Development and characterization of expressed sequence tag-derived simple sequence repeat markers in tropical forage legume Stylosanthes guianensis (Aubl.) Sw.
Tóm tắt
Most species of Stylosanthes (stylo) genus are important tropical pasture legumes with very versatile, widely adapted, and productive characteristics. These legumes are commercially used in various agricultural systems in many tropical and subtropical regions. However, the few molecular markers for the stylo species limit their genetic improvement. In this study, 36,558 expressed sequence tags (ESTs) have been de novo assembled using Illumina paired-end sequencing in Stylosanthes guianensis (Aubl.) Sw. to develop simple sequence repeat (SSR) markers. We searched these ESTs for SSRs and identified 4115 SSR loci from 3643 ESTs (9.96 %). Dinucleotide and trinucleotide repeat motifs were the most abundant types (30.50 and 50.33 %, respectively), whereas tetranucleotide, pentanucleotide, and hexanucleotide motifs represented <10 % of all SSRs. The motif AG/CT was the most abundant, accounting for 21.7 % of all SSRs. Moreover, 2008 SSR markers were developed using 1873 SSR-containing unigenes. A total of 115 EST-SSR markers located in the coding region were amplified using polymerase chain reaction to detect 29 S.
guianensis accessions. Of these 115 markers, 96 produced reliable bands with expected sizes, and 81 markers were polymorphic, with 2–6 alleles among the 29 accessions. Analysis of the genetic diversity of all 29 accessions revealed similarity coefficients that ranged from 0.528 to 0.983. The EST-SSR markers developed in this study represent the first large-scale development of SSR markers for S.
guianensis. These SSR markers will provide a valuable resource for genetic diversity studies, cultivar fingerprinting, construction of genetic maps, identification of quantitative trait loci for important traits, and molecular marker-assisted selection breeding in stylo species.
Tài liệu tham khảo
Aggarwal RK, Hendre PS, Varshney RK, Bhat PR, Krishnakumar V, Singh L (2007) Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species. Theor Appl Genet 114:359–372
Billotte N, Lagoda PJ, Risterucci AM, Baurens FC (1999) Microsatellite-enriched libraries: applied methodology for the development of SSR markers in tropical crops. Fruits 54:277–288
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331
Brandão M, Costa NM, Schultze-Kraft R (1985) Pauciflora: uma nova variedade de Stylosanthes guianensis (Aub.) Sw. Anais do 36 Congresso Nacional de Botanica, Curitiba: Sociedade Botanica do Brasil 235–241
Bushman BS, Larson SR, Tuna M, West MS, Hernandez AG, Vullaganti D, Gong G, Robins JG, Jensen KB, Thimmapuram J (2011) Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability. Theor Appl Genet 123:119–129
Calles T, Schultze-Kraft R (2010) Stylosanthes falconensis (Leguminosae, Papilionoideae, Dalbergieae), a new species endemic to Venezuela. Kew Bull 65:73–76
Chandra A (2006) A partial genetic map of Stylosanthes developed using inter-specific F2 cross. Cytologia 71:353–358
Chandra A, Tiwari KK, Nagaich D, Dubey N, Kumar S, Roy AK (2011) Development and characterization of microsatellite markers from tropical forage Stylosanthes species and analysis of genetic variability and cross-species transferability. Genome 54:1016–1028
Chen S, Huang X, Yan X, Liang Y, Wang Y, Li X, Peng X, Ma X, Zhang L, Cai Y et al (2013) Transcriptome analysis in sheepgrass (Leymus chinensis): a dominant perennial grass of the Eurasian Steppe. PLoS ONE 8:e67974
Cho YG, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch SR, Park WD, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722
Costa N (2006) Revisão do género Stylosanthes. PhD thesis, Universidade Técnica de Lisboa, Portugal, 470 pp
Dutta S, Kumawat G, Singh BP, Gupta DK, Singh S, Dogra V, Gaikwad K, Sharma TR, Raje RS, Bandhopadhya TK et al (2011) Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea (Cajanus cajan (L.) Millspaugh). BMC Plant Biol 11:17
Ellis JR, Burke JM (2007) EST-SSRs as a resource for population genetic analyses. Heredity 99:125–132
Eujayl I, Sorrells M, Baum M, Wolters P, Powell W (2001) Assessment of genotypic variation among cultivated durum wheat based on EST-SSRs and genomic SSRs. Euphytica 119:39–43
Huang C, Liu G, Bai C, Wang W, Tang J (2014) Application of SRAP markers in the identification of Stylosanthes guianensis hybrids. Mol Biol Rep 41:5923–5929
Kalia RK, Mai MK, Kalia S, Singh R, Dhawan AK (2011) Microsatellite markers: an overview of the recent progress in plants. Euphytica 177:309–334
Kantety RV, La Rota M, Matthews DE, Sorrells ME (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510
Kumpatla SP, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48:985–998
Liu CJ, Musial JM, Thomas BD (1999) Genetic relationships among Stylosanthes species revealed by RFLP and STS analyses. Theor Appl Genet 99:1179–1186
Liu T, Zhu S, Fu L, Tang Q, Yu Y, Chen P, Luan M, Wang C, Tang S (2013a) Development and characterization of 1,827 expressed sequence tag-derived simple sequence repeat markers for ramie (Boehmeria nivea L. Gaud). PLoS ONE 8:e60346
Liu Z, Chen T, Ma L, Zhao Z, Zhao PX, Nan Z, Wang Y (2013b) Global transcriptome sequencing using the Illumina platform and the development of EST-SSR markers in autotetraploid alfalfa. PLoS ONE 8:e83549
Maass BL, Sawkins M (2004) History, relationships and diversity among Stylosanthes species of commercial significance. In: Chakraborty S (ed) High-yielding anthracnose-resistant Stylosanthes for agricultural systems. Australian Centre for International Agricultural Research (ACIAR), Canberra, pp 9–26
Mace ES, Varshney RK, Mahalakshmi V, Seetha K, Gafoor A, Leeladevi Y, Crouch JH (2008) In silico development of simple sequence repeat markers within the aeschynomenoid/dalbergoid and genistoid clades of the Leguminosae family and their transferability to Arachis hypogaea, groundnut. Plant Sci 174:51–60
Nagaich D, Chandra A (2009) Assessment of genetic diversity and identification of informative molecular markers for germplasm characterization in Caribbean Stylo (Stylosanthes hamata). J Plant Biochem Biotechnol 18:257–260
Nagaich D, Tiwari KK, Srivastva N, Chandra A (2013) Assessment of genetic diversity and morpho-physiological traits related to drought tolerance in Stylosanthes scabra. Acta Physiol Plant 35:3127–3136
Rohlf FJ (2000) NTSYS-pc. Numerical taxonomy and multivariate analysis system, version 2.10. Exeter Software, New York
Santos MO, Karia CT, Resende RM, Chiari L, Jungmann L, Zucchi MI, Souza AP (2009a) Isolation and characterization of microsatellite loci in the tropical forage legume Stylosanthes guianensis (Aubl.) Sw. Conserv Genet Resour 1:43–46
Santos MO, Sassaki RP, Ferreira TH, Resende RM, Chiari L, Karia CT, Faleiro FG, Jungmann L, Zucchi MI, Souza AP (2009b) Polymorphic microsatellite loci for Stylosanthes macrocephala Ferr. et Costa, a tropical forage legume. Conserv Genet Resour 1:481–485
Santos MO, Sassaki RP, Chiari L, Resende RM, Souza AP (2009c) Isolation and characterization of microsatellite loci in tropical forage Stylosanthes capitata Vogel. Mol Ecol Resour 9:192–194
Santos-Garcia MO, Resende RM, Chiari L, Zucchi MI, Souza AP (2011) Mating systems in tropical forages: Stylosanthes capitata Vog. and Stylosanthes guianensis (Aulbl.) Sw. Euphytica 178:185–193
Santos-Garcia MO, Karia CT, Resende RM, Chiari L, Vieira ML, Zucchi MI, Souza AP (2012a) Identification of Stylosanthes guianensis varieties using molecular genetic analysis. AoB Plants 2012:pls001
Santos-Garcia MO, Toledo-Silva G, Sassaki RP, Ferreira TH, Resende RM, Chiari L, Karia CT, Carvalho MA, Faleiro FG, Zucchi MI et al (2012b) Using genetic diversity information to establish core collections of Stylosanthes capitata and Stylosanthes macrocephala. Genet Mol Biol 35:847–861
Tan C, Wu Y, Taliaferro CM, Anderson MP, Tauer C, Samuels T (2012) Development of simple sequence repeat markers for bermudagrass from its expressed sequence tag sequences and preexisting sorghum SSR markers. Mol Breed 29:23–30
Tan LQ, Wang LY, Wei K, Zhang CC, Wu LY, Qi GN, Cheng H, Zhang Q, Cui QM, Liang JB (2013) Floral transcriptome sequencing for SSR marker development and linkage map construction in the tea plant (Camellia sinensis). PLoS ONE 8:e81611
Tang Y, Wu Z, Liu G, Yi K (2009) Research advances in germplasm resources of Stylosanthes. Chin Bull Bot 44:752–762
Thumma BR, Naidu BP, Chandra A, Cameron DF, Bahnisch LM, Liu C (2001) Identification of causal relationships among traits related to drought resistance in Stylosanthes scabra using QTL analysis. J Exp Bot 52:203–214
Vander Stappen J, Weltjens II, Volckaert G (1999) Microsatellite markers in Stylosanthes guianensis. Mol Ecol 8:514–517
Vander Stappen J, Weltjens I, Gama Lopez S, Volckaert G (2000) Genetic diversity in Mexican Stylosanthes humilis as revealed by AFLP, compared to variability of S. humilis accessions of South American origin. Euphytica 113:145–154
Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55
Wang Z, Li J, Luo Z, Huang L, Chen X, Fang B, Li Y, Chen J, Zhang X (2011) Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas). BMC Plant Biol 11:139
Wang S, Wang X, He Q, Liu X, Xu W, Li L, Gao J, Wang F (2012) Transcriptome analysis of the roots at early and late seedling stages using Illumina paired-end sequencing and development of EST-SSR markers in radish. Plant Cell Rep 31:1437–1447
Wang Z, Yu G, Shi B, Wang X, Qiang H, Gao H (2014) Development and characterization of simple sequence repeat (SSR) markers based on RNA-sequencing of Medicago sativa and in silico mapping onto the M. truncatula genome. PLoS ONE 9(3):e92029
Wu J, Cai C, Cheng F, Cui H, Zhou H (2014) Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences. Mol Breed 34:1853–1866
Xin D, Sun J, Wang J, Jiang H, Hu G, Liu C, Chen Q (2012) Identification and characterization of SSRs from soybean (Glycine max) ESTs. Mol Biol Rep 39:9047–9057
Yadav HK, Ranjan A, Asif MH, Mantri S, Sawant SV, Tuli R (2011) EST-derived SSR markers in Jatropha curcas L.: development, characterization, polymorphism, and transferability across the species/genera. Tree Genet Genomes 7:207–219
Yeh FC, Yang RC, Boyle T (1999) POPGENE, version 1.32: the user friendly software for population genetic analysis. Molecular Biology and Biotechnology Centre, University of Alberta, Edmonton
Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16