Root architecture critically influences a plant’s ability to forage for nutrients and water in so... more Root architecture critically influences a plant’s ability to forage for nutrients and water in soil. In this issue of Cell, Ogura et al. (2019) report a new regulatory gene and elegant molecular mechanism that links auxin-dependent root-angle regulation with improved plant fitness under variable rainfall conditions.
Phosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive me... more Phosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive mechanisms to forage for P in soil. Root hair elongation is particularly important since P is immobile. Here we report that auxin plays a critical role promoting root hair growth in Arabidopsis in response to low external P. Mutants disrupting auxin synthesis (taa1) andtransport (aux1) attenuate the low P root hair response. Conversely, targeting AUX1 expression in lateral root cap and epidermal cells rescues this low P response in aux1. Hence auxin transport from the root apex to differentiation zone promotes auxin-dependent hair response to low P. Low external P results in induction of root hair expressed auxin-inducible transcription factors ARF19, RSL2, and RSL4. Mutants lacking these genes disrupt the low P root hair response. We conclude auxin synthesis, transport and response pathway components play critical roles regulating this low P root adaptive response.
Root traits such as root angle and hair length influence resource acquisition particularly for im... more Root traits such as root angle and hair length influence resource acquisition particularly for immobile nutrients like phosphorus (P). Here, we attempted to modify root angle in rice by disrupting the OsAUX1 auxin influx transporter gene in an effort to improve rice P acquisition efficiency. We show by X-ray microCT imaging that root angle is altered in the osaux1 mutant, causing preferential foraging in the top soil where P normally accumulates, yet surprisingly, P acquisition efficiency does not improve. Through closer investigation, we reveal that OsAUX1 also promotes root hair elongation in response to P limitation. Reporter studies reveal that auxin response increases in the root hair zone in low P environments. We demonstrate that OsAUX1 functions to mobilize auxin from the root apex to the differentiation zone where this signal promotes hair elongation when roots encounter low external P. We conclude that auxin and OsAUX1 play key roles in promoting root foraging for P in rice.
Root angle has a major impact on acquisition of nutrients like phosphate that accumulate in topso... more Root angle has a major impact on acquisition of nutrients like phosphate that accumulate in topsoil and in many species; low phosphate induces shallower root growth as an adaptive response. Identifying genes and mechanisms controlling root angle is therefore of paramount importance to plant breeding. Here we show that the actin-binding protein Rice Morphology Determinant (RMD) controls root growth angle by linking actin filaments and gravity-sensing organelles termed statoliths. RMD is upregulated in response to low external phosphate and mutants lacking of RMD have steeper crown root growth angles that are unresponsive to phosphate levels. RMD protein localizes to the surface of statoliths, and rmd mutants exhibit faster gravitropic response owing to more rapid statoliths movement. We conclude that adaptive changes to root angle in response to external phosphate availability are RMD dependent, providing a potential target for breeders.
Diverse environmental stimuli largely affect the ionic balance of soil, which have a direct effec... more Diverse environmental stimuli largely affect the ionic balance of soil, which have a direct effect on growth and crop yield. Details are fast emerging on the genetic/molecular regulators, at whole-genome levels, of plant responses to mineral deficiencies in model and crop plants. These genetic regulators determine the root architecture and physiological adaptations for better uptake and utilization of minerals from soil. Recent evidence also shows the potential roles of epigenetic mechanisms in gene regulation, driven by minerals imbalance. Mineral deficiency or sufficiency leads to developmental plasticity in plants for adaptation, which is preceded by a change in the pattern of gene expression. Notably, such changes at molecular levels are also influenced by altered chromatin structure and methylation patterns, or involvement of other epigenetic components. Interestingly, many of the changes induced by mineral deficiency are also inheritable in the form of epigenetic memory. Unravelling these mechanisms in response to mineral deficiency would further advance our understanding of this complex plant response. Further studies on such approaches may serve as an exciting interaction model of epigenetic and genetic regulations of mineral homeostasis in plants and designing strategies for crop improvement.
Phosphorus (P) is one of the most essential nutrients for the adequate growth and
development of ... more Phosphorus (P) is one of the most essential nutrients for the adequate growth and development of plants as well as a crucial component of all life forms. Plants absorb P only in the inorganic form of orthophosphate (Pi). The availability of soluble Pi in most of the world’s soil is poor as compared to its requirement for optimum growth and crop yield. Application of P fertilizers is a common practice to grow crop plants in P-poor soils. However, highly reactive Pi easily forms insoluble complexes in soil and a large fraction of applied Pi fertilizer becomes unavailable to plants. This problem is further compounded as the source of P fertilizers (i.e., P rocks) may be exhausted in the near future. Plants have evolved physiologically, biochemically, and morphologically to cope with Pi starvation through modification of the root system architecture for better Pi uptake and remobilize the internal Pi content. Genetic regulation of these adaptations has been explored to some extent and thus provides the resource for crop improvement using transgenics or plant breeding. This complex network is regulated by transcription factors, microRNAs, membrane transporters, kinases/phosphatases, ubiquitin conjugase, and various hormones. Sugars have also been shown to play important roles in Pi starvationmediated gene expression. Here, we review the recent progress made in delineating the functions of genetic elements in terms of modulating the Pi starvation response in plants. We further explore the possible strategies for crop improvement using available resources.
Jasmonates (JA) are well-known phytohormones which play important roles in plant
development and ... more Jasmonates (JA) are well-known phytohormones which play important roles in plant development and defense against pathogens. Jasmonate ZIM domain (JAZ) proteins are plant-specific proteins and act as transcriptional repressors of JA-responsive genes. JA regulates both biotic and abiotic stress responses in plants; however, its role in nutrient deficiency responses is very elusive. Although, JA is well-known for root growth inhibition, little is known about behavior of JAZ genes in response to nutrient deficiencies, under which root architectural alteration is an important adaptation. Using protein sequence homology and a conserved-domains approach, here we identify 10 novel JAZ genes from the recently sequenced Chickpea genome, which is one of the most nutrient efficient crops. Both rice and chickpea JAZ genes express in tissue- and stimuli-specific manners. Many of which are preferentially expressed in root. Our analysis further showed differential expression of JAZ genes under macro (NPK) and micronutrients (Zn, Fe) deficiency in rice and chickpea roots. While both rice and chickpea JAZ genes showed a certain level of specificity toward type of nutrient deficiency, generally majority of them showed induction under K deficiency. Generally, JAZ genes showed an induction at early stages of stress and expression declined at later stages of macro-nutrient deficiency. Our results suggest that JAZ genes might play a role in early nutrient deficiency response both in monocot and dicot roots, and information generated here can be further used for understanding the possible roles of JA in root architectural alterations for nutrient deficiency adaptations
Phosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes
are se... more Phosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes are sensitive to Pi deficiency whereas traditional rice genotypes are naturally compatible with low Pi ecosystems. However, the underlying molecular mechanisms for low Pi tolerance in traditional genotypes remain largely elusive. To delineate the molecular mechanisms for low Pi tolerance, two contrasting rice genotypes, Dular (low Pi tolerant), and PB1 (low Pi sensitive), have been selected. Comparative morphophysiological, global transcriptome and lipidome analyses of root and shoot tissues of both genotypes grown under Pi deficient and sufficient conditions revealed potential low Pi tolerance mechanisms of the traditional genotype. Most of the genes associated with enhanced internal Pi utilization (phospholipid remobilization) and modulation of root system architecture (RSA) were highly induced in the traditional rice genotype, Dular. Higher reserves of phospholipids and greater accumulation of galactolipids under low Pi in Dular indicated it has more efficient Pi utilization. Furthermore, Dular also maintained greater root growth than PB1 under low Pi, resulting in larger root surface area due to increased lateral root density and root hair length. Genes involved in enhanced low Pi tolerance of the traditional genotype can be exploited to improve the low Pi tolerance of modern high yielding rice cultivars.
Soil Phosphorus (P) deficiency is one of the major challenges to rice crop world-wide. Modern ric... more Soil Phosphorus (P) deficiency is one of the major challenges to rice crop world-wide. Modern rice genotypes are highly P-responsive and rely on high input of P fertilizers. However, low P tolerant traditional cultivars and landraces have genetic potential to sustain well under low P. Identification of high resolution DNA polymorphisms (SNPs and InDels) in such contrasting genotypes is largely missing for low P response at gene levels. Here, we report high quality DNA polymorphisms in low P sensitive genotype, PB1 and tolerant traditional genotype, Dular. We performed whole genome resequencing using Illumina NGS platform and identified a total of 5,157,939 sequence variants in PB1 and Dular with reference to Nipponbare genome. We have identified approximately 2.3 million and 2.9 million high quality polymorphisms in PB1 and Dular, respectively, with an average read depth of ≥24X. We further mapped several DNA polymorphisms (non-synonymous and regulatory variants) having potential functional significance to key Phosphate Starvation Responsive (PSR) and root architecture genes in Dular and Kasalath using a compiled list of low P responsive genes. These identified variants can serve as a useful source of genetic variability for improving low P tolerance and root architecture of high yielding modern genotypes
Root architecture critically influences a plant’s ability to forage for nutrients and water in so... more Root architecture critically influences a plant’s ability to forage for nutrients and water in soil. In this issue of Cell, Ogura et al. (2019) report a new regulatory gene and elegant molecular mechanism that links auxin-dependent root-angle regulation with improved plant fitness under variable rainfall conditions.
Phosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive me... more Phosphate (P) is an essential macronutrient for plant growth. Roots employ adaptive mechanisms to forage for P in soil. Root hair elongation is particularly important since P is immobile. Here we report that auxin plays a critical role promoting root hair growth in Arabidopsis in response to low external P. Mutants disrupting auxin synthesis (taa1) andtransport (aux1) attenuate the low P root hair response. Conversely, targeting AUX1 expression in lateral root cap and epidermal cells rescues this low P response in aux1. Hence auxin transport from the root apex to differentiation zone promotes auxin-dependent hair response to low P. Low external P results in induction of root hair expressed auxin-inducible transcription factors ARF19, RSL2, and RSL4. Mutants lacking these genes disrupt the low P root hair response. We conclude auxin synthesis, transport and response pathway components play critical roles regulating this low P root adaptive response.
Root traits such as root angle and hair length influence resource acquisition particularly for im... more Root traits such as root angle and hair length influence resource acquisition particularly for immobile nutrients like phosphorus (P). Here, we attempted to modify root angle in rice by disrupting the OsAUX1 auxin influx transporter gene in an effort to improve rice P acquisition efficiency. We show by X-ray microCT imaging that root angle is altered in the osaux1 mutant, causing preferential foraging in the top soil where P normally accumulates, yet surprisingly, P acquisition efficiency does not improve. Through closer investigation, we reveal that OsAUX1 also promotes root hair elongation in response to P limitation. Reporter studies reveal that auxin response increases in the root hair zone in low P environments. We demonstrate that OsAUX1 functions to mobilize auxin from the root apex to the differentiation zone where this signal promotes hair elongation when roots encounter low external P. We conclude that auxin and OsAUX1 play key roles in promoting root foraging for P in rice.
Root angle has a major impact on acquisition of nutrients like phosphate that accumulate in topso... more Root angle has a major impact on acquisition of nutrients like phosphate that accumulate in topsoil and in many species; low phosphate induces shallower root growth as an adaptive response. Identifying genes and mechanisms controlling root angle is therefore of paramount importance to plant breeding. Here we show that the actin-binding protein Rice Morphology Determinant (RMD) controls root growth angle by linking actin filaments and gravity-sensing organelles termed statoliths. RMD is upregulated in response to low external phosphate and mutants lacking of RMD have steeper crown root growth angles that are unresponsive to phosphate levels. RMD protein localizes to the surface of statoliths, and rmd mutants exhibit faster gravitropic response owing to more rapid statoliths movement. We conclude that adaptive changes to root angle in response to external phosphate availability are RMD dependent, providing a potential target for breeders.
Diverse environmental stimuli largely affect the ionic balance of soil, which have a direct effec... more Diverse environmental stimuli largely affect the ionic balance of soil, which have a direct effect on growth and crop yield. Details are fast emerging on the genetic/molecular regulators, at whole-genome levels, of plant responses to mineral deficiencies in model and crop plants. These genetic regulators determine the root architecture and physiological adaptations for better uptake and utilization of minerals from soil. Recent evidence also shows the potential roles of epigenetic mechanisms in gene regulation, driven by minerals imbalance. Mineral deficiency or sufficiency leads to developmental plasticity in plants for adaptation, which is preceded by a change in the pattern of gene expression. Notably, such changes at molecular levels are also influenced by altered chromatin structure and methylation patterns, or involvement of other epigenetic components. Interestingly, many of the changes induced by mineral deficiency are also inheritable in the form of epigenetic memory. Unravelling these mechanisms in response to mineral deficiency would further advance our understanding of this complex plant response. Further studies on such approaches may serve as an exciting interaction model of epigenetic and genetic regulations of mineral homeostasis in plants and designing strategies for crop improvement.
Phosphorus (P) is one of the most essential nutrients for the adequate growth and
development of ... more Phosphorus (P) is one of the most essential nutrients for the adequate growth and development of plants as well as a crucial component of all life forms. Plants absorb P only in the inorganic form of orthophosphate (Pi). The availability of soluble Pi in most of the world’s soil is poor as compared to its requirement for optimum growth and crop yield. Application of P fertilizers is a common practice to grow crop plants in P-poor soils. However, highly reactive Pi easily forms insoluble complexes in soil and a large fraction of applied Pi fertilizer becomes unavailable to plants. This problem is further compounded as the source of P fertilizers (i.e., P rocks) may be exhausted in the near future. Plants have evolved physiologically, biochemically, and morphologically to cope with Pi starvation through modification of the root system architecture for better Pi uptake and remobilize the internal Pi content. Genetic regulation of these adaptations has been explored to some extent and thus provides the resource for crop improvement using transgenics or plant breeding. This complex network is regulated by transcription factors, microRNAs, membrane transporters, kinases/phosphatases, ubiquitin conjugase, and various hormones. Sugars have also been shown to play important roles in Pi starvationmediated gene expression. Here, we review the recent progress made in delineating the functions of genetic elements in terms of modulating the Pi starvation response in plants. We further explore the possible strategies for crop improvement using available resources.
Jasmonates (JA) are well-known phytohormones which play important roles in plant
development and ... more Jasmonates (JA) are well-known phytohormones which play important roles in plant development and defense against pathogens. Jasmonate ZIM domain (JAZ) proteins are plant-specific proteins and act as transcriptional repressors of JA-responsive genes. JA regulates both biotic and abiotic stress responses in plants; however, its role in nutrient deficiency responses is very elusive. Although, JA is well-known for root growth inhibition, little is known about behavior of JAZ genes in response to nutrient deficiencies, under which root architectural alteration is an important adaptation. Using protein sequence homology and a conserved-domains approach, here we identify 10 novel JAZ genes from the recently sequenced Chickpea genome, which is one of the most nutrient efficient crops. Both rice and chickpea JAZ genes express in tissue- and stimuli-specific manners. Many of which are preferentially expressed in root. Our analysis further showed differential expression of JAZ genes under macro (NPK) and micronutrients (Zn, Fe) deficiency in rice and chickpea roots. While both rice and chickpea JAZ genes showed a certain level of specificity toward type of nutrient deficiency, generally majority of them showed induction under K deficiency. Generally, JAZ genes showed an induction at early stages of stress and expression declined at later stages of macro-nutrient deficiency. Our results suggest that JAZ genes might play a role in early nutrient deficiency response both in monocot and dicot roots, and information generated here can be further used for understanding the possible roles of JA in root architectural alterations for nutrient deficiency adaptations
Phosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes
are se... more Phosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes are sensitive to Pi deficiency whereas traditional rice genotypes are naturally compatible with low Pi ecosystems. However, the underlying molecular mechanisms for low Pi tolerance in traditional genotypes remain largely elusive. To delineate the molecular mechanisms for low Pi tolerance, two contrasting rice genotypes, Dular (low Pi tolerant), and PB1 (low Pi sensitive), have been selected. Comparative morphophysiological, global transcriptome and lipidome analyses of root and shoot tissues of both genotypes grown under Pi deficient and sufficient conditions revealed potential low Pi tolerance mechanisms of the traditional genotype. Most of the genes associated with enhanced internal Pi utilization (phospholipid remobilization) and modulation of root system architecture (RSA) were highly induced in the traditional rice genotype, Dular. Higher reserves of phospholipids and greater accumulation of galactolipids under low Pi in Dular indicated it has more efficient Pi utilization. Furthermore, Dular also maintained greater root growth than PB1 under low Pi, resulting in larger root surface area due to increased lateral root density and root hair length. Genes involved in enhanced low Pi tolerance of the traditional genotype can be exploited to improve the low Pi tolerance of modern high yielding rice cultivars.
Soil Phosphorus (P) deficiency is one of the major challenges to rice crop world-wide. Modern ric... more Soil Phosphorus (P) deficiency is one of the major challenges to rice crop world-wide. Modern rice genotypes are highly P-responsive and rely on high input of P fertilizers. However, low P tolerant traditional cultivars and landraces have genetic potential to sustain well under low P. Identification of high resolution DNA polymorphisms (SNPs and InDels) in such contrasting genotypes is largely missing for low P response at gene levels. Here, we report high quality DNA polymorphisms in low P sensitive genotype, PB1 and tolerant traditional genotype, Dular. We performed whole genome resequencing using Illumina NGS platform and identified a total of 5,157,939 sequence variants in PB1 and Dular with reference to Nipponbare genome. We have identified approximately 2.3 million and 2.9 million high quality polymorphisms in PB1 and Dular, respectively, with an average read depth of ≥24X. We further mapped several DNA polymorphisms (non-synonymous and regulatory variants) having potential functional significance to key Phosphate Starvation Responsive (PSR) and root architecture genes in Dular and Kasalath using a compiled list of low P responsive genes. These identified variants can serve as a useful source of genetic variability for improving low P tolerance and root architecture of high yielding modern genotypes
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development of plants as well as a crucial component of all life forms. Plants absorb
P only in the inorganic form of orthophosphate (Pi). The availability of soluble Pi in
most of the world’s soil is poor as compared to its requirement for optimum
growth and crop yield. Application of P fertilizers is a common practice to grow
crop plants in P-poor soils. However, highly reactive Pi easily forms insoluble
complexes in soil and a large fraction of applied Pi fertilizer becomes unavailable to
plants. This problem is further compounded as the source of P fertilizers (i.e., P
rocks) may be exhausted in the near future. Plants have evolved physiologically,
biochemically, and morphologically to cope with Pi starvation through modification
of the root system architecture for better Pi uptake and remobilize the internal Pi
content. Genetic regulation of these adaptations has been explored to some extent
and thus provides the resource for crop improvement using transgenics or plant
breeding. This complex network is regulated by transcription factors, microRNAs,
membrane transporters, kinases/phosphatases, ubiquitin conjugase, and various
hormones. Sugars have also been shown to play important roles in Pi starvationmediated
gene expression. Here, we review the recent progress made in
delineating the functions of genetic elements in terms of modulating the Pi
starvation response in plants. We further explore the possible strategies for crop
improvement using available resources.
development and defense against pathogens. Jasmonate ZIM domain (JAZ) proteins are
plant-specific proteins and act as transcriptional repressors of JA-responsive genes. JA
regulates both biotic and abiotic stress responses in plants; however, its role in nutrient
deficiency responses is very elusive. Although, JA is well-known for root growth inhibition,
little is known about behavior of JAZ genes in response to nutrient deficiencies, under
which root architectural alteration is an important adaptation. Using protein sequence
homology and a conserved-domains approach, here we identify 10 novel JAZ genes
from the recently sequenced Chickpea genome, which is one of the most nutrient efficient
crops. Both rice and chickpea JAZ genes express in tissue- and stimuli-specific manners.
Many of which are preferentially expressed in root. Our analysis further showed differential
expression of JAZ genes under macro (NPK) and micronutrients (Zn, Fe) deficiency in rice
and chickpea roots. While both rice and chickpea JAZ genes showed a certain level of
specificity toward type of nutrient deficiency, generally majority of them showed induction
under K deficiency. Generally, JAZ genes showed an induction at early stages of stress
and expression declined at later stages of macro-nutrient deficiency. Our results suggest
that JAZ genes might play a role in early nutrient deficiency response both in monocot
and dicot roots, and information generated here can be further used for understanding
the possible roles of JA in root architectural alterations for nutrient deficiency adaptations
are sensitive to Pi deficiency whereas traditional rice genotypes are naturally compatible
with low Pi ecosystems. However, the underlying molecular mechanisms for low Pi
tolerance in traditional genotypes remain largely elusive. To delineate the molecular
mechanisms for low Pi tolerance, two contrasting rice genotypes, Dular (low Pi tolerant),
and PB1 (low Pi sensitive), have been selected. Comparative morphophysiological,
global transcriptome and lipidome analyses of root and shoot tissues of both genotypes
grown under Pi deficient and sufficient conditions revealed potential low Pi tolerance
mechanisms of the traditional genotype. Most of the genes associated with enhanced
internal Pi utilization (phospholipid remobilization) and modulation of root system
architecture (RSA) were highly induced in the traditional rice genotype, Dular. Higher
reserves of phospholipids and greater accumulation of galactolipids under low Pi in Dular
indicated it has more efficient Pi utilization. Furthermore, Dular also maintained greater
root growth than PB1 under low Pi, resulting in larger root surface area due to increased
lateral root density and root hair length. Genes involved in enhanced low Pi tolerance of
the traditional genotype can be exploited to improve the low Pi tolerance of modern high
yielding rice cultivars.
genotypes are highly P-responsive and rely on high input of P fertilizers. However, low P tolerant
traditional cultivars and landraces have genetic potential to sustain well under low P. Identification
of high resolution DNA polymorphisms (SNPs and InDels) in such contrasting genotypes is largely
missing for low P response at gene levels. Here, we report high quality DNA polymorphisms in low
P sensitive genotype, PB1 and tolerant traditional genotype, Dular. We performed whole genome
resequencing using Illumina NGS platform and identified a total of 5,157,939 sequence variants in
PB1 and Dular with reference to Nipponbare genome. We have identified approximately 2.3 million
and 2.9 million high quality polymorphisms in PB1 and Dular, respectively, with an average read
depth of ≥24X. We further mapped several DNA polymorphisms (non-synonymous and regulatory
variants) having potential functional significance to key Phosphate Starvation Responsive (PSR) and
root architecture genes in Dular and Kasalath using a compiled list of low P responsive genes. These
identified variants can serve as a useful source of genetic variability for improving low P tolerance
and root architecture of high yielding modern genotypes
development of plants as well as a crucial component of all life forms. Plants absorb
P only in the inorganic form of orthophosphate (Pi). The availability of soluble Pi in
most of the world’s soil is poor as compared to its requirement for optimum
growth and crop yield. Application of P fertilizers is a common practice to grow
crop plants in P-poor soils. However, highly reactive Pi easily forms insoluble
complexes in soil and a large fraction of applied Pi fertilizer becomes unavailable to
plants. This problem is further compounded as the source of P fertilizers (i.e., P
rocks) may be exhausted in the near future. Plants have evolved physiologically,
biochemically, and morphologically to cope with Pi starvation through modification
of the root system architecture for better Pi uptake and remobilize the internal Pi
content. Genetic regulation of these adaptations has been explored to some extent
and thus provides the resource for crop improvement using transgenics or plant
breeding. This complex network is regulated by transcription factors, microRNAs,
membrane transporters, kinases/phosphatases, ubiquitin conjugase, and various
hormones. Sugars have also been shown to play important roles in Pi starvationmediated
gene expression. Here, we review the recent progress made in
delineating the functions of genetic elements in terms of modulating the Pi
starvation response in plants. We further explore the possible strategies for crop
improvement using available resources.
development and defense against pathogens. Jasmonate ZIM domain (JAZ) proteins are
plant-specific proteins and act as transcriptional repressors of JA-responsive genes. JA
regulates both biotic and abiotic stress responses in plants; however, its role in nutrient
deficiency responses is very elusive. Although, JA is well-known for root growth inhibition,
little is known about behavior of JAZ genes in response to nutrient deficiencies, under
which root architectural alteration is an important adaptation. Using protein sequence
homology and a conserved-domains approach, here we identify 10 novel JAZ genes
from the recently sequenced Chickpea genome, which is one of the most nutrient efficient
crops. Both rice and chickpea JAZ genes express in tissue- and stimuli-specific manners.
Many of which are preferentially expressed in root. Our analysis further showed differential
expression of JAZ genes under macro (NPK) and micronutrients (Zn, Fe) deficiency in rice
and chickpea roots. While both rice and chickpea JAZ genes showed a certain level of
specificity toward type of nutrient deficiency, generally majority of them showed induction
under K deficiency. Generally, JAZ genes showed an induction at early stages of stress
and expression declined at later stages of macro-nutrient deficiency. Our results suggest
that JAZ genes might play a role in early nutrient deficiency response both in monocot
and dicot roots, and information generated here can be further used for understanding
the possible roles of JA in root architectural alterations for nutrient deficiency adaptations
are sensitive to Pi deficiency whereas traditional rice genotypes are naturally compatible
with low Pi ecosystems. However, the underlying molecular mechanisms for low Pi
tolerance in traditional genotypes remain largely elusive. To delineate the molecular
mechanisms for low Pi tolerance, two contrasting rice genotypes, Dular (low Pi tolerant),
and PB1 (low Pi sensitive), have been selected. Comparative morphophysiological,
global transcriptome and lipidome analyses of root and shoot tissues of both genotypes
grown under Pi deficient and sufficient conditions revealed potential low Pi tolerance
mechanisms of the traditional genotype. Most of the genes associated with enhanced
internal Pi utilization (phospholipid remobilization) and modulation of root system
architecture (RSA) were highly induced in the traditional rice genotype, Dular. Higher
reserves of phospholipids and greater accumulation of galactolipids under low Pi in Dular
indicated it has more efficient Pi utilization. Furthermore, Dular also maintained greater
root growth than PB1 under low Pi, resulting in larger root surface area due to increased
lateral root density and root hair length. Genes involved in enhanced low Pi tolerance of
the traditional genotype can be exploited to improve the low Pi tolerance of modern high
yielding rice cultivars.
genotypes are highly P-responsive and rely on high input of P fertilizers. However, low P tolerant
traditional cultivars and landraces have genetic potential to sustain well under low P. Identification
of high resolution DNA polymorphisms (SNPs and InDels) in such contrasting genotypes is largely
missing for low P response at gene levels. Here, we report high quality DNA polymorphisms in low
P sensitive genotype, PB1 and tolerant traditional genotype, Dular. We performed whole genome
resequencing using Illumina NGS platform and identified a total of 5,157,939 sequence variants in
PB1 and Dular with reference to Nipponbare genome. We have identified approximately 2.3 million
and 2.9 million high quality polymorphisms in PB1 and Dular, respectively, with an average read
depth of ≥24X. We further mapped several DNA polymorphisms (non-synonymous and regulatory
variants) having potential functional significance to key Phosphate Starvation Responsive (PSR) and
root architecture genes in Dular and Kasalath using a compiled list of low P responsive genes. These
identified variants can serve as a useful source of genetic variability for improving low P tolerance
and root architecture of high yielding modern genotypes