Akshay Singh

Genetic diversity in ber (Ziziphus spp.) revealed by AFLP markers

Summary Ber (Ziziphus spp.), belonging to the buckthorn family Rhamnaceae, is an important fruit crop that grows naturally in harsh environmental conditions. Commercial cultivars have been developed in India, mostly through selection of productive natural variants propagated by budding on wild rootstocks and used for orchard plantations. There is a complete lack of information on the extent of genetic diversity in this fruit crop. In the present study, 33 accessions of cultivated Z. mauritiana (Lam.) and eight accessions of its wild relative Z. nummularia (Burm.f.) Wight & Arn. were investigated using AFLP. Eleven primer pairs used in AFLP analysis detected 952 fragments, of which 789 (83.8%) were polymorphic. Similarity coefficients ranging from 0.14 – 0.86 suggested that the 41 Ziziphus accessions used in this study were divergent. The wild relative being used as a rootstock showed greater diversity than the cultivated species. The range (0.37 – 0.86) and average (0.62) similarity among the 33 cultivated species accessions indicated the broad genetic base of the commercial cultivars. Cluster analysis revealed the complete separation of the 33 cultivated species accessions and the eight wild species accessions into two distinct groups. Morphologically similar cultivars clustered together with a high degree of similarity. A high correlation of the similarity matrix using a single primer combination with that based on all eleven primer combinations suggested that one or a few primer combinations could be used to estimate diversity in ber. Nine primer combinations detected 86 accession-specific amplified fragments and each primer combination gave a discrimination rate of 1. Any of these primers can thus be used to maintain the quality of both scions and rootstocks to establish productive orchards.

Paclobutrazol minimises the effects of salt stress in mango (Mangifera indica L.)

Summary We investigated the effects of paclobutrazol (PBZ) on 1-year-old plants of ‘Olour’ mango subjected to NaCl stress under polythene tunnel conditions. Plants were treated with two levels of salt [0.0 g NaCl kg−1 soil (control) or 1 g NaCl kg−1 soil] and three concentrations of paclobutrazol [PBZ; 0.0 mg l−1 (control), 750 mg l−1 or 1,500 mg l−1] after 30 d of establishment. Mortality in saline-treated mango plants was reduced significantly (LSD = 8.55; P ≤ 0.05) following the application of PBZ. NaCl-stress reduced the survival of plants without PBZ treatment by 89%, but only by 28.4% for 1,500 mg l−1 PBZ-treated plants. PBZ-treated plants also showed less defoliation, and fewer leaves per plant exhibited salt stress symptoms. It was also evident that treatment with PBZ increased the relative water and chlorophyll contents of mango seedlings, and reduced membrane injury, under salt stress. Furthermore, saline treatment without PBZ increased the Na+ and Cl− ion contents of leaves and roots; however, application of PBZ consistently and significantly lowered these ion contents (P ≤ 0.05). The Na+ content of leaves on saline-treated plants was reduced by 1.96- to 2.12-fold, whereas Cl− ion contents were reduced by 22 – 39% by PBZ treatment compared to salt-treated seedlings without PBZ. Our results suggest a role for PBZ in promoting the avoidance of salt stress in mango by increasing the levels of photosynthetic pigments, water content, K+ uptake and accumulation, and by reducing defoliation, the membrane injury index, and the uptake and accumulation of harmful Na+ and Cl− ions. These findings may be used to improve the yields and quality of mango trees grown in salt-affected areas.

Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety ‘Amrapali’ (Mangifera indica L.)

Mango (Mangifera indica L.) is called “king of fruits” due to its sweetness, richness of taste, diversity, large production volume and a variety of end usage. Despite its huge economic importance genomic resources in mango are scarce and genetics of useful horticultural traits are poorly understood. Here we generated deep coverage leaf RNA sequence data for mango parental varieties ‘Neelam’, ‘Dashehari’ and their hybrid ‘Amrapali’ using next generation sequencing technologies. De-novo sequence assembly generated 27,528, 20,771 and 35,182 transcripts for the three genotypes, respectively. The transcripts were further assembled into a non-redundant set of 70,057 unigenes that were used for SSR and SNP identification and annotation. Total 5,465 SSR loci were identified in 4,912 unigenes with 288 type I SSR (n ≥ 20 bp). One hundred type I SSR markers were randomly selected of which 43 yielded PCR amplicons of expected size in the first round of validation and were designated as validated genic-SSR markers. Further, 22,306 SNPs were identified by aligning high quality sequence reads of the three mango varieties to the reference unigene set, revealing significantly enhanced SNP heterozygosity in the hybrid Amrapali. The present study on leaf RNA sequencing of mango varieties and their hybrid provides useful genomic resource for genetic improvement of mango.

Influence of tillage, water regimes and integrated nitrogen management practices on soil quality indices in rice (Oryza sativa L.) in the Indo-Gangetic plains

A field experiment was conducted on sandy clay-loam soil at New Delhi, during 2004 and 2005 to investigate the effect of irrigation regimes, namely, continuous submergence, one-day drainage, and three-day drainage, and integrated nutrient management practices on the soil biological health parameters under rice cultivation. The non-puddled soils showed significantly high soil respiration (17.32%) and soil microbial biomass carbon (45.51%) activity than the puddled soils. However, the soil dehydrogenase enzyme activity was 65.26% higher under puddled soils than the non-puddled. Among the integrated nitrogen management, substitution of 25% recommended dose of nitrogen (RDN) as biofertilizer resulted in highest (560.02 μg TPF g−1 soil 24 h−1) enzyme dehydrogenase (DH) activity and application of entire RDN as organics supported the highest soil microbial biomass carbon (218.29 μg g−1 soil) and respiration activity (56.67 mg CO2 [100 g−1 soil 24 h−1). In comparison with other organic N inputs, substitution of sewage-sludge for 25% RDN resulted in the least soil respiration (47.67 mg CO2 100 g−1 soil 24 h−1), low DH enzyme activity (313.37 μg TPF g−1 soil 24 h−1) and soil microbial biomass carbon content (183.85 μg g−1 soil). The present study suggests that inorganic, organic and bio-fertilizer combinations significantly improved soil health parameters.

EFFECT OF PACLOBUTRAZOL AND PUTRESCINE ON ANTIOXIDANT ENZYMES ACTIVITY AND NUTRIENTS CONTENT IN SALT TOLERANT CITRUS ROOTSTOCK SOUR ORANGE UNDER SODIUM CHLORIDE STRESS

The effects of paclobutrazol (PBZ) and putrescine (Put) on antioxidant enzymes activity, proline contents and nutrients uptake were studied on salt tolerant citrus rootstock sour orange. Six-month-old nucellar seedlings grown in pots and subjected to three levels of PBZ and two levels each of salinity and Put for 90 days. Seedlings treated with PBZ or Put alone or in combination had higher anti-oxidant enzymes activities, accumulation of proline and nutrients contents like potassium (K+) and calcium (Ca2+) under both saline and non-saline conditions. Further, application of PBZ or Put alone or in combination also reduced the accumulation of both Na+ and Cl− ions in leaves and roots in NaCl stressed seedlings. A combined application of 250 mg L−1 PBZ and 50 mg L−1 Put proved to be more effective in improving proline and Ca2+ content and restricting accumulation of Na+ ions in leaf tissues.

PpTFDB: A pigeonpea transcription factor database for exploring functional genomics in legumes

Pigeonpea (Cajanus cajan L.), a diploid legume crop, is a member of the tribe Phaseoleae. This tribe is descended from the millettioid (tropical) clade of the subfamily Papilionoideae, which includes many important legume crop species such as soybean (Glycine max), mung bean (Vigna radiata), cowpea (Vigna ungiculata), and common bean (Phaseolus vulgaris). It plays major role in food and nutritional security, being rich source of proteins, minerals and vitamins. We have developed a comprehensive Pigeonpea Transcription Factors Database (PpTFDB) that encompasses information about 1829 putative transcription factors (TFs) and their 55 TF families. PpTFDB provides a comprehensive information about each of the identified TFs that includes chromosomal location, protein physicochemical properties, sequence data, protein functional annotation, simple sequence repeats (SSRs) with primers derived from their motifs, orthology with related legume crops, and gene ontology (GO) assignment to respective TFs. (PpTFDB: http://14.139.229.199/PpTFDB/Home.aspx) is a freely available and user friendly web resource that facilitates users to retrieve the information of individual members of a TF family through a set of query interfaces including TF ID or protein functional annotation. In addition, users can also get the information by browsing interfaces, which include browsing by TF Categories and by, GO Categories. This PpTFDB will serve as a promising central resource for researchers as well as breeders who are working towards crop improvement of legume crops.

The draft genome of Corchorus olitorius cv. JRO-524 (Navin)

Here, we present the draft genome (377.3 Mbp) of Corchorus olitorious cv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv. Sudan Green) and indigenous (cv. JRO-632) types. We predicted from the draft genome a total of 57,087 protein-coding genes with annotated functions. We identified a large number of 1765 disease resistance-like and defense response genes in the jute genome. The annotated genes showed the highest sequence similarities with that of Theobroma cacao followed by Gossypium raimondii. Seven chromosome-scale genetically anchored pseudomolecules were constructed with a total size of 8.53 Mbp and used for synteny analyses with the cocoa and cotton genomes. Like other plant species, gypsy and copia retrotransposons were the most abundant classes of repeat elements in jute. The raw data of our study are available in SRA database of NCBI with accession number SRX1506532. The genome sequence has been deposited at DDBJ/EMBL/GenBank under the accession LLWS00000000, and the version described in this paper will be the first version (LLWS01000000).

Effect of NaCl in the irrigation water on growth, anti-oxidant enzyme activities, and nutrient uptake in five citrus rootstocks

Summary Seven–month-old, uniform-sized seedlings of five citrus rootstocks [sour orange (Citrus aurantiam), Attani-2 (C. rugulosa), Troyer citrange (C. sinensis × Poncirus trifoliata), billikhichlli (C. reshni), and RLC-6 (C. jambhiri)] were irrigated to 70% of field capacity with water containing 0, 50, 100, or 200 mM NaCl for 180 d. Growth, in terms of plant heights and the numbers of leaves, decreased with increasing levels of salinity in all five rootstocks. The decrease in plant height was greatest in the salt-susceptible Troyer citrange and billikhichlli at higher levels of salinity. However, in the salt-tolerant sour orange and Attani-2, NaCl caused only a slight decrease in plant height. Defoliation was maximum in the salt-susceptible Troyer citrange and billikhichlli. The maximum increases in superoxide dismutase (SOD) and peroxidase (POD) activities were found in the salt-susceptible Troyer citrange at higher levels of salinity. Leaf proline contents increased most in Attani-2, sour orange, and RLC-6 at higher levels of salinity.The concentration of Na+ ions in leaf tissues increased to a maximum in Attani-2; while, in root tissues, RLC-6 and Troyer had the highest Na+ ion contents. The maximum increase in leaf Cl– ion levels occurred in Troyer citrange, and the minimum was in RLC-6, at 200 mM NaCl. These data suggest that higher levels of proline accumulation and leaf abscission could be used as indicators for screening citrus rootstocks for resistance to NaCl stress. Sour orange and Attani-2 were able to exclude Cl– ions, whereas Troyer citrange appeared to exclude Na+ ions at lower levels of NaCl. Further studies are required to observe the translocation of harmful and beneficial mineral elements to scion cultivars grafted onto sour orange and Attani-2 and grown under NaCl stress. Overall, salt-tolerance increased in the following order: Troyer ì billikhichlli ì RLC-6 ì Attani-2 ì sour orange.

Prospects of Understanding the Molecular Biology of Disease Resistance in Rice

Rice is one of the important crops grown worldwide and is considered as an important crop for global food security. Rice is being affected by various fungal, bacterial and viral diseases resulting in huge yield losses every year. Deployment of resistance genes in various crops is one of the important methods of disease management. However, identification, cloning and characterization of disease resistance genes is a very tedious effort. To increase the life span of resistant cultivars, it is important to understand the molecular basis of plant host–pathogen interaction. With the advancement in rice genetics and genomics, several rice varieties resistant to fungal, bacterial and viral pathogens have been developed. However, resistance response of these varieties break down very frequently because of the emergence of more virulent races of the pathogen in nature. To increase the durability of resistance genes under field conditions, understanding the mechanismof resistance response and its molecular basis should be well understood. Some emerging concepts like interspecies transfer of pattern recognition receptors (PRRs) and transgenerational plant immunitycan be employed to develop sustainable broad spectrum resistant varieties of rice.

A web-based microsatellite database for the Magnaporthe oryzae genome

Microsatellites have been widely utilized for molecular marker development. Codominant and multiallelic nature of these simple repeats have several advantages over other types of molecular markers. Their broad applicability in the area of molecular biology like gene mapping, genome characterization, genome evolution, and gene regulation has been reported in various crop plants, animals and fungi. Considering these benefits of the SSR markers, a MMDB (Magnaporthe oryzae Microsatellite Database) was developed to help in understanding about the pathogen and its diversity at strains level of a particular geographic region, which can help us to make a proper utilization of blast resistance genes in the region. This microsatellite database is based on whole genome sequence of two M. oryzae isolates, RML-29 (2665 SSRs from 43037792 bp) and RP-2421 (3169 SSRs from 45510614 bp). Although, first M. oryzae genome (70-15) was sequenced in 2005, but this sequenced isolate is not a true field isolate of M. oryzae. Therefore, MMDB has great potential in the study of diversification and characterization of M. oryzae and other related fungi. Availability: http://14.139.229.199/home.aspx