INDIAN JOURNAL OF GENETICS AND PLANT BREEDING

A comprehensive transcriptome analysis reveals the key mechanism related to leaf colour variation in a xantha mutant of Cucumis melo L

Qin Shao — 2025-07-01

This study aimed to investigate the key mechanisms underlying variation in leaf colour in the xantha mutant of Cucumis melo. The normal green C. melo inbred line ‘Baishami NO.1’ (wild type) and its spontaneous mutant’ 9388-1’ (xantha mutant) were collected. A comprehensive transcriptome analysis was conducted to identify differentially expressed genes (DEGs) between wild-type and xantha mutant C. melo in both the cotyledon and euphylla stages. A functional enrichment analysis, transcription factor (TF) prediction and a protein-protein interaction (PPI) network analysis for differentially expressed genes (DEGs) were subsequently conducted. In total, 234 up- and 551 down-regulated common DEGs in both the cotyledon and euphylla stages of xantha mutant C. melo were identified. These DEGs were significantly enriched in functions or pathways associated with photosynthesis and chloroplast development. Moreover, 18 common DEGs were identified as TFs that belonged to the ERF family. Notably, the photosynthesis-related gene MELO3C010813 (ZAT10) that was identified was also found to be a TF that belongs to the ethylene response factor family. A PPI network analysis showed that MELO3C023986 had the highest with TOP2 in Arabidopsis thaliana, and our findings revealed that expression of the xantha mutant phenotype may be associated with the abnormal expression of ZAT10, MAPK3, CRD1, PORA and ERF TFs, as well as the dysregulation of photosynthesis and chloroplast development.

Unraveling genetic diversity and yield traits in mungbean (Vigna radiata L.) through morpho-molecular approach

Audil Gull — 2025-07-01

The present study was carried out to analyze the genetic variability in 124 genotypes of mungbean (Vigna radiata L.) following an augmented block design in kharif over two years. The analysis of variance revealed significant variation among genotypes for all the traits except the number of branches. Pearson correlation coefficients demonstrated significant correlations between several traits, notably between seed yield and traits such as the number of branches, number of pods per plant, pod length, no. of seeds per pod, and 100-seed weight. Principal component analysis (PCA) identified three principal components explaining 74.68% of the total variation. Yield-related traits predominantly influenced the first principal component (PC1); the second (PC2) by seeds per pod and days to 50% flowering, and the third (PC3) by growth-related traits such as days to flowering, days to maturity and number of branches. Cluster analysis based on morphological traits and SSR marker analysis grouped the genotypes into two distinct clusters, respectively, corroborating the morphological clustering results with SSR markers. Overall, the results of the study provide a detailed understanding of the genetic diversity and variability in morphological traits among mung bean genotypes, offering valuable insights for breeding programs and genetic improvement efforts.

Dissection of genotype × environment interaction for selection of elite stable genotypes of cumin (Cuminum cyminum L.)

Ramesh — 2025-07-01

Cumin (Cuminum cyminum L.) is a versatile seed spice containing 2-4% essential oil with a distinctive aroma and flavor. About 21 diverse cumin genotypes were evaluated for their stability under field conditions over three consecutive years in the rabi seasons. The phenotypic stability of cumin genotypes for seed yield was analyzed using multivariate analysis through AMMI and GGE biplots. Which-won-where biplot identified MCU-6 as a high-yielding vertex genotype for E1 environment, while MCU-73 and MCU-105 were suitable for E2 and E3. The multi-trait stability index identified three genotypes, namely MCU-73, MCU-105, and MCU-25, with higher phenotypic stability and mean performance across all the traits studied. The identified genotypes may be recommended for cultivation.

Identification and characterization of cold shock domain proteins (CSPs) for their response to cold stress in pigeonpea [Cajanus cajan (L.) Millsp.]

Shruti Sinha — 2025-07-01

Chilling stress arrests plant metabolism, slowly perturbing homeostasis, which eventually leads to senescence. If imposed for a long time, it can cause plant death. Prokaryotes possess cold shock domain-containing proteins (CSPs) in their genomes that help them acclimate to chilling stress by acting as RNA chaperones, ensuring the maintenance of cellular functions. Considering this as an important class of genes in maintaining homeostasis during chilling stress, the present study was conducted to carry out a genome-wide survey of these genes in Cajanus cajan, which has not been studied to date. In-silico genome-wide characterization of the Cajanus genome identified 4 CSPs (CcCSP1, CcCSP2, CcCSP3 and CcCSP4) members. Domains prediction identified each containing at least one CSD (cold shock domain), Glycine-rich repeats and CCHC-type zinc fingers, suggesting their role as nucleic acid binding proteins and protein-protein interactions. All, except the CcCSP2 gene, were found to be intronless. Additionally, CcCSP2 was found to be divergent from the rest of the three genes and phylogenetically close to Medicago MtCSP3. Spatiotemporal expression in genotypes contrasting for cold stress response showed the highest expression of the CcCSP2 gene (almost 6-fold) in flowering bud tissue of tolerant genotypes, suggesting it may be involved in the cold adaptation mechanism. The study establishes that less-explored cold acclimation proteins, such as CSPs, are transcriptionally regulated genes in Cajanus when it experiences chilling stress during extreme weather conditions. This suggests that this subtropical crop may have the potential to cold-acclimate. Further studies are needed to establish the details so that crop damage is mitigated in these times of climate change.

Development and validation of candidate gene specific markers for salinity responsiveness in chickpea (Cicer arietinum L.)

Neeraj Kumar — 2025-07-01

Soil salinity is a crucial abiotic stress that significantly reduces the yield and productivity of crops, it reduces chickpea annual yields by 8 to 10% globally. The efficient utilization of marker-aided selection would increase precision and expedite the development of salt-tolerant chickpea varieties. This study intends to identify and analyze microsatellite regions from identified candidate genes related to salinity in chickpeas. A total of 195 putative candidate genes were sort listed, out of which 158 genes contained microsatellite loci with mono- (32%) and di- (32%) nucleotides, followed by tri- (18%), tetra- (11%), penta- (4%) and hexa-nucleotides (3%) motifs for salt tolerance. Gene-based SSR (cg-SSR) primer sets were used to validate the results in a panel of tolerant and sensitive genotypes. The polymorphic cg-SSR loci gave a polymorphic information content (PIC) ranging from 0.21 to 0.37 with an average of 0.34. A neighbor-joining (N-J) tree was created to depict the relationships between genotypes, classifying them into two distinct clusters. The first group was most salt-sensitive, while the second mainly contained salt-tolerant genotypes, which were congruent with the phenotypic data. The analysis of population structure unveiled the presence of two sub-populations. Sub-population 1 consisted of salt-tolerant genotypes, while sub-population 2 comprised salt-sensitive genotypes. The study ultimately revealed that the Cg-SSR markers designed for salinity were effective in deciphering the functional diversity and salinity responses in chickpeas.

Allele mining and haplotype-based association studies for nitrogen stress-responsive gene Os06g0291500 in indica rice (Oryz sativa L.) panel

Ankur Poudel — 2025-06-30

Improving nitrogen use efficiency (NUE) in rice is critical for reducing nitrogen-induced environmental pollution and enhancing yield. Identifying natural allelic variants associated with NUE-related traits and utilizing them in breeding programs is an important approach. In this study, Os06g0291500, a novel, unannotated candidate gene associated with NUE, was used. Allelic variations were analyzed in 91 diverse rice genotypes through Illumina NovaSeq 6000 sequencing of the gene (3,078 bp) and its promoter (2,000 bp) regions. Mutation analysis revealed ample genetic variation of the gene across a panel of rice genotypes under study. The released varieties were found to accumulate more mutations, indicating limited selection for this gene in breeding programs. The phenotypic study showed differential N-response traits among genotypes, but association analysis did not reveal significant genotype-phenotype correlations due to the low phenotypic variance explained (PVE). Consequently, haplotype-based analysis was employed, identifying seven haplotypes within the panel. Among these, Hap_5 and Hap_7 were identified as the best and poorest haplotypes, respectively, based on phenotypic performance and SSI scores. The results highlight the potential of Os06g0291500 for NUE improvement in rice through functional validation and haplotype-based breeding. This study provides valuable insights into the genetic regulation of NUE and underscores the importance of exploring natural allelic diversity to develop nitrogen-efficient rice varieties.

Determining the potential and adaptability of multi-cut forage sorghum (Sorghum bicolor L. Moench) genotypes through AMMI, genotype by environment interaction and GGE biplot analysis

Pummy Kumari — 2025-07-01

Forage sorghum (Sorghum bicolor L. Moench) is a vital crop in the global fodder supply chain, especially in arid and semi-arid regions, due to its high biomass yield, efficient water utilization and adaptability to diverse climates. The challenge in optimizing forage sorghum productivity lies in the intricate interaction between genotype and environment (G × E interactions). Seventeen multi-cut forage sorghum genotypes were evaluated under field conditions for their green fodder yield (GFY) and dry fodder yield (DFY) during the kharif season (Wet season) at three locations, namely, Pantnagar, Ludhiana and Hisar employing biplot models such as genotype + genotype × environment (GGE), and additive main effects and multiplicative interaction (AMMI). Statistical analysis revealed significant effects of genotype, environment, and their interactions on the target traits, with AMMI and GGE biplot models capturing over 87.9% of the total variance, thus demonstrating their applicability. The environment accounted for the majority of the variability in GFY and DFY, highlighting its influence on sorghum production. The genotypes CSH 43MF and SPH 2018 emerged as superior hybrids across all environments, while CSV 33MF (variety), SPH 2024 and SPH 2043 showed specific adaptability to the Pantnagar, Ludhiana and Hisar environments, respectively. The findings also underscore the potential of multicut forage sorghum varieties/hybrids, CSH 43MF and SPH 2018, for enhancing green and dry fodder production under three different mega-environments in northern India, thereby contributing to the region’s agricultural sustainability and fodder security.

Assessment of Flue Cured Virginia tobacco genotype performance in the light soil tobacco growing regions based on GGE biplot and AMMI analysis

P.V. Venugopala Rao — 2025-07-01

Flue Cured Virginia (FCV) tobacco is a major commercial crop grown as a rainfed crop in Andhra Pradesh and Karnataka states during rabi and kharif seasons, respectively. The tobacco leaf yield is often affected by aberrant weather conditions leading to significant reduction in leaf yield and quality. To identify yielding and stable FCV genotypes, two groups of genotypes were evaluated, consisting of 9 light-cast and 7 medium-cast FCV tobacco types, along with three checks, over a period of three years in the rabi season. The stability analysis was carried out using AMMI and GGE analysis and identified three breeding lines (KB 32, KB 50, and KB 67) in respect of stable leaf yield and quality grade index. These lines were selected on the bases of yield stability indices and genotype stability index for cured leaf yield. They were further evaluated at four locations during 2021 representing the southern light soils, northern light soils and Karnataka light soils regions of FCV tobacco growing regions of the country. The superior performance of genotype KB 67 for high leaf yield was advanced for further large-scale testing in SLS areas of Andhra Pradesh.

Identification of polymorphic SSR markers by examining their cross-transferability and investigation of genetic diversity within Pterocarpus species

Mohana Kumara p — 2025-07-01

Pterocarpus dalbergioides and P. marsupium are deciduous tropical trees in the Fabaceae family, with P. dalbergioides native to India’s Andaman Islands and P. marsupium found in various Asian countries. This research investigated the applicability of specific primers for P. santalinus across these species. DNA isolation and PCR amplification were performed on 15 samples from each species. Out of 33 primers, 7 markers were amplified in P. dalbergioides and 15 in P. marsupium, yielding transferability rates of 21 and 33%, respectively. For P. dalbergioides, the effective population size (Ne) was 3.82 ± 1.84, observed heterozygosity (He) 0.42 ± 0.15, and allelic richness (Pa) 5.29 ± 2.01. In P. marsupium, Ne was 4.83 ± 0.91, He was 0.56 ± 0.10, and Pa was 7.07 ± 1.27. The average polymorphic information content (PIC) was 0.49 for P. dalbergioides and 0.54 for P. marsupium. The study underscores the potential of transferred SSR markers to assess genetic diversity in Pterocarpus species.

Genetic potential unravelling for anaerobic germination tolerances in North-eastern Indian rice (Oryza sativa L.) germplasm

Umakanta Ngangkham — 2025-06-30

Anaerobic germination is one of the constraints faced by direct seeded seeds (DSR) rice plants causing poor and irregular germination. In this study, 281 rice germplasm were screened for anaerobic germination. Based on the phenotypic variation of root length, coleoptile length or and percentage of germination, twenty-four rice genotypes were identified as anaerobic germination tolerant. The correlation analysis showed significant association among phenotypic traits in the aerobic and anaerobic germination. The genetic diversity among the 48 selected germplasm using 48 SSR markers of 12 rice chromosomes revealed prevalence of enough diversity for marker-trait association analysis. The PIC value ranged from 0 to 0.375, with the maximum (0.375) in RM16238, RM7311, RM20228, RM22321, RM25866 and RM26603 markers. A PCoA showed the first two components accounted for 25.72% and 9.42% of the genetic variation respectively accounting a total genetic variation of 35.14%. The dendrogram based on UPGMA-based clustered analysis and population structure clustered the 48 individuals into two major groups. The analysis of molecular variance (AMOVA) showed 92% variation within the population whereas 8% variation was observed among the population (P<0.001). Marker-traits association analyses identified five SSR markers (RM20948, RM26033, RM16730, RM23732, RM25866) that strongly associated with Root length and coleoptile length with a phenotypic variance of 1.1% to 9.9%. These findings provide valuable insights into the genetic architecture and population structure underlying anaerobic germination tolerance in rice, facilitating future breeding efforts to develop improved DSR varieties.

Transgenerational analyses and transcript memory profiling of SKP1 gene expression after seed priming with IAA and GA3 shows positive modulation of terminal heat stress tolerance in bread wheat (Triticum aestivum L.)

Praful Jaiswal — 2025-06-30

Obligate exposure to high temperatures during the anthesis of wheat is a reality and one of the major challenges in wheat breeding today. Seed priming is a valuable technology to increase seed vigour and stress resilience. Seed priming of wheat cv. HD2967 was carried out with two plant hormones, auxin (IAA) and gibberellins (GA3) and the primed plants were analyzed in two consecutive seasons in a field at two planting times. The main aim was to determine how these hormones modulate various pre-germinative metabolic pathways, which lead to enhanced stress tolerance and finally affect crop yield after a triggered high-temperature stress at the anthesis stage. At the molecular genetic level, transcriptional memory was analyzed by expression profiling of the SKP1(S-phase kinase protein1)gene, an essential component of the ubiquitin-proteasome system that is specifically involved in protein homeostasis and plant hormonal signaling. The results revealed that the grain yield at all sowing times was significantly increased by IAA and GA3 seed priming (50 mg/L) under high ambient temperature. The SKP1 transcript showed maximum induction in the P1-D, P2-D, and P2-N conditions in the flag leaf and ear head under heat stress. The SKP1 gene expression showed a higher correlation with chlorophyll content at the post-anthesis stage (S3) by SKP1-FL r = .92 and SKP1-EH r=0.85 (p < 0.01) and a strong positive correlation with S3 r = 0.77and NOGPH r=0.77 (p < 0.01). These results document the potential of this technology as an effective approach to cope with severe high-temperature stresses during grain filling in wheat cultivation. To the best of our knowledge, this is one of the first reports of IAA, GA3, in combination with heat priming of seeds and analyses in natural field conditions in wheat.

Novel marker haplotypes and starch quality parameters in relation to glycaemic response of temperate rice (Oryza sativa L.) landraces and germplasm

Nowsheen Noor — 2025-06-30

The study investigates the quality of various rice genotypes, focusing on the identification of rice (Oryza sativa L.) genotypes with low GI to promote healthy dietary options. Given the link between amylose content and GI, evaluation was carried out for grain and kernel characteristics, amylose content, pasting and thermal properties. Significant variability in amylose content, with NR-AB 1 showing the lowest at 12.42% and Pusa Basmati 1509, the highest at 25.01%, was recorded. Pasting properties evaluated through RVA showed a wide range of viscosities, indicating differences in the thickening and water-binding capacities of the rice flour from various genotypes. Molecular marker analysis and allelic profiling at loci controlling starch properties further provided a genetic perspective on rice quality. The research offered valuable insights for rice breeders, food scientists, and the culinary industry, where the low GI genotypes were identified, which can be further promoted for product development.

Exploring arsenic (As) tolerant and exclusion donors for use in rice (Oryza sativa L.) breeding

Swapan Kumar Tripathy — 2025-06-30

Growing rice under arsenic (As) stress inevitably invites a huge risk of As exposure to humans and livestock in Asian countries. Identification of As-tolerant rice genotype(s) with accumulation of As in straw and grains below the threshold limit can be a way forward to mitigate such a life-threatening problem. The present study systematically evaluated 131 diverse rice genotypes for As tolerance based on germination and seedling growth parameters and selected a few elite As tolerant genotypes at appropriate lethal (LD50). The rice genotypes responded differentially with marked differences in tolerance under As stress. Exposure to As adversely affected germination and seedling growth. Significantly higher estimates of relative seedling vigor index and both stress tolerance indices and relative tolerance indices are coherently associated with tolerant rice genotypes with no symptoms of damage on leaves. A major proportion of As uptake was shown to be retained in roots in tolerant genotypes with a progressive decrease in the order of leaf sheath> leaf blade> husk> kernel under As stress, although the extent of partitioning was genotype-specific, signifying As exclusion in shoot and grains. The first Principal component alone explained 78.16% of the total phenotypic variation. Seedling tolerance indices, vigor indices and germination percentage were shown to be important criteria for As tolerance based on PCA and correlation analysis. PCA biplot revealed highly As tolerant genotypes, e.g., Ashutosh, BRRI Dhan-72, CST Sel. 4, Mahanadi, MI 156, OR(CZ) 78-1, PB-1, Pusa Sugandha 3 and Pusa Sugandha 3-1 with higher positive score value on 1st Principal Component. The As-tolerant genotypes identified in this pursuit would certainly help in planning As tolerance breeding in rice.

Application of GGE biplot analysis for assessing stability in Recombinant Inbred Lines (RILs) of rice (Oryza sativa L.)

Aziz Ur Rahman — 2025-06-30

This study was conducted to assess the genetic differences among 87 rice (Oryza sativa L.) recombinant inbred lines (RILs), identify productive environments, and measure the impacts of genotype by environment interaction (GEI) on yield across four locations. The pooled ANOVA showed significant differences among the environments, genotypes, and GEI for grain yield. A graphical method for analyzing experimental data from multiple environments is to consider genotype as the main effect and genotype x environment interaction (GGE) biplot, which visually assesses the total number of genotypes. The first two primary components cumulatively explained 50.9% of the variation in grain yield. GEI is responsible for more than half of the overall variation for this trait. Peshawar and Charsadda form one mega environment, while Swat and Mansehra constitute another mega environment for grain yield. Recombinant inbred lines, AUP-3 and AUP-30 were identified as the highest-yielding, stable, and ideal genotypes across the environments for grain yield.

Mapping of QTL for anaerobic germination using the donor AC39416A in the genetic background of variety Swarna Sub-1 of rice (Oryza sativa L.)

B. Saimohan — 2025-06-30

Climate change is causing a decline in rice productivity and sustainability in coastal irrigated areas due to abiotic stresses. Flooding during
germination, triggered by unexpected and heavy rainfall, poses a significant threat to the growth and survival of rice plants. Anaerobic
germination (AG) is an important trait in particular circumstances for cultivation under the direct seeding method in kharif season. To
identify QTLs responsible for AG, phenotypic screening was carried out using the 188 F2:3 population of Swarna Sub1/AC39416A in the
present investigation. The mean anaerobic germination percent recorded after the 2 weeks of submergence ranged from 0 to 95%, with
an overall mean of 47.51%, whereas, for 3 weeks of submergence, the mean anaerobic germination percent recorded between 0 and 95%,
with an overall mean of 37.66%. Parental polymorphism studies revealed that 134 out of 687 SSR markers were polymorphic. Linkage
analysis with 83 polymorphic SSR markers was done using the QTL IciMapping software version 4.1.1. The length of the linkage map
constructed across the whole genome was 3600.8 cM. Four QTLs were identified viz., qAG7-1, qAG7-2, qAG10 and qAG12 with the ICIM
method. All these 4 QTLs explained a phenotypic variance of about 18.81% collectively for AG trait, with their individual contributions
ranging from 2.99 to 8.67% of phenotypic variation and LOD scores of 5.05 to 5.86. The LOD score and phenotypic variance is 5.86 and
8.67% respectively for qAG10 a novel QTL identified in the present study using ICIM method.

Performance of seedless and sparse-seeded mutants in sweet orange and mandarin genotypes induced through Gamma-irradiation mutagenesis

Ashutosh A. Murkute — 2025-07-01

Citrus fruits, a globally significant crop, face consumer and processing challenges due to the presence of seed. Conventional breeding
methods to develop seedless varieties are time-consuming and often unsuccessful due to the complex genetic nature of citrus. This study
explores the potential of gamma-irradiation mutagenesis in producing seedless or sparsely-seeded mutants. Dormant budwoods of sweet
orange cv. Mosambi (Tm-33), Kinnow, and Nagpur mandarin (N-4 and N-74) were irradiated with gamma doses (5–40 Gy) and grafted
onto rough lemon rootstocks. Observations were recorded from mutant generations (MV2) and analyzed over two seasons. Significant
variations in fruit weight, size, rind thickness, juice content, and total soluble solids (TSS) were observed. On average, the physical
parameters of the fruit, such as weight, length, diameter, axis diameter, and rind thickness, were found to be inversely proportional to
increasing doses of gamma-irradiation. Notably, a sweet orange mutant (Tm33-5-B2R2-P01) exhibited reduced seed count (3.67 seeds/
fruit) with satisfactory TSS (9.70°Brix) compared to the parent (12.25 seeds/fruit). Kinnow mandarin mutant KM-40-B2R1-P19 showed
the lowest seed count (1.50 seeds/fruit) and good TSS (9.03°Brix) compared to the parent (14.75 seeds/fruit). Nagpur mandarin mutant
N4-5-B3R1-P05 was identified as seedless (0 seeds/fruit), maintaining favorable TSS (10.07°Brix) compared to parent (12.23 seeds/fruit).
The results demonstrate the potential of gamma-irradiation in citrus breeding to meet consumer demands for quality seedless fruits.

Physio-biochemical trait characterization using generation mean analysis in chickpea (Cicer arietinum L.) under timely and late sown conditions

Mahaveer Prasad OIa — 2025-07-01

Limited information is available regarding the interaction effects, particularly for physio-biochemical traits under heat stress conditions
in chickpeas, which are critical for identifying heat-tolerant genotypes. To address this gap, a field experiment was conducted to study
gene effects for various physio-biochemical traits of four specific crosses, namely, RSG-973 × HC-5, RSG-963 × RSG-973, CSJD-884 ×
Avrodhi and RSG-974 × CSJ-515 during the rabi seasons of 2019-20 to 2021-20 under two sowing environments. Results revealed
duplicate epistasis for specific traits observed in different cross-environment combinations, such as membrane stability index in RSG-973
× HC-5 under E2 and in CSJD-884 × Avrodhi under both E1 and E2, total chlorophyll content in RSG-973 × HC-5 under E2, carotenoid
content in RSG-974 × CSJ-515 under E2, proline content in RSG-974 × CSJ-515 under E1, protein content in RSG-973 × HC-5 under E1,
and seed yield per plant in CSJD-884 × Avrodhi under E2. The predominance of additive (d) and/or additive × additive ‘i’ gene effects,
along with significant contributions of non-additive gene effects (h and/or j and/or l), for protein content in RSG-973 × HC-5 under E2
condition. Overall, non-additive gene effects (h, j, and l) were predominant for most traits across the studied crosses under both timely
and late-sown conditions.

Studies on combining ability for grain yield and resistance to banded leaf and sheath blight disease in maize (Zea mays L.) improvement

Duggempudi Venkata Ramana — 2025-06-30

Twelve maize inbred lines, differing for resistance to BLSB were crossed in a half-diallel mating design and the F₁s were evaluated during Kharif-2023, at Delhi and Peddapuram. The combining ability of these inbred lines for BLSB resistance under artificial inoculation and grain yield in artificial and natural conditions was assessed. The ANOVA revealed highly significant GCA variances (P<0.01) for grain yield in both conditions as well as for BLSB disease scores, indicating additive genetic variance of both traits. In addition, crosses and SCA effects also showed significant variances for both traits suggesting the presence of sufficient variability among half-diallel crosses and non-additive genetic variance. Notably, the mean squares for GCA in BLSB disease resistance were much higher than those for SCA, indicating that additive genetic effects predominantly contributed to disease resistance. The results indicate that the selection for BLSB resistance under artificial epiphytotic conditions at hotspot locations would be effective in breeding programs. P5 and P7 were the most desirable inbreds for developing high-yielding, BLSB-resistant hybrids due to their higher magnitude of positive GCA effects for grain yield and higher magnitude of negative GCA effects for BLSB disease. P4×P12, P5×P7, P6×P12, and P6×P1 exhibited significant negative SCA effects for BLSB resistance and significant positive SCA effects for grain yield under artificial inoculation conditions, making them promising combinations for further breeding programs.

Screening for submergence tolerant varieties via association of Sub1 gene related markers in rice (Oryza sativa L.)

Norliza Abu Bakar — 2025-06-30

Complete submergence from flooding and stagnant water seriously injures the plant’s growth and survival. The aim of the study was to identify local rice varieties that can be used as breeding materials for submergence tolerant varieties development using SSR and CAPS markers. Phenotypic screening revealed a significant difference whereby the mean elongation was higher for susceptible lines compared to tolerant lines. A strong negative correlation at -0.933 existed between survival percentage and elongation height in the submerged group. The elongation for the control group was also higher at 24.541 ± 5.119 cm than the submerged group at 14.806 ± 8.196 cm. Genotypic screening using the GNS2 CAPS marker has revealed the presence of the Sub1 gene and the gene polymorphism in the identified tolerant varieties with SSR markers, RM8303 that showed the highest PIC value (0.5174) and gene diversity (0.5816). It is expected that the results obtained may significantly help the development of better varieties in the upcoming rice breeding programmes.