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Bacterial leaf blight (BLB) is one of the major and oldest diseases of rice. The best cost effective management of this disease is the development of resistant cultivars. Morphological and molecular screening are widely used approach in the recent scenario for identifying BLB resistant cultivar. In present study, two experiments were carried out to identify the BLB resistant rice lines and varieties. An active strain of Xanthomonas oryzae pv. oryaze (Xoo.) BXO-09 was used for the inoculation experiments. Then, morphological rating was done to find out the resistant rice lines and varieties whereas three RFLP primers (RG136, RG556 and pTA248) were used for identifying the BLB resistant genes. Through morphological analysis, the rice line RC251 was recorded as susceptible where the rest of the rice lines resulted moderately susceptible or moderately resistant. Among the rice varieties, BR-26, BRRI Dhan31, IRBB5, IRBB21, IRBB60, IRBB65, and Kumragur were recorded as resistant where BR-11, Binadhan-8, and Binadhan-10 were found highly susceptible to BLB. In case of RFLP marker based analysis, a specific type of banding pattern was observed for IRBB5 for RG556 primer which indicated the presence of xa5 gene. For RG136 primer 8 kb single band was formed for different lines and varieties whereas only IRBB60 showed 2 fragments of 8 kb and 5 kb which also indicated the presence of xa13 gene. Finally, DNA amplification of 27 rice lines and varieties using pTA248 primer showed the band at 4 kb position for the BLB resistant lines and varieties and 3.7 kb position for the susceptible lines and varieties. The findings of morpho-molecular characterization information could be useful to the breeders for further planning of developing BLB resistant cultivars.

To detect DNA polymorphisms in the peanut, we screened 26 polymorphic primers using intron-exon splice junction (ISJ), universal rice primer (URP), and directed amplification of minisatellite region DNA (DAMD) techniques. Amplification of genomic DNA of 16 peanut accessions yielded 121 ISJ, 50 URP, and 25 DAMD fragments, of which 34, 25 and 16 were polymorphic, respectively. The range of polymorphism was 10.0-62.5%, averaging 27.7%, for ISJ; 20-80%, averaging 49.5%, for URP; and 28.6-50.0%, averaging 36.3%, for DAMD. In comparisons of multiplex ratio, average polymorphism information content, and marker index, the URP markers were relatively more efficient than ISJ and DAMD markers. Clustering results remained more or less the same with ISJ and URP markers. To the best of our knowledge, this is the first report on the study of the genetic diversity of the peanut using ISJ, URP, and DAMD markers.

The illness known as kernel smut, which is brought on by Tilletia horrida, is typified by the sooty black masses of teliospores or chlamydospores that replace rice grains. The color of the chlamydospores in kernel smut is different from that of rice fake smut, which is generated by Ustilaginoidea virens. Spore balls that are globose and velvety, with colors ranging from orangish yellow to greenish black, are the hallmark of false smut. Due to their irregular breakouts and little economic impact, kernel smut and fake smut which were first identified in the late 1870s and continued to persist are regarded as minor illnesses in many nations. However, in many nations, particularly the US, kernel smut and fake smut have become two of the most commercially significant illnesses affecting rice, including organic rice, in recent years. Grain production and quality have significantly decreased as a result of the growing use of sensitive rice cultivars particularly hybrids, excessive nitrogen fertilizer use, and short crop rotations. These factors have also led to a rise in kernel smut and fake smut. The distribution and economic significance of kernel smut are reviewed in this article, along with our current knowledge of the taxonomy, biology, and epidemiology of kernel smut and the genomics of the kernel smut fungus in comparison to fake smut and its causative agent. We also provide an update on the current management strategies of pathogen exclusion, cultivar resistance, fungicides, biological control, and cultural practices for kernel smut and false smut of rice.

ABSTRACTXanthomonas oryzae pv. oryzae (Xoo) is the causal agent of bacterial leaf blight (BLB) disease in rice, exerting a detrimental impact on the yield of various rice cultivars in Vietnam, notably the Bacthom 7 (BT7) variety. Xoo possesses transcription activator‐like effectors (TALEs) which modulate the expression of host genes by specifically binding to the effector‐binding element (EBE) sequence in target promoter regions, thereby facilitating bacterial proliferation and pathogenesis on rice plants. Notably, OsSWEET13, a member of the Sugar Will Eventually be Exported Transporter (SWEET) gene family encoding sugar transporter proteins, has been identified as a prominent susceptibility (S) gene for BLB. This investigation focuses on elucidating the role of OsSWEET13 in the susceptibility of BT7 to BLB disease in Vietnam. Vietnamese Xoo (VXO) strains were observed to elicit characteristic BLB symptoms on BT7 and trigger the expression of OsSWEET13 during the course of infection. To further probe this, a clustered regularly interspaced palindromic repeats/CRISPR‐associated protein 9 (CRISPR/Cas9) construct targeting the EBE PthXo2A site on the OsSWEET13 promoter was designed and introduced into BT7 rice plants through Agrobacterium tumefaciens, resulting in the creation of rice lines with OsSWEET13 promoter modifications. Upon conducting detailed genotype and phenotype analyses of the gene‐edited rice plants, it was ascertained that the mutation exhibited no adverse effects on the principal agronomic traits under scrutiny. Notably, a transgene‐free homozygous 3‐nucleotide deletion modified rice line displayed diminished OsSWEET13 gene expression and a significant reduction in BLB development upon inoculation with VXO strains. This study unequivocally establishes OsSWEET13 as an S gene for VXO, underscoring its significance in breeding programs aimed at enhancing BLB resistance in the BT7 variety through the utilization of CRISPR/Cas9 technology.

Improvement of nutrient-use efficiency (NUE) in rice is important for increasing productivity. Rice varieties with tolerance to phosphorus (P) deficiency increase the productivity in P-deficient fields. Therefore, the objective of this study was to develop high yielding, P-deficiency tolerant rice varieties to enhance the NUE. High yielding and popular rice varieties (Bg300 and Bg94-1) and known P-deficiency tolerant rice varieties (H4 and At353) were used as female and male parents, respectively, in a crossing program. Single seed descent approach was used for rapid generation advancement. Bg300/At353 and Bg94-1/H4 crosses were advanced from F2 to F6 in planthouse condition under minimum fertigation for restricted growth. In F7 generation, 310 recombinant inbred lines (RIL) in both crosses were space-planted and 40 RILs were selected from each cross. Selected RILs were screened in a hydroponic system at 10 μM P level to select the best lines for P-deficiency tolerance. Multiple plant traits were used for selection and the most promising 20 rice lines were selected as the best performers under P-deficient hydroponic conditions. Marker assisted selection was carried out to confirm the presence of PSTOL1 gene. Selected rice lines were evaluated for agronomic traits and yield parameters. Ten promising rice lines were identified as high yielding lines with accepted agronomic traits.

The 5' ends of Leishmania mRNAs contain an identical 35-nucleotide sequence termed the spliced leader (SL) or 5' mini-exon. The SL sequence is at the 5' end of an 85-nucleotide primary transcript that contains a consensus eucaryotic 5' intron-exon splice junction immediately 3' to the SL. The SL is added to protein-coding genes immediately 3' to a consensus eucaryotic 3' intron-exon splice junction. Our previous work demonstrated possible intermediates in discontinuous mRNA processing that contain the 50 nucleotides of the SL primary transcript 3' to the SL, the SL intron sequence (SLIS). These RNAs have a 5' terminus at the splice junction of the SL and the SLIS. We examined a Leishmania nuclear extract for these RNAs in ribonucleoprotein (RNP) particles. Density centrifugation analysis showed that the SL RNA is predominantly in RNP complexes at 60S, while the SLIS-containing RNAs are in complexes at 40S. We also demonstrated that the SLIS can be released from polyadenylated RNA by incubation with a HeLa cell extract containing debranching enzymatic activity. These data suggested that Leishmania enriettii mRNAs are assembled by bimolecular or trans splicing as has been recently demonstrated for Trypanosoma brucei. Furthermore, we determined the partial sequence of the Leishmania U2 equivalent RNA and demonstrated that it cosediments with the SL RNA at 60S in a nuclear extract. These RNP particles may be analogous to so-called spliceosomes that have been demonstrated in other systems.

Soil salinity has turned out to be an important global concern, which affects tenable rice production in many agricultural countries like Bangladesh. A cross was made between Binadhan-7 with FL-478 for developing salt tolerant advance lines to assess phenotypic and genotypic diversity in rice for salinity tolerance. Twenty advance rice lines (Binadhan-7/FL-478) along with check varieties were screened for salinity tolerance at reproductive stage using sea site saline water having electrical conductivity (EC) 10 dS m-1. Among the twenty rice lines, seven lines were tolerant, three were moderately tolerant, six were susceptible, four were highly susceptible on the basis of phenotypic evaluation. Seven simple sequence repeat (SSR) markers linked with salt tolerance quantitative trait loci were used for investigation of salt tolerant rice lines. The result revealed that an average number of 6.286 alleles per locus were detected, with polymorphism information content (PIC) values ranging from 0.672 (RM490) to 0.838 (RM562). The highest gene diversity value (0.812) was found in RM562 and the lowest (0.684) was in RM490. A dendrogram constructed from the genetic distance of the genotypes produced four distinct clusters of twenty rice genotypes. Considering both phenotypic and genotypic observation, seven genotypes viz., Binadhan-10, FL-478, SL-51, SL-56, SL-77, EFSD-59 and IZSD-45 were identified as salt-tolerant; on the other hand, EFSD-21, SL-28, SL-32, SL-10, BRRI dhan28, and Binadhan-7 were identified as salt-susceptible. The identified salt-tolerant rice genotypes could be used in the improvement of rice breeding programs. Bangladesh J. Nuclear Agric, 37(2): 1-18, 2023

Among abiotic stresses, salt stress is the most complicated problem posing a major challenge for maintaining world food supplies as well as food security as it covers 1125 m ha globally and 6.73 m ha in India. It is very essential to increase rice productivity in salt-affected soils for food security and sustainability in salt-affected environments. The pass port data of 9000 rice Germplasm has been established for 30 traits and a mini core of 1500 lines has been developed. Approximately 20,000 rice lines have been screened for salinity and sodicity for both seedling and reproductive stages. The highly tolerant rice lines are being used in breeding programme to enhance the genetic diversity. The six QTLs in chromosomes 1, 2, 8, 9, 10 has been identified for the Na/K ratio, spikelet fertility and grain yield for the reproductive stage salt tolerance. The Saltol QTL has been transferred to Indian mega rice varieties namely, Pusa44 and Sarjoo52, to improve the salinity tolerance at the seedling stage. Similarly, the qSSISFHS8.1 (QTL for spikelet fertility) QTL is being transferred into mega rice varieties namely, PR114, Pusa44 and Sarjoo52, to improve the salinity tolerance at the reproductive stage. The marker assisted selection accelerates the breeding activities to develop the salt-tolerant varieties as well as transfer the QTLs to HVYs through marker assisted back cross breeding. The Central Soil Salinity Research Institute (CSSRI) has developed 13 salt-tolerant rice varieties, namely CSR10, CSR13, CSR23, CSR27, Basmati CSR30, CSR36, CSR43, CSR46, CSR49, CSR52, CSR56, CSR60 and CSR76, through conventional breeding approaches to increase the productivity of salt-affected soils for resource poor farmers. The popularity of these salt-tolerant rice varieties can be ascertained from the facts that large quantity of breeder seeds (1056 quintals) and truthfully labelled seeds (3126 quintals) has been produced and sold during last 22 years (2000–2021), more demand from the farmers and large area app. One point two million hectares is covered by these salt-tolerant rice varieties every year. Numerous salt-tolerant rice lines are being developed at CSSRI to cope with salt-affected soils and enable sustainable agriculture under salt-affected soils.

This study was conducted to clarify the relationship between the number of pollen grains per anther and spikelet fertility under low temperature conditions in the rice cultivars and lines including lines with quantitative trait loci (QTL) for cold tolerance, adapted to the Tohoku region of northern Japan. Cold-water treatment decreased anther length, the number of pollen grains per anther, and spikelet fertility in all cultivars and lines. The number of pollen grains was proportional to anther length in all cultivars and lines and under all temperatures. Spikelet fertility decreased with decreasing the number of pollen grains in cold-water treatments at 18.5 and 19.3 °C. ‘Ouu 415’, with the qLTB3 QTL for cold tolerance, had 28% more pollen grains and 9% higher spikelet fertility than the recurrent parent, ‘Hitomebore’, in the 18.5 °C cold-water treatment, suggesting that qLTB3 increased both parameters. Lines with the qCTB8 QTL for cold tolerance had significantly more pollen grains in two of the three years and significantly higher spikelet fertility in all three years in the 19.3 °C cold-water treatment, suggesting that qCTB8 reinforced cold tolerance. Ctb1, a proposed cold-tolerance QTL, had no effect on the number of pollen grains or spikelet fertility. In conclusion, the cultivars and lines with more pollen grains had a higher cold tolerance. Some of QTLs were inferred to increase the number of pollen grains and reinforce cold tolerance.

Virulence assays and DNA polymorphism analyses were used to characterize 33 Xanthomonas oryzae pv. oryzae (Xoo) strains collected from the coastline region of Fangchenggang city in China. Two new pathogenic races (FXP1 and FXP2), were determined by leaf-clipping inoculation of 12 near-isogenic International Rice-Bacterial Blight (IRBB) rice lines, each containing a single resistance gene. Race FXP1 consisted of twenty-eight strains that were incompatible on IRBB5 and IRBB7, while race FXP2 included five strains that were incompatible on IRBB5 and IRBB7 and moderately virulent on IRBB8 containing the xa8 gene. Restriction fragment length polymorphism (RFLP) analysis revealed that each probe of avrXa10 and IS1112 resolved two haplotypes. In a dendrogram generated from the combined RFLP data, the 33 Xoo strains were resolved into two clusters. There was a weak correlation (r = 0.53) between race and haplotype. All of the rice cultivars planted in the coastline region of Fangchenggang city were susceptible to the representative Xoo strains tested above. However, we found that four rice cultivars used as breeding materials in the laboratory could fully resist infection by the Xoo strains, suggesting that the isolated Xoo strains could be used to detect resistant rice cultivars suitable for planting in the local rice field.

Kernel smut of rice caused by Tilletia barclayana (Bref.) Sacc. and Syd., becomes a serious disease for seed production of rice under favourable environmental conditions. The disease has been listed as objectionable disease under the Indian Minimum Seed Certification Standards. In this study, effort has been made to generate information on the most suitable time of sowing of rice in relation to minimum disease parameters of kernel smut. Ten rice cultivars viz., PR 111, PR 114, PR 116, PR 118, PR 121, PR 122, PR 124, PR 126, PR 127 and PAU 201 were sown on three different dates of sowing (28 May; 10 June; and 24 June) at an interval of 14 days during the crop season 2019 and 2020 under natural epiphytotic conditions for disease development so as to focus on the most crucial time of disease development under natural field conditions. There was a gradual decrease in disease parameters of kernel smut with delayed sowing in case of all cultivars under study except variety PR 111. Coefficient of infection reduced uniformly with the delay in sowing time in different cultivars during the two consecutive crop seasons in all the test cultivars. Test weight (1000 grain weight) of rice did not vary significantly in response to alteration in sowing time indicating no adverse effect of late planting on the seed quality.

The demand for aromatic rice has increased in the United States during the last two decades. Jazzman, the first US-bred jasmine-type rice variety, was released by the Louisiana State University (LSU) AgCenter Rice Research Station in 2008 to compete for a market share of jasmine-type rice. Jazzman, a long grain aromatic rice variety, was developed from a cross between Ahrent and an unreleased aromatic Chinese rice line 96a-8. In pre-release field tests and laboratory scale evaluation, Jazzman rice yield and milling quality compared favorably with two high-yielding and good-milling non-aromatic long grain varieties, Cypress and Cheniere. Pilot scale evaluation of Jazzman for milling quality supported laboratory scale evaluation while providing additional data for milling optimization. Pilot scale milling uses larger rice samples than laboratory scale testing and employs a continuous process instead of the batch process used at laboratory scale. As a result, pilot scale milling offers more comprehensive information regarding the milling yield and quality of rice varieties as they are considered for industrial scale release. Another consideration for new rice varieties involves their potential for value-added processing, in which waste streams during processing can be used to create valuable products. The oil from rice bran is one such product. The objective of this study was to use pilot scale milling to determine the potential of Jazzman for industrial scale release, including its potential for value-added processing. Results showed that bran was easily removed during milling; the head rice recovery ranged from 66% to 74% as a function of milling flow rate. Water polishing had little effect on head rice recovery, but improved the final degree of milling (DOM) to a commercially acceptable level of 87 - 90. Additionally, rice bran oil concentration decreased as pilot scale flow rate increased, indicating that oil was concentrated in the outer bran layer of Jazzman. Pilot scale milling shows that Jazzman is a high-yielding and good-milling aromatic long grain rice variety.

Improvement of local rice variety could be conducted by crossing it with superior varieties. C3 is improved line of Acehnese rice ‘Cantik Manis’ by crossing it with the introduced Chinese rice variety Yin Zhan to make their progenies have shorter lifespan and good productivity. Although C3 line has been improved, this variety still has lifespan for about ± 135 days. Koshihikari is Japanese rice variety with its lifespan about 80-90 days. It is though that Koshihikari has various semidwarf gene such as sd-1 or other semidwarf genes. The strategy that can be used to decrease harvesting period of C3 is by crossing this variety with Koshihikari to insert semi-dwarf gene such as sd-1. The research was conducted to analyse the existing of sd-1 gen and phenotypic performance of their progenies specially in BC1F1. The seed of BC1F1 were found by crossing 2 prospective F1 plants (T8 and T10) with C3 parent. Molecular analysis showed that the whole progenies BC1F1-T8 inherit sd-1 gene (100%). Phenotypic observation showed the whole progenies had similar architecture as their parents with average heights at 45 DAP ranged from 74-91 cm, and number of tiller range from 3-9 tillers. Whereas in BC1F1-T10 progenies, there were 11 plant from 12 plants inherit sd-1 gene (91.7%). These progenies had average heights at 45 DAP ranged from 75-88 cm, and number of tiller range from 6-13 tillers.

A simple and rapid method for the detection of Tilletia horrida, the causal agent of rice kernel smut, in rice seeds is developed based on specific polymerase chain reaction (PCR). To design the specific primers for the detection of T. horrida, partial sequences of internal transcribed spacer (ITS) DNA region of T. horrida, T. controversa, T. walkeri, T. ehrhartae, T. indica and T. caries were analyzed and compared. A 503-bp fragment was amplified with the designed primers from the T. horrida genomic DNA. However, no PCR product was obtained from the DNA of other five Tilletia species and 22 fungal plant pathogens tested in the present work indicating the specificity of the primers for the detection of T. horrida. The PCR was performed by directly using the spores, isolated from the 21 different rice seed samples, as template DNA. The T. horrida was detected in 6 of the samples, indicating that 28.6% of the rice samples were contaminated with the kernel smut pathogen. This simple PCR based diagnostic assay can be applied for the direct and rapid detection and identification of T. horrida to screen large numbers of rice seed samples.

Rice (Oryza sativa) is one of the most profitable and popular cereal crops in Pakistan. In July 2012, symptoms consisting of circular, black, necrotic spots, 2 to 4 mm in diameter, were observed on leaves of a commonly grown rice cultivar, Basmati-198, in private rice fields at Lahore (Punjab). This disease was observed later on rice cultivar KSK-133 grown at Faisalabad (Punjab) during the same cropping season. Disease incidence was ~35% and 25% for Basmati-198 and KSK-133, respectively. To our knowledge, the pathogen was confined only in these areas and cultivars and was not present on other rice varieties or crops. Ten infected plants were selected randomly from each field of two rice cultivars and one infected leaf for each of the 10 infected plants was selected for the isolation of fungal pathogen. Necrotic lesions were cut into pieces of ~2 mm2, surface-disinfected with 0.5% sodium hypochlorite, placed on 2% malt extract agar (MEA) (Sigma, Dorset, UK), and incubated at 25 ± 2°C for 4 to 5 days. Emerging fungal colonies were transferred aseptically to fresh MEA petri plates for purification. Alternaria spp. were consistently recovered from infected leaves. Three isolates per variety were selected for detailed morphological studies. Each isolate was grown at 25°C on MEA and potato carrot agar (PCA) for 7 days. All isolates displayed similar morphological features including black radiate, floccose colonies with irregular margins, 6 to 7 cm in diameter on MEA and 2 to 3 cm with 1 to 2 pairs of concentric growth rings on PCA. Conidial chains were not crowded with 1 to 10 conidia per branch and bearing several lateral branches. Conidiophores were tapering and narrow, 40 to 200 × 2 μm. Conidia were ovoid within a size range of 10 to 30 × 5 to 14 μm, with 1 to 5 transverse and 1 longitudinal septum. Conidial color darkens from a dull tan to a medium brown as the culture matures. Based on morphology, the pathogen was identified as Alternaria arborescens (1). A pure culture of the pathogen was deposited in First Fungal Culture Bank of Pakistan (FCBP) with accession FCBP1351. Identification based on morphology was verified by sequencing the internal transcribed spacer (ITS) region. For this, a DNA fragment of ~650 bp was amplified using total genomic DNA as template and ITS1 and ITS4 primers (2). The nucleotide sequence of the ITS region was submitted to GenBank under accession KF679683. Comparison of the sequence with those in GenBank revealed that the sequence was 99% identical with A. arborescens, isolate ALT-242 (KC415808), causing Eucalyptus leaf spot in India and strain STE-U4345 (AF404667), a causal pathogen of apple core rot in South Africa. Pathogenicity testing was performed on both cultivars. One-month-old plants grown in greenhouse were sprayed with 10 ml of spore suspension (2 × 105 spores/ml) as well as 10 ml of this spore suspension in soil at the time of sowing. Control plants were sprayed with sterilized water. The plants were covered with plastic bags for 48 h and kept under observation for 2 weeks in a glasshouse at 30 ± 2°C. Lesions appeared on leaves after 10 days of inoculation whereas control plants remained healthy. Pathogenicity tests were repeated in triplicate. Similar disease symptoms and re-isolation of A. arborescens fulfilled Koch's postulates. To our knowledge, this is the first report of A. arborescens leaf spot of rice in Pakistan. At present, the distribution of this disease is limited to the fields where it was observed.