Table 4. Summary of identified polymorphisms in LD with the leading SNPs from the epistatic GWA analysis.
Four unique interacting pairs of loci were significantly associated with root length (Table 2). Here, the genes located within 1000bp of the leading SNPs, together with the mutational effects of the identified polymorphisms, are listed.
| Chr | SNP position (bp) | In pair | Locus | # Mutations (# in LD) 1 | Mutation Effects |
|---|---|---|---|---|---|
| 3 | 66596 | 1, 4 | At3g01180 | 1 (0) | 1 upstream |
| At3g01185 | 1 (0) | 1 syn | |||
| 3 | 9,272,294 | 1 | At3g25520 | 4 (21) | 1 intron, 3 upstream |
| 9,273,674 | At3g25530 | 14 (21) | 1 mis, 1 splice, 1 syn, 2 intron, 9 upstream | ||
| At3g25540 | 17 (21) | 1 mis, 4 syn, 2 intron, 5 5'UTR, 5 upstream | |||
| At3g25545 | 3 (21) | 3 upstream | |||
| 5 | 18,241,640 | 4 | At5g45120 | 6 (5) | 2 mis, 4 syn |
| 1 | 17,257,526 | 2 | At1g46624 | 1 (0) | 1 non-coding exon |
| 5 | 15,862,026 | 2 | At5g39610 | 2 (4) | 6 upstream 3 |
| 15,862,525 | At5g39620 | 2 (4) | 6 downstream 3 | ||
| 3 | 10,891,195 | 3 | At3g28865 | 4 (7) | 4 non-coding exon |
| At3g28870 | 2 (7) | 1 mis, 1 syn | |||
| At3g28880 | 3 (7) | 3 upstream | |||
| 5 | 1,027,939 | 3 | At5g03840 | 1 (1) | 1 upstream |
| At5g03850 | 1 (1) | 1 downstream |
1The number of polymorphisms associated with each listed gene, with the number of these polymorphisms that are in LD with the leading SNP in parenthesis. Some mutations are associated with more than one gene.
2Abbreviations for mutational effects: syn = synonymous variant; mis = missense variant; splice = splice site variant.
3SNPs more than 1000bp away from the nearest gene