Morpho-Molecular Characterization and Screening of Rice (Oryza Sativa L.) Genotypes for Salinity Tolerance at Seedling Stage

SAARC J. Agric., 18(2): 1-15 (2020) DOI: https://doi.org/10.3329/sja.v18i2.51104 Research Article MORPHO-MOLECULAR CHARACTERIZATION AND SCREENING OF RICE (Oryza sativa l.) GENOTYPES FOR SALINITY TOLERANCE AT SEEDLING STAGE S.A.A. Muti1, M.I. Hoque2*, M.M. Islam3, M.A. Siddique4 and M.S. Islam5 1&5 Department of Biotechnology, Bangladesh Agricultural University (BAU), Mymensingh-2202, Bangladesh 2* Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture (BINA), BAU Campus, Mymensingh-2202, Bangladesh, 3 Biotechnology Division, Bangladesh Institute of Nuclear Agriculture (BINA), BAU Campus, Mymensingh-2202, Bangladesh, 4 GRSD, Bangladesh Rice Research Institute (BRRI), Gazipur-1701, Bangladesh ABSTRACT Salinity is one of the major abiotic stresses which severely affect the production of crops across the world. Twenty rice genotypes of diverse origins were assessed to examine salt tolerance potentiality at seedling stage as well as to elucidate the genetic variation using SSR markers. Consequently, IRRI standard protocol was applied to screen out those varieties for tolerance at the glasshouse laboratory of Bangladesh Institute of Nuclear Agriculture, maintaining salt stress level at 6dS m-1, 8dS m-1, 10dS m-1 and 12 dS m-1. Data on morphological parameter were recorded as shoot length (cm), root length (cm) and total dry matter (TDM). For molecular characterization thirteen SSR markers were exploited to determine the genetic diversity and in this context, 53alleles were revealed while the mean number of alleles per locus was 4.The Polymorphism Information Content (PIC) value ranged from 0.370.78 having an average of 0.58. The Un-weighted Pair Group Method with Arithmetic Mean (UPGMA) displayed three major clusters including some sub-clusters, where in Cluster 1, Binadhan8, Binadhan-10, Pokkali and FL478 were very close in their vicinity. Information obtained from this experiment, thus can be taken into account for stress breeding program and prospective genetic materials could be utilized for exploring the genetic architecture in favor of salt tolerance as well as for developing better salt tolerant rice varieties in near future. Keywords: Rice, Abiotic stress, Salinity, Tolerance, SSR marker, Diversity, Polymorphism * Corresponding author: Received: 07.07.2020 Accepted: 02.10.2020 2 Muti et al. INTRODUCTION Rice (O. sativa) is the staple food of an estimated 3.5 billion people throughout the world. Nowadays, rice is produced in every continent of the world except the Antarctica. Thousands of rice cultivars are cultivated across 100 countries (IRRI, 2013). However, worldwide, different biotic and abiotic stresses (drought, flood, salinity) are responsible for the stagnant production of rice (Shelly et al., 2016). Salinity is one of the major hindrances to increase rice production worldwide. Onefifth of the irrigated arable lands are recorded to be severely affected by high salinity throughout the world (Negrao et al., 2011). Bangladesh has a considerable amount of coastal areas that are affected to salinity and occupies 30 % of net cultivable land (Mamun et al., 2019). Coastal land of Bangladeshis affected by varying degrees of salinity. Saline soils occur in the river deltas in strip of land extending from few kilometers to 180 km from the coast. The flow of fresh water in the upstream river plays an important role to control the salinity intrusion. The upstream withdrawal of the Ganges water has reduced the flow tremendously and increased salinity in the tidal river, decreased surface water availability in the rivers and canals, lowered ground water table and reduced soil moisture content. About 1.02 million hectares in the coastal areas (out of 1.459 million hectares of cultivated land in the country) are affected by various degrees of salinity. Very slight salinity (2.0 - 4.0 dS m-1) exists in about 0.282 million ha, slight salinity (4.1–8.0 dS m-1 in 0.297 million ha, moderate salinity (8.1-12.0 dS m-1) in 0.191 million ha, strong salinity (12.1–16.0 dS m-1) in 0.45 million hectares of land. About 0.087 million ha of coastal land is affected by very strong salinity (>16.0 dS m-1). The salinity varies considerably by seasons. In dry season soil and river water salinity increase, while during the monsoon season, it goes down. Therefore, land use also has temporal and spatial variation with season (Hussain, 2008). If salinity increases with time it is estimated that there will be reduction in production by 10 % by 2050 (IPCC, 2007). Salinity in soils is characterized by the excess presence of sodium ions along with dominant anions like chlorine and sulfate which combine together to increased electrical conductivity (Ali et al., 2013). The effects of salinity on different parameters like morphological, physiological and biochemical traits have been studied in rice which showed reduced tillering, Although the genetics of salt tolerance is useful for the researchers to develop salt tolerant varieties, there are some problems those are required to be assessed. The main reason is that salinity is not uniformly distributed throughout a given area and thus it is difficult to recognize tolerant variety added that there are some variations which are found among species and some among cultivars within species (Arzani, 2008; Ashraf and Foolad, 2013). Hydroponic system is perfectly compatible with screening. Moreover, assessment of genetic diversity and identification of superior genotypes are important as well as necessary for any crop improvement program (Bhuiyan, 2005). Molecular markers have been proved to be very useful for crop evaluation in many species. A rapid as well as technically simple method include SSR analysis which is based on PCR MORPHO-MOLECULAR CHARACTERIZATION OF RICE 3 assay requiring only small quantity of DNA and thus inexpensive (Litt and Lutty, 1989). Through PCR different alleles at a locus can be detected by using conserved DNA sequence flanking SSR as primers. SSR have become a popular type of codominant molecular marker in genetic analysis and plant breeding application (Choi et al., 2003). Twenty rice genotypes of diverse origins were assessed to examine salt tolerance potentiality at seedling stage as well as to elucidate the genetic variation using SSR markers. MATERIALS AND METHODS This experiment was carried out both glass house and laboratory of the Biotechnology Division of Bangladesh Institute of Nuclear Agriculture (BINA), during the period from February 2019 to June 2019. Modified hydroponic system (Gregorio et al., 1997) was used at the glasshouse to evaluate salt tolerance of the 20 rice genotypes using Peter's solution (Yoshida et al., 1976). The salinization levels were EC at 6 dS m-1, 8 dS m-1, 10 dS m-1 and 12 dS m-1. The salinity level was measured through EC using the EC meter and maintained pH at 5.1 daily. Salt stresses were applied at 7th days old seedling. The data were recorded at the age of 7 days, (...truncated)