TABLE 2.
Significant genotype–environment associations with heat stress in Acropora millepora, Pocillopora damicornis and Pocillopora acuta
| (a) Number of significant genotype–environment associations | |||
|---|---|---|---|
| ENV | collinear ENV | # SNPs | #uSNPs |
| Acropora millepora | |||
| BAF5 | SST5.osd, SST5.hsd | 10 | 20 |
| BAF1 | – | 14 | |
| Pocillopora damicornis | |||
| BAF5 | SST5.hsd, SST5.osd | 18 | 25 |
| BAF1 | – | 10 | |
| Pocillopora acuta | |||
| BAF5 | SST5.hsd, SSS.om, SSS.hm | 4 | 9 |
| BAF1 | – | 7 | |
| (b) Top five significant genotype–environment associations | |||||
|---|---|---|---|---|---|
| Closest gene | |||||
| Chr/Contig | Position | Name | Distance | ENV | q‐value |
| Acropora millepora | |||||
| chr2 | 15023481 | MICOS complex subunit MIC60 | 14044 BFE | BAF5 | 4.08E‐11 |
| Sc0000070 | 588818 | Low‐density lipoprotein receptor‐related protein 6 | 7929 BFS | BAF1 | .0001 |
| chr12 | 3092569 | Adipose triglyceride lipase | 1902 BFS | BAF1 | .0001 |
| chr3 | 16787176 | Enoyl‐[acyl‐carrier‐protein] reductase | CDS | BAF1 | .0002 |
| chr11 | 5209122 | Hemicentin‐2 | 16601 BFE | BAF1 | .0007 |
| Pocillopora damicornis | |||||
| NW_020846863.1 | 50886 | Melanocyte‐stimulating hormone receptor | 43840 BFE | BAF1 | 7.43E‐07 |
| NW_020844635.1 | 120593 | Omega‐3 fatty acid desaturase fat‐1 | 8241 BFS | BAF5 | 1.92E‐05 |
| NW_020846229.1 | 44431 | Protocadherin Fat 3 | CDS | BAF1 | .0001 |
| NW_020847397.1 | 2088 | Tumour necrosis factor receptor superfamily member 27 | 2079 BFS | BAF1 | .0005 |
| NW_020846232.1 | 92716 | Glutamine and serine‐rich protein 1 | 3792 BFE | BAF5 | .0007 |
| Pocillopora acuta | |||||
| NW_020845243.1 | 143820 | Quinone oxidoreductase PIG3 | Intronic | BAF1 | .0003 |
| NW_020847027.1 | 161943 | Multidrug resistance‐associated protein 4 | CDS | BAF1 | .0004 |
| NW_020845228.1 | 63533 | Receptor‐type tyrosine‐protein phosphatase delta | CDS | BAF1 | .0011 |
| NW_020845314.1 | 124 | — | — | BAF1 | .0013 |
| NW_020847378.1 | 374764 | Golgin subfamily A member 1 | Intronic | BAF1 | .0040 |
Table (a) displays the number of SNPs significantly associated (#SNPs; q < .01) with the environmental variables (ENV) describing bleaching alert frequency (BAF5 and BAF1, computed out of sea surface temperature data at 5 and 1 km of resolution, respectively). The ‘collinear ENV’ column displays the identifiers of environmental variables highly correlated (R > .9) with ENV. The #uSNPs column shows the number of SNPs found significant for at least one of the two BAF variables. Table (b) displays the five significant SNPs more strongly associated with BAF5 and BAF1. For every SNP, the table shows the genomic position (chromosome or contig, and position), the name of the closest known gene with the distance from the SNP (number of nucleotides before start—BFS—or before end—BFE, intronic or in coding sequence—CDS), the environmental variable involved in the association (ENV) and the q‐value of the association. The panel in top right position displays the key of the abbreviations for the identifiers of the environmental variables. Table S5 displays the count of significant SNPs for all the other (non‐collinear) environmental variables; Table S6 shows the complete list of SNPs significantly associated with BAF5 and BAF1. Environmental variables identifiers key: BAF5 = bleaching alert frequency (5‐km resolution) BAF1 = bleaching alert frequency (1‐km resolution) SST5 = sea surface temperature (5‐km resolution) SSS = sea surface salinity; .om = overall mean .hm = highest monthly mean .osd = overall standard deviation .hsd = standard dev. of month with highest mean.