Skip to main content
SpringerLink
Log in

Genetic diversity analysis of specialty glutinous and low-amylose rice (Oryza sativa L.) landraces of Assam based on Wx locus and microsatellite diversity

  • Published:
Journal of Biosciences Aims and scope Submit manuscript

Abstract

The sticky rice of Assam is traditionally classified as bora (glutinous) and chokuwa (semi-glutinous) based on their stickiness after cooking. The Waxy (Wx) gene encodes for granule-bound starch synthase (GBSS) that controls the synthesis of amylose, which is a key determinant of rice end-use quality attributes. In this report, we analysed the level of variation in grain quality traits in a collection of bora and chokuwa cultivars, and examined the nucleotide diversity at the Wx locus of selected rice accessions to identify the possible cause of low-amylose in these rice cultivar groups. The Wx gene sequencing from 24 bora and chokuwa cultivars revealed several nucleotide variations that can explain the variation in the amylose phenotypes. The nucleotide polymorphisms in the downstream intron regions were similar to those reported in Bangladeshi Beruin cultivars. Among the Wx polymorphisms, the CTn microsatellite in exon 1 and G/T SNP in intron 1 (G/T-Int1) should be considered for marker assisted breeding involving bora cultivars. The Wx gene tree, classified the bora accessions possessing the G/T-Int1 SNP as japonicas. However, cluster analysis using microsatellite markers classified the bora and chokuwa cultivars as indica, and intermediate of indica-aus. The findings of this study supplemented our understanding on the evolution of the Wx gene under human selection. The results will assist plant breeders to effectively improve the bora and chokuwa landraces.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6

Similar content being viewed by others

References

  • Ayres NM, McClung AM, Larkin PD, Bligh HF, Jones CA and Park WD 1997 Microsatellites and a single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germplasm. Theor. Appl. Genet. 94 773–781

    CAS  Google Scholar 

  • Bao JS, Corke H and Sun M 2002 Microsatellites in starch-synthesizing genes in relation to starch physicochemical properties in waxy rice (Oryza sativa L.). Theor. Appl. Genet. 105 898–905

    CAS  PubMed  Google Scholar 

  • Biselli C, Cavalluzzo D, Perrini R, Gianinetti A, Bagnaresi P, Urso S, Orasen G, Desiderio F, et al. 2014 Improvement of marker-based predictability of Apparent Amylose Content in japonica rice through GBSSI allele mining. Rice 7 1

    PubMed  PubMed Central  Google Scholar 

  • Bligh HF, Larkin PD, Roach PS, Jones CA, Fu H and Park WD 1998 Use of alternate splice sites in granule-bound starch synthase mRNA from low-amylose rice varieties. Plant Mol. Biol. 38 407–415

    CAS  PubMed  Google Scholar 

  • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y and Buckler ES 2007 TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23 2633–2635

    CAS  PubMed  Google Scholar 

  • Cagampang GB, Perez CM and Juliano BO 1973 A gel consistency test for eating quality of rice. J. Sci. Food Agric. 24 1589–1594

    CAS  PubMed  Google Scholar 

  • Cai XL, Wang ZY, Xing YY, Zhang JL and Hong MM 1998 Aberrant splicing of intron 1 leads to the heterogeneous 5′ UTR and decreased expression of waxy gene in rice cultivars of intermediate amylose content. Plant J. 14 459–465

    CAS  PubMed  Google Scholar 

  • Chen MH, Bergman C, Pinson S ane Fjellstrom R 2008 Waxy gene haplotypes: Associations with apparent amylose content and the effect by the environment in an international rice germplasm collection. J. Cereal Sci. 47 536–545

    CAS  Google Scholar 

  • Choudhury BI, Khan ML and Dayanandan S 2014 Genetic relatedness among indigenous rice varieties in the Eastern Himalayan region based on nucleotide sequences of the Waxy gene. BMC Res. Notes 7 953

    PubMed  PubMed Central  Google Scholar 

  • Chung HJ, Liu Q, Lee L and Wei D 2011 Relationship between the structure, physicochemical properties and in vitro digestibility of rice starches with different amylose contents. Food Hydrocoll. 25 968–975

    CAS  Google Scholar 

  • Das B, Sengupta S, Parida SK, Roy B, Ghosh M, Prasad M and Ghose TK 2013 Genetic diversity and population structure of rice landraces from Eastern and North Eastern States of India. BMC Genet. 14 71

    CAS  PubMed  PubMed Central  Google Scholar 

  • Dobo M, Ayres N, Walker G and Park WD 2010 Polymorphism in the GBSS gene affects amylose content in US and European rice germplasm. J. Cereal Sci. 52 450–456

    CAS  Google Scholar 

  • Dutta L and Barua JN 1978 Nutrient composition of glutinous and non-glutinous rice varieties grown in Assam [India]. Ind. J. Agric. Sci. 48 610–613

    CAS  Google Scholar 

  • Fan CC, Yu XQ, Xing YZ, Xu CG, Luo LJ and Zhang Q 2005 The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population. Theor. Appl. Genet. 110 1445–1452

    CAS  PubMed  Google Scholar 

  • Fortune PM, Schierenbeck KA, Ainouche AK, Jacquemin J, Wendel JF and Aïnouche ML 2007 Evolutionary dynamics of Waxy and the origin of hexaploid Spartina species (Poaceae). Mol. Phylogenet. Evol. 43 1040–1055

    CAS  PubMed  Google Scholar 

  • Golomb L 1976 The origin, spread and persistence of glutinous rice as a staple crop in mainland Southeast Asia. J. Southeast Asian Stud. 71–5

  • Hammer O, Harper DA and Ryan PD 2001 Paleontological statistics software: package for education and data analysis. Palaeontol. Electron. 4 9

    Google Scholar 

  • Hirano HY, Eiguchi M and Sano Y 1998 A single base change altered the regulation of the Waxy gene at the posttranscriptional level during the domestication of rice. Mol. Biol. Evol. 15 978–987

    CAS  PubMed  Google Scholar 

  • Hirano HY and Sano Y 1991 Molecular characterization of the waxy locus of rice (Oryza sativa). Plant Cell Physiol. 32 989–997

    CAS  Google Scholar 

  • Hore DK 2005 Rice diversity collection, conservation and management in northeastern India. Genet. Resour. Crop Evol. 52 1129–1140

    Google Scholar 

  • Hori Y, Fujimoto R, Sato Y and Nishio T 2007 A novel wx mutation caused by insertion of a retrotransposon-like sequence in a glutinous cultivar of rice. Theor. Appl. Genet. 115 217–224

    CAS  PubMed  Google Scholar 

  • IBM Corp. Released 2016 IBM SPSS statistics for Macintosh, version 24.0. Armonk, New York: IBM Corp

  • Ingram AL and Doyle JJ 2003 The origin and evolution of Eragrostis tef (Poaceae) and related polyploids: evidence from nuclear waxy and plastid rps16. Am. J. Bot. 90 116–122

    CAS  PubMed  Google Scholar 

  • International Rice Research Institute 2013 Standard Evaluation System (SES) for Rice, 5th ed. IRRI, Manila

    Google Scholar 

  • Isshiki M, Morino K, Nakajima M, Okagaki RJ, Wessler SR, Izawa T and Shimamoto K 1998 A naturally occurring functional allele of the rice waxy locus has a GT to TT mutation at the 5′ splice site of the first intron. Plant J. 15 133–138

    CAS  PubMed  Google Scholar 

  • Jayamani P, Negrao S, Brites C and Oliveira MM 2007 Potential of Waxy gene microsatellite and single-nucleotide polymorphisms to develop japonica varieties with desired amylose levels in rice (Oryza sativa L.). J. Cereal Sci. 46 178–186

    CAS  Google Scholar 

  • Juliano B 1985 Criteria and test for rice grain quality; in Rice chemistry and technology. (Saint Paul: American Association of Cereal Chemists) pp. 443–513

  • Juliano BO, Perez CM, Blakeney AB, Castillo T, Kongseree N, Laignelet B, Lapis ET, Murty VV et al. 1981 International cooperative testing on the amylose content of milled rice. Starch-Stärke 33 157–162

    CAS  Google Scholar 

  • Juliano BO and Villareal CP 1993 Grain quality evaluation of world rices. IRRI: Manila, Philippines

    Google Scholar 

  • Juliano BO 1992 Structure and function of the rice grain and its fractions. Cereal Foods World 37 772–774

    CAS  Google Scholar 

  • Larkin PD and Park WD 2003 Association of waxy gene single nucleotide polymorphisms with starch characteristics in rice (Oryza sativa L.). Mol. Breed. 12 335–339

    CAS  Google Scholar 

  • Librado P and Rozas J 2009 DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25 1451–1452

    CAS  PubMed  Google Scholar 

  • Liu K and Muse SV 2005 PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21 2128–2129

    CAS  PubMed  Google Scholar 

  • Liu L, Ma X, Liu S, Zhu C, Jiang L, Wang Y, Shen Y, Ren Y et al. 2009 Identification and characterization of a novel Waxy allele from a Yunnan rice landrace. Plant Mol. Biol. 71 609–626

    CAS  PubMed  Google Scholar 

  • Mason-Gamer RJ, Weil CF and Kellogg EA 1998 Granule-bound starch synthase: structure, function, and phylogenetic utility. Mol. Biol. Evol. 15 1658–1673

    CAS  PubMed  Google Scholar 

  • McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R et al. 2002 Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9 199–207

    CAS  PubMed  Google Scholar 

  • Mikami I, Aikawa M, Hirano HY and Sano Y 1999 Altered tissue-specific expression at the Wx gene of the opaque mutants in rice. Euphytica 105 91–97

    CAS  Google Scholar 

  • Mikami I, Uwatoko N, Ikeda Y, Yamaguchi J, Hirano HY, Suzuki Y and Sano Y 2008 Allelic diversification at the wx locus in landraces of Asian rice. Theor. Appl. Genet. 116 979–989

    CAS  PubMed  Google Scholar 

  • Morishima HI, Sano YO and Oka H-I 1992 Evolutionary studies in cultivated rice and its wild relatives; in Oxford Surveys in Evolutionary Biology vol 8 (eds) D Futuyma, J Antonovics (New York: Oxford University Press) pp 135–184

    Google Scholar 

  • Olsen K, Caicedo A, Polato N, McClung A, McCouch S and Purugganan M 2006 Selection under domestication: Evidence for a sweep in the rice Waxy genomic region. Genetics 173 975–983

    CAS  PubMed  PubMed Central  Google Scholar 

  • Olsen KM and Purugganan MD 2002 Molecular evidence on the origin and evolution of glutinous rice. Genetics 162 941–950

    CAS  PubMed  PubMed Central  Google Scholar 

  • Peakall R and Smouse PE 2012 GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research – an update. Bioinformatics 28 2537–2539

    CAS  PubMed  PubMed Central  Google Scholar 

  • Prathepa P and Baimai V 2004 Variation of Wx microsatellite allele, waxy allele distribution and differentiation of chloroplast DNA in a collection of Thai rice (Oryza sativa L.). Euphytica 140 231–237

    Google Scholar 

  • Rathi S and Sarma RN 2012 Microsatellite diversity in indigenous glutinous rice landraces of Assam. Ind. J. Biotechnol. 11 23–29

    Google Scholar 

  • Roy S, Banerjee A, Mawkhlieng B, Misra AK, Pattanayak A, Harish GD, Singh SK, Ngachan SV et al. 2015 Genetic diversity and population structure in aromatic and quality rice (Oryza sativa L.) landraces from Northeastern India. PloS one 10 e0129607

    PubMed  PubMed Central  Google Scholar 

  • Roy S, Marndi BC, Mawkhlieng B, Banerjee A, Yadav RM, Misra AK and Bansal KC 2016 Genetic diversity and structure in hill rice (Oryza sativa L.) landraces from the Northeastern Himalayas of India. BMC Genet. 17 107

    PubMed  PubMed Central  Google Scholar 

  • Sano Y, Katsumata M and Amano E 1985 Correlations between the amounts of amylose and Wx protein in rice endosperm. SABRAO J. 17 121–127

    Google Scholar 

  • Shahid S, Begum R, Razzaque S and Seraj ZI 2016 Variability in amylose content of Bangladeshi rice cultivars due to unique SNPs in Waxy allele. J. Cereal Sci. 71: 1–9

    CAS  Google Scholar 

  • Shaptadvipa B and Sarma RN 2009 Study on apparent amylose content in context of polymorphism information content along with indices of genetic relationship derived through SSR markers in Birain, Bora and Chokuwa groups of traditional glutinous rice (Oryza sativa L.) of Assam. Asian J. Biochem. 4 45–54.

    CAS  Google Scholar 

  • Shu QY, Wu DX, Xia YW, Gao MW, Ayres NM, Larkin PD and Park WD 1999 Microsatellites polymorphism on the waxy gene locus and their relationship to amylose content in indica and japonica rice, Oryza sativa L. Acta Genet. Sin. 26 350–358

    CAS  Google Scholar 

  • Sridharan V and Singh RA 2007 conditional role of U2AF in splicing of introns with unconventional polypyrimidine tracts. Mol. Cell Biol. 27 7334–7344

    CAS  PubMed  PubMed Central  Google Scholar 

  • Swofford DL 1998 PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods) (Sunderland: Sinauer Associates)

    Google Scholar 

  • Tian Z, Qian Q, Liu Q, Yan M, Liu X, Yan C, Liu G, Gao Z et al. 2009 Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc. Natl. Acad. Sci. USA 106 21760–21765

    CAS  PubMed  Google Scholar 

  • Wanchana S, Toojinda T, Tragoonrung S and Vanavichit A 2003 Duplicated coding sequence in the waxy allele of tropical glutinous rice (Oryza sativa L.). Plant Sci. 165 1193–1199

    CAS  Google Scholar 

  • Wang ZY, Zheng FQ, Shen GZ, Gao JP, Snustad DP, Li MG, Zhang JL and Hong MM 1995 The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J. 7 613–622

    CAS  PubMed  Google Scholar 

  • Watabe T 1967 Glutinous rice in northern Thailand (Kyoto: CSEAS, Kyoto University)

    Google Scholar 

  • Wei-Hua Q, You-Tao C, Rong-Sheng W, Xin W, Li-Rong C, Wan-Xia Z and Qing-Wen Y 2012 Nucleotide diversity in Waxy gene and validation of single nucleotide polymorphism in relation to amylose content in Chinese microcore rice germplasm. Crop Sci. 52 1689–1697

    Google Scholar 

Download references

Acknowledgements

The authors thank Dr. N. Umakanta, ICAR-RC for NEHR, Umiam, Meghalaya, for helping with the association analysis.

Author information

Authors and Affiliations

  1. Central Rainfed Upland Rice Research Station, ICAR-NRRI, Hazaribag, Jharkhand, 825301, India

    Somnath Roy, Amrita Banerjee & Nimai Prasad Mandal

  2. ICAR-National Rice Research Institute, Cuttack, Odisha, India

    Nabaneeta Basak, Torit Baran Bagchi & Bhaskar Chandra Patra

  3. Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, 110 001, India

    Anup Kumar Misra

  4. ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110 012, India

    Sanjeev Kumar Singh & Ranbir Singh Rathi

  5. ICAR-Vivekananda Parvatiya Krishi Anusandha Sansthan, Almora, Uttarakhand, 263 601, India

    Arunava Pattanayak

  6. ICAR-National Bureau of Plant Genetic Resources, Regional Station, Umiam, Meghalaya, 793 103, India

    Somnath Roy, Anup Kumar Misra & Sanjeev Kumar Singh

  7. ICAR Research Complex for NEH Region, Umiam, Meghalaya, 793 103, India

    Amrita Banerjee & Arunava Pattanayak

Authors
  1. Somnath Roy
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Amrita Banerjee
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nabaneeta Basak
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Torit Baran Bagchi
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Nimai Prasad Mandal
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Bhaskar Chandra Patra
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Anup Kumar Misra
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Sanjeev Kumar Singh
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Ranbir Singh Rathi
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Arunava Pattanayak
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Somnath Roy.

Additional information

Corresponding editor: Ashis Kumar Nandi.

Corresponding editor: Ashis Kumar Nandi

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Roy, S., Banerjee, A., Basak, N. et al. Genetic diversity analysis of specialty glutinous and low-amylose rice (Oryza sativa L.) landraces of Assam based on Wx locus and microsatellite diversity. J Biosci 45, 86 (2020). https://doi.org/10.1007/s12038-020-00059-w

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s12038-020-00059-w

Keywords

Search

Navigation