Data on genetic potentiality of folk rice (Oryza sativa L.) genotypes from Koraput, India in reference to drought tolerance traits

Precise physiological and molecular marker-based assessment provides information about the extent of genetic diversity, which helps for effective breeding programmes. We have conducted detailed physiological and molecular marker-based assessment of selected eight indigenous rice landraces from Koraput, India along with tolerant (N22) and susceptible (IR64) check varieties under control and simulated drought stress using polyethylene glycol (PEG) 6000. After exposure to different levels of drought stress, relative germination performance (RGP), seedling vigour index (SVI) and relative growth index (RGI) were significantly declined in all the rice landraces compared to the control plants and significant varietal differences were observed. Genetic relationship among the studied rice landraces was assessed with 24 previously reported drought tolerance linked Simple Sequence Repeat (SSR) markers. A total of 53 alleles were detected at the loci of the 24 markers across the 10 rice accessions. The Nei's gene diversity (He) and the polymorphism information content (PIC) ranged from 0 to 0.665 and 0 to 0.687, respectively. Six SSR loci, RM276, RM411, RM3, RM263, RM216 and RM28199, provided the highest PIC values and are potential for exploring the genetic diversity of studied rice lines for drought tolerance. Four rice genotypes (Butkichudi, Haldichudi, Machakanta and Kalajeera) showed the highest genetic distance with tolerant check variety (N22) and can be considered as valuable genetic resources for drought breeding program.


a b s t r a c t
Precise physiological and molecular marker-based assessment provides information about the extent of genetic diversity, which helps for effective breeding programmes. We have conducted detailed physiological and molecular marker-based assessment of selected eight indigenous rice landraces from Koraput, India along with tolerant (N22) and susceptible (IR64) check varieties under control and simulated drought stress using polyethylene glycol (PEG) 6000. After exposure to different levels of drought stress, relative germination performance (RGP), seedling vigour index (SVI) and relative growth index (RGI) were significantly declined in all the rice landraces compared to the control plants and significant varietal differences were observed. Genetic relationship among the studied rice landraces was assessed with 24 previously reported drought tolerance linked Simple Sequence Repeat (SSR) markers. A total of 53 alleles were detected at the loci of the 24 markers across the 10 rice accessions. The Nei's gene diversity (He) and the polymorphism information content (PIC) ranged from 0 to 0.665 and 0 to 0.687, respectively. Six SSR loci, RM276, RM411, RM3, RM263, RM216 and RM28199, provided the highest PIC values and are potential for exploring the genetic diversity of studied rice lines for drought tolerance. Four

Data
The dataset contains tables, graphs and images derived from the analysis of the raw data obtained from the various growth and genetic diversity parameters of the folk rice varieties from Koraput, India under control and drought condition. Details of genotypes with their origin, ecotype and special characters were presented in Table 1. Variations of relative germination performance (RGP), relative growth index (RGI) and seedling vigour index (SVI) of studied rice genotypes in different concentration of PEG induced drought stress was shown in Fig. 1. Analysis of variance (ANOVA) of studied parameters in rice seedlings grown under different levels drought stress was presented in Table 2. Genotyping of the studied genotypes was carried out by taking 24 reported simple sequence repeat (SSR) markers

Value of the data
The first open-access visual feature data set that describes genetic potentiality of folk rice (Oryza sativa L.) genotypes from Koraput for drought tolerance traits.
Our data provides information about the description of variety, tables and graphs for physiological and molecular analysis and also microsatellite panel along with the genetic relationship. Hence, it gives a holistic and clear view of genetic potentiality of the studied genotypes for drought tolerance. The data presented can be a benchmark to conserve the existing rice gene pool as well as popularization of the rice genotypes for future breeding programs.
linked to different drought tolerance QTL [2] and details of SSR markers are presented in Table 3. Different alleles, in form of variation in molecular weight of each amplified products for each SSR marker against studied ten genotypes are given in a Microsatellite Panel (Fig. 2). The markers amplified a total of 53 alleles with an average of 2.2 per locus. Genetic diversity parameters such as number of alleles, number of effective alleles, expected homozygosity, expected heterozygosity, Nei's genetic diversity, Shannon's information index and polymorphism information content was presented in Table  4. The pair-wise genetic similarity calculated for all the studied genotypes with 24 SSR markers ranged from 0.431 to 0.813 (Table 5). Cluster analysis based on the Bray-Curtis paired linkage revealed the percent of similarity in SSR marker data among studied rice genotypes were presented in Fig. 3.

Plant materials and growth conditions
The experiment was conducted by taking eight folk rice genotypes from Koraput, India along with N22 (drought-tolerant improved rice variety) and IR64 (drought-susceptible irrigated variety) as check varieties. The details of the rice landraces used in this study are presented in Table 1. Uniform sized seeds of each variety were selected, surface sterilized and kept for germination. The seeds were  placed in sterilized petriplates over saturated tissue paper and transferred to an incubator with a 12h light/12-h dark photoperiod with daily maximum photosynthetic photon flux density (PPFD) about 380 ± 40 m mol m À2 s À1 at 25 C in the laboratory. After sowing seeds immediately the drought stress was simulated with variations in osmotic potential by application of different concentrations (19.6%, 29.6% and 36.0%) of polyethylene glycol (PEG) that produced À0.5, À1.0 and À1.5 MPa water potential, respectively for 15 days. A control set was also run along with the treatment without application of PEG.

Determination of early growth performances
The seed germination rate was recorded 9 days after sowing. The seedling vigour characteristics of 15-days-old seedlings were measured by taking root and shoot length, fresh and dry weight of five Table 2 Sum square is the absolute value and percentage of total (in bracket) of main effect resulting from analysis of variance (ANOVA) of studied parameters in rice seedlings grown under different levels drought stress. df, Degrees of freedom; Total df ¼ 49; The P of overall ANOVA for variety, treatment and variety Â treatment interaction for each parameters *P < 0.05,**P < 0.01.

Parameters
Source of Variation

Genotyping with drought tolerance linked rice microsatellite loci
Genotyping with drought tolerance linked rice microsatellite loci was done by taking 24 reported simple sequence repeat (SSR) markers linked to different drought tolerance QTL. Total genomic DNA was extracted and purified from the young leaves by a modified CTAB (cetyl-trimethylammonium bromide) method described by Murray and Thompson [5]. The PCR amplification was performed in thermal cycler (BioRad, USA) by taking 20 ml volumes mixed with 2 ml of genomic DNA (25 ng ml À1 ), 1.5 ml of MgCl 2 (25 mM L À1 ), 0.3 ml of dNTP mixtures (10 mM L À1 ), 2 ml of 10 PCR buffer, 2 ml of SSR primer (2 mM L À1 ), 0.2 ml of Taq polymerase (10 U ml À1 ) and 12 ml of ddH 2 O, following the method of Panaud et al. [6]. The PCR amplification was an initial denaturation at 94 C for 5 min followed by 35 cycles of denaturation at 94 C for 30 sec, annealing (depending on TM value of primer) at 50e60 C for 45 sec, extension at 72 C for 1 min and a final extension of 7 min at 72 C. The amplified products were resolved through 2.5% ethidium bromide stained (1 mg ml À1 ) agarose gel and documented using a gel documentation system (BioRad, USA). The different allelic forms (variation in molecular weight of the amplicons) of individual SSR loci were scored as 1 or 0 based on their presence or absence, respectively across the studied rice genotypes. A proximity matrix was constructed from the 1/ 0 matrix using PAST-3 (Palaeontological Statistics) software to construct a dendrogram using average linkage among the studied genotypes. Marker based population genetics study was performed with calculation of polymorphic information content (PIC), effective number of alleles (Ne), Shannon's Information index (I), and Nei's heterozygosity (He) was performed using genetic diversity analysis software POPGENE 1.31 [7].

Statistical analysis
Growth parameters were analyzed by two-way analysis of variance (ANOVA) with the variety and different treatment levels by using CROPSTAT (International Rice Research Institute, Philippines) software.