The exploitation of genetic diversity plays a pivotal role in determining the success of breeding program (Borborah et al., 2020). Populations that actively display significant levels of genetic variation are particularly valuable, as they can expand the genetic diversity in any breeding program (Nachimuthu et al., 2015). Ye et al. (2021) stated that the QTLs identified for heat tolerance in rice can only account for approximately 20% of the variation and introgressing one or a few QTLs into the genetic background may not be sufficient to significantly enhance heat tolerance. Therefore, there is a pressing need to identify heat tolerance donors. With this objective, the current study was taken up to identify tolerant donors. The study comprised of 49 rice genotypes, which consist of breeding lines and released varieties, to assess the genetic diversity related to thermotolerance should be utilized in breeding programmes to develop thermotolerant varieties. Harnessing the genetic diversity among the rice germplasm available at Maruteru research station to enhance thermotolerance in rice genotypes already grown in tropical climates, with focus on actively seeking thermotolerance in existing varieties will be beneficial.
In this direction researchers reported numerous results using SSR markers. Mohapatra et al. (2017) analysed 48 rice accessions using 35 SSR markers and identified a total of 86 alleles with an average of 2.87 alleles per locus. Similarly, Islam et al. (2018) reported 162 alleles with an average of 3.24 alleles per locus by genotyping 50 entries using 50 SSR markers. In the present study, a total of 113 alleles with an average of 2.31 alleles per locus were detected.
Shannon’s information index and genetic diversity revealed the information about high rate of genetic exchange among the selected cultivars. In this study, Shannon's information index varied between 0.09 (RM210, RM 247) to 1.07 (RM 4108) with a mean of 0.56 and Nei's genetic diversity index (He) values varied considerably among the loci in the present study. Nei’s genetic diversity index ranged from 0.64 (RM 4108) to 0.04 (RM 210 and RM 247) with a mean value of 0.35. The Nei's genetic diversity index (He) values varied considerably among the loci in the present study. Heterozygosity or genetic diversity index is related to the polymorphic nature or genetic variation of each locus. A high value of heterozygosity indicates high genetic variation among the individuals. Jasim Aljumaili et al. (2018) reported heterozygosity with 0.25 to 0.98 in 50 aromatic rice accessions using 32 SSR markers. Gene diversity was similar to the reports of Pradhan et al. (2023) which ranged between 0.08 and 0.86, indicating a suitable genetic exchange among cultivars.
Polymorphic information content (PIC) of 49 markers ranged from 0.04 to 0.65 with an average PIC value of 0.36 which indicated the potential of these markers for assessing molecular diversity. The highest PIC value was exhibited by the markers, RM 4108 (0.65) closely followed by RM 3586 (0.63), RM 228 (0.62) and RM 225 (0.58). The banding pattern obtained by genotyping the 49 genotypes using RM 212, RM 225 and RM 547 on chromosomes 1, 6 and 8 respectively were presented in Fig. 6. Markers with high PIC values can efficiently distinguish the genotypes and are said to be more informative. Hence, these markers may be used for diversity studies, gene mapping related studies etc. The lowest PIC value was exhibited by RM 3916 (0.04), RM 1089 (0.04), RM 3351 (0.04), RM 210 (0.04) and RM 247 (0.04) indicating less discriminatory power of these markers in distinguishing the genotypes. PIC offers a more accurate assessment of diversity and it also signifies the discriminatory power of a locus, because it takes into consideration of the number of expressed alleles and the relative frequencies of each allele. In the present study out of 49 markers screened, 13 markers viz., RM 212, RM 4108, RM 3586, RM 2431, RM 3471, RM 16575, RM 5633, RM 592, RM 225, RM 219, RM 286, RM 228 and RM 209 were found to be highly informative with ≥ 0.5 PIC. Thus, based on the PIC values, the markers used in the present study showed appreciable level of polymorphism in the rice genotypes. The average PIC value (0.36), in the present study is more than the previous studies of Mazal (2021) who reported an average PIC value of 0.28. The range of the PIC values reported in the present study was similar to the findings of Mohapatra et al. (2017) for heat stress in rice using 30 SSR markers.
AMOVA and PCoA which was performed based on two classes of rice cultivars (29 released varieties and 20 breeding lines) clearly depicted the high genetic divergence among the cultivars. The PCoA represented a mixed positions of the cultivars with co-ordinate 1 showing majority of the released varieties and few breeding lines and vice versa in co-ordinate 3. The AMOVA analysis along with Fst value supplemented the PCoA analysis with mere 5% genetic difference among the populations, 51% within the individuals and 49% among the individuals. Similar findings with the variation of 36% among the individuals and slightly higher variation of 59% within individuals was reported by Pradhan et al., 2023.
Genetic distance is used to evaluate the variety of populations within a species as well as between them. The population structure analysis performed using both distances based and model-based approach represented the cultivars into three clusters/populations. The tolerant genotypes N22, Rasi, L 663, L 672, L 674, CL 448, CL 452, MTU 1239 and MTU 1223 identified during phenotypic evaluation were diversified into three separate clusters I, II and III. The sub cluster IIB, comprised of 8 genotypes, which exhibited moderate tolerance to heat stress. Most of the susceptible genotypes (MTU 1001, Vandana, MTU 1166 and MTU 1253) were grouped under sub cluster IB (Fig. 5). Most of the advanced breeding lines were clustered into IA and IIA. Similar results were reported by Khalequzzaman et al. (2022) in assessing the genetic diversity of boro rice landraces.