[Show abstract][Hide abstract] ABSTRACT: Genomic prediction is meant for estimating the breeding value using molecular marker data which has turned out to be a powerful tool for efficient utilization of germplasm resources and rapid improvement of cultivars. Model-based techniques have been widely used for prediction of breeding values of genotypes from genomewide association studies. However, application of the random forest (RF), a model-free ensemble learning method, is not widely used for prediction. In this study, the optimum values of tuning parameters of RF have been identified and applied to predict the breeding value of genotypes based on genomewide single-nucleotide polymorphisms (SNPs), where the number of SNPs (P variables) is much higher than the number of genotypes (n observations) (P > > n). Further, a comparison was made with the model-based genomic prediction methods, namely, least absolute shrinkage and selection operator (LASSO), ridge regression (RR) and elastic net (EN) under P > > n. It was found that the correlations between the predicted and observed trait response were 0.591, 0.539, 0.431 and 0.587 for RF, LASSO, RR and EN, respectively, which implies superiority of the RF over the model-based techniques in genomic prediction. Hence, we suggest that the RF methodology can be used as an alternative to the model-based techniques for the prediction of breeding value at genome level with higher accuracy.
Journal of Genetics 05/2015; 94(2). DOI:10.1007/s12041-015-0501-5 · 1.01 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Water stress is one of the most severe constraints to crop productivity. Plants
display a variety of physiological and biochemical responses both at cellular and
whole organism level upon sensing water stress. Leaf rolling, stomatal closure,
deeper root penetration, higher relative water content and better osmotic adjustment
are some of the mechanisms plants employ to overcome water stress. In the current
study, we report a mutant, ewst1 with enhanced water stress tolerance, identified
from the EMS induced mutant population of rice variety Nagina22, by field screening
followed by withdrawal of irrigation in pots and hydroponics (PEG 6000). Though
ewst1 was morphologically similar to the wild type (WT) for 35 of the 38
morphological descriptors (except chalky endosperm/expression of white core,
decorticated grain colour and grain weight), it showed enhanced germination in PEG
infused medium. It exhibited increased maximum root length without increase in its
root weight, root volume and total root number on crown as compared to the WT
under stress in PVC tube experiment. It also showed better performance for various
physiological parameters such as relative water content, cell membrane stability and
chlorophyll concentration upon water stress in pot experiment. Alterations in number
of xylem, phloem, dimension of central metaxylem and number of closed stomata
were observed in ewst1 as compared to the WT in root anatomy and stomatal
microscopy studies. Comparative genomewide transcriptome analysis identified
genes related to exocytosis, secondary metabolites, tryptophan biosynthesis, protein
phosphorylation and other signaling pathways to be playing a role in enhanced
response to water stress in ewst1. Possible involvement of a candidate gene with
respect to the observed morpho-physiological and transcriptional changes and its
role in stress tolerance are discussed. The mutant identified and characterized in this
study will be useful for further dissection of water stress tolerance in rice.
[Show abstract][Hide abstract] ABSTRACT: Identification of a small core germplasm set representing the available
genetic diversity is essential for its proper evaluation and subsequent utilization
in rice improvement programmes. For constituting a small diverse
mini-core panel of Indian rice germplasm, a representative set of 6912
accessions drawn based on their geographic origin from the whole rice
germplasm collection available in the National Gene Bank was genotyped
using 36 microsatellite markers. Automated fragment analysis of amplicons
yielded a total of 435 alleles, with an average 12.4 and range of 3–29
alleles per locus. Polymorphism information content (PIC) ranged from
0.08 (RGNMS190) to 0.86 (RM552) with an average of 0.528. Based on
genotyping data, a mini-core consisting of 98 genotypes was identified.
Ninety-four per cent of the alleles present in the core set were present in
the mini-core. The identified small but diverse panel will be useful for further
intensive trait-specific evaluation and utilization in allele mining.
[Show abstract][Hide abstract] ABSTRACT: A study was carried out for characterization of 60 farmers’ varieties using grain characters and 40 SSR (Simple
Sequence Repeat) markers. Only a set of 8 (20%) primers were polymorphic yielding 16 bands (alleles) among these
60 varieties. The size of amplicons ranged from 120 bp (RM238) to 240 bp (RM551). The number of alleles per
microsatellite ranged from 1 (RM238, RM119 and RM120) to 3 (RM259, RM234 and RM551) with an average of 2
alleles per locus. Major allele frequency ranged from 0.51 to 0.97 averaging 0.74. Genetic diversity ranged from
0.045 to 0.588 with a mean of 0.34. Considering the entire genotypic array, the mean value for polymorphism
information content (PIC) for all microsatellites was 0.27. Microsatellite RM122 with 2 alleles had the maximum
PIC value (0.37) and the microsatellite RM205 with 2 alleles had the minimum (0.27) value. The UPGMA cluster
analysis grouped varieties into three main clusters with 58% genetic similarity and homing 24, 23 and 13 varieties,
respectively. Grain characteristic-based clustering was better than molecular markers as accessions were in expected
cluster. However, few accessions showed scattering to other sub-clusters. The diversity analysis revealed the distinct
nature of farmers’ varieties in a large number of clusters indicating greater diversity, which could be exploited in
breeding programmes to combine grain traits and early vigor.
Indian Journal of Agricultural Sciences 01/2015; 85(1):118-124. · 0.18 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A study was undertaken to examine the interactive effects of rice genotypes, media composition and desiccation treatment on regeneration frequency (RF) and total number of regenerated plantlets (green shoot induction, GSI). Out of four tested genotypes, the aromatic indica rice variety Pusa Sugandh2 (PS2) showed similar regeneration frequency (94±12.81) and green shoot induction (387.33±2.91) on RM-1 medium as that of japonica genotype Taipei 309 (TP309), which was significantly higher than those in Pusa Basmati1 (PB1) and IR64. The better performing genotype (PS2) was subjected to genetic transformation using AtDREB1A by biolistic method. The regeneration frequency of transformed embryogenic calli of PS2 was found to be 87.02% which was not significantly different from non-transformed embryogenic calli of PS2, where as 50% lower frequency was observed in case of GSI (178.66±0.28). Successful transformants were analysed by PCR using hptII and DREB specific primers. High frequency regeneration coupled with genetic transformation makes PS2 a preferred genotype for large scale functional validation of candidate genes in transgenics.
[Show abstract][Hide abstract] ABSTRACT: Earlier studies were focused on the genetics of temperate and tropical maize under drought. We identified genetic loci and their association with functional mechanisms in 240 accessions of subtropical maize using a high-density marker set under water stress.
Out of 61 significant SNPs (11 were false-discovery-rate-corrected associations), identified across agronomic traits, models, and locations by subjecting the accessions to water stress at flowering stage, 48% were associated with drought-tolerant genes. Maize gene models revealed that SNPs mapped for agronomic traits were in fact associated with number of functional traits as follows: stomatal closure, 28; flowering, 15; root development, 5; detoxification, 4; and reduced water potential, 2. Interactions of these SNPS through the functional traits could lead to drought tolerance. The SNPs associated with ABA-dependent signalling pathways played a major role in the plant's response to stress by regulating a series of functions including flowering, root development, auxin metabolism, guard cell functions, and scavenging reactive oxygen species (ROS). ABA signalling genes regulate flowering through epigenetic changes in stress-responsive genes. ROS generated by ABA signalling are reduced by the interplay between ethylene, ABA, and detoxification signalling transductions. Integration of ABA-signalling genes with auxin-inducible genes regulates root development which in turn, maintains the water balance by regulating electrochemical gradient in plant.
Several genes are directly or indirectly involved in the functioning of agronomic traits related to water stress. Genes involved in these crucial biological functions interacted significantly in order to maintain the primary as well as exclusive functions related to coping with water stress. SNPs associated with drought-tolerant genes involved in strategic biological functions will be useful to understand the mechanisms of drought tolerance in subtropical maize.
[Show abstract][Hide abstract] ABSTRACT: Determination of maintainer and restorer status of germplasm collections is a prerequisite for their use in development of hybrid employing CMS system. In the present study, restorer and maintainer status of 372 Indian genotypes was determined using fertility restoration (Rf) linked microsatellite marker RM6100. A total of seven alleles for the marker locus, including four novel and three known, were identified in the study material. Maximum frequency was observed for the 144bp allele (44.89%) while minimum frequency was for 138bp allele (0.27%). Though most of the novel alleles were minor, occurring in less than 5% frequency, cumulatively they accounted for 9.2% frequency in the study material. Of the known alleles, which were found in 90.8% (338 genotypes) of the tested rice genotypes, 36% had maintainer type allele (132bp allele similar to Pusa 6B) while the rest had restorer type (144 or 150 bp) alleles. The spikelet fertility data generated on a subset of the study material agreed well with the established associations for the already reported alleles. Of the novel alleles, two (141 and 147 bp) were represented in the spikelet fertility dataset, both of which restored fertility, though their representation was low. This allelic information would be useful in selection of parental lines for development of hybrids in rice.
Indian Journal of Genetics and Plant Breeding 12/2014; 74(4):409-413. DOI:10.5958/0975-6906.2014.00863.3 · 0.19 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Dwarf plant height and tillering ability are two of the most important agronomic traits that determine the plant architecture, and have profound influence on grain yield in rice. To understand the molecular mechanism controlling these two traits, an EMS-induced recessive dwarf and increased tillering1 (dit1) mutant was characterized. The mutant showed proportionate reduction in each internode as compared to wild type revealing that it belonged to the category of dn-type of dwarf mutants. Besides, exogenous application of GA3 and 24-epibrassinolide, did not have any effect on the phenotype of the mutant. The gene was mapped on the long arm of chromosome 4, identified through positional candidate approach and verified by cosegregation analysis. It was found to encode carotenoid cleavage dioxygenase7 (CCD7) and identified as an allele of htd1. The mutant carried substitution of two nucleotides CC to AA in the sixth exon of the gene that resulted in substitution of serine by a stop codon in the mutant, and thus formation of a truncated protein, unlike amino acid substitution event in htd1. The new allele will facilitate further functional characterization of this gene, which may lead to unfolding of newer signalling pathways involving plant development and architecture.. 2014 A substitution mutation in OsCCD7 cosegregates with dwarf and increased tillering phenotype in rice. J. Genet. 93, xx–xx]
Journal of Genetics 08/2014; 93(2). DOI:10.1007/s12041-014-0389-5 · 1.01 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Moth bean (Vigna aconitifolia (Jacq.) Marechal), an important grain-legume crop grown in hot desert regions of Thar, under scorching sun rays, was investigated for heat tolerance at molecular level. In the present study, we constructed a forward suppression subtractive hybridization (SSH) cDNA library of heat tolerant genotype RMO-40 to identify genes expressing under delayed response to elevated temperature. Heat induction was carried out by exposing 14-day-old seedlings to elevated temperature of 42 °C for 30 min. A total of 125 unigenes (33 contigs and 92 singletons) were derived by cluster assembly and sequence alignment of 200 ESTs; out of 125 unigenes, 21 (16 %) were found to be novel to moth bean. Gene ontology functional classification terms were retrieved for 98 (78.4 %) unigenes of which 73 (58.4 %) ESTs were functionally annotated (GO consensus) where 19 unigenes were annotated with 11 enzyme commission (EC) codes and were mapped to 25 different KEGG pathways. We have identified a majority of heat-shock proteins (constituting 35 % of the present library) aiding heat stress tolerance to moth bean. An expression level of 22 ESTs generated from the above SSH cDNA library was studied through semiquantitative RT-PCR assay simultaneously under 5 and 30 min of heat stress at 42 °C.
[Show abstract][Hide abstract] ABSTRACT: Rice (Oryza sativa) is the staple food of more than half of the world‟s population. The
International Rice Genome Sequencing Project (IRGSP) generated very high quality
sequences that were used to predict the number and type of genes, and the non-genic
regions containing repeats and mobile genetic elements. Concerted efforts are required
to understand the function of individual genes, and their interactions among themselves
as well as with environment in relation to variation in traits for a directed genetic
manipulation of this important crop for the benefit of the mankind. One of the
approaches to determine functions of genes employs natural mutants available in the
germplasm or those induced by physical, chemical or biological agents. Mutants
facilitate unveiling the causal relationships between coding/regulatory sequences and
plant performance, and also cloning of the corresponding genes. Therefore a number of
international efforts are underway for generation, collection and characterization of
mutants for providing technological platform for functional genomics. In an indigenous
effort funded by the Department of Biotechnology (DBT), Government of India, a set of
22, 292 EMS mutagenised lines have been generated in the background of an upland
rice variety Nagina-22. EMS was chosen since it gives high point mutation densities by
base substitution either in the transcribed regions or in the regulatory elements of a
gene that might alter gene function leading to creation of a series of alleles of a gene.
The uniqueness of this national effort is phenotyping for a range of traits. Elaborate
phenotyping by different partner institutions has led to identification of mutants for plant
growth and architecture, flowering, maturity, grain number, shape and size, yield,
resistance to blast and bacterial leaf blight diseases, phosphorus use efficiency, and
tolerance to herbicide, drought and salinity. Inheritance of selected mutants has been
carried out using F2 populations developed from the cross of the mutants with wild type
Nagina22. Mutant loci for seed size and plant height have been mapped using SSR
markers on chromosomes 5 and 4, respectively. Transcriptome profiling using rice
microarrays has revealed altered expression of only a limited set of genes in these
mutants. In contrast, hundreds of genes were found differentially regulated in a gain-offunction
mutant having higher level of tolerance to moisture deficit stress. This mutant
also showed longer roots and more of partially closed stomata under stress. Two of the
mutants, one for plant height and the other for seed size were characterized in detail.
The dwarf mutant showed proportionate reduction in each of the internodes as
compared to wild type. The gene, identified through positional candidate approach and
verified by co-segregation analysis, was found to encode Carotenoid Cleavage
Dioxygenase7 (CCD7) and identified as an allele of htd1. The mutant carried
substitution of two nucleotides CC to AA in the sixth exon of the gene that resulted in
substitution of serine by a stop codon in the mutant. The short grain mutant had shorter,
narrower, and lesser cells in as compared to the wild type. The candidate gene region
on the short arm of chromosome 5 includes srs3, which was already reported to control
grain size in rice. It encodes kinesin 13 family proteins with a major role in mediation of
microtubule organisation during mitosis. Sequencing of 11kb srs3 gene region revealed
a substitution of C to T in the coding region of the mutant leading to creation of a stop
codon. Sequencing of the kinesin motor domain region of the gene did not reveal
presence of this mutation in 96 germplasm lines having significant grain size variation.
Results suggested utility of the mutant resource in rice functional genomics including
discovery of new genes for traits agronomic importance and allele mining.
[Show abstract][Hide abstract] ABSTRACT: Development of a representative and well-diversified core with minimum duplicate accessions and maximum diversity from a larger population of germplasm is highly essential for breeders involved in crop improvement programmes. Most of the existing methodologies for the identification of a core set are either based on qualitative or quantitative data. In this study, an approach to the identification of a core set of germplasm based on the response from a mixture of qualitative (single nucleotide polymorphism genotyping) and quantitative data was proposed. For this purpose, six different combined distance measures, three for quantitative data and two for qualitative data, were proposed and evaluated. The combined distance matrices were used as inputs to seven different clustering procedures for classifying the population of germplasm into homogeneous groups. Subsequently, an optimum number of clusters based on all clustering methodologies using different combined distance measures were identified on a consensus basis. Average cluster robustness values across all the identified optimum number of clusters under each clustering methodology were calculated. Overall, three different allocation methods were applied to sample the accessions that were selected from the clusters identified under each clustering methodology, with the highest average cluster robustness value being used to formulate a core set. Furthermore, an index was proposed for the evaluation of diversity in the core set. The results reveal that the combined distance measure A
2 – the distance based on the average of the range-standardized absolute difference for quantitative data with the rescaled distance based on the average absolute difference for qualitative data – from which three clusters that were identified by using the k-means clustering algorithm along with the proportional allocation method was suitable for the identification of a core set from a collection of rice germplasm.
[Show abstract][Hide abstract] ABSTRACT: Maize is an increasingly important food crop in southeast Asia. The elucidation of its genetic architecture, accomplished by exploring quantitative trait loci and useful alleles in various lines across numerous breeding programs, is therefore of great interest. The present study aimed to characterize subtropical maize lines using high-quality SNPs distributed throughout the genome.
We genotyped a panel of 240 subtropical elite maize inbred lines and carried out linkage disequilibrium, genetic diversity, population structure, and principal component analyses on the generated SNP data. The mean SNP distance across the genome was 70 Kb. The genome had both high and low linkage disequilibrium (LD) regions; the latter were dominant in areas near the gene-rich telomeric portions where recombination is frequent. A total of 252 haplotype blocks, ranging in size from 1 to 15.8 Mb, were identified. Slow LD decay (200-300 Kb) at r2 <= 0.1 across all chromosomes explained the selection of favorable traits around low LD regions in different breeding programs. The association mapping panel was characterized by strong population substructure. Genotypes were grouped into three distinct clusters with a mean genetic dissimilarity coefficient of 0.36.
The genotyped panel of subtropical maize lines characterized in this study should be useful for association mapping of agronomically important genes. The dissimilarity uncovered among genotypes provides an opportunity to exploit the heterotic potential of subtropical elite maize breeding lines.
[Show abstract][Hide abstract] ABSTRACT: Assessment of genetic diversity in a crop germplasm is a vital part of plant breeding. DNA markers such as microsatellite or simple sequence repeat markers have been widely used to estimate the genetic diversity in rice. The present study was carried out to decipher the pattern of genetic diversity in terms of both phenotypic and genotypic variability, and to assess the efficiency of random vis-á-vis QTL linked/gene based simple sequence repeat markers in diversity estimation. A set of 88 rice accessions that included landraces, farmer's varieties and popular Basmati lines were evaluated for agronomic traits and molecular diversity. The random set of SSR markers included 50 diversity panel markers developed under IRRI's Generation Challenge Programme (GCP) and the trait-linked/gene based markers comprised of 50 SSR markers reportedly linked to yield and related components. For agronomic traits, significant variability was observed, ranging between the maximum for grains/panicle and the minimum for panicle length. The molecular diversity based grouping indicated that varieties from a common centre were genetically similar, with few exceptions. The trait-linked markers gave an average genetic dissimilarity of 0.45 as against that of 0.37 by random markers, along with an average polymorphic information constant value of 0.48 and 0.41 respectively. The correlation between the kinship matrix generated by trait-linked markers and the phenotype based distance matrix (0.29) was higher than that of random markers (0.19). This establishes the robustness of trait-linked markers over random markers in estimating genetic diversity of rice germplasm.
Journal of Genetics 12/2013; 92(3):545-57. DOI:10.1007/s12041-013-0312-5 · 1.01 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Grain size is one of the three productivity related traits in rice and hence a major target for genetic improvement. Since understanding genetic variation in grain size between Basmati and indica genotypes is important for rice improvement, a recombinant inbred population was developed from a traditional aromatic cultivar ‘Basmati 370’ and a non-aromatic indica genotype ‘IRBB60’. This population was phenotyped in two locations for grain length (GL), grain breadth (GB), GL/GB ratio (LBR) and grain weight (GW). Though the RIL population reported in the current study exhibited segregation distortion (SD) for 54 % of the markers, they were utilized in analysis using an appropriate statistical package, PROC QTL in the SAS environment. Interval mapping revealed a total of 15 QTLs for GL, seven for GB, 15 for LBR and two for GW. Among them 13 were not reported earlier and thus novel. For a known major QTL identified in the study, GW8 for GB, a PCR based functional marker was designed and validated. This is the first report wherein a very high proportion of markers (>50 %) exhibiting SD have been successfully used for QTL mapping.