Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

/pdf/genome-sequence-of-the-palaeopolyploid-soybean-2s3cr5djfl.pdf

Genome sequence of the palaeopolyploid soybean

Contents
I. Introduction  424
II. The phosphorus conundrum 424
III. Adaptations to low P 424
IV. Uptake of P  424
V. P deficiency alters root development and function 426
VI. P deficiency modifies carbon metabolism 431
VII. Acid phosphatase 436
VIII. Genetic regulation of P responsive genes 437
IX. Improving P acquisition 439
X. Synopsis  440


Summary
Phosphorus (P) is limiting for crop yield on > 30% of the world's arable land and, by some estimates, world resources of inexpensive P may be depleted by 2050. Improvement of P acquisition and use by plants is critical for economic, humanitarian and environmental reasons. Plants have evolved a diverse array of strategies to obtain adequate P under limiting conditions, including modifications to root architecture, carbon metabolism and membrane structure, exudation of low molecular weight organic acids, protons and enzymes, and enhanced expression of the numerous genes involved in low-P adaptation. These adaptations may be less pronounced in mycorrhizal-associated plants. The formation of cluster roots under P-stress by the nonmycorrhizal species white lupin (Lupinus albus), and the accompanying biochemical changes exemplify many of the plant adaptations that enhance P acquisition and use. Physiological, biochemical, and molecular studies of white lupin and other species response to P-deficiency have identified targets that may be useful for plant improvement. Genomic approaches involving identification of expressed sequence tags (ESTs) found under low-P stress may also yield target sites for plant improvement. Interdisciplinary studies uniting plant breeding, biochemistry, soil science, and genetics under the large umbrella of genomics are prerequisite for rapid progress in improving nutrient acquisition and use in plants.

/pdf/phosphorus-acquisition-and-use-critical-adaptations-by-56im8qzi8m.pdf

Phosphorus acquisition and use: critical adaptations by plants for securing a nonrenewable resource

Contents

 Summary

I Introduction
II Variability of N : P ratios in response to nutrient  supply
III Critical N : P ratios as indicators of nutrient  limitation
IV Interspecific variation in N : P ratios
V Vegetation properties in relation to N : P ratios
VI Implications of N : P ratios for human impacts  on ecosystems
VII Conclusions

 Acknowledgements


 References



Summary
Nitrogen (N) and phosphorus (P) availability limit plant growth in most terrestrial ecosystems. This review examines how variation in the relative availability of N and P, as reflected by N : P ratios of plant biomass, influences vegetation composition and functioning. Plastic responses of plants to N and P supply cause up to 50-fold variation in biomass N : P ratios, associated with differences in root allocation, nutrient uptake, biomass turnover and reproductive output. Optimal N : P ratios – those of plants whose growth is equally limited by N and P – depend on species, growth rate, plant age and plant parts. At vegetation level, N : P ratios 20 often (not always) correspond to N- and P-limited biomass production, as shown by short-term fertilization experiments; however long-term effects of fertilization or effects on individual species can be different. N : P ratios are on average higher in graminoids than in forbs, and in stress-tolerant species compared with ruderals; they correlate negatively with the maximal relative growth rates of species and with their N-indicator values. At vegetation level, N : P ratios often correlate negatively with biomass production; high N : P ratios promote graminoids and stress tolerators relative to other species, whereas relationships with species richness are not consistent. N : P ratios are influenced by global change, increased atmospheric N deposition, and conservation managment.

https://nph.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1469-8137.2004.01192.x

N : P ratios in terrestrial plants: variation and functional significance

Phosphate (Pi) is considered to be one of the least available plant nutrients in the soil. High-affinity Pi transporters are generally accepted as entry points for Pi in the roots. The physiological, genetic, molecular and biochemical analysis of phosphate starvation response mechanisms highlight the ability of plants to adapt and thrive under phosphate limiting conditions. These responses help them enhance the availability of Pi, increase its uptake and improve the use-efficiency of Pi within a plant. Enhanced ability to acquire Pi appears to be regulated at the level of transcription of high-affinity phosphate transporters. These transporters are encoded by a family of small number of genes having characteristic tissue and organ associated expression patterns. Many of them are strongly induced during phosphate deficiency thus providing plants with enhanced ability to acquire and transfer phosphate. In addition, plants also activate biochemical mechanisms that could lead to increased acquisition of phosphate from both inorganic and organic phosphorus sources in the soil. Furthermore, altered root morphology and mycorrhizal symbiosis further enhance the ability of plants to acquire Pi. Interestingly most of these responses appear to be coordinated by changes in cellular phosphate levels. It is becoming apparent that phosphate acquisition and utilization are associated with activation or inactivation of a host of genes in plants. In this article we describe molecular, biochemical and physiological factors associated with phosphate acquisition by plants.

Phosphate Acquisition

As the result of intensive research and breeding efforts over the last 20 years, the yield potential and yield quality of cereals have been greatly improved. Nowadays, yield safety has gained more importance because of the forecasted climatic changes. Drought and high temperature are especially considered as key stress factors with high potential impact on crop yield. Yield safety can only be improved if future breeding attempts will be based on the valuable new knowledge acquired on the processes determining plant development and its responses to stress. Plant stress responses are very complex. Interactions between plant structure, function and the environment need to be investigated at various phases of plant development at the organismal, cellular as well as molecular levels in order to obtain a full picture. The results achieved so far in this field indicate that various plant organs, in a definite hierarchy and in interaction with each other, are involved in determining crop yield under stress. Here we attempt to summarize the currently available information on cereal reproduction under drought and heat stress and to give an outlook towards potential strategies to improve yield safety in cereals.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-3040.2007.01727.x

The effect of drought and heat stress on reproductive processes in cereals.

As most soil phosphates exist as insoluble inorganic phosphate and organic phosphates, higher plants have developed several strategies for adaptation to low phosphorus (P). These include the secretion of acid phosphatase and organic acids, induction of the inorganic phosphate (Pi) transporter and the substitution of some enzyme activities as alternative pathways to increase P utilization efficiency. It has been proposed that plants also have a ‘pho regulon’ system, as observed in yeast and Escherichia coli; however, the detail of the regulation system for gene expression on P status is still unclear in plants. To investigate the alteration of gene expression of rice roots grown under P-deficient conditions, a transcriptomic analysis was conducted using a cDNA microarray on rice. Based on the changes of gene expression under a –P treatment, the up-regulation of some genes due to P deficiency was confirmed . Some new important metabolic changes are suggested, namely: (1) acceleration of carbon supply for organic acid synthesis through glycolysis; (2) alteration of lipid metabolism; (3) rearrangement of compounds for cell wall; and (4) changes of gene expression related to the response for metallic elements such as Al, Fe and Zn.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-3040.2003.01074.x

Transcriptomic analysis of metabolic changes by phosphorus stress in rice plant roots

We studied the effects of the application of organic matter (OM) and chemical fertilizer (CF) on soil alkaline phosphatase (ALP) activity and ALP-harboring bacterial communities in the rhizosphere and bulk soil in an experimental lettuce field in Hokkaido, Japan. The ALP activity was higher in soils with OM than in soils with CF, and activity was higher in the rhizosphere for OM than in the bulk soil. Biomass P and available P in the soil were positively related to the ALP activity of the soil. As a result, the P concentration of lettuce was higher in OM soil than in CF soil. We analyzed the ALP-harboring bacterial communities using polymerase chain reaction based denaturing gradient gel electrophoresis (DGGE) on the ALP genes. Numerous ALP genes were detected in the DGGE profile, regardless of sampling time, fertilizer treatment or sampled soil area, which indicated a large diversity in ALP-harboring bacteria in the soil. Several ALP gene fragments were closely related to the ALP genes of Mesorhizobium loti and Pseudomonas fluorescens. The community structures of the ALP-harboring bacteria were assessed using principal component analysis of the DGGE profiles. Fertilizer treatment and sampled soil area significantly affected the community structures of ALP-harboring bacteria. As the DGGE bands contributing to the principal component were different from sampling time, it is suggested that the major bacteria harboring the ALP gene shifted. Furthermore, there was, in part, a significant correlation between ALP activity and the community structure of the ALP-harboring bacteria. These results raise the possibility that different ALP-harboring bacteria release different amounts and/or activity of ALP, and that the structure of ALP-harboring bacterial communities may play a major role in determining overall soil ALP activity.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1747-0765.2007.00210.x

Analysis of bacterial communities on alkaline phosphatase genes in soil supplied with organic matter

The present paper alms at determining how carbon (C) and nitrogen (N) compounds are redistributed from leaves to harvesting organs during maturation in several major field crops. In order to illustrate these processes in the case of C and N compounds, 6 major crops in Hokkaido were grown and compared during maturation. The results obtained were as follows. 1) The N-redistribution rate during maturation was in the order of wheat, soybean and potato > maize > rice. The percentage of distributed nitrogen among the different nitrogenous fractions in leaves and stems was remained constant during maturation, suggesting that each nitrogen compound was equally decomposed. 2) The composition of protein amino acids was similar regardless of organs or crops. The composition of free amino acids differed widely among organs and crops, and differed from that of protein amino acids. Therefore during the translocation of amino acids from leaves to harvesting organs through stems, the composition of free amino ac...

https://www.tandfonline.com/doi/pdf/10.1080/00380768.1991.10415017

Redistribution of carbon and nitrogen compounds from the shoot to the harvesting organs during maturation in field crops

The roots of white lupin (Lupinus albus L. cv. Kievskij mutant) secrete acid phosphatase, S-APase, when they grow under conditions of low available phosphorus (P). S-APases hydrolyze organic phosphate compounds in the rhizosphere and supply inorganic phosphate to the plants. Low phosphorus availability also induces vigorous growth of cluster roots. In this study, the function of cluster roots was investigated with reference to S-APase secretion. White lupins were grown in hydroponic culture in a greenhouse under P-deficient and P-sufficient conditions. S-APase in the excised roots after treatment was detected by staining with 4-methylumbelliferone phosphate (MUP). Gene expression of S-APase in cluster and normal roots was also investigated. Activity was greatest in the roots of plants grown under conditions of P -deficiency, particularly in cluster roots. S-APase gene expression was induced by a decrease in internal P concentrations, and was especially high in cluster roots formed under conditions of P -deficiency. It was suggested that decrease of internal P concentration stimulated both of the S-APase expression and cluster root formation.

Secreted acid phosphatase is expressed in cluster roots of lupin in response to phosphorus deficiency

Levels of cytokinins and abscisic acid (ABA) and the expression of senescence-related genes were investigated in two maize (Zea mays L.) cultivars of different senescence type, cv. P3845 (stay-green) and cv. Hokkou 55 (earlier senescent), in a field study. The delay in leaf senescence in P3845 was correlated with increased levels of chlorophyll and nitrogen and a higher photon-saturated photosynthetic rate (P(sat)). Compared with the earlier senescent Hokkou 55, P3845 showed enhanced contents of cytokinins (trans-zeatin riboside, t-ZR; dihydrozeatin riboside, DHZR; isopentenyladenosine, iPA) and reduced levels of ABA in its leaves. In roots, P3845 had increased levels of t-ZR, DHZR, and ABA, but decreased concentrations of iPA. It was concluded that a higher rate of cytokinin transport from roots to leaves contributes to the delay of senescence in P3845. By contrast, the translocation of ABA from roots to shoots may be blocked in the stay-green cultivar, which also results in retarded leaf senescence. P3845 ear leaves contained more malondialdehyde (MDA) and higher catalase (CAT) and superoxide dismutase (SOD) activities than Hokkou 55. Since the accumulation of the mRNAs for Rubisco small subunit (rbcS), phosphoenolpyruvate carboxylase (PEPC), and SOD peaked after Chl content and P(sat) had reached their maxima, it is speculated that when leaf senescence is initiated, Chl contents decrease first, followed by the degradation of the photosynthetic apparatus and of photosynthesis-related enzymes. See1 and See2 encode senescence-related cysteine proteases; their mRNAs were most abundant in yellowing leaves, suggesting that these proteins are involved in the process of senescence rather than its initiation. mRNAs of both genes were more abundant in Hokkou 55 than in P3845, which suggests a regulation of leaf senescence at the transcriptional level.

Takuro Shinano

Papers

Transcriptomic analysis of metabolic changes by phosphorus stress in rice plant roots

Analysis of bacterial communities on alkaline phosphatase genes in soil supplied with organic matter

Redistribution of carbon and nitrogen compounds from the shoot to the harvesting organs during maturation in field crops

Secreted acid phosphatase is expressed in cluster roots of lupin in response to phosphorus deficiency

Endogenous hormones and expression of senescence-related genes in different senescent types of maize