Advertisement

Euphytica

, 215:149 | Cite as

Integrating marker-assisted selection and doubled haploidy for rapid introgression of semi-dwarfing and blast resistance genes into a Basmati rice variety ‘Ranbir Basmati’

  • Prabhudutt Samal
  • T. D. Pote
  • S. Gopala Krishnan
  • Ashok K. Singh
  • R. K. Salgotra
  • R. RathourEmail author
Article
  • 34 Downloads

Abstract

Ranbir Basmati, an early maturing pure line selection of traditional Basmati 370, is widely cultivated Basmati variety in the Indian state of Jammu and Kashmir. The variety is tall statured, prone to lodging and highly susceptible to rice blast. The present study was carried out for genetic improvement of Ranbir Basmati for semi dwarf stature and resistance to blast by introgressing semi-dwarfing gene, sd1, and blast resistance gene, Pi9 from an improved Basmati rice variety, Pusa Basmati 1637 (PB 1637).The selfed progenies of two superior BC2F1 recombinants of the cross Ranbir Basmati/PB 1637 showing maximum recovery of recurrent parent genome and phenome were analyzed with gene-based markers to select plants homozygous for both Pi9 and sd1. These plants were processed via anther culture to produce homozygous doubled haploid (DH) lines. All the anther culture derived DH plants were short-statured compared to Ranbir Basmati and exhibited high level of resistance to blast. The analysis of yield and its component traits revealed the presence of superior transgressive segregants for various traits namely, effective tillers, grains per panicle and yield per plant. Combined use of marker-assisted selection and anther culture ensured speedy conversion of Ranbir Basmati into semi-dwarf genotypes with in-built resistance to rice blast. The study demonstrated the utility of anther culture as an adjunct to marker-assisted backcross breeding schemes for instant elimination of the residual background heterozygosity of the selected recombinants.

Keywords

Basmati Pi9 sd1 Blast resistance Semi-dwarfing Anther culture 

Notes

Acknowledgements

The corresponding author gratefully acknowledges the financial support (San No. BT/PR10966/AGII/106/960/2014) received from the Department of Biotechnology, Govt. of India for the work reported in this paper.

Author’s contribution

RR conceived and designed the experiments and wrote the final manuscript. PS performed MAS and anther culture experiments.TP performed crossing and background analysis. SGK and AKS helped in grain quality analysis. SGK, AKS and RKS also read and edited the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10681_2019_2473_MOESM1_ESM.pptx (1.2 mb)
Supplementary Fig. 1 Comparison of plant height of sd-1 homozygous doubled haploids with parental genotypes Ranbir Basmati and PB 1637 (PPTX 1194 kb)

References

  1. Amante-Bordeos A, Sitch LA, Nelson R, Dalmacio RD, Oliva NP, Aswidinnoor H, Leung H (1992) Transfer of bacterial blight and blast resistance from the tetraploid wild rice Oryza minuta to cultivated rice, Oryza sativa. Theor Appl Genet 84(4):345–354PubMedCrossRefGoogle Scholar
  2. Amarawathi Y, Singh R, Singh AK, Singh VP, Mohapatra T, Sharma TR, Singh NK (2008) Mapping of quantitative trait loci for basmati quality traits in rice (Oryza sativa L.). Mol Breed 21(1):49–65CrossRefGoogle Scholar
  3. APEDA (2017) Basmati acreage and production. Basmati export development foundation, agricultural and processed food products export development authority (APEDA), New Delhi, Report–6. p 4Google Scholar
  4. Basavaraj SH, Singh VK, Singh A, Singh A, Singh A, Anand D, Yadav S, Ellur RK, Singh D, Krishnan SG, Nagarajan M (2010) Marker-assisted improvement of bacterial blight resistance in parental lines of Pusa RH10, a superfine grain aromatic rice hybrid. Mol Breed 26(2):293–305CrossRefGoogle Scholar
  5. Bhatia D, Sharma R, Vikal Y, Mangat GS, Mahajan R, Sharma N, Lore JS, Singh N, Bharaj TS, Singh K (2011) Marker-assisted development of bacterial blight resistant, dwarf, and high yielding versions of two traditional basmati rice cultivars. Crop Sci 51(2):759–770CrossRefGoogle Scholar
  6. Bishnoi U, Jain RK, Rohilla JS, Chowdhury VK, Gupta KR, Chowdhury JB (2000) Anther culture of recalcitrant indica × Basmati rice hybrids. Euphytica 114(2):93–101CrossRefGoogle Scholar
  7. Chen CC, Wu YH (1983) Segmentations in microspores of rice during anther culture. Proc Natl Sci Counc ROC 7B:151–157Google Scholar
  8. Chu CC, Wang CS, Sun CS, Hsu C, Yin KC, Chu CY, Bi FY (1975) Establishment of an efficient medium for anther culture of rice through comparative experiments on the nitrogen sources. Sci Sin 18(5):659–668Google Scholar
  9. Ellis MH, Spielmeyer W (2002) Perfect markers for the semi dwarfing gene sd-1 in rice. IRRI Notes 27(2):13–14Google Scholar
  10. Ellur RK, Khanna A, Yadav A, Pathania S, Rajashekara H, Singh VK, Krishnan SG, Bhowmick PK, Nagarajan M, Vinod KK, Prakash G (2016) Improvement of Basmati rice varieties for resistance to blast and bacterial blight diseases using marker assisted backcross breeding. Plant Sci 242:330–341PubMedCrossRefGoogle Scholar
  11. Germana MA (2011) Anther culture for haploid and doubled haploid production. Plant Cell, Tissue Organ Cult 104(3):283–300CrossRefGoogle Scholar
  12. Glaszmann JC (1987) Isozymes and classification of Asian rice varieties. Theor Appl Genet 74(1):21–30PubMedCrossRefGoogle Scholar
  13. Guiderdoni E, Galinato E, Luistro J, Vergara G (1992) Anther culture of tropical japonica × indica hybrids of rice (Oryza sativa L.). Euphytica 62(3):219–224CrossRefGoogle Scholar
  14. Hedden P (2003) The genes of the green revolution. Trends Genet 19(1):5–9PubMedCrossRefGoogle Scholar
  15. Imam J, Alam S, Mandal NP, Variar M, Shukla P (2014) Molecular screening for identification of blast resistance genes in North East and Eastern Indian rice germplasm (Oryza sativa L.) with PCR based makers. Euphytica 196(2):199–211CrossRefGoogle Scholar
  16. IRRI (2002) Standard evaluation system for rice. International Rice Research Institute, ManilaGoogle Scholar
  17. Juliano BO (1971) A simplified assay for milled rice amylose. Cereal Sci Today 16(10):334–340Google Scholar
  18. Kaushal L, Balachandran SM, Ulaganathan K, Shenoy V (2014) Effect of culture media on improving anther culture response of rice (Oryza sativa L.). Int J Agric Innov Res 3(1):218–224Google Scholar
  19. Khanna A, Sharma V, Ellur RK, Shikari AB, Krishnan SG, Singh UD, Prakash G, Sharma TR, Rathour R, Variar M, Prashanthi SK (2015) Development and evaluation of near-isogenic lines for major blast resistance gene(s) in Basmati rice. Theor Appl Genet 128(7):1243–1259PubMedCrossRefGoogle Scholar
  20. Khush GS (1995) Breaking the yield frontier of rice. Geo Journal 35(3):329–332Google Scholar
  21. Kumar I, Khush GS (1986) Genetics of amylose content in rice (Oryza sativa L.). J Genet 65(2):1–11CrossRefGoogle Scholar
  22. Lanceras JC, Huang Z, Naivikul O, Vanavichit A, Ruanjaichon V, Tragoonrung S (2000) Mapping of genes for cooking and eating qualities in Thai Jasmine rice (KDML105). DNA Res 7(2):93–101PubMedCrossRefGoogle Scholar
  23. Lee YT, Lim MS, Kim HS, Shin HT, Kim CH, Bae SH, Cho CI (1989) An anther-derived new high quality rice variety with disease and insect resistance” Hwacheongbyeo”. Res Rep Rural Dev Admin-Rice 31(2):27–34Google Scholar
  24. Little RR, Hilder GB, Dawson EH (1958) Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chem 35(2):111–126Google Scholar
  25. Lorieux M, Petrov M, Huang N, Guiderdoni E, Ghesquiere A (1996) Aroma in rice: genetic analysis of a quantitative trait. Theor Appl Genet 93(7):1145–1151PubMedCrossRefGoogle Scholar
  26. Luo Y, Yin Z (2013) Marker-assisted breeding of Thai fragrance rice for semi-dwarf phenotype, submergence tolerance and disease resistance to rice blast and bacterial blight. Mol Breed 32(3):709–721CrossRefGoogle Scholar
  27. Ma J, Lei C, Xu X, Hao K, Wang J, Cheng Z, Ma X, Ma J, Zhou K, Zhang X, Guo X, Wu F, Lin Q, Wang C, Zhai H, Wang H, Wan J (2015) Pi-64, encoding a novel CC-NBS-LRR protein, confers resistance to leaf and neck blast in rice. Mole Plant Microbe Interact 28(5):558–568CrossRefGoogle Scholar
  28. Mackill DJ, Bonman JM (1992) Inheritance of blast resistance in near-isogenic lines of rice. Phytopathology 82(7):746–749CrossRefGoogle Scholar
  29. Monna L, Kitazawa N, Yoshino R, Suzuki J, Masuda H, Maehara Y, Tanji M, Sato M, Nasu S, Minobe Y (2002) Positional cloning of rice semi dwarfing gene, sd-1: rice “green revolution gene” encodes a mutant enzyme involved in gibberellin synthesis. DNA Res 9(1):11–17PubMedCrossRefGoogle Scholar
  30. Murai M, Takamure I, Sato S, Tokutome T, Sato Y (2002) Effects of the dwarfing gene originating from ‘Dee-geo-woo-gen’ on yield and its related traits in rice. Breed Sci 52(2):95–100CrossRefGoogle Scholar
  31. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15(3):473–497CrossRefGoogle Scholar
  32. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8(19):4321–4325PubMedPubMedCentralCrossRefGoogle Scholar
  33. 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):5836–5841PubMedCrossRefGoogle Scholar
  34. Patil VD, Nerkar YS, Misal MB, Harkal SR (1997) Parag 401, a semi-dwarf rice variety developed through anther culture. IRRI Notes 22(2):1Google Scholar
  35. Pauk J, Janeso M, Simon-Kiss I (2009) Rice doubled haploids and breeding. In: Touraev A, Forster BP, Jain SM (eds) Advances in haploid production in higher plants. Springer, Berlin, pp 189–197CrossRefGoogle Scholar
  36. Pinthus MJ (1974) Lodging in wheat, barley, and oats: the phenomenon, its causes, and preventive measures. Adv Agron 25:209–263CrossRefGoogle Scholar
  37. Qu S, Liu G, Zhou B, Bellizzi M, Zeng L, Han B, Wang GL (2006) The broad-spectrum blast resistance gene Pi-9 encodes a nucleotide-binding site–leucine-rich repeat protein and is a member of a multigene family in rice. Genetics 172(3):1901–1914PubMedPubMedCentralCrossRefGoogle Scholar
  38. Raina SK, Zapata FJ (1997) Enhanced anther culture efficiency of indica rice (Oryza sativa L.) through modification of the culture media. Plant Breed 116(4):305–315CrossRefGoogle Scholar
  39. Raina SK, Irfan ST (1998) High-frequency embryogenesis and plantlet regeneration from isolated microspores of Indica rice. Plant Cell Rep 17:957–962PubMedCrossRefGoogle Scholar
  40. Raina SK, Sathish P, Sarma KS (1987) Plant regeneration from in vitro cultures of anthers and mature seeds of rice (Oryza sativa L.) cv. Basmati-370. Plant Cell Rep 6(1):43–45PubMedCrossRefGoogle Scholar
  41. Rajpurohit D, Kumar R, Kumar M, Paul P, Awasthi A, Basha PO, Puri A, Jhang T, Singh K, Dhaliwal HS (2011) Pyramiding of two bacterial blight resistance and a semi dwarfing gene in Type 3 Basmati using marker-assisted selection. Euphytica 178(1):111–126CrossRefGoogle Scholar
  42. Rani NS, Singh RK (2003) Efforts on aromatic rice improvement in India. In: Singh RK, Singh US (eds) A treatise on the scented rices of India. Kalyani Publishers, New Delhi, pp 23–72Google Scholar
  43. Rathour R, Singh BM, Sharma TR (2004) Population structure of Magnaporthe grisea from north western Himalayas and its implications for blast resistance breeding of rice. J Phytopathol 152(5):304–312CrossRefGoogle Scholar
  44. Rathour R, Katoch A, Kusum Kaushik RP, Sharma TR (2011) Virulence analysis of Magnaporthe oryzae for resistance gene deployment in north-western Himalayas. Plant Dis Res 26(2):183Google Scholar
  45. Rathour R, Krishnan SG, Khanna A, Dhatwalia S, Kachra A, Sharma TR, Singh AK (2016) Development and validation of co-dominant gene based markers for Pi-9, a gene governing broad-spectrum resistance against blast disease in rice. Mol Breed 36(12):168CrossRefGoogle Scholar
  46. Roy B, Mandal AB (2005) Anther culture response in indica rice and variations in major agronomic characters among the androclones of a scented cultivar, Karnal local. Afr J Biotechnol 4(2):235–240Google Scholar
  47. Senadhira D, Zapata-Arias FJ, Gregorio GB, Alejar MS, De LaCruz HC, Padolina TF, Galvez AM (2002) Development of the first salt tolerant rice cultivar through indica/indica anther culture. Field Crops Res 76(3):103–110CrossRefGoogle Scholar
  48. Singh P (2014) Development of bacterial blight resistant basmati rice doubled haploids through anther culture. M.Sc. thesis. School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, IndiaGoogle Scholar
  49. Singh RK, Singh US, Kush GS (2000) Aromatic rices. Oxford & IBH Publishing Co. Pvt. Ltd., New DelhiGoogle Scholar
  50. Singh VK, Singh A, Singh SP, Ellur RK, Choudhary V, Sarkhel S, Singh D, Gopala Krishnan S, Nagarajan M, Vinod KK, Singh UD, Rathore R, Prasanthi SK, Agrawal PK, Bhatt JC, Mohapatra T, Prabhu KV, Singh AK (2012) Incorporation of blast resistance into “PRR78”, an elite Basmati rice restorer line, through marker assisted backcross breeding. Field Crops Res 128:8–16CrossRefGoogle Scholar
  51. Singh AK, Gopala Krishnan S, Nagarajan M, Bhowmick PK, Ellur RK, Haritha B, Vinod KK, Prabhu KV, Khanna A, Singh UD, Sharma TR, Prakash G, Seth R, Kumar D (2017) Notification of Basmati rice variety Pusa Basmati 1637. Indian J Genet 77(4):583–584Google Scholar
  52. Singh V, Singh AK, Mohapatra T, Gopala Krishnan S, Ellur RK (2018) Pusa Basmati 1121—a rice variety with exceptional kernel elongation and volume expansion after cooking. Rice 11:19.  https://doi.org/10.1186/s12284-018-0213-6 PubMedPubMedCentralCrossRefGoogle Scholar
  53. Snape JW (1989) Doubled haploid breeding: theoretical basis and practical applications. In: Mujeeb-Kazi A, Sitch LA (eds) Review of advances in plant biotechnology, 1985–1988: 2nd international symposium on genetic manipulation in crops. CIMMYT and IRRI, Mexico and Manila, pp 19–30Google Scholar
  54. Sood BC, Siddiq EA (1978) A rapid technique for scent determination in rice. Indian J Genet Plant Breed 38(2):268–275Google Scholar
  55. 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):9043–9048PubMedCrossRefGoogle Scholar
  56. Takemoto-Kuno Y, Mitsueda H, Suzuki K, Hirabayashi H, Ideta O, Aoki N, Umemoto T, Ishii T, Ando I, Kato H, Nemoto H (2015) qAC2, a novel QTL that interacts with Wx and controls the low amylose content in rice (Oryza sativa L.). Theor Appl Genet 128(4):563–573PubMedCrossRefGoogle Scholar
  57. Thakur S, Gupta YK, Singh PK, Rathour R, Variar M, Prashanthi SK (2013) Molecular diversity in rice blast resistance gene Pi-ta makes it highly effective against dynamic population of Magnaporthe oryzae. Funct Integr Genomics 13:309–322PubMedCrossRefGoogle Scholar
  58. Tian D, Chen Z, Chen Z, Zhou Y, Wang Z, Wang F, Chen S (2016) Allele-specific marker-based assessment revealed that the rice blast resistance genes Pi-2 and Pi-9 have not been widely deployed in Chinese indica rice cultivars. Rice 9(1):19PubMedPubMedCentralCrossRefGoogle Scholar
  59. Tomita M, Ishii K (2018) Genetic performance of the semi dwarfing allele sd-1 derived from a japonica rice cultivar and minimum requirements to detect its single-nucleotide polymorphism by miSeq whole-genome sequencing. Biomed Res Int.  https://doi.org/10.1155/2018/4241725 PubMedPubMedCentralCrossRefGoogle Scholar
  60. Trijatmiko KR, Prasetiyono J, Thomson MJ, Cruz CM, Moeljopawiro S, Pereira A (2014) Meta-analysis of quantitative trait loci for grain yield and component traits under reproductive-stage drought stress in an upland rice population. Mol Breed 34(2):283–295PubMedPubMedCentralCrossRefGoogle Scholar
  61. Xu X, Hayashi N, Wang CT, Fukuoka S, Kawasaki S, Takasuji H, Jiang CJ (2014) Rice blast resistance gene Pikahei-1(t), a member of a resistance gene cluster on chromosome 4, encodes a nucleotide-binding site and leucine-rich repeat protein. Mol Breed 34:691–700CrossRefGoogle Scholar
  62. Yan J, Xue Q, Zhu J (1996) Genetic studies of anther culture ability in rice (Oryza sativa). Plant Cell, Tissue Organ Cult 45:253–258CrossRefGoogle Scholar
  63. Yin KC, Hsu C, Chu CY, Pi FY, Wang ST, Liu TY, Chu CC, Wang CC, Sun CS (1976) A study of the new cultivar of rice raised by haploid breeding method. Sci Sin 19(2):227–242Google Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.CSK Himachal Pradesh Agricultural UniversityPalampurIndia
  2. 2.Division of GeneticsIndian Agricultural Research InstituteNew DelhiIndia
  3. 3.School of BiotechnologySher-e-Kashmir University of Agricultural Sciences and TechnologyJammuIndia

Personalised recommendations