Genetic diversity, allelic variation and marker trait associations in gamma irradiated mutants of rice (Oryza sativa L.)

References

• Albani M, Wilkinson M. 1998. Inter simple sequence repeat polymerase chain reaction for the detection of somaclonal variation. Plant Breed. 117:573–575.
   Web of Science ®Google Scholar
• Ali A, Pan Y-B, Wang Q-N, Wang J-D, Chen J-L, Gao S-J. 2019. Genetic diversity and population structure analysis of Saccharum and Erianthus genera using microsatellite (SSR) markers. Sci Rep. 9(1):395.
   PubMed Web of Science ®Google Scholar
• Aliyu B, Ng N, Fawole I. 2000. Inheritance of pubescence in crosses between cowpea (Vigna unguiculata (L.) Walp) and Vigna rhomboidea Burtt. Davy. Niger J Genet. 15(1):9–14.
   Google Scholar
• Anderson J, Churchill G, Autrique J, Tanksley S, Sorrells M. 1993. Optimizing parental selection for genetic linkage maps. Genome. 36(1):181–186.
   PubMed Web of Science ®Google Scholar
• Aryanti A, Ishak I. 2018. Evaluation of drought tolerance rice mutant lines and identification using SSR markers. Vienna (Austria): International Atomic Energy Agency (IAEA).
   Google Scholar
• Ashikari M, Sasaki A, Ueguchi-Tanaka M, Itoh H, Nishimura A, Swapan D, Ishiyama K, Saito T, Kobayashi M, Khush GS, et al. 2002. Loss-of-function of a rice gibberellin biosynthetic gene, GA20 oxidase (GA20ox-2), led to the rice green revolution. Breeding Sci. 52:143–150.
   Web of Science ®Google Scholar
• Baloch A, Soomro A, Javed M, Bughio M, Mastoi N. 2002. Impact of reduced culm length on yield and yield parameters in rice. Asian J Plant Sci. 1(1):39–40.
   Google Scholar
• Becker J, Vos P, Kuiper M, Salamini F, Heun M. 1995. Combined mapping of AFLP and RFLP markers in barley. Mol Gen Genet. 249(1):65–73.
   PubMedGoogle Scholar
• Bharadwaj C, Tara Satyavathi C, Subramanyam D. 2001. Evaluation of different classificatory analysis methods in some rice (Oryza sativa) collections. Ind J Agricult Sci. 71(2):123–125.
   Web of Science ®Google Scholar
• Blair MW, Panaud O, McCouch SR. 1999. Inter-simple sequence repeat (ISSR) amplification for analysis of microsatellite motif frequency and fingerprinting in rice (Oryza sativa L.). Theor Appl Genet. 98(5):780–792.
   Web of Science ®Google Scholar
• Botstein D, White RL, Skolnick M, Davis RW. 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet. 32(3):314–331.
   PubMed Web of Science ®Google Scholar
• Chakravorty A, Ghosh P, Sahu P. 2012. Multivariate analysis of phenotypic diversity of landraces of rice of West Bengal. J Exp Agricult Int. 3(1):110–123.
   Google Scholar
• CIMMYT. 2005. Laboratory protocols: CIMMYT applied molecular genetics laboratory. 3rd ed. Mexico (D.F.): CIMMYT.
   Google Scholar
• FAO/IAEA-MVD. 2019. Food and agriculture organization of the United Nations/International atomic energy agency – mutant variety database. https://mvd.iaea.org/
   Google Scholar
• Field D, Wills C. 1996. Long, polymorphic microsatellites in simple organisms. Proc Biol Sci. 263(1367):209–215.
   PubMed Web of Science ®Google Scholar
• Futsuhara T, Kikuchi F. 1997. Inheritance of morphological characters. 2. Inheritance of dwarfism. In Sci Rice Plant. 3:300–308.
   Google Scholar
• Hameed K, Sadia B, Habib M, Ul Qamar Z, Awan FS. 2020. Detection of genetic divergence among putative ethyl methanesulfonate mutants of super basmati using microsatellite markers. Res Square. doi:https://doi.org/10.21203/rs.3.rs-34720/v1
   Google Scholar
• IRRI. 2019. World Rice Statistics. [accessed 2021 April 10]. http://ricestat.irri.org:8080/wrs
   Google Scholar
• Issac. SC. 2006. Line x tester analysis for earliness yield and its components in rice (Oryza sativa L.) for the Cauvery delta zone. Ind J Agricult Res. 40(4):255–261.
   Google Scholar
• Kalivas A, Xanthopoulos F, Kehagia O, Tsaftaris A. 2011. Agronomic characterization, genetic diversity and association analysis of cotton cultivars using simple sequence repeat molecular markers. Genet Mol Res. 10(1):208–217.
   PubMed Web of Science ®Google Scholar
• Kapil A, Rai PK, Shanker A. 2014. ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants. J Biol Databases Curation. 2014:bau107.
   PubMed Web of Science ®Google Scholar
• Kotaiah K, Rao C, Reddi N, Sarma Y. 1986. Mahalanobis's D2 and metroglyph analyses in mid-duration genotypes of rice. Ind J Agricult Sci. 56(3):151–156.
   Web of Science ®Google Scholar
• Kumar M, Kapil A, Shanker A. 2014. MitoSatPlant: mitochondrial microsatellites database of viridiplantae. Mitochondrion. 19 (Pt B):334–337.
   PubMed Web of Science ®Google Scholar
• Kumar V, Bhagwat S. 2009. SSR-based DNA fingerprinting and analysis of genetic diversity in radiation-induced mutants of rice (Oryza sativa L.). Proceedings of International Conference on Emerging Trends in Biotechnology; December 4–6, 2009; Banaras Hindu University, Varanasi, India.
   Google Scholar
• Kumari N, Kumar R, Kumar A. 2019. Genetic variability and association of traits in mutant lines of rice (Oryza sativa L.) for submergence tolerance. Curr J Appl Sci Technol. 33(2):1–7.
   Google Scholar
• Lagoda PJL. 2012. Chapter 11, Effects of radiation on living cells and plants. In: Shu QY, Forster BP, Nakagawa H, editors. Plant mutation breeding and biotechnology. Vienna, Austria: Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency; p. 123–134.
   Google Scholar
• Leon AP, Ramchander S, Kumar KK, Muthamilarasan M, Pillai MA. 2021. Assessment of efficacy of mutagenesis of gamma-irradiation in plant height and days to maturity through expression analysis in rice. PLOS One. 16(1):e0245603.
   PubMed Web of Science ®Google Scholar
• Levinson G, Gutman GA. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol. 4(3):203–221.
   PubMed Web of Science ®Google Scholar
• Li F, Shimizu A, Nishio T, Tsutsumi N, Kato H. 2019. Comparison and characterization of mutations induced by gamma-ray and carbon-ion irradiation in rice (Oryza sativa L.) using whole-genome resequencing. G3 Genes|Genomes|Genetics. 9(11):3743–3751.
   Web of Science ®Google Scholar
• Liang F, Xin X, Hu Z, Xu J, Wei G, Qian X, Yang J, He H, Luo X. 2011. Genetic analysis and fine mapping of a novel semidominant dwarfing gene LB4D in rice. J Integr Plant Biol. 53:312–323.
   PubMed Web of Science ®Google Scholar
• Lin Y, Wu S, Chen S, Tseng T, Chen C, Kuo S, Wu H, Hsing Y. 2011. Mapping of quantitative trait loci for plant height and heading date in two inter-subspecific crosses of rice and comparison across Oryza genus. Bot Stud. 52(1):1–4.
   Google Scholar
• Mackill DJ, Zhang Z, Redoña ED, Colowit PM. 1996. Level of polymorphism and genetic mapping of AFLP markers in rice. Genome. 39(5):969–977.
   PubMed Web of Science ®Google Scholar
• Maji A, Shaibu A. 2012. Application of principal component analysis for rice germplasm characterization and evaluation. J Plant Breed Crop Sci. 4(6):87–93.
   Google Scholar
• Monfared S, Mardi M, Hossienzadeh A, Naghavi M. 2008. Association analysis of important agronomic traits to retrotransposon markers SSAPs in durum wheat accessions. J Modern Genet. 3:29–36.
   Google Scholar
• Nagaraju J, Kathirvel M, Kumar RR, Siddiq EA, Hasnain SE. 2002. Genetic analysis of traditional and evolved Basmati and non-Basmati rice varieties by using fluorescence-based ISSR-PCR and SSR markers. Proc Natl Acad Sci USA. 99(9):5836–5841.
   PubMed Web of Science ®Google Scholar
• Oladosu Y, Rafii MY, Abdullah N, Malek MA, Rahim HA, Hussin G, Ismail MR, Latif MA, Kareem I. 2015. Genetic variability and diversity of mutant rice revealed by quantitative traits and molecular markers. Agrociencia. 49:249–266.
   Web of Science ®Google Scholar
• Paran I, Michelmore RW. 1993. Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Theor Appl Genet. 85(8):985–993.
   PubMed Web of Science ®Google Scholar
• Peng Y, Hu Y, Qian Q, Ren D. 2021. Progress and prospect of breeding utilization of green revolution gene SD1 in rice. Agriculture. 11:611.
   Web of Science ®Google Scholar
• Piao R, Chu SH, Jiang W, Yu Y, Jin Y, Woo MO, Lee J, Kim S, Koh HJ. 2014. Isolation and characterization of a dominant dwarf gene, D-h, in rice. PLOS One. 9:e86210.
   PubMed Web of Science ®Google Scholar
• Pookamana P. 1985. The use of mutant stock for semi-dwarf plant type and early maturity as cross-breeding materials in rice (coordinated programme on semi-dwarf mutants for rice improvement in Asia and the Pacific Region – RCA). Vienna (Austria): International Atomic Energy Agency (IAEA).
   Google Scholar
• Ramchander S, Ushakumari R, Arumugam Pillai M. 2015. Lethal dose fixation and sensitivity of rice varieties to gamma radiation. Ind J Agricult Res. 45(1):24–31.
   Google Scholar
• Roy JK, Bandopadhyay R, Rustgi S, Balyan HS, Gupta PK. 2006. Association analysis of agronomically important traits using SSR, SAMPL and AFLP markers in bread wheat. Curr Sci. 90(5):683–689.
   Web of Science ®Google Scholar
• Rutger J. 2009. The induced sd1 mutant and other useful mutant genes in modern rice varieties. In: Shu Q, editor. Induced plant mutations in the genomics era. Rome: Food and Agriculture Organization of the United Nations; p. 44–47.
   Google Scholar
• Sakamoto T, Miura K, Itoh H, Tatsumi T, Tanaka MU, Ishiyama K, Kobayashi M, Agrawal GK, Takeda S, Abe K, et al. 2004. An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiol. 134:1642–1653.
   PubMed Web of Science ®Google Scholar
• Sasaki A, Ashikari M, Tanaka MU, Itoh H, Nishimura A, Swapan D, Ishiyama K, Saito T, Kobayashi M, Khush GS, et al. 2002. Green revolution: a mutant gibberellin-synthesis gene in rice. Nature. 416(6882):701–702.
   PubMed Web of Science ®Google Scholar
• Sharma D, Das B, Kumar V, Tiwari A, Sahu P. 2017. Development of semidwarf and mid-late maturing Jawaphool mutant through the use of gamma radiation. Int J Pure Appl Biosci. 5(5):228–233.
   Google Scholar
• Songsri P, Suriharn B, Sanitchon J, Srisawangwong S, Kesmala T. 2011. Effects of gamma radiation on germination and growth characteristics of physic nut (Jatropha curcas L.). J Biol Sci. 11(3):268–274.
   Google Scholar
• Spielmeyer W, Ellis MH, Chandler PM. 2002. Semidwarf (sd- 1), “green revolution” rice, contains a defective gibberellin 20-oxidase gene. Proc Natl Acad Sci USA. 99(13):9043–9048.
   PubMed Web of Science ®Google Scholar
• Tautz D, Renz M. 1984. Simple sequences are ubiquitous repetitive components of eukaryotic genomes. Nucleic Acids Res. 12(10):4127–4138.
   PubMed Web of Science ®Google Scholar
• Thomas CM, Vos P, Zabeau M, Jones DA, Norcott KA, Chadwick BP, Jones JDG. 1995. Identification of amplified restriction fragment polymorphism (AFLP) markers tightly linked to the tomato Cf-9 gene for resistance to Cladosporium fulvum. Plant J. 8(5):785–794.
   PubMed Web of Science ®Google Scholar
• Tingey SV, del Tufo JP. 1993. Genetic analysis with random amplified polymorphic DNA markers. Plant Physiol. 101(2):349–352.
   PubMed Web of Science ®Google Scholar
• Tomita M, Ishimoto K. 2019. Rice novel semidwarfing gene d60 can be as effective as green revolution gene sd1. Plants. 8:464.
   Web of Science ®Google Scholar
• Tu Anh TT, Khanh TD, Dat TD, Xuan TD. 2018. Identification of phenotypic variation and genetic diversity in rice (Oryza sativa L.) mutants. Agriculture. 8(2):30.
   Web of Science ®Google Scholar
• Vieux EF, Kwok P-Y, Miller RD. 2002. Primer design for PCR and sequencing in high-throughput analysis of SNPs. BioTechniques. 32(6S):S28–S32.
   PubMed Web of Science ®Google Scholar
• Vos P, Hogers R, Bleeker M, Reijans M, Tvd L, Hornes M, Friters A, Pot J, Paleman J, Kuiper M, et al. 1995. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23(21):4407–4414.
   PubMed Web of Science ®Google Scholar
• Wenzl P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A. 2004. Diversity arrays technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA. 101(26):9915.
   PubMed Web of Science ®Google Scholar
• Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18(22):6531–6535.
   PubMed Web of Science ®Google Scholar
• Xu Y, Beachell H, McCouch SR. 2004. A marker-based approach to broadening the genetic base of rice in the USA. Crop Sci. 44(6):1947–1959.
   Web of Science ®Google Scholar
• Yoshihara R, Hase Y, Sato R, Takimoto K, Narumi I. 2010. Mutational effects of different LET radiations in rpsL transgenic Arabidopsis. Int J Radiat Biol. 86(2):125–131.
   PubMed Web of Science ®Google Scholar
• Zhang W, Wu L, Wu X, Ding Y, Li G, Li J, Weng F, Liu Z, Tang S, Ding C, et al. 2016. Lodging Resistance of Japonica rice (Oryza Sativa L.): morphological and anatomical traits due to top-dressing nitrogen application rates. Rice. 9(1):31.
   PubMed Web of Science ®Google Scholar
• Zhang YH, Bian XF, Zhang SB, Ling J, Wang YJ, Wei XY, Fang XW. 2016. Identification of a novel gain-of-function mutant allele, slr1-d5, of rice DELLA protein. J Integ Agri. 15:1441–1448.
   Web of Science ®Google Scholar
• Zhu J, Gale MD, Quarrie S, Jackson MT, Bryan GJ. 1998. AFLP markers for the study of rice biodiversity. Theor Appl Genet. 96(5):602–611.
   Web of Science ®Google Scholar