Abstract
A total 177 simple sequence repeat (SSR) markers were screened using a set of 47 Upland cotton genotypes comprising 14 commercial varieties, 14 germplasm accessions and 19 advanced breeding lines to identify informative markers for genetic diversity assessment and fingerprinting in G. hirsutum. Only 21% (381177) of SSR markers tested showed polymorphism with a mean of 2.18 alleles per locus and with average polymorphism information content (PIC) of 0.32. The SSR markers revealed a Jaccard’ similarity coefficient ranging between 0.43 and 0.89, with an average of 0.67 among accessions. Cluster analysis using unweighted pair group method with arithmetic averages (UPGMA) and principal component analysis (PCA) indicated that majority of the genotypes were very closely related. All the 47 genotypes showed heterorygosity for at least one of the SSR loci. We discovered 19 rare and 6 unique alleles among the tested genotypes of cotton. Fingerprint based on all the 38 loci revealed a probability of identical match by chance of 3.98x10. A set of ten SSR markers was identified which could distinguish all the 47 genotypes with a moderate probability of identical match by chance (X̅D n = 0.01).
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Abbreviations
- BNL:
-
Brookhaven National Laboratory
- PCA:
-
principal component analysis
- PIC:
-
polymorphism information content
- SSR:
-
simple sequence repeat
- UPGMA:
-
unweighted paired group method using arithmetic averages
References
Meshram LD, Wadodkar MR & Ladole MY, J Cotton Res Dev, 17 (2003) 224.
Wu L, Lin ZX & Zhang XL, J Genetics Genomics, 34 (2007) 634.
Bowman DT, J Cotton Sci, 4 (2000) 130.
Meredith WR Jr, CSSA Spec. Publ, 17 (1991) 127.
Reif JC, Hamrit S, Heckenberger M, Schipprack W, Maurer HP, Bohn M & Melchinger AE, Theor Appl Genet, 111 (2005) 838.
Xu SX, Liu J & Liu GS, Hereditas, 141 (2004) 207.
Rakshit A, Vashisht V, Rakshit S, Dadlani M, Seed Res, 36 (2008) 28.
Rana MK & Bhat KV, Current Sci, 66 (2005) 1956.
Vamadevaiah HM, Katageri IS, Anita B, Thippeswamy S & Soregaon CD, Annals Biology, 22 (2006) 107.
Kumar B, Rakshit S, Singh RD, Gadag RN, Nath R, Paul AK & Wasialam , J Plant Biochem Biotech, 17 (2008) 133.
Tatineni V, Cantrell RG & Davis DD, Crop Sci, 36 (1996) 186.
Iqbal MJ, Aziz N, Saced NA, Zafar Y & Malik KA, Theor Appl Genet, 67 (1997) 934.
Lu HJ & Myers GO, Theor Appl Genet, 105 (2002) 325.
Wendel JF & Brubaker CL, Am J Bot, 60 (1993) 71.
Pillay M & Meyers GO, Crop Sci, 39 (1999) 1881.
Abdalla AM, Reddy OUK, EL-Zik KM & Pepper AE, Theor Appl Genet, 102 (2001) 222.
Rana MK, Singh VP & Bhat KV, Genet Resour Crop Evol, 52 (2005) 989.
Rungis D, Lewellyn D, Dennis ES & Lyon BR, Aust J Agric Res, 56 (2005) 301.
Liu S, Contrail RG, McCarty JC Jr & Stewart JM, Crop Sci, 40 (2000) 1459.
Nguyen TB, Giband M, Brottler P, Risterucci AM & Lacape JM, Theor Appl Genet, 109 (2004) 167.
Xlao J, Wu K, David DF, David MS, John Y & Roy GC, J Cotton Sci, 13 (2009) 75.
Wang BH, Guo WZ, Zhu XF, Wu YT, Huang NT & Zhang TZ, Euphytica, 152 (2006) 367.
Lacape JM, Dessauw D, Rajab M, Noyer JL & Hau B, Mot Breed, 19 (2007) 45.
Li Z, Wang X, Zhang Y, Zhang G, Wu L, Chi J & Ma Z, Front Agriculture in China, 2 (2008) 245.
Bertini CHCdeM, Ivan S, Tocio S, Everaldo GdeB & Maurillo AM, Genet Mot Bio, 29 (2006) 321.
Chen H, Clan N, Guo W, Song Q, Li B, Deng F, Dong C, Zhang T, Theor Appl Genet, 119 (2009) 605.
Liu DO, Gua XP, Lin ZX, Nie YC & Zhang XL, Genet Resour Crop Evol, 53 (2006) 1145.
Liu K & Muse CV, Biointormatics, 21 (2005) 2128.
Jaccard P, Bull Soc Vaudolse Sci Nat, 44 (1908) 223.
Rohlf FJ, NTSYS-pc numerical taxonomy and multi-variate analysis system, version 2.02. Exeter Publications, New York (1989).
Roy Choudhury P, Kohli S, Srinivasan S, MohapatraT & Sharma RP, Euphytica, 116 (2001) 243.
Zhang YX, Lin ZX, Li W, Tu LL, Nie YC & Zhang XL, Chinese Sci Bulletin, 52 (2007) 2522.
Qureshi SN, Saha S, Kantety RV & Jenkins JN, J Cotton Sci, 6 (2004), 112.
Pang CY, Du XM & Ma ZY, Acta Agronomica Sinica, 32 (2006) 1371.
Bhat KV, in: Advances in Data Analytical Techniques (Prasad R; Gupta V K; Bhar L M; Bhatia V K, eds), New Delhi: IASRI, (2008) 101.
Gunjaca J, Buhinicek I, Jukic M, Sercevic H, Bargolovic A, Kozic Z, Jambrovic A & Pejic I, Euphytica, 161 (2008) 165.
Ibáñez, J., Vélez, M.D., Andrés, M.T. & Borrego, J, Theor Appl Genet, 119 (2009) 1213.
Van Deynze AE, Sundstrom FJ & Bradford KJ, Crop Sci, 45 (2005)1565.
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Rakshit, A., Rakshit, S., Santhy, V. et al. Evaluation of SSR Markers for the Assessment of Genetic Diversity and Fingerprinting of Gossypium hirsutum Accessions. J. Plant Biochem. Biotechnol. 19, 153–160 (2010). https://doi.org/10.1007/BF03263335
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DOI: https://doi.org/10.1007/BF03263335