Please wait a minute...
Journal of Integrative Agriculture  2023, Vol. 22 Issue (3): 679-690    DOI: 10.1016/j.jia.2022.07.001
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Development of new aromatic rice lines with high eating and cooking qualities

Kanokwan KAEWMUNGKUN1, 2, Keasinee TONGMARK1, Sriprapai CHAKHONKAEN1, Numphet SANGARWUT1, Thiwawan WASINANON1, Natjaree PANYAWUT1, Khanittha DITTHAB1, Kannika SIKAEWTUNG1, QI Yong-bin3, Sukanya DAPHA4, Atikorn PANYA1, Natthaporn PHONSATTA1, Amorntip MUANGPROM1#

1 National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Pathum Thani 12120, Thailand  

2 Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Pathum Thani 12120, Thailand

3 Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P.R.China

4 Khlong Luang Rice Research Center, Rice Department, Pathum Thani 12120, Thailand

Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      

Rice is the staple food for about half of the world’s population.  Preferred by consumers, aromatic rice is a special type of rice with great commercial value.  Cooking and eating qualities and aroma are the major grain qualities favored by most consumers.  Currently, most of the available aromatic varieties have low yields and some undesirable agronomic traits.  Thus, there is an urgent need to develop better aromatic rice varieties.  This work aims to identify rice germplasm lines that have good grain quality and to develop new varieties with desirable traits.  Thirty-six out of 188 germplasm lines were found to have betaine aldehyde dehydrogenase 2 (badh2) controlling the aroma and were analyzed for their 2-acetyl-1-pyrroline (2AP) contents.  Then, 17 of those lines were found to have alleles for low amylose content and low gelatinization temperature, controlled by waxy and starch synthase IIa (SSIIa), respectively, suggesting that they are aromatic rice lines with high cooking and eating qualities.  A total of 158 F7 recombinant inbred lines (RILs) generated from five crosses of the selected germplasm lines were planted for phenotypic and yield observations, resulting in 27 F8 RILs selected for yield evaluation and genotyping.  Finally, four out of the seven F9 aromatic RILs showed high yield, high 2AP production, and low amylose content, in agreement with their genotypes.  The other three F9 RILs were aromatic rice lines with high amylose content and high yield.  Because consumer preferences for grain quality vary depending on regions and ethnic groups, the high-yielding aromatic RILs generated from this study can be used to increase the yield of Thai rice and to raise market value and farm profits.

Keywords:  germplasm       functional marker        aromatic rice        badh2        waxy        SSIIa        RILs  
Received: 03 December 2021   Accepted: 16 February 2022

This research was funded by the Project of the Science and Technology Department of Zhejiang Province, China (LGN21C130005, 2021C02063-2) and the Agricultural Research Development Agency, Thailand (ARDA, PRP6205031170).  

About author:  #Correspondence Amorntip Muangprom, Tel: +66-2-5646700 ext 3348, Fax: +66-2-5646707, E-mail:

Cite this article: 

Kanokwan KAEWMUNGKUN, Keasinee TONGMARK, Sriprapai CHAKHONKAEN, Numphet SANGARWUT, Thiwawan WASINANON, Natjaree PANYAWUT, Khanittha DITTHAB, Kannika SIKAEWTUNG, QI Yong-bin, Sukanya DAPHA, Atikorn PANYA, Natthaporn PHONSATTA, Amorntip MUANGPROM. 2023. Development of new aromatic rice lines with high eating and cooking qualities. Journal of Integrative Agriculture, 22(3): 679-690.

Addison C K, Angira B, Kongchum M, Harrell D L, Baisakh N, Linscombe S D, Famoso A N. 2020. Characterization of haplotype diversity in the BADH2 aroma gene and development of a KASP SNP assay for predicting aroma in U.S. rice. Rice, 13, 47.
Ahn S N, Bollich C N, Tanksley S D. 1992. RFLP tagging of a gene for aroma in rice. Theoretical and Applied Genetics, 84, 825–828.
Akhter M, Mahmood A, Haider Z, Saleem U. 2019. Development of an aromatic high yielding basmati rice variety having extra long grains and short duration. Journal of Rice Research, 7, 1–6.
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.). Molecular Breeding, 21, 49–65.
Andersen J R, Lübberstedt T. 2003. Functional markers in plants. Trends in Plant Science, 8, 554–560.
Bao J, Corke H, Sun M. 2006. Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.). Theoretical and Applied Genetics, 113, 1171–1183.
Bora A, Choudhury P R, Pande V, Mandal A B. 2016. Assessment of genetic purity in rice (Oryza sativa L.) hybrids using microsatellite markers. 3 Biotech, 6, 1–7.
Bradbury L M T, Fitzgerald T L, Henry R J, Jin Q, Waters D L E. 2005. The gene for fragrance in rice. Plant Biotechnology Journal, 3, 363–370.
Bradbury L M T, Gillies S A, Brushett D J, Waters D L, Henry R J. 2008. Inactivation of an aminoaldehyde dehydrogenase is responsible for fragrance in rice. Plant Molecular Biology, 68, 439–449.
Bradbury L M T, Henry R J, Jin Q, Reinke R F, Waters D L. 2005. A perfect marker for fragrance genotyping in rice. Molecular Breeding, 16, 279–283. 
Buttery R G, Ling L C, Juliano B O, Turnbaugh J G. 1983. Cooked rice aroma and 2-acetyl-1-pyrroline. Journal of Agricultural and Food Chemistry, 31, 823–826.
Champagne E T, Lyon B G, Min B K, Vinyard B T, Bett K L, Barton F E, Webb B D, McClung A M, Moldenhauer K A, Linscombe S. 1998. Effects of postharvest processing on texture profile analysis of cooked rice. Cereal Chemistry, 75, 181–186.
Fitzgerald T L, Waters D L E, Henry R J. 2008. The effect of salt on betaine aldehyde dehydrogenase transcript levels and 2-acetyl-1-pyrroline concentration in fragrant and non-fragrant rice (Oryza sativa L.). Plant Sciences, 175, 539–546.
Fu D, Xiao M, Hayward A, Fu Y, Liu G, Jiang G, Zhang H. 2014. Utilization of crop heterosis: A review. Euphytica, 197, 161–173. 
Gao L, Zhou M, Chen R, Gao H, Yan Q, Zhou W, Deng G. 2012. Developing and validating the functional marker of rice waxy gene, M-Wx. Rice Genomics and Genetics, 3, 61–65.
Gaur A, Wani S, Deepika P, Bharti N, Malav A, Shikari A, Bhat A. 2016. Understanding the fragrance in rice. Rice Research, 4, e125. 
Goufo P, Duan M, Wongpornchai S, Tang X. 2010. Some factors affecting the concentration of the aroma compound 2-acetyl-1-pyrroline in two fragrant rice cultivars grown in South China. Frontiers of Agriculture in China, 4, 1–9.
Grimm C C, Bergman C, Delgado J T, Bryant R. 2001. Screening for 2-acetyl-1-pyrroline in the headspace of rice using SPME/GC-MS. Journal of Agricultural and Food Chemistry, 49, 245–249.
Guo J, Xu X, Li W, Zhu W, Zhu H, Liu Z, Luan X, Dai Z, Liu G, Zhang Z. 2016. Overcoming inter-subspecific hybrid sterility in rice by developing indica-compatible japonica lines. Scientific Reports, 6, 1–9.
Hashemi F S G, Rafii M Y, Ismail M R, Mahmud T M M, Rahim H A, Asfaliza R, Malek M A, Latif M A. 2013. Biochemical, genetic and molecular advances of fragrance characteristics in rice. Critical Reviews in Plant Sciences, 32, 445–457. 
He Q, Park Y J. 2015. Discovery of a novel fragrant allele and development of functional markers for fragrance in rice. Molecular Breeding, 35, 217.
Ingvardsen C R, Schejbel B, Lübberstedt T. 2008. Functional markers in resistance breeding. In: Lüttge U, Beyschlag W, Murata J, eds., Progress in Botany. Springer Berlin Heidelberg, Berlin, Heidelberg. pp. 61–87.
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 Production Science, 7, 178–183.
Ji Q, Lu J, Chao Q, Zhang Y, Zhang M, Gu M, Xu M. 2010. Two sequence alterations, a 136 bp InDel and an A/C polymorphic site, in the S5 locus are associated with spikelet fertility of indica–japonica hybrid in rice. Journal of Genetics and Genomics, 37, 57–68.
Jin L, Lu Y, Shao Y, Zhang G, Xiao P, Shen S, Corke H, Bao J. 2010. Molecular marker assisted selection for improvement of the eating, cooking and sensory quality of rice (Oryza sativa L.). Journal of Cereal Science, 51, 159–164.
Juliano B O. 1971. A simplified assay for milled rice amylose. Cereal Science Today, 16, 334–360.
Juliano B O, Villareal C. 1993. Grain Quality Evaluation of World Rices. International Rice Research Institute, Manila, Philippines. 
Kim S R, Ramos J, Ashikari M, Virk P S, Torres E A, Nissila E, Hechanova S L, Mauleon R, Jena K K. 2016. Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L. Rice, 9, 1–17.
Kobayashi A, Hori K, Yamamoto T, Yano M. 2018. Koshihikari: A premium short-grain rice cultivar - Its expansion and breeding in Japan. Rice, 11, 1–12.
Kumar I, Khush G S. 1986. Gene dosage effects of amylose content in rice endosperm. Japanese Journal of Genetics, 61, 559–568.
Kumar M, Vishwanath K, Shivakumar N, Prasad R, Radha S, Ramegowda B. 2012. Utilization of SSR markers for seed purity testing in popular rice hybrids (Oryza sativa L.). Annals of Plant Sciences, 1, 1–5.
Lapitan V C, Brar D S, Abe T, Redoña E D. 2007. Assessment of genetic diversity of Philippine rice cultivars carrying good quality traits using SSR markers. Breeding Science, 57, 263–270.
Li H, Gilbert R G. 2018. Starch molecular structure: The basis for an improved understanding of cooked rice texture. Carbohydrate Polymers, 195, 9–17. 
Li H, Prakash S, Nicholson T M, Fitzgerald M A, Gilbert R G. 2016. The importance of amylose and amylopectin fine structure for textural properties of cooked rice grains. Food Chemistry, 196, 702–711. 
Limjumroon T. 2017. Rice. [2021-07-19]. 
Little R R. 1958. Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chemistry, 35, 111–126. 
Liu Y, Zhang A, Wang F, Wang J, Bi J, Kong D, Zhang F, Luo L, Liu G, Yu X. 2019. Development and validation of a PCR-based functional marker system for identifying the low amylose content-associated gene Wxh in rice. Breeding Science, 69, 702–706.
Mathure S, Shaikh A, Renuka N, Wakte K, Jawali N, Thengane R, Nadaf A. 2011. Characterisation of aromatic rice (Oryza sativa L.) germplasm and correlation between their agronomic and quality traits. Euphytica, 179, 237–246.
Mo Z, Li W, Pan S, Fitzgerald T L, Xiao F, Tang Y, Wang Y, Duan M, Tian H, Tang X. 2015. Shading during the grain filling period increases 2-acetyl-1-pyrroline content in fragrant rice. Rice, 8, 1–10.
Murray M, Thompson W F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research, 8, 4321–4326.
Nakata M, Miyashita T, Kimura R, Nakata Y, Takagi H, Kuroda M, Yamaguchi T, Umemoto T, Yamakawa H. 2018. MutMapPlus identified novel mutant alleles of a rice starch branching enzyme II b gene for fine-tuning of cooked rice texture. Plant Biotechnology Journal, 16, 111–123.
Nelson O E, Rines H W. 1962. The enzymatic deficiency in the waxy mutant of maize. Biochemical and Biophysical Research Communications, 9, 297–300.
Ouyang Y, Zhang Q. 2018. The molecular and evolutionary basis of reproductive isolation in plants. Journal of Genetics and Genomics, 45, 613–620.
Pratap A, Bisen P, Loitongbam B, Singh P. 2018. Assessment of genetic variability for yield and yield components in rice (Oryza sativa L.) germplasms. International Journal of Bio-Resource and Stress Management, 9, 87–92.
Prodhan Z H, Shu Q Y. 2020. Rice aroma: A natural gift comes with price and the way forward. Rice Science, 27, 86–100.
Shao G, Tang A, Tang S, Luo J, Jiao G, Wu J, Hu P. 2011. A new deletion mutation of fragrant gene and the development of three molecular markers for fragrance in rice. Plant Breeding, 130, 172–176.
Singh A, Singh P, Nandan R, Rao M. 2012. Grain quality and cooking properties of rice germplasm. Annals of Plant and Soil Research, 14, 52–57. 
Song J M, Arif M, Zhang M, Sze S H, Zhang H B. 2019. Phenotypic and molecular dissection of grain quality using the USDA rice mini-core collection. Food Chemistry, 284, 312–322.
Sun J, Liu D, Wang J Y, Ma D R, Tang L, Gao H, X Z J, Chen W F. 2012. The contribution of intersubspecific hybridization to the breeding of super-high-yielding japonica rice in northeast China. Theoretical and Applied Genetics, 125, 1149–1157. 
Tian Z, Qian Q, Liu Q, Yan M, Liu X, Yan C, Liu G, Gao Z, Tang S, Zeng D. 2009. Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proceedings of the National Academy of Sciences of the United States of America, 106, 21760–21765.
Tongmark K, Chakhonkaen S, Sangarwut N, Wasinanon T, Panyawut N, Ditthab K, Sikaewtung K, Janbuathong S, Taprab S, Deerusamee C. 2021. Development of high yielding two-line hybrid rice in Thailand. ScienceAsia, 47, 153–162.
Wanchana S, Toojinda T, Tragoonrung S, Vanavichit A. 2003. Duplicated coding sequence in the waxy allele of tropical glutinous rice (Oryza sativa L.). Plant Science, 165, 1193–1199.
Wang C, Zhang Y, Zhu Z, Chen T, Zhao L, Lin J, Zhou L. 2010. Development of a new japonica rice variety Nan-jing 46 with good eating quality by marker assisted selection. Rice Genomics and Genetics, 7, 1070–1076. 
Zhang G Q. 2020. Prospects of utilization of inter-subspecific heterosis between indica and japonica rice. Journal of Integrative Agriculture, 19, 1–10.
[1] ZHANG Yong-fang, ZHANG Chun-yan, ZHANG Bo, YIN Man, HONG Hui-long, YU Li-li, GAO Hua-wei, GU Yong-zhe, LIU Zhang-xiong, LI Fu-heng, QIU Li-juan. Establishment and application of an accurate identification method for fragrant soybeans[J]. >Journal of Integrative Agriculture, 2021, 20(5): 1193-1203.
[2] GU Xiao-zhen, CAO Ya-cong, ZHANG Zheng-hai, ZHANG Bao-xi, ZHAO Hong, ZHANG Xiao-min, WANG Hai-ping, LI Xi-xiang, WANG Li-hao. Genetic diversity and population structure analysis of Capsicum germplasm accessions[J]. >Journal of Integrative Agriculture, 2019, 18(6): 1312-1320.
[3] Wasan Jaruchai, Tidarat Monkham, Sompong Chankaew, Bhalang Suriharn, Jirawat Sanitchon. Evaluation of stability and yield potential of upland rice genotypes in North and Northeast Thailand[J]. >Journal of Integrative Agriculture, 2018, 17(01): 28-36.
[4] LENG Peng-fei, Thomas Lübberstedt, XU Ming-liang. Genomics-assisted breeding - A revolutionary strategy for crop improvement[J]. >Journal of Integrative Agriculture, 2017, 16(12): 2674-2685.
[5] LI Zai-yun, WANG You-ping. Cytogenetics and germplasm enrichment in Brassica allopolyploids in China[J]. >Journal of Integrative Agriculture, 2017, 16(12): 2698-2708.
[6] CHEN Dan, WU Xiao-yang, WU Kuo, ZHANG Jin-peng, LIU Wei-hua, YANG Xin-ming, LI Xiu-quan, LU Yu-qing, LI Li-hui. Novel and favorable genomic regions for spike related traits in a wheat germplasm Pubing 3504 with high grain number per spike under varying environments[J]. >Journal of Integrative Agriculture, 2017, 16(11): 2386-2401.
[7] WANG Jian, HOU Lu, WANG Ruo-yu, HE Miao-miao, LIU Qing-chang. Genetic diversity and population structure of 288 potato (Solanum tuberosum L.) germplasms revealed by SSR and AFLP markers[J]. >Journal of Integrative Agriculture, 2017, 16(11): 2434-2443.
[8] SHENG Fang, CHEN Shu-ying, TIAN Jia, LI Peng, QIN Xue, WANG Lei, LUO Shu-ping, LI Jiang. Morphological and ISSR molecular markers reveal genetic diversity of wild hawthorns (Crataegus songorica K. Koch.) in Xinjiang, China[J]. >Journal of Integrative Agriculture, 2017, 16(11): 2482-2498.
[9] SHI Xiao-hua, HU Rui-fa. Rice variety improvement and the contribution of foreign germplasms in China[J]. >Journal of Integrative Agriculture, 2017, 16(10): 2337-2345.
[10] ZHANG Xiao-min, ZHANG Zheng-hai, GU Xiao-zhen, MAO Sheng-li, LI Xi-xiang, Jo?l Chadoeuf, Alain Palloix, WANG Li-hao, ZHANG Bao-xi. Genetic diversity of pepper (Capsicum spp.) germplasm resources in China reflects selection for cultivar types and spatial distribution[J]. >Journal of Integrative Agriculture, 2016, 15(9): 1991-2001.
[11] GUO Xiu-hua, CAI Cai-ping, YUAN Dong-dong, ZHANG Ren-shan, XI Jing-long, GUO Wang-zhen. Development and identification of Verticillium wilt-resistant upland cotton accessions by pyramiding QTL related to resistance[J]. >Journal of Integrative Agriculture, 2016, 15(3): 512-520.
[12] QIU Cai-ling, ZHANG Zhi-xiang, LI Shi-fang, BAI Yan-ju, LIU Shang-wu, FAN Guo-quan, GAO Yan-ling, ZHANG Wei, ZHANG Shu, Lü Wen-he, Lü Dian-qiu. Occurrence and molecular characterization of Potato spindle tuber viroid (PSTVd) isolates from potato plants in North China[J]. >Journal of Integrative Agriculture, 2016, 15(2): 349-363.
[13] JIA Yin-hua, SUN Jun-ling, WANG Xi-wen, ZHOU Zhong-li, PAN Zao-e, HE Shou-pu, PANG Bao-yin, WANG Li-ru , DU Xiong-ming. Molecular Diversity and Association Analysis of Drought and Salt Tolerance in Gossypium hirsutum L. Germplasm[J]. >Journal of Integrative Agriculture, 2014, 13(8): 1845-1853.
No Suggested Reading articles found!