Table 3 Assignments of SNP assay nucleotides to A and C (sub)genomes
Assay(Category) | Brassica rapa | Brassica oleracea | Brassica napus | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
No1 | No2 | No1 | No2 | Express | BAC A | BAC C | ||||
SNP | SNP | WGS | SNP | SNP | WGS (GSS) | SNP | Sequences of PCR amplicons | |||
#386-17c(1) | C | C | C | G | G | G | C/G | S | C | G |
#386-17a(1) | T | T | T | C | C | C | T/C | Y | T | C |
#386-14d(4) | A | - | A | G | G | G | G | S | C | G |
#386-14c(1) | A | A | A | G | G | G | A/G | R | A | G |
#386-13(1) | A | A | A | G | G | G | A/G | R | A | G |
#386-8(2) | C | C | C | T | C | T | T/C | Y | C | T |
#637-3(1) | T | T | T | G | G | G | T/G | K | T | G |
#637-5(2) | A/C | C | A | A | A | A | A/C | M | C | A |
#637-8a(1) | T | T | T | C | C | C | T/C | Y | T | C |
#637-8b(1) | C | C | C | T | T | T | T/C | Y | C | T |
#637-11(1) | G | G | G | A | A | A | A/G | R | G | A |
#11428(1) | A | A | A | T | T | T (T) | T/A | W | A | T |
#11426(1) | A | A | A | G | G | G (G) | A/G | R | A | G |
#11424(5) | A | A | A | T | T | T (T) | T | T | T | T |
#11411(3) | T/G | T | T | G | T | T (T) | T/G | K | T | G |
#11410(2) | A | A | A | A | A | A (T) | A/T | W | A | T |
#11406(3) | A | A | A | A | A | A (A) | A/G | R | A | G |
#11405(1) | G | G | G | T | T | T (T) | T/G | K | G | T |
#11396(5) | C | C | C | C | C | C (G) | C | C | C | C |
#11395(1) | G | G | G | A | A | A (A) | A/G | R | G | A |
#11392a(4) | T | T | T | C | - | T (C) | T | T | T | T |
#11392b(2) | A | A | A | C | C | A (C) | A/C | M | A | C |
#11385-b(1) | G | G | G | A | A | A (A) | A/G | R | G | A |
#11385-c(1) | G | G | G | T | T | T (T) | T/G | K | G | T |
#11382a(1) | T | T | T | C | C | C (C) | T/C | nd | T | C |
#11382b(2) | G | G | G | G | C | C (G) | G/C | S | G | C |
#11376(1) | A | A | A | T | T | T (T) | T/A | W | A | T |
#11372(5) | C | A | C | A | A | A (A) | A | nd | A | A |
#11356(3) | nd | - | A | G | G | A (G) | A/G | nd | A | G |
#11355(1) | A | A | A | G | G | G (G) | A/G | R | A | G |
#11354(1) | T | T | T | G | G | G (G) | T/G | K | T | G |
#479-18(1) | G | G | G | C | C | C | nd | S | G | C |
#479-13d(2) | G | A/G | A | A | A | A | A/G | R | G | A |
#479-13b(2) | A | A/G | A | G | G | G | A/G | R | A | G |
#479-12b(2) | G | T | G | T | T | T | T/G | K | G | T |
#479-12a(3) | T | T | T | T | T | T | T/C | Y | T | C |
#479-9(4) | nd | G | G | A | A | A | A | A | A | nd |
#479-3(2) | A | G | G | - | G | G | A/G | R | A | G |
#BolI-5(2) | T/C | T | T | C | C | C | nd | T | T | C |
#BolI-3(4) | C | C | C | T | T | T | C | C | C | nd |
#11308(1) | T | T | T | C | C | C (C) | T/C | Y | T | C |
#11307(2) | C | C | C | T | C | T (C) | T/C | Y | C | T |
#11303 | nd | nd | G | nd | nd | A (A) | nd | nd | G | G |
#11301 | nd | nd | T | nd | nd | C (C) | nd | Y | T | C |
#217-1(1) | A | A | A | G | G | G | A/G | R | A | G |
#217-5(5) | G | G | G | A | A | A | A | nd | A | A |
#217-6a(3) | A | A | A | A | A | A | A/C | M | C | A |
#217-6b(2) | G | G | G | nd | nd | T | nd | K | G | T |
#217-7(2) | C | C | G | G | G | G | C/G | S | C | G |
#217-9(1) | G | G | G | A | A | A | A/G | R | G | A |
#578-5(3) | G | G | G | G | G | G | A/G | R | A | G |
#578-6(1) | A | A | A | C | C | C | A/C | C | nd | C |