Developing Rice with High Yield under Phosphorus Deficiency: Pup1 Sequence to Application    

Abstract

The major quantitative trait locus (QTL) Phosphorus uptake1 (Pup1) confers tolerance of phosphorus deficiency in soil and is currently one of the most promising QTLs for the development of tolerant rice (Oryza sativa) varieties. To facilitate targeted introgression of Pup1 into intolerant varieties, the gene models predicted in the Pup1 region in the donor variety Kasalath were used to develop gene-based molecular markers that are evenly distributed over the fine-mapped 278-kb QTL region. To validate the gene models and optimize the markers, gene expression analyses and partial allelic sequencing were conducted. The markers were tested in more than 80 diverse rice accessions revealing three main groups with different Pup1 allele constitution. Accessions with tolerant (group I) and intolerant (group III) Pup1 alleles were distinguished from genotypes with Kasalath alleles at some of the analyzed loci (partial Pup1; group II). A germplasm survey additionally confirmed earlier data showing that Pup1 is largely absent from irrigated rice varieties but conserved in varieties and breeding lines adapted to drought-prone environments. A core set of Pup1 markers has been defined, and sequence polymorphisms suitable for singlenucleotide polymorphism marker development for high-throughput genotyping were identified. Following a marker-assisted backcrossing approach, Pup1 was introgressed into two irrigated rice varieties and three Indonesian upland varieties. First phenotypic evaluations of the introgression lines suggest that Pup1 is effective in different genetic backgrounds and environments and that it has the potential to significantly enhance grain yield under field conditions.

Identifying markers associated with yield traits in Nagina22 rice mutants grown in low phosphorus field or in alternate wet/dry conditions

“…The sequenced gene, Pup1 in Kasalath rice variety was reported to provide tolerance to P deficiency under field conditions in Japan (Wissuwa et al, 1998;Wissuwa et al, 2002;Chin et al, 2010Chin et al, , 2011 and it was independently mapped on chromosome 12 by Ni et al (1998). Introgression lines with Pup1 region in different genetic backgrounds have the potential to significantly increase grain yield under P deficient field conditions (Chin et al, 2011). In the present study also, it is significant that K-1(one of the Pup1 markers) was linked to tiller number only in low P conditions but not in normal and AWD conditions.…”

“…For genotyping, polymerase chain reaction (PCR) was done with 44 SSR markers from RM series (McCouch et al, 2002) and four Pup1 gene specific markers (Chin et al, 2011). The amplified fragments were evaluated as present (1) and absent (0) bands.…”

Application of Pup1 Markers for Identification of Rice (Oryza Sativa L.) Cultivars with Tolerance to Phosphorus Deficiency

“…13 Recently quantitative genetic studies were begun to dissect the underlying genetics of PD tolerance in rice (Chin et al, 2011). A major quantitative trait locus (QTL) controlling PD tolerance was identified on the rice chromosome 12 using recombinant inbred lines (RILs) generated from a cross between a PD tolerant landrace Kasalath and sensitive landrace Nipponbare (Wissuwa et al, 2002).…”

“…A major quantitative trait locus (QTL) controlling PD tolerance was identified on the rice chromosome 12 using recombinant inbred lines (RILs) generated from a cross between a PD tolerant landrace Kasalath and sensitive landrace Nipponbare (Wissuwa et al, 2002). Later this QTL was fine mapped and labeled as Pup1 (Chin et al, 2011).…”

A REVIEW OF MOLECULAR MARKERS TO GENES INVOLVED IN MINERAL NUTRITION EFFICIENCY CONTROL IN RICE (Oryza sativa L.)

“…QTL for NUE were mapped on chromosomes 1, 2, 3, 4, 6, 7, 9, 10 and 11 in rice variety of subspecies indica (Zhenshan 97 ½ Minghui 63) ( Table 1) [33][34][35][36][37][38][39][40]. Four genomic regions in chromosomes 1, 3, 4 and 7 involved in expression of both studied traits, NDT and NUE, are flanked by markers G393-C922, RM232-C63, G235-G102 and RG678-R1440, receptively.…”