Germplasm Resources, Genes and Perspective for Aromatic Rice

doi:10.1016/j.rsci.2023.03.011

Abstract

Abstract:

Aromatic rice is considered an important commodity in the global market because of its strong aroma and eating and cooking quality. Asian countries, such as India and Pakistan, are the leading traders of Basmati rice, whereas Thailand is the major supplier of Jasmine rice in the international market. The strong aroma of rice is associated with more than 300 volatile compounds, among which 2-acetyl-1-pyrroline (2-AP) is the principal component. 2-AP is a phenotypic expression of spontaneous mutations in the recessive gene OsBadh2 or Badh2. The present review focuses on the origin, evolution and diversity of genetic resources of aromatic rice available worldwide. A brief discussion is presented on the genes responsible for quality traits along with details of their molecular genetics. This compilation and discussion will be useful for future breeding programs and the biofortification of quality traits of aromatic rice to ensure food security and nutritional need.

Key words: aromatic rice, 2-acetyl-1-pyrroline, polyamine degradation pathway, quality trait

Prafulla Kumar Behera, Debabrata Panda. Germplasm Resources, Genes and Perspective for Aromatic Rice[J]. Rice Science, 2023, 30(4): 294-305.

Figures/Tables 4

References 91

[1]	Ahn S N, Bollich C N, Tanksley S D. 1992. RFLP tagging of a gene for aroma in rice. Theor Appl Genet, 84(7): 825-828.
[2]	Amarawathi Y, Singh R, Singh A K, Singh V P, Mohapatra T, Sharma T R, Singh N K. 2008. Mapping of quantitative trait loci for basmati quality traits in rice (Oryza sativa L.). Mol Breed, 21(1): 49-65.
[3]	Anik A R, Talukder R K. 2002. Economic and financial profitability of aromatic and fine rice production in Bangladesh. Bangladesh J Agric Econ, 25(2): 103-113.
[4]	Ashokkumar S, Jaganathan D, Ramanathan V, Rahman H, Palaniswamy R, Kambale R, Muthurajan R. 2020. Creation of novel alleles of fragrance gene OsBADH2 in rice through CRISPR/Cas9 mediated gene editing. PLoS One, 15(8): e0237018.
[5]	Baliyan N, Malik R, Rani R, Mehta K, Vashisth U, Dhillon S, Boora K S. 2018. Integrating marker-assisted background analysis with foreground selection for pyramiding bacterial blight resistance genes into Basmati rice. C R Biol, 341(1): 1-8.
[6]	Bao G G, Ashraf U, Wan X R, Zhou Q, Li S Y, Wang C L, He L X, Tang X R. 2021. Transcriptomic analysis provides insights into foliar zinc application induced upregulation in 2-acetyl-1-pyrroline and related transcriptional regulatory mechanism in fragrant rice. J Agric Food Chem, 69(38): 11350-11360.
[7]	Bergman C J, Delgado J T, Bryant R, Grimm C, Cadwallader K R, Webb B D. 2000. Rapid gas chromatographic technique for quantifying 2-acetyl-1-pyrroline and hexanal in rice (Oryza sativa L.). Cereal Chem J, 77(4): 454-458.
[8]	Bounphanousay C, Jaisil P, Sanitchon J, Fitzgerald M, Hamilton N S. 2008. Chemical and molecular characterization of fragrance in black glutinous rice from Lao PDR. Asian J Plant Sci, 7(1): 1-7.
[9]	Bradbury L M T, Fitzgerald T L, Henry R J, Jin Q S, Waters D L E. 2005. The gene for fragrance in rice. Plant Biotechnol J, 3(3): 363-370. PMID
[10]	Bradbury L M T, Gillies S A, Brushett D J, Waters D L E, Henry R J. 2008. Inactivation of an aminoaldehyde dehydrogenase is responsible for fragrance in rice. Plant Mol Biol, 68(4/5): 439-449.
[11]	Buttery R G. 1982. 2-Acetyl-1-pyrroline: An important aroma component of cooked rice. Chem Ind, 12: 958-959.
[12]	Caicedo A L, Williamson S H, Hernandez R D, Boyko A, Fledel-Alon A, York T L, Polato N R, Olsen K M, Nielsen R, McCouch S R, Bustamante C D, Purugganan M D. 2007. Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet, 3(9): 1745-1756. PMID
[13]	Chakraborty D, Deb D, Ray A. 2016. An analysis of variation of the aroma gene in rice (Oryza sativa L. subsp. indica Kato) landraces. Genet Resour Crop Evol, 63(6): 953-959.
[14]	Chen S H, Wu J, Yang Y, Shi W W, Xu M L. 2006. The fgr gene responsible for rice fragrance was restricted within 69 kb. Plant Sci, 171(4): 505-514.
[15]	Chen S H, Yang Y, Shi W W, Ji Q, He F, Zhang Z D, Cheng Z K, Liu X N, Xu M L. 2008. Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. Plant Cell, 20(7): 1850-1861. PMID
[16]	Chen Y B, Wang Z D, Wang C R, Li H, Huang D Q, Zhou D G, Zhao L, Pan Y Y, Gong R, Zhou S C. 2022. Comparisons of metabolic profiles for carbohydrates, amino acids, lipids, fragrance and flavones during grain development in indica rice cultivars. Rice Sci, 29(2): 155-165.
[17]	Dela Cruz N, Khush G S. 2000. Rice grain quality evaluation procedures. In: Singh R K, Singh U S, Khush G S. Aromatic Rices. New Delhi, India: Oxford and IBH Publishing Co Pvt. Ltd: 15-28.
[18]	Fitzgerald T L, Lex Ean Waters D, Brooks L O, Henry R J. 2010. Fragrance in rice (Oryza sativa) is associated with reduced yield under salt treatment. Environ Exp Bot, 68(3): 292-300.
[19]	Fukuoka S, Suu T D, Ebana K, Trinh L N, Nagamine T, Okuno K. 2006. Diversity in phenotypic profiles in landrace populations of Vietnamese rice: A case study of agronomic characters for conserving crop genetic diversity on farm. Genet Resour Crop Evol, 53(4): 753-761.
[20]	Garris A J, Tai T H, Coburn J, Kresovich S, McCouch S. 2005. Genetic structure and diversity in Oryza sativa L. Genetics, 169(3): 1631-1638.
[21]	Ghosh P, Roychoudhury A. 2020. Aromatic rice:Biochemical and molecular basis of aroma production and stress response. In: Roychoudhury A. Rice Research for Quality Improvement: Genomics and Genetic Engineering. Singapore: Springer: 373-408.
[22]	Glaszmann J C. 1987. Isozymes and classification of Asian rice varieties. Theor Appl Genet, 74(1): 21-30. PMID
[23]	Gopalakrishnan S, Sharma R K, Anand Rajkumar K, Joseph M, Singh V P, Singh A K, Bhat K V, Singh N K, Mohapatra T. 2008. Integrating marker assisted background analysis with foreground selection for identification of superior bacterial blight resistant recombinants in Basmati rice. Plant Breed, 127(2): 131-139.
[24]	Grimm C C, Champagne E T, Lloyd S W, Easson M, Condon B, McClung A. 2011. Analysis of 2-acetyl-1-pyrroline in rice by HSSE/GC/MS. Cereal Chem, 88(3): 271-277.
[25]	He Q, Yu J, Kim T S, Cho Y H, Lee Y S, Park Y J. 2015. Resequencing reveals different domestication rate for BADH1 and BADH2 in rice (Oryza sativa). PLoS One, 10(8): e0134801.
[26]	Hien N L, Ahmad Sarhadi W, Oikawa Y, Hirata Y. 2007. Genetic diversity of morphological responses and the relationships among Asia aromatic rice (Oryza sativa L.) cultivars. Tropics, 16(4): 343-355.
[27]	Hinge V, Zanan R, Rashmi D, Nadaf A. 2019. Aroma volatiles as biomarkers for characterizing rice (Oryza sativa L.): Flavor types and their biosynthesis. In: Verma D K, Srivastav P P. Science and Technology of Aroma, Flavor and Fragrance in Rice. Florida, USA: Apple Academic Press: 200-269.
[28]	Hinge V R, Patil H B, Nadaf A B. 2016. Aroma volatile analyses and 2AP characterization at various developmental stages in Basmati and non-Basmati scented rice (Oryza sativa L.) cultivars. Rice, 9(1): 38.
[29]	Hofmann T, Schieberle P. 1998. 2-Oxopropanal, hydroxy-2-propanone, and 1-pyrrolineImportant intermediates in the generation of the roast-smelling food flavor compounds 2-acetyl-1-pyrroline and 2-acetyltetrahydropyridine. J Agric Food Chem, 46(6): 2270-2277.
[30]	Hu X Q, Lu L, Guo Z L, Zhu Z W. 2020. Volatile compounds, affecting factors and evaluation methods for rice aroma: A review. Trends Food Sci Technol, 97: 136-146.
[31]	Huang T C, Teng C S, Chang J L, Chuang H S, Ho C T, Wu M L. 2008. Biosynthetic mechanism of 2-acetyl-1-pyrroline and its relationship with Δ¹-pyrroline-5-carboxylic acid and methylglyoxal in aromatic rice (Oryza sativa L.) callus. J Agric Food Chem, 56(16): 7399-7404.
[32]	Imran M, Liu Y H, Shafiq S, Abbas F, Ilahi S, Rehman N, Ahmar S, Fiaz S, Baran N, Pan S G, Mo Z W, Tang X R. 2022. Transcriptional cascades in the regulation of 2-AP biosynthesis under Zn supply in fragrant rice. Physiol Plant, 174(3): e13721.
[33]	IRGSP International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. Nature, 436: 793-800.
[34]	Itani T. 2002. Agronomic characteristics of rice cultivars collected from Japan and other countries. Jpn J Crop Sci, 71: 68-75. (in Japanese with English abstract)
[35]	Itani T, Tamaki M, Hayata Y, Fushimi T, Hashizume K. 2004. Variation of 2-acetyl-1-pyrroline concentration in aromatic rice grains collected in the same region in Japan and factors affecting its concentration. Plant Prod Sci, 7(2): 178-183.
[36]	Kaikavoosi K, Kad T D, Zanan R L, Nadaf A B. 2015. 2-Acetyl-1-pyrroline augmentation in scented indica rice (Oryza sativa L.) varieties through Δ(1)-pyrroline-5-carboxylate synthetase (P5CS) gene transformation. Appl Biochem Biotechnol, 177(7): 1466-1479. PMID
[37]	Kamath S, Stephen J C, Suresh S, Barai B K, Sahoo A K, Reddy K R, Bhattacharya K R. 2008. Basmati rice: Its characteristics and identification. J Sci Food Agric, 88(10): 1821-1831.
[38]	Khush G S. 2000. Taxonomy and origin of rice. In: Singh R K, Singh U S, Khush G S. Aromatic Rices. New Delhi, India: Oxford and IBH Publishing Co Pvt. Ltd: 5-13.
[39]	Kiani G, Nematzadeh G A, Ghareyazie B, Sattari M. 2012. Pyramiding of cry1Ab and fgr genes in two Iranian rice cultivars Neda and Nemat. J Agric Sci Technol, 14: 1087-1092.
[40]	Kishor D S, Seo J, Chin J H, Koh H J. 2020. Evaluation of whole-genome sequence, genetic diversity, and agronomic traits of Basmati rice (Oryza sativa L.). Front Genet, 11: 86. PMID
[41]	Korinsak S, Sriprakhon S, Sirithanya P, Jairin J, Korinsak S, Vanavichit A, Toojinda T. 2009. Identification of microsatellite markers (SSR) linked to a new bacterial blight resistance gene xa33(t) in rice cultivar ‘Ba7’. Maejo Int J Sci Technol, 3(2): 235-247.
[42]	Kovach M J, Calingacion M N, Fitzgerald M A, McCouch S R. 2009. The origin and evolution of fragrance in rice (Oryza sativa L.). Proc Natl Acad Sci USA, 106(34): 14444-14449.
[43]	Kumari A, Kumar J, Kumar A, Gaur A K. 2019. Physico-chemical and epigenetic aspects towards revealing aroma biology in Oryza sativa L. Genome Gene Ther Int J, 3(1): 000111.
[44]	Lorieux M, Petrov M, Huang N, Guiderdoni E, Ghesquière A. 1996. Aroma in rice: Genetic analysis of a quantitative trait. Theor Appl Genet, 93(7): 1145-1151. PMID
[45]	Luo H W, He L X, Du B, Pan S G, Mo Z W, Yang S Y, Zou Y B, Tang X R. 2022. Epoxiconazole improved photosynthesis, yield formation, grain quality and 2-acetyl-1-pyrroline biosynthesis of fragrant rice. Rice Sci, 29(2): 189-196.
[46]	Maraval I, Sen K, Agrebi A, Menut C, Morere A, Boulanger R, Gay F, Mestres C, Gunata Z. 2010. Quantification of 2-acetyl-1-pyrroline in rice by stable isotope dilution assay through headspace solid-phase microextraction coupled to gas chromatography-tandem mass spectrometry. Anal Chim Acta, 675(2): 148-155. PMID
[47]	Mathure S V, Jawali N, Thengane R J, Nadaf A B. 2014. Comparative quantitative analysis of headspace volatiles and their association with BADH2 marker in non-basmati scented, basmati and non-scented rice (Oryza sativa L.) cultivars of India. Food Chem, 142: 383-391. PMID
[48]	Nadaf A, Mathure S, Jawali N. 2016. Quality parameter assessment in scented rice cultivars. In: Nadaf A, Mathure S, Jawali N. Scented Rice (Oryza sativa* L.) Cultivars of India:A Perspective on Quality and Diversity*. New Delhi, India: Springer: 31-56.
[49]	Nagaraju J, Kathirvel M, Kumar R R, Siddiq E A, Hasnain S E. 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. PMID
[50]	Nematzadeh G A, Karbalaie M T, Farrokhzad F, Ghareyazie B. 2000. Aromatic rices of Iran. In: Singh R K, Singh U S, Khush G S. Aromatic Rices. New Delhi, India: Oxford and IBH Publishing Co Pvt. Ltd: 191-200.
[51]	Ootsuka K, Takahashi I, Tanaka K, Itani T, Tabuchi H, Yoshihashi T, Tonouchi A, Ishikawa R. 2014. Genetic polymorphisms in Japanese fragrant landraces and novel fragrant allele domesticated in northern Japan. Breed Sci, 64(2): 115-124.
[52]	Pachauri V, Singh M K, Singh A K, Singh S, Shakeel N A, Singh V P, Singh N K. 2010. Origin and genetic diversity of aromatic rice varieties, molecular breeding and chemical and genetic basis of rice aroma. J Plant Biochem Biotechnol, 19(2): 127-143.
[53]	Pachauri V, Mishra V, Mishra P, Singh A K, Singh S, Singh R, Singh N K. 2014. Identification of candidate genes for rice grain aroma by combining QTL mapping and transcriptome profiling approaches. Cereal Res Commun, 42(3): 376-388.
[54]	Peng B, Zuo Y H, Hao Y L, Peng J, Kong D Y, Peng Y, Nassirou T Y, He L L, Sun Y F, Liu L, Pang R H, Chen Y X, Li J T, Zhou Q Y, Duan B, Song X H, Song S Z, Yuan H Y. 2018. Studies on aroma gene and its application in rice genetics and breeding. J Plant Stud, 7(2): 29.
[55]	Prasad G S V, Padmavathi G, Suneetha K, Madhav M S, Muralidharan K. 2020. Assessment of diversity of Indian aromatic rice germplasm collections for morphological, agronomical, quality traits and molecular characters to identify a core set for crop improvement. CABI Agric BioSci, 1: 13.
[56]	Prodhan Z H, Shu Q Y. 2020. Rice aroma: A natural gift comes with price and the way forward. Rice Sci, 27(2): 86-100.
[57]	Ramaiah K, Rao M V. 1953. Rice Breeding and Genetics. New Delhi, India: Indian Council of Agricultural Research.
[58]	Roy S, Banerjee A, Basak N, Kumar J, Mandal N P. 2020. Aromatic rice. In: de Oliveira A C, Pegoraro C, Viana V E. The Future of Rice Demand: Quality Beyond Productivity. Cham: Springer: 251-282.
[59]	Sakthivel K, Sundaram R M, Shobha Rani N, Balachandran S M, Neeraja C N. 2009. Genetic and molecular basis of fragrance in rice. Biotechnol Adv, 27(4): 468-473. PMID
[60]	Samal P, Pote T D, Krishnan S G, Singh A K, Salgotra R K, Rathour R. 2019. Integrating marker-assisted selection and doubled haploidy for rapid introgression of semi-dwarfing and blast resistance genes into a basmati rice variety ‘Ranbir Basmati’. Euphytica, 215: 149.
[61]	Sansenya S, Hua Y L, Chumanee S. 2018. The correlation between 2-acetyl-1-pyrroline content, biological compounds and molecular characterization to the aroma intensities of Thai local rice. J Oleo Sci, 67(7): 893-904. PMID
[62]	Shan Q W, Wang Y P, Chen K L, Liang Z, Li J, Zhang Y, Zhang K, Liu J X, Voytas D F, Zheng X L, Zhang Y, Gao C X. 2013. Rapid and efficient gene modification in rice and Brachypodium using TALENs. Mol Plant, 6(4): 1365-1368.
[63]	Shao G N, Tang A, Tang S Q, Luo J, Jiao G A, Wu J L, Hu P S. 2011. A new deletion mutation of fragrant gene and the development of three molecular markers for fragrance in rice. Plant Breed, 130(2): 172-176.
[64]	Shi Y Q, Zhao G C, Xu X L, Li J Y. 2014. Discovery of a new fragrance allele and development of functional markers for identifying diverse fragrant genotypes in rice. Mol Breed, 33(3): 701-708.
[65]	Siangliw M, Toojinda T, Tragoonrung S, Vanavichit A. 2003. Thai jasmine rice carrying QTLch9 (SubQTL) is submergence tolerant. Ann Bot, 91(S2): 255-261.
[66]	Siddiq E A, Vemireddy L R, Nagaraju J. 2012. Basmati rices: Genetics, breeding and trade. Agric Res, 1(1): 25-36.
[67]	Singh R K, Singh U S, Khush G S, Rohilla R. 2000. Genetics and biotechnology of quality traits in aromatic rices. In: Singh R K, Singh U S, Khush G S. Aromatic Rices. New Delhi, India: Oxford and IBH Publishing Co Pvt. Ltd: 47-70.
[68]	Singh S P, Singh M K, Kumar S, Sravan U S. 2019. Cultivation of aromatic rice: A review. In: Hasanuzzaman M. Agronomic Crops. Singapore: Springer: 175-198.
[69]	Singh V K, Singh B D, Kumar A, Maurya S, Krishnan S G, Vinod K K, Singh M P, Ellur R K, Bhowmick P K, Singh A K. 2018. Marker-assisted introgression of Saltol QTL enhances seedling stage salt tolerance in the rice variety Pusa Basmati 1. Int J Genom, 2018: 8319879.
[70]	Singh V P. 2000. Basmati rice of India. In: Singh R K, Singh U S, Khush G S. Aromatic Rices. New Delhi, India: Oxford and IBH Publishing Co Pvt. Ltd: 135-154.
[71]	Singh V P, Singh A K. 2010. Role of Indian agricultural research institute in collection, acquisition, evaluation, enhancement, utilization and conservation of rice germplasm. In: Sharma S D, Rap P. Genetic Resources of Rice in India. New Delhi, India: Today and Tomorrow’s Printers and Publications: 135-150.
[72]	Singh V P, Singh A K, Mohapatra T, Gopala Krishnan S, Ellur R K. 2018. Pusa Basmati 1121: A rice variety with exceptional kernel elongation and volume expansion after cooking. Rice, 11: 19.
[73]	Srivastava D, Shamim M, Mishra A, Yadav P, Kumar D, Pandey P, Khan N A, Singh K N. 2019. Introgression of semi-dwarf gene in Kalanamak rice using marker-assisted selection breeding. Curr Sci, 116(4): 597-603.
[74]	Sun P Y, Zhang W H, Zhang L, Shu F, He Q, Xu N, Peng Z R, Zeng J, Fang P P, Deng H F. 2023. Development and application of a novel functional marker for fragrance in rice. Rice Sci, 30(3): 176-180.
[75]	Talukdar P R, Rathi S, Pathak K, Chetia S K, Sarma R N. 2017. Population structure and marker-trait association in indigenous aromatic rice. Rice Sci, 24(3): 145-154.
[76]	Tama R A Z, Begum I A, Alam M J, Islam S. 2015. Financial profitability of aromatic rice production in some selected areas of Bangladesh. Int J Innov Appl Stud, 12(1): 235-242.
[77]	Tanchotikul U, Hsieh T C Y. 1991. An improved method for quantification of 2-acetyl-1-pyrroline, a “popcorn”-like aroma, in aromatic rice by high-resolution gas chromatography/mass spectrometry/selected ion monitoring. J Agric Food Chem, 39(5): 944-947.
[78]	van Quoc G, Huynh K, Nguyen C T T, Nguyen L H, van Nguyen M, Nguyen N T, Vo C T, Swee K Y. 2023. Novel deletion in exon 7 of Betaine Aldehyde Dehydrogenase 2 (BADH2). Rice Sci, 30(2): 104-112.
[79]	Vanavichit A, Yoshihashi T, Wanchana S, Areekit S, Saengsraku D, Kamolsukyunyong W. 2005. Cloning of Os2AP, the aromatic gene controlling the biosynthetic switch of 2-acetyl-1-pyrroline and gamma aminobutyric acid (GABA) in rice. In: 5th International Rice Genetics Symposium. Manila, the Philippines: IRRI: 44.
[80]	Vanavichit A, Kamolsukyeunyong W, Siangliw M, Siangliw J L, Traprab S, Ruengphayak S, Chaichoompu E, Saensuk C, Phuvanartnarubal E, Toojinda T, Tragoonrung S. 2018. Thai hom Mali rice: Origin and breeding for subsistence rainfed lowland rice system. Rice, 11(1): 20. PMID
[81]	Vemireddy L R, Tanti B, Lahakar L, Shandilya Z M. 2021. Aromatic rices: Evolution, genetics and improvement through conventional breeding and biotechnological methods. In: Hossain M A, Hassan L, Iftekharudaula K M, Kumar A, Henry R. Molecular Breeding for Rice Abiotic Stress Tolerance and Nutritional Quality. NY, USA: John Wiley & Sons Ltd: 341-357.
[82]	Verma D K, Mohan M, Yadav V K, Asthir B, Soni S K. 2012. Inquisition of some physico-chemical characteristics of newly evolved basmati rice. Environ Ecol, 30(1): 114-117.
[83]	Verma D K, Mohan M, Asthir B. 2013. Physicochemical and cooking characteristics of some promising basmati genotypes. Asian J Food Agro-Ind, 6(2): 94-99.
[84]	Verma D K, Mohan M, Prabhakar P K, Srivastav P P. 2015. Physico-chemical and cooking characteristics of Azad basmati. Int Food Res J, 22(4): 1380-1389.
[85]	Verma D K, Srivastav P P. 2017. Proximate composition, mineral content and fatty acids analyses of aromatic and non-aromatic Indian rice. Rice Sci, 24(1): 21-31.
[86]	Verma D K, Srivastav P P, Nadaf A. 2019. Aromatic rice from different countries: An overview. In: Verma D K, Srivastav P P. Science and Technology of Aroma, Flavour and Fragrance in Rice. Florida, USA: Apple Academic Press: 35-58.
[87]	Wakte K, Zanan R, Hinge V, Khandagale K, Nadaf A, Henry R. 2017. Thirty-three years of 2-acetyl-1-pyrroline, a principal basmati aroma compound in scented rice (Oryza sativa L.): A status review. J Sci Food Agric, 97(2): 384-395.
[88]	Yang D S, Shewfelt R L, Lee K S, Kays S J. 2008. Comparison of odor-active compounds from six distinctly different rice flavor types. J Agric Food Chem, 56(8): 2780-2787.
[89]	Yang S Y, Zou Y B, Liang Y Z, Xia B, Liu S K, Ibrahim M, Li D Q, Li Y Q, Chen L, Zeng Y, Liu L, Chen Y, Li P, Zhu J W. 2012. Role of soil total nitrogen in aroma synthesis of traditional regional aromatic rice in China. Field Crops Res, 125: 151-160.
[90]	Yi M, Nwe K T, Vanavichit A, Chai-arree W, Toojinda T. 2009. Marker assisted backcross breeding to improve cooking quality traits in Myanmar rice cultivar Manawthukha. Field Crops Res, 113(2): 178-186.
[91]	Yoshihashi T. 2002. Quantitative analysis on 2-acetyl-1-pyrroline of an aromatic rice by stable isotope dilution method and model studies on its formation during cooking. J Food Sci, 67(2): 619-622.

Country	Popular variety	Reference
Afghanistan	Bahra, Lawangi, Sela Takhar, Bala, Lawangin, Pashadi, Germa Bala, Sarda Bala, Luke Qasan, Torishi, Sela Doshi, Surkha-Bala, Pashadi Konar	Singh, 2000; Itani, 2002
Bangladesh	Kataribhog, Bau-pagal, Badshabhog, Kala Namak, Dadkhani, Kalazira, Banshful, Kataribagh, Tulshimala, BR36, BR6, BR26, Dolhabhog (BR5), Chinigura, BRRI dhan 70, Binadhan 13, BRRI dhan 38	Anik and Talukder, 2002; Vemireddy et al, 2021
Cambodia	Somali, Phka Rumduol, Phka Rumdeng, Phka Roment	Pachauri et al, 2010; Roy et al, 2020
China	Xianggeng 3, Xiangyou 63, Zhe 9248, Ganwanxian 22, SR5041, Dechangxiangmi, Beijingkoutou, Shuangzhuzhan, Xiangnuo 4, Tainung Sen 20, Yongshunxingdao, Qingbuxiangjingmi, Congjiangxixiangmi, Jingxixiangdao, Huanglongxiangmi, Jingcixiangdao, Jiangyongxiangdao, Qufuxiangmi	Yang et al, 2012; Verma et al, 2019
India	Basmati 370, Haryana Basmati 1, Kalanamak, Ranbir Basmati, Taraori Basmati, Basmati 386, Type 3, Pusa Basmati 1, Pusa Basmati 1121, Punjab Basmati 1, CSR30, Pusa 33, Amritsari Basmati	Nagaraju et al, 2002; Kiani et al, 2012; Singh et al, 2018; Verma et al, 2019
Indonesia	Rojo Lele, Bengwan Solo, Pare Kembang, Batang Gadis, Mentik Wangi, Sukanandi, Sinyanur, Pulu Mandoti, Pandanawangi, Gunung Perak	Kamath et al, 2008; Pachauri et al, 2010; Verma et al, 2019
Iran	Tarom Mahalli, Anbar-boo, Mirza, Fajr, Champa, Mir tarom, Hassani, Shiroudi, Nemat, Mehr, Mosa Tarom, Poya, Domsiah, Hasan, Sadri, Hashemi	Fukuoka et al, 2006; Kiani et al, 2012; Vemireddy et al, 2021
Iraq	Anbarboo	Pachauri et al, 2010
Japan	Miyakaori, Iwaga, Sari Queen, Kouikuka 37, Hieri, Jakou, Kabashiko, Oitakoutou	Hien et al, 2007; Ootsuka et al, 2014
Malaysia	MRQ74	Vemireddy et al, 2021
Myanmar	Boke Hmwe, Balugyun, Taungpyan Hmwe, Nyakywe, Nama Tha Lay, Pawsan Hmwe	Pachauri et al, 2010
Nepal	Basamati Pahade, Basmati Gola, Brahmaphool, Jetho Budho, Rato Basmati, Kalo, Basmati Uzarka, Basmati Dhan, Lamo, Basmati Red	Pachauri et al, 2010; Kishor et al, 2020
Pakistan	Basmati Pak, Basmati 385, Super Basmati, PK50005-3, Basmati 185, Basmati 50021-1, Basmati 377, Sathi Basmati	Khush, 2000; Kishor et al, 2020
Thailand	Buer Neo Moo, Hawm Klong Luang, Buer Ner Moo Pho Phi, Hawn Mali, RD15, Baow Hawm 62, Buer Ner Moo Phardo, Jao Mali, KDML105, Siamati, Hawm, Som Hung, Hawm Baow, RD6, Hawm Supanburi, Pla Sew, Nahng Nuan, Khao Dawk Mali, Thung Kula Rang-Hai Tahi Hom Mali	Itani et al, 2004; Pachauri et al, 2010; Verma et al, 2019; Roy et al, 2020
the Philippines	Azucena, Milagrosa, Binicol, Mangareez, Milfore 6(2)	Pachauri et al, 2010; Ootsuka et al, 2014
the USA	Texamati, Della, Carolina, A201, Dellamont, Kasmati, Jasmine 85, Sierra, Delrose, Delmont, Jazzman, JES	Khush, 2000; Verma et al, 2019
Vietnam	Di Huang, Tam Xuan Hai Hau, VD 20, Nang Thom, Nep Hoa Vang, Tam On, Nang Huong Ran, Nang Thom Muong, Tam Canh, Lam Thao, Hai Hau, Nep Bac, Tam Xoan, Can Duoc, Nep Rong, Lua Tam, Nam Dinh	Hien et al, 2007; Pachauri et al, 2010; Verma et al, 2019

Country	Popular variety	Reference
Afghanistan	Bahra, Lawangi, Sela Takhar, Bala, Lawangin, Pashadi, Germa Bala, Sarda Bala, Luke Qasan, Torishi, Sela Doshi, Surkha-Bala, Pashadi Konar	Singh, 2000; Itani, 2002
Bangladesh	Kataribhog, Bau-pagal, Badshabhog, Kala Namak, Dadkhani, Kalazira, Banshful, Kataribagh, Tulshimala, BR36, BR6, BR26, Dolhabhog (BR5), Chinigura, BRRI dhan 70, Binadhan 13, BRRI dhan 38	Anik and Talukder, 2002; Vemireddy et al, 2021
Cambodia	Somali, Phka Rumduol, Phka Rumdeng, Phka Roment	Pachauri et al, 2010; Roy et al, 2020
China	Xianggeng 3, Xiangyou 63, Zhe 9248, Ganwanxian 22, SR5041, Dechangxiangmi, Beijingkoutou, Shuangzhuzhan, Xiangnuo 4, Tainung Sen 20, Yongshunxingdao, Qingbuxiangjingmi, Congjiangxixiangmi, Jingxixiangdao, Huanglongxiangmi, Jingcixiangdao, Jiangyongxiangdao, Qufuxiangmi	Yang et al, 2012; Verma et al, 2019
India	Basmati 370, Haryana Basmati 1, Kalanamak, Ranbir Basmati, Taraori Basmati, Basmati 386, Type 3, Pusa Basmati 1, Pusa Basmati 1121, Punjab Basmati 1, CSR30, Pusa 33, Amritsari Basmati	Nagaraju et al, 2002; Kiani et al, 2012; Singh et al, 2018; Verma et al, 2019
Indonesia	Rojo Lele, Bengwan Solo, Pare Kembang, Batang Gadis, Mentik Wangi, Sukanandi, Sinyanur, Pulu Mandoti, Pandanawangi, Gunung Perak	Kamath et al, 2008; Pachauri et al, 2010; Verma et al, 2019
Iran	Tarom Mahalli, Anbar-boo, Mirza, Fajr, Champa, Mir tarom, Hassani, Shiroudi, Nemat, Mehr, Mosa Tarom, Poya, Domsiah, Hasan, Sadri, Hashemi	Fukuoka et al, 2006; Kiani et al, 2012; Vemireddy et al, 2021
Iraq	Anbarboo	Pachauri et al, 2010
Japan	Miyakaori, Iwaga, Sari Queen, Kouikuka 37, Hieri, Jakou, Kabashiko, Oitakoutou	Hien et al, 2007; Ootsuka et al, 2014
Malaysia	MRQ74	Vemireddy et al, 2021
Myanmar	Boke Hmwe, Balugyun, Taungpyan Hmwe, Nyakywe, Nama Tha Lay, Pawsan Hmwe	Pachauri et al, 2010
Nepal	Basamati Pahade, Basmati Gola, Brahmaphool, Jetho Budho, Rato Basmati, Kalo, Basmati Uzarka, Basmati Dhan, Lamo, Basmati Red	Pachauri et al, 2010; Kishor et al, 2020
Pakistan	Basmati Pak, Basmati 385, Super Basmati, PK50005-3, Basmati 185, Basmati 50021-1, Basmati 377, Sathi Basmati	Khush, 2000; Kishor et al, 2020
Thailand	Buer Neo Moo, Hawm Klong Luang, Buer Ner Moo Pho Phi, Hawn Mali, RD15, Baow Hawm 62, Buer Ner Moo Phardo, Jao Mali, KDML105, Siamati, Hawm, Som Hung, Hawm Baow, RD6, Hawm Supanburi, Pla Sew, Nahng Nuan, Khao Dawk Mali, Thung Kula Rang-Hai Tahi Hom Mali	Itani et al, 2004; Pachauri et al, 2010; Verma et al, 2019; Roy et al, 2020
the Philippines	Azucena, Milagrosa, Binicol, Mangareez, Milfore 6(2)	Pachauri et al, 2010; Ootsuka et al, 2014
the USA	Texamati, Della, Carolina, A201, Dellamont, Kasmati, Jasmine 85, Sierra, Delrose, Delmont, Jazzman, JES	Khush, 2000; Verma et al, 2019
Vietnam	Di Huang, Tam Xuan Hai Hau, VD 20, Nang Thom, Nep Hoa Vang, Tam On, Nang Huong Ran, Nang Thom Muong, Tam Canh, Lam Thao, Hai Hau, Nep Bac, Tam Xoan, Can Duoc, Nep Rong, Lua Tam, Nam Dinh	Hien et al, 2007; Pachauri et al, 2010; Verma et al, 2019

Candidate gene	Chr	Response to stress	Tissue specificity	Protein interaction	Subcellular localization	Reference
OsBadh1	8	Submergence, anoxia, salinity	Flowers, roots before flowering	Glutamate synthase	Peroxisome, chloroplast, cytoplsam, nucleus	Amarawathi et al, 2008; Pachauri et al, 2014
OsBadh2	3, 4 and 8	Anoxia, salinity, submergence	Flower buds, flowers	Glutamate synthase	Chloroplast, peroxisome, cytoplasm, nucleus	IRGSP, 2005
OsP5CS1	5	Salinity, anoxia, osmoregulation	Milk grains, flower buds	Ferredoxin- dependent glutamate synthase	Chloroplast, endoplasmic reticulum, nucleus, cytoplasm, mitochondria, plasma membrane, extracellular, vacuole	Kaikavoosi et al, 2015
OsP5CS2	5	Osmoregulation, anoxia, salinity	Flower buds, flowers	Glutamate synthase	Chloroplast, extracellular, nucleus, vacuole	Kaikavoosi et al, 2015
OsGlyI	5	Salinity, anoxia	Flower buds, leaves before flowering		Chloroplast, cytoplasm	Talukdar et al, 2017
OsGlyII	3	Anoxia, salinity	Flowers, flower buds	Glyoxalase	Cytoplasm, chloroplast, nucleus, extracellular	Huang et al, 2008; Pachauri et al, 2014
OsGlyIII	3	Salinity, anoxia	Leaves and roots before flowering	Ferredoxin-nitrite reductase	Chloroplast, peroxisome, cytoplasm, Golgi apparatus	Huang et al, 2008; Pachauri et al, 2014

Candidate gene	Chr	Response to stress	Tissue specificity	Protein interaction	Subcellular localization	Reference
OsBadh1	8	Submergence, anoxia, salinity	Flowers, roots before flowering	Glutamate synthase	Peroxisome, chloroplast, cytoplsam, nucleus	Amarawathi et al, 2008; Pachauri et al, 2014
OsBadh2	3, 4 and 8	Anoxia, salinity, submergence	Flower buds, flowers	Glutamate synthase	Chloroplast, peroxisome, cytoplasm, nucleus	IRGSP, 2005
OsP5CS1	5	Salinity, anoxia, osmoregulation	Milk grains, flower buds	Ferredoxin- dependent glutamate synthase	Chloroplast, endoplasmic reticulum, nucleus, cytoplasm, mitochondria, plasma membrane, extracellular, vacuole	Kaikavoosi et al, 2015
OsP5CS2	5	Osmoregulation, anoxia, salinity	Flower buds, flowers	Glutamate synthase	Chloroplast, extracellular, nucleus, vacuole	Kaikavoosi et al, 2015
OsGlyI	5	Salinity, anoxia	Flower buds, leaves before flowering		Chloroplast, cytoplasm	Talukdar et al, 2017
OsGlyII	3	Anoxia, salinity	Flowers, flower buds	Glyoxalase	Cytoplasm, chloroplast, nucleus, extracellular	Huang et al, 2008; Pachauri et al, 2014
OsGlyIII	3	Salinity, anoxia	Leaves and roots before flowering	Ferredoxin-nitrite reductase	Chloroplast, peroxisome, cytoplasm, Golgi apparatus	Huang et al, 2008; Pachauri et al, 2014

Developed improved variety	Target trait	Parent	QTL/gene used	Reference
HM80	Submergence resistance	IR49830-7-1-2-2 and KDML105	Sub1	Siangliw et al, 2003
Pusa 1460	Bacterial blight tolerance	IRBB55 and Pusa Basmati 1	xa13 and Xa21	Gopalakrishnan et al, 2008
HM812	Bacterial blight tolerance	IR1188 and KDML105	Xa21, xa5, xa33(t), xa34(t) and qBB11	Korinsak et al, 2009
IC-R28, IC-R68, IC-R32 and IC-R42	Bacterial blight tolerance	IRBB60 and CSR30	Xa21, xa13 and xa5	Baliyan et al, 2018
Pusa Basmati 1	Salt tolerance	FL478 and Pusa Basmati 1	Saltol QTL	Singh V K et al, 2018
Pusa Basmati 1718	Bacterial blight tolerant	SPS97 and PB1121	xa13 and Xa21	Singh V P et al, 2018
HM84	Brown planthopper, blast resistant, and salinity and drought tolerance	Abhaya, Rathu Heenati and KDML105	Sub1A, Xa21, xa5, BphQ12, Bph32, Bph3 and BLQ1	Vanavichit et al, 2018
Two superior BC₂F₁ recombinants	Semi-dwarf and blast tolerance	Pusa Basmati 1637 and Ranbir Basmati	Pi9 and sd1	Samal et al, 2019
Improved Kalanamak lines	Semi-dwarf trait	CSR10 and Kalanamak	Sd1	Srivastava et al, 2019