Table 6.

Primer sequences used in the SNP genotyping format for foreground selection

No.	SNP name	Chr.	Trait	Tag number	SNP type	Amplicon size (bp)	Forward primer (5′---3′)	Reverse primer (5′---3′)	SNP-specific primer (5′---3′)
1	Sub1C	9	Sub	9	A/G	111	ACGAGCCGACGACGACGA	ATCTCCGACGCCCACCTC	CCGCCAGTAAGACCTAGACGCGGCGGCGGCGGCGGCGGAGGGAGA
2	xa5*	5	BB	2	C/G	303	GGCCACCTTCGAGCTCTACC	CAACATTGCAACTCCGTGATAAG	CTCAGACTACGAATCCACGTGTAAAGTAGATACCTTATCAAACTG
3	Xa21	11	BLQ11	40	T/C	141	AAAGCTAGGCTGCTAGTGCTG	AAAATAGTATATATGTACCACTGCTTCTT	AAGTACCACGTCAACGTCACTATGCTTCAAGGTCAGGGTGGTCGA
4	SSIIa	6	GT	25	G/T	89	CCACTGCCTCGAGACGTA	CGTGGTCCCAGCTGAGGT	CCATAACAACTTACCAGCCAGCAAGTACAAGGAGAGCTGGAGGGG
5	Waxy	6	AC	31	G/T	141	TTCACTTCTCTGCTTGTGTTGT	TACTTGTAAGGAAAAACGAGCAA	CAGAACATCCTCAGAAGCAAGTTCATCAGGAAGAACATCTGCAAG
6	aromarker*	8	FR	41	A/G	400	AATCATGTATACCCCATCAA	TTTCCACCAAGTTCCAGTGA	TACCTATGACCAGCAAGCACAACCTTAACCATAGGAGCAGCTGAA
7	Hd1	6	Photo	13	C/G	152	TCCAAAGATTCCGACAACA	TTGTCGTAGTACGAATTGTACCC	CAACAATACGAGCCAGCAAGACAACAACAACGACAACGACAATAA
8	TPS_Chr4_ATHB1*	4	Bph3	27	T/G	264	AAGCGCTTATATTCAAGCAGAA	TCCATTCTTCCGATCTCTGG	GCAAGCCATCAGCTAATACATTCATGAAACAGTTCTAGCAATAAT
9	Bph_Chr6_1210*	6	Bph3	17	T/C	287	GAAAGCCTTTGAAACAAAGTATTGA	CTTGAATTTGAAGTTGATTTTAGGG	GCAGACAACGAACAACTACCAAACGGCATATTTGCAAACAGAAAA
10	Bph_Chr6_3380*	6	Bph3	22	T/C	300	AGAGGAAATGATTCAAGGAG	AGCTAGCAGGCGTAGCTTAT	GCAACATAAGACCGCTCAACTAGTTAATTTCACGCCATGACAGAT
11	Bph_Chr6_1380*	6	Bph3	19	A/G	296	TTTTGTTTTCTTCTTGAGAGTGGTC	CAAGGTAATGACATCAAGAACCAAT	CCACTCAACTCCACGAATACCACATGTTTATTTTTAATTTCACAG
12	TBGI055716	1	BLQ1	24	T/A	169	ACGATGCGGCACTCGTCG	TGTTCTTGAACGCGGCGA	CAACAAGACATAACAACGCAGTGGAGTGGTGGATGAAGCGGAAGA
13	TBGI055578	1	BLQ1	42	A/G	93	ATTTGCTGCTCATGGTGG	TGGGGAAGCCGAGGAGAT	CTCACTATCTGACAAGCCACGTGGAGCCTCCTCACCAGGAAGTGC
14	TBGI055841	1	BLQ1	46	T/C	115	ATTGGCATCGTTTGGTCTG	ATTCCGTGCATATATACGAACTTC	ACAGATCACTCACCGACTAAATACCTGCGTCGAGTAGAGACGATG
15	TBGI454069	11	BLQ11	14	A/G	142	TGAATTGTCGTCCTCTAACAAC	TATGGAATATCTGCATCATGAAC	AACATACAGACGCACTCCTCTCTTTGCTATGCCAAAGTCTGCTAC
16	TBGI453598	11	BLQ11	23	C/T	90	TTTGCTGTGACGGGAAGA	AAAAAGGAACTAGCCAGTTTTG	AGTAGCCTAACAGCACTCGAAAGATCGAGTGCTCTATTGCAACCG
17	TBGI453126	11	BLQ11	32	C/T	92	ACCGACGCTGCTGCAGAA	AGCGGTTATGGATGGCTAA	CAAGCAACGACCTACTACAAGCATGGCGTTTGAGCGCGTCCTGGG
18	TBGI454717	11	BLQ11	36	T/A	132	ATCCTACCGTCCGCTCTG	AATTCGGTCTTCGTAAACACG	CACCGCTATCAACAGACTTGGTGCGGTAGTTTCTGGGAAGCTACG
19	TBGI454800	11	BLQ11	38	G/C	113	TACTACAACAACAGGAACGCC	TTGATGATGAAGTGGATGAGC	ACGTAAGACCACTCAAGACCAGAAGACGCTGAACAGGATGGCGAT

*These primer designs were optimized manually.