Papers by Alagu Manickavelu
Molecular Breeding, Aug 29, 2016
Fungal diseases are among the most devastating biotic stresses and often cause significant losses... more Fungal diseases are among the most devastating biotic stresses and often cause significant losses in wheat production worldwide. A set of 173 synthetic hexaploid wheat (SHW) characterized for resistance against fungal pathogens that cause leaf, stem and yellow rusts, yellow leaf spot, Septoria nodorum and crown rot were used in genome-wide association study (GWAS). Diversity Arrays Technology (DArT) and DArTSeq markers were employed for marker-trait association in which 74 markers associated with 35 quantitative trait loci (QTL) were found to be significantly linked with disease resistances using a unified mixed model (P = 10-3 to 10-5); Of these 15 QTL originated from D genome. Six markers on 1BL, 3BS, 4BL, 6B, and 6D conferred resistance to two diseases representing 10 of the 35 QTL. A further set of 147 SHW genotyped with DArT only markers validated 11 QTL detected in the previous 173 SHW. We also confirmed the presence of the gene Lr46/Yr29/Sr58/Pm39/Ltn2 on 1BL in the SHW germplasm. In addition, gene-gene interactions between significantly associated loci and all loci across the genome revealed five significant interactions at FDR \0.05. Two significant leaf rust and one stem rust interactions were thought to be synergistic, while another two QTL for yellow leaf spot involved antagonistic relations. To the best of our knowledge, this is the first GWAS for six fungal diseases using Electronic supplementary material The online version of this article (
DNA Research, Feb 14, 2012
About 1 million expressed sequence tag (EST) sequences comprising 125.3 Mb nucleotides were accre... more About 1 million expressed sequence tag (EST) sequences comprising 125.3 Mb nucleotides were accreted from 51 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including abiotic stresses and pathogen challenges in common wheat (Triticum aestivum). Expressed sequence tags were assembled with stringent parameters after processing with inbuild scripts, resulting in 37 138 contigs and 215 199 singlets. In the assembled sequences, 10.6% presented no matches with existing sequences in public databases. Functional characterization of wheat unigenes by gene ontology annotation, mining transcription factors, full-length cDNA, and miRNA targeting sites were carried out. A bioinformatics strategy was developed to discover single-nucleotide polymorphisms (SNPs) within our large EST resource and reported the SNPs between and within (homoeologous) cultivars. Digital gene expression was performed to find the tissue-specific gene expression, and correspondence analysis was executed to identify common and specific gene expression by selecting four biotic stress-related libraries. The assembly and associated information cater a framework for future investigation in functional genomics.
Molecular Genetics and Genomics, 2022
Researchers stand at the vanguard of advancement and application of next-generation sequencing te... more Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for developing dominant strategies for the sustainable management of genetically diverse crops. We attempt to fill the existing research lacuna in the molecular characterization of potent rice landraces in Kerala. Genotyping-by-sequencing (GBS) was performed on 96 Kerala rice accessions to identify single-nucleotide polymorphisms (SNPs), to examine the genetic diversity, population structure, and to delineate linkage disequilibrium (LD) pattern. GBS identified 5856 high-quality SNPs. The structure analysis indicated three subpopulations with the highest probability for population clustering with significant genetic differentiation, confirmed by principal component analysis. The genome-wide LD decay distance was 772 kb, at which the r 2 dropped to half its maximum value. The analysis of genetic properties of the identified SNP panel with an average polymorphism information content (PIC) value of 0.22 and a minor allele frequency (MAF) > 0.1 unveiled their efficacy in genome-wide association studies (GWAS). High F ST (0.266) and low Nm (0.692) portray a strong genetic differentiation among the rice landraces, complementing the genetic structuring observed in the studied population. Slow LD decay in the rice landraces reflects their self-pollinating behavior and the indirect selection of desired traits by domestication. Moreover, the high LD entails only a minimum number of SNP markers for detecting marker–trait association. The diverse germplasm utilized in this study can be further utilized to disclose genetic variants associated with phenotypic traits and define signatures of selection via GWAS and selective sweep, respectively.
Springer eBooks, Sep 27, 2013
Lentil is a diploid (2n = 2X = 14) self-pollinating crop with a genome size of 4 Gbp. The use of ... more Lentil is a diploid (2n = 2X = 14) self-pollinating crop with a genome size of 4 Gbp. The use of genomics tools in lentil breeding programs has been limited, since available genomic resources are not adequate. Recent advances in high-throughput genotyping and sequencing technologies have brought in new impetus in the development of genetic and genomic resources and high resolution marker-trait association in lentil. Their integration in marker-assisted breeding is expected to improve the precision and efficiency in breeding programs with accelerated and directed genetic gains in crops like lentil. Molecular markers are expected to facilitate indirect selection for difficult traits, introgression of novel genes into adapted varieties, pyramiding genes from different sources, and combining multiple stress resistance. The present review highlights recent advances in lentil genomics and future outlook in the light of rapid advancement in the genomics tools.
Science Publishers eBooks, Aug 25, 2010
Egyptian Journal of Medical Human Genetics, Sep 2, 2022
Background: Non-communicable diseases such as cardiovascular diseases, respiratory diseases and d... more Background: Non-communicable diseases such as cardiovascular diseases, respiratory diseases and diabetes contribute to the majority of deaths in India. Public health programmes on non-communicable diseases (NCD) prevention primarily target the behavioural risk factors of the population. Hereditary is known as a risk factor for most NCDs, specifically, type 2 diabetes mellitus (T2DM), and hence, understanding of the genetic markers of T2DM may facilitate prevention, early case detection and management. Main body: We reviewed the studies that explored marker-trait association with type 2 diabetes mellitus globally, with emphasis on India. Globally, single nucleotide polymorphisms (SNPs) rs7903146 of Transcription Factor 7-like 2 (TCF7L2) gene was common, though there were alleles that were unique to specific populations. Within India, the state-wise data were also taken to foresee the distribution of risk/susceptible alleles. The findings from India showcased the common and unique alleles for each region. Conclusion: Exploring the known and unknown genetic determinants might assist in risk prediction before the onset of behavioural risk factors and deploy prevention measures. Most studies were conducted in non-representative groups with inherent limitations such as smaller sample size or looking into only specific marker-trait associations. Genome-wide association studies using data from extensive prospective studies are required in highly prevalent regions worldwide. Further research is required to understand the singular effect and the interaction of genes in predicting diabetes mellitus and other comorbidities.
Genetic Resources and Crop Evolution, Jan 29, 2015
Journal of Plant Sciences, Sep 15, 2006
Plant Science, Nov 1, 2016
Mining of new genetic resources is of paramount importance to combat the alarming spread of strip... more Mining of new genetic resources is of paramount importance to combat the alarming spread of stripe rust disease and breakdown of major resistance genes in wheat. We conducted a genome wide association study on 352 unutilized Afghan wheat landraces against stripe rust resistance in eight locations. High level of disease variation was observed among locations and a core-set of germplasm showed consistence performance. Linkage disequilibrium (LD) decayed rapidly (R 2 ≈0.16 at 0 cM) due to germplasm peerless diversity. The mixed linear model resulted in ten marker-trait associations (MTAs) across all environments representing five QTL. The extensively short LD blocks required us to repeat the analysis with less diverse subset of 220 landraces in which R 2 decayed below 0.2 at 0.3 cM. The subset GWAS resulted in 36 MTAs clustered in nine QTL. The subset analysis validated three QTL previously detected in the full list analysis. Overall, the study revealed that stripe rust epidemics in the geographical origin of this germplasm through time have permitted for selecting novel resistance loci.
Asian Journal of Plant Sciences, Dec 15, 2005
DNA Research, Apr 1, 2010
Gene expression after leaf rust infection was compared in near-isogenic wheat lines differing in ... more Gene expression after leaf rust infection was compared in near-isogenic wheat lines differing in the Lr10 leaf rust resistance gene. RNA from susceptible and resistant plants was used for cDNA library construction. In total, 55 008 ESTs were sequenced from the two libraries, then combined and assembled into 14 268 unigenes for further analysis. Of these ESTs, 89% encoded proteins similar to (E value of 10 25) characterized or annotated proteins from the NCBI non-redundant database representing diverse molecular functions, cellular localization and biological processes based on gene ontology classification. Further, the unigenes were classified into susceptible and resistant classes based on the EST members assembled from the respective libraries. Several genes from the resistant sample (14-3-3 protein, wali5 protein, actin-depolymerization factor and ADP-ribosylation factor) and the susceptible sample (brown plant hopper resistance protein, caffeic acid O-methyltransferase, pathogenesis-related protein and senescence-associated protein) were selected and their differential expression in the resistant and susceptible samples collected at different time points after leaf rust infection was confirmed by RT-PCR analysis. The molecular pathogenicity of leaf rust in wheat was studied and the EST data generated made a foundation for future studies.
Compendium of plant genomes, 2021
Molecular Biology Reports, Jul 28, 2021
I. Background: As rice is the staple food for more than half of the world population, enhancing g... more I. Background: As rice is the staple food for more than half of the world population, enhancing grain yield irrespective of the variable climatic conditions is indispensable. Many of the traditionally cultivated rice landraces are well adapted to severe environmental conditions and have high genetic diversity that could play an important role in crop improvement. II. Methods and Results: The present study disclosed high level of genetic diversity among the unexploited rice landraces cultivated by farmers of Kerala. Twelve polymorphic markers detected a total of seventy-seven alleles with an average of 6.416 alleles per locus. PIC value ranged from 0.459 to 0.809 and to differentiate the rice genotypes, RM 242 was found to be the most appropriate marker with the highest value of 0.809. The current study indicated that the rice landraces were highly diverse with higher values of the effective number of alleles, PIC, and Shannon information index and utilizing these informative SSR markers for future molecular characterization and population genetic studies in rice landraces are advisable. Haplotypes are sets of genomic regions within a chromosome that are inherited together and haplotype-based breeding is a promising strategy for designing next-generation rice varieties. Here, haplotype analysis explored 270 haplotype blocks and 775 haplotypes from all the chromosomes of landraces under study. The number of SNPs in each haplotype block ranged from two to 28. Haplotypes of genes related to biotic and abiotic stress tolerance, yield-enhancing, and growth and development in rice landraces were also elucidated in the current study. III. Conclusions: The present investigation revealed genetic diversity of rice landraces and the haplotype analysis will open the way for genome wide association studies, QTL identi cation, and marker assisted selection in the unexplored rice landraces collected from Kerala.
Molecular Biology Reports, Dec 18, 2008
FSH, which binds to specific receptors on granulosa cells in mammals, plays a key role in follicu... more FSH, which binds to specific receptors on granulosa cells in mammals, plays a key role in folliculogenesis. Its biological activity involves stimulation of intercellular communication and upregulation of steroidogenesis, but the entire spectrum of the genes regulated by FSH has yet to be fully characterized. In order to find new regulated transcripts, however rare, we have used a Suppression Subtractive Hybridization approach (SSH) on pig granulosa cells in primary culture treated or not with FSH. Two SSH libraries were generated and 76 clones were sequenced after selection by differential screening. Sixty four different sequences were identified, including 3 novel sequences. Experiments demonstrated the presence of 25 regulated transcripts. A gene ontology analysis of these 25 genes revealed (1) catalytic; (2) transport; (3) signal transducer; (4) binding; (5) anti-oxidant and (6) structural activities. These findings may deepen our understanding of FSH's effects. Particularly, they suggest that FSH is involved in the modulation of peroxidase activity and remodelling of chromatin.
International Journal of Agricultural Research, Oct 15, 2006
Breeding Science, 2009
The crossability of common wheat with alien species, e.g., rye, wild and cultivated barley, is kn... more The crossability of common wheat with alien species, e.g., rye, wild and cultivated barley, is known to be controlled by the Kr gene family. The reproduction barrier caused by Kr genes decreases hybrid seed set; however, the molecular mechanism is still unclear. We attempted to localize the QTLs controlling the crossability of wheat in wheat-rye crosses by using molecular markers on wheat chromosome 5B on which the most effective Kr gene is known to be located. QTL mapping was carried out using the F 7 population derived from a cross between Chinese Spring (high crossability) and a chromosome substitution line of Chinese Spring which has its chromosome 5B of Cheyenne (low crossability), and pollinated with rye cv. Petkus. In this population, a major QTL region controlling crossability with rye was detected on the locus closely linked to a SSR marker, Xgwm443, on the short arm of chromosome 5B which was supposed to be Skr locus.
Breeding Science, 2016
This study was carried out with the aim of developing the methodology to determine elemental comp... more This study was carried out with the aim of developing the methodology to determine elemental composition in wheat and identify the best germplasm for further research. Orphan and genetically diverse Afghan wheat land races were chosen and EDXRF was used to measure the content of some of the elements to establish elemental composition in grains of 266 landraces using 10 reference lines. Four elements, K, Mg, P, and Fe, were mea sured by standardizing sample preparation. The results of hierarchical cluster analysis using elemental compo sition data sets indicated that the Fe content has an opposite pattern to the other elements, especially that of K. By systematic analysis the best wheat germplasms for P content and Fe content were identified. In order to compare the sensitivity of EDXRF, the ICP method was also used and the similar results obtained confirmed the EDXRF methodology. The sampling method for measurement using EDXRF was optimized resulting in high-throughput profiling of elemental composition in wheat grains at low cost. Using this method, we have characterized the Afghan wheat landraces and isolated the best genotypes that have highelemental content and have the potential to be used in crop improvement.
BMC Plant Biology, Nov 29, 2014
Background: Landraces are an important source of genetic diversity in common wheat, but archival ... more Background: Landraces are an important source of genetic diversity in common wheat, but archival collections of Afghan wheat landraces remain poorly characterised. The recent development of array based marker systems, particularly single nucleotide polymorphism (SNP) markers, provide an excellent tool for examining the genetic diversity of local populations. Here we used SNP analysis to demonstrate the importance of Afghan wheat landraces and found tremendous genetic diversity and province-specific characteristics unique to this geographic region. Results: A total of 446 Afghan wheat landraces were analysed using genotype by sequencing (GBS) arrays containing~10 K unique markers. Pair-wise genetic distance analyses revealed significant genetic distances between landraces, particularly among those collected from distanced provinces. From these analyses, we were able to divide the landraces into 14 major classes, with the greatest degree of diversity evident among landraces isolated from Badakhshan province. Population-based analyses revealed an additional 15 sub-populations within our germplasm, and significant correlations were evident in both the provincial and botanical varieties. Genetic distance analysis was used to identify differences among provinces, with the strongest correlations seen between landraces from Herat and Ghor province, followed closely by those between Badakhshan and Takhar provinces. This result closely resembles existing agro-climatic zones within Afghanistan, as well as the wheat varieties commonly cultivated within these regions. Molecular variance analysis showed a higher proportion of intra-province variation among landraces compared with variation among all landraces as a whole. Conclusion: The SNP analyses presented here highlight the importance and genetic diversity of Afghan wheat landraces. Furthermore, these data strongly refute a previous analysis that suggested low genetic diverse within this germplasm. Ongoing analyses include phenotypic characterisation of these landraces to identify functional traits associated with individual genotypes. Taken together, these analyses can be used to help improve wheat cultivation in Afghanistan, while providing insights into the evolution and selective pressures underlying these distinct landraces.
Journal of Experimental Botany, Mar 28, 2015
Climate change has generated unpredictability in the timing and amount of rain, as well as extrem... more Climate change has generated unpredictability in the timing and amount of rain, as well as extreme heat and cold spells that have affected grain yields worldwide and threaten food security. Sources of specific adaptation related to drought and heat, as well as associated breeding of genetic traits, will contribute to maintaining grain yields in dry and warm years. Increased crop photosynthesis and biomass have been achieved particularly through disease resistance and healthy leaves. Similarly, sources of drought and heat adaptation through extended photosynthesis and increased biomass would also greatly benefit crop improvement. Wheat landraces have been cultivated for thousands of years under the most extreme environmental conditions. They have also been cultivated in lower input farming systems for which adaptation traits, particularly those that increase the duration of photosynthesis, have been conserved. Landraces are a valuable source of genetic diversity and specific adaptation to local environmental conditions according to their place of origin. Evidence supports the hypothesis that landraces can provide sources of increased biomass and thousand kernel weight, both important traits for adaptation to tolerate drought and heat. Evaluation of wheat landraces stored in gene banks with highly beneficial untapped diversity and sources of stress adaptation, once characterized, should also be used for wheat improvement. Unified development of databases and promotion of data sharing among physiologists, pathologists, wheat quality scientists, national programmes, and breeders will greatly benefit wheat improvement for adaptation to climate change worldwide.
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Papers by Alagu Manickavelu