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Table 1 Marker-trait associations from GWAS scanning for ACR, PHC and plant sex and associated candidate genes in D. rotundata

From: Association mapping of plant sex and cross-compatibility related traits in white Guinea yam (Dioscorea rotundata Poir.) clones

Trait Method Markers Chr Marker position (bp) QTN effect LOD score log10(P) R2 (%) MAF GfC1 Orthologs Putative function
Sex mrMLM chr10_867,049 10 867,049 −0.66 4.61 5.40 20.33 0.46 C ABA_WDS Controls sex before transpiration in vascular plants
  mrMLM chr16_9,051,658 16 9,051,658 0.92 5.82 6.65 0.00 0.15 C   
  FASTmrMLM chr10_867,049 10 867,049 −0.54 4.50 5.27 13.81 0.46 C   
  FASTmrMLM chr16_9,051,658 16 9,051,658 0.71 4.45 5.22 0.00 0.14 C   
  FASTmrEMMA chr10_867,049 10 867,049 −1.09 4.61 5.39 9.90 0.46 C   
  FASTmrEMMA chr16_9,051,658 16 9,051,658 1.61 5.82 6.65 13.25 0.14 C   
  pLARmEB chr10_867,049 10 867,049 −0.55 5.54 6.36 14.29 0.46 C   
  pKWmEB chr10_867,049 10 867,049 −0.55 5.60 6.42 20.22 0.46 C   
  mrMLM chr11_4,499,228 11 4,499,228 0.11 4.79 5.99 11.23 0.27 C WD40_repeat Key regulator of plant-specific developmental events
ACR FASTmrEMMA chr03_4,353,133 3 4,353,133 54.81 5.09 5.89 12.78 0.12 C   
  pLARmEB chr05_15,917,143 5 15,917,143 −7.80 4.16 4.92 2.11 0.11 T ATS3 Plant seed-specific proteins
  pLARmEB chr12_140,889 12 140,889 10.06 4.95 5.75 0.00 0.11 G Cupin_1 Plant seed storage proteins
            WRKY_dom Involved in the gibberellic acid-induced expression
PHC FASTmrEMMA chr03_4,353,133 3 4,353,133 68.35 6.41 7.26 19.87 0.02 C   
  1. ACR average crossability rate, PHC percentage high crossability, Chr chromosome, R2 phenotypic variance explained, QTN quantitative trait nucleotide, MAF minor allele frequency, GfC1 genotype for code 1