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Genetic Diversity and Conservation of Pterocarpus santalinus L.f. Through Molecular Approaches

  • B. K. Indu
  • Sudipta Kumar Mohonty
  • Savithri Bhat
  • Mallappa Kumara Swamy
  • M. Anuradha
Chapter

Abstract

The research and development of molecular tools in recent years has significantly influenced the tree improvement and conservation. Molecular markers, such as restriction fragment length polymorphism, random amplified polymorphic DNAs, amplified fragment length polymorphism, inter simple sequence repeat, single strand conformation polymorphism, single sequence repeats are indispensable in identifying elite lines, studying genetic diversity and phylogenetic relationships and utilizing genetic resources for crop improvement. The advancements in these DNA-based marker technologies along with high-throughput sequencing platforms have further geared plant biotechnology and have a unique role in selection of plants with desired characters. Genetic diversity though contributes to adaptability and sometimes hampers the morphological selection of plants particularly tree species. There are certain features which are expressed only after several years of juvenile growth. Pterocarpus santalinus, commonly known as ‘red sanders’, is one such tree which has elite and nonelite types. This is an endemic and endangered medicinally and commercially valued tree species with wavy grained wood and smooth grained wood impregnated with different levels of santalin. The commercial significance of this tree is attributed for its wavy grained nature with deep red coloured dye santalin. Thus, precise characterization and identification of selectable markers play a crucial role for an effective conservation of P. santalinus and sustainable utilization. Molecular studies and marker identification are widely used for varietal identification, documentation of genetic diversity and genetic mapping and also to know about phylogenetic relationships. This chapter presents a detailed review on the molecular studies of P. santalinus with an emphasis on genetic conservation and diversity.

Keywords

Red sanders Authentication Diversity DNA markers RAPD Sequencing 

Notes

Acknowledgements

The first author Indu BK thanks the Department of Science and Technology, Government of India, for the financial support under DST (WOS-A) scheme.

References

  1. Arif IA, Khan HA, Bahkali AH, Homaidan AA, Farhan AH, Al Sadoon M, Shobrak M (2011) DNA marker technology for wildlife conservation. Saudi J Biol Sci 18(3):219–225.  https://doi.org/10.1016/j.sjbs.2011.03.002PubMedPubMedCentralCrossRefGoogle Scholar
  2. Arokiyaraj S, Martin S, Perinbam K, Marie Arockianathan P, Beatrice V (2008) Free radical scavenging activity and HPTLC finger print of Pterocarpus santalinus L. – an in vitro study. Indian J Sci Technol 1(7):1–3Google Scholar
  3. Arunkumar AN, Joshi G (2014) Pterocarpus santalinus (Red Sanders) an endemic, endangered tree of India: current status, improvement and the future. J Trop For Environ 4:1–10Google Scholar
  4. Bal P, Panda PC, Mohapatra UB (2014) Genetic diversity and phylogenetic relationships in Pterocarpus species and its closely related genus Tipuana (Fabaceae) as revealed by RAPD and ISSR markers. Plant Sci Res 36(1&2):68–76Google Scholar
  5. Beckmann J, Soller M (1990) Towards a unified approach to genetic mapping of eukaryotes based on sequence tagged microsatellites. Biotechnology 8:930–932PubMedPubMedCentralGoogle Scholar
  6. Caetano-Anolles G, Bassam BJ, Gresshoff PM (1991) DNA amplification fingerprinting using very short arbitrary oligonucleotide primers. Biotechnology 9:553–557PubMedPubMedCentralGoogle Scholar
  7. Chaitanya PJ, Chandrashekar R, Bhavani NL (2014) Isolation of Pterocarpus santalinus L genomic DNA, for quality check and quantification with reference to Telangana region, Andhra Pradesh, India. Indian J Sci 8(19):21–24Google Scholar
  8. Chaitanya PJ, Chandrashekar R, Bhavani NL (2015) Analysis of genetic diversity in the populations of Pterocarpus santalinus L. detected by Random Amplified Polymorphic (RAPD) DNA markers. J Pharm Biol 5(1):1–6Google Scholar
  9. Collard BC, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans R Soc B Biol Sci 363(1491):557–572CrossRefGoogle Scholar
  10. Ender A, Schwenk K, Stadler T, Streit B, Schierwater B (1996) Rapid identification of microsatellites in Daphnia. Mol Ecol 5:437–447PubMedCrossRefGoogle Scholar
  11. Frankham R (1996) Relationship of genetic variation to population size in wildlife. Conserv Biol 10:1500–1508CrossRefGoogle Scholar
  12. Fukuoka S, Inoue T, Miyao A, Monna L, Zhong HS, Sasaki T, Minobe Y (1994) Mapping of sequence tagged sites in rice by single strand confirmation polymorphism. DNA Res 1:271–275PubMedCrossRefGoogle Scholar
  13. Ganal MW, Altmann T, Röder MS (2009) SNP identification in crop plants. Curr Opin Plant Biol 12(2):211–217PubMedCrossRefGoogle Scholar
  14. Gasser RB, Hu M, Chilton NB, Campbell BE, Jex AJ, Otranto D, Cafarchia C, Beveridge I, Zhu X (2006) Single-strand conformation polymorphism (SSCP) for the analysis of genetic variation. Nat Protoc 1(6):3121–3128PubMedCrossRefGoogle Scholar
  15. Ghareyazie B, Huang N, Second G, Bennet J, Kuhush GS (1995) Classification of rice germplasm I. Analysis using ALP and PCR-based RFLP. Theor Appl Genet 91:218–227PubMedCrossRefGoogle Scholar
  16. Grover A, Sharma PC (2016) Development and use of molecular markers: past and present. Crit Rev Biotechnol 36(2):290–302PubMedCrossRefGoogle Scholar
  17. Hearne CM, Ghosh S, Todd JA (1992) Microsatellites for linkage analysis of genetic traits. Trends Genet 8:288–294PubMedCrossRefGoogle Scholar
  18. Heywood VH (2014) An overview of in situ conservation of plant species in the Mediterranean. Flora Mediterr 24:5–24.  https://doi.org/10.7320/FlMedit24.005CrossRefGoogle Scholar
  19. Indu BK, Anuradha M (2018) Optimization of marker assisted technology for screening, selection and micropropagation of elite genotypes of Pterocarpus santalinus (Red Sandalwood). Project report submitted to Dept. Sci. Tech., Government of India (unpublished). http://online-wosa.gov.in:8080/wosa/wos/projectReceived_viewProjectRecieved.action (2014) 75
  20. IUCN (2014) IUCN Red list of threatened plants. Species survival commission IUCN. Gland, Switzerland and Cambridge, UKGoogle Scholar
  21. Jaisankar I, Subramani T, Velmurugan A, Singh AK (2017) Genetic diversity revealed among Rattan genotypes from Andaman and Nicobar based on RAPD and ISSR markers. For Res Eng Int J 1(2):45–50Google Scholar
  22. Jarwan AP, Wells RA (1989) Hypervariable minisatellites: recombinators or innocent bystanders? Trends Genet 5:367–371CrossRefGoogle Scholar
  23. Jhansi Rani S, Usha R (2013) Development of RAPD and specific scar markers for the identification of Pterocarpus santalinus L. J Cell Tissue Res 13(3):3809–3816Google Scholar
  24. Jiao L, Yu M, Wiedenhoeft AC, He T, Li J et al (2018) DNA barcode authentication and library development for the wood of six commercial Pterocarpus species: the critical role of Xylarium specimens. Sci Rep 8:1945.  https://doi.org/10.1038/s41598-018-20381-6PubMedPubMedCentralCrossRefGoogle Scholar
  25. Kalender R, Grob T, Regina M, Suoniemi A, Schulman A (1999) IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques. Theor Appl Genet 98:704–711CrossRefGoogle Scholar
  26. Karp A, Seberg O, Buiatti M (1996) Molecular techniques in the assessment of botanical diversity. Ann Bot 78:143–149CrossRefGoogle Scholar
  27. Karp AKS, Bhat KV, Ayad WG, Hodgkin T (1997) Molecular tools in plant genetic resources conservation: a guide to the technologies. International Plant Genetic Resources Institute, Rome. IPGRI Technical Bulletin No. 2Google Scholar
  28. Kundan KM, Fougat RS, Ballani AT, Thakur V, Jha Y, Bora M (2014) Potential and application of molecular markers techniques for plant genome analysis. Int J Pure Appl Biosci 2(1):169–188Google Scholar
  29. Lakshmi TBV, Sriramamurthy K (2013) Molecular phylogeny of Pterocarpus marsupium and Pterocarpus santalinus. World J Pharm Pharm Sci 2(6):6668–6681Google Scholar
  30. Leimu R, Mutikainen P, Koricheva J, Fischer M (2006) How general are positive relationships between plant population size, fitness and genetic variation? J Ecol 94:942–952CrossRefGoogle Scholar
  31. Lyamichev V, Brow MA, Dahlberg JE (1993) Structure specific endonucleotide cleavage of nucleic acids by eubacterial DNA polymerases. Science 260:778–783PubMedPubMedCentralCrossRefGoogle Scholar
  32. Lynch M, Walsh B (1998) Genetics and analysis of quantitative traits. Sinauer, SunderlandGoogle Scholar
  33. Meyer W, Mitchell TG, Freedmann EZ, Vilgalys R (1993) Hybridisation probes for conventional DNA fingerprinting used as a single primers in the polymerase chain reaction to distinguish strains of Cryptococcus neoformans. J Clin Biol 31:2274–2280Google Scholar
  34. Mishra KK, Fougat RS, Ballani A, Thakur V, Jha Y, Madhumati B (2014) Potential and application of molecular markers techniques for plant genome analysis. Int J Pure Appl Biosci 2(1):169–188Google Scholar
  35. Moraes VA, Haddad D, Craessaerts K, De Bock PJ, Swerts J, Vilain S, Aerts L, Overbergh L, Grünewald A, Seibler P, Klein C, Gevaert K, Verstreken P, De Strooper B (2014) PINK1 loss-of-function mutations affect mitochondrial complex I activity via NdufA10 ubiquinone uncoupling. Science 344(6180):203–207CrossRefGoogle Scholar
  36. Nadeem MA, Nawaz MA, Shahid MQ, Dgan Y, Comertpay G, Yildiz M, Hatipoglu R, Ahmad F, Alsaleh A, Labhne N, Ozkan H (2018) DNA molecular markers in plant breeding. Current status and recent advancements in genomic selection and genome editing. Biotechnol Biotechnol Equip 32(2):261–285CrossRefGoogle Scholar
  37. Ng WL, Tan SG (2015) Inter-simple sequence repeat (ISSR) markers: are we doing it right? ASM Sci J 9:30–39Google Scholar
  38. Nikiforov TT, Rendle RB, Goelet P, Rogers YH, Kotewicz ML, Anderson S, Trainor GL, Knapp MR (1994) Genetic bit analysis a solid phase method for typing single nucleotide polymorphisms. Nucleic Acids Res 22:4167–4175PubMedPubMedCentralCrossRefGoogle Scholar
  39. Orita M, Suzuki Y, Sekiya T, Hayashi K (1989) Rapid and sensitive detection of point mutations and DNA polymorphism using the polymerase chain reaction. Genomics 5:874–879PubMedPubMedCentralCrossRefGoogle Scholar
  40. Padmalatha K (2005) Ex-situ conservation molecular diversity of Pterocarpus santalinus L.f. and Rauvolfia serpentina (L.) Benth. ex Kurz. using RAPD markers: endangered medicinal plants. Ph.D. thesis, University of Hyderabad, HyderabadGoogle Scholar
  41. Padmalatha K, Prasad MNV (2007) Morphological and molecular diversity in Pterocarpus santalinus L.f – an endemic and endangered medicinal plant. Med Aromat Plant Sci Biotechnol 1(2):263–273Google Scholar
  42. Peñas J, Barrios S, Bobo-Pinilla J, Lorite J, Martínez-Ortega MM (2016) Designing conservation strategies to preserve the genetic diversity of Astragalus edulis Bunge, an endangered species from western Mediterranean region. Peer J 4:e1474.  https://doi.org/10.7717/peerj.1474PubMedCrossRefGoogle Scholar
  43. Perez-Collazos E, Segarra-Moragues JG, Catalan P (2008) Two approaches for the selection of relevant genetic units for conservation in the narrow European endemic steppe plant Boleum asperum (Brassicaceae). Biol J Linn Soc 94:341–354CrossRefGoogle Scholar
  44. Porth I, El-Kassaby YA (2014) Assessment of the genetic diversity in forest tree populations using molecular markers. Diversity. 4 6(2):283–295CrossRefGoogle Scholar
  45. Raju KK, Nagaraju A (1999) Geobotany of Red Sanders (Pterocarpus santalinus) – a case study from the south-eastern portion of Andhra Pradesh. Environ Geol 37(4):340–344CrossRefGoogle Scholar
  46. Rao R, Hoskela J (2001) Actions plan and research need to conserve forest genetic resources in Asia. In: Uma Shaanker R, Ganeshaiah KN et al (eds) Forest genetic resources: status, threats and conservation strategies. Oxford & IBH Publishing Company Private Limited, CalcuttaGoogle Scholar
  47. Rongwen J, Akkaya MS, Bhagwat AA, Lavi U, Cregan PV (1995) The use of microsatellite DNA markers for soybean genotype identification. Theor Appl Genet 90:43–48PubMedCrossRefGoogle Scholar
  48. Sarkar G, Cassady J, Bottema CDK, Sommer SS (1990) Characterization of polymerase chain reaction amplification of specific alleles. Anal Biochem 186:64–68PubMedPubMedCentralCrossRefGoogle Scholar
  49. Sun M, Wong KC, Lee JSY (1998) Reproduction biology and population genetic structure of Kandelia candel (Rhizophoraceae) a viviparous mangrove species. Am J Bot 85:1631–1637PubMedPubMedCentralCrossRefGoogle Scholar
  50. Swamy MK, Anuradha M (2011) Analysis of genetic variability in Patchouli cultivars (Pogostemon cablin Benth.) by using RAPD markers. Res Biotechnol 2(6):64–71Google Scholar
  51. Usha R, Jhansi Rani S, Geethaprasuna T (2013) Genetic relationship between quality and non quality wood of Pterocarpus santalinus (Red Sanders) an endemic tree species by using molecular markers. J Chem Pharm Sci 6(3):189–194Google Scholar
  52. Vieira ML, Santini L, Diniz AL, Munhoz CD (2016) Microsatellite markers: what they mean and why they are so useful. Genet Mol Biol 39(3):312–328PubMedPubMedCentralCrossRefGoogle Scholar
  53. Vipranarayana S, Prasad TNVKV, Rajinikanth A, Damodharam T (2013) Genomic DNA isolation and purification of two endemic medicinal plants (Pterocarpus santalinus Linn.f. & Pimpinella tirupatiensis Bal. & Subr.) of Seshachalam Hills, Tirumala. J Biol Life Sci 4(1):415–420Google Scholar
  54. Volis S, Blecher M (2010) Quasi in situ: a bridge between ex situ and in situ conservation of plants. Biodivers Conserv 19:2441–2454.  https://doi.org/10.1007/s10531-010-9849-2CrossRefGoogle Scholar
  55. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23(21):4407–4414PubMedPubMedCentralCrossRefGoogle Scholar
  56. Welsh J, McClelland M (1990) Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res 18(24):7213–7218PubMedPubMedCentralCrossRefGoogle Scholar
  57. Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV (1990) DNA polymorphism amplified by arbitrary primers are useful as genetic markers. Nucleic Acid Res 18:6531–6535PubMedCrossRefGoogle Scholar
  58. Williams MNV, Pande N, Nair S, Mohan M, Bennet J (1991) Restriction fragment length polymorphism analysis of polymerase chain reaction products amplified from mapped loci of rice (Oryza sativa L.) Genome DNA. Theor Appl Genet 82:489–498PubMedCrossRefGoogle Scholar
  59. Xu Y (2010) Molecular plant breeding. CABI, WallingfordCrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  • B. K. Indu
    • 1
  • Sudipta Kumar Mohonty
    • 2
  • Savithri Bhat
    • 3
  • Mallappa Kumara Swamy
    • 4
  • M. Anuradha
    • 2
  1. 1.Rishi FoundationBangaloreIndia
  2. 2.Department of BiotechnologyPadmashree Institute of Management and SciencesBangaloreIndia
  3. 3.BMS College of EngineeringBangaloreIndia
  4. 4.Department of Crop Science, Faculty of AgricultureUniversity Putra MalaysiaSerdangMalaysia

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