Diagnostic markers for a major phosphorous uptake QTL (Pup1)

Product Description/Background:

Globally, more than half of all cropland is low in plant-available phosphorus, posing a serious problem for poor, remote, rice-farming communities that must manage without fertilisers. The major rice QTL Phosphate Uptake 1 (Pup1) was originally identified in a screening in a phosphorus (P) – deficient field under upland conditions in Japan.   Phenotypic data derived from Nipponbare contrasting near isogenic lines (NILs) with and without the QTL showed that Pup1increases P uptake (Wissuwa and Ae, 2001aWissuwa et al., 2002) and confers a significant yield advantage (2- to 4-fold higher grain weight per plant) in pot experiments using different P-deficient soil types and environments (Chin et al., 2010). After fine mapping, the Pup1 locus was sequenced in the tolerant donor variety Kasalath. Based on comparative sequence analyses, gene-specific Pup1 markers (Table 1) have been developed that are diagnostic for Pup1 in a wide range of rice varieties.. These markers, in conjunction with SSR and SNP background markers are now being used to develop Pup1 introgression lines of three Indonesian upland varieties at ICABIOGRAD and two irrigated indica varieties at IRRI (Philippines) by a marker-assisted backcrossing approach.  

*Extracted From Table II, page 1210 of: Chin JHGamuyao RDalid CBustamam MPrasetiyono JMoeljopawiro SWissuwa MHeuer S. Developing rice with high yield under phosphorous deficiency. Plant Physiology. July 2011 vol. 156 no. 3 1202-1216

** Markers in bold are currently considered the most important (JH Chin, personal communication)

*** Bsp 12861 = enzyme at CAPS marker locus

Pup1 gene models and marker positions may also be found in the above publication.

Also refer to:

Chin J.H., X. Lu, S.M. Haefele, R. Gamuyao, A.M. Ismail, M. Wissuwa and S. Heuer (2010) Development and Application of Gene-Based Markers for the Major Rice QTL Phosphate Uptake 1 (Pup1), Theoretical and Applied Genetics, 120 (6), pp. 1073-1086.

Diagnostic SNP markers (ID codes) for the Pup1 locus on the KASPar (KBiosciences) platform

Heuer, et al. (2009) reported the fine mapping of the Pup1 locus to the long arm of chromosome 12  at 59.10 – 59.47 Cm. The following SNP markers: :id12005384 at 59.0796 Cm and K_id12005428 at 58.4842 Cm were found to approximate the locus closely and as such are considered diagnostic, as well. SNP markers id12005339 at 58.5835 Cm and K_id12005540 at 60.4958 Cm closely flank these, respectively.

Examples of phenotypic expression of Pup1 in the field:

Lowland Rice

Figure 1. Field evaluation and selection of IR64-Pup1 and IR74-Pup1 breeding lines. A, Sister lines with (+Pup1) and without (2Pup1) the tolerant Pup1 locus and control plants were grown under irrigated field conditions in P-deficient soil (P2) and in a P-fertilized parallel control plot (P+) in three replicates. Phenotypic data from the BC2F3 populations were collected in 2010. Data were analyzed by paired t test (95%). Significance levels are as follows: * 0.05.P$0.01, ** 0.01. P $ 0.001, *** 0.001 . P. No asterisk indicates not significant.*

*Extracted from: Figure 7 in Joong Hyoun Chin, Rico Gamuyao, Cheryl Dalid, Masdiar Bustamam, Joko Prasetiyono, Sugiono Moeljopawiro, Matthias Wissuwa, and Sigrid Heuer. Developing Rice with High Yield under Phosphorus Deficiency: Pup1 Sequence to Application Plant Physiology. July 2011, Vol. 156, pp. 1202–1216














Upland Rice

Figure 2. Twenty-three rice accessions with contrasting Pup1 haplotype (KK= tolerant Pup1 alleles; KN= tolerant dirigent allele, intolerant protein kinase allele; NK= intolerant dirigent allele, tolerant protein kinase allele; NN= intolerant Pup1 alleles) were screened during the DS2008 at the IRRI upland farm under well-watered and drought stressed conditions (a). A subset of 17 accessions was additionally screened during the DS2009. Residual P at the upland farm is high and plants generally show no P-deficiency symptoms even if P fertilizer is not applied.

Extracted from: Figure 16 in G4008.41 GCP Project G4008.41- Application and Validation of the Major QTL Phosphate Uptake 1 (Pup1) - Final Technical Report.

Marker Access/Availability:

The above marker information can be used freely to generate markers and used to genotype germplasm.  For SSR and STS marker services in Africa and Asia  we suggest BecA, Nairobi, Kenya and ICRISAT, Patancheru, India. SNP markers can be accessed through KBiosciences, Hoddesdon, Herts, UK. Click here for a list and description of laboratories and services. See the following information for details.  In addition, the Integrated Breeding Platform Genotyping Service provides a set of options for users to access different marker service laboratories in the public and private sector with clear contractual conditions. The service identifies laboratories able to provide services for genetic diversity analysis and plant breeding applications and negotiates favourable terms for IBP clients. Laboratories are selected on the basis of competitive cost, fit with quality control requirements and expeditious delivery.  Click on  Service request for details of how to access genotyping services through the platform. For additional information and help on using the IBP Marker Service, contact Chunlin He.

If you need assistance in the use of these markers refer to  IBP Breeding Services or for more information contact Mark Sawkins or Chunlin He.


These markers were validated in part through the GCP supported multi-institutional project G4008.41 “Application and Validation of the Major QTL Phosphate Uptake 1 (Pup1)”, completed in 2011. Sigrid Heuer, International Rice Research Institute, Los Baños, The Philippines, was the Principal Investigator. Contact: Sigrid Heuer, Australian Centre for Plant Functional Genomics, Adelaide, Australia sigrid.heuer@acpfg.com.au.

Supporting Germplasm Resources

If it is determined that the local collection contains little or insufficient tolerance to low P conditions, introgression of the Pup1 allele from outsourced germplasm may be necessary.  The following table indicates consensus recommendations of Drs. Joong Hyoun Chin, IRRI, Los Banos, Philippines and Sigrid Heuer (formerly of IRRI), Australian Centre for Functional Plant Genomics, Adelaide, Australia both of whom have been instrumental in the elucidation of Pup1 functionality and development of Pup1 breeding materials. 

*Subject to commercial fees for requests from commercial companies.

**Available pending agreements between IRRI and ICABIOGRAD, Indonesia.  Subject to commercial fees for requests from commercial companies.

To request germplasm from IRRI send a request either by:

1)  letter addressed to Dr. Nigel Ruaraidh Sackville Hamilton, Head, Genetic Resources Center, IRRI, DAPO Box 7777 Metro Manila, Philippines; or

2) electronic mail to Dr. N. Ruaraidh Sackville Hamilton (r.hamilton@cgiar.org) or

3) access germplasm information directly thru the System-wide Information Network for Genetic Resources (SINGER) website (http://www.cgiar.org/singer)

Supporting Publications:

Heuer S, Lu X, Chin JH, Tanaka JP, Kanamori H, Matsumoto T, De Leon T, Ulat VJ, Ismail AM, Yano M, Wissuwa M (2009). Comparative sequence analyses of the major QTL Phosphate uptake 1 (Pup1) reveal a complex genetic structureJournal of Plant Biotechnology: 456–471.

Gamuyao R., J.H. Chin, J. Pariasca-Tanaka, P. Pesaresi, S. Catausan, C. Dalid, I. Slamet-Loedin, E.M. Tecson-Mendoza, M. Wissuwa and S. Heuer (2012) The Protein Kinase PSTOL1 from Traditional Rice Confers Tolerance of Phosphorus Deficiency, Nature, 488 (7412), pp. 535-539.

Heuer S., X. Lu, J.H. Chin, J.P. Tanaka, H. Kanamori, T. Matsumoto, T. De Leon, V.J. Ulat, A.M. Ismail, M. Yano and M. Wissuwa (2009) Comparative Sequence Analyses of the Major QTL Phosphate Uptake 1 (Pup1) Reveal a Complex Genetic Structure, Plant Biotechnology Journal, 7 (5), pp. 456-471.

Other Resources:

GCP Project G4008.41- Application and Validation of the Major QTL Phosphate Uptake 1 (Pup1) - Final Technical Report.

European Initiative for Agricultural Research for Development (EIARD) Impact Study 2013 - Rooting for more phosphorus

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