Abstract
BackgroundThe genetic mechanism of aluminum (Al) tolerance in rice is great complicated. Uncovering genetic mechanism of Al tolerance in rice is the premise for Al tolerance improvement. Mining elite genes within rice landrace is of importance for improvement of Al tolerance in rice.ResultsGenome-wide association study (GWAS) performed in EMMAX for rice Al tolerance was carried out using 150 varieties of Ting’s core collection constructed from 2262 Ting’s collections with more than 3.8 million SNPs. Within Ting’s core collection of clear population structure and kinship relatedness as well as high rate of linkage disequilibrium (LD) decay, 17 genes relating to rice Al tolerance including cloned genes like NRAT1, ART1 and STAR1 were identified in this study. Moreover, 13 new candidate regions with high LD and 69 new candidate genes were detected. Furthermore, 20 of 69 new candidate genes were detected with significant difference between Al treatment and without Al toxicity by transcriptome sequencing. Interestingly, both qRT-PCR and sequence analysis in CDS region demonstrated that the candidate genes in present study might play important roles in rice Al tolerance.ConclusionsThe present study provided important information for further using these elite genes existing in Ting’s core collection for improvement of rice Al tolerance.
Highlights
The genetic mechanism of aluminum (Al) tolerance in rice is great complicated
High quality Single Nucleotide Polymorphisms (SNPs) (Additional file 7: Table S3) distribution along position on each chromosome were shown in Additional file 2: Figure S2. 3,808,730 SNPs were generated totally, while there were 386,562 SNPs found in the Coding sequence (CDS) region (Additional file 7: Table S3)
Population structure and linkage disequilibrium (LD) estimation Principal component analysis (PCA) were performed with all SNPs for identifying the population structure of Ting’s core collection, and two subpopulations were observed (Fig. 1b)
Summary
The genetic mechanism of aluminum (Al) tolerance in rice is great complicated. Over 50% of the world’s arable land is acidic and about 13% of global rice were produced on acidic soils [1,2,3]. Improving Al tolerance is significantly useful for rice production. Uncovering genetic mechanism of Al tolerance in rice is the premise for Al tolerance improvement. Plant physiologists and breeders have been focusing on revealing genetic mechanism of Al tolerance in rice [7,8,9,10,11,12,13,14,15,16,17]. Two detoxification mechanisms under Al3+ toxicity were illuminated in above studies, i.e. called exclusion of Al3+ producing in root cells and excreting chelating chemicals [18] and accumulation of Al3+ called internal detoxification [10, 14, 19, 20]
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