Population Structure and Marker-Trait Association in Indigenous Aromatic Rice
Received date: 2016-04-09
Accepted date: 2016-08-18
Online published: 2017-03-03
Joha rice of Assam is a class of rice with aroma, good cooking qualities and excellent palatability, which are grown in different places of Assam with their adaptability to local situations. A total of 143 simple sequence repeat markers were used in this study to reveal sufficient genetic variations among the 40 Joha and 14 non-Joha rice genotypes. Polymorphism information content of these markers were from 0.17 to 0.88, where the average of 3.7 alleles were observed. The model-based population assignment and dendrogram analysis identified three distinct groups in the 54 rice accessions, which established a clear identity of Joha accessions from the Basmati accessions, indicating high diversity and strong population structure in Joha rice. Furthermore, a total of 29 significant marker-trait associations (P < 0.05) for 10 characters were detected. The QTLs related with yield and grain quality can be used effectively in crop improvement programs and for further fine mapping and validation of specific genes to develop gene-based perfect markers in rice breeding and for mining of better alleles of these genes in Joha rice collections.
Rekha Talukdar Preeti, Rathi Sunayana, Pathak Khanin, Kumar Chetia Sanjay, Nath Sarma Ramendra . Population Structure and Marker-Trait Association in Indigenous Aromatic Rice[J]. Rice Science, 2017 , 24(3) : 145 -154 . DOI: 10.1016/j.rsci.2016.08.009
| 1 | Ahmed N, Mir J I, Mir R R, Rather N A, Rashid R, Wani S H, Shafi W, Mir H, Sheikh M A.2012. SSR and RAPD analysis of genetic diversity in walnut (Juglans regia L.) genotypes from Jammu and Kashmir, India. Physiol Mol Biol Plants, 18(2): 149-156. |
| 2 | Allard R W.1992. Predictive methods for germplasm identification. In: Stalker H T, Murphy J P. Plant Breeding in the 1990s. Wallingford Oxon, UK, CAB International: 119-146. |
| 3 | 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 Breeding, 21(1): 49-65. |
| 4 | Bai X F, Luo L J, Yan W H, Kovi M R, Zhan W, Xing Y Z.2010. Genetic dissection of rice grain shape using a recombinant inbred line population derived from two contrasting parents and fine mapping a pleiotropic quantitative trait locusqGL7. BMC Genet, 11: 16. |
| 5 | Besnier F, Glover K A.2013. Parallel structure: A R package to distribute parallel runs of the population genetics program structure on multi-core computers.PLoS One, 8: e70651. |
| 6 | Bian J M, He H H, Shi H, Zhu C L, Peng X S, Li C J, Fu J R, He X P, Chen X R, Hu L R, Ouyang L J.2013. Dynamic QTL detection and analysis of tiller number before and after heading in japonica rice.Aust J Crop Sci, 7(8): 1189-1197. |
| 7 | Blair M W, McCouch S R.1997. Microsatellite and sequenced- tagged site markers diagnostic for the rice bacterial leaf blight resistance genexa-5. Theor Appl Genet, 95: 174-184. |
| 8 | Bradbury L M T, Henry R J, Jin Q, Reinke R F, Waters D L.2005. A perfect marker for fragrance genotyping in rice.Mol Breeding, 16(4): 279-283. |
| 9 | Brondani C, Rangel P H N, Brondani R P V, Ferreira M E.2002. QTL mapping and introgression of yield-related traits fromOryza glumaepatula to cultivated rice(Oryza sativa) using microsatellite markers. Theor Appl Genet, 104(6): 1192-1203. |
| 10 | Das A, Kesari T V, Rangan L.2010. Aromatic Joha rice of Assam: A review.Agric Rev, 31(1): 1-10. |
| 11 | Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu H O, Buffalo V, Zerbino D R, Diekhans M, Nguyen N, Ariyaratne P N, Sung W K, Ning Z M, Haimel M, Simpson J T, Fonseca N A, Birol I, Docking T R, Ho I Y, Rokhsar D S, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz M C, Kelley D R, Phillippy A M, Koren S, Yang S P, Wu W, Chou W C, Srivastava A, Shaw T I, Ruby J G, Skewes-Cox P, Betegon M, Dimon M T, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez Gonzalez R, Leggett R, MacLean D, Xia F F, Luo R B, Li Z Y, Xie Y L, Liu B H, Gnerre S, MacCallum I, Przybylski D, Ribeiro F J, Yin S Y, Sharpe T, Hall G, Kersey P J, Durbin R, Jackman S D, Chapman J A, Huang X Q, DeRisi J L, Caccamo M, Li Y G, Jaffe D B, Green R E, Haussler D, Korf I, Paten B.2011. Assemblathon 1: A competitive assessment of de novo short read assembly methods.Genome Res, 21(12): 2224-2241. |
| 12 | Evanno G, Regnaut S, Goudet J.2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study.Mol Ecol, 14: 2611-2620. |
| 13 | Falush D, Stephens M, Pritchard J K.2003. Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies.Genetics, 164(4): 1567-1587. |
| 14 | Garris A J, Tai T H, Coburn J, Kresovich S, McCouch S.2005. Genetic structure and diversity inOryza sativa L. Genetics, 169(3): 1631-1638. |
| 15 | Grist D.1983. Rice: Longman. New York, USA. |
| 16 | Johanson H W, Robinson H F, Comstock R E.1955. Estimates of genetic and environmental variability in soybean.Agron J, 47: 314-318. |
| 17 | Joshi S P, Gupta V S, Aggarwal R K, Ranjekar P K, Brar D S.2000. Genetic diversity and phylogenetic relationship as revealed by inter simple sequence repeat (ISSR) polymorphism in the genusOryza. Theor Appl Genet, 100(8): 1311-1320. |
| 18 | Kaw R N, Aquino R C, Moon H P, Yae J D, Haq N.1999. Variability and interrelations in rice under cold stress environments.Oryza, 36(1): 1-4. |
| 19 | Liu G F, Yang J, Xu H M, Hayat Y, Zhu J.2008. Genetic analysis of grain yield conditioned on its component traits in rice (Oryza sativa L.). Aust J Agric Res, 59(2): 189-195. |
| 20 | Marri P R, Sarla N, Reddy L V, Siddiq E A.2005. Identification and mapping of yield-related QTL from an Indian accession ofOryza rufipogon. BMC Genet, 6(1): 33. |
| 21 | Moncada P, Martínez C P, Borrero J, Chatel M, Gauch Jr H, Guimaraes E, Tohme J, McCouch S R.2001. Quantitative trait loci for yield and yield components in anOryza sativa × Oryza rufipogon BC2F2 population evaluated in an upland environment. Theor Appl Genet, 102(1): 41-52. |
| 22 | Nachimuthu V V, Muthurajan R, Duraialaguraja S, Sivakami R, Pandian B A, Ponniah G, Gunasekaran K, Swaminathan M, Suji K K, Sabariappan R.2015. Analysis of population structure and genetic diversity in rice germplasm using SSR markers: An initiative towards association mapping of agronomic traits inOryza sativa. Rice, 8: 30. |
| 23 | Nei M.1973. Analysis of gene diversity in subdivided populations.Proc Natl Acad Sci USA, 70(12): 3321-3323. |
| 24 | Ni J J, Colowit P M, Mackill D J.2002. Evaluation of genetic diversity in rice sub-species using microsatellite markers.Crop Sci, 42(2): 601-607. |
| 25 | Parikh M, Motiramani N K, Rastogi N K, Sharma B.2012. Agro-morphological characterization and assessment of variability in aromatic rice germplasm.Bangl J Agric Res, 37(1): 1-8. |
| 26 | Plaschke J, Ganal M W, Roder M S.1995. Detection of genetic diversity in closely related bread wheat using microsatellite markers.Theor Appl Genet, 91(6): 1001-1007. |
| 27 | Pritchard J K, Stephens M, Donnelly P.2000. Inference of population structure using multilocus genotype data.Genetics, 155: 945-959. |
| 28 | 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. |
| 29 | Ram S G, Thiruvengadam V, Vinod K K.2007. Genetic diversity among cultivars, landraces and wild relatives of rice as revealed by microsatellite markers.J Appl Genet, 48(4): 337-345. |
| 30 | Rathi S, Yadav R N S, Sarma R N.2010. Variability in grain quality characters of upland rice of Assam, India.Rice Sci, 17(4): 330-333. |
| 31 | Rathi S, Yadav R N S, Pathak K, Sarma R N.2014. Genetic diversity in upland rice of Assam detected by SSR markers.Ind J Genet, 74(2): 238-242. |
| 32 | Rohlf F.1998. Taxonomy, NTSYS-pc Numerical, Multivariate Analysis System. New York, USA: Exeter Software, Applied Biostatistics Inc. |
| 33 | Roy S, Banerjee A, Mawkhlieng B, Misra A K, Pattanayak A, Harish G D, Singh S K, Ngachan S V, Bansal K C.2015. Genetic diversity and population structure in aromatic and quality rice (Oryza sativa L.) landraces from North-Eastern India. PLoS One, 10(6): e0129607. |
| 34 | Sakthivel K, Sundaram R M, Rani N S, Balachandran S M, Neereja C N.2009. Genetic and molecular basis of fragrance in rice.Biotechn Adv, 27(4): 468-473. |
| 35 | Samal K C, Rout G R, Das S R.2014. Study of genetic divergence of indigenous aromatic rice (Oryza sativa L.): Potentials and consequences of on farm management in traditional farming. Int J Agric Sci, 4(4): 176-189. |
| 36 | Sandhu N, Jain S, Kumar A, Mehla B S, Jain R.2013. Genetic variation, linkage mapping of QTL and correlation studies for yield, root, and agronomic traits for aerobic adaptation.BMC Genet, 14: 4. |
| 37 | Shenoy V V, Kalagudi G M.2004. Amplified fragment length polymorphism in select specialty rice of India. New directions for a diverse planet. Proceedings of the 4th International Crop Science Congress, Brisbane, Australia. |
| 38 | Sneath P H, Sokal R R.1973. Numerical Taxonomy: The Principles and Practice of Numerical Classification. W H Freeman and Company, San Fransisco, USA. |
| 39 | Sood B C, Siddiq E A.1978. A rapid technique for scent determination in rice.Ind J Genet Plant Breeding, 38(2): 268-275. |
| 40 | Sun S X, Gao F Y, Lu X J, Wu X J, Wang X D, Ren G J, Luo H.2008. Genetic analysis and gene fine mapping of aroma in rice (Oryza sativa L. Cyperales, Poaceae). Genet Mol Biol, 31(2): 532-538. |
| 41 | Temnykh S, Park W D, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho Y G, McCouch S R.2000. Mapping and genome organization of microsatellites in rice (Oryza sativa L.). Theor Appl Genet, 100(5): 697-712. |
| 42 | Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S.2001. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Fequency, length variation, transposon associations, and genetic marker potential. Genome Res, 11: 1441-1452. |
| 43 | Thomson M J, Tai T H, McClung A M, Lai X H, Hinga M E, Lobos K B, Xu Y, Martinez C P, McCouch S R.2003. Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced backcross population betweenOryza rufipogon and the Oryza sativa cultivar Jefferson. Theor Appl Genet, 107(3): 479-493. |
| 44 | Travis A J, Norton G J, Datta S, Sarma R, Dasgupta T, Savio F L, Macaulay M, Hedley P E, McNally K, Sumon M H, Islam M R, Price A H.2015. Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal.Rice, 8: 35. |
| 45 | Tuwar A K, Singh S K, Sharma A, Bhati P K.2013. Appraisal of genetic variability for yield and its component characters in rice (Oryza sativa L.). Biolofe, 1(3): 84-89. |
| 46 | Vhora Z, Trivedi R V, Chakraborty S, Ravikiran R, Sasidharan N.2013. Molecular studies of aromatic and non aromatic rice (Oryza sativa L.) genotypes for quality traits using microsatellite markers. Biosacn, 8(2): 359-362. |
| 47 | Virk P S, Ford-Lloyd B V, Jackson M T, Newbury H J.1995. Use of RAPD for the study of diversity within plant germplasm collections.Heredity, 74: 170-179. |
| 48 | Yoon D B, Kang K H, Kim H J, Ju H G, Kwon S J, Suh J P, Jeong O Y, Ahn S N.2006. Mapping quantitative trait loci for yield components and morphological traits in an advanced backcross population betweenOryza grandiglumis and the O. sativa japonica cultivar Hwaseongbyeo. Theor Appl Genet, 112: 1052-1062. |
| 49 | Yu J M, Pressoir G, Briggs W H, Bi I V, Yamasaki M, Doebley J F, McMullen M D, Gaut B S, Nielsen D M, Holland J B, Kresovich S, Buckler E S.2006. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness.Nat Genet, 38(2): 203-208. |
| 50 | Zhao K Y, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali M L, Tung C W, Reynolds A, Bustamante C D, McCouch S R.2010. Genomic diversity and introgression inO. sativa reveal the impact of domestication and breeding on the rice genome. PLoS One, 5(5): e10780. |
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