Marker-Assisted Introgression of Saltol QTL Enhances Seedling Stage Salt Tolerance in the Rice Variety "Pusa Basmati 1"

Marker-assisted selection is an unequivocal translational research tool for crop improvement in the genomics era. Pusa Basmati 1 (PB1) is an elite Indian Basmati rice cultivar sensitive to salinity. Here, we report enhanced seedling stage salt tolerance in improved PB1 genotypes developed through marker-assisted transfer of a major QTL, Saltol. A highly salt tolerant line, FL478, was used as the Saltol donor. Parental polymorphism survey using 456 microsatellite (SSR)/QTL-linked markers revealed 14.3% polymorphism between PB1 and FL478. Foreground selection was carried out using three Saltol-linked polymorphic SSR markers RM8094, RM493, and RM10793 and background selection by 62 genome-wide polymorphic SSR markers. In every backcross generation, foreground selection was restricted to the triple heterozygotes of foreground markers, which was followed by phenotypic and background selections. Twenty-four near isogenic lines (NILs), with recurrent parent genome recovery of 96.0-98.4%, were selected after two backcrosses followed by three selfing generations. NILs exhibited agronomic traits similar to those of PB1 and additional improvement in the seedling stage salt tolerance. They are being tested for per se performance under salt-affected locations for release as commercial varieties. These NILs appear promising for enhancing rice production in salinity-affected pockets of Basmati Geographical Indication (GI) areas of India.

Effect of qGN4.1 QTL for Grain Number per Panicle in Genetic Backgrounds of Twelve Different Mega Varieties of Rice

BACKGROUND

Rice is a major source of food, particularly for the growing Asian population; hence, the utilization of genes for enhancing its yield potential is important for ensuring food security. Earlier, we have mapped a major quantitative trait loci (QTL) for the grain number per panicle, qGN4.1, using biparental recombinant inbred line (RIL) populations involving a new plant type Indica rice genotype Pusa 1266. Later, three independent studies have confirmed the presence of a major QTL for spikelet number by three different names (SPIKE, GPS and LSCHL4) in the same chromosomal region, and have implicated the overexpression of Nal1 gene as the causal factor for high spikelet number. However, the effect of qGN4.1 in different rice genetic backgrounds and expression levels of the underlying candidate genes is not known.

RESULTS

Here, we report the effect of qGN4.1 QTL in the genetic backgrounds of 12 different high-yielding mega varieties of rice, introgressed by marker assisted-backcross breeding (MABB) using two QTL positive markers for foreground selection and two QTL negative flanking markers for recombinant selection together with phenotypic selection for the recovery of recipient parent genetic background. Analysis of the performance of BC₂F₃ plants showed a significant increase in the average number of well-filled grains per panicle in all the backgrounds, ranging from 21.6 in CSR 30-GN4.1 to 147.6 in Samba Mahsuri-GN4.1. Furthermore, qGN4.1 caused a significant increase in flag leaf width and panicle branching in most backgrounds. We identified BC₃F₃ qGN4.1 near-isogenic lines (NILs) with 92.0-98.0% similarity to the respective recipient parent by background analysis using a 50 K rice SNP genotyping chip. Three of the NILs, namely Pusa Basmati 1121-GN4.1, Samba Mahsuri-GN4.1 and Swarna-GN4.1, showed a significant yield superiority to their recipient parents. Analysis of differential gene expression revealed that high grain number in these QTL-NILs was unlikely due to the overexpression of Nal1 gene (LOC_Os04g52479). Instead, another tightly linked gene (LOC_Os04g52590) coding for a protein kinase domain-containing protein was consistently overexpressed in the high grain number NILs.

CONCLUSION

We have successfully introgressed the qGN4.1 QTL for high grain number per panicle into 12 different mega varieties of rice using marker-assisted backcross breeding. The advanced near-isogenic lines are promising for the development of even higher yielding versions of these high-yielding mega varieties of rice.

Mining the Cicer arietinum genome for the mildew locus O (Mlo) gene family and comparative evolutionary analysis of the Mlo genes from Medicago truncatula and some other plant species

The mildew locus O (Mlo) gene family is ubiquitous in land plants. Some members of this gene family are involved in negative regulation of powdery mildew resistance, while others are involved in several other biological functions. Mlo proteins have characteristic seven transmembrane domains and a calmodulin-binding domain at their C-termini, and are associated with plasma membrane. The Mlo gene family has been studied in several economically important cereals, but little information is available on this gene family in the important legumes, Medicago truncatula Gaertn. and Cicer arietinum L. We carried out a comprehensive and comparative investigation of the Mlo gene family in these two species using the genome sequences available at the M. truncatula genome database (Mt v4.0) and NCBI (C. arietinum). A genome-wide homology-based search using Arabidopsis Mlo proteins as query identified 16 MtMlo (M. truncatula Mlo) and 14 CarMlo (C. arietinum Mlo) genes. The MtMlo and CarMlo genes had comparable gene structure, protein sequence and topology. Their chromosomal locations indicated the occurrence of extensive reorganization in the genomes of the two species after their divergence from the common ancestor. A multiple sequence alignment of 53 Mlo proteins from these two and several other species showed a highly conserved sequence block of seven amino acids, viz., L-ETPTW, towards their N-termini. The evolutionary phylogenetic analysis grouped the MtMlo and CarMlo members into four clusters, and most of the MtMlo and CarMlo members formed one-to-one ortholog pairs. The ka/ks analyses indicated that the MtMlo and CarMlo genes are subjected to intense purifying selection.

Comparative analysis of genome-wide Mlo gene family in Cajanus cajan and Phaseolus vulgaris

The Mlo gene was discovered in barley because the mutant 'mlo' allele conferred broad-spectrum, non-race-specific resistance to powdery mildew caused by Blumeria graminis f. sp. hordei. The Mlo genes also play important roles in growth and development of plants, and in responses to biotic and abiotic stresses. The Mlo gene family has been characterized in several crop species, but only a single legume species, soybean (Glycine max L.), has been investigated so far. The present report describes in silico identification of 18 CcMlo and 20 PvMlo genes in the important legume crops Cajanus cajan (L.) Millsp. and Phaseolus vulgaris L., respectively. In silico analysis of gene organization, protein properties and conserved domains revealed that the C. cajan and P. vulgaris Mlo gene paralogs are more divergent from each other than from their orthologous pairs. The comparative phylogenetic analysis classified CcMlo and PvMlo genes into three major clades. A comparative analysis of CcMlo and PvMlo proteins with the G. max Mlo proteins indicated close association of one CcMlo, one PvMlo with two GmMlo genes, indicating that there was no further expansion of the Mlo gene family after the separation of these species. Thus, most of the diploid species of eudicots might be expected to contain 15-20 Mlo genes. The genes CcMlo12 and 14, and PvMlo11 and 12 are predicted to participate in powdery mildew resistance. If this prediction were verified, these genes could be targeted by TILLING or CRISPR to isolate powdery mildew resistant mutants.

Development and evaluation of near-isogenic lines for major blast resistance gene(s) in Basmati rice

A set of NILs carrying major blast resistance genes in a Basmati rice variety has been developed. Also, the efficacy of pyramids over monogenic NILs against rice blast pathogen Magnaporthe oryzae has been demonstrated. Productivity and quality of Basmati rice is severely affected by rice blast disease. Major genes and QTLs conferring resistance to blast have been reported only in non-Basmati rice germplasm. Here, we report incorporation of seven blast resistance genes from the donor lines DHMASQ164-2a (Pi54, Pi1, Pita), IRBLz5-CA (Pi2), IRBLb-B (Pib), IRBL5-M (Pi5) and IRBL9-W (Pi9) into the genetic background of an elite Basmati rice variety Pusa Basmati 1 (PB1). A total of 36 near-isogenic lines (NILs) comprising of 14 monogenic, 16 two-gene pyramids and six three-gene pyramids were developed through marker-assisted backcross breeding (MABB). Foreground, recombinant and background selection was used to identify the plants with target gene(s), minimize the linkage drag and increase the recurrent parent genome (RPG) recovery (93.5-98.6 %), respectively, in the NILs. Comparative analysis performed using 50,051 SNPs and 500 SSR markers revealed that the SNPs provided better insight into the RPG recovery. Most of the monogenic NILs showed comparable performance in yield and quality, concomitantly, Pusa1637-18-7-6-20 (Pi9), was significantly superior in yield and stable across four different environments as compared to recurrent parent (RP) PB1. Further, among the pyramids, Pusa1930-12-6 (Pi2+Pi5) showed significantly higher yield and Pusa1633-7-8-53-6-8 (Pi54+Pi1+Pita) was superior in cooking quality as compared to RP PB1. The NILs carrying gene Pi9 were found to be the most effective against the concoction of virulent races predominant in the hotspot locations for blast disease. Conversely, when analyzed under artificial inoculation, three-gene pyramids expressed enhanced resistance as compared to the two-gene and monogenic NILs.

Validation of SSR markers associated with rust (Uromyces fabae) resistance in pea (Pisum sativum L.)

Pea rust is a devastating disease of peas especially in the sub-tropical regions of the world and greatly influenced by the environmental conditions during disease development. Molecular markers associated with pea rust resistance would be useful in marker assisted selection (MAS). Utility of molecular markers associated with the pea rust resistance were evaluated in 30 diverse pea genotypes using four SSR markers (AA446 and AA505 flanking the major QTL Qruf; AD146 and AA416 flanking the minor QTL, Qruf1). QTL, Qruf flanking markers were able to identify all the resistant genotypes when used together, except Pant P 31. While, SSR markers AD146 and AA416 flanking the minor QTL, Qruf1 were able to identify all the pea resistant genotypes used for validation, except for HUDP-11 by AD146 and Pant P 31 by AA416. Similarly, SSR markers AA446 and AA505 were able to identify all the susceptible pea genotypes, except IPFD 99-13, HFP 9415 and S- 143. SSR markers AD146 and AA416 were together able to identify all the pea susceptible genotypes used for validation, except KPMR 526, KPMR 632 and IPFD 99-13. On the basis of marker allele analysis it may be concluded that SSR markers (AA446, AA505, AD146 and AA416) can be used in MAS of pea rust resistance.

Fibro-epithelial hyperplasia mimicking mucocele

The effects of chronic local irritation have been seen commonly in the form of fibroma or mucocele in children. We report a ten year old girl with the chief complaint of swelling in the lower right region of labial mucosa which was diagnosed clinically as mucocele and histologically as fibro-epithelial hyperplasia. Surgical excision was done under local anesthesia with no post-operative complication.

Comparative phylogenetic analysis of genome-wide Mlo gene family members from Glycine max and Arabidopsis thaliana

Powdery mildew locus O (Mlo) gene family is one of the largest seven transmembrane protein-encoding gene families. The Mlo proteins act as negative regulators of powdery mildew resistance and a loss-of-function mutation in Mlo is known to confer broad-spectrum resistance to powdery mildew. In addition, the Mlo gene family members are known to participate in various developmental and biotic and abiotic stress response-related pathways. Therefore, a genome-wide similarity search using the characterized Mlo protein sequences of Arabidopsis thaliana was carried out to identify putative Mlo genes in soybean (Glycine max) genome. This search identified 39 Mlo domain containing protein-encoding genes that were distributed on 15 of the 20 G. max chromosomes. The putative promoter regions of these Mlo genes contained response elements for different external stimuli, including different hormones and abiotic stresses. Of the 39 GmMlo proteins, 35 were rich (8.7-13.1 %) in leucine, while five were serine-rich (9.2-11.9 %). Furthermore, all the GmMlo members were localized in the plasma membrane. Phylogenetic analysis of the GmMlo and the AtMlo proteins classified them into three main clusters, and the cluster I comprised two sub-clusters. Multiple sequence alignment visualized the location of seven transmembrane domains, and a conserved CaM-binding domain. Some of the GmMlo proteins (GmMlo10, 20, 22, 23, 32, 36, 37) contained less than seven transmembrane domains. The motif analysis yielded 27 motifs; out of these, motif 2, the only motif present in all the GmMlos, was highly conserved and three amino acid residues were essentially invariant. Five of the GmMlo members were much smaller in size; presumably they originated through deletion following a gene duplication event. The presence of a large number of GmMlo members in the G. max genome may be due to its paleopolyploid nature and the large genome size as compared to that of Arabidopsis. The findings of this study may further help in characterization and isolation of individual GmMlo members.

Distinct role of core promoter architecture in regulation of light-mediated responses in plant genes

In the present study, we selected four distinct classes of light-regulated promoters. The light-regulated promoters can be distinctly grouped into either TATA-box-containing or TATA-less (initiator-containing) promoters. Further, using either native promoters or their swapped versions of core promoter elements, we established that TATA-box and Inr (Initiator) elements have distinct mechanisms which are involved in light-mediated regulation, and these elements are not swappable. We identified that mutations in either functional TATA-box or Inr elements lead to the formation of nucleosomal structure. The nucleotide diversity in either the TATA-box or Inr element in Arabidopsis ecotypes proposes that the nucleotide variation in core promoters can alter the gene expression. We show that motif overrepresentation in light-activated promoters encompasses different specific regulatory motifs present downstream of TSS (transcription start site), and this might serve as a key factor in regulating light promoters which are parallel with these elements. Finally, we conclude that the TATA-box or Inr element does not act in isolation, but our results clearly suggests the probable involvement of other distinct core promoter elements in concurrence with the TATA-box or Inr element to impart selectivity to light-mediated transcription.

Computational tridimensional protein modeling of Cry1Ab19 toxin from Bacillus thuringiensis BtX-2

We report the computational structural simulation of the Cry1Ab19 toxin molecule from B. thuringiensis BtX-2 based on the structure of Cry1Aa1 deduced by x-ray diffraction. Validation results showed that 93.5% of modeled residues are folded in a favorable orientation with a total energy Z-score of -8.32, and the constructed model has an RMSD of only 1.13. The major differences in the presented model are longer loop lengths and shortened sheet components. The overall result supports the hierarchical three-domain structural hypothesis of Cry toxins and will help in better understanding the structural variation within the Cry toxin family along with facilitating the design of domain-swapping experiments aimed at improving the toxicity of native toxins.

Molecular mapping for resistance to pea rust caused by Uromyces fabae (Pers.) de-Bary

Pea rust caused by Uromyces fabae (Pers.) de-Bary is a major problem in warm humid regions causing huge economic losses. A mapping population of 136 F(6:7) recombinant inbred lines (RILs) derived from the cross between pea genotypes, HUVP 1 (susceptible) and FC 1 (resistant) was evaluated in polyhouse as well as under field conditions during two consecutive years. Infection frequency (IF) and area under disease progress curve (AUDPC) were used for evaluation of rust reaction of the RILs. A linkage map was constructed with 57 polymorphic loci selected from 148 simple sequence repeats (SSRs), 3 sequence tagged sites (STS), and 2 random amplified polymorphic (RAPD) markers covering 634 cM of genetic distance on the seven linkage groups of pea with an average interval length of 11.3 cM. Composite interval mapping (CIM) revealed one major (Qruf) and one minor (Qruf1) QTL for rust resistance on LGVII. The LOD (5.2-15.8) peak for Qruf was flanked by SSR markers, AA505 and AA446 (10.8 cM), explaining 22.2-42.4% and 23.5-58.8% of the total phenotypic variation for IF and AUDPC, respectively. The minor QTL was environment-specific, and it was detected only in the polyhouse (LOD values 4.2 and 4.8). It was flanked by SSR markers, AD146 and AA416 (7.3 cM), and explained 11.2-12.4% of the total phenotypic variation. The major QTL Qruf was consistently identified across all the four environments. Therefore, the SSR markers flanking Qruf would be useful for marker-assisted selection for pea rust (U. fabae) resistance.

Shoot bud regeneration from different explants of Bacopa monniera (L.) Wettst. by trimethoprim and bavistin

A mass in vitro propagation system devoid of growth regulators for Bacopa monniera (L.) Wettst., a traditional Indian medicinal plant, has been developed. Direct shoot bud regeneration was induced by culturing internode and leaf explants on Murashige and Skoog's (MS) medium supplemented with an antibiotic (trimethoprim) or a fungicide (bavistin). Bavistin showed a marked cytokinin-like activity, as evident from high number of shoot buds induced in node, internode and leaf explants. Optimum adventitious shoot buds induction occurred at 300 mg/l bavistin from internode explants. In vitro regenerated shoots were elongated and rooted before transferred to field with 85% survival. The regeneration protocol developed in this study illustrates the usefulness of additives for mass propagation and germplasm conservation of B. monniera.

Agrobacterium-mediated transformation of cauliflower: optimization of protocol and development of Bt-transgenic cauliflower

A number of factors that are known to influence genetic transformation were evaluated to optimize Agrobacterium-mediated transformation of hypocotyl explants of cauliflower variety Pusa Snowball K-1. The binary vector p35SGUSINT mobilized into Agrobacterium strain GV2260 was used for transformation and transient GUS expression was used as the basis for identifying the most appropriate conditions for transformation. Explant age, preculture period, bacterial strain and density were found to be critical determinants of transformation efficiency. Using the optimized protocol, the synthetic cryIA(b) gene was mobilized into cauliflower. Molecular analyses of transgenics established the integration and expression of the transgene. Insect bioassays indicated the effectiveness of the transgene against infestation by diamondback moth (Plutella xylostella) larvae

Ectodermal dysplasia with total anodontia: rehabilitation of a seven year old child

Total anodontia in a paediatric patient is a difficult prosthetic problem. Upper and lower complete dentures were fabricated for a 7 year old patient with anodontia. The problems encountered on account of the age of the child, the absence of alveolar processes, the tooth size and acceptability of the dentures are discussed herein.

Non-familial cherubism--a case report

A case of cherubism in a 9 year old boy with no familial history is presented. Clinical features, histologic appearance, radiographic findings, differential diagnosis and rationale for treatment is discussed.

Xanthomonas campestris pv. parthenii pathovar nov. incitant of leaf blight of parthenium

A new bacterial leaf blight disease of parthenium (Parthenium hysterophorus L.) is described for the first time. The disease-causing bacterium was isolated and its morphological, physiological and biochemical characters were determined. The pathogenicity of bacterium is apparently limited only to parthenium. The pathogen was identified as Xanthomonas campestris pv. parthenii pathovar nov. on the basis of morphological, physiological, biochemical and pathogenic characteristics.

Transfer of nitrate reductase genes of the cyanobacterium Nostoc muscorum into Rhizobium japonicum

Transformation of Rhizobium japonicum CB1809 was studied using DNA from the cyanobacterium Nostoc muscorum ATCC 27893. A spontaneous nitrate reductase deficient (Nar-) mutant (NR-6) of R. japonicum CB1809 was isolated with a frequency of 8.4 X 10(-7). Streptomycin (Sm) and Neomycin (Neo) resistance markers were introduced into strain NR-6, and the resulting strain was designated NR-6 SmR NeoR. Experiments with cyanobacterial DNA and live cells of strain NR-6 SmR NeoR indicated transformation of nitrate reductase (nar) genes of N. muscorum into this strain. This conclusion was supported by the reversion frequency of strain NR-6 SmR NeoR to Nar+ and the transformation frequency when recipient cells were exposed to N. muscorum DNA (with heat-treated DNA as control). Comparisons of growth, nitrate uptake, assimilatory nitrate reductase activity and nodulation of parent CB1809, NR-6 SmR NeoR and five transformant clones (Nar+) suggest that there may be considerable homology between the nar genes of R. japonicum CB1809 and N. muscorum.

Inhibition of photosystem II of nitrogen-fixing blue-green alga Nostoc linckia by the rice-field herbicide benthiocarb

Effects of rice-field herbicide benthiocarb (S(4-chlorobenzyl)-N,N-diethyl thiolcarbamate) was studied on the nitrogen-fixing blue-green alga Nostoc linckia. The herbicide caused inhibition of growth and heterocyst formation, an increase in intensity of photoacoustic signals, and a four-fold reduction in oxygen evolution, but did not affect dark O2-uptake. The inhibition of growth and heterocyst formation was relieved by 500 micrograms/ml glucose. A Het-Nif- mutant of Nostoc muscorum failed to show an increase in reversion, frequency after treatment with 10 micrograms/ml benthiocarb for 1 hr.

Morphology and general characteristics of viruses active against cowpea Rhizobium CB756 and 32H1

Two newly isolated viruses, RS1 and RS2, infective on two strains of cowpea Rhizobium capable of N2-fixation in vitro, were characterized. RS1 parasitizes CB756 but RS2 infects both 32H1 and CB756. RS1 has an isometric, polyhedral head and a long contractile tail, while RS2 has an oblate, polyhedral head and a long flexible non-contractile tail; RS1 is considerably larger than RS2. The phages were relatively stable between pH 5 and 9 (1 hour incubation). RS1 appeared to be more thermal sensitive and exhibited one component inactivation, while RS2 showed two component inactivation at 58, 60 and 62 degrees C. RS1 had a slower adsorption rate (3.3 X 10(-10) ml minutes-1) than RS2 (1.2 X 10(-9) ml minutes-1, on 32H1). The latent period of RS1 and RS2 was 180 and 225 minutes, and the burst size was 15 and 9 particles/cell, respectively.