Mining Beneficial Genes for Aluminum Tolerance Within a Core Collection of Rice Landraces Through Genome-Wide Association Mapping With High Density SNPs From Specific-Locus Amplified Fragment Sequencing.

Minghui Zhao,Jiayu Song,Jinquan Li,Tao Hu,Aiting Wu

doi:10.3389/fpls.2018.01838

Abstract

Trivalent Aluminum (Al3+) in acidic soils is harmful to root growth and significantly reduce crop yields. Therefore, mining beneficial genes for Al tolerance is valuable for rice production. The objective of this research is to identify some beneficial genes for Al tolerance from rice landraces with high density SNP set from SLAF-seq (Specific-Locus Amplified Fragment sequencing). A total of 67,511 SNPs were obtained from SLAF-seq and used for genome-wide association study (GWAS) for Al tolerance with the 150 accessions of rice landraces in the Ting's rice core collection. The results showed that rice landraces in the Ting's rice core collection possessed a wide-range of variation for Al tolerance, measured by relative root elongation (RRE). With the mixed linear models, GWAS identified a total of 25 associations between SNPs and Al tolerant trait with p < 0.001 and false discovery rate (FDR) <10%. The explained percentage by quantitative trait locus (QTL) to phenotypic variation was from 7.27 to 13.31%. Five of twenty five QTLs identified in this study were co-localized with the previously cloned genes or previously identified QTLs related to Al tolerance or root growth/development. These results indicated that landraces are important sources for Al tolerance in rice and the mapping results could provide important information to breed Al tolerant rice cultivars through marker-assisted selection.

Highlights

Rice (Oryza sativa L.) is an important crop in the world
Previous researchers have identified a number of quantitative trait loci (QTLs) for Al tolerance in rice (Nguyen et al, 2002; Ma and Furukawa, 2003; Mao et al, 2004; Xue et al, 2007; Famoso et al, 2011), and found a few genes linked to Al tolerance (e.g., Yokosho et al, 2011; Chen et al, 2012; Huang et al, 2012; Xia et al, 2013; Li et al, 2014)
In the context of quantitative trait locus (QTL) mapping for Al tolerance, most of these previous researches were conducted with bi-parent segregation populations and linkage mapping

Summary

Introduction

Rice (Oryza sativa L.) is an important crop in the world. There is about 13% of global rice field on acidic soils (Vonuexkull and Mutert, 1995). Exploring the genetic mechanism of Al tolerance in rice is of importance to understand why Al3+ is toxic to the plants and to breed Al tolerant varieties for rice production. Serval researches on the genetic mechanism of Al tolerance in rice have been reported (e.g., Famoso et al, 2010, 2011; Cai et al, 2011). Previous researchers have identified a number of quantitative trait loci (QTLs) for Al tolerance in rice (Nguyen et al, 2002; Ma and Furukawa, 2003; Mao et al, 2004; Xue et al, 2007; Famoso et al, 2011), and found a few genes linked to Al tolerance (e.g., Yokosho et al, 2011; Chen et al, 2012; Huang et al, 2012; Xia et al, 2013; Li et al, 2014). It is important to apply GWAS with modern genotyping technology for QTL mapping for Al tolerance

Objectives

Methods

Results