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Table 1 Gene diversity, linkage disequilibrium and genetic differentiation between populations estimated by FST statistic

From: Evolutionary Processes Involved in the Emergence and Expansion of an Atypical O. sativa Group in Madagascar

      Asian panel Malagasy panel
Population N Gene diversity Distancea (kb) for r2 ≤ 0.2 Genetic differentiation between subpopulations estimated by FST statistic
indica XI-1A XI-1B XI-2 XI-3 cAus japonica GJ- trop GJ-sbtrop GJ-temp cBas G1 Gm G6
Indica (XI) 1139 0.19 ± 0.09 75–100               
- XI-1A 178 0.13 ± 0.06 250–300   0.00             
- XI-1B 49 0.15 ± 0.07 250–300   0.25 0.00            
- XI-2 179 0.18 ± 0.08 125–150   0.23 0.17 0.00           
- XI-3 392 0.16 ± 0.06 125–150   0.25 0.18 0.15 0.00          
cAus 169 0.16 ± 0.08 200–250 0.42 0.53 0.49 0.42 0.49 0.00 0.73        
japonica (GJ) 495 0.11 ± 0.04 350–400 0.66              
- GJ-trop 210 0.09 ± 0.04 500–600   0.74 0.74 0.68 0.68 0.70   0.00       
- GJ-sbtrop 105 0.05 ± 0.02 700–800   0.76 0.78 0.69 0.69 0.71   0.25 0.00      
- GJ-temp 150 0.03 ± 0.01 700–800   0.79 0.83 0.72 0.71 0.75   0.30 0.43 0.00     
cBas 62 0.12 ± 0.06 500–600 0.54 0.65 0.62 0.56 0.59 0.56 0.51 0.48 0.56 0.64 0.00    
G1 156 0.14 ± 0.09 125–150 0.07 0.14 0.14 0.11 0.16 0.44 0.73 0.69 0.70 0.74 0.56 0.00   
Gm 220 0.09 ± 0.05 600–700 0.42 0.57 0.58 0.41 0.52 0.55 0.78 0.77 0.80 0.82 0.70 0.46 0.00  
G6 45 0.10 ± 0.05 1250–1500 0.66 0.70 0.69 0.63 0.65 0.64 0.17 0.13 0.34 0.43 0.46 0.62 0.75 0.00
  1. N number of accessions; in the cases of indica (XI) and japonica (GJ), N includes 342 XI-adm and 30 GJ-adm accessions, respectively. r2: Linkage disequilibrium (LD); a: threshold of pairwise distance between markers above which the mean r2 reaches values below 0.2. The 64 Admix accessions of the A-panel, the 196 Admix, 1 cAus and 2 cBas accessions of the M-Panel were excluded from LD, gene diversity and genetic differentiation analyses