November 2009 issue

SSR polymorphism in Artemisia annua: Recognition of hotspots for dynamics mutation

Kumar Parijat Tripathi, Sudeep Roy, Neha Maheshwari, Feroz Khan*, Abha Meena, Ashok Sharma

Abstract

Simple sequence repeats or micro-satellites form an important class of molecular markers for genomic and plant breeding applications. In the studied work, publicly available data of 85,252 expressed sequence tagged sites of Artemisa annua (an anti-malarial plant) have been assembled and clustered into 20,588 non-redundant sequences by using EGassembler program. Results indicate 75.8% reduction of data redundancy and simple sequence repeats in only 20.74% (i.e., 4272) EST sequences. We have also identified the frequency, density, composition and distribution of SSR containing ESTs. Among all the SSR motifs, maximum frequency was showed by trinucleotide SSR motifs i.e., 47.84% while minimum by pentanucleotide SSR motifs i.e., 5.2%. The ESTs containing the unique SSRs were functionally annotated with the help of SwissProt protein database using BLASTx program. After GO based functional classification, only 18.8% of the total significant matches revealed the putative function, which is of agronomic importance. Approximately 4000 SSR-ESTs were analysed for their polymorphism both in ORF and non-ORF regions showing their importance in regulating the function of important genes.

Keywords: Aartemisia annua; Contig assembly; Expressed Sequence Tags; Microsatellites; Polymorphism; Simple Sequence Repeats

Pages 228-237 Full Text PDF

Regulation of Polygalacturonase-inhibitory proteins in plants is highly dependent on stress and light responsive elements

Guguloth Mahesh Kumar, Praveen Mamidala And Appa Rao Podile

Abstract

PG inhibiting proteins (PGIPs) are extracellular plant proteins capable of inhibiting fungal endoPGs. The identification of cis-regulatory elements is one of the major challenges in bioinformatics and integrates comparative, structural, and functional genomics. We have detected cis-acting upstream regulatory elements of PGIP-encoding genes, based on sequence analysis in seven different plant species at PLACE and PlantCARE. The upstream sequences of PGIPs contain different regulatory elements such as TATA box, CAAT box, ABRE box, ERE box, wound responsive elements, drought response elements etc., which help in induction of gene expression during plant growth and development, and biotic and abiotic stress. On the basis of the analysis of the regulatory elements we confirm the assigned function of PGIPs in plants like Lycopersicon esculentum, Arabidopsis thaliana, Oryza sativa cv.japonica, Vitis venifera, Brassica napus, Brassica rapa and Medicago sativa. We have also identified the presence of the most important elements, at a high frequency, responsive to light apart from wounding, salicylic acid, abscisic acid, fungal elicitors, ethylene in the upstream sequences across genera providing a link to the light and stress mediated signaling in plant defense responses.

Keywords: PGIP; cis regulatory elements; Light responsive elements; biotic and abiotic stress

Pages 238-249 Full Text PDF

Studies on genetic identification and genetic fidelity of cultivated banana using ISSR markers

G.R. Rout, S. K. Senapati, S. Aparajita, S.K. Palai

Abstract

Molecular identification of different varieties is an important element for efficient and effective management of banana genetic resources. Genetic uniformity of in vitro raised plants also a prerequisite for production of quality planting material of banana. Present study showed the use of ISSR marker for identification of different varieties of banana and detection of genetic uniformity of micropropagated plantlets. Fifteen ISSR primers used to differentiate the four cultivated banana. Based on those identity markers, the genetic distance between varieties was estimated and their genetic relationship was found out. The banana varieties having genome constitution AAA were grouped together whereas ‘Bantala’ variety is out grouped with genome constitution BBB. A homogenous amplification profile was observed for all the micropropagated plants of ‘Bantala’ when compared to mother plant. In case of ‘Grand Naine’, few plants showed variation at the DNA level in primer IG-13. But, morphologically they are identical as compared with original mother plant. The results confirmed that the clonal fidelity of in vitro raised plantlets and corroborate the fact that in vitro multiplication is the safest mode for multiplying of true to type plants.

Keywords: Banana; genetic stability; ISSR marker; In vitro; Shoot multiplication

Pages 250-258 Full Text PDF

Highly efficient plant regeneration through somatic embryogenesis in 20 elite commercial cotton (Gossypium hirsutum L.) cultivars

Baohong Zhang, Qinglian Wang, Fang Liu, Kunbo Wang, and Taylor P. Frazier

Abstract

A protocol was established for cotton somatic embryogenesis and plant regeneration. Using this protocol, highly efficient plant regeneration via somatic embryogenesis was obtained from more than 20 Chinese and Australian commercialized cotton cultivars including CCRI 12, CCRI 19, and Simian No 3. These three cultivars alone comprise more than 50% of the total cultivated cotton in China. Based on three criteria, the 20 tested cotton cultivars were classified into three different groups: easily embryogenesis-induced cultivars (such as CCRI 19, Simian No 3, Lumian 6, Sikral 1-3, Coker 201), moderately easy embryogenesis-induced cultivars (such as CCRI 16, CCRI 24, Simian No 4 and CCRI 29), and not easily embryogenesis-induced cultivars (such as CCRI 17, CCRI 30 and CCRI 27). The three criteria used included (1) the somatic embryogenesis ratios, (2) the time required to produce somatic embryogenesis, and (3) the number of the somatic embryos produced in each culture. Also, the plant hormone Zeatin (ZT) was used to induce direct somatic embryogenesis and had the highest induction ratio of 33.3%. Overall, this procedure simplifies cotton somatic embryogenesis from a multi-step culture process to a one-step culture process and shortens the culture cycle from 180 to 60-120 days. This protocol also makes it easier to control the somaclonal variation in plant tissue culture and facilitates the application of plant genetic engineering on cotton genetic improvement.

Keywords: cotton; somatic embryogenesis; genotype-independent; dehydration; plant regeneration; plant growth regulator; hormone

Pages 259-268 Full Text PDF