A novel allele of the P-starvation tolerance gene OsPSTOL1 from African rice (Oryza glaberrima Steud) and its distribution in the genus Oryza.

Juan Pariasca-Tanaka,Joong Hyoun Chin,Matthias Wissuwa,Sigrid Heuer,Cheryl Dalid,Khady Nani Dramé

doi:10.1007/s00122-014-2306-y

Abstract

Key message We have developed allele-specific markers for molecular breeding to transfer the PSTOL1 gene from Kasalath to African mega-varieties, including NERICAs, to improve their tolerance to P-deficient soil. The deficiency of phosphorus (P) in soil is a major problem in Sub-Saharan Africa due to general nutrient depletion and the presence of P-fixing soils. Developing rice cultivars with enhanced P efficiency would, therefore, represent a sustainable strategy to improve the livelihood of resource-poor farmers. Recently the Pup1 locus, a major QTL for tolerance to P deficiency in soil, was successfully narrowed-down to a major gene, the protein kinase OsPSTOL1 (P-starvation tolerance), which was found to be generally absent from modern irrigated rice varieties. Our target is to improve the tolerance of African mega-varieties to P deficiency through marker-assisted introgression of PSTOL1. As a first step, we have determined the Pup1 haplotype and surveyed the presence or absence of PSTOL1 and other genes of the Pup1 locus in African mega-varieties, NERICAs (New Rice for Africa) and their Oryza glaberrima parents. Here, we report the presence of a novel PSTOL1 allele in upland NERICAs that was inherited from the O. glaberrima parent CG14. This allele showed a 35 base-pair substitution when aligned to the Kasalath allele, but maintained a fully conserved kinase domain, and is present in most O. glaberrima accessions evaluated. In-silico and marker analysis indicated that many other genes of the Kasalath Pup1 locus were missing in the O. glaberrima genome, including the dirigent-like gene OsPupK20-2, which was shown to be downstream of PSTOL1. We have developed several allele-specific markers for the use for molecular breeding to transfer the PSTOL1 gene from Kasalath to African mega-varieties, including NERICAs.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-014-2306-y) contains supplementary material, which is available to authorized users.

Highlights

The deficiency of phosphorus (P) in soil is a worldwide problem affecting about 50 % of the rice-cultivated area
To survey the presence of PSTOL1 in NERICAs and other important African varieties, we have initially used PSTOL1-specific PCR-based molecular markers that were designed based on the sequence of the Phosphorus uptake 1 (Pup1) donor variety Kasalath (Chin et al 2011)
These may represent recent mutations in the second PSTOL1 allele or slight differences between parental accessions used in this study and in making the crosses resulting in NERICA varieties

Summary

Introduction

The deficiency of phosphorus (P) in soil is a worldwide problem affecting about 50 % of the rice-cultivated area. Annual average nutrient loss in SSA was estimated at 22 kg of nitrogen (N), 2.5 kg of phosphorus (P), and 15 kg of potassium (K) per hectare of cultivated land, which accounted for an annual loss equivalent to US $4 billion in fertilizer (Sanchez et al 1997). These rates are several times higher than Africa’s annual fertilizer consumption, which accounts for only 0.8 % (1.29 Mt) of the global fertilizer consumption (International Fertilizer Development Center 2013). The development of low-cost technologies for alleviating P deficiency, such as direct use of low-grade phosphate rock in conjunction with organic resources (Nakamura et al 2013; Appleton 2002) could offer a sustainable solution

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Conclusion