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Table 1 AmpliSeq results and classification of markers

From: Targeted amplicon sequencing + next-generation sequencing–based bulked segregant analysis identified genetic loci associated with preharvest sprouting tolerance in common buckwheat (Fagopyrum esculentum)

  Cross A_1 (n = 94) Cross B_1 (n = 87) Cross C (n = 84)
Sh linka PHS linka Whole-genomea Total Sh link PHS link Whole-genome Total Sh link PHS link Whole-genome Total
Number of SNP detected markers 67 56 176 299 74 41 124 239 68 34 140 242
After filtering and before removing duplicateb 57 48 112 217 50 14 61 125 43 11 55 109
Remove duplicated markers (no. of duplicated marker) 12 (45) 18 (30) 98 (14) 127 (90) 10 (40) 10 (4) 54 (7) 74 (51) 5 (38) 8 (3) 49 (6) 62 (47)
 LG1 12 (45) 2 (1) 13 (2) 27 (48) 10 (40) 1 (1) 8 (3) 19 (44) 5 (38) 2 (1) 6 (3) 13 (42)
 LG2 0 0 11 (3) 11 (3) 0 0 10 10 0 0 4 (1) 4 (1)
 LG3 0 2 (3) 11 (4) 13 (7) 0 2 (2) 6 8 (2) 0 2 (1) 11 13 (1)
 LG4 0 7 (1) 11 (3) 18 (4) 0 4 (1) 7 (1) 11 (2) 0 4 (1) 6 10 (1)
 LG5 0 0 15 15 0 0 7 7 0 0 9 9
 LG6 0 7 (25) 11 (1) 18 (26) 0 3 1 4 0 0 3 (1) 3 (1)
 LG7 0 0 20 20 0 0 8 (1) 8 (1) 0 0 5 5
 LG8 0 0 5 (1) 5 (1) 0 0 7 (2) 7 (2) 0 0 5 (1) 5 (1)
  1. aExpected marker linkage: Sh-link, self-compatibility; PHS link, tolerance to preharvest sprouting; whole-genome, whole genome region
  2. bFiltering steps: drop duplicate markers; drop samples with < 80 genotypes; drop marker subsets in which < 90% of population is genotyped; drop markers with an abnormal genotyping distribution