Rice ( Oryza sativa L.) is one of the most important food crops in the world, especially in Asian countries, and salinity is a major constraint to the sustainability and expansion of rice cultivation. Genetically improving salt tolerance of rice is a highly important objective of rice breeding programs. Traits such as salt tolerance are quantitatively inherited. Hence, mapping quantitative trait loci (QTL) with molecular markers can be very helpful to plant breeders in the field of agricultural genomics (AgriGenomics). In this investigation, QTL analysis of physiological traits related to salt tolerance was carried out using F _2:4 population of rice derived from a cross between a salt-tolerant variety, Gharib (indica), and a salt-sensitive variety, Sepidroud (indica). A linkage map based on 148 F ₂ individuals was constructed with 131 SSR markers and 105 AFLP markers, covering 2475.7 cM of rice genome with an average distance of 10.48 cM between flanking markers. A total of 41 QTLs for twelve physiological traits under salinity stress were detected distributed on all rice chromosomes, some of them being reported for the first time. Also, overlapping of QTLs related to salt tolerance were observed in this study. Some of the identified QTLs on specific chromosomal regions explaining high phenotypic variance could be used for marker-assisted selection (MAS) programs. New QTLs retrieved in this study play an important role in growth of rice at seedling stage in an Iranian local population under high salinity conditions.

Oryza sativa L. F₂ population and F_2:3 derived from a cross between salt tolerance cv. Tarommahali and salt sensitive cv. Khazar were used in this study. A linkage map based on F₂ population was constructed (74 SSR markers on 192 individuals), which covered a total of 1231.50 cM with an average two locus interval of 19.83 cM. Two QTLs related to Na⁺/K⁺ ratio were found on chromosome 3 and 6. qDM-3 and qDM-8 (for dry mass of shoot) are major QTLs with very large effects explained 20.90 and 17.72 % of the total phenotypic variance, respectively. Major locus for DM (qDM-3) was bracketed by RM1022 — RM6283 spread over 13.6 cM on chromosome 3. Major part of the variability for standard tolerance ranking (STR) was explained by the qSTR-6 flanked by RM3727 — RM340 on chromosome 6, which exhibited phenotypic variance of 17.25 % and peak likelihood ratio (LR) of 17.51. The length of this QTL is 8.8 cM and identification of any tightly linked markers in this region will serve as a candidate gene for fine-mapping. qSTR-3 overlapped with qNA-3 and qNAK-3. The qSTR-3 may contain a new major gene for salt stress tolerance at seedling stage in rice. Major QTLs identified in this paper, after fine-mapping, could be used for marker assisted selection.

Selection and breeding for drought tolerance in rice have always been one of the leading objectives for rice breeders in water-deficient farming areas. In the present study, we applied the potential of recombinant inbred lines (RILs) population, which were derived from cross Shahpasand (Iranian landrace) and IR28, for the development of drought-tolerant rice lines. One hundred fifty-two lines along with five check varieties were investigated from 2017 to 2019 under non-stress and drought stress conditions. The yield reduction caused by drought based on overall mean during 2017, 2018, and 2019 were estimated to be 89.40, 57.95, and 35.31%, respectively. Using different statistical methods, certain lines, including L33, L90, and L109, which are considered as the best lines in most environments, were found to be promising for being utilized to increase rice drought tolerance. The averages of grain yield of the above-mentioned lines were respectively 6.45, 5.80, and 5.70 t ha⁻¹ under non-stress condition, and respectively 2.77, 2.66, and 2.59 t ha⁻¹ under drought stress condition. The yield reduction of the selected lines were significantly lower than that of others indicating the significant transgressive segregation. The results revealed using the combination of the best identified tolerance and susceptibility indices and GT-biplot are effective methods for screening superior lines. However, their utilization is not easy and requires specialized packages. For the first time, we introduced a new composite index as a combination of significant indices (CSI). CSI is in the form of a linear function of indices which effectiveness is determined by their correlation coefficient with grain yield. According to our results, using CSI, the identified rice drought-tolerant lines were in high agreement with those obtained by other methods, demonstrating that CSI is a simple but reliable composite index.

Rice blast disease, caused by the fungus Magnaporthe oryzae, poses a significant threat to rice cultivation. One effective way to deal with this disease is to identify and introduce resistant varieties using different breeding methods. This study utilized a population of 153 recombinant inbred lines (RILs) derived from the crossing of the Shahpasand (SH) and IR28 varieties, characterized by susceptibility and resistance to leaf blast, respectively. In combination with 12 control varieties, these genotypes were subjected to an extensive evaluation of disease severity (5 stages), the area under the disease progress curve (AUDPC), type, and the infection rate in 2021 and 2022. Analysis of variance revealed significant genetic variation, highlighting the potential of the RIL population for identifying and selecting resistant lines. Employing cluster analysis and the multi-trait genotype-ideotype distance index (MGIDI), 17 lines were identified as the most resistant over a two-year evaluation period. The average AUDPC for these resistant lines was estimated at 2.435 ± 0.114, and lines 17 and 111 had the lowest AUDPC (1.526 and 1.630, respectively) and showed the least infection in two years. Conversely, lines 42 and 43 showed the highest AUDPC values (255.312 and 248.209) along with heightened sensitivity. The use of MGIDI yielded a substantial selection differential (SD) of −59.12% for traits related to leaf blast disease resistance, demonstrating the effectiveness of this method. Furthermore, new recombinant populations are expected to be developed in future plant breeding projects by crossing the most susceptible and resistant lines, which will be new sources of resistance to this disease.