Table S1.
Primers used in this study
| Name | Type | Forward primer (5′–3′) | Reverse primer (5′–3′) |
| M1 | Mapping | AACAAGCTAAGCAAGCAGAA | GATTGCAACCAGTAATCCAT |
| M2 | Mapping | CCAAATCATGTTTCACTCTGT | TAGTTTGATGTGCAGTGTGC |
| M3 | Mapping | AGAGGCCTTTGTAAGGTGAC | TCCACGTATATTTGGAAGAAG |
| M4 | Mapping | ATGGGTGTGTAAGAGCAACT | AGACTCTCCAAGTTTGACCA |
| M5 | Mapping | TATGCACAGCTAACCAACTG | GAATTTTGACCGTGTTTGAT |
| M6 | Mapping | AGAGTAGAAGAAGTCGGAAGAA | TCATTAACATCTATATGAACGTAGG |
| M7 | Mapping | CCAGTGAAGTCAATTGTGG | TCCTCTTCCATACTGCAAAT |
| M8 | Mapping | AGCAACACAAACATCATCAA | ACTGCACAACAGCAACACT |
| M9 | Mapping | TATACATGCTAAATGGCGAA | GAACCTAAGTGACAACTCGC |
| SSIIIa-1 | Sequencing | GAGCAGGCTGAAGGTCGTC | CGTATGAAGGGAAATCGTCC |
| SSIIIa-2 | Sequencing | CAAGTTCAGGTTTGTGTAGGATAGC | GCTTCATCCACCACATCCAC |
| SSIIIa-3 | Sequencing | CTTCAAGCACTGTAATGTATGGG | GACTGGCTTTTCCTATGGACAC |
| SSIIIa-4 | Sequencing | CCAGCGTTTATCAACAAGAAGG | GACTAAACGACCATTGAAGAACAC |
| SSIIIa-5 | Sequencing | TGTCCACATCAAAGGAGCATTC | AGCCAACAAAATACATCAGAACC |
| SSIIIa-6 | Sequencing | ATCAGAGAACGGGAGGAAGC | CTCCAGTTACAGAATTGTCGTAGC |
| SSIIIa-7 | Sequencing | CAAGCACTGTTGAAGTATATGTCTAGC | CTAACTGAGAAAGGAAGGACAACAC |
| SSIIIa-8 | Sequencing | GTTTCTGTGGTGGTTTTGTCG | GCAAAACACATTACATGGATTCTC |
| SSIIIa-9 | Sequencing | CTTTCTTTGTTTCCATGTTTTGC | AAGAGGAGTAAAGTGAATGTAAGGTG |
| SSIIIa-10 | Sequencing | GTTCTTGTTTTCCATGCTTGC | AACCACCTAAAAAGCAAACACATC |
| SSIIIa-11 | Sequencing | ACTTGAACGCAATGGACAGG | GCAGAGGGAGTGGAACCAAC |
| SSIIIa-12 | Sequencing | GCTTGGTGGTCTATTGTTTATGTG | GGCTTTAGGAATCGTGATGG |
| SSIII-2RNAi | RNAi construction | TGCTGTCAGCGAACAAAATC | CTCTTGTGCAGTCTTTCGGTG |
| SSIIIa-OE1 | Overexpression construction | ATGGAGATGGCTCTCCGGCCTCAAA | GCATGAAAATCTTGTCGACCATTGTTGT |
| SSIIIa-OE2 | Overexpression construction | ACAACAATGGTCGACAAGATTTTCATGC | AAACCTAGGCTAAATCAAGTATTCATAATTAAAACTG |
| gSSIIIa-1 | Complementation construction | CGCATGCTTCACCGCCGCTCGTCT | GCTTCCTCCCGTTCTCTGATCTCGTGGA |
| gSSIIIa-2 | Complementation construction | CTGGGTTTTTGCTGACGGGCCACCT | TCACGGCTCAGATCGACGAGTAGACCCA |
| SSIIIa-Pro | Complementation construction | CGCATGCTTCACCGCCGCTCGTCT | TGGCACTGCTAGCTGGCCGGATGACGA |
| rSSIIIa-1 | Sequencing for cDNA | ACACTTAGTGGGGATAAACTTTATAGA | ACTTTCAGACGATCTCATAGACTTGCCA |
| rSSIIIa-2 | Sequencing for cDNA | ACTGGAGCTGCCCATAATGGTTTACCA | ATTGAGAATTCGTAGGCACGCCCAG |
| rSSIIIa-3 | Sequencing for cDNA | ACTAGAGATTATGTAAGCTAACCACGCT | TTAGTGGAGTTTTGCACTGTCCTGACA |
| rSSIIIa-4 | Sequencing for cDNA | ACAGTATGCCACTTACATATTCCTTGTGT | AGGCTTCACTTCAAAACTGAACAG |
| SSIIIa-CAPS | Genotyping | TTGGAACTTTGGTTGGTATATCG | CTTACCTTTGCAATGGGTGC |
| Wx MII | Genotyping | GACAAGGCAAGAATGAGTGACA | GTGCCGACGACCTTGATGG |
| SSIIIa-DJ 1F | Genotyping | CAATTTGGCATGTCTTGTGG | |
| SSIIIa-DJ 1R | Genotyping | TGAGGTGGATACCCTTCTGG | |
| SSIIIa-DJ 2F | Genotyping | ACCCGGGACTGCATATAACCTGC | |
| SSIIIa-DJ 2R | Genotyping | ACCCTTCTGGGCTGTCAGACG | |
| SSIIIa-ZH11 3F | Genotyping | AAGCAATGACATACTGCGACAA | |
| SSIIIa-ZH11 3R | Genotyping | ACCGCAAGGTTCAAAGATGG | |
| SSIIIa-ZH11 4F | Genotyping | AATCCAGATCCCCCGAATTA | |
| Actin | Real-time PCR | CTTCATAGGAATGGAAGCTGCGGGTA | CGACCACCTTGATCTTCATGCTGCTA |
| SSIIIa | Real-time PCR | GAGGAAGTGGATGTGGTAGATGAA | TCTGTTTCGGTGATTGAAGCATTT |
| Wx | Real-time PCR | GGACCTGACACTGGAGTTG | TTTGAAGTATGGGTTGTTGTTGAG |
| PHOH | Real-time PCR | CACCAAGACGAAGCTCATCAAG | TTCACTCGTTGCTGGGTTCTC |
| PHOL | Real-time PCR | TTGGCAGGAAGGTTTCGCT | CGAAGCCTGAAGTGAACTTGCT |
| DPE1 | Real-time PCR | GGCGGTGGTTCTGACAATC | GTCTGCTTCTCTTCCTCTGGTA |
| DPE2 | Real-time PCR | CATTGGATTCGCTGTTGGA | GATACCCTTCGGCTGTTCT |
| AGPL1 | Real-time PCR | GTTGATTCCACATGGCAGAGAA | GTTGCTGCTGCTACTTCACT |
| AGPL2 | Real-time PCR | AGTTCGATTCAAGACGGATAGC | CGACTTCCACAGGCAGCTTATT |
| AGPL3 | Real-time PCR | GGAGAACTGCTGGCTGAA | AATACGATGGTGATGCCTGAT |
| AGPL4 | Real-time PCR | TCCCTTCTGGTTTGTTGCATTTG | CCTCAGTTCCTAGCCTCATTCAT |
| AGPS1 | Real-time PCR | GTGCCACTTAAAGGCACCATT | CCCACATTTCAGACACGGTTT |
| AGPS2a | Real-time PCR | ACTCCAAGAGCTCGCAGACC | GCCTGTAGTTGGCACCCAGA |
| AGPS2b | Real-time PCR | AACAATCGAAGCGCGAGAAA | GCCTGTAGTTGGCACCCAGA |
| GBSSII | Real-time PCR | GCTTGCTGGCTTGTTTAG | TGAAGTAGACGAGAGAAATGG |
| SSI | Real-time PCR | GTGAGCAGGAGTCTGAGAT | TGACCACGAAGAGCAAGA |
| SSIIa | Real-time PCR | CCTATTCCTGCGGTAGAAGA | CCGAATCGTCATCCTGGT |
| SSIIb | Real-time PCR | GTAGGAGCAACGGTGGAAGTG | GGTAATTCAGCGTGAACGTGAGT |
| SSIIIb | Real-time PCR | ATTCCGCTCGCAAGAACTGA | CAACCGCAGGATAACGGAAA |
| SSIIc | Real-time PCR | ACGGTTGTTCAGTCATTCAT | GTCCGCTGCTGTATTCAC |
| SSIVa | Real-time PCR | ATGCAGGAAGCCGAGATGTT | ACGACAATGGGTGCCAAGAT |
| SSIVb | Real-time PCR | GGGAGCGGCTCAAACATAAA | CCGTGCACTGACTGCAAAAT |
| SBEI | Real-time PCR | CCTGCTTCACCTACCATCAA | CGACAAGGCTCCACTGAC |
| SBEIIb | Real-time PCR | CGGTTTCAGCAGGTTCAGA | CTCCAGATGACTCAATCTCAACTT |
| SBEIIa | Real-time PCR | GGAGTTGGTGGTAATGAC | CCCTGGTCTATTTCCTTCA |
| ISA1 | Real-time PCR | TGCTCAGCTACTCCTCCATCATC | AGGACCGCACAACTTCAACATA |
| ISA2 | Real-time PCR | TAGAGGTCCTCTTGGAGG | AATCAGCTTCTGAGTCACCG |
| ISA3 | Real-time PCR | ACAGCTTGAGACACTGGGTTGAG | GCATCAAGAGGACAACCATCTG |
| PUL | Real-time PCR | ACCTTTCTTCCATGCTGG | CAAAGGTCTGAAAGATGGG |
AGPL1, ADP glucose pyrophosphorylase large subunit 1; AGPS1, ADP glucose pyrophosphorylase small subunit 1; DPE1, disproportionating enzyme 1; ISA1, isoamylose 1; PHOH, phosphorylase H; PUL, pullulanase.