Mapping and cloning of quantitative trait loci for phosphorus efficiency in crops: opportunities and challenges

Abstract

Phosphorus (P) is an essential mineral element required in large quantities by plants. Globally, the availability of P in many soils is poor. Breeding crops that can acquire and utilise this limited resource with high efficiency is an important goal for agricultural sustainability in the future. The mapping and cloning of quantitative trait loci (QTLs) provides an effective tool in analyzing the genetic mechanisms underlying P efficiency and breeding P-efficient varieties. This paper describes the QTL mapping of traits related to P efficiency which impact on shoot biomass or yield of crops in the past 20 years. It summarises the progress of studies on crop P-efficiency related QTLs and discusses the challenges for the cloning of QTLs. It proposes a scheme to develop crop genotypes with improved P efficiency. It also describes emerging methods, such as QTL-seq, genome-wide association analysis, and RNA-seq, that aid the rapid identification of P-efficiency related genes in crops. Traits conferring P efficiency are heritable. Thus, it is feasible to incorporate phenotyping and selection for P efficiency in crop breeding programs. Identification of QTLs for target traits is a key step to enhancing the P efficiency of crops. Numerous QTLs have been identified that affect P efficiency in key crops, but few causal genes have been identified and breeding P-efficient crop varieties using marker-assisted selection (MAS) has not progressed far. The challenge now is to identify the specific genes controlling P-efficiency related traits. The availability of complete genome sequences for more crops, and the combination of conventional linkage mapping, association mapping, QTL-seq, transcriptomics and gene editing technologies can accelerate the cloning and confirmation of genes underlying QTL affecting P-efficiency related traits. Knowledge of these genes will be helpful in revealing the molecular mechanisms underlying P efficiency in crops, as well as providing the opportunity to improve crop P efficiency through MAS or gene manipulation.