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Rice false smut (RFS), an emerging major fungal disease worldwide caused by Ustilaginoidea virens, affects rice grain quality and yield. RFS cause 2.8-49% global yield loss depending upon disease severity and cultivars. In India, the yield loss due to RFS ranged from 2 to 75%. Identification of the genes or quantitative trait loci (QTLs) governing disease resistance would be of utmost importance towards mitigating the economic losses incurred due to RFS. Here, we report mapping of RFS resistance QTLs from a resistant breeding line RYT2668. The mapping population was evaluated for RFS resistance under the field condition in three cropping seasons 2013, 2015, and 2016. A positive correlation among infected panicle/plant, total smut ball/panicle, and disease score was observed in the years 2013, 2015, and the mean data. A total of seven QTLs were mapped on rice chromosomes 2, 4, 5, 7, and 9 using 2326 single nucleotide polymorphism markers. Of these, two QTLs, qRFSr5.3 and qRFSr7.1a, were associated with the infected panicle per plant, one QTL qRFsr9.1 with total smut ball per panicle, and four QTLs qRFSr2.2, qRFSr4.3, qRFSr5.4, and qRFSr7.1b with disease score. Among them, a novel QTL qRFSr9.1 on chromosome 9 exhibits the largest phenotypic effect. The prediction of putative candidate genes within the qRFSr9.1 revealed four nucleotide-binding sites-leucine-rich repeat (NBS-LRR) domain-containing disease resistance proteins. In summary, our findings mark the hotspot region of rice chromosomes carrying genes/QTLs for resistance to the RFS disease.

Rice is a principal food crop for more than half of the global population. Grain number and grain weight (2Gs) are the two complex traits controlled by several quantitative trait loci (QTLs) and are considered the most critical components for yield enhancement in rice. Novel molecular biology and QTL mapping strategies can be utilized in dissecting the complex genetic architecture of these traits. Discovering the valuable genes/QTLs associated with 2Gs traits hidden in the rice genome and utilizing them in breeding programs may bring a revolution in rice production. Furthermore, the positional cloning and functional characterization of identified genes and QTLs may aid in understanding the molecular mechanisms underlying the 2Gs traits. In addition, knowledge of modern genomic tools aids the understanding of the nature of plant and panicle architecture, which enhances their photosynthetic activity. Rice researchers continue to combine important yield component traits (including 2Gs for the yield ceiling) by utilizing modern breeding tools, such as marker-assisted selection (MAS), haplotype-based breeding, and allele mining. Physical co-localization of

The temporal and spatial progress of sheath blight was assessed on a set of mega rice varieties of South Asia and local varieties of North India in field experiments for two consecutive years. With artificially created disease focus disease severity was recorded on five un-inoculated plants from the focus in four directions after two, four and six weeks of inoculation. The mega varieties differed in their level of susceptibility to sheath blight. The temporal progression of the disease was significantly increased in Swarna and Swarna Sub-1 followed by PR 114 and PR 121 varieties. Area under disease progress curve (AUDPC) ranged 184.92 – 683.67 in tested varieties. The disease severity decreased as the distance from the disease focus increased in all varieties, the significance of the spatial spread depended on the susceptibility level of the variety. Swarna and Swarna Sub-1 showed higher level of susceptibility. The exponential regression model explained the increased severity with time which get decreased with increase in distance from the disease focus. Relationship of week after inoculation with disease severity indicated that model explained 96.0% variability of the response data in Swarna. The morphological traits like plant height, number of tillers per hill and tiller angle of the varieties had a significant correlation with the disease severity and incidence. In the absence of genetic resistance, this study provides evidence of requirement of a six-week period for differentiating the susceptible or resistant response of rice varieties to sheath blight under field conditions. Plant morphological traits are the key factor which can be consider in disease resistant breeding programme.

Wild relatives of rice (Oryza sativa L.) represent enormous genetic diversity for many traits. Many domestication related traits found only in wild species that are lost from cultivated species during domestication. In this study, we report high-resolution mapping of two domestications related quantitative trait locus (QTL) controlling purple sheath color and plant height using high-density SNP based linkage map in an interspecific F2 population derived from a cross between O. nivara Sharma & Shastry and O. sativa. The segregation ratio of purple sheath color fit into 3:1 indicated that the presence of a dominant gene. The segregation of plant height trait exhibited a normal distribution in F2 and F2:3 generations. QTL analysis showed the identification of two QTLs controlling purple sheath color (designated as qPsh6.1 and qPsh6.2) on chromosome 6 explaining 27.12% and 14% phenotypic variance, respectively. The only plant height QTL (tentatively designated as qPh1.9) was mapped on chromosome 1 contributing 18.3% phenotypic variance. The qPsh6.1 covers 25.17 Kb region flanked by AX-95928721 and AX-95954573 containing five open reading frames (ORFs) while qPsh6.2 spanned in 118.2 Kb region containing 19 ORFs flanked by markers AX-95956260 and AX-95928295. The qPh1.9 gene controlling plant height was mapped between two SNP markers, AX-95944819 and AX-95964796 co-segregated with the locus LOC_Os01g66690 encoding for ZIP4/SPO22 protein. The detailed genetic study of the location of these genes will be useful for the map-based cloning.

A novel recessive bacterial blight resistance locus designated as a xa-45(t) was identified from Oryza glaberrima accession IRGC 102600B, transferred to O. sativa and mapped to the long arm of chromosome 8 using ddRAD sequencing approach. The identified QTL spans 80 kb region on Nipponbare reference genome IRGSP-1.0 and contains 9 candidate genes. An STS marker developed from the locus LOC_Os08g42410 was found co-segregating with the trait and will be useful for marker-assisted transfer of this recessive resistance gene in breeding programs. Bacterial blight, caused by Xanthomonas oryzae pv. oryzae, is one of the major constraints of rice productivity in Southeast Asia. In spite of having 44 bacterial blight resistance genes from cultivated rice and wild species, the durability of resistance is always at stake due to the continually evolving nature of the pathogen and lack of suitable chemical control. Here, we report high-resolution genetic mapping of a novel bacterial blight resistance gene tentatively designated as a xa-45(t) from an introgression line derived from Oryza glaberrima accession IRGC 102600B. This introgression line was crossed with the susceptible rice indica cultivar cv. Pusa 44 to generate F2 and F2:3 populations for inheritance and mapping studies. The inheritance studies revealed the presence of single recessive locus controlling resistance to the Xanthomonas pathotype seven. A high-density linkage map was constructed using double-digest restriction-associated DNA sequencing of 96 F2 populations along with the parents. The QTL mapping identified a major locus on the long arm of rice chromosome 8 with a LOD score of 33.22 between the SNP markers C8.26737175 and C8.26818765. The peak marker, C8.26810477, explains 49.8% of the total phenotypic variance and was positioned at 202.90 cM on the linkage map. This major locus spans 80 kb region on Nipponbare reference genome IRGSP-1.0 and contains 9 candidate genes. A co-segregating STS marker was developed from the LOC_Os08g42410 for efficient transfer of this novel gene to elite cultivars.

Rice bran oil is good quality edible oil, rich in antioxidants and comprised typically of oleic-linoleic type fatty acids. However, presence of a highly lipolytic enzyme Phospholipase D alpha1 (OsPLDα1) increases free fatty acid content in the oil which further leads to stale flavor and rancidity of the oil, making it unfit for human consumption. In this study, we compared the upstream regions of OsPLDα1 orthologs across 34 accessions representing 5 wild Oryza species and 8 cultivars, to uncover sequence variations and identify cis-elements involved in differential transcription of orthologs. Alignment of the upstream sequences to the Nipponbare OsPLDα1 reference sequence revealed the presence of 39 SNPs. Phylogenetic analysis showed that all the selected cultivars and wild species accessions are closely related to the reference except for three accessions of O. rufipogon (IRGC89224, IRGC104425, and IRGC105902). Furthermore, using exon-specific qRT-PCR, OsPLDα1 expression patterns in immature grains indicated significant differences in transcript abundance between the wild species accessions. In comparison to the control, lowest gene expression was observed in IRGC89224 accession (0.20-fold) followed by IRGC105902 (0.26-fold) and IRGC104425 (0.41-fold) accessions. In-silico analysis of the OsPLDα1 promoter revealed that the copy number variations of CGCGBOXAT, GT1CONSENSUS, IBOXCORE, NODCON2GM, OSE2ROOTNODULE, SURECOREATSULTR11, and SORLIP1AT cis-elements play an important role in the transcriptional activities of orthologous genes. Owing to the presence of ARFAT and SEBF elements only in the IRGC89224 accession, which had the lowest gene expression as well, these putative upstream regulatory sequences have been identified as novel cis-elements which may act as repressors in regulating the OsPLDα1 gene expression. The accessions identified with low OsPLDα1 expressions could be further deployed as potential donors of ideal OsPLDα1 allele for transfer of the desired trait into elite rice cultivars.

The present investigation was carried out to exploit bacterial endophytes associated with root and leaf tissue of rice plant for plant growth promotion (PGP) and colonization study in vitro. Total 10 endophytic bacterial isolates (Pseudomonas sp.) were evaluate for PGP traits like P solubilization, production of Indole acetic acid (IAA), siderophore, ACC deaminase, protease, cellulase, fluorescent pigment, urease and denitrification activity. Out of 10 endophytic bacteria 30 %, 60 %, 20 %, 70 %, 10 % and 10 % were positive for siderophore, protease, cellulase, fluorescent pigment, urease and denitrification respectively. Maximum IAA production was recorded with isolate LRBLE7 (18.8 μgml-1) followed by LRBRE4 (16.0 μgml-1) and maximum P-solubilization was recorded with isolate LRBRE4 (5.8 mg 100 ml-1) followed by LRBLE7 (4.4 mg 100 ml-1). ACC deaminase production was recorded with isolate LRBLE6 (O.D=0.352 nm) followed by LRBRE5 (O.D=0.324nm). Three potential isolates (LRBRE4, LRBRE6 and LRBLE7) were selected on the basis of multiple PGP traits and were subjected to colonization study of rice seedling in vitro. Potential bacterial isolates can be exploited for improving growth and productivity in rice under sustainable management system.

Bacterial blight (BB) of rice caused byXanthomonas oryzaepv.oryzae(Xoo) is a major biotic constraint of rice production in all the major irrigated/lowland rice growing regions of Asia, including Punjab and its adjoining states in India. None of the individual BB resistantXa/xagenes is effective against Punjab pathotypes. In the present study, we have screened 1176 accessions, comprising 1007 accessions of A genome speciesOryza glaberrima, O. barthii, O. nivara, O. rufipogon, O. longistaminata, O. meridionalis, O. glumaepatulaand 169 accessions from ten other wild species having CC, FF, EE, BBCC and CCDD genomes against two most recently evolvedXoopathotypes viz. PbXo-10 and PbXo-8 in Punjab state of India, for two constitutive years 2014 and 2015. Based on 2 years of data, four accessions ofO. glaberrima(IRGC102206, IRGC1022445, IRGC102512 and IRGC102520) and two of theO. longistaminataaccessions (IRGC92624 and IRGC101754) were identified with immune reaction against PbXo-8. For PbXo-10,O. longistaminatashowed large number of accessions with complete to partial resistance followed byO. rufipogon(8),O. nivara(2),O. punctata(2) andO. officinalis(1). Two of theO. longistaminataaccessions IRGC92624 and IRGC92644 from Mali were found to have resistance against both theXoopathotypes indicating presence of BB resistance gene other thanXa21. These can be transferred to elite cultivars ofO. sativafor better management of BB.

Rhizoctonia solani Kuhn, a highly variable pathogen, causes sheath blight of rice globally leading to serious yield losses under favourable environmental conditions. Sixty-four Rhizoctonia isolates collected from diverse rice growing agro-ecological zones of the north Indian state of Punjab were analyzed for species identification, genetic diversity, morphological features and virulence pattern. Accurate identification of the fungal species using internal transcribed spacer species-specific primers confirmed presence of R. solani (84.4 %), R. oryzae-sativae (10.9 %), R. oryzae (1.5 %) and mixed infection of these Rhizoctonia sp. Genetic structure of the isolates resolved using inter simple sequence repeat primers revealed high degree of polymorphism (PIC value ranging from 0.80 to 0.90), clustering the pathogen population into four major groups. The virulence pattern of 18 isolates representing genetically diverse groups generated by ISSR profile was quantified on seven rice genotypes/cultivars i.e., Tetep, Jasmine 85, Te-Qing, D-256, D-6766, PR108 and PAU201 with different levels of resistance to rice sheath blight. The hierarchical cluster analysis based on different disease variables classified isolates into six main groups. Reaction of individual isolate to each genotype revealed different levels of virulence pointing towards high evolutionary potential, thus enabling it to adapt to diverse geographical regions.

BACKGROUND Antioxidative properties and physicochemical characteristics of introgression lines (ILs) and their recurrent parents were analyzed. In addition, catalase (CAT) and superoxide dismutase (SOD) activities and free radical-scavenging capacity were evaluated, since these are important antioxidative properties for developing nutraceutical and functional foods. RESULTS Comparative analysis of the brown and milled rice fractions of ILs with their respective recurrent parents revealed 2.26- and 1.22-fold increase in total phenolics, 1.95- and 2.09-fold increase in flavonoids, 8.38- and 6.80-fold increase in proanthocyanidins and 1.55- and 1.20-fold increase in tannins in brown and milled rice fractions respectively. Higher CAT (1.36- and 1.89-fold) and SOD (1.71- and 2.02-fold) activities and Trolox equivalent antioxidant capacity (TEAC, 7.13- and 1.98-fold) were observed in brown and milled rice fractions respectively of ILs compared with their respective recurrent parents. A high and positive correlation was obtained between TEAC and total phenols (0.73, P ≤ 0.01), flavonoids (0.66, P ≤ 0.05) and proanthocyanidins (0.69, P ≤ 0.05). The yield parameters and physicochemical characteristics of the grains, in general, were comparable in the ILs and their respective recurrent parents. CONCLUSION The ILs of rice reported in the present study exhibited significant positive differences in the content of phenolic constituents and antioxidant properties with good grain quality characteristics over their recurrent parents, indicating their potential as a natural source of phytochemicals for nutraceutical and functional food development. © 2014 Society of Chemical Industry

Basmati rice, owing to its characteristic aroma and long, slender grains, is a specialized group of rice (Oryza sativa L.) and is high in demand. Traditional basmati cultivars are tall, low yield- ing, and susceptible to diseases, especially bacterial blight. Conventional plant breeding approaches could bring only marginal improve- ment in basmati yield. This study reports improvement of traditional basmati cultivars for bacterial blight resistance and plant height. Using marker-assisted backcrossing we trans- ferred two bacterial blight resistance genes, xa13 and Xa21, and semidwarfi ng gene, sd-1, into two traditional basmati cultivars, Basmati 370 and Basmati 386. Markers were also used for selecting aroma and amylose content of basmati cultivars. Along with marker-assisted selection (MAS), we practiced stringent pheno- typic selection in the target environment in all the generations for faster recovery of the recur- rent parent genotype. A set of BC 2 F 6 progenies selected for semidwarf stature, bacterial blight resistance, aroma and nonsticky grains and having more than 90% of the recurrent-parent genome were evaluated for yield and yield com- ponents. Lines that signifi cantly outyielded the recurrent parent and the check cultivars in sta- tion trials are being evaluated in multiple loca- tions in national-level nurseries for identifying the lines that could be released as varieties. These lines, in addition to being released as cul- tivars, can also be used as immediate donors for further basmati improvement.

Modern rice varieties that ushered in the green revolution brought about dramatic increase in rice production worldwide but at the cost of genetic diversity at the farmers’ fields. The wild species germplasm can be used for broadening the genetic base and improving productivity. Mining of alleles at productivity QTL from related wild species under simultaneous backcrossing and evaluation, accompanied by molecular marker analysis has emerged as an effective plant breeding strategy for utilization of wild species germplasm. In the present study, a limited backcross strategy was used to introgress QTL associated with yield and yield components from Oryza rufipogon (acc. IRGC 105491) to cultivated rice, O. sativa cv IR64. A set of 12 BC2F6 progenies, selected from among more than 100 BC2F5 progenies were evaluated for yield and yield components. For plant height, days to 50% flowering and tillers/plant, the introgression lines did not show any significant change compared to the recurrent parent IR64. For yield, 9 of the 12 introgression lines showed significantly higher yield (19–38%) than the recurrent parent IR64. Four of these lines originating from a common lineage showed higher yield due to increase in grain weight and another three also from a common lineage showed yield increase due to increase in grain number per panicle. For analyzing the introgression at molecular level all the 12 lines were analyzed for 259 polymorphic SSR markers. Of the total 259 SSR markers analyzed, only 18 (7.0%) showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6 and 11. Graphical genotypes have been prepared for each line and association between the introgression regions and the traits that increased yield is reported. Based on marker trait association it appears that some of the QTL are stable across the environments and genetic backgrounds and can be exploited universally.

PAU 201, a high yielding variety of rice released by Punjab Agricultural University in 2007, was withdrawn from cultivation in the year 2010 mainly due to its red coloured pericarp. It also became susceptible to a new pathotype (PbXo-8) of bacterial blight (BB) pathogen. To improve these specific defects, PAU 201 was mutagenized with ethyl methane sulphonate in different concentrations of 0.6, 0.8 and 1.0% in water (v/v). A total of 841 M1 single panicles were harvested and advanced to M4 generation following selfing and selection for white pericarp colour in each generation. A set of promising 68 M4 progenies was also screened for BB resistance and one putative mutant possessing white pericarp colour as well as BB resistance (designated as RYT 3207) was identified. On further evaluation, RYT 3207 was found to be resistant to all the ten pathotypes of BB pathogen prevalent in the Punjab state and it yielded at par with the PAU 201 in multi-location trials during 2011 to 2013. Molecular marker analysis showed presence of xa13 locus in RYT 3207. The acquired resistance to all the ten pathotypes in RYT 3207, compared to nine pathotypes in PAU 201, could be due to modified function of xa13 gene. The new genotype RYT 3207 is a mutagenized version of the high yielding rice cultivar PAU 201 possessing white pericarp and enhanced resistance to bacterial blight.

A number of maize (Zea mays L.) genotypes were tested for their influence on induction and regeneration of haploid wheat (Triticum aestivum L.) embryos to improve further the efficiency of the wheat × maize system of haploid production. Fifteen maize genotypes were crossed to five diverse wheat F, hybrids in a line x tester fashion in three replications. Two efficiency parameters, caryopses formation frequency (CFF-number of caryopses/100 pollinated florets) and embryo formation frequency (EFF-number of embryo-carrying caryopses/100 pollinated florets), were estimated. Analysis of variance revealed that lines (wheat genotypes), testers (maize genotypes), and their interaction showed significant effects on both efficiency parameters, but the effect of maize genotypes was greater than that of wheat genotypes. The EFF of individual maize genotypes ranged from 1.1 to 23.4% and the EFF of individual wheat genotypes ranged from 8.4 to 10.2%. Maize genotypes also showed significant differences for general combining ability estimates. In addition to EFF, maize genotypes had a striking effect on haploid embryo regeneration as analyzed using one of the wheat genotypes. The values ranged from 0.0 to 87.8%. For maize genotypes producing the highest EFFs, the regeneration frequency was not necessarily higher. Hence, we suggest a new index, haploid formation efficiency (HFE-number of haploid plants formed /100 pollinated florets), be used for identification of efficient pollinators. The HFE ranged from 0.0 to 9.9%. In this study. a pop corn cultivar, Pearl Pop Corn, was identified as the best pollinator with an average EFF of 15.1% across five wheat genotypes and an HFE of 9.9% with the one wheat genotype tested.

One thousand and eighteen rice germplasm lines were evaluated against the prevalent pathotypes viz., PbXo-7 and PbXo-10 of Xanthomonas oryzae pv. oryzae causing bacterial blight, brown spot and sheath blight diseases under artificial inoculation conditions. Virulence/avirulence of the two pathotypes to Xa/xa genes indicated that all the pathotypes were virulent on the most of bacterial blight resistant single Xa/xa gene (s). Pathotype PbXo-7 was virulent to known Xa genes namely Xa 1, Xa 3, Xa 4, xa 5, Xa 7, xa 8, Xa 10 and Xa 11 and cultivars PR 114, PR 116 and PR 118 growing in Northern regions of India. PbXo-10 was virulent on all these genes including newly identified gene Xa38. None of the single gene is effective against the pathotypes prevalent in Punjab. Two years data revealed that 46 lines (5.4%) showed resistant reaction to pathotype PbXo-7 and 30 lines (2.9%) showed resistance to newly emerged pathotype PbXo-10. Twenty two lines showed resistant reaction to both the pathotypes. Most of the entries which were resistant to PbXo-10 also showed resistant to the PbXo-7. Germplasm line IC No.346207 showed resistant reaction and IC Nos. 114315 and 320826 showed moderately resistant reaction to brown spot. None of the germplasm line showed resistance to sheath blight. These resistant entries can either be released as new varieties or further utilized as donors in multiple disease resistance breeding programmes.

Embryo rescue is an important step in the wheat × maize system of induced haploidy in wheat. On average, only one-third of the seeds carry embryos, but they all have to be dissected because no morphological distinction is available to distinguish between seeds with and without embryos. We here report a simple technique in which immature seeds from wheat × maize crosses are placed on a transparent surface and illuminated from above. The free-floating embryo, settled at the bottom of the seed, can be seen from below or in an image reflected on a plane mirror. Using this technique 97.8% of the embryo-containing seeds could be detected prior to dissection. The technique will be useful in reducing the time and labour involved in embryo culture, thereby scaling up haploid production.

Exogenous application of 1-amino; 4-sulphonate, β-naphthol; 8-amino; 3–6 disulphonate, γ-naphthol; 1, 3-dihydroxybenzene and 4, 6-Bis (diazonaphthalene sulphonate-resorcinol) 5, 20, 50 ppm) increased number of pods per plant, number of seeds/pod and improved the yield (kg/ha) in chickpea. Some of the compounds enhanced total free amino acids and soluble protein and total soluble sugars. The effects of the phenolic acids on growth and development were independent of their structural configuration.

Out of 1 989 wild accessions sown in seed boxes for screening, only 1 003 wild accessions with good germination were screened against brown planthopper (BPH), Nilaparvata lugens (Stal) under greenhouse conditions. The collection comprised of accessions from 11 wild species and African cultivated rice. The germplasm was screened for BPH following standard seed box screening technique in the greenhouse. As many as 159 accessions were identified as resistant during the year 2012 based on one year screening. A selected set of BPH resistant accessions were screened again during 2013. Based on the two years screening, seven accessions of O. nivara (AA), one accession of O. officinalis (CC), seven accessions of O. australiensis (EE), five accessions of O. punctata (BB and BBCC) and nine accessions of O. latifolia (CCDD) were confirmed to be resistant to BPH. So far no BPH resistance genes have been identified and designated from O. nivara and O. punctata , hence these may act as new sources of resistance.