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Studies on genetic variability and identification of sequence variations among cultivars and landraces of rice (Oryza sativa L.) for apparent amylose and amylopectin contents

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Abstract

Starch is the main component of cereals like rice. It is mainly composed of amylose and amylopectin. Apparent amylose content (AAC) in rice grain controlled by granule bound starch synthase enzyme (GBSS) is the key factor determining cooking and processing quality. The present study has been attempted to decipher the genetic variability among 36 cultivars of rice for agro-morphological parameters along with AAC and amylopectin content, to determine the extent of association among yield and its contributing characters and to detect the sequence variations among the cultivars having differential AAC. Results revealed the presence of adequate genetic variability among the tested rice cultivars for yield attributing traits, as well as their AAC and amylopectin content. Most of the yield attributing traits was under control of additive genes. Genetic diversity study of the tested rice cultivars grouped them into four clusters. The nucleotide sequence and derived amino acid sequence variations among the region spanning between the intron 7 and exon 10 of GBSSI allele from the rice cultivars differing in AAC detected the presence of several SNPs, deletions and insertions within the tested exon and intron regions. Presence of methionine (M) or isoleucine (I) at 308 aa position and presence of phenylalanine (F) at 425 or 434 aa position of GBSSI protein across the tested rice cultivars can be exploited in marker-assisted breeding programme for developing high yielding rice cultivars with proper grain quality as per consumer’s preference.

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References

  • Adjah KL, Abe A, Adetimirin VO, Asante MD (2020) Genetic variability, heritability and correlations for milling and grain appearance qualities in some accessions of rice (Oryza sativa L.). Physiol Mol Biol Plants 26:1309–1317

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ahuja S, Malhotra PK, Bhatia VK, Prasad R (2008) Statistical package for agricultural research (SPAR 2). J Ind Soc Agric Stat 62:65–74

    Google Scholar 

  • Akinwale MG, Gregorio G, Nwilene F, Akinyele BO, Ogunbayo SA, Odiyi AC (2011) Heritability and correlation coefficient analysis for yield and its components in rice (Oryza sativa L.). Afr J Plant Sci 5(3):207–212

    Google Scholar 

  • Ayres NM, McClung AM, Larkin PD, Bligh HFJ, Jones CA, Park WD (1997) Microsatellites and a single-nucleotide polymorphism differentiate apparent amylose classes in an extended pedigree of US rice germ plasm. Theor Appl Genet 94(6–7):773–781

    Article  CAS  Google Scholar 

  • Biselli C, Daniela C, Rosaria P, Alberto G, Paolo B, Simona U, Gabriele O et al (2014) Improvement of marker-based predictability of apparent amylose content in japonica rice through GBSSI allele mining. Rice. https://doi.org/10.1186/1939-8433-7-1

    Article  PubMed  PubMed Central  Google Scholar 

  • Biswas T, Das A, Bhattacharyya S (2012) Microsatellite marker-based diversity analysis for submergence tolerance in some Bengal landraces of rice (Oryza sativa L.). J Trop Agril 50(1):67–71

    CAS  Google Scholar 

  • Carrijo DR, Lundy ME, Linquist BA (2017) Rice yields and water use under alternate wetting and drying irrigation: a meta-analysis. Field Crops Res 203:173–180. https://doi.org/10.1016/j.fcr.2016.12.002

    Article  Google Scholar 

  • Chen MH, Bergman C, Pinson S, 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(3):536–545

    Article  CAS  Google Scholar 

  • Choudhury B, Khan ML, Dayanandan S (2013) Genetic structure and diversity of indigenous rice (Oryza sativa) varieties in the Eastern Himalayan region of Northeast India. Springer plus 2(1):228

    Article  PubMed  PubMed Central  Google Scholar 

  • Das A, Pramanik K, Sharma R, Gantait S, Banerjee J (2019) In-silico study of biotic and abiotic stress-related transcription factor binding sites in the promoter regions of rice germin-like protein genes. PLoS ONE 14(2):e0211887

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deng N, Ling X, Sun Y, Zhang C, Fahad S, Peng S et al (2015) Influence of temperature and solar radiation on grain yield and quality in irrigated rice system. Eur J Agron 64:37–46

    Article  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  • FAO (2018) FAOSTAT database. Rome: FAO. http://www.fao.org/faostat/en/#data/QC/

  • Hanashiro I, Itoh K, Kuratomi Y, Yamazaki M, Igarashi T, Matsugasako JI, Takeda Y (2008) Granule-bound starch synthase I is responsible for biosynthesis of extra-long unit chains of amylopectin in rice. Plant Cell Physiol 49(6):925–933

    Article  CAS  PubMed  Google Scholar 

  • Hirose T, Terao T (2004) A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.). Planta 220(1):9–16. https://doi.org/10.1007/s00425-004-1314-6 (Epub 2004 Jun 30 PMID: 15232694)

    Article  CAS  PubMed  Google Scholar 

  • Hizukuri S, Abe JI, Hanashiro I (2006) Starch: analytical aspects. Food Sci Technol 159:305

    CAS  Google Scholar 

  • Jennings PR (1979) Rice improvement, International Rice Research Institute, Los Baños, Laguna, Philippines

  • Johnson HW, Robinson HF, Comstock RE (1955) Estimates of genetic and environmental variability in soybeans. Agron J 47(7):314–318

    Article  Google Scholar 

  • Juliano BO, Perez CM, Blakeney AB, Castillo T, Kongseree N, Laignelet B et al (1981) International cooperative testing on the amylose content of milled rice. Starch Stärke 33(5):157–162

    Article  CAS  Google Scholar 

  • Kong X, Zhu P, Sui Z, Bao J (2015) Physicochemical properties of starches from diverse rice cultivars varying in apparent amylose content and gelatinisation temperature combinations. Food Chem 172:433–440

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Chauhan MP, Tomar A, Kasana RK, Kumar N (2018) Correlation and path coefficient analysis in rice (Oryza sativa L.). Pharma Innov J 7(6):20–26

    Google Scholar 

  • Mahalanobis PC (1963) On the generalized distance in statistics. Proc Natl Acad Sci (india) 2:49–55

    Google Scholar 

  • Nakamura Y, Ono M, Ozaki N (2019) Structural features of α-glucans in the very early developmental stage of rice endosperm. J Cereal Sci 89:102778

  • Nirmaladevi G, Padmavathi G, Kota S, Babu VR (2015) Genetic variability, heritability and correlation coefficients of grain quality characters in rice (Oryza sativa L.). Sabrao J Breed Genet 47(4):424–433

    Google Scholar 

  • Okagaki RJ (1992) Nucleotide sequence of a long cDNA from the rice waxy gene. Plant Mol Biol 19:513. https://doi.org/10.1007/BF00023402

    Article  CAS  PubMed  Google Scholar 

  • Pandey MK, Rani NS, Madhav MS, Sundaram RM, Varaprasad GS, Sivaranjani AK, Bohra A, Kumar GR, Kumar A (2012) Different isoforms of starch-synthesizing enzymes controlling amylose and amylopectin content in rice (Oryza sativa L.). Biotechnol Adv 30(6):1697–1706. https://doi.org/10.1016/j.biotechadv.2012.08.011

    Article  CAS  PubMed  Google Scholar 

  • PPV & FRA, Protection of Plant Varieties and Farmer’s Rights Authority (PPV&FRA) (2007) Specific DUS test guidelines for twelve notified crops – rice (Oryza sativa L.). Plant Var J India 1:151–169

    Google Scholar 

  • Raigond P, Ezekiel R, Raigond B (2015) Resistant starch in food: A review. J Sci Food Agric 95(10):1968–1978

    Article  CAS  PubMed  Google Scholar 

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

    Google Scholar 

  • Sarawgi AK, Subba Rao LV, Parikh M, Sharma B, Ojha GC (2013) Assessment of variability of Rice (Oryza sativa L.) germplasm using agro-morphological characterization. J Rice Res 6(1):14–19

    Google Scholar 

  • Singh RK, Chaudhary BD (1979) Biometrical methods in quantitative genetic analysis. Kalyani Publishers, Dudhiano

    Google Scholar 

  • Tian Z, Qian Q, Liu Q, Yan M, Liu X, Yan C et al (2009) Allelic diversities in rice starch biosynthesis leadled to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci 106(51):21760–21765

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Veni B, Krishna D, Sandeep R, Rama Rao CV, Sridevi P (2020) Characterization of colored rice genotypes for nutritional traits and functional properties. Extended Summ 2020:63

    Google Scholar 

  • Vrinten PL, Nakamura T (2000) Wheat granule-bound starch synthase I and II are encoded by separate genes that are expressed in different tissues. Plant Physiol 122:255–264

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang W, Wei X, Jiao G, Chen W, Wu Y, Sheng Z, Hu S, Xie L, Wang J, Tang S, Hu P (2020) GBSS-binding protein, encoding a CBM48 domain-containing protein, affects rice quality and yield. J Integr Plant Biol 62(7):948–966. https://doi.org/10.1111/jipb.12866 (Epub 2019 Oct 18 PMID: 31449354)

    Article  CAS  PubMed  Google Scholar 

  • Zhao C, Zhao L, Zhao Q et al (2020) Genetic dissection of eating and cooking qualities in different subpopulations of cultivated rice (Oryza sativa L.) through association mapping. BMC Genet 21:119. https://doi.org/10.1186/s12863-020-00922-7

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou H, Wang L, Liu G, Meng X, Jing Y, Shu X, Kong X, Sun J, Yu H, Smith SM, Wu D (2016) Critical roles of soluble starch synthase SSIIIa and granule-bound starch synthase Waxy in synthesizing resistant starch in rice. Proc Natl Acad Sci 113(45):12844–12849

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Author notes

  1. Moumita Ghosh and Joydeep Banerjee have contributed equally to this work.

Authors and Affiliations

  1. Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, Nadia, West Bengal, 741252, India

    Moumita Ghosh, Sudip Bhattacharya, Krishnendu Pramanik, Anita Roy & Arpita Das

  2. Department of Agricultural and Food Engineering, Indian Institute of Technology, Kharagpur, West Bengal, 721302, India

    Joydeep Banerjee

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  1. Moumita Ghosh
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  2. Joydeep Banerjee
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  3. Sudip Bhattacharya
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  4. Krishnendu Pramanik
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  5. Anita Roy
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Correspondence to Arpita Das.

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Communicated by A. Das.

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Ghosh, M., Banerjee, J., Bhattacharya, S. et al. Studies on genetic variability and identification of sequence variations among cultivars and landraces of rice (Oryza sativa L.) for apparent amylose and amylopectin contents. CEREAL RESEARCH COMMUNICATIONS 50, 1085–1094 (2022). https://doi.org/10.1007/s42976-021-00231-4

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  • DOI: https://doi.org/10.1007/s42976-021-00231-4

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