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A preliminary genetic analysis of fibre traits and the use of new genomic SSRs for genetic diversity in jute

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Abstract

Jute is one of the most important fibre crops, which is second only to cotton in providing environment-friendly (biodegradable and renewable) ligno-cellulose fibre. In order to improve this largely neglected crop, we conducted a preliminary study involving the following: (i) analysis of nature and extent of the genetic variability for fibre yield and four other related traits in a set of 81 genotypes belonging to two commercially cultivated Corchorus species (45 genotypes of C. olitorius + 36 genotypes of C. capsularis), (ii) development and analysis of a set of simple sequence repeat (SSR) markers from C. olitorius, and (iii) use of a sub-set of SSRs for assessment of genetic diversity in the above set of 81 genotypes. The results suggested quantitative nature of fibre yield and other related traits, with a preponderance of dominance component in genetic variance. A sub-set of 45 SSRs derived from C. olitorius, when used for a study of DNA polymorphism and genetic diversity, showed high transferability of these C. olitorius SSRs to C. capsularis. The average number of alleles for individual SSRs was surprisingly low (3.04 for both species, 2.02 for C. capsularis and 2.51 for C. olitorius), and so was the average polymorphic information content (PIC; 0.23 and 0.24 in two species). In the dendrogram obtained using a similarity matrix, the 81 genotypes were grouped into three clusters, which largely corresponded to the two species, Cluster I belonging mainly to C. capsularis and the other two closely related clusters (clusters II and III) belonging to C. olitorius. It was also shown that a minimum of 15 SSRs could give the same information as 41 SSRs, thus making many SSRs redundant. The SSR markers developed during the present study and to be developed in future will prove useful not only for evaluation of genetic diversity, but also for molecular mapping/QTL analysis, and for comparative genome analysis of the two Corchorus species.

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References

  • Akkaya MS, Bhagwat AA, Cregan PB (1992) Length polymorphism of simple sequence repeat DNA in soybean. Genetics 132:1131–1139

    PubMed  CAS  Google Scholar 

  • Ali MA (1984) Correlation and regression studies between fibre yield and some anatomical characters in white jute (Corchorus capsularis L.). Bang J Jute Fib Res 9:25–30

    Google Scholar 

  • Ali MA (1994) Genetic estimates of anatomical characters of white jute. Bang J Jute Fib Res 21:43–50

    Google Scholar 

  • Ali MA, Naher Z, Rhaman M, Haque A, Alim A (2002) Selection prediction for yield of fibre in jute (Corchorus capsularis and C. olitorius). OnLine J Biol Sci 2:295–297

    Google Scholar 

  • Bandopadhyay R, Sharma S, Rustgi S, Singh R, Kumar A, Balyan HS, Gupta PK (2004) DNA polymorphism among 18 species of Triticum-Aegilops complex using wheat EST-SSRs. Plant Sci 166:349–356

    Article  CAS  Google Scholar 

  • Basu A, Ghosh M, Meyer R, Powell W, Basak SL, Sen SK (2004) Analysis of genetic diversity in cultivated jute determined by means of SSR markers and AFLP profiling. Crop Sci 44:678–685

    Article  CAS  Google Scholar 

  • Bell CJ, Ecker JR (1994) Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19:137–144

    Article  PubMed  CAS  Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331

    PubMed  CAS  Google Scholar 

  • Burstin J, Deniot G, Potier J, Weinachter C, Aubert G, Baranger A (2001) Microsatellite polymorphism in Pisum sativum. Plant Breed 120:311–317

    Article  CAS  Google Scholar 

  • Cardle L, Ramsay L, Milbourne D, Macaualy M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–854

    PubMed  CAS  Google Scholar 

  • Decroocq V, Fave MG, Hagen L, Bordenave L, Decroocq S (2003) Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 106:912–922

    PubMed  CAS  Google Scholar 

  • Edmonds JM (1990) Herbarium survey of African Corchorus L. species. Systematic and ecogeographic studies on crop gene pools 4. IBPGR/IJO, Rome, p 284

    Google Scholar 

  • Gascuel O (1997) Concerning the NJ algorithm and its unweighted version, UNJ. In: Mirkin B, McMorris FR, Roberts F, Rzhetsky A (eds) Mathematical hierarchies and biology. DIMACS workshop, series in discrete mathematics and theoretical computer science, vol 37. American Mathematical Society, Providence, RI, pp 149–170

    Google Scholar 

  • Griffing B (1956) Concepts of general and specific combining ability in relation to diallel crossing systems. Aust J Biol Sci 9:463–493

    Google Scholar 

  • Gupta PK, Balyan HS, Sharma PC, Ramesh B (1996) Microsatellites in plants: a new class of molecular markers. Curr Sci 70:45–54

    CAS  Google Scholar 

  • Gupta PK, Rustgi S, Sharma S, Singh R, Kumar N, Balyan HS (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Mol Genet Genomics 270:315–323

    Article  PubMed  CAS  Google Scholar 

  • Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–185

    Article  CAS  Google Scholar 

  • Hamza S, Hamida WB, Rebaï A, Harrabi M (2004) SSR-based genetic diversity assessment among Tunisian winter barley and relationship with morphological traits. Euphytica 135:107–118

    Article  CAS  Google Scholar 

  • Hirata M, Cai H, Inoue M, Yuyama N, Miura Y, Komatsu T, Takamizo T, Fujimori M (2006) Development of simple sequence repeat (SSR) markers and construction of an SSR-based linkage map in Italian ryegrass (Lolium multiflorum Lam.). Theor Appl Genet 113:270–279

    Article  PubMed  CAS  Google Scholar 

  • Hossain MB, Awal A, Rahman MA, Haque S, Khan H (2003) Distinction between cold-sensitive and -tolerant jute by DNA polymorphisms. J Biochem Mol Biol 36:427–432

    PubMed  CAS  Google Scholar 

  • Hossain MB, Haque S, Khan H (2002) DNA fingerprinting of jute germplasm by RAPD. J Biochem Mol Biol 35:414–419

    PubMed  CAS  Google Scholar 

  • Hüttel B, Winter P, Weising K, Choumane W, Weigand F, Kahl G (1999) Sequence-tagged microsatellite site markers for chickpea (Cicer arietinum L.). Genome 42:210–217

    Article  PubMed  Google Scholar 

  • Islam AS, Rashid A (1960) First successful hybridization between the two jute yielding species. Nature 185:258–259

    Article  Google Scholar 

  • Islam AS (1964) A rare hybrid combination through application of hormone and embryo culture. Nature 210:320

    Article  Google Scholar 

  • Kumpatla SP, Mukhopadhyay S (2005) Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 48:985–998

    Article  PubMed  CAS  Google Scholar 

  • Liu ZW, Biyashev RM, Saghai-Maroof MA (1996) Development of simple sequence repeat DNA markers and their integration into a barley linkage map. Theor Appl Genet 93:869–876

    Article  CAS  Google Scholar 

  • Martinez-Gomez P, Arulsekar S, Potter D, Gradziel TM (2003) Relationships among peach, almond, and related species as detected by simple sequence repeat markers. J Am Soc Hortic Sci 128:667–671

    Google Scholar 

  • McCouch SR, Chen X, Panaud O, Temnykh S, Xu Y, Cho YG, Huang N, Ishii T, Blair M (1997) Microsatellite marker development, mapping and applications in rice genetics and breeding. Plant Mol Biol 35:88–89

    Article  Google Scholar 

  • Odeny DA, Jayashree B, Ferguson M, Hoisington D, Crouch J, Gebhardt C (2007) Development, characterization and utilization of microsatellite markers in pigeonpea. Plant Breed 126:130–136

    Article  CAS  Google Scholar 

  • Palit P, Sasmal BC, Bhattacharryya AC (1996) Germplasm diversity and estimate of genetic advance of four morpho-physiological traits in a world collection of jute. Euphytica 90:89–110

    Google Scholar 

  • Palve SM, Sinha MK, Mandal RK (2003) Preliminary evaluation of wild species of jute (Corchorus species). Plant Genet Resour Newsl 134:10–12

    Google Scholar 

  • Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Enfield, Science Publishers, Montpellier, pp 43–76

    Google Scholar 

  • Prasad M, Varshney RK, Roy JK, Balyan HS, Gupta PK (2000) The use of microsatellites for detecting DNA polymorphism, genotype identification and genetic diversity in wheat. Theor Appl Genet 100:584–592

    CAS  Google Scholar 

  • Qi J, Zhou D, Wu W, Lin L, Wu J, Fang P (2003a) Application of ISSR technology in genetic diversity detection of jute. Ying Yong Sheng Tai Xue Bao 14:1473–1477

    PubMed  CAS  Google Scholar 

  • Qi J, Zhou D, Wu W, Lin L, Fang P, Wu J (2003b) The application of RAPD technology in genetic diversity detection of Jute. Yi Chuan Xue Bao 30:926–932

    PubMed  CAS  Google Scholar 

  • Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149:2007–2023

    PubMed  Google Scholar 

  • Rossetto M (2001) Sourcing of SSR markers from related plant species. In: Henry RJ (ed) Plant genotyping: the DNA fingerprinting of plants. CABI Publishing, CAB International, Wallingford, UK, pp 211–224

    Google Scholar 

  • Roy A, Bandyopadhyay A, Mahaptra AK, Ghosh SK, Singh NK, Bansal KC, Koundal KR, Mohapatra T (2006) Evaluation of genetic diversity in jute (Corchorous species) using STMS, ISSR and RAPD markers. Plant Breed 125:292–297

    Article  CAS  Google Scholar 

  • Saghai-Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018

    Article  PubMed  CAS  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York

    Google Scholar 

  • Scott KD, Eaggler P, Seaton G, Rossetto M, Ablett EM, Lee LS, Henry RJ (2000) Analysis of SSRs derived from grape ESTs. Theor Appl Genet 100:723–726

    Article  CAS  Google Scholar 

  • Sengupta D, Nandy S, Mitra S, Dutta P, Sinha MK, Kole PC, Chakraborty S (2005) Genetical study on tossa jute (Corchorous olitorius L.) for fibre yield and quality parameters. Ind J Genet 65:29–32

    Google Scholar 

  • Sethy NK, Shokeen B, Edwards KJ, Bhatia S (2006) Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). Theor Appl Genet 112:1416–1428

    Article  PubMed  CAS  Google Scholar 

  • Shaikh MAQ, Ahamed ZU, Khan AI, Majid MA (1980) An anatomical screening approach to selection of high yielding mutants of jute. Environ Exp Bot 20:287–296

    Article  Google Scholar 

  • Sharopova N, McMullen MD, Schultz L, Schroeder S, Sanchez-Villeda H, Gardiner J, Bergstrom D, Houchins K, Melia-Hancock S, Musket T, Duru N, Polacco M, Edwards K, Ruff T, Register JC, Brouwer C, Thompson R, Velasco R, Chin E, Lee M, Woodman-Clikeman W, Jane Long M, Liscum E, Cone K, Davis G, Coe EH Jr (2002) Development and mapping of SSR markers for maize. Plant Mol Biol 48:463–481

    Article  PubMed  CAS  Google Scholar 

  • Sharma S, Balyan HS, Kulwal PL, Kumar N, Varshney RK, Prasad M, Gupta PK (2002) Study of interspecific SSR polymorphism among 14 species from Triticum-Aegilops group. Wheat Inf Serv 95:23–28

    Google Scholar 

  • Singh DP (1973) Combining ability in jute. Ind J Genet 33:77–81

    Google Scholar 

  • Singh DP (1975) The analysis of additive and dominance genetic variances in a diallel cross of jute (C. olitorius L). Acta Agron Acad Sci Hungary 24:167–172

    Google Scholar 

  • Sinha MK, Guharoy MK, Sasmal BC (1989) Triallel cross approach to genetical analysis of fibre yield in jute. Phytobreedon 5:13–18

    Google Scholar 

  • Sinha MK, Sengupta D, Sen HS, Ghosh T (2004a) Jute and jute like fibres: current situation. Sci Cult 70:23–27

    Google Scholar 

  • Sinha MK, Mitra S, Nandy S, Sengupta D, Dutta P, Das F, Chakrabarty SC (2004b) Interspecific hybrid between two jute (Corchorus) species for textile quality fibre. Ind J Genet 64:310–316

    Google Scholar 

  • Stachel M, Lelley T, Grausgruber H, Vollmann J (2000) Application of microsatellites in wheat (Triticum aestivum L.) for studying genetic differentiation caused by selection for adaptation and use. Theor Appl Genet 100:242–248

    Article  Google Scholar 

  • Swaminathan MS, Iyer RD, Sulbha K (1961) Morphology, cytology and breeding behaviour of hybrids between Corchorus olitorius and C. capsularis. Curr Sci 30:67–68

    Google Scholar 

  • Tegelstrom H (1992) Detection of mitochondrial DNA fragments. In: Hoelzel AR (ed) Molecular genetic analysis of populations: a practical approach. IRL Press, Oxford, pp 89–114

    Google Scholar 

  • Wessa P (2007) Free statistics software, office for research development and education, version 1.1.21, URL http://www.wessa.net/. Accessed May 2007

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Acknowledgements

Financial support from the International Centre for Genetic Engineering and Biotechnology (ICGEB) to carry out this study and the award of JRF/SRF/RA to RRM, SR, SS, RS, AG, and JK by CSIR, DBT, and DAE-BRNS are gratefully acknowledged. Support of DBT to AKT, and the award of a position of INSA-Senior Scientist by INSA to PKG are also acknowledged. Funds provided under FIST Programme by DST for equipments used to carry out this study are also acknowledged.

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Correspondence to Pushpendra Kumar Gupta.

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Mir, R.R., Rustgi, S., Sharma, S. et al. A preliminary genetic analysis of fibre traits and the use of new genomic SSRs for genetic diversity in jute. Euphytica 161, 413–427 (2008). https://doi.org/10.1007/s10681-007-9597-x

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