Development and application of gene-based markers for the major rice QTL Phosphorus uptake 1

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Abstract

Marker-assisted breeding is a very useful tool for breeders but still lags behind its potential because information on the effect of quantitative trait loci (QTLs) in different genetic backgrounds and ideal molecular markers are unavailable. Here, we report on some first steps toward the validation and application of the major rice QTL Phosphate uptake 1 (Pup1) that confers tolerance of phosphorus (P) deficiency in rice (Oryza sativa L.). Based on the Pup1 genomic sequence of the tolerant donor variety Kasalath that recently became available, markers were designed that target (1) putative genes that are partially conserved in the Nipponbare reference genome and (2) Kasalath-specific genes that are located in a large insertion-deletion (INDEL) region that is absent in Nipponbare. Testing these markers in 159 diverse rice accessions confirmed their diagnostic value across genotypes and showed that Pup1 is present in more than 50% of rice accessions adapted to stress-prone environments, whereas it was detected in only about 10% of the analyzed irrigated/lowland varieties. Furthermore, the Pup1 locus was detected in more than 80% of the analyzed drought-tolerant rice breeding lines, suggesting that breeders are unknowingly selecting for Pup1. A hydroponics experiment revealed genotypic differences in the response to P deficiency between upland and irrigated varieties but confirmed that root elongation is independent of Pup1. Contrasting Pup1 near-isogenic lines (NILs) were subsequently grown in two different P-deficient soils and environments. Under the applied aerobic growth conditions, NILs with the Pup1 locus maintained significantly higher grain weight plant−1 under P deprivation in comparison with intolerant sister lines without Pup1. Overall, the data provide evidence that Pup1 has the potential to improve yield in P-deficient and/or drought-prone environments and in diverse genetic backgrounds.

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Acknowledgments

We would like to thank Jennylyn Trinidad and Cheryl Dalid, as well as Miladie Penarubia, Manolo Balanial, and Ricardo Eugenio for their contributions to this paper and excellent technical assistance. Also, we would like to thank Susan McCouch for conducting the SNP genotyping. This project is fully supported by the Generation Challenge Program (GCP).

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Correspondence to Sigrid Heuer.

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An erratum to this article can be found at http://dx.doi.org/10.1007/s00122-010-1286-9

Communicated by L. Xiong.

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Supplementary Fig. S1. Pup1 haplotype in diverse rice accessions. A set of accessions belonging to different varietal groups (A = aus, I = indica, J = japonica, TV = traditional variety, MV = modern variety) and adapted to different agro-ecosystems (L = lowland, U = upland) were genotyped with seven Pup1-specific markers. (PDF 57 kb)

a

Supplementary Fig. S2. Kasalath introgressions in Pup1 near isogenic lines. Graphical genotypes of three pairs of near isogenic lines (NILs) with contrasting Pup1 haplotypes that had shown co-segregation of Pup1 with a P efficient phenotype (Heuer et al. 2009): (a) NILs 14-4 (+Pup1, left) and 14-6 (−Pup1, right); (b) NILs 6-4 (+Pup1, left) and 6-3 (−Pup1, right); (c) NILs 24-4 (+Pup1, left) and 24-6 (−Pup1, right). Genotyping was done using the 1536 GoldenGate assay (Zhao et al., Cornell University, personal communication). The Pup1 locus is located at 15.3–15.5 Mb on chromosome 12 (indicated in red). (PDF 31 kb)

a

Supplementary Fig. S3. Pup1 allelic variation and phosphorus (P) uptake. The Pup1 haplotype of 19 rice accessions was determined with seven Pup1-specific markers (for details see Table 2 in main text). Genotypes that possess Kasalath Pup1 alleles of the targeted genes showed a significantly higher P-uptake under high and low P conditions (a). This was also observed when the markers were analyzed individually (b). The marker Pup1-K48 showed the least diagnostic value (see also Fig. 1a, main text). (PDF 27 kb)

Supplementary Table S1. See excel file “Chin et al._Supplementary Table S1_final (Nov 12 2009)” (PDF 291 kb)

Supplementary Table S2. Shoot and root length of accessions with contrasting Pup1 haplotypes in hydroponics solution (DOCX 12 kb)

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Chin, J.H., Lu, X., Haefele, S.M. et al. Development and application of gene-based markers for the major rice QTL Phosphorus uptake 1 . Theor Appl Genet 120, 1073–1086 (2010). https://doi.org/10.1007/s00122-009-1235-7

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Keywords

  • International Rice Research Institute
  • Rice Accession
  • Hydroponic Experiment
  • Upland Condition
  • Upland Variety