Association Mapping for Aluminum Tolerance in a Core Collection of Rice Landraces.

Peng Zhang,Jinquan Li,Muhammad Qasim Shahid,Kaizhen Zhong,Hanhua Tong

doi:10.3389/fpls.2016.01415

Abstract

Trivalent aluminum (Al3+) has drastic effect on the rice production in acidic soils. Elite genes for aluminum (Al) tolerance might exist in rice landraces. Therefore, the purpose of this research is to mine the elite genes within rice landraces. Association mapping for Al tolerance traits [i.e., relative root elongation (RRE)] was performed by using a core collection of 150 accessions of rice landraces (i.e., Ting’s rice core collection). Our results showed that the Ting’s rice core collection possessed a wide-range of phenotypic variation for Al tolerance, and the index of Al tolerance (RRE) was ranged from 0.22 to 0.89. Moreover, the groups with different origins and compositions of indica and japonica rice showed different degrees of tolerance to varying levels of Al. These rice landraces were further screened with 274 simple sequence repeat markers, and association mapping was performed using a mixed linear model approach. The mapping results showed that a total of 23 significant (P < 0.05) trait–marker associations were detected for Al tolerance. Of these, three associations (13%) were identical to the quantitative trait loci reported previously, and other 20 associations were reported for the first time in this study. The proportion of phenotypic variance (R2) explained by 23 significant associations ranged from 5.03 to 20.03% for Al tolerance. We detected several elite alleles for Al tolerance based on multiple comparisons of allelic effects, which could be used to develop Al tolerant rice cultivars through marker-assisted breeding.

Highlights

Acidic soils occupy approximately 30% of the world’s ice-free area, and over 50% of the world’s arable land is acidic (Vonuexkull and Mutert, 1995; Kochian et al, 2004; Ryan et al, 2011)
Most of the previous studies on quantitative trait locus (QTL) mapping for Al tolerance were based on the selection of typical Al tolerant and sensitive rice accessions for constructing a segregating population and mapping
A core collection consisted of rice landraces was used for association mapping for Al tolerance in the present study

Summary

Introduction

Acidic soils occupy approximately 30% of the world’s ice-free area, and over 50% of the world’s arable land is acidic (Vonuexkull and Mutert, 1995; Kochian et al, 2004; Ryan et al, 2011). Al has been shown to be beneficial to some plant species including rice when supplied at low concentrations, and Al’s benefits were summarized in Abbreviations: Al3+, trivalent aluminum; GLM, general linear model; MLM, mixed linear model; PIC, polymorphism information content; QTL, quantitative trait locus; RRE, relative root elongation; SD, standard deviation; SSR, simple sequence repeat. Up to 60% of the acidic soils in the world occur in developing countries, where food production is affected by Al toxicity in acid land and always a major area of research for plant physiologists and breeders (Kochian et al, 2005; Delhaize et al, 2012a; Fujii et al, 2012; Xia et al, 2013; Caniato et al, 2014; Li et al, 2014). Identification of elite genes for Al tolerance is of paramount importance for plant growth and production in the world

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