High-Density Genetic Mapping Identifies New Major Loci for Tolerance to Low-Phosphorus Stress in Soybean.

Dan Zhang,Shanshan Chu,Hongyan Li,Jinshe Wang,Deyue Yu,Haiyan Lv,Zhenbin Hu,Hengyou Zhang

doi:10.3389/fpls.2016.00372

Abstract

Phosphorus (P) is essential for all living cells and organisms, and low-P stress represents a major constraint on plant growth and yield worldwide. Soybean is an important economical resource of protein and oil for human and animals, and soybean is also a high-P demand species that is sensitive to low-P stress, which is considered a major constraint on soybean production. However, P efficiency is an important complex quantitative trait involving multiple genes, and the mechanisms underlying soybean P efficiency are largely unknown. Here, we reported the construction of a high-density genetic map using a specific-locus amplified fragment sequencing (SLAF-seq) strategy in soybean. This map, spanning 3020.59 cM in length, contained 6159 markers on 20 chromosomes, with an average distance of 0.49 cM between adjacent markers. Based on this map, 20 loci, including eight novel loci, associated with P efficiency-related traits were identified across multiple years and treatments. The confidence intervals of almost all QTLs were refined significantly, and the accuracy of this map was evidenced by coincident detections of the previously identified P efficiency-related genes GmACP1 and GmPT1. Notably, a highly significant novel QTL located on chromosome 4, q4-2, was identified across traits, years and treatments. Several candidate genes, such as a pectin methylesterase-encoding gene (Glyma.04G214000) and a protein kinase gene (Glyma.13G161900), with significantly differential expression upon low-P stress were considered as promising candidates involved in regulating soybean P efficiency. Markers that tightly associated with P efficiency could be used for marker-assisted selection in a soybean P efficient breeding program. Further, dissection of these QTLs will facilitate gene cloning underlying P efficiency in soybean, and increase our understanding of efficient use of P in enhancing crop yield.

Highlights

Phosphorus (P) involves in all living cells and organisms through the synthesis of nucleic acids (e.g., DNA and RNA) and the cellular energy storage molecule adenine tri-phosphate (ATP) as well as all cellular phosphorylation events (Johnston et al, 2000; Khan et al, 2009)
These traits include plant height (PH), root day weight (RDW), shoot dry weight (SDW), total dry weight (TDW), phosphorus acquisition efficiency (PAE), phosphorus use efficiency (PUE), P concentration (PC) and acid phosphatase activity (APA) under different P conditions
A total of 188.77 M paired-end reads were obtained for both parents and 146 recombinant inbred line (RIL), with an average of 1.29 M reads for each individual line

Summary

Introduction

Phosphorus (P) involves in all living cells and organisms through the synthesis of nucleic acids (e.g., DNA and RNA) and the cellular energy storage molecule adenine tri-phosphate (ATP) as well as all cellular phosphorylation events (Johnston et al, 2000; Khan et al, 2009). Because almost half of the world’s agricultural lands are known to be severely deficient in this element (Elser, 2012) due to its low mobility and high fixation in soils (Kochian, 2012), P has become a worldwide constraint for crop productivity. Insufficient P content in soil becomes more severe in some developing countries because of rapidly expanding population growth and a lack of financial support to obtain P-containing fertilizers. To meet these present and future challenges of limited P resources, identification and dissection of P-efficient genes represent the important steps for the subsequent development of P-efficient crops, securing sustainable food supply and agriculture (Gaxiola et al, 2012)

Methods

Results

Conclusion