, Mian MR, Eujayl I, Zwonitzer JC, Wang L, May GD (2004). Tall fescue EST-SSR markers with transferability across several grass species. Theor. Appl. Genet. 109(4):783-791.
Crossref

 
 

Schlötterer C (2000). Evolutionary dynamics of microsatellite DNA. Chromosoma 109(6):365-371.
Crossref

 
 

Schmutz J, Mcclean PE, Mamidi S, Wu GA, Cannon SB, Grimwood J, Jenkins J, Shu S, Song Q, Chavarro C (2014). A reference genome for common bean and genome-wide analysis of dual domestications. Nat. Genet. 46(7):707-713.
Crossref

 
 

Silva OF, Wander AE (2013). O feijão-comum no Brasil passado, presente e futuro.

 
 

Sterky F, Regan S, Karlsson J, Hertzberg M, Rohde A, Holmberg A, Amini B, Bhalerao R, Larsson M, Villarroel R (1998). Gene discovery in the wood-forming tissues of poplar: analysis of 5,692 expressed sequence tags. Proc. Natl. Acad. Sci. 95(22):13330-13335.
Crossref

 
 

Vallone PM, Butler JM (2004). AutoDimer: a screening tool for primer-dimer and hairpin structures. Biotechniques 37(2): 226-231.

 
 

Victoria FC, Maia LC, Oliveira AC (2011). In silico comparative analysis of SSR markers in plants. BMC Plant Biol. 11(1):15.
Crossref

 
 

Vieira C, Paula Júnior T, Borém A (1998). Adubação mineral e calagem. Feijão 2:115-142.

 
 

Walber R, Juliatti F, Santos M (2003). Avaliação de acessos de feijoeiro em relação aos nematóides das galhas. In: Congresso Brasileiro de Fitopatologia. Soc. Bras. Fitopatol. 293-294.

 
 

Wander AE (2005). Perspectivas de mercado interno e externo para o feijão. In: Congresso Nacional De Pesquisa De Feijão. pp. 892-895.

 
 

Wang B, Zhu P, Yuan Y, Wang C, Yu C, Zhang H, Zhu X, Wang W, Yao C, Zhuang Z (2014). Development of EST-SSR markers related to salt tolerance and their application in genetic diversity and evolution analysis in Gossypium. Genet. Mol. Res. 13(2):3732-3746.
Crossref

 
 

Yokoyama L (2007). Cultivo do feijoeiro comum: importância econômica. Sistemas de Produção. 2.

 
 

Zane L, Bargelloni L, Patarnello T (2002). Strategies for microsatellite isolation: a review. Mol. Ecol. 11(1):1-16.
Crossref

 
 

Zhai C, Xu P, Zhang X, Guo Q, Zhang X, Xu Z, Shen X (2015). Development of Gossypium anomalum-derived microsatellite markers and their use for genome-wide identification of recombination between the G. anomalum and G. hirsutum genomes. Theor. Appl. Genet. 128(8):1531-1540.
Crossref