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United States Department of Agriculture

Agricultural Research Service

Research Project: Characterization of Pup1 Candidate Genes

Location: Plant, Soil and Nutrition Research

2013 Annual Report


1a.Objectives (from AD-416):
A multidisciplinary team involving USDA, Embrapa, JIRCAS, IRRI and Moi University will work on the identification and characterization of genes associated with maize P efficiency (tolerance to low P). The objectives for this research project include: 1. Pup-1 candidate gene identification in maize 2. QTL/gene mapping for P use efficiency in maize 3. Inheritance studies on maize root architecture under high and low P 4. Validation of maize Pup-1 candidate genes and if necessary, novel P efficiency QTL (if maize Pup1 homologues are not functional in P efficiency)


1b.Approach (from AD-416):
A multidisciplinary team involving USDA, Embrapa, JIRCAS, IRRI and Moi University will work on the identification and characterization of genes associated with maize P efficiency (tolerance to low P). Bioinformatics will be used to identify homologues of the rice Pup-1 (P uptake efficiency) gene in maize and a set of markers for these genes will be developed. An Embrapa inbred line panel that was developed for breeding for P efficiency be phenotyped in the field for this trait measured as grain yield under contrasting P conditions and in the greenhouse/lab for root architecture traits; also the Buckler association panel will be phenotyped for P efficiency and root architecture traits in the green house/lab at USDA-ARS. Finally, a maize RIL population from the cross of a highly P efficient tropical maize line (L3) with a P inefficient line (L22) will be phenotyped to identify QTLs for P acquisition, internal P efficiency and root architecture traits. Also, candidate genes for p efficiency will be mapped on the same RIL population, in order to verify the co-segregation of Pup-1 homologs with QTLs for different P-efficiency traits. Finally, association analysis using Embrapa’s elite inbred lines panel and the Buckler maize association panel will be carried out to validate candidate genes.


3.Progress Report:

Our initial research involved bioinformatics-based search of maize homologs using the rice phosphate (P) acquisition efficiency gene, OsPSTOL1 as the query. This gene is responsible for the rice P efficiency (which is ability to maintain yields under low P soil conditions) QTL, Pup1 (P uptake 1). This analysis identified four predicted genes in the maize genome sharing more than 65% of sequence identity with OsPSTOL1, which are our initial candidate genes for analysis. These genes are located on chromosomes 3, 4 and 8. Genetic markers (SNPs or single nucleotide polymorphisms) diagnostic for these 4 genes between the parents of a maize genetic mapping population were identified and converted to a type of genetic marker that was used to map their physical position on the maize genome. We identified maize lines that carry interesting versions of the maize PSTOL1 genes and these maize lines are being grown on nutrient sufficient and low P soils to see if any of these genes confer increases in yield on the low P soil (increased P efficiency).


Last Modified: 7/24/2014
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