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Mining simple sequence repeats in Picrorhiza kurroa transcriptomes for assessing genetic diversity among accessions varying for picrosides contents

Published online by Cambridge University Press:  28 September 2015

Kirti Shitiz ,
Saurabh Pandit ,
Sreekrishna Chanumolu ,
Hemant Sood ,
Harvinder Singh ,
Jagdish Singh  and
Rajinder Singh Chauhan
Kirti Shitiz
Affiliation:
Department of Biotechnology and Bioinformatics, Jaypee University, Waknaghat-173234, Solan, Himachal Pradesh, India
Saurabh Pandit
Affiliation:
Department of Biotechnology and Bioinformatics, Jaypee University, Waknaghat-173234, Solan, Himachal Pradesh, India
Sreekrishna Chanumolu
Affiliation:
Department of Biotechnology and Bioinformatics, Jaypee University, Waknaghat-173234, Solan, Himachal Pradesh, India
Hemant Sood
Affiliation:
Department of Biotechnology and Bioinformatics, Jaypee University, Waknaghat-173234, Solan, Himachal Pradesh, India
Harvinder Singh
Affiliation:
Department of Biotechnology and Bioinformatics, Jaypee University, Waknaghat-173234, Solan, Himachal Pradesh, India
Jagdish Singh
Affiliation:
Agroforestry and Extension Division, Himalayan Forest Research Institute, Panthaghati-171009, Shimla, Himachal Pradesh, India
Rajinder Singh Chauhan*
Affiliation:
Department of Biotechnology and Bioinformatics, Jaypee University, Waknaghat-173234, Solan, Himachal Pradesh, India
*
*Corresponding author. E-mail: [email protected]
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Abstract

Picrorhiza kurroa (family Scrophulariaceae) is a high value medicinal herb used in herbal drug formulations like picroliv, picrolax, etc. It has been collected recklessly from its natural habitat posing endangered status for its existence, thereby necessitating characterization of genetic diversity for its sustainable utilization and conservation. In this study, picrosides content and genetic profiles of 26 accessions of P. kurroa from different locations in north-western Himalayas have been analysed. Picroside-I (P-I) content ranged from 0.37 to 2.7% in fresh shoots whereas total picrosides content (P-I+P-II) ranged from 3.7 to 10.9% in dry rhizomes. High picrosides content accession PKS-1 was identified, both for shoots and rhizomes. To study genetic diversity and correlate picrosides content with their genetic factors, genetic profiling was done using simple sequence repeats (SSRs) identified from P. kurroa transcriptomes. Out of 361 SSR primers tested on 26 accessions, 35 primers yielded polymorphic profiles. Overall low genetic diversity was observed in P. kurroa accessions. The highest polymorphism information content (PIC) of 0.55 was given by SSR marker PKSTS-P9 (TGGTG)4. Mean allele number was 2.97. Mean observed and expected heterozygosities were 0.597 and 0.452, respectively. Among all accessions Nei's genetic diversity (H) was 0.39 and Shannon's information index (I) was 0.58. Cluster analysis of STRUCTURE was comparable to DARWIN. Microsatellite markers would be helpful in the development of DNA diagnostics for the authentication of quality plant material as well as planning a genetic improvement strategy.

Keywords

genetic diversityHPLCmarkersPicrorhiza kurroapicrosidesSSR
Type
Research Article
Information
Plant Genetic Resources , Volume 15 , Issue 1 , February 2017 , pp. 79 - 88
Copyright
Copyright © NIAB 2015 

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References

Belaj, A, Muñoz-Diez, C, Baldoni, L, Porceddu, A, Barranco, D and Satovic, Z (2007) Genetic diversity and population structure of wild olives from the north-western Mediterranean assessed by SSR markers. Annals of Botany 100: 449–458.Google Scholar
Cardle, L, Ramsay, L, Milbourne, D, Macaulay, M, Marshall, D and Waugh, R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156: 847–854.Google Scholar
Castillo, A, Varshney, RK, Graner, A and Hernández, P (2008) High transferability and polymorphism of barley EST-SSR markers for the analysis of gene biodiversity in Hordeum chilense . In: Molina-Cano, JL, Christou, P, Graner, A, Hammer, K, Jouve, N, Keller, B, Lasa, JM, Powell, W, Royo, C, Shewry, P and Stanca, AM (eds) Cereal Science and Technology for Feeding Ten Billion People: Genomics Era and Beyond. Zaragoza: CIHEAM/IRTA, pp. 53 (Options Méditerranéennes: Série A. Séminaires Méditerranéens, n. 81).Google Scholar
Chabane, K, Ablett, GA, Cordeiro, GM, Valkoun, J and Henry, RJ (2005) EST versus genomic-derived microsatellite markers for genotyping wild and cultivated barley. Genetic Resources and Crop Evolution 52: 903–909.Google Scholar
Chandra, B, Palni, LMS and Nandi, SK (2006) Propagation and conservation of Picrorhiza kurroa Royle ex Benth.: an endangered Himalayan medicinal herb of high commercial value. Biodiversity and Conservation 15: 2325–2338.Google Scholar
Cho, YG, Ishii, T, Temnykh, S, Chen, X, Lipovich, L, McCouch, SR, Park, WD, Ayres, N and Cartinhour, S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theoretical and Applied Genetics 100: 713–722.Google Scholar
Fagen, LI and Nianhe, XIA (2005) Population structure and genetic diversity of an endangered species Glyptostrobus pensilis (Cupressaceae). Botanical Bulletin – Academia Sinica Taipei 46: 155–162.Google Scholar
Frankham, R (1995) Conservation genetics. Annual Review of Genetics 29: 305–327.Google Scholar
Fu, N, Wang, P, Liu, X and Shen, H (2014) Use of EST-SSR markers for evaluating genetic diversity and fingerprinting celery (Apium graveolens L.) cultivars. Molecules 19: 1939–1955.Google Scholar
Gadaleta, A, Giancasproa, A, Zacheoa, S, Nigroa, D, Giovea, SL, Colasuonnoa, P and Blancoa, A (2011) Comparison of genomic and EST-derived SSR markers in phylogenetic analysis of wheat. Plant Genetic Resources 9: 243–246.Google Scholar
Gahlan, P, Singh, HR, Shankar, R, Sharma, N, Kumari, A, Chawla, V, Ahuja, PS and Kumar, S (2012) De novo sequencing and characterization of Picrorhiza kurroa transcriptome at two temperatures showed major transcriptome adjustments. BMC Genomics 13: 126.Google Scholar
Gong, Y, Xu, S, Mao, W, Hu, Q, Zhang, G, Ding, J and Ya-dan, L (2010) Developing new SSR markers from ESTs of pea (Pisum sativum L.). Journal of Zhejiang University Science B 11: 702–707.Google Scholar
Gupta, PK, Rustgi, S, Sharma, S, Singh, R, Kumar, N and Balyan, HS (2003) Transferable EST-SSR markers for the study of polymorphism and genetic diversity in bread wheat. Molecular Genetics and Genomics 270: 315–323.CrossRefGoogle Scholar
Hamrick, JL and Godt, MJW (1989) Allozyme diversity in plant species. In: Brown, AHD, Clegg, MT, Kahler, AL and Weir, BS (eds) Plant Population Genetics, Breeding, and Genetic Resources. Sunderland: Sinauer, pp. 43–63.Google Scholar
Hu, J, Wang, L and Li, J (2010) Comparison of genomic SSR and EST-SSR markers for estimating genetic diversity in cucumber. Biologia Plantarum 55: 577–580.CrossRefGoogle Scholar
Huang, Y, Zhang, C and Li, D (2009) Low genetic diversity and high genetic differentiation in the critically endangered Omphalogramma souliei (Primulaceae): implications for its conservation. Journal of Systematics and Evolution 47: 103–109.Google Scholar
Hussain, MA and Bedi, YS (2012) Authentication of Picrorhiza kurroa Royle ex Benth. using DNA fingerprint. International Journal of Agricultural Sciences 2: 511–521.Google Scholar
Katoch, M, Fazli, IS, Suri, KA, Ahuja, A and Qazi, GN (2011) Effect of altitude on picroside content in core collections of Picrorhiza kurrooa from the north western Himalayas. Journal of Natural Medicine 65: 578–582.Google Scholar
Katoch, M, Hussain, MA and Ahuja, A (2013) Comparison of SSR and cytochrome P-450 markers for estimating genetic diversity in Picrorhiza kurroa L. Plant Systematics and Evolution 299: 1637–1643.Google Scholar
Katti, MV, Ranjekar, PK and Gupta, VS (2001) Differential distribution of simple sequence repeats in eukaryotic genome sequences. Molecular Biology and Evolution 18: 1161–1167.CrossRefGoogle ScholarPubMed
Kumar, R, Bhandari, P, Singh, B and Ahuja, PS (2012) Evaluation of Picrorhiza kurroa accessions for growth and quality in north western Himalayas. Journal of Medicinal Plants Research 6: 2660–2665.Google Scholar
Li, YC, Korol, AB, Fahima, T and Nevo, E (2004) Microsatellites within genes: structure, function, and evolution. Molecular Biology and Evolution 21: 991–1007.Google Scholar
Marshall, TC, Slate, J, Kruuk, LEB and Pemberton, JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Molecular Ecology 7: 639–655.Google Scholar
McCouch, SR, Teytelman, L, Xu, Y, Lobos, KB, Clare, K, Walton, M, Fu, B, Maghirang, R, Li, Z, Xing, Y, Zhang, Q, Kono, I, Yano, M, Fjellstrom, R, DeClerck, G, Schneider, D, Cartinhour, S, Ware, D and Stein, L (2002) Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Research 9: 199–207.Google Scholar
Metzgar, D, Bytof, J and Wills, C (2000) Selection against frameshift mutations limits microsatellite expansion in coding DNA. Genome Research 10: 72–80.Google Scholar
Mishra, RK, Gangadhar, BH, Yu, JW, Kim, DH and Park, SW (2011) Development and characterization of EST-based SSR markers in Madagascar periwinkle (Catharanthus roseus) and their transferability in other medicinal plants. Plant Omics 4: 154–162.Google Scholar
Mostafa, N, Omar, H, Tan, SG and Napis, S (2011) Studies on the genetic variation of the green unicellular alga Haematococcus pluvialis (Chlorophyceae) obtained from different geographical locations using ISSR and RAPD molecular markers. Molecules 16: 2599–2608.Google Scholar
Murray, MG and Thompson, WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research 8: 4321–4325.Google Scholar
Pandey, SP and Somssich, IE (2009) The role of WRKY transcription factors in plant immunity. Plant Physiology 150: 1648–1655.CrossRefGoogle ScholarPubMed
Pandit, S, Shitiz, K, Sood, H and Chauhan, RS (2012) Differential biosynthesis and accumulation of picrosides in an endangered medicinal herb Picrorhiza kurroa . Journal of Plant Biochemistry and Biotechnology 22: 335–342.Google Scholar
Patial, V, Devi, K, Sharma, M, Bhattacharya, A and Ahuja, PS (2012) Propagation of Picrorhiza kurroa Royle ex Benth: an important medicinal plant of Western Himalaya. Journal of Medicinal Plants Research 6: 4848–4860.Google Scholar
Peakall, R and Smouse, PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288–295.Google Scholar
Pritchard, JK, Stevens, M and Donnelly, P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945–959.Google Scholar
Qiu, Y, Zhou, X, Fu, C and Chan, YG (2005) A preliminary study of genetic variation in the endangered, Chinese endemic species Dysosma versipellis (Berberidaceae). Botanical Bulletin – Academia Sinica Taipei 46: 61–69.Google Scholar
Raina, R, Mehra, TS, Chand, R and Sharma, YP (2010) Reproductive biology of Picrorhiza kurroa – a critically endangered high value temperate medicinal plant. Open Access Journal of Medicinal and Aromatic Plants 1: 40–43.Google Scholar
Rushton, PJ, Somssich, IE, Ringler, P and Shen, QJ (2010) WRKY transcription factors. Trends in Plant Science 15: 247–258.Google Scholar
Sharma, A and Chauhan, RS (2011) Repertoire of SSRs in the castor bean genome and their utilization in genetic diversity analysis in Jatropha curcas . Comparative and Functional Genomics 2011: Article ID 286089, 9.CrossRefGoogle ScholarPubMed
Sharma, N, Pathania, V, Singh, B and Gupta, RC (2012) Intraspecific variability of main phytochemical compounds in Picrorhiza kurroa Royle ex Benth. from North Indian higher altitude Himalayas using reversed-phase high-performance liquid chromatography. Journal of Medicinal Plants Research 6: 3181–3187.Google Scholar
Sood, H and Chauhan, RS (2010) Biosynthesis and accumulation of a medicinal compound, Picroside-I, in cultures of Picrorhiza kurroa Royle ex Benth. Plant Cell, Tissue and Organ Culture 100: 113–117.Google Scholar
Tabbasam, N, Zafar, Y and Mehboob-ur-Rahman, (2013) Pros and cons of using genomic SSRs and EST-SSRs for resolving phylogeny of the genus Gossypium . Plant Systematics and Evolution 300: 559–575.Google Scholar
Torii, KU (2004) Leucine-rich repeat receptor kinases in plants: structure, function, and signal transduction pathways. International Review of Cytology 234: 1–46.Google Scholar
Verma, V, Smelcerovic, A, Zuehlke, S, Hussain, MA, Ahmad, SM, Ziebach, T, Qazi, GN and Spiteller, M (2008) Phenolic constituents and genetic profile of Hypericum perforatum L. from India. Biochemical Systematics and Ecology 36: 201–206.Google Scholar
Wang, L, Xu, C, Wang, C and Wang, Y (2012) Characterization of a eukaryotic translation initiation factor 5A homolog from Tamarix androssowii involved in plant abiotic stress tolerance. BMC Plant Biology 12: 118.Google Scholar
Weising, K, Atkinson, RG and Gardner, RC (1995a) Genomic fingerprinting by microsatellite-primed PCR: a critical evaluation. PCR Methods and Applications 4: 249–255.Google Scholar
Weising, K, Nybom, H, Wolff, K and Meyer, W (1995b) DNA Fingerprinting in Plants and Fungi. Boca Raton, FL: CRC Press.Google Scholar
Wen, M, Wang, H, Xia, Z, Zou, M, Lu, C and Wang, W (2010) Development of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha curcas L. BMC Research Notes 3: 42–49.Google Scholar
Yang, GP, Saghai, MMA, Xu, CG, Zhang, Q and Biyashev, RM (1994) Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars. Molecular Genetics and Genomics 245: 187–194.Google Scholar
Zhang, L, Yuan, D, Yu, S, Li, Z and Cao, Y (2004) Preference of simple sequence repeats in coding and non-coding regions of Arabidopsis thaliana . Bioinformatics 20: 1081–1086.Google Scholar
Zhang, Q, Li, J, Zhao, Y, Korban, SS and Han, Y (2012) Evaluation of genetic diversity in Chinese wild apple species along with apple cultivars using SSR markers. Plant Molecular Biology Reporter 30: 539–546.Google Scholar
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