Future Perspectives in Plant Biology

Quantitative Trait Loci, , Sugars, and MicroRNAs: Quaternaries in Phosphate Acquisition and Use

Carroll P. Vance* United States Department of /Agricultural Research Service, Plant Science Research Unit, Agronomy and Plant Department, University of Minnesota, St. Paul, Minnesota 55108

Phosphorus (P) is a critical element for plant growth the tropics and subtropics are particularly prone to P and is frequently the limiting nutrient in many soils. deficiency. Continued production and application of P fertilizer Mined rock phosphate, a nonrenewable resource, is relies on a nonrenewable resource that will peak in the primary source of P fertilizer (Steen, 1998; Tiessen, about 2050. This will result in significantly increased 2008; Cordell et al., 2009). Easily mined, high-quality cost, particularly for developing countries. Significant rock phosphate sources are projected to be depleted research efforts in the of P stress have shown within 30 to 50 years. In addition, the world’s major that many suites of regulated in a coordinated reserves of rock phosphate are located in Morocco and fashion are involved in plant acclimation to P defi- China. Uncertain political issues could limit access to ciency. These genomic studies, in conjunction with tra- the world’s P resources. Coalescence of these factors ditional , have shown that P-acclimation as well as production of food for energy has seen traits are controlled by multiple genes, most probably P-fertilizer costs increase 6- to 9-fold in the past few in quantitative trait loci (QTLs). Future development years. A potential phosphate crisis looms for agricul- of near isogenic lines (NILs) and recombinant inbred ture in the 21st century (Abelson, 1999; Tiessen, 2008). lines (RILs) coupled to next-generation Application of P fertilizer, however, is problematic will facilitate the cloning of genes in QTLs regulating for both the intensive and extensive agriculture of the P-deficiency acclimation. Defining the role of epigenetic developed and developing worlds, respectively. Un- regulation of expression in adaptation to abiotic der adequate P fertilization, only 20% or less of that stress will provide new targets for improving plant applied is removed in the first year’s growth. This adaptation to P starvation. Cross talk between sugars, results in P loading of prime agricultural land and microRNAs (miRNAs), and P-starvation-induced gene increased P runoff (Kirkby and Johnston, 2008; White expression may be significant to understanding the and Hammond, 2008). An even greater concern is the fundamental underpinning of plant adaptation to nu- lack of available P fertilizers for extensive agriculture trient stresses. Plants with highly efficient P acquisition in the tropics and subtropics, where the majority of and use could reduce the need for P fertilizer in the Earth’s people live. Lack of infrastructure, money, and developed world, thereby ameliorating the overuse of P transportation make P fertilization unattainable for while concurrently enhancing yield in the developing these areas. It is imperative that within the next 40 world, where P is frequently unavailable. years plant biologists understand the genetic basis for acclimation to P deficiency and through traditional selection and/or biotechnology develop germplasm sources with improved P-use efficiency. IMPORTANCE OF P Plant responses to P-stress conditions involve changes in both shoot and root development (Lynch, P is one of 17 essential elements (nutrients) required 1995; Lynch and Brown, 2001; Lo´pez-Bucio et al., 2003; for plant growth (Tiessen, 2008; Cordell et al., 2009). Bucciarelli et al., 2006; Lambers et al., 2006; Herna´ndez The P concentration in plants ranges from 0.05% to et al., 2007). P-deficient plants display (1) delayed leaf 0.50% dry weight. The concentration gradient from the development and reduced photosynthetic capacity, (2) soil solution P to plant cells exceeds 2,000-fold, with an m reduced axillary shoot emergence and elongation average free P of 1 to 5 M in the soil solution (Bieleski, (stunted plants), (3) impaired flower development, 1973; Schachtman et al., 1998). Although bound P is (4) increased anthocyanin accumulation, (5) increased quite abundant in many soils, it is largely unavailable root-shoot ratio, (6) altered root architecture, and (7) for uptake, and P is frequently the most limiting increased exudation from roots of organic acids, phe- element for plant growth and development (Tiessen, nolics, protons, and enzymes. 2008; Cordell et al., 2009). The acid-weathered soils of Because roots are the primary site for acquiring P, they have become a rich topic for developmental and * E-mail [email protected]. genetic studies. Soil P limitation is a primary effector www.plantphysiol.org/cgi/doi/10.1104/pp.110.161067 of root architecture (Dinkelaker et al., 1995; Williamson

Ò 582 Plant Physiology , October 2010, Vol. 154, pp. 582–588, www.plantphysiol.org Ó 2010 American Society of Plant Biologists Plant Phosphorus Stress et al., 2001; Lo´pez-Bucio et al., 2003; Lambers et al., et al., 2006), soybean (Glycine max; Li et al., 2005; 2006) and is known to impact all aspects of root growth Zhang et al., 2009), barley (Hordeum vulgare; Gahoonia and development. Phenotypic and genotypic adapta- and Nielsen, 2004), and maize (Zea mays; Zhu et al., tions to P deficiency involve changes in root architec- 2005; Chen et al., 2009; Hochholdinger and Tuberosa, ture that facilitate the acquisition of P from the topsoil. 2009). Adaptations that enhance acquisition of P from topsoil Utilizing a mapping population derived from a are important because of the relative immobility of P cross of the intolerant ‘Nipponbare’ cultivar with the in soil, with the highest concentrations usually found tolerant landrace ‘Kasalath,’ Wissuwa et al. (2002) in the topsoil. Lynch and Brown (2001) refer to identified a QTL for tolerance to low P in rice desig- P-deficiency-induced modifications of root architecture nated Phosphorus uptake1 (Pup1). of as adaptations for topsoil foraging. Root characteris- Pup1 into NILs allowed fine mapping of the Pup1 tics associated with improved topsoil foraging for to the long arm of 12 (15.31–15.47 scarce P are a more shallow horizontal basal root Mb) on the basis of the Nipponbare reference genome growth angle, increased adventitious root formation, (Heuer et al., 2009). Next-generation sequencing was enhanced lateral root proliferation, and increased root used to characterize the genomic (278 kb) introgres- hair density and length. The phenotypic complexity of sion region. Although the gene(s) regulating the Pup1 plant acclimation to P deficiency reflects the polygenic has yet to be identified, it is worthwhile to nature of these processes. note that the Pup1 region is found in 50% of the rice In recent years, significant inroads into understand- accessions adapted to stress-prone environments (Chin ing biochemical and molecular events involved in et al., 2010). plant acclimation to P stress have been made through In common bean, RILs were developed for shallow- comparative microarray and macroarray studies of rooted and deep-rooted (Rubio et al., P-deficient plants as compared with P-sufficient plants. 2003). Under field conditions, when available P was In addition, definition of single-gene mutants in Arab- concentrated in the topsoil layer, the shallow-rooted idopsis (Arabidopsis thaliana) that show impaired P RILs were more productive and had a competitive signaling has demonstrated the role of transcription advantage over deep-rooted RILs. Further analysis of factors involved in P-induced gene expression. The the RILs by Liao et al. (2004) showed 16 QTLs control- importance of miR399 in P signal transduction has also ling the root traits. Adventitious root formation in 84 been a fruitful avenue of research. In coming years, RILs grown under limiting P conditions was shown to complementary research approaches that utilize next- be important for P acquisition in common bean (Ochoa generation sequencing coupled to analysis of well- et al., 2006). The QTLs for root traits related to low P defined plant germplasm containing QTLs for enhanced tolerance were mainly located on linkage groups B2 P-stress tolerance will lead to the identity of genome and B9. One QTL on linkage group B9 accounted for regulatory elements. Moreover, plants exposed to biotic 61% of the total phenotypic variation. Beebe et al. stress, such as diseases, undergo epigenetic changes (2006) evaluated 71 RILs grown under either low P or leading to resistance responses, but the importance of high P and identified 26 QTLs affecting P accumula- epigenetic mechanisms in adaptation to abiotic stress is tion and root architecture. Enhanced P uptake was an underdeveloped discipline. Lastly, while sugars can associated with basal root development. Development act as signal molecules in several developmental re- of NILs of common bean having enhanced P tolerance sponses and have been implicated in P-stress responses, and shallow basal roots will provide the germplasm it is unclear how sugars moderate the transcriptional resources for further fine mapping of important traits. regulation of gene expression. This contribution will The common bean genome is currently being se- address the implications of next-generation sequencing, quenced. Having a reference genome and NIL genetic QTLs, epigenetics, and sugar-miRNA cross talk in plant resources for common bean coupled with next-generation acclimation to P deficiency. high-throughput RNA sequencing (RNA-seq) will fa- cilitate fine mapping and (s) identifica- tion regulating P tolerance and root traits in common bean. QTLS ASSOCIATED WITH P-STRESS TOLERANCE AND ACCLIMATION Tuberosa and Salvi (2007) developed a library of maize introgressed lines from B73 (recurrent parent) Genetic variability for the complex root and shoot crossed with Gaspe Flint (donor parent) to identify responses to P-limiting conditions has been demon- major QTLs for root architecture and growth that map strated for a wide range of species. Variation for to maize bin 1.06. Utilizing other maize RILs grown complex phenotypic traits are frequently controlled under low and high P, Chen et al. (2008) identified a by many genetic loci, QTLs, scattered throughout QTL at bin 1.06 for P efficiency and topsoil root dry the genome (Price, 2006). QTLs for traits related to weight. They found several QTLs for interactions P-deficiency tolerance have been found in rice (Oryza () located near bin 1.06. The bin 1.06 region sativa; Wissuwa et al., 2002), wheat (Triticum aestivum; on maize chromosome 1 has been reported to control a Su et al., 2009), common bean (Phaseolus vulgaris; Beebe QTL for root architecture in five maize genetic back- et al., 2006; Ochoa et al., 2006), Arabidopsis (Reymond grounds (Hochholdinger and Tuberosa, 2009). The

Plant Physiol. Vol. 154, 2010 583 Vance

QTL at bin 1.06 has also been associated with nitrogen- generally linked with repressive chromatin in gene use efficiency. This region of the maize genome is promoters and repression of gene expression, while currently under evaluation for candidate genes. hypomethylation leads to enhanced transcription. En- Building upon a number of approaches, a gene has hanced expression of a glycerophodiesterase (GPXPD) been identified in Arabidopsis that is involved in a gene in tobacco (Nicotiana tabacum) in response to QTL controlling root growth response (Reymond et al., aluminum, salt, and cold stresses has been associated 2006; Svistoonoff et al., 2007). As noted earlier, when with demethylation in the coding region of the GPXPD grown on low P, Arabidopsis primary root growth is gene (Choi and Sano, 2007). These authors, however, inhibited while lateral root growth is stimulated. did not find demethylation in the promoter region of Reymond et al. (2006) generated NILs by segregating the gene. Many genes showing enhanced transcription an F6 RIL mapped for root growth response to low P. in response to aluminum stress are also induced Fine mapping of the low-phosphate root (LPR1) QTL during P stress. As with aluminum stress, GPXPDs trait located it to a 2.5-Mb region at the top of chro- are known to be highly expressed in response to P mosome 1. Further fine mapping by Svistoonoff et al. starvation and return to basal levels as P stress is (2007) refined the LPR1 trait to a 36-kb region. They relieved (Misson et al., 2005; Morcuende et al., 2007). then mutagenized the LPR1 line and screened for The methylation status of GPXPDs has not been eval- progeny with long roots on low-P medium. Moreover, uated during P stress, but it as well as many other Svistoonoff et al. (2007) also developed T-DNA inser- genes that respond quickly to P status may be under a tion mutants for LPR1. Utilizing fine mapping of the similar form of epigenetic regulation. With the soon to locus and mutagenesis, they defined the LPR1 QTL be available single-molecule real-time DNA sequenc- locus as encoding a multicopper oxidase enzyme. ing capabilities, laboratories will be able to do direct Transcripts for LPR1 were most abundant in the root sequencing for methylated DNA rather than bisulfite meristem and root cap. Ticconi et al. (2009) have sequencing (Flusberg et al., 2010). This will allow for recently proposed that LPR1 interacts with phosphate immediate and direct evaluation of the epigenetic deficiency 2 (PDR2) to adjust root meristem activity. status of plants grown under any stress condition. The authors suggested that the root cap played a Smith et al. (2010) have implicated the actin-related critical role in local P sensing. protein 6 (APR6) as an epigenetic modulator of some As evidenced by the cloning of LPR1 in Arabidopsis, P-starvation response (PSR) genes. APR6 is a key complementary approaches will lead to cloning of component of the SWR1 complex involved in chroma- genes controlling QTLs involved in tolerance to P tin remodeling and is required for histone H2A.Z deficiency. Progress on cloning these QTLs will be incorporation into chromatin (Jarillo et al., 2009). The dependent upon several factors, including (1) the physiological and molecular phenotypes of apr6 mu- development of RILs segregating for the desired trait, tants were noticeably similar to those displayed by followed by the development of NILs having the P-starved Arabidopsis plants (Smith et al., 2010). Loss introgressed trait; (2) fine mapping of the trait utilizing of function of APR6 resulted in a dramatic decrease in molecular markers, derived preferably from single H2A.Z abundance at several PSR gene sites accompa- nucleotide polymorphisms generated by RNA-seq nied by an increase in gene transcription. Chromatin comparisons of the NILs; (3) mutations in or near the remodeling is an integral mechanism in regulating locus; and (4) a reference genome. In the near future, yeast structural phosphate regulon (PHO) gene ex- low-cost next-generation sequencing will rapidly ad- pression (Barbaric et al., 2007; Wippo et al., 2009). In vance cloning of QTLs for not only P deficiency addition, chromatin remodeling has also been impli- tolerance but also other traits. cated as a component of adaptation to pathogen stress in Arabidopsis (March-Diaz et al., 2008). Another epigenetic mechanism involved in adap- tation to stress appears to involve posttranslational ACCLIMATION TO PHOSPHATE STRESS INVOLVES EPIGENETIC CHANGES? modifications to the N-terminal region of nucleosome core complex histones through acetylation, phosphor- Acclimation and resistance to abiotic and biotic ylation, ubiquitination, and sumolaytion (Boyko and stresses involve significant biochemical and develop- Kovalchuk, 2008; Chinnusamy and Zhu, 2009). The mental plasticity. While much of this plasticity is the WD-40 protein gene HOS15 of Arabidopsis has been direct result of either increased or decreased transcrip- shown to be important in histone deacetylation and tion of several suites of genes, some may be derived is crucial for the repression of genes associated from epigenetic modifications that alter gene expres- with plant acclimation and tolerance to cold stress sion (Lukens and Zhan, 2007; Zhang, 2008; Chinnusamy (Zhu et al., 2008). HOS15 mutants accumulate higher and Zhu, 2009). In recent years, epigenetic changes amounts of stress-related transcripts and are hyper- have been noted as salient features in adaptation sensitive to cold temperatures. Phosphorylation of to abiotic and biotic stresses. Changes in DNA meth- histone H3,S10 and acetylation of histone H4 is corre- ylation are a hallmark of the epigenetic regulation lated with increased abundance of salt tolerance tran- of gene expression (Boyko and Kovalchuk, 2008; scripts in tobacco and Arabidopsis (Sokol et al., 2007). Zhang, 2008). In plants, DNA hypermethylation is The limited information available on the epigenetic

584 Plant Physiol. Vol. 154, 2010 Plant Phosphorus Stress regulation of plant response to P deficiency makes this many developmental processes in plants and animals topic rich for exploration. (Bartel, 2004; Jones-Rhodes and Bartel, 2004; Xie et al., 2005). miRNAs are noncoding small RNAs, about 20 to 24 nucleotides in length in plants, that function as posttranscriptional negative regulators or repressors SIGNALING OF PHOSPHATE STRESS: SUGARS AND MIRNAS CROSS TALK? through base pairing to complementary or partially complementary sequences in target mRNAs, leading The plethora of biochemical and developmental to cleavage of that RNA. Most known miRNAs in adaptations displayed in plants subjected to P defi- plants are predicted to target the expression of several ciency result from both local and systemic signaling, classes of genes, including transcription factors, indi- which activates the coordinated expression of a med- cating their importance in regulating various plant ley of genes (Franco-Zorrilla et al., 2004; Mu¨ ller et al., developmental aspects (Bartel and Bartel, 2004). Re- 2007; Tesfaye et al., 2007; Hammond and White, 2008). cently, miR399, first identified in Arabidopsis and rice Suc derived from photosynthate and miRNAs have (Sunkar and Zhu, 2004), was shown to be induced by P been implicated as critical molecules signaling P status stress after 24 and 48 h of P starvation (Fujii et al., 2005; of the plant. Chiou and Bush (1998) showed that Suc Aung et al., 2006; Bari et al., 2006; Chiou et al., 2006). could act as a signal molecule in assimilate partition- Transcript abundance of miR399 declines rapidly fol- ing. A growing body of evidence now supports Suc lowing the addition of P in the medium (Bari et al., derived from photosynthate as part of the systemic 2006) and is not detected at all under P-sufficient con- signaling leading to P-deficiency-induced increase in ditions. Chiou et al. (2006) found that while miR399 was lateral root formation and increased root hair density highly up-regulated during P stress, transcripts for a (Hermans et al., 2006; Jain et al., 2007; Karthikeyan ubiquitin-conjugating E2 enzyme (UBC24) were re- et al., 2007; Zhou et al., 2008). Moreover, Suc has been duced by 5-fold. By comparison, plants grown under shown to be required for enhanced expression of P sufficiency had significantly reduced miR399 but P-starvation-induced genes. To test the role of photosyn- UBC24 was abundant. Computational analysis of the thate and phloem Suc on P-stress transcript induction, 5# upstream region of UBC24 showed several target- shoots of white lupin (Lupinus albus) plants were either binding sites for miR399. Overexpression of miR399 darkened or stems were girdled to block phloem suppressed the accumulation of UBC24 transcripts and transport, and the starvation-enhanced expression of resulted in enhanced accumulation of P in the shoot. genes in roots was evaluated (Liu et al., 2005; Tesfaye Moreover, P remobilization was impaired in plants et al., 2007). Both treatments reduced gene expres- overexpressing miR399. Enhanced accumulation of P in sion in P-stressed roots to nondetectable levels within shoots and impaired P remobilization in plants over- a few hours. Returning darkened plants to light re- expressing miR399 phenocopied the Arabidopsis pho2 stored P-starvation-induced gene expression in roots. mutant (Dong et al., 1998). In P-stressed Arabidopsis roots, P-starvation-induced In concurrent studies, Bari et al. (2006) using map- genes showed further enhanced expression when based cloning identified the impaired gene in the pho2 supplemented with 3% Suc (Franco-Zorrilla et al., mutant as the ubiquitin-conjugating enzyme UBC24. 2005; Karthikeyan et al., 2007). Mu¨ ller et al. (2007) They also found that UBC24 had five complementary evaluated the interaction between P and Suc in Arabi- miR399-binding sites in the 5# upstream region. Bari dopsis leaves. Using a 2-fold cutoff, they found that et al. (2006) extended the understanding of the PHO2- 187 transcripts responded to P starvation while 644 miR399 interaction by showing that plants with the responded to Suc. They identified 149 transcripts that phr1-MYB protein mutation failed to accumulate were regulated by the interaction between P starvation miR399 transcripts. Their observations showed that and Suc availability. One group of 47 genes having PHR1-MYB was required for miR399 expression. increased expression in response to P deficiency was Thus, PHO2, miR399, and PHR1 define a critical further enhanced by Suc. Many of the transcripts in phosphate signaling pathway (Doerner, 2008). The this group encode proteins involved in P remobiliza- MYB PHR1 regulates miR399 ex- tion and carbohydrate metabolism. Although Suc pression, which in turn regulates the UBC24 E2 ligase appears to be important in signaling P status and PHO2. PHO2 then regulates a subset of P-starvation the full expression of P-starvation genes, the mecha- genes. Studies have now clearly shown that miR399 nism remains elusive. The sucrose nonfermenting1 can move in the phloem sap and serve as a long- kinase:calcineurin B-like protein kinase (SNF1:CIPK) distance signal for phosphate homeostasis (Lin et al., pathway has been implicated as the transduction 2008; Pant et al., 2008). A novel genetic concept super- system for sugar signaling (Hummel et al., 2009; Rosa imposed upon miR399 and P signaling has been et al., 2009). Whether the SNF1:CIPK pathway regu- demonstrated by Franco-Zorrilla et al. (2007). They lates sugar signaling during P starvation deserves found that along with transcriptional control, miR399 attention. activity is also regulated by “target mimicry.” The Computational and molecular cloning approaches non-protein-coding gene Induced by Phosphate Starva- revealed a group of endogenous noncoding small tion (IPS1) contains a motif with sequence comple- RNAs that may play important roles in the control of mentarity to miR399. IPS1 is induced along with

Plant Physiol. Vol. 154, 2010 585 Vance miR399 during P stress. However, rather than being ductionoftheyeastPHO5promoterinvivo.JBiolChem282: 27610– cleaved by miR399, IPS1 transcripts can bind to and 27621 Bari R, Pant BD, Stitt M, Scheible WR (2006) Pho2, microRNA399, and sequester miR399, thereby acting to attenuate the PHR1 define a phosphate-signaling pathway in plants. Plant Physiol inhibitory activity of miR399. Target mimicry by IPS1 141: 988–999 and other non-protein-coding genes may be a mech- Bartel B, Bartel DP (2004) Micro RNAs: at the root of plant development. anism to coregulate numerous miRNAs. Plant Physiol 132: 709–717 A recently proposed unique aspect of P signaling Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism and func- tion. Cell 116: 281–297 and miRNA involves potential cross talk between Beebe SE, Rojas-Pierce M, Yan X, Blair MW, Pedraza F, Mun˜ oz F, Tohme J, photosynthate (Suc) availability and miRNA expres- Lynch JP (2006) Quantitative trait loci for root architecture traits sion during P deficiency (Liu et al., 2010). The authors correlated with phosphorus acquisition in common bean. Crop Sci 46: found that expression of miR399 in either shoots or 413–423 roots required photosynthetic carbon assimilation. Bieleski RL (1973) Phosphate pools, phosphate transport, and phosphate availability. Annu Rev Plant Physiol 24: 225–252 When P-sufficient bean plants were subjected to P Boyko A, Kovalchuk I (2008) Epigenetic control of plant stress response. starvation, miR399 was strongly induced in roots and Environ Mol Mutagen 49: 61–72 shoots within 24 h. Surprisingly, miR399 was not Bucciarelli B, Hanan J, Palmquist D, Vance CP (2006) A standardized expressed in roots of dark-treated and stem-girdled method for analysis of Medicago truncatula phenotype development. P-starved plants. Moreover, expression of miR399 Plant Physiol 142: 207–219 Chen J, Xu L, Cai Y, Xu J (2008) QTL mapping of phosphorus efficiency and transcript expression was blocked in dark-treated relative biologic characteristics in maize (Zea mays L.) at two sites. Plant leaves of P-deficient plants. Whether light and sugars Soil 313: 251–266 modulate the expression of miR399 and other miRNAs Chen J, Xu L, Cai Y, Xu J (2009) Identification of QTLs for phosphorus known to be involved in abiotic and biotic stress needs utilization efficiency in maize (Zea mays L.) across P levels. Euphytica to be addressed. 167: 245–252 Chin JH, Haefele SM, Gamuyao R, Ismail A, Wissuwa M, Heuer S (2010) Development and application of gene based markers for the major rice QTL phosphorus uptake 1. Theor Appl Genet 120: 1073–1086 CONCLUSION Chinnusamy V, Zhu JK (2009) Epigenetic regulation of stress responses in plants. Curr Opin Plant Biol 12: 1–7 P is required for plant growth and development, but Chiou TJ, Aung K, Lin SL, Wu CC, Chiang SF, Su CL (2006) Regulation of phosphate homeostasis by microRNA in Arabidopsis. Plant Cell 18: its availability is frequently limiting. Plants have 412–421 evolved numerous adaptive mechanisms for acclima- Chiou TJ, Bush DR (1998) Sucrose is a signal molecule in assimilate tion to P deficiency. These mechanisms involve the partitioning. Proc Natl Acad Sci USA 95: 4784–4788 activation of metabolic, molecular, developmental, Choi CH, Sano H (2007) Abiotic-stress induces demethylation and tran- and regulatory processes that modify root architec- scriptional activation of a gene encoding a glycerophosphodiesterase- like protein in tobacco plants. Mol Genet Genomics 277: 589–600 ture to increase soil volume exploration and recycling Cordell D, Drangert JO, White S (2009) The story of phosphorus: of internal P. Modification of root architecture is global food security and food for thought. Glob Environ Change 19: frequently accompanied by increased exudation of 292–305 organic acids, protons, and enzymes to increase P Dinkelaker B, Hengeler C, Marschner H (1995) Distribution and function availability. Recent advances in genomics and genetics of proteoid roots and other root clusters. Acta Bot 108: 183–200 Doerner P (2008) Phosphate starvation signaling: a threesome controls suggest that plant acclimation to P deficiency involves systemic Pi homeostasis. Curr Opin Plant Biol 11: 536–540 cross talk between sugars and gene expression, in- Dong B, Rengel Z, Delhaize E (1998) Uptake and translocation of phos- cluding expression of miR399. The development of phate by pho2 mutant and wild-type seedlings of Arabidopsis thaliana. well-defined RILs and NILs having P tolerance cou- Planta 205: 251–256 pled to next-generation sequencing will lead to the FlusbergBA,WebsterDR,LeeJH,TraversKJ,OlivaresEC,ClarkTA, Karlach J, Turner SW (2010) Direct detection of DNA methylation identification of genes regulating adaptation to P during single-molecular, real-time sequencing. Nat Methods 7: stress. Next-generation sequencing will also be critical 461–465 to defining whether epigenetic changes are involved in Franco-Zorrilla JM, Gonza´lez E, Bustos R, Linhares F, Leyva A, Paz-Ares J P-stress responses. Further understanding of the bio- (2004) The transcriptional control of plant responses to phosphate chemical and genetic regulation of these quaternaries limitation. J Exp Bot 55: 285–293 Franco-Zorrilla JM, Martı´n AC, Leyva A, Paz-Ares J (2005) Interaction in plant acclimation to P stress will pave the way to between phosphate-starvation, sugar, and cytokinin signaling in Arabi- developing crop plants with enhanced P acquisition dopsis and the roles of cytokinin receptors CRE1/AHK4 and AHK3. and use. Plant Physiol 138: 847–857 Franco-Zorrilla JM, Valli A, Todesco M, Mateos I, Puga MI, Rubio- Received June 11, 2010; accepted July 1, 2010; published October 6, 2010. Somoza I, Leyva A, Weigel D, Garcia JA, Paz-Ares J (2007) Target mimicry provides a new mechanism for regulation of microRNA activ- ity. Nat Genet 39: 1033–1037 LITERATURE CITED Fujii H, Chiou TZ, Lin SI, Aung K, Zhu JK (2005) A miRNA involved in phosphate starvation response in Arabidopsis.CurrBiol15: Abelson PH (1999) A potential phosphate crisis. Science 283: 2015 2038–2043 Aung K, Lin SI, Wu CC, Huang YT, Su CL, Chiou TJ (2006) Pho2,a Gahoonia TS, Nielsen NE (2004) Root traits as tools for creating phospho- phosphate overaccumulator, is caused by a nonsense mutation in a rus efficient crop varieties. Plant Soil 260: 47–57 microRNA399 target gene. Plant Physiol 141: 1000–1011 Hammond JP, White PJ (2008) Sucrose transport in the phloem: integrating Barbaric S, Luckenbach T, Schmid A, Blaschke D, Horz W, Korber P root responses to phosphorus starvation. J Exp Bot 59: 93–109 (2007) Redundancy of chromatin remodeling pathways for the in- Hermans C, Hammond JP, White PJ, Verbruggen N (2006) How do plants

586 Plant Physiol. Vol. 154, 2010 Plant Phosphorus Stress

respond to nutrient shortage by biomass allocation? Trends Plant Sci 11: reprogramming of metabolism and regulatory networks of Arabidopsis 610–617 in response to phosphorus. Plant Cell Environ 30: 85–112 Herna´ndez G, Ramirez M, Valde´s-Lopez O, Tesfaye M, Graham MA, Mu¨ ller R, Morant M, Jarmer H, Nilsson L, Nielsen TH (2007) Genome- Czechowski T, Schlereth A, Wandrey M, Erban A, Cheung F, et al wide analysis of Arabidopsis leaf transcriptome reveals interaction of (2007) Phosphorus stress in common bean: root transcript and metabolic phosphate and sugar metabolism. Plant Physiol 143: 156–171 responses. Plant Physiol 144: 752–767 Ochoa IE, Blair MW, Lynch JP (2006) QTL analysis of adventitious root HeuerS,LuX,ChinJH,TanakaJP,KanamoriH,MatsumotoT,DeLeon formationincommonbeanundercontrastingphosphorusavailability. T, Ulat VJ, Ismail AM, Yano M, Wissuwa M (2009) Comparative Crop Sci 46: 1609–1621 sequence analyses of the major quantitative trait locus Phosphorus uptake Pant BD, Buhtz A, Kehr J, Scheible WR (2008) MicroRNA399 is a long- 1 (Pup1) reveal a complex genetic structure. Plant Biotechnol J 7: distance signal for the regulation of plant phosphate homeostasis. Plant 456–471 J 53: 731–738 Hochholdinger F, Tuberosa R (2009) Genetic and genomic dissection of Price AH (2006) Believe it or not, QTLs are accurate. Trends Plant Sci 11: maize root development and architecture. Curr Opin Plant Biol 12: 213–216 172–177 Reymond M, Svistoonoff S, Loudet O, Nussaume L, Desnos T (2006) Hummel M, Rahamani F, Smeekens S, Hanson J (2009) Sucrose mediated Identification of QTL controlling root growth response to phosphate translational control. Ann Bot (Lond) 104: 1–7 starvation in Arabidopsis thaliana. Plant Cell Environ 29: 115–125 Jain A, Poling MD, Karthikeyan AS, Blakeslee JJ, Peer WA, Titapiwatanakun Rosa M, Prado C, Podazzo G, Interdonato R, Gonzalez JA, Hilal M, Prado B, Murphy AS, Raghothama KG (2007) Differential effects of sucrose FE (2009) Soluble sugars: metabolism, sensing, and abiotic stress. Plant and auxin on localized phosphate deficiency-induced modulation of differ- Signal Behav 4: 388–393 ent traits of root system architecture in Arabidopsis. Plant Physiol 144: Rubio G, Liao H, Yan X, Lynch JP (2003) Topsoil foraging and its role in 232–247 plant competitiveness for phosphorus in common bean. Crop Sci 43: Jarillo JA, Pin˜ eiro M, Cubas P, Martinez-Zapater JM (2009) Chromatin 598–607 remodeling in plant development. Int J Dev Biol 53: 1581–1596 Schachtman DP, Reid RJ, Ayling SM (1998) Phosphorus uptake by plants: Jones-Rhodes MW, Bartel DP (2004) Computational identification of plant from soil to cell. Plant Physiol 116: 447–453 microRNAs and their targets, including a stress-induced miRNA. Mol Smith AP, Jain A, Deal RB, Nagarajan VK, Poling MD, Raghothama KG, Cell 14: 787–799 Meagher RB (2010) Histone H2A.Z regulates the expression of several Karthikeyan AS, Varadarajan DK, Jain A, Held MA, Carpita NC, classes of phosphate starvation response genes but not as transcrip- Raghothama KG (2007) Phosphate starvation responses are mediated tional activator. Plant Physiol 152: 217–225 by sugar signaling in Arabidopsis. Planta 225: 907–918 Sokol A, Kwiathowska A, Jerzmanowski A, Prymakowska-Bosak M Kirkby EA, Johnston AE (2008) Soil and fertilizer phosphorus in relation to (2007) Up-regulation of stress-inducible genes in tobacco and Arabidop- crop nutrition. In PJ White, JP Hammond, eds, Ecophysiology of Plant- sis cells in response to abiotic stresses and ABA treatment correlates Phosphorus Interactions. Springer Science & Business Media, New with dynamic changes in histone H3 and H4 modifications. Planta 227: York, pp 177–223 245–254 Lambers HY, Shane MW, Cramer MD, Pearse SJ, Veneklaas EJ (2006) Root Steen I (1998) Phosphorus availability in the 21st century: management of a structure and functioning for efficient acquisition of phosphorus: non-renewable resource. Phosphorus and Potassium 217: 25–31 matching morphological and physiological traits. Ann Bot (Lond) 98: Su JY, Zheng Q, Li HW, Li B, Jing RL, Tong YP, Li ZS (2009) Detection of 693–713 QTLs for phosphorus use efficiency in relation to agronomic perfor- Li YD, Wang YJ, Tong YP, Gao JG, Zhang JS, Chen SY (2005) QTL mapping mance in wheat grown under phosphorus sufficient and limited condi- of phosphorus deficiency tolerance in soybean (Glycine max L. Merr.). tions. Plant Sci 176: 824–836 Euphytica 142: 137–142 Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other Liao H, Yan X, Rubio G, Beebe SE, Blair MW, Lynch JP (2004) Genetic small RNAs from Arabidopsis. Plant Cell 16: 2001–2019 mapping of basal root gravitropism and phosphorus acquisition effi- Svistoonoff S, Creff A, Reymond M, Sigoillot-Claude C, Ricaud L, ciency in common bean. Funct Plant Biol 31: 959–970 Blanchet A, Nussaume L, Desnos T (2007) Root tip contact with low Lin SI, Chiang SF, Lin WY, Chen JW, Tseng CY, Wu PC, Chiou TJ (2008) phosphate media reprograms plant root architecture. Nat Genet 19: Regulatory network of microRNA399 and PHO2 by systemic signaling. 792–796 Plant Physiol 147: 732–746 Tesfaye M, Liu J, Allan DL, Vance CP (2007) Genomic and genetic control LiuJ,AllanDL,VanceCP(2010) Systemic signaling and local sensing of of phosphate stress in legumes. Plant Physiol 144: 594–603 phosphate in common bean: cross-talk between photosynthate and Ticconi CA, Lucero RD, Sakhonwasee S, Adamson AW, Creff A, Nussaume microRNA399. Mol Plant 3: 428–437 L, Desnos T, Abel S (2009) ER-resident proteins PDR2 and LPR1 mediate the Liu J, Samac DA, Bucciarelli B, Allan DL, Vance CP (2005) Signaling of developmental response of root meristems to phosphate availability. Proc phosphorus deficiency-induced gene expression in white lupin requires Natl Acad Sci USA 106: 14174–14179 sugar and phloem transport. Plant J 41: 257–268 Tiessen H (2008) Phosphorus in the global environment. In PJ White, JP Lo´pez-Bucio J, Cruiz-Ramirez A, Herrera-Estrella L (2003) The role of Hammond, eds, Ecophysiology of Plant-Phosphorus Interactions. nutrient availability in regulating root architecture. Curr Opin Plant Biol Springer Science & Business Media, New York, pp 1–8 6: 280–287 Tuberosa R, Salvi S (2007) From QTLs to genes controlling root traits in Lukens LN, Zhan S (2007) The plant genome’s methylation status and maize. In JHJ Spiertz, PC Struik, HH van Laar, eds, Scale and Complex- response to stress: implications for plant improvement. Curr Opin Plant ity in Plant Systems Research: Gene-Plant-Crop Relations. Springer, Biol 10: 317–322 Wageningen, The Netherlands, pp 15–24 Lynch JP (1995) Root architecture and plant productivity. Plant Physiol White PJ, Hammond JP (2008) Phosphorus nutrition of terrestrial plant. 109: 7–13 In PJ White, JP Hammond, eds, Ecophysiology of Plant-Phosphorus Lynch JP, Brown KM (2001) Topsoil foraging: an architectural adaptation of Interactions. Springer Science & Business Media, New York, pp plants to low phosphorus availability. Plant Soil 237: 225–237 51–81 March-Diaz R, Garcia-Dominguez M, Lozano-Juste J, Leo´nJ,Florencio Williamson LC, Ribrioux SP, Fitter AH, Ottoline Leyser HM (2001) FJ, Reyes JC (2008) Histone H2A.Z and homologues of components of Phosphate availability regulates root system architecture in Arabidop- the SWR1 complex are required to control immunity in Arabidopsis. sis. Plant Physiol 126: 875–882 Plant J 53: 475–487 Wippo CJ, Krstulovic BS, Ertel F, Musladin S, Blaschke D, Sturzl S, Yuan MissonJ,RaghothamaKG,JainA,JouhetJ,BlockMA,BlingnyR,Ortet GC, Horz W, Korber P, Barbaric S (2009) Differential cofactor require- P, Creff A, Somerville S, Rolland N, et al (2005) A genome-wide ments for histone eviction from two nucleosomes at the yeast PHO84 transcriptional analysis using Arabidopsis thaliana Affymetrix gene chips promoter are determined by intrinsic nucleosome stability. Mol Cell Biol determined plant responses to phosphate deprivation. Proc Natl Acad 29: 2960–2981 Sci USA 102: 11934–11939 WissuwaM,WegnerJ,AeN,YanoM(2002) Substitution mapping of Pup1: Morcuende R, Bari R, Gibon Y, Zheng W, Pant BD, Blasing O, Usadel B, a major QTL increasing phosphorus uptake of rice. Theor Appl Genet CzechowskiT,UdvardiMK,StittM,etal(2007) Genome-wide 105: 890–897

Plant Physiol. Vol. 154, 2010 587 Vance

Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC mediates cluster root formation and phosphorus starvation-induced (2005) Expression of Arabidopsis MIRNA genes. Plant Physiol 138: gene expression in white lupin. J Exp Bot 59: 2749–2756 2145–2154 Zhu J, Jeong JC, Zhu Y, Sokolchik I, Miyazaki S, Zhu JK, Hasegawa PM, Zhang D, Cheng H, Geng L, Kan G, Cui S, Meng Q, Gai J, Yu D (2009) Bohnert HJ, Shi H, Yun DJ, et al (2008) Involvement of Arabidopsis Detection of quantitative trait loci for phosphorus deficiency tolerance HOS15 in histone deacetylation and cold tolerance. Proc Natl Acad Sci at soybean seedling stage. Euphytica 167: 313–322 USA 105: 4945–4950 Zhang X (2008) The epigenetic landscape of plants. Science 320: Zhu J, Kaeppler SM, Lynch JP (2005) Mapping of QTL controlling root hair 489–492 length in maize (Zea mays L.) under phosphorus deficiency. Plant Soil Zhou K, Yamagishi M, Osaki M, Masuda K (2008) Sugar signaling 270: 299–310

588 Plant Physiol. Vol. 154, 2010