Assessment of Genetic Diversity of Drought Tolerant and Susceptible Rice Genotypes Using Microsatellite Markers
Received date: 2018-11-14
Accepted date: 2019-01-14
Online published: 2019-04-04
The introgression of wild chromosomal segments into popular rice varieties is one of the potential approaches for developing varieties for drought stress condition. Sixteen genotypes, including nine indica, two tropical japonica and five chromosome segments substitution lines (CSSLs) with different levels of tolerance/susceptibility to drought stress, were selected for diversity study. Sixty-three microsatellite markers were utilized for assessing genetic diversity. A total of 95 alleles were amplified, and out of them, 60 were polymorphic. Six unique alleles, amplified by the microsatellite loci RM276, RM472, RM488, RM537, RM541 and RM28089, were identified in six genotypes, namely FR13A, Brahamanakhi, RUF44, Swarna-sub1, Brahamanakhi and Satyabhama. The highest genetic similarity was found among CSSLs. Polymorphism information content (PIC) value varied from 0 to 1.00 with an average of 0.66 per locus. Twenty-eight microsatellites were found to be polymorphic, which could be used in marker-assisted selection programme. All the sixteen genotypes were grouped into two major clusters at genetic similarity of 0.64. In the cluster I, five CSSLs identified as diverse genotypes had wild ancestor segments responsible for drought tolerance, and hence they could be utilized as potential donors. The popular Indian varieties, Swarna-sub1 and IR64-sub1, could be used as recurrent parents in the future breeding program for developing varieties for abiotic stresses such as submergence and drought.
Donde Ravindra, Kumar Jitendra, Gouda Gayatri, Kumar Gupta Manoj, Mukherjee Mitadru, Yasin Baksh Sk, Mahadani Pradosh, Kumar Sahoo Khirod, Behera Lambodar, Kumar Dash Sushanta . Assessment of Genetic Diversity of Drought Tolerant and Susceptible Rice Genotypes Using Microsatellite Markers[J]. Rice Science, 2019 , 26(4) : 239 -247 . DOI: 10.1016/j.rsci.2019.01.004
| [1] | Anandan A, Anumalla M, Pradhan S K, Ali J.2016. Population structure, diversity and trait association analysis in rice (Oryza sativa L.) germplasm for early seedling vigor (ESV) using trait linked SSR markers. PLoS One, 11(3): e0152406. |
| [2] | Anderson J A, Churchill G A, Autrique J E, Tanksley S D, Sorrells M E.1993. Optimizing parental selection for genetic linkage maps.Genome, 36(1): 181-186. |
| [3] | Arbelaez J D, Moreno L T, Singh N, Tung C W, Maron L G, Ospina Y, Martinez C P, Grenier C, Lorieux M, McCouch S.2015. Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice,O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga. Mol Breeding, 35: 81. |
| [4] | Barik M, Dash S K, Padhi S, Swain P.2017. Effect of drought on morpho-physiological, yield and yield traits of chromosome segment substitution lines (CSSLs) derived from wild species of rice.ORYZA-Int J Rice, 54(1): 65-72. |
| [5] | Behera L, Patra B C, Sahu R K, Nanda A, Sahu S C, Patnaik A, Rao G J N, Singh O N.2012. Assessment of genetic diversity in medicinal rices using microsatellite markers.Aust J Crop Sci, 6(9): 1369-1376. |
| [6] | Behera L, Mohanty S, Pradhan S, Singh S, Singh O, Sahu R, Sahu S, Dash S, Mohapatra T.2013. Assessment of genetic diversity of rainfed lowland rice genotypes using microsatellite markers.Indian J Genet, 73: 142-152. |
| [7] | Charcosset A, Moreau L.2004. Use of molecular markers for the development of new cultivars and the evaluation of genetic diversity.Euphytica, 137(1): 81-94. |
| [8] | Choudhary G, Ranjitkumar N, Surapaneni M, Deborah D A, Vipparla A, Anuradha G, Siddiq E A, Vemireddy L R.2013. Molecular genetic diversity of major Indian rice cultivars over decadal periods.PLoS One, 8(6): e66197. |
| [9] | Dellaporta S L, Wood J, Hicks J B.1983. A plant DNA minipreparation: Version II.Plant Mol Biol Rep, 1: 19-21. |
| [10] | Flint-Garcia S A, Thuillet A C, Yu J, Pressoir G, Romero S M, Mitchell S E, Doebley J, Kresovich S, Goodman M M, Buckler E S.2005. Maize association population: A high-resolution platform for quantitative trait locus dissection.Plant J, 44: 1054-1064. |
| [11] | Gaikwad K B, Singh N, Bhatia D, Kaur R, Bains N S, Bharaj T S, Singh K.2014. Yield-enhancing heterotic QTL transferred from wild species to cultivated riceOryza sativa L. PLoS One, 9(6): e96939. |
| [12] | Ganie S A, Borgohain M J, Kritika K, Talukdar A, Pani D R, Mondal T K.2016. Assessment of genetic diversity ofSaltol QTL among the rice(Oryza sativa L.) genotypes. Physiol Mol Biol Pla, 22(1): 107-114. |
| [13] | Gawenda I, Schrӧder-Lorenz A, Debener T.2012. Markers for ornamental traits inPhalaenopsis orchids: Population structure, linkage disequilibrium and association mapping. Mol Breeding, 30(1): 305-316. |
| [14] | Ismail A M, Singh U S, Singh S, Dar M H, Mackill D J.2013. The contribution of submergence-tolerant (sub1) rice varieties to food security in flood-prone rainfed lowland areas in Asia. Field Crops Res, 152: 83-93. |
| [15] | Jasim Aljumaili S, Rafii M Y, Latif M, Sakimin S Z, Arolu I W, Miah G.2018. Genetic diversity of aromatic rice germplasm revealed by SSR markers.BioMed Res Int, 2018: 1-11. |
| [16] | Khush G S.2005. What it will take to feed 5.0 billion rice consumers in 2030.Plant Mol Biol, 59: 1-6. |
| [17] | Kumbhar S D, Kulwal P L, Patil J V, Sarawate C D, Gaikwad A P, Jadhav A S.2015. Genetic diversity and population structure in landraces and improved rice varieties from India.Rice Sci, 22(3): 99-107. |
| [18] | Marathi B, Guleria S, Mohapatra T, Parsad R, Mariappan N, Kurungara V K, Atwal S S, Prabhu K V, Singh N K, Singh A K.2012. QTL analysis of novel genomic regions associated with yield and yield related traits in new plant type based recombinant inbred lines of rice (Oryza sativa L.). BMC Plant Boil, 12: 137. |
| [19] | Molden D, Oweis T, Steduto P, Bindraban P, Hanjra M A, Kijne J.2010. Improving agricultural water productivity: Between optimism and caution.Agr Water Manage, 97(4): 528-535. |
| [20] | 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. |
| [21] | Patel S, Ravikiran R, Chakraborty S, Macwana S, Sasidharan N, Trivadi R, Aher B.2014. Genetic diversity analysis of colored and white rice genotypes using microsatellite (SSR) and insertion-deletion (INDEL) markers.Emir J Food Agr, 26(6): 497-507. |
| [22] | Pradhan S K, Barik S R, Sahoo A, Mohapatra S, Nayak D K, Mahender A, Meher J, Anandan A, Pandit E.2016. Population structure, genetic diversity and molecular marker-trait association analysis for high temperature stress tolerance in rice.PLoS One, 11: e0160027. |
| [23] | Rohlf F J.1988. NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System. Exeter Publishing. |
| [24] | Roy P S, Rao G J N, Jena S, Samal R, Patnaik A, Patnaik S S C, Jambhulkar N N, Sharma S, Mohapatra T.2016. Nuclear and chloroplast DNA variation provides insights into population structure and multiple origin of native aromatic rices of Odisha, India.PLoS One, 11(9): e0162268. |
| [25] | Roy S, Banerjee A, Mawkhlieng B, Misra1 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: e0129607. |
| [26] | Saini N, Jain N, Jain S, Jain R K.2004. Assessment of genetic diversity within and among Basmati and non-Basmati rice varieties using AFLP, ISSR and SSR markers.Euphytica, 140(3): 133-146. |
| [27] | Sajib A M, Hossain M, Mosnaz A, Hossain H, Islam M, Ali M, Prodhan S H.2012. SSR marker-based molecular characterization and genetic diversity analysis of aromatic landreces of rice (Oryza sativa L.). J BioSci Biotechnol, 1: 107-116. |
| [28] | Septiningsih E M, Pamplona A M, Sanchez D L, Neeraja C N, Vergara G V, Heuer S, Ismail A M, Mackill D J.2009. Development of submergence-tolerant rice cultivars: Thesub1 locus and beyond. Ann Bot, 103(2): 151-160. |
| [29] | Shah S M, Arif M, Aslam K, Shabir G, Thomson M J.2016. Genetic diversity analysis of Pakistan rice (Oryza sativa) germplasm using multiplexed single nucleotide polymorphism markers. Genet Res Crop Ev, 63(7): 1113-1126. |
| [30] | Singh N, Dang T T M, Vergara G V, Pandey D M, Sanchez D, Neeraja C N, Septiningsih E M, Mendioro M, Tecson-Mendoza E M, Ismail A M, Mackill D J.2010. Molecular marker survey and expression analyses of the rice submergence-tolerance geneSUB1A. Theor Appl Genet, 121(8): 1441-1453. |
| [31] | Singh N, Choudhury D R, Tiwari G, Singh A K, Kumar S, Srinivasan K, Tyagi R K, Sharma A D, Singh N K, Singh R.2016. Genetic diversity trend in Indian rice varieties: An analysis using SSR markers.BMC Genet, 17: 127. |
| [32] | Sun J, Qian Q, Ma D R, Xu Z J, Liu D, Du H B, Chen W F.2013. Introgression and selection shaping the genome and adaptive loci of weedy rice in northern China.New Phytol, 197(1): 290-299. |
| [33] | Sweeney M, McCouch S.2007. The complex history of the domestication of rice.Ann Bot, 100(5): 951-957. |
| [34] | Tian F, Li D J, Fu Q, Zhu Z F, Fu Y C, Wang X K, Sun C Q.2006. Construction of introgression lines carrying wild rice (Oryza rufipogon Griff.) segments in cultivated rice(Oryza sativa L.) background and characterization of introgressed segments associated with yield-related traits. Theor Appl Genet, 112(3): 570-580. |
| [35] | Upadhyay P, Singh V K, Neeraja C.2011. Identification of genotype specific alleles and molecular diversity assessment of popular rice (Oryza sativa L.) varieties of India. Int J Plant Breeding Genet, 5(2): 130-140. |
| [36] | Varshney R K, Bansal K C, Aggarwal P K, Datta S K, Craufurd P Q.2011. Agricultural biotechnology for crop improvement in a variable climate: Hope or hype?Trends Plant Sci, 16(7): 363-371. |
| [37] | Venuprasad R, Bool M, Dalid C O, Bernier J, Kumar A, Atlin G N.2009a. Genetic loci responding to two cycles of divergent selection for grain yield under drought stress in a rice breeding population.Euphytica, 167(2): 261-269. |
| [38] | Venuprasad R, Dalid C O, Del Valle M, Zhao D, Espiritu M, Sta Cruz M T, Amante M, Kumar A, Atlin G N.2009b. Identification and characterization of large-effect quantitative trait loci for grain yield under lowland drought stress in rice using bulk-segregant analysis.Theor Appl Genet, 120(1): 177-190. |
| [39] | Venuprasad R, Bool M E, Quiatchon L, Sta Cruz M T, Amante M, Atlin G.2012. A large-effect QTL for rice grain yield under upland drought stress on chromosome 1.Mol Breeding, 30(1): 535-547. |
| [40] | Xu Q, Yuan X P, Wang S, Feng Y, Yu H Y, Wang Y P, Yang Y L, Wei X H, Li X M.2016. The genetic diversity and structure ofindica rice in China as detected by single nucleotide polymorphism analysis. BMC Genet, 17: 53. |
| [41] | Yang F, Chen Y L, Tong C, Huang Y, Xu F F, Li K H, Corke H, Sun M, Bao J S.2014. Association mapping of starch physicochemical properties with starch synthesis-related gene markers in nonwaxy rice (Oryza sativa L.). Mol Breeding, 34(4): 1747-1763. |
| [42] | Zhao Y L, Wang H M, Chen W, Li Y H.2014. Genetic structure, linkage disequilibrium and association mapping of Verticillium wilt resistance in elite cotton (Gossypium hirsutum L.) germplasm population. PLoS One, 9(1): e86308. |
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