Arun Prabhu Dhanapal

Chlorophyll is a major component of chloroplasts and a better understanding of the genetic basis of chlorophyll in soybean [Glycine max (L.) Merr.] might contribute to improving photosynthetic capacity and yield in regions with adverse environmental conditions. A collection of 332 diverse soybean genotypes were grown in 2 years (2009 and 2010) and chlorophyll a (eChl_A), chlorophyll b (eChl_B), and total chlorophyll (eChl_T) content as well as chlorophyll a/b ratio (eChl_R) in leaf tissues were determined by extraction and spectrometric determination. Total chlorophyll was also derived from canopy spectral reflectance measurements using a model of wavelet transformed spectra (tChl_T) as well as with a spectral reflectance index (iChl_T). A genome-wide associating mapping approach was employed using 31,253 single nucleotide polymorphisms (SNPs) to identify loci associated with the extract based eChl_A, eChl_B, eChl_R and eChl_T measurements and the two canopy spectral reflectance-based methods (tChl_T and iChl_T). A total of 23 (14 loci), 15 (7 loci) and 14 SNPs (10 loci) showed significant association with eChl_A, eChl_B and eChl_R respectively. A total of 52 unique SNPs were significantly associated with total chlorophyll content based on at least one of the three approaches (eChl_T, tChl_T and iChl_T) and likely tagged 27 putative loci for total chlorophyll content, four of which were indicated by all three approaches. Results presented here show that markers for chlorophyll traits can be identified in soybean using both extract-based and canopy spectral reflectance-based phenotypes, and confirm that high-throughput phenotyping-amenable canopy spectral reflectance measurements can be used for association mapping.

Ureides are the N-rich products of N-fixation that are transported from soybean nodules to the shoot. Ureides are known to accumulate in leaves in response to water-deficit stress and this has been used to identify genotypes with reduced N-fixation sensitivity to drought. Our objectives in this research were to determine shoot ureide concentrations in 374 Maturity Group IV soybean accessions and to identify genomic regions associated with shoot ureide concentration. The accessions were grown at two locations (Columbia, MO and Stuttgart, AR) in two years (2009 and 2010) and characterized for ureide concentration at beginning flowering to full bloom. Average shoot ureide concentrations across all four environments (two locations and two years) and 374 accessions ranged from 12.4 to 33.1 µmol g(-1) and were comparable to previously reported values. SNP-ureide associations within and across the four environments were assessed using 33,957 SNPs with a MAF ≥ 0.03. In total, 53 putative lo...

Carotenoids are organic pigments that are produced predominantly by photosynthetic organisms and provide antioxidant activity to a wide variety of plants, animals, bacteria, and fungi. The carotenoid biosynthetic pathway is highly conserved in plants and occurs mostly in chromoplasts and chloroplasts. Leaf carotenoids play important photoprotective roles and targeted selection for leaf carotenoids may offer avenues to improve abiotic stress tolerance. A collection of 332 soybean [Glycine max (L.) Merr.] genotypes was grown in two years and total leaf carotenoid content was determined using three different methods. The first method was based on extraction and spectrophotometric determination of carotenoid content (eCaro) in leaf tissue, whereas the other two methods were derived from high-throughput canopy spectral reflectance measurements using wavelet transformed reflectance spectra (tCaro) and a spectral reflectance index (iCaro). An association mapping approach was employed using...

The deduced amino-acid sequences of 17 protein disulphide isomerase (PDI) and PDI-like cDNAs of wheat assigned to nine homoeologous groups were searched for conserved motives by comparison with characterized sequences in different protein databases. The wheat protein sequences encoded by genes of different homoelogous groups showed a high level of structural similarity with the corresponding protein sequences of other species clustering into the same phylogenetic group. The proteins of five groups (I–V) share two thioredoxin-like active domains and show structural similarities with the corresponding proteins of higher eukaryotes, whereas those of the remaining three groups (VI–VIII) contain a single thioredoxin-like active domain. The expression analysis of the nine non-homoeologous wheat genes, which was carried out by quantitative RT-PCR in developing caryopses and in seedlings subjected to temperature stresses, showed their constitutive although highly variable transcription rate...

ABSTRACT An investigation was conducted to evaluate twenty sugarcane genotypes for cane and fodder yield. Apart from primary use for sugar extraction, other byproducts such as sugarcane molasses sugarcane bagasse pressmud and sugarcane tops were obtained from sugarcane, which can be used to feed livestock. Sugarcane juice is also fed to animals in some western countries. Sugarcane tops is major byproduct of sugarcane cultivation which is left in field after harvest, retains its nutritional value over a long period when compared to other grasses. In many parts of Tamil Nadu, the matured leaves removed from the growing sugarcane crop are used as fodder. Considering the nutritional significance of sugarcane tops an attempt was made to study promising sugarcane genotypes for dual purpose. Path analysis between different characters is very essential in any crop improvement programme. Study for seven biometrical characters plant height, number of tillers, leaf length, leaf breadth, number of leaves, leaf / stem ratio, green fodder field (leaf weight) and dry fodder yield. By path analysis, it is possible to measure the direct influence of one variable upon another and separate the correlation co-efficient into components of direct, indirect effects and residual effects.

African Journal of Biotechnology Vol. 8 (22), pp. 6046-6052, 16 November, 2009 Available online at http://www.academicjournals.org/AJB ISSN 1684–5315 © 2009 Academic Journals ... Genetic diversity analysis of pearl millet (Pennisetum ... M. Govindaraj*, B. Selvi, D. Arun Prabhu and S. Rajarathinam ... Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641003, India. ... Random amplified polymorphic DNA (RAPD) analysis was applied to pearl millet genotypes in order to assess the degree of polymorphisms ...

The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences.The importance of databases keeps increasing as the volume of datasets fromdirect and indirect genomics, as well as other omics approaches, keeps expanding in recent years.The databases and associated web portals provide at a minimum a uniformset of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants.The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away.

Ozone treatments are used to preserve quality during cold storage of commercially important fruits due to its ethylene oxidizing capacity and its antimicrobial attributes. To address whether or not ozone also modulates ripening by directly affecting fruit physiology, kiwifruit (Actinidia deliciosa cv. ‘Hayward’) were stored in very low ethylene atmosphere at 0 °C (95% RH) in air (control) or in the presence of ozone (0.3 μL L−1) for 2 or 4 months and subsequently ripened at 20 °C (90% RH) for up to 8 d. Ozone-treated kiwifruit showed a significant delay of ripening during maintenance at 20 °C, accompanied by a marked decrease in ethylene biosynthesis due to inhibited AdACS1 and AdACO1 expression and reduced ACC synthase (ACS) and ACC oxidase (ACO) enzyme activity. Furthermore, ozone-treated fruit exhibited a marked reduction in flesh softening and cell wall disassembly. This effect was associated with reduced cell wall swelling and pectin and neutral sugar solubilization and was correlated with the inhibition of cell wall degrading enzymes activity, such as polygalacturonase (PG) and endo-1,4-β-glucanase/1,4-β-glucosidase (EGase/glu). Conclusively, the present study indicated that ozone may exert major residual effects in fruit ripening physiology and suggested that ethylene biosynthesis and cell walls turnover are specifically targeted by ozone.

Pearl millet is a staple food crop for millions of people living in the arid and semi-arid tropics. Molecular markers have been used to identify genomic regions linked to traits of interest by conventional QTL mapping and association analysis. Phenotypic recurrent selection is known to increase frequencies of favorable alleles and decrease those unfavorable for the traits under selection. This study was undertaken (i) to quantify the response to recurrent selection for phenotypic traits during breeding of the pearl millet open-pollinated cultivar “CO (Cu) 9” and its four immediate progenitor populations and (ii) to assess the ability of simple sequence repeat (SSR) marker alleles to identify genomic regions linked to grain and stover yield-related traits in these populations by association analysis. A total of 159 SSR alleles were detected across 34 selected single-copy SSR loci. SSR marker data revealed presence of subpopulations. Association analysis identified genomic regions associated with flowering time located on linkage group (LG) 6 and plant height on LG4, LG6, and LG7. Marker alleles on LG6 were associated with stover yield, and those on LG7 were associated with grain yield. Findings of this study would give an opportunity to develop marker-assisted recurrent selection (MARS) or marker-assisted population improvement (MAPI) strategies to increase the rate of gain for pearl millet populations undergoing recurrent selection.

Peach and nectarine (Prunus persica L.) are highly perishable; they ripen and deteriorate quickly at ambient temperature. Storage at low temperature (0–5 °C) is a common strategy used to slow the ripening processes and to extend shelf life. However, if susceptible varieties are held too long at a low temperature, they will not ripen properly and will develop chilling injury (CI) symptoms like mealiness (M), flesh browning (FB), and flesh bleeding (FBL). Understanding the genetic control of these traits to produce CI resistant cultivars will greatly benefit producers, shippers and consumers. In this study, we evaluated a population of 51 individuals from Pop-DG across 4 years with CI traits observed in one or two time points to detect molecular marker association with selected 960 single-nucleotide polymorphisms (SNPs) from 1,536 SNPs chip. Genotypic and phenotypic data were analyzed by general linear model and mixed linear model to see comparative results from both analyses. Among 960 SNPs used, 22 SNPs were found associated with CI susceptibility traits like M, FB, and FBL. Many SNP markers were located in or close to previously reported quantitative trait loci mapped by linkage analysis.

Peach and nectarine (Prunus persica L) are highly perishable; they ripen and deteriorate quickly at ambient temperature. Storage at low temperature (0–5°C) is a common strategy used to slow the ripening processes and extending shelf life. However, if susceptible varieties are held too long at a low temperature, they will not ripen properly and will develop chilling injury (CI) symptoms like mealiness, flesh browning, and flesh bleeding. Understanding the genetic control of these traits to produce CI resistant cultivars will greatly benefit producers, shippers and consumers. Mapping approach for a set of 40 candidate genes (CGs) obtained after a transcriptomic analysis of peach between high tolerant and sensitivity to CI were used, to identify CI controlling genes in Pop-DG progeny population and CI-susceptible (hermoza) and chilling injury-resistant (oded) peaches. A set of 142 CGs from detailed transcriptomic analysis of two different peach cultivars studied previously and additional 10 CGs nominated from published works and review articles of physiology and transcriptomic study of peach fruit subjected to CI were localized in this study. In present study 12 CGs have been mapped on Pop-DG population with 8 SSR and 26 SNP markers.

Plant genetic resources collection and utilization had made a huge impact in balancing the genetic diversity of the existing crop plant species and their application in genome based studies had also increased widely. Primarily studies were based on model species, although it now enhances the transferability of information to crops and related species. With the tremendous outbreak of new high-throughput technologies like next-generation sequencing (NGS) and reduction in their costs are bringing many more plants within the range of genome and transcriptome level analysis. The completion of reference genome sequences for many important crops and the ability to perform high-throughput resequencing are providing opportunities for improving our understanding of the crop plant genetic resources to accelerate crop improvement. The future of crop improvement will be centred on comparisons of individual crop plant genomes, and some of the best opportunities may lie in using combinations of new genetic mapping strategies and evolutionary analyses to direct and optimize the discovery and use of genetic variation. Here I review the importance of crop plant genetic resources and insights that have been emerged in recent years.

Protein disulphide isomerase (PDI) is an oxidoreductase enzyme abundant in the endoplasmic reticulum (ER). In plants, PDIs have been shown to assist the folding and deposition of seed storage proteins during the biogenesis of protein bodies in the endosperm. Cloning and characterization of the complete set of genes encoding PDI and PDI like proteins in bread wheat (Triticum aestivum cv. Chinese Spring) and the comparison of their sequence, structure and expression with homologous genes from other plant species were reported in our previous publications. Promoter sequences of three homoeologous genes encoding typical PDI, located on chromosome group 4 of bread wheat, and PDI promoter sequence analysis of Triticum urartu, Aegilops speltoides and Aegilops tauschii had also been reported previously. In this study, we report the isolation and sequencing of a ~700 bp region, comprising ~600 bp of the putative promoter region and 88 bp of the first exon of the typical PDI gene, in five accessions each from Triticum urartu (AA), Aegilops speltoides (BB) and Aegilops tauschii (DD). Sequence analysis indicated large variation among sequences belonging to the different genomes, while close similarity was found within each species and with the corresponding homoeologous PDI sequences of Triticum aestivum cv. CS (AABBDD) resulting in an overall high conservation of the sequence con- ferring endosperm-specific expression.

"The deduced amino-acid sequences of 17 protein disulphide isomerase (PDI) and PDI-like
cDNAs of wheat assigned to nine homoeologous groups were searched for conserved motives
by comparison with characterized sequences in different protein databases. The wheat protein
sequences encoded by genes of different homoelogous groups showed a high level of structural
similarity with the corresponding protein sequences of other species clustering into the same
phylogenetic group. The proteins of five groups (I–V) share two thioredoxin-like active domains
and show structural similarities with the corresponding proteins of higher eukaryotes, whereas
those of the remaining three groups (VI–VIII) contain a single thioredoxin-like active domain.
The expression analysis of the nine non-homoeologous wheat genes, which was carried out
by quantitative RT-PCR in developing caryopses and in seedlings subjected to temperature stresses,
showed their constitutive although highly variable transcription rate. The comprehensive
structural and transcriptional characterization of the PDI and PDI-like genes of wheat performed
in this study represents a basis for future functional characterization of the PDI gene family in the
hexaploid context of bread wheat."

Eight genes encoding protein disulphide isomerase (PDI)-like proteins in bread wheat were cloned and characterized and their genomic structure was compared with that of homoeologous genes isolated from other plant species. Fourteen wheat cDNA sequences of PDI-like genes were amplified and cloned; eight of them were relative to distinct PDI-like genes, whereas six corresponded to homoeologous sequences. Also, the genomic sequences of the eight non-homoeologous genes were amplified and cloned. Phylogenetic analysis, which included eight genes encoding PDI-like proteins and the gene encoding the typical PDI, assigned at least one of them to each of the eight major clades identified in the phylogenetic tree of the PDI gene family of plants. The close chromosome synteny between wheat and rice was confirmed by the location of the homoeologous genes of the PDI family in syntenic regions of the two species. Within the same phylogenetic group, a high level of conservation, in terms of sequence homology, genomic structure and domain organization, was detected between wheat and the other plant species. The high level of conservation of sequence and genomic organization within the PDI gene family, even between distant plant species, might be ascribed to the key metabolic roles of their protein products.

Protein disulphide isomerase (PDI) catalyses the formation, reduction and isomerization of disulphide bonds in the newly synthesized secretory proteins. Plant PDIs have been shown to be involved in the folding and deposition of seed storage proteins, which makes this enzyme particularly interesting in wheat, as flour quality is strongly affected by composition and structure of seed storage proteins. In hexaploid wheat cultivar (AABBDD) Chinese Spring (CS), the genomic, complementary DNA and promoter sequences of the three homoeologous gene encoding PDI had been isolated and characterized in a previous study revealing high levels of sequence conservation. In this study, we report the isolation and sequencing of a ,700 bp region, comprising ,600 bp of the putative promoter region and 88 bp of the first exon of the typical PDI gene, in five accessions each from Triticum urartu (AA), Aegilops speltoides (BB) and Aegilops tauschii (DD). Sequence analysis indicated large variation among sequences belonging to the different genomes, while close similarity was found within each species and with the corresponding homoeologous PDI sequences of Triticum aestivum cv. CS (AABBDD) resulting in an overall high conservation of the regulatory motifs conferring endosperm-specific expression.

"Background:
The Protein Disulfide Isomerase (PDI) gene family encodes several PDI and PDI-like proteins containing thioredoxin domains and controlling diversified metabolic functions, including disulfide bond formation and isomerisation during protein folding. Genomic, cDNA and promoter sequences of the three homoeologous wheat genes encoding the "typical" PDI had been cloned and characterized in a previous work. The purpose of present research was the cloning and characterization of the complete set of genes encoding PDI and PDI like proteins in bread wheat (Triticum aestivum cv Chinese Spring) and the comparison of their sequence, structure and expression with homologous genes from other plant species.
Results: Eight new non-homoeologous wheat genes were cloned and characterized. The nine PDI and PDI-like sequences of wheat were located in chromosome regions syntenic to those in rice and assigned to eight plant phylogenetic groups. The nine wheat genes differed in their sequences, genomic organization as well as in the domain composition and architecture of their deduced proteins; conversely each of them showed high structural conservation with genes from other plant species in the same phylogenetic group. The extensive quantitative RT-PCR analysis of the nine genes in a set of 23 wheat samples, including tissues and developmental stages, showed their constitutive, even though highly variable expression.
Conclusions: The nine wheat genes showed high diversity, while the members of each phylogenetic group were highly conserved even between taxonomically distant plant species like the moss Physcomitrella patens. Although constitutively expressed the nine wheat genes were characterized by different expression profiles reflecting their different genomic organization, protein domain architecture and probably promoter sequences; the high conservation among species indicated the ancient origin and diversification of the still evolving gene family. The comprehensive structural and expression characterization of the complete set of PDI and PDI-like wheat genes represents a basis for the functional characterization of this gene family in the hexaploid context of bread wheat."