Background: Whole genome sequencing provides the most comprehensive collection of an organism's g... more Background: Whole genome sequencing provides the most comprehensive collection of an organism's genetic information. The availability of complete genome sequences is expected to dramatically deliver a high impact on biology. However, to achieve this impact in the area of crop improvement, significant efforts are still required on functional genomics, including the areas of gene annotation, cloning, expression profiling, and functional validation.
Background SWEET (MtN3_saliva) domain proteins, a recently identified group of efflux transporter... more Background SWEET (MtN3_saliva) domain proteins, a recently identified group of efflux transporters, play an indispensable role in sugar efflux, phloem loading, plant-pathogen interaction and reproductive tissue development. The SWEET gene family is predominantly studied in Arabidopsis and members of the family are being investigated in rice. To date, no transcriptome or genomics analysis of soybean SWEET genes has been reported. Results In the present investigation, we explored the evolutionary aspect of the SWEET gene family in diverse plant species including primitive single cell algae to angiosperms with a major emphasis on Glycine max. Evolutionary features showed expansion and duplication of the SWEET gene family in land plants. Homology searches with BLAST tools and Hidden Markov Model-directed sequence alignments identified 52 SWEET genes that were mapped to 15 chromosomes in the soybean genome as tandem duplication events. Soybean SWEET (GmSWEET) genes showed a wide range of...
Circadian clocks are a great evolutionary innovation and provide competitive advantage during the... more Circadian clocks are a great evolutionary innovation and provide competitive advantage during the day/night cycle and under changing environmental conditions. The circadian clock mediates expression of a large proportion of genes in plants, achieving a harmonious relationship between energy metabolism, photosynthesis, and biotic and abiotic stress responses. Here it is shown that multiple paralogues of clock genes are present in soybean (Glycine max) and mediate flooding and drought responses. Differential expression of many clock and SUB1 genes was found under flooding and drought conditions. Furthermore, natural variation in the amplitude and phase shifts in PRR7 and TOC1 genes was also discovered under drought and flooding conditions, respectively. PRR3 exhibited flooding- and drought-specific splicing patterns and may work in concert with PRR7 and TOC1 to achieve energy homeostasis under flooding and drought conditions. Higher expression of TOC1 also coincides with elevated leve...
Root system architecture is important in soybean to improve the acquisition and use efficiency of... more Root system architecture is important in soybean to improve the acquisition and use efficiency of water and nutrients in resource limited growing environments. Root architectural traits are very desirable to govern avoidance mechanisms under drought stress conditions. Due to the complexities involved with root phenotyping, limited efforts have been made to improve the genetic potential of soybean root traits. We developed few root screening phenotyping platforms to study root development and its plasticity in soybean. Quantitative Trait Loci (QTL) research on soybean intra-specific populations have identified few root QTLs, but none of them have identified key genes involved in regulating root architectural traits. Moreover, the genetic potential available in wild soybean, Glycine soja, has not been employed to improve root system architecture in cultivated soybean. Rare and conserved non-synonymous Single Nucleotide Polymorphism (SNP) alleles specific to wild soybeans for root arch...
Background: Drought stress is a major limitation to rainfed rice production and yield stability. ... more Background: Drought stress is a major limitation to rainfed rice production and yield stability. Identifying yield-associated quantitative trait loci (QTLs) that are consistent under drought stress predominant in target production environments, as well as across different genetic backgrounds, will help to develop high-yielding rice cultivars suitable for water-limited environments through marker-assisted breeding (MAB). Considerable progress has been made in mapping QTLs for drought resistance traits in rice; however, few have been successfully used in MAB. Results: Recombinant inbred lines of IR20 × Nootripathu, two indica cultivars adapted to rainfed target populations of environments (TPEs), were evaluated in one and two seasons under managed stress and in a rainfed target drought stress environment, respectively. In the managed stress environment, the severity of the stress meant that measurements could be made only on secondary traits and biomass. In the target environment, the lines experienced varying timings, durations, and intensities of drought stress. The rice recombinant inbred lines exhibited significant genotypic variation for physio-morphological, phenological, and plant production traits under drought. Nine and 24 QTLs for physio-morphological and plant production traits were identified in managed and natural drought stress conditions in the TPEs, respectively. Yield QTLs that were consistent in the target environment over seasons were identified on chromosomes 1, 4, and 6, which could stabilize the productivity in high-yielding rice lines in a water-limited rainfed ecosystem. These yield QTLs also govern highly heritable key secondary traits, such as leaf drying, canopy temperature, panicle harvest index and harvest index.
Journal of integrative plant biology, Jan 14, 2015
Limited information available for soybean root traits and their plasticity under drought stress. ... more Limited information available for soybean root traits and their plasticity under drought stress. To date, no studies have focused on examining diverse soybean germplasm for regulation of shoot and root response under water limited conditions across varying soil types. In this study, 17 genetically diverse soybean germplasm lines were selected to study root response to water limited conditions in clay (trial 1) and sandy soil (trial 2) in two target environments. Physiological data on shoot traits, phenotypic root traits, and biomass accumulation was measured at multiple crop stages ranging from early vegetative to pod filling. In trial 1, the number of lateral roots and forks were positively correlated with plot yield under water limitation and in trial 2, lateral root thickness was positively correlated with the hill plot yield. Plant Introduction (PI) 578477A and 088444 were found to have higher later root number and forks in clay soil with higher yield under water limitation. In ...
Cultivated soybean (Glycine max L.) cv. Dunbar (PI 552538) and wild G. soja (PI 326582A) exhibite... more Cultivated soybean (Glycine max L.) cv. Dunbar (PI 552538) and wild G. soja (PI 326582A) exhibited significant differences in root architecture and root-related traits. In this study, phenotypic variability for root traits among 251 BC 2 F 5 backcross inbred lines (BILs) developed from the cross Dunbar/PI 326582A were identified. The root systems of the parents and BILs were evaluated in controlled environmental conditions using a cone system at seedling stage. The G. max parent Dunbar contributed phenotypically favorable alleles at a major quantitative trait locus on chromosome 8 (Satt315-I locus) that governed root traits (tap root length and lateral root number) and shoot length. This QTL accounted for >10% of the phenotypic variation of both tap root and shoot length. This QTL region was found to control various shoot-and root-related traits across soybean genetic backgrounds. Within the confidence interval of this region, eleven transcription factors (TFs) were identified. Based on RNA sequencing and Affymetrix expression data, key TFs including MYB, AP2-EREBP and bZIP TFs were identified in this QTL interval with high expression in roots and nodules. The backcross inbred lines with different parental allelic combination showed different expression pattern for six transcription factors selected based on their expression pattern in root tissues. It appears that the marker interval Satt315-I locus on chromosome 8 contain an essential QTL contributing to early root and shoot growth in soybean.
Background: Root system architecture is important for water acquisition and nutrient acquisition ... more Background: Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed composition traits, but have never been investigated to improve root system architecture. Therefore, in this study, high-density single-feature polymorphic markers and simple sequence repeats were used to map quantitative trait loci (QTLs) governing root system architecture in an inter-specific soybean mapping population developed from a cross between Glycine max and Glycine soja.
Small RNAs are ubiquitous, versatile repressors and include (1) microRNAs (miRNAs), processed fro... more Small RNAs are ubiquitous, versatile repressors and include (1) microRNAs (miRNAs), processed from mRNA forming stem-loops; and (2) small interfering RNAs (siRNAs), the latter derived in plants by a process typically requiring an RNA-dependent RNA polymerase. We constructed and analyzed an expression atlas of soybean (Glycine max) small RNAs, identifying over 500 loci generating 21-nucleotide phased siRNAs (phasiRNAs; from PHAS loci), of which 483 overlapped annotated protein-coding genes. Via the integration of miRNAs with parallel analysis of RNA end (PARE) data, 20 miRNA triggers of 127 PHAS loci were detected. The primary class of PHAS loci (208 or 41% of the total) corresponded to NB-LRR genes; some of these small RNAs preferentially accumulate in nodules. Among the PHAS loci, novel representatives of TAS3 and noncanonical phasing patterns were also observed. A noncoding PHAS locus, triggered by miR4392, accumulated preferentially in anthers; the phasiRNAs are predicted to targ...
Many sources of drought and flooding tolerance have been identified in soybean, however underlyin... more Many sources of drought and flooding tolerance have been identified in soybean, however underlying molecular and physiological mechanisms are poorly understood. Therefore, it is important to illuminate different plant responses to these abiotic stresses and understand the mechanisms that confer tolerance. Towards this goal we used four contrasting soybean (Glycine max) genotypes (PI 567690 e drought tolerant, Pana e drought susceptible, PI 408105A e flooding tolerant, S99-2281 e flooding susceptible) grown under greenhouse conditions and compared genotypic responses to drought and flooding at the physiological, biochemical, and cellular level. We also quantified these variations and tried to infer their role in drought and flooding tolerance in soybean. Our results revealed that different mechanisms contribute to reduction in net photosynthesis under drought and flooding stress. Under drought stress, ABA and stomatal conductance are responsible for reduced photosynthetic rate; while under flooding stress, accumulation of starch granules played a major role. Drought tolerant genotypes PI 567690 and PI 408105A had higher plastoglobule numbers than the susceptible Pana and S99-2281. Drought stress increased the number and size of plastoglobules in most of the genotypes pointing to a possible role in stress tolerance. Interestingly, there were seven fibrillin proteins localized within the plastoglobules that were up-regulated in the drought and flooding tolerant genotypes PI 567690 and PI 408105A, respectively, but down-regulated in the drought susceptible genotype Pana. These results suggest a potential role of Fibrillin proteins, FBN1a, 1b and 7a in soybean response to drought and flooding stress.
Soybean production is greatly influenced by abiotic stresses imposed by environmental factors suc... more Soybean production is greatly influenced by abiotic stresses imposed by environmental factors such as drought, water submergence, salt, and heavy metals. A thorough understanding of plant response to abiotic stress at the molecular level is a prerequisite for its effective management. The molecular mechanism of stress tolerance is complex and requires information at the omic level to understand it effectively. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. The emerging field of ionomics is also being employed for investigating abiotic stress tolerance in soybean. Omic approaches generate a huge amount of data, and adequate advancements in computational tools have been achieved for effective analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. In this review, we have described advances in omic tools in the view of conventional and modern approaches being used to dissect abiotic stress tolerance in soybean. Emphasis was given to approaches such as quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). Comparative genomics and candidate gene approaches are also discussed considering identification of potential genomic loci, genes, and biochemical pathways involved in stress tolerance mechanism in soybean. This review also provides a comprehensive catalog of available online omic resources for soybean and its effective utilization. We have also addressed the significance of phenomics in the integrated approaches and recognized high-throughput multi-dimensional phenotyping as a major limiting factor for the improvement of abiotic stress tolerance in soybean.
This study was to estimate the GCA of the parents and SCA considered for the development of high ... more This study was to estimate the GCA of the parents and SCA considered for the development of high yielding and better quality cultivars. Eleven genotypes and 28 F 1 hybrids obtained by crossing 4 lines and 7 testers in line X tester mating system were sown in randomized complete block design. L X T analysis revealed significant GCA and SCA effects for all the traits except earliness. Among the parents: MCU 12 for number of bolls per plant, boll weight, seed cotton yield per plant, F 1861 for seed cotton yield and number of bolls per plant, SOCC 17 for earliness, SURABHI for number of sympodia and TCH 1641 for ginning outturn and lint index with high GCA. Parent F 776 and F1861 were good combiners for fibre quality traits. The high yielding quality hybrids were deducted with significant SCA effects for seed cotton yield and fibre characteristics.
Sampling the sequence of a relatively small fraction of the genome in large numbers of individual... more Sampling the sequence of a relatively small fraction of the genome in large numbers of individuals is an important objective for population genetics and association genetics approaches. However, currently available 'sequence capture' methods either require expensive instrumentation or have problems dealing with high sample numbers and relatively small target sizes. We have developed Genome-Tagged Amplification (GTA) as a flexible PCR-based method for preparing pools of hundreds of amplicons from hundreds of samples for next generation sequencing. The method involves tagging of genomic DNA with barcode adapters at restriction sites, followed by PCR amplification from flanking DNA. It is freely scalable for both sample number and amplicon number and has no specialized equipment requirement. An optimized protocol is presented which provides a matrix of 96 9 192 combinations of samples x amplicons, corresponding to a complete 454 Titanium run. Initially, we used 454 sequencing; however, GTA could easily be adapted to Illumina sequencing platforms as read lengths have significantly increased in this system.
Drought stress is the major constraint in rainfed rice production. Deep and thick roots are thoug... more Drought stress is the major constraint in rainfed rice production. Deep and thick roots are thought to contribute in drought resilience. Selection for root traits is hampered by difficulty in phenotypic measurements. Mapping quantitative trait loci (QTLs) for root traits and their use in marker assisted breeding (MAB) will hasten the development of genotypes with improved root system. Consistent QTLs for root traits have been mapped in rice. Developing and testing near iso-genic lines (NILs) with QTLs for root traits in target populations of environment (TPE) will help to verify the agronomic value of the QTLs. NILs were developed by introgression of three root QTLs from CT9993, an upland japonica into IR20, a lowland indica cultivar through MAB. Considerable variation in drought response and grain yield under rainfed condition in TPE was observed among the NILs. Five out of 41 NILs gave higher yields under rain-fed and irrigated conditions as compared to IR20. Two NILs viz., 212 and 297, with three and two root QTLs, respectively had thicker and longer nodal roots and higher total and deep nodal root weights than IR20. In addition, NIL 297 had more nodal root volume and surface area, while NIL 212 had more number of nodal roots compared to IR20. Further evaluation of the NILs with farmers for yield and grain quality may help in identification of high-yielding, resilient rice suitable for drought-prone rainfed ecosystems. The NILs may also be useful to study the genes underlying the QTLs and their functions for drought resilience improvement in rice.
An experiment was undertaken to identify heterotic rice hybrids for aerobic condition based on ph... more An experiment was undertaken to identify heterotic rice hybrids for aerobic condition based on physiological and root characters associated with water stress tolerance in rice. Panicle harvest index, a substitute for spikelet fertility is used as a secondary trait in the selection of drought tolerant genotypes. Deep roots are required to explore the soil profile for effectively absorbing water at deeper layers. A cultivar which partitions more of its dry weight in root can explore more soil volume for extracting water and thus can effectively sustain drought. Four hybrids viz., IR 68885A / IR 73718-3-1-3-3, IR 67684A / CT-6510-24-1-2, IR 70369A / IR 73718-3-1-3-3 and IR 70372A/ PSBRC 80 exhibited heterotic vigour for yield and maximum number of yield components and showed better adaptability to aerobic conditions. These hybrids can be commercially exploited under aerobic condition.
Background: Whole genome sequencing provides the most comprehensive collection of an organism's g... more Background: Whole genome sequencing provides the most comprehensive collection of an organism's genetic information. The availability of complete genome sequences is expected to dramatically deliver a high impact on biology. However, to achieve this impact in the area of crop improvement, significant efforts are still required on functional genomics, including the areas of gene annotation, cloning, expression profiling, and functional validation.
Background SWEET (MtN3_saliva) domain proteins, a recently identified group of efflux transporter... more Background SWEET (MtN3_saliva) domain proteins, a recently identified group of efflux transporters, play an indispensable role in sugar efflux, phloem loading, plant-pathogen interaction and reproductive tissue development. The SWEET gene family is predominantly studied in Arabidopsis and members of the family are being investigated in rice. To date, no transcriptome or genomics analysis of soybean SWEET genes has been reported. Results In the present investigation, we explored the evolutionary aspect of the SWEET gene family in diverse plant species including primitive single cell algae to angiosperms with a major emphasis on Glycine max. Evolutionary features showed expansion and duplication of the SWEET gene family in land plants. Homology searches with BLAST tools and Hidden Markov Model-directed sequence alignments identified 52 SWEET genes that were mapped to 15 chromosomes in the soybean genome as tandem duplication events. Soybean SWEET (GmSWEET) genes showed a wide range of...
Circadian clocks are a great evolutionary innovation and provide competitive advantage during the... more Circadian clocks are a great evolutionary innovation and provide competitive advantage during the day/night cycle and under changing environmental conditions. The circadian clock mediates expression of a large proportion of genes in plants, achieving a harmonious relationship between energy metabolism, photosynthesis, and biotic and abiotic stress responses. Here it is shown that multiple paralogues of clock genes are present in soybean (Glycine max) and mediate flooding and drought responses. Differential expression of many clock and SUB1 genes was found under flooding and drought conditions. Furthermore, natural variation in the amplitude and phase shifts in PRR7 and TOC1 genes was also discovered under drought and flooding conditions, respectively. PRR3 exhibited flooding- and drought-specific splicing patterns and may work in concert with PRR7 and TOC1 to achieve energy homeostasis under flooding and drought conditions. Higher expression of TOC1 also coincides with elevated leve...
Root system architecture is important in soybean to improve the acquisition and use efficiency of... more Root system architecture is important in soybean to improve the acquisition and use efficiency of water and nutrients in resource limited growing environments. Root architectural traits are very desirable to govern avoidance mechanisms under drought stress conditions. Due to the complexities involved with root phenotyping, limited efforts have been made to improve the genetic potential of soybean root traits. We developed few root screening phenotyping platforms to study root development and its plasticity in soybean. Quantitative Trait Loci (QTL) research on soybean intra-specific populations have identified few root QTLs, but none of them have identified key genes involved in regulating root architectural traits. Moreover, the genetic potential available in wild soybean, Glycine soja, has not been employed to improve root system architecture in cultivated soybean. Rare and conserved non-synonymous Single Nucleotide Polymorphism (SNP) alleles specific to wild soybeans for root arch...
Background: Drought stress is a major limitation to rainfed rice production and yield stability. ... more Background: Drought stress is a major limitation to rainfed rice production and yield stability. Identifying yield-associated quantitative trait loci (QTLs) that are consistent under drought stress predominant in target production environments, as well as across different genetic backgrounds, will help to develop high-yielding rice cultivars suitable for water-limited environments through marker-assisted breeding (MAB). Considerable progress has been made in mapping QTLs for drought resistance traits in rice; however, few have been successfully used in MAB. Results: Recombinant inbred lines of IR20 × Nootripathu, two indica cultivars adapted to rainfed target populations of environments (TPEs), were evaluated in one and two seasons under managed stress and in a rainfed target drought stress environment, respectively. In the managed stress environment, the severity of the stress meant that measurements could be made only on secondary traits and biomass. In the target environment, the lines experienced varying timings, durations, and intensities of drought stress. The rice recombinant inbred lines exhibited significant genotypic variation for physio-morphological, phenological, and plant production traits under drought. Nine and 24 QTLs for physio-morphological and plant production traits were identified in managed and natural drought stress conditions in the TPEs, respectively. Yield QTLs that were consistent in the target environment over seasons were identified on chromosomes 1, 4, and 6, which could stabilize the productivity in high-yielding rice lines in a water-limited rainfed ecosystem. These yield QTLs also govern highly heritable key secondary traits, such as leaf drying, canopy temperature, panicle harvest index and harvest index.
Journal of integrative plant biology, Jan 14, 2015
Limited information available for soybean root traits and their plasticity under drought stress. ... more Limited information available for soybean root traits and their plasticity under drought stress. To date, no studies have focused on examining diverse soybean germplasm for regulation of shoot and root response under water limited conditions across varying soil types. In this study, 17 genetically diverse soybean germplasm lines were selected to study root response to water limited conditions in clay (trial 1) and sandy soil (trial 2) in two target environments. Physiological data on shoot traits, phenotypic root traits, and biomass accumulation was measured at multiple crop stages ranging from early vegetative to pod filling. In trial 1, the number of lateral roots and forks were positively correlated with plot yield under water limitation and in trial 2, lateral root thickness was positively correlated with the hill plot yield. Plant Introduction (PI) 578477A and 088444 were found to have higher later root number and forks in clay soil with higher yield under water limitation. In ...
Cultivated soybean (Glycine max L.) cv. Dunbar (PI 552538) and wild G. soja (PI 326582A) exhibite... more Cultivated soybean (Glycine max L.) cv. Dunbar (PI 552538) and wild G. soja (PI 326582A) exhibited significant differences in root architecture and root-related traits. In this study, phenotypic variability for root traits among 251 BC 2 F 5 backcross inbred lines (BILs) developed from the cross Dunbar/PI 326582A were identified. The root systems of the parents and BILs were evaluated in controlled environmental conditions using a cone system at seedling stage. The G. max parent Dunbar contributed phenotypically favorable alleles at a major quantitative trait locus on chromosome 8 (Satt315-I locus) that governed root traits (tap root length and lateral root number) and shoot length. This QTL accounted for >10% of the phenotypic variation of both tap root and shoot length. This QTL region was found to control various shoot-and root-related traits across soybean genetic backgrounds. Within the confidence interval of this region, eleven transcription factors (TFs) were identified. Based on RNA sequencing and Affymetrix expression data, key TFs including MYB, AP2-EREBP and bZIP TFs were identified in this QTL interval with high expression in roots and nodules. The backcross inbred lines with different parental allelic combination showed different expression pattern for six transcription factors selected based on their expression pattern in root tissues. It appears that the marker interval Satt315-I locus on chromosome 8 contain an essential QTL contributing to early root and shoot growth in soybean.
Background: Root system architecture is important for water acquisition and nutrient acquisition ... more Background: Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed composition traits, but have never been investigated to improve root system architecture. Therefore, in this study, high-density single-feature polymorphic markers and simple sequence repeats were used to map quantitative trait loci (QTLs) governing root system architecture in an inter-specific soybean mapping population developed from a cross between Glycine max and Glycine soja.
Small RNAs are ubiquitous, versatile repressors and include (1) microRNAs (miRNAs), processed fro... more Small RNAs are ubiquitous, versatile repressors and include (1) microRNAs (miRNAs), processed from mRNA forming stem-loops; and (2) small interfering RNAs (siRNAs), the latter derived in plants by a process typically requiring an RNA-dependent RNA polymerase. We constructed and analyzed an expression atlas of soybean (Glycine max) small RNAs, identifying over 500 loci generating 21-nucleotide phased siRNAs (phasiRNAs; from PHAS loci), of which 483 overlapped annotated protein-coding genes. Via the integration of miRNAs with parallel analysis of RNA end (PARE) data, 20 miRNA triggers of 127 PHAS loci were detected. The primary class of PHAS loci (208 or 41% of the total) corresponded to NB-LRR genes; some of these small RNAs preferentially accumulate in nodules. Among the PHAS loci, novel representatives of TAS3 and noncanonical phasing patterns were also observed. A noncoding PHAS locus, triggered by miR4392, accumulated preferentially in anthers; the phasiRNAs are predicted to targ...
Many sources of drought and flooding tolerance have been identified in soybean, however underlyin... more Many sources of drought and flooding tolerance have been identified in soybean, however underlying molecular and physiological mechanisms are poorly understood. Therefore, it is important to illuminate different plant responses to these abiotic stresses and understand the mechanisms that confer tolerance. Towards this goal we used four contrasting soybean (Glycine max) genotypes (PI 567690 e drought tolerant, Pana e drought susceptible, PI 408105A e flooding tolerant, S99-2281 e flooding susceptible) grown under greenhouse conditions and compared genotypic responses to drought and flooding at the physiological, biochemical, and cellular level. We also quantified these variations and tried to infer their role in drought and flooding tolerance in soybean. Our results revealed that different mechanisms contribute to reduction in net photosynthesis under drought and flooding stress. Under drought stress, ABA and stomatal conductance are responsible for reduced photosynthetic rate; while under flooding stress, accumulation of starch granules played a major role. Drought tolerant genotypes PI 567690 and PI 408105A had higher plastoglobule numbers than the susceptible Pana and S99-2281. Drought stress increased the number and size of plastoglobules in most of the genotypes pointing to a possible role in stress tolerance. Interestingly, there were seven fibrillin proteins localized within the plastoglobules that were up-regulated in the drought and flooding tolerant genotypes PI 567690 and PI 408105A, respectively, but down-regulated in the drought susceptible genotype Pana. These results suggest a potential role of Fibrillin proteins, FBN1a, 1b and 7a in soybean response to drought and flooding stress.
Soybean production is greatly influenced by abiotic stresses imposed by environmental factors suc... more Soybean production is greatly influenced by abiotic stresses imposed by environmental factors such as drought, water submergence, salt, and heavy metals. A thorough understanding of plant response to abiotic stress at the molecular level is a prerequisite for its effective management. The molecular mechanism of stress tolerance is complex and requires information at the omic level to understand it effectively. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. The emerging field of ionomics is also being employed for investigating abiotic stress tolerance in soybean. Omic approaches generate a huge amount of data, and adequate advancements in computational tools have been achieved for effective analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. In this review, we have described advances in omic tools in the view of conventional and modern approaches being used to dissect abiotic stress tolerance in soybean. Emphasis was given to approaches such as quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). Comparative genomics and candidate gene approaches are also discussed considering identification of potential genomic loci, genes, and biochemical pathways involved in stress tolerance mechanism in soybean. This review also provides a comprehensive catalog of available online omic resources for soybean and its effective utilization. We have also addressed the significance of phenomics in the integrated approaches and recognized high-throughput multi-dimensional phenotyping as a major limiting factor for the improvement of abiotic stress tolerance in soybean.
This study was to estimate the GCA of the parents and SCA considered for the development of high ... more This study was to estimate the GCA of the parents and SCA considered for the development of high yielding and better quality cultivars. Eleven genotypes and 28 F 1 hybrids obtained by crossing 4 lines and 7 testers in line X tester mating system were sown in randomized complete block design. L X T analysis revealed significant GCA and SCA effects for all the traits except earliness. Among the parents: MCU 12 for number of bolls per plant, boll weight, seed cotton yield per plant, F 1861 for seed cotton yield and number of bolls per plant, SOCC 17 for earliness, SURABHI for number of sympodia and TCH 1641 for ginning outturn and lint index with high GCA. Parent F 776 and F1861 were good combiners for fibre quality traits. The high yielding quality hybrids were deducted with significant SCA effects for seed cotton yield and fibre characteristics.
Sampling the sequence of a relatively small fraction of the genome in large numbers of individual... more Sampling the sequence of a relatively small fraction of the genome in large numbers of individuals is an important objective for population genetics and association genetics approaches. However, currently available 'sequence capture' methods either require expensive instrumentation or have problems dealing with high sample numbers and relatively small target sizes. We have developed Genome-Tagged Amplification (GTA) as a flexible PCR-based method for preparing pools of hundreds of amplicons from hundreds of samples for next generation sequencing. The method involves tagging of genomic DNA with barcode adapters at restriction sites, followed by PCR amplification from flanking DNA. It is freely scalable for both sample number and amplicon number and has no specialized equipment requirement. An optimized protocol is presented which provides a matrix of 96 9 192 combinations of samples x amplicons, corresponding to a complete 454 Titanium run. Initially, we used 454 sequencing; however, GTA could easily be adapted to Illumina sequencing platforms as read lengths have significantly increased in this system.
Drought stress is the major constraint in rainfed rice production. Deep and thick roots are thoug... more Drought stress is the major constraint in rainfed rice production. Deep and thick roots are thought to contribute in drought resilience. Selection for root traits is hampered by difficulty in phenotypic measurements. Mapping quantitative trait loci (QTLs) for root traits and their use in marker assisted breeding (MAB) will hasten the development of genotypes with improved root system. Consistent QTLs for root traits have been mapped in rice. Developing and testing near iso-genic lines (NILs) with QTLs for root traits in target populations of environment (TPE) will help to verify the agronomic value of the QTLs. NILs were developed by introgression of three root QTLs from CT9993, an upland japonica into IR20, a lowland indica cultivar through MAB. Considerable variation in drought response and grain yield under rainfed condition in TPE was observed among the NILs. Five out of 41 NILs gave higher yields under rain-fed and irrigated conditions as compared to IR20. Two NILs viz., 212 and 297, with three and two root QTLs, respectively had thicker and longer nodal roots and higher total and deep nodal root weights than IR20. In addition, NIL 297 had more nodal root volume and surface area, while NIL 212 had more number of nodal roots compared to IR20. Further evaluation of the NILs with farmers for yield and grain quality may help in identification of high-yielding, resilient rice suitable for drought-prone rainfed ecosystems. The NILs may also be useful to study the genes underlying the QTLs and their functions for drought resilience improvement in rice.
An experiment was undertaken to identify heterotic rice hybrids for aerobic condition based on ph... more An experiment was undertaken to identify heterotic rice hybrids for aerobic condition based on physiological and root characters associated with water stress tolerance in rice. Panicle harvest index, a substitute for spikelet fertility is used as a secondary trait in the selection of drought tolerant genotypes. Deep roots are required to explore the soil profile for effectively absorbing water at deeper layers. A cultivar which partitions more of its dry weight in root can explore more soil volume for extracting water and thus can effectively sustain drought. Four hybrids viz., IR 68885A / IR 73718-3-1-3-3, IR 67684A / CT-6510-24-1-2, IR 70369A / IR 73718-3-1-3-3 and IR 70372A/ PSBRC 80 exhibited heterotic vigour for yield and maximum number of yield components and showed better adaptability to aerobic conditions. These hybrids can be commercially exploited under aerobic condition.
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Papers by Silvas Prince