title: Identification of quantitative trait loci for phosphorus use efficiency traits in rice using a high density SNP map.
abstract: BACKGROUND
  Soil phosphorus (P) deficiency is one of the major limiting factors to crop production. The development of crop varieties with improved P use efficiency (PUE) is an important strategy for sustainable agriculture. The objectives of this research were to identify quantitative trait loci (QTLs) linked to PUE traits using a high-density single nucleotide polymorphism (SNP) map and to estimate the epistatic interactions and environmental effects in rice (Oryza sativa L.).
  
  
  RESULTS
  We conducted a two-year field experiment under low and normal P conditions using a recombinant inbred population of rice derived from Zhenshan 97 and Minghui 63 (indica). We investigated three yield traits, biomass (BIOM), harvest index (HI), and grain yield (Yield), and eight PUE traits: total P uptake (PUP), P harvest index (PHI), grain P use efficiency (gPUE) based on P accumulation in grains, straw P use efficiency (strPUE) based on P accumulation in straw, P use efficiency for biomass (PUEb) and for grain yield (PUEg) based on P accumulation in the whole plant, P translocation (PT), and P translocation efficiency (PTE). Of the 36 QTLs and 24 epistatic interactions identified, 26 QTLs and 12 interactions were detected for PUE traits. The environment affected seven QTLs and three epistatic interactions. Four QTLs (qPHI1 and qPHI2 for PHI, qPUEg2 for PUEg, and qPTE8 for PTE) with strong effects were environmentally independent. By comparing our results with similar QTLs in previous studies, three QTLs for PUE traits (qPUP1 and qPUP10 for PUP, and qPHI6 for PHI) were found across various genetic backgrounds. Seven regions were shared by QTLs for yield and PUE traits.
  
  
  CONCLUSIONS
  Most QTLs linked to PUE traits were different from those linked to yield traits, suggesting different genetic controls underlying these two traits. Those chromosomal regions with large effects that are not affected by different environments are promising for improving P use efficiency. The seven regions shared by QTLs linked to yield and PUE traits imply the possibility of the simultaneous improvement of yield and PUE traits.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. wkhzau@sina.com.|MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. wkhzau@sina.com.
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. cuikehui@mail.hzau.edu.cn.|MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. cuikehui@mail.hzau.edu.cn.
authors.forename: Kehui
authors.initials: K
authors.lastname: Cui
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. liuguoling1222@sina.com.|MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. liuguoling1222@sina.com.
authors.forename: Guoling
authors.initials: G
authors.lastname: Liu
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. weibo.xie@mail.hzau.edu.cn.
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. yingcai@webmail.hzau.edu.cn.
authors.forename: Huihui
authors.initials: H
authors.lastname: Yu
authors.affiliation: MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. junfeng401@163.com.|Rice Research Institute, Guangdong Academy of Agricultural Science, Guangzhou, 510640, Guangdong, China. junfeng401@163.com.
authors.forename: Junfeng
authors.initials: J
authors.lastname: Pan
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. jhuang@mail.hzau.edu.cn.|MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. jhuang@mail.hzau.edu.cn.
authors.forename: Jianliang
authors.initials: J
authors.lastname: Huang
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. nielixiao@mail.hzau.edu.cn.|MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. nielixiao@mail.hzau.edu.cn.
authors.forename: Lixiao
authors.initials: L
authors.lastname: Nie
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. farooqagronomist@googlemail.com.|MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. farooqagronomist@googlemail.com.|Department of Agriculture, Anbar Campus of Abdul Wali Khan University, Mardan, Khyber Pakhtunkhwa, Pakistan. farooqagronomist@googlemail.com.
authors.forename: Farooq
authors.initials: F
authors.lastname: Shah
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. speng@mail.hzau.edu.cn.|MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China. speng@mail.hzau.edu.cn.
authors.forename: Shaobing
authors.initials: S
authors.lastname: Peng
mesh_terms: D002874:Chromosome Mapping; D004843:Epistasis, Genetic; D008040:Genetic Linkage; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010641:Phenotype; D010758:Phosphorus / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
chemical_list: D010758:Phosphorus