Full Length Research Paper
ABSTRACT
Expressed sequences are important sources in the development of functional heterologous microsatellite markers in phylogenetic related groups, that is, soybean and commom bean. The objective of this work was to identify and characterize expressed sequence tag (EST)-simple sequence repeats (SSRs) in silico candidates of resistance to Meloidogyne spp. in common bean. Seven DNA sequences from soybean associated with genetic resistance have been identified and obtained in the NCBI database. Its homology in common bean genome was verified using the BLAST tool. The cellular processes involved were also checked using the Blast2GO program. The identification of microsatellite markers and design of the primer pairs was performed using the SSRLocator and Primer3 programs, respectively. The transferability rate of common beans the target sequences identified was 86%, demonstrating the power of success of this method. All the cellular processes involved in the original DNA sequences were verified from EST on beans, with E-value between 0 and 2.9×10-168. Fifteen EST-SSRs candidates for common bean resistance were identified, which have proved to be suitable for their amplification by PCR. The transferability analysis of ESTs related to resistance to Meloidogyne spp., especially among soybeans and common beans is efficient. Based on this study, 15 EST-SSRs candidates are available for validation and later use.
Key words: simple sequence repeats (SSRs) markers, assisted selection, ontology, pre-breeding.
INTRODUCTION
MATERIALS AND METHODS
RESULTS AND DISCUSSION
CONCLUSION
CONFLICT OF INTERESTS
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. |
|
Andersen JR, Lübberstedt T (2003). Functional markers in plants. Trends Plant. Sci. 8(11):554-560. |
|
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. |
|
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. |
|
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. |
|
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. |
|
Buso G,Amaral Z, Brondani R, Ferreira M (2006). Microsatellite markers for the common bean Phaseolus vulgaris. Mol. Ecol. Notes 6(1):252-254. |
|
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. |
|
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. |
|
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. |
|
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. |
|
Ellegren H (2004). Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 5(6):435-445. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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 |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
Schlötterer C (2000). Evolutionary dynamics of microsatellite DNA. Chromosoma 109(6):365-371. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
|
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. |
Copyright © 2024 Author(s) retain the copyright of this article.
This article is published under the terms of the Creative Commons Attribution License 4.0