This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
IntroductionMango (Mangifera indica L.), acclaimed as the ‘king of fruits’ in the tropical world,... more IntroductionMango (Mangifera indica L.), acclaimed as the ‘king of fruits’ in the tropical world, has historical, religious, and economic values. It is grown commercially in more than 100 countries, and fresh mango world trade accounts for ~3,200 million US dollars for the year 2020. Mango is widely cultivated in sub-tropical and tropical regions of the world, with India, China, and Thailand being the top three producers. Mango fruit is adored for its taste, color, flavor, and aroma. Fruit color and firmness are important fruit quality traits for consumer acceptance, but their genetics is poorly understood.MethodsFor mapping of fruit color and firmness, mango varieties Amrapali and Sensation, having contrasting fruit quality traits, were crossed for the development of a mapping population. Ninety-two bi-parental progenies obtained from this cross were used for the construction of a high-density linkage map and identification of QTLs. Genotyping was carried out using an 80K SNP chip ...
the past, an excellent infrastructure in terms of equipment and other physical facilities and als... more the past, an excellent infrastructure in terms of equipment and other physical facilities and also a high degree of scientific competence. Development of transgenic crops for biotic and abiotic stress management, exploitation of heterosis through marker and genomic approaches, marker assisted selection and molecular breeding of major crops for productivity and quality enhancement, search for novel genes and promoters for efficient native and transgene expression are the major activities taken up by the centre. There is now considerable emphasis on structural and functional genomics of crop species such as rice, wheat, chickpea, pigeonpea, and mustard in the centre. In addition to research, the centre is contributing significantly to competent human resource development by way of offering regular M.Sc. and Ph.D. programmes by partnering with PG School, IARI.
The present report is in continuation to our earlier reports on the identification and fine mappi... more The present report is in continuation to our earlier reports on the identification and fine mapping of three aroma QTLs in basmati rice using a bi-parental mapping population derived from a cross between Pusa 1121, a basmati rice variety, and Pusa 1342, a non-aromatic rice variety. We used a combination of genetic mapping and transcriptome profiling to narrow down the number of differentially expressed genes in rice to identify potential candidate genes for rice grain aroma. Highly aromatic and non-aromatic recombinant inbred lines (RILs) were identified through sensory analysis of mature milled grains. RILs with similar phenotypes were bulked together using bulk segregant analysis approach which drastically reduced the number of differentially expressed genes from 4016 to 1344. The transcriptome profiles generated were analyzed through Affymetrix rice genome array containing probe sets designed from all the predicted rice gene sequences. Microarray-based transcriptome profiling revealed one down-regulated gene co-located in QTL region aro3.1 on chromosome 3, eight genes co-located in the aro4.1 region on chromosome 4 and the badh2 gene on chromosome 8 to be differentially expressed in the aromatic parent and aromatic bulk. These genes are the most suitable candidates for future validation and development of new molecular functional markers to facilitate marker assisted breeding.
Indian Journal of Genetics and Plant Breeding (The), 2015
ABSTRACT In the present study, genetic diversity among 73 genotypes comprising of cultivars and s... more ABSTRACT In the present study, genetic diversity among 73 genotypes comprising of cultivars and stable inter-specific derivatives from pigeonpea (Cajanus cajan x C. scarabaeoides) was assessed based on thirteen agro-morphological and quality traits and 42 genic microsatellite markers. Cluster analysis based on Tocher’s methods of pooled fielddata of agromorphological traits from all three environment and two locations grouped pigeonpea genotypes into nine clusters. Genetic divergence was mainly contributed by days to 50% flowering (30.14%) followed by100 seed weight (20.78%) and protein content (12.56%). The range of polymorphic information content (PIC) for microsatellites was 0.055-0.695. A total of 104 alleles were amplified with 42 SSR markers with an average of 2.48 alleles per locus. Ten alleles were unique to inter-specific derivatives. Based on Shannon’s information index (I), ASSR 17 was the most informative locus for all the genotypes. Two loci, ASSR114 and ASSR317 were polymorphic only among the inter-specific derivatives. Cophenetic correlations were statistically significant for phenograms based on Euclidean distances and average Manhattan distance analysis. The first three principal coordinates explained 60.17% and 57.22% of the accumulated variation in case of agromorphological traits and microsatellite data respectively. The information accrued is potential for broadening the genetic base in pigeonpea.
Journal of Plant Biochemistry and Biotechnology, 2019
Flowering is a complicated developmental process of physiological and morphological stages under ... more Flowering is a complicated developmental process of physiological and morphological stages under the control of a number of external signals and internal factors. Floral malformation occurring during flower development stage is serious constraint having crippling effect on mango flowering and production leading to heavy economic losses. In mango there is lack of information about the gene expression profile during flower development. We therefore performed transcriptome analysis of Mangifera indica cultivar Amrapalli, by isolating total RNA from different stages of bud development in healthy and malformed tissues. The next generation sequencing were performed using 2 9 150 PE chemistry on the
Flax (Linum usitatissimum L.) is a self-pollinating, annual, diploid crop grown for multi-utility... more Flax (Linum usitatissimum L.) is a self-pollinating, annual, diploid crop grown for multi-utility purposes for its quality oil, shining bast fiber, and industrial solvent. Being a cool (Rabi) season crop, it is affected by unprecedented climatic changes such as high temperature, drought, and associated oxidative stress that, globally, impede its growth, production, and productivity. To precisely assess the imperative changes that are inflicted by drought and associated oxidative stress, gene expression profiling of predominant drought-responsive genes (AREB, DREB/CBF, and ARR) was carried out by qRT-PCR. Nevertheless, for normalization/quantification of data obtained from qRT-PCR results, a stable reference gene is mandatory. Here, we evaluated a panel of four reference genes (Actin, EF1a, ETIF5A, and UBQ) and assessed their suitability as stable reference genes for the normalization of gene expression data obtained during drought-induced oxidative stress in flax. Taking together, f...
A3 and Glu-A1 loci coding for gliadins, LMW glutenin subunits and HMW glutenin subunits on dough ... more A3 and Glu-A1 loci coding for gliadins, LMW glutenin subunits and HMW glutenin subunits on dough resistance and extensibility was analysed in 56 Fz-derived F 6 families from a cross between bread wheats MKR(111/8) and 'Kite'. Extensograph data from two sites giving widely different flour protein levels (approximately 7% and 14%) revealed that the Glu-A3m and Glu-Alb alleles were associated with larger effects on dough resistance and extensibility than the null alleles Glu-A3k and Glu-Ale, respectively, and moreover, their effects were additive at both protein levels. The effect of the LMW glutenin allele Glu-A3m on both dough resistance and dough extensibility was relatively larger than that of the HMW glutenin allele Glu-Alb at both sites. Variation at the Gli-At locus did not appear to contribute towards dough strength. The results also showed the large effect of flour protein content on dough properties.
Indian Journal of Genetics and Plant Breeding (The), 2014
Bakanae or foot rot disease caused by Fusarium fujikuroi (teleomorph: Gibberella fujikuroi, Sawad... more Bakanae or foot rot disease caused by Fusarium fujikuroi (teleomorph: Gibberella fujikuroi, Sawada, Wollenweber) is emerging as a serious disease of rice. A simple, reliable and high-throughput method for screening the disease would enable rapid screening of germplasm aimed at identifying resistance sources, mapping QTLs/genes and developing resistant rice cultivars. In the present study, a highthroughput, reliable bioassay to screen rice germplasm for resistance to bakanae disease was developed and compared with the conventional screening technique. This technique involves soaking of rice seeds in fungal spore suspension (1.0x10 6 spores ml-1) for 24 hours at room temperature. Seedling growth at 30°/25° (±3)°C day/night temperature and 60/80(±10)% day/night relative humidity in glasshouse gave the best results. The new protocol described here produces consistent and reproducible bakanae disease symptoms and enables screening of hundreds of rice germplasm within 15 days without any loss of precision in screening of rice genotypes against bakanae disease. The resistant and susceptible genotypes can be used for developing mapping population and identification of QTLs/genes conferring resistance to bakanae disease.
The genes controlling resistance to three wheat rusts, viz., leaf rust (Lr26), stem rust (St31) a... more The genes controlling resistance to three wheat rusts, viz., leaf rust (Lr26), stem rust (St31) and stripe or yellow rust (Yr9), and co-secalins (Secl), located on the short arm of rye chromosome IR, were mapped with respect to each other and the centromere. Analysis of 214 seeds (or families derived from them) from testcrosses between a IBL.IRS/IR heterozygote and 'Chinese Spring' ditelocentric 1BL showed no recombination between the genes for resistance to the three rusts, suggesting very tight linkage or perhaps a single complex locus conferring resistance to the three rusts. The rust resistance genes were located 5.4_+ 1.7 cM from the Secl locus, which in turn was located 26.1 _+ 4.3 cM from the centromere; the gene order being centromere-Seel-Lr26/Sr31/Yr9 telomere. In a second test-cross, using a different IBL.1RS translocation which had only stem rust resistance (SrR), the above gene order was confirmed despite a very large proportion of aneuploids (45.8%) among the progeny. Furthermore, a map distance of 16.0 + 4.8 cM was estimated for SrR and the telomeric heterochromatin (C-band) on I RS. These results suggest that a very small segment of 1RS chromatin is required to maintain resistance to all three wheat rusts. It should be possible but difficult to separate the rust resistance genes from the secalin gene(s), which are thought to contribute to dough stickiness of wheat-rye translocation lines carrying 1RS.
Oryza coarctata Roxb. is a wild halophytic species found mostly on South Asian seashore. It can t... more Oryza coarctata Roxb. is a wild halophytic species found mostly on South Asian seashore. It can tolerate salinity up to 4 S m-1 , which is equivalent to 479 mM NaCl. This species has unique morphological, anatomical, as well as physiological adaptations, which helps it to survive under high salinity and submerged conditions. Thus, it is considered to be a reservoir of salinity and submergence tolerance genes. For quantification of gene expressions, it is necessary to identify stable reference genes and validate stress responsive genes by real time quantitative PCR. The present study deals with the expression analyses of eight candidate reference genes, namely, ubiquitin 2, histone 3, β-tubulin, α-tubulin, glyceraldehyde-3-phosphate dehydrogenase, eukaryotic initiation factor 4-α (eIF4-α), cyclophilin, and actin (ACT) under different abiotic stresses such as salinity, cold, drought, heat, submergence, submergence with saline water (dual stress), and abscisic acid treatment. The four different statistical algorithms, namely, Bestkeeper, NormFinder, geNorm, and RefFinder were used to rank the genes in order of stability. The analysis revealed that ACT and eIF4-α were the two most stable reference genes, which was further validated by determining the expressions of two well-known stress responsive genes alcohol dehydrogenase and dehydration responsive element binding protein 2A under submergence and drought stress, respectively. This study is the first report to analyse the reference genes for O. coarctata.
Earthworms are one of the most important and beneficial macrofauna, and are used extensively in o... more Earthworms are one of the most important and beneficial macrofauna, and are used extensively in organic farming. Earthworms mediate soil biological regulation systems, and produce biogenic structures. They help to maintain soil structure, water infiltration, and regulate the availability of nutrients assimilated by plants. The objectives of this study were to perform morphological and molecular characterizations of 24 earthworm individuals collected from geographically diverse locations to assess the level of genetic variation. For molecular analysis, the effectiveness of RAPD, ISSR, and Universal rice primers (URPs) markers was investigated to identify polymorphism among 24 isolates of earthworms. A total of 62 molecular markers were used for amplification of genomic DNA of earthworms. Of these, 10 RAPD, 10 ISSR, and 10 URPs markers were used for characterization, which showed 95.7%, 96.7% and 98.3% polymorphism, respectively. The dendrogram, generated from the DNA markers by the unweighted pair group method using arithmetic averages, grouped all the isolates into two main clusters. All Eisenia fetida isolates were clustered in group A, whereas group B included three isolates belonging to Eudrilus eugeniae. Molecular markers allowed a rapid assessment of genetic variation among these closely related isolates of earthworms. These results suggest that molecular markers are a good choice for diversity analysis of earthworm individuals.
A translocation mapping procedure was used to map gene-centromere distances for the genes control... more A translocation mapping procedure was used to map gene-centromere distances for the genes controlling endosperm proteins on the short arm of each of the chromosomes 1A, 1B and 1D in wheat. The genes controlling triplet proteins (tentatively designated Tri-1) were found to be closely linked to the centromere on chromosome arms 1AS and 1DS and loosely linked to the gliadin genes (Gli-1) on the same arms. The Gli-1 genes segregated independently or were very loosely linked to their respective centromeres. The Gli-Bl-centromere map distance on 1BS was also estimated using conventional telocentric mapping and the result was similar to that obtained with the translocation mapping. A simple two-step one-dimensional electrophoretic procedure is described which allows the lowmolecular-weight (LMW) glutenin subunits to be separated from the gliadin bands, thus facilitating the genetic analysis of these LMW subunits. No recombination was observed between the genes (designated Glu-3) controlling some major LMW glutenin subunits and those controlling gliadins on chromosome alms 1AS and 1DS. However, in a separate experiment, the genes controlling LMW glutenin subunits on 1BS (Glu-B3) showed a low frequency of recombination with the gliadin genes.
We have obtained several amino acid sequences from purified polypeptides of a wheat endosperm sto... more We have obtained several amino acid sequences from purified polypeptides of a wheat endosperm storage globulin previously described as 'triplet' protein. The amino acid sequence data supported by immunochemical analysis using anti-oat 12S globulin antibodies, provide definitive evidence that the triplet protein is homologous to pea legumin and related seed storage proteins of oats, rice and several dicotyledonous species. Thus, it is now proposed that the triplet protein of wheat be renamed 'triticin'. The oat globulin antibodies also cross-reacted strongly with the high-molecular-weight (HMW) glutenin subunits which have been implicated in bread-making quality.
This study reports generation of large-scale genomic resources for pigeonpea, a so-called 'orphan... more This study reports generation of large-scale genomic resources for pigeonpea, a so-called 'orphan crop species' of the semi-arid tropic regions. FLX/454 sequencing carried out on a normalized cDNA pool prepared from 31 tissues produced 494 353 short transcript reads (STRs). Cluster analysis of these STRs, together with 10 817 Sanger ESTs, resulted in a pigeonpea trancriptome assembly (CcTA) comprising of 127 754 tentative unique sequences (TUSs). Functional analysis of these TUSs highlights several active pathways and processes in the sampled tissues. Comparison of the CcTA with the soybean genome showed similarity to 10 857 and 16 367 soybean gene models (depending on alignment methods). Additionally, Illumina 1G sequencing was performed on Fusarium wilt (FW)-and sterility mosaic disease (SMD)-challenged root tissues of 10 resistant and susceptible genotypes. More than 160 million sequence tags were used to identify FW-and SMD-responsive genes. Sequence analysis of CcTA and the Illumina tags identified a large new set of markers for use in genetics and breeding, including 8137 simple sequence repeats, 12 141 single-nucleotide polymorphisms and 5845 intron-spanning regions. Genomic resources developed in this study should be useful for basic and applied research, not only for pigeonpea improvement but also for other related, agronomically important legumes.
Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu Univ... more Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi-221005, India. National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012, India. STRASA-IRRI-India Office, Rajendra Place, 9 floor, Aggrawal Corporate Tower, New Delhi, 110008, India. Corresponding author’s email: [email protected] Co-authors’ email addresses: [email protected], [email protected], [email protected], [email protected], [email protected], [email protected]
This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY
IntroductionMango (Mangifera indica L.), acclaimed as the ‘king of fruits’ in the tropical world,... more IntroductionMango (Mangifera indica L.), acclaimed as the ‘king of fruits’ in the tropical world, has historical, religious, and economic values. It is grown commercially in more than 100 countries, and fresh mango world trade accounts for ~3,200 million US dollars for the year 2020. Mango is widely cultivated in sub-tropical and tropical regions of the world, with India, China, and Thailand being the top three producers. Mango fruit is adored for its taste, color, flavor, and aroma. Fruit color and firmness are important fruit quality traits for consumer acceptance, but their genetics is poorly understood.MethodsFor mapping of fruit color and firmness, mango varieties Amrapali and Sensation, having contrasting fruit quality traits, were crossed for the development of a mapping population. Ninety-two bi-parental progenies obtained from this cross were used for the construction of a high-density linkage map and identification of QTLs. Genotyping was carried out using an 80K SNP chip ...
the past, an excellent infrastructure in terms of equipment and other physical facilities and als... more the past, an excellent infrastructure in terms of equipment and other physical facilities and also a high degree of scientific competence. Development of transgenic crops for biotic and abiotic stress management, exploitation of heterosis through marker and genomic approaches, marker assisted selection and molecular breeding of major crops for productivity and quality enhancement, search for novel genes and promoters for efficient native and transgene expression are the major activities taken up by the centre. There is now considerable emphasis on structural and functional genomics of crop species such as rice, wheat, chickpea, pigeonpea, and mustard in the centre. In addition to research, the centre is contributing significantly to competent human resource development by way of offering regular M.Sc. and Ph.D. programmes by partnering with PG School, IARI.
The present report is in continuation to our earlier reports on the identification and fine mappi... more The present report is in continuation to our earlier reports on the identification and fine mapping of three aroma QTLs in basmati rice using a bi-parental mapping population derived from a cross between Pusa 1121, a basmati rice variety, and Pusa 1342, a non-aromatic rice variety. We used a combination of genetic mapping and transcriptome profiling to narrow down the number of differentially expressed genes in rice to identify potential candidate genes for rice grain aroma. Highly aromatic and non-aromatic recombinant inbred lines (RILs) were identified through sensory analysis of mature milled grains. RILs with similar phenotypes were bulked together using bulk segregant analysis approach which drastically reduced the number of differentially expressed genes from 4016 to 1344. The transcriptome profiles generated were analyzed through Affymetrix rice genome array containing probe sets designed from all the predicted rice gene sequences. Microarray-based transcriptome profiling revealed one down-regulated gene co-located in QTL region aro3.1 on chromosome 3, eight genes co-located in the aro4.1 region on chromosome 4 and the badh2 gene on chromosome 8 to be differentially expressed in the aromatic parent and aromatic bulk. These genes are the most suitable candidates for future validation and development of new molecular functional markers to facilitate marker assisted breeding.
Indian Journal of Genetics and Plant Breeding (The), 2015
ABSTRACT In the present study, genetic diversity among 73 genotypes comprising of cultivars and s... more ABSTRACT In the present study, genetic diversity among 73 genotypes comprising of cultivars and stable inter-specific derivatives from pigeonpea (Cajanus cajan x C. scarabaeoides) was assessed based on thirteen agro-morphological and quality traits and 42 genic microsatellite markers. Cluster analysis based on Tocher’s methods of pooled fielddata of agromorphological traits from all three environment and two locations grouped pigeonpea genotypes into nine clusters. Genetic divergence was mainly contributed by days to 50% flowering (30.14%) followed by100 seed weight (20.78%) and protein content (12.56%). The range of polymorphic information content (PIC) for microsatellites was 0.055-0.695. A total of 104 alleles were amplified with 42 SSR markers with an average of 2.48 alleles per locus. Ten alleles were unique to inter-specific derivatives. Based on Shannon’s information index (I), ASSR 17 was the most informative locus for all the genotypes. Two loci, ASSR114 and ASSR317 were polymorphic only among the inter-specific derivatives. Cophenetic correlations were statistically significant for phenograms based on Euclidean distances and average Manhattan distance analysis. The first three principal coordinates explained 60.17% and 57.22% of the accumulated variation in case of agromorphological traits and microsatellite data respectively. The information accrued is potential for broadening the genetic base in pigeonpea.
Journal of Plant Biochemistry and Biotechnology, 2019
Flowering is a complicated developmental process of physiological and morphological stages under ... more Flowering is a complicated developmental process of physiological and morphological stages under the control of a number of external signals and internal factors. Floral malformation occurring during flower development stage is serious constraint having crippling effect on mango flowering and production leading to heavy economic losses. In mango there is lack of information about the gene expression profile during flower development. We therefore performed transcriptome analysis of Mangifera indica cultivar Amrapalli, by isolating total RNA from different stages of bud development in healthy and malformed tissues. The next generation sequencing were performed using 2 9 150 PE chemistry on the
Flax (Linum usitatissimum L.) is a self-pollinating, annual, diploid crop grown for multi-utility... more Flax (Linum usitatissimum L.) is a self-pollinating, annual, diploid crop grown for multi-utility purposes for its quality oil, shining bast fiber, and industrial solvent. Being a cool (Rabi) season crop, it is affected by unprecedented climatic changes such as high temperature, drought, and associated oxidative stress that, globally, impede its growth, production, and productivity. To precisely assess the imperative changes that are inflicted by drought and associated oxidative stress, gene expression profiling of predominant drought-responsive genes (AREB, DREB/CBF, and ARR) was carried out by qRT-PCR. Nevertheless, for normalization/quantification of data obtained from qRT-PCR results, a stable reference gene is mandatory. Here, we evaluated a panel of four reference genes (Actin, EF1a, ETIF5A, and UBQ) and assessed their suitability as stable reference genes for the normalization of gene expression data obtained during drought-induced oxidative stress in flax. Taking together, f...
A3 and Glu-A1 loci coding for gliadins, LMW glutenin subunits and HMW glutenin subunits on dough ... more A3 and Glu-A1 loci coding for gliadins, LMW glutenin subunits and HMW glutenin subunits on dough resistance and extensibility was analysed in 56 Fz-derived F 6 families from a cross between bread wheats MKR(111/8) and 'Kite'. Extensograph data from two sites giving widely different flour protein levels (approximately 7% and 14%) revealed that the Glu-A3m and Glu-Alb alleles were associated with larger effects on dough resistance and extensibility than the null alleles Glu-A3k and Glu-Ale, respectively, and moreover, their effects were additive at both protein levels. The effect of the LMW glutenin allele Glu-A3m on both dough resistance and dough extensibility was relatively larger than that of the HMW glutenin allele Glu-Alb at both sites. Variation at the Gli-At locus did not appear to contribute towards dough strength. The results also showed the large effect of flour protein content on dough properties.
Indian Journal of Genetics and Plant Breeding (The), 2014
Bakanae or foot rot disease caused by Fusarium fujikuroi (teleomorph: Gibberella fujikuroi, Sawad... more Bakanae or foot rot disease caused by Fusarium fujikuroi (teleomorph: Gibberella fujikuroi, Sawada, Wollenweber) is emerging as a serious disease of rice. A simple, reliable and high-throughput method for screening the disease would enable rapid screening of germplasm aimed at identifying resistance sources, mapping QTLs/genes and developing resistant rice cultivars. In the present study, a highthroughput, reliable bioassay to screen rice germplasm for resistance to bakanae disease was developed and compared with the conventional screening technique. This technique involves soaking of rice seeds in fungal spore suspension (1.0x10 6 spores ml-1) for 24 hours at room temperature. Seedling growth at 30°/25° (±3)°C day/night temperature and 60/80(±10)% day/night relative humidity in glasshouse gave the best results. The new protocol described here produces consistent and reproducible bakanae disease symptoms and enables screening of hundreds of rice germplasm within 15 days without any loss of precision in screening of rice genotypes against bakanae disease. The resistant and susceptible genotypes can be used for developing mapping population and identification of QTLs/genes conferring resistance to bakanae disease.
The genes controlling resistance to three wheat rusts, viz., leaf rust (Lr26), stem rust (St31) a... more The genes controlling resistance to three wheat rusts, viz., leaf rust (Lr26), stem rust (St31) and stripe or yellow rust (Yr9), and co-secalins (Secl), located on the short arm of rye chromosome IR, were mapped with respect to each other and the centromere. Analysis of 214 seeds (or families derived from them) from testcrosses between a IBL.IRS/IR heterozygote and 'Chinese Spring' ditelocentric 1BL showed no recombination between the genes for resistance to the three rusts, suggesting very tight linkage or perhaps a single complex locus conferring resistance to the three rusts. The rust resistance genes were located 5.4_+ 1.7 cM from the Secl locus, which in turn was located 26.1 _+ 4.3 cM from the centromere; the gene order being centromere-Seel-Lr26/Sr31/Yr9 telomere. In a second test-cross, using a different IBL.1RS translocation which had only stem rust resistance (SrR), the above gene order was confirmed despite a very large proportion of aneuploids (45.8%) among the progeny. Furthermore, a map distance of 16.0 + 4.8 cM was estimated for SrR and the telomeric heterochromatin (C-band) on I RS. These results suggest that a very small segment of 1RS chromatin is required to maintain resistance to all three wheat rusts. It should be possible but difficult to separate the rust resistance genes from the secalin gene(s), which are thought to contribute to dough stickiness of wheat-rye translocation lines carrying 1RS.
Oryza coarctata Roxb. is a wild halophytic species found mostly on South Asian seashore. It can t... more Oryza coarctata Roxb. is a wild halophytic species found mostly on South Asian seashore. It can tolerate salinity up to 4 S m-1 , which is equivalent to 479 mM NaCl. This species has unique morphological, anatomical, as well as physiological adaptations, which helps it to survive under high salinity and submerged conditions. Thus, it is considered to be a reservoir of salinity and submergence tolerance genes. For quantification of gene expressions, it is necessary to identify stable reference genes and validate stress responsive genes by real time quantitative PCR. The present study deals with the expression analyses of eight candidate reference genes, namely, ubiquitin 2, histone 3, β-tubulin, α-tubulin, glyceraldehyde-3-phosphate dehydrogenase, eukaryotic initiation factor 4-α (eIF4-α), cyclophilin, and actin (ACT) under different abiotic stresses such as salinity, cold, drought, heat, submergence, submergence with saline water (dual stress), and abscisic acid treatment. The four different statistical algorithms, namely, Bestkeeper, NormFinder, geNorm, and RefFinder were used to rank the genes in order of stability. The analysis revealed that ACT and eIF4-α were the two most stable reference genes, which was further validated by determining the expressions of two well-known stress responsive genes alcohol dehydrogenase and dehydration responsive element binding protein 2A under submergence and drought stress, respectively. This study is the first report to analyse the reference genes for O. coarctata.
Earthworms are one of the most important and beneficial macrofauna, and are used extensively in o... more Earthworms are one of the most important and beneficial macrofauna, and are used extensively in organic farming. Earthworms mediate soil biological regulation systems, and produce biogenic structures. They help to maintain soil structure, water infiltration, and regulate the availability of nutrients assimilated by plants. The objectives of this study were to perform morphological and molecular characterizations of 24 earthworm individuals collected from geographically diverse locations to assess the level of genetic variation. For molecular analysis, the effectiveness of RAPD, ISSR, and Universal rice primers (URPs) markers was investigated to identify polymorphism among 24 isolates of earthworms. A total of 62 molecular markers were used for amplification of genomic DNA of earthworms. Of these, 10 RAPD, 10 ISSR, and 10 URPs markers were used for characterization, which showed 95.7%, 96.7% and 98.3% polymorphism, respectively. The dendrogram, generated from the DNA markers by the unweighted pair group method using arithmetic averages, grouped all the isolates into two main clusters. All Eisenia fetida isolates were clustered in group A, whereas group B included three isolates belonging to Eudrilus eugeniae. Molecular markers allowed a rapid assessment of genetic variation among these closely related isolates of earthworms. These results suggest that molecular markers are a good choice for diversity analysis of earthworm individuals.
A translocation mapping procedure was used to map gene-centromere distances for the genes control... more A translocation mapping procedure was used to map gene-centromere distances for the genes controlling endosperm proteins on the short arm of each of the chromosomes 1A, 1B and 1D in wheat. The genes controlling triplet proteins (tentatively designated Tri-1) were found to be closely linked to the centromere on chromosome arms 1AS and 1DS and loosely linked to the gliadin genes (Gli-1) on the same arms. The Gli-1 genes segregated independently or were very loosely linked to their respective centromeres. The Gli-Bl-centromere map distance on 1BS was also estimated using conventional telocentric mapping and the result was similar to that obtained with the translocation mapping. A simple two-step one-dimensional electrophoretic procedure is described which allows the lowmolecular-weight (LMW) glutenin subunits to be separated from the gliadin bands, thus facilitating the genetic analysis of these LMW subunits. No recombination was observed between the genes (designated Glu-3) controlling some major LMW glutenin subunits and those controlling gliadins on chromosome alms 1AS and 1DS. However, in a separate experiment, the genes controlling LMW glutenin subunits on 1BS (Glu-B3) showed a low frequency of recombination with the gliadin genes.
We have obtained several amino acid sequences from purified polypeptides of a wheat endosperm sto... more We have obtained several amino acid sequences from purified polypeptides of a wheat endosperm storage globulin previously described as 'triplet' protein. The amino acid sequence data supported by immunochemical analysis using anti-oat 12S globulin antibodies, provide definitive evidence that the triplet protein is homologous to pea legumin and related seed storage proteins of oats, rice and several dicotyledonous species. Thus, it is now proposed that the triplet protein of wheat be renamed 'triticin'. The oat globulin antibodies also cross-reacted strongly with the high-molecular-weight (HMW) glutenin subunits which have been implicated in bread-making quality.
This study reports generation of large-scale genomic resources for pigeonpea, a so-called 'orphan... more This study reports generation of large-scale genomic resources for pigeonpea, a so-called 'orphan crop species' of the semi-arid tropic regions. FLX/454 sequencing carried out on a normalized cDNA pool prepared from 31 tissues produced 494 353 short transcript reads (STRs). Cluster analysis of these STRs, together with 10 817 Sanger ESTs, resulted in a pigeonpea trancriptome assembly (CcTA) comprising of 127 754 tentative unique sequences (TUSs). Functional analysis of these TUSs highlights several active pathways and processes in the sampled tissues. Comparison of the CcTA with the soybean genome showed similarity to 10 857 and 16 367 soybean gene models (depending on alignment methods). Additionally, Illumina 1G sequencing was performed on Fusarium wilt (FW)-and sterility mosaic disease (SMD)-challenged root tissues of 10 resistant and susceptible genotypes. More than 160 million sequence tags were used to identify FW-and SMD-responsive genes. Sequence analysis of CcTA and the Illumina tags identified a large new set of markers for use in genetics and breeding, including 8137 simple sequence repeats, 12 141 single-nucleotide polymorphisms and 5845 intron-spanning regions. Genomic resources developed in this study should be useful for basic and applied research, not only for pigeonpea improvement but also for other related, agronomically important legumes.
Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu Univ... more Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi-221005, India. National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110 012, India. STRASA-IRRI-India Office, Rajendra Place, 9 floor, Aggrawal Corporate Tower, New Delhi, 110008, India. Corresponding author’s email: [email protected] Co-authors’ email addresses: [email protected], [email protected], [email protected], [email protected], [email protected], [email protected]
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