Identification of quantitative trait loci for phosphorus use efficiency traits in rice using a high density SNP map.

Kai Wang,Shaobing Peng,Lixiao Nie,Farooq Shah,Weibo Xie,Jianliang Huang,Guoling Liu,Huihui Yu,Kehui Cui,Junfeng Pan

doi:10.1186/s12863-014-0155-y

Abstract

BackgroundSoil 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.).ResultsWe 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.ConclusionMost 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.

Highlights

Soil phosphorus (P) deficiency is one of the major limiting factors to crop production
Lines with too short a growth duration and with very low grain yield were not used for the field experiments because it is less significant to estimate P use efficiency (PUE) traits based on low grain yield or biomass from the viewpoint of crop production
P use efficiencies based on the P stored in a specific part of plant is distinct from those based on the total P in an entire plant

Summary

Introduction

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. Low levels of available P in soils and P use efficiency (PUE) are becoming the two major constraints for crop production. For soils with low total P content, strategies include regular applications of small doses of P and the improvement of internal PUE. For soils with high unavailable P content, the most common strategy is the increase in P uptake efficiency through the proliferation and extension of plant roots, including the selection of deep rooting, thick roots, and strong root penetration ability [5]. Most investigations have focused on increasing P acquisition abilities by improving features such as root traits, root exudates, mycorrhiza, and high-affinity P transporters [7,8,9,10]

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