Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping
Figure 4
Haplotype analysis of the Nrat1 gene region.
A) Haplotypes observed in 373 accessions using the 44,000 SNP data. Haplotype 1 was unique to aus ancestry and associated with Al susceptibility within the aus subpopulation, explaining 40% of the Al tolerance variation within aus. Haplotypes 1, 2, and 3 share the same 4-SNP haplotype (id2001231-id2001243) flanking the Nrat1 gene (1.66 Mb). SNP positions are based on MSU6 annotation and subpopulations are abbreviated as follows: IND = indica, TEJ = temperate japonica, TRJ = tropical japonica, G.V. = groupV/aromatic, Admix = admixed lines without 80% ancestry to any one subpopulation. B) Haplotypes at the Nrat1 gene (1.66 Mb) in the (9) aus and (6) indica accessions sharing the 4-SNP haplotype flanking the Nrat1 gene. Polymorphisms are identified with numbers along bottom of figure. A STOP codon occurs in exon 13 between polymorphism 17 and 18. Gray shaded cells represent the reference allele and plant ID# 173 is the reference genotype ‘Nipponbare’. Yellow shaded cells represent polymorphisms in introns or synonymous polymorphisms in exons. Red shaded cells represent polymorphisms that result in amino acid substitutions (Indel or non-synonymous), unshaded cells marked with “−” indicate missing data, and +* indicates an intron insertion >500 bp.