Skip to main content

Table 2 Description of 1-Mb windows that explained more than 0.8% of genetic variance and significant SNPs within those windows for genome-wide recombination number in white layers

From: Identification of recombination hotspots and quantitative trait loci for recombination rate in layer chickens

GGA_Mb # SNP GV%a WPPAb Most significant SNPc SPPId GV% SNP MAFe Position, Mb P- valuef Candidate gene
1_54 126 1.00 0.27 AX-80768024 0.02 0.05 0.132 54.56 0.003 TDG, NFYB
1_84 112 8.39 0.54 AX-80984549 0.52 8.38 0.151 84.06 0.04 RPL24, IMPG2
1_158 165 1.00 0.23 AX-75313537 0.01 0.42 0.349 158.73 0.005  
1_162–165 801 4.39 0.89 AX-75325622 0.02 1.3 0.189 165.07 0.006 RGCC, WBP4, LECT1
1_171 198 1.00 0.34 AX-75341236 0.02 0.1 0.316 171.68 0.03 CCNA1
2_76–77 408 4.13 0.76 AX-76154814 0.02 0.15 0.346 77.43 0.06 ANKH
2_81–82 196 3.91 0.64 AX-76163810 0.01 0.38 0.312 82.25 0.04  
3_85 468 3.92 0.79 AX-76572482 0.01 0.16 0.357 86.15 0.04 PRIM2
4_44 183 7.93 0.56 AX-76669056 0.48 7.88 0.126 44.57 0.08 EPGN, AREGB, EREG
5_13 398 2.23 0.64 AX-76779213 0.01 0.26 0.355 13.59 0.02 IGF2, MRPL23, RAG1, RAG2
10_1 382 1.08 0.39 AX-75574022 0.01 0.1 0.472 1.06 0.03 RPS17L
13_3 166 2.37 0.50 AX-75754286 0.01 0.77 0.465 3.62 0.02  
20_5 283 1.02 0.35 AX-76217814 0.01 0.2 0.316 5.09 0.02 YWHAB
20_10 189 1.15 0.29 AX-76199322 0.03 0.12 0.385 10.96 0.005 SPO11
  1. aGV%, proportion of the genetic variance explained by window or SNP
  2. bWPPA, window posterior probability of association
  3. cMost significant SNP, SNP with the highest SPPI in the 1 Mb region
  4. dSPPI, SNP posterior probability of inclusion
  5. eMAF, minor allele frequency
  6. fP-value, the significance of the single SNP as a fixed effect in ASREML