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Front. Plant Sci. | doi: 10.3389/fpls.2018.01838

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 Zhao1,  Jiayu Song1, Aiting Wu1, Tao Hu1 and  Jinquan Li2, 3*
  • 1Rice Research Institute, Shenyang Agricultural University, China
  • 2College of Agriculture, South China Agricultural University, China
  • 3Department of Plant Breeding and Genetics, Max Planck Institut für Pflanzenzüchtungsforschung, Germany

Trivalent Aluminium (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 26 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 26 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 importance sources for Al tolerance in rice and the mapping results could provide important information to breed Al tolerant rice cultivars through marker-assisted selection.

Keywords: Aluminium tolerance, Genome-wide association mapping, Relative root elongation, Rice landraces, Al tolerant QTL, SLAF-seq

Received: 09 Mar 2018; Accepted: 27 Nov 2018.

Edited by:

Peter Ryan, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Australia

Reviewed by:

Harsh Raman, New South Wales Department of Primary Industries, Australia
Wricha Tyagi, Central Agricultural University, India
Saul J. Newman, Research School of Biology, Australian National University, Australia  

Copyright: © 2018 Zhao, Song, Wu, Hu and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Jinquan Li, South China Agricultural University, College of Agriculture, Guangzhou, 510642, Guangdong, China, jqli@mpipz.mpg.de