Validation of molecular markers linked to grain physical and chemical characteristics in recombinant inbred lines of Iranian rice (Oryza sativa L.)

Document Type : Research Paper

Authors

1 M.Sc. Graduated, Department of Plant Production and Genetics Engineering, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.

2 Professor, Department of Plant Production and Genetics Engineering, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.

3 Research Assist. Prof, Rice Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Rasht, Iran.

Abstract

Rice grain quality is a complex characteristic that can be divided into milling quality, appearance quality, cooking quality, and nutritional quality. Most studies on rice grain quality show the importance of chromosomes number one and six in the genetic control of various traits in rice. In the present study, the validation of 35 microsatellite markers linked to grain quality characteristics which all located on two chromosomes one and six, was performed in 144 recombinant inbred lines of F10 population resulted from the cross between Sepidrood (an Iranian improved cultivar with inferior quality) and Gharib (an Iranian local cultivar with good quality). The results of regression analysis showed that 25 markers were linked to different quantitative and qualitative traits, and explained from 16 to 39% of the variance of different traits, but the markers RM253, RM246, RM190, RM104, RM314, RM3827 and RM7434 had stronger linkage. Construction of the linkage map of 35 microsatellite markers in the studied population showed that the map length was 236.5 cM and the average distance between adjacent markers was 6.95 cM. QTL analysis by the composite interval mapping method showed that 40 QTLs controlled the measured traits in the studied population and the phenotypic variance controlled by the identified QTLs ranged from 7.57 to 37.41% for milling quality and head rice percentage, respectively. Based on this analysis, 23 markers were closer to the QTLs controlling the studied traits in this research. Of these, some markers were linked to several different traits. In total, the results of regression analysis and QTL analysis showed that the markers RM253, RM246, RM340, RM243, RM4128, RM314, RM3827, RM7434, RM104 and RM190 were the informative markers linked to grain quality characteristics, which can be used in marker-assisted selection programs in the future.

Keywords

Main Subjects


Allahgholipour M, Moumeni A, Nahvi M, Yekta, M, Zarbafi SS (2012) Identification of parental combinations for improvement of rice grain quality, yield and yield components in rice. Cereal Research. 1(1): 1-10. Aluko G, Martinez C, Tohme J, Castano C, Bergman C, Oard JH (2004) QTL mapping of grain quality traits from the interspecific cross Oryza sativa×O.glaberrima. Theoretical and Applied Genetics. 109(3): 630-639.‏ 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.). Molecular Breeding. 21(1): 49-65. Bao J (2014) Genes and QTLs for rice grain quality improvement. InTech–Open Science Open Mind. 239-278. Bao J, Xie J, Xia Y (2001) Genetic analysis of cooked rice elongation in Indica rice (Oryza sativa L.). Zuo wu xue bao. 27(4): 489-492. Bastin C, Zeng B (2001) QTL Cartigrapher: A refrens manual and toturial for QTL mapping. North Carolina State Univercity.USA. PP.163. Bazrkar-Khatibani L, Fakheri BA, Hosseini-Chaleshtori M, Mahender A, Mahdinejad N, Ali J (2019) Genetic Mapping and Validation of Quantitative Trait Loci (QTL) for the Grain Appearance and Quality Traits in Rice (Oryza sativa L.) by Using Recombinant Inbred Line (RIL) Population. International Journal of Genomics. 2019. Bernier J, Kumar A, Ramaiah V, Spaner D, Atlin G (2007) A large‐effect QTL for grain yield under reproductive‐stage drought stress in upland rice. Crop Science. 47(2): 507-516.‏ Bian J, Li C, He H, Shi H, Yan S (2014) Identification and analysis of QTLs for grain quality traits in rice using an introgression lines population. Euphytica. 195(1): 83-93. Borale SU, Kumbhar SD (2021) Use of Simple Sequence Repeat Marker to Assess the Segregating Population of Rice (Oryza sativa L.) in field for Grain Length Quality Parameter. European Journal of Agriculture and Food Sciences. 3(1): 132-135.‏ Dai L, Wang L, Leng Y, Yang Y, Huang L, Chen L, Zhu L (2016) Quantitative trait loci mapping for appearance quality in short-grain rice. Crop Science. 56(4): 1484-1492. Deborah DA, Vemireddy LR, Roja V, Patil S, Choudhary GP, Noor S, Anuradha G (2017) Molecular dissection of QTL governing grain size traits employing association and linkage mapping in Basmati rice. Molecular Breeding. 37(6). 77. Ebadi AA, Farshadfar E, Rabiei B (2013) Mapping QTLs controlling cooking and eating quality indicators of Iranian rice using RILs across three years. Australian Journal of Crop Science. 7(10). 1494.‏ Eizenga GC, Neves PC, Bryant RJ, Agrama HA, Mackill DJ (2016) Evaluation of a M-202× Oryza nivara advanced backcross mapping population for seedling vigor, yield components and quality. Euphytica. 208(1): 157-171.‏ Fan CC, Yu XQ, Xing YZ, Xu CG, Luo LJ, Zhang Q (2005) The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population. Theoretical and Applied Genetics. 110(8): 1445-1452.‏ Fu JR, Zhu LX, Sun XT, Zhou DH, Ouyang LJ, Bian JM, Xu J (2015) Genetic analysis of grain shape and weight after cutting rice husk. Genet Mol Res. 14(4): 17739-17748.‏ Gaikwad KB, Singh N, Bhatia D, Sharma N, Bains NS, Bharaj TS, Singh K (2018) Heterotic response of genomic regions derived from Oryza rufipogon and O.nivara in improving grain morphology and quality of indica rice (Oryza sativa L.). Indian J. Genet. 78(2): 155-165.‏ Gao YM, Zhu J, Song, YS, He CX, Shi CH, Xing YZ (2004) Analysis of digenic epistatic effects and QE interaction effects QTL controlling grain weight in rice. Journal of Zhejiang University-SCIENCE A. 5(4): 371-377.‏ Guleria S, Sharma V, Marathi B, Anand S, Singh N.K, Mohapatra T, Singh A.K (2012) Molecular mapping of grain physico-chemical and cooking quality traits using recombinant inbred lines in rice (Oryza sativa L.). Journal of plant biochemistry and biotechnology. 21(1): 1-10.‏ Hagiwara WE, Onishi K, Takamure I, Sano Y (2006) Transgressive segregation due to linked QTLs for grain characteristics of rice. Euphytica. 150(1): 27-35.‏ Halder T, Hoque ME, Islam MM, Ali L, Chowdhury AK (2016) Morphomolecular characterization of local boro rice (Oryza sativa L.) germplasm. Bangladesh Journal of Plant Breeding and Genetics. 29(2): 01-09.‏ Hosseini-Chaleshtori M, Sorkheh K (2014) Rice Quality (Aspects of Quantitative, Molecular and Genomic).‬ Sina-Teb Press, Tehran, Iran, P. 178. Ishimaru K, Hirotsu N, Madoka Y, Murakami N, Hara N, Onodera H, Katoh E (2013) Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nature genetics. 45(6): 707-711.‏ Juliano BO, Villareal CP (1993) Grain quality evaluation of world rices. Int. Rice Res. Inst. Kim HY, Kim KM (2016) Mapping of grain alkali digestion trait using a Cheongcheong/Nagdong doubled haploid population in rice. Journal of Plant Biotechnology. 43(1): 76-81.‏ Kordrostami M, Rabiei B, Sabouri A, Sabouri H (2015) Identification of QTLs Controlling Cooking and Milling Quality Traits in an F2: 4 Population of Rice (Oryza sativa L.). Journal of Crop Breeding. 7(16): 16-26. Kosambi DD (1943) The estimation of map distance from recombination values, Annals of Human Genetics. 12: 172-175.‏ Lee SH (2005) Analysis of rice quality and environmental factors based on different agricultural regions in Gyeongbuk province (Doctoral dissertation, Ph D. Dissertation Thesis, Kyungpook National University, Daegu).‏ Li SQ, CUI GK, GUAN CR, Jun WANG, LIANG GH (2011) QTL detection for rice grain shape using chromosome single segment substitution lines. Rice Science. 18(4): 273-278.‏ Li-Feng L, Hong-Liang Z, Ping M, Yan-Ying Q, Zi-Chao L (2007) Construction and evaluation of near-isogenic lines for major QTLs of basal root thickness and 1000-grain-weight in lowland and upland rice. Chinese Journal of Agricultural Biotechnology. 4(3): 199-205.‏ Lou J, Chen L, Yue G, Lou Q, Mei H, Xiong L, Luo L (2009) QTL mapping of grain quality traits in rice. Journal of cereal science. 50(2): 145-151. Mallikarjuna BP, Shivakumar N, Devendrappa J, Sheela VD, Bharamappa G, Halikatti G (2014) Combining ability analysis for grain yield and its attributes in Rice (Oryza sativa L.). SAARC Journal of Agriculture. 12(1): 1-8.‏ Maroof MS, Biyashev RM, Yang GP, Zhang Q, Allard RW (1994) Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics. Proceedings of the National Academy of Sciences. 91(12): 5466-5470. Mei D, Yu Z, Gong C, Chen X, Zhu Q, Wang S (2018) Validation and Fine Mapping a Multifunction Region qPCG10/qDC10 Conferring Chalkiness and Grain Shape of Rice. Crop Science. 58(2): 639-649. Ooijen J W, Voorrips RE (2002) JoinMap: version 3.0: software for the calculation of genetic linkage maps. University and Research Center.‏ Pang Y, Ali J, Wang X, Franje NJ, Revilleza JE, Xu J, Li Z (2016) Relationship of rice grain amylose, gelatinization temperature and pasting properties for breeding better eating and cooking quality of rice varieties. PLoSOne. 11(12). e0168483.‏ Ponce KS, Ye G, Zhao X (2018) Qtl identification for cooking and eating quality in indica rice using multi-parent advanced generation intercross (MAGIC) population. Frontiers in plant science. 9.‏868. Qi P, Lin YS, Song XJ, Shen JB, Huang W, Shan JX and Lin HX (2012) The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3. Cell research. 22(12): 1666-1680.‏ Qiu X, Chen K, Lv W, Ou X, Zhu Y, Xing D, Li Z (2017a) Examining two sets of introgression lines reveals background-independent and stably expressed QTL that improve grain appearance quality in rice (Oryza sativa L.). Theoretical and Applied Genetics. 130(5): 951-967.‏ Qiu X, Du B, Hu H, Ou X, Lv W, Yang L, Wang X (2017b) Scanning QTLs for Grain Shape using Two Sets of Introgression Lines in Rice. International Journal of Agriculture and Biology. 19(3).‏ Rabiei B, Kordrostami M, Sabouri A (2015) Identifi cation of QTLs for yield related traits in indica type rice using SSR and ALFP markers, Agriculturae Conspectus Scientificus. 80: 91-99. Rabiei B, Valizadeh M, Ghareyazie B, Moghaddam M, Ali A J (2004) Identification of QTLs for rice grain size and shape of Iranian cultivars using SSR markers. Euphytica. 137(3): 325-332.‏ Sabouri A, Rabiei B, Toorchi M, Aharizad S, Moumeni A (2012) Mapping quantitative trait loci (QTL) associated with cooking quality in rice (Oryza sativa L.). Australian Journal of Crop Science. 6(5): 808-814.‏ Song XJ, Kuroha T, Ayano M, Furuta T, Nagai K, Komeda N, Ashikari M (2015) Rare allele of a previously unidentified histone H4 acetyltransferase enhances grain weight, yield, and plant biomass in rice. Proceedings of the National Academy of Sciences. 112(1): 76-81.‏ Sravani D, Neeraja CN, Ravindrababu V, Reddy MR (2020) Identification of SSR Markers Linked to Regions Associated with Protein Content in F2 Population of Rice (Oryza sativa L.). Current Journal of Applied Science and Technology. 32-37.‏ Swamy B M, Kaladhar K, Shobha Rani N, Prasad GSV, Viraktamath BC, Reddy GA, Sarla N (2012) QTL analysis for grain quality traits in 2 BC2F2 populations derived from crosses between Oryza sativa cv Swarna and 2 accessions of O.nivara. Journal of Heredity. 103(3): 442-452.‏ Tavassoli F (2003) Assessment of periodical storage on cooking Rice quality. Rice Research Institute of Iran (RRII) Edt. 23 pp. Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q, Ma H (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nature genetics. 40(11). 1370. Wang LQ, Liu WJ, Xu Y, He YQ, Luo LJ, Xing YZ, Zhang Q (2007) Genetic basis of 17 traits and viscosity parameters characterizing the eating and cooking quality of rice grain. Theoretical and Applied Genetics. 115(4): 463-476.‏ Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X, Fu X (2012) Control of grain size, shape and quality by OsSPL16 in rice. Nature genetics. 44(8). 950.‏ Yamamoto T, Nagasaki H, Yonemaru JI, Ebana K, Nakajima M, Shibaya T, Yano M (2010) Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. BMC genomics. 11(1): 1-14.‏ Yan B, Liu R, Li Y, Wang Y, Gao G, Zhang Q, He Y (2014) QTL analysis on rice grain appearance quality, as exemplifying the typical events of transgenic or backcrossing breeding. Breeding science. 64(3): 231-239.‏ Yao X, Wang J, Liu J, Zhang J, Ren C, Ma D, Xu Z (2017) Mapping quantitative trait loci associated with starch paste viscosity in rice (Oryza sativa L.) under different environmental conditions. Plant Breeding. 136(5): 591-602. Yoshida S, Ikegami M, Kuze J, Sawada K, Hashimoto Z, Ishii T, Kamijima O (2002) QTL analysis for plant and grain characters of sake-brewing rice using a doubled haploid population. Breeding Science. 52(4): 309-317. Yu J, Miao J, Zhang Z, Xiong H, Zhu X, Sun X, Li Z (2018) Alternative splicing of Os LG 3b controls grain length and yield in japonica rice. Plant biotechnology journal 16(9):1667-1678.‏ Yun BW, Kim MG, Handoyo T, Kim KM (2014) Analysis of rice grain quality-associated quantitative trait loci by using genetic mapping. American Journal of Plant Sciences. 5(09). 1125. Zhang QF, Zhang YD, Zhen ZHU, Ling ZHAO, Zhao QY, Ling XU, Wang CL (2008) Inheritance analysis and QTL mapping of rice starch viscosity (rapid visco analyzer profile) characteristics. Rice Science. 15(3): 186-194.‏ Zhang S, Hao H, Liu X, Li Y, Ma X, Liu W, Luan W (2021) SDG712, a Putative H3K9-Specific Methyltransferase Encoding Gene, Delays Flowering through Repressing the Expression of Florigen Genes in Rice. Rice 14(1):1-13.‏ Zhao D, Li P, Wang L, Sun LXiaD, Luo L, He Y (2017) Genetic dissection of large grain shape in rice cultivar ‘Nanyangzhan’and validation of a grain thickness QTL (qGT3.1) and a grain length QTL (qGL3.4). Molecular breeding. 37(3). 42.‏ Zhao X, Zhou L, Ponce K, Ye G (2015) The usefulness of known genes/QTLs for grain quality traits in an indica population of diverse breeding lines tested using association analysis. Rice. 8(1): 1-13.‏ Zheng TQ, Xu JL, Li ZK, Zhai HQ, Wan JM (2007) Genomic regions associated with milling quality and grain shape identified in a set of random introgression lines of rice (Oryza sativa L.). Plant breeding. 126(2): 158-163.‏ Zhou H, Xia D, He Y (2020) Rice grain quality traditional traits for high quality rice and health-plus substances. Molecular Breeding. 40(1): 1-17. Zhou J, You A, Ma Z, Zhu L, He G (2012) Association analysis of important agronomic traits in japonica rice germplasm. African journal of Biotechnology. 11(12): 2957-2970.‏