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Table 2 RAD sequence reads of the 38 SNP candidate markers linked to anthracnose disease resistance gene Lanr1 in cultivar Tanjil of Lupinus angustifolius discovered by RAD sequencing on NGS platform Solexa HiSeq2000

From: Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

Candidate markers*

Coverage depth**

DNA sequences (5’-3’)***

Candidate marker 1

7.0/6.4

AATTCAGATTCAAGCGTGAAATATTTATACGTAGGAGAAAATGAGAGAAGGGAGGTCTGTGAGAGAAAGAGTA[G/A]AAAGAAAAAAATAAAAAA

Candidate marker 2

5.7/6.7

AATTCAACACACCGCTCATCTCA[A/C]CTACTTTCAAAATCAACCGTCTATGGATTATCTCCACTAAGATAATATATATTATAATAAAAAATGAA

Candidate marker 3

7.1/7.5

AATTCCACAAATTGAAAAACCCGACCGCTTTTTTCATGAAATGCCAATGAAAATG[T/C]TGTTAGTACTAATACTAATTAATTGACTTCTATAAG

Candidate marker 4

11.9/13.9

AATTCCACCAGGATTGCACAACACTAATCTCAACTTGGTCTTGTTGTTTTTCATAATTGGCATCTACACCAATTG[C/G]ATATCAACACTGCTTT

Candidate marker 5

7.2/7.7

AATTCTTCTTCAGAAACAAGGAGCCAATC[G/C]GATTCCAAATGCACTGAAGGAAGCTCAAGCAGAAAGCAAAATCTAAAGAGATTAATCTGATA

Candidate marker 6

9.0/8.8

AATTCTTACAATGAACTTCTATTTTCATTTTGCACTACTAAATCATATTTGCAATATATATGTGTTATATTATGCAAACTGAATCTTT[A/G]TAT

Candidate marker 7

13.7/13.3

AATTCATCTGTACTGATTTCTTTCATATCAAATAGCAGCAGTGGCAATCCTAAAAATAGAATGACCTCT[C/T]GATGTGTGTGCATTATGTGTAT

Candidate marker 8

8.7/9.1

AATTCTTTAAACTTTTGTTCCTTTATTTGAAGTTCTCTTGCTTTTTCTAAATCAAGTAAATTAGGAGTC[A/C]TAACAAAGTTTACCTTAGAGCA

Candidate marker 9

9.1/8.8

AATTCAGAGACAGGACTCATGGCTTATTGGTAATTGGAACATT[C/T]GGAAATAGCAATGAAATCAAAGAAATTCTAGATAACCAAAAAAACACT

Candidate marker 10

15.4/15.8

AATTCTTAAAACAAATTTATACAAGTTTCTCTTTTATTCATTCATGAGAATAAGTCAAAATTGAAAATGGAAGGTAACCC[A/T]TATCAAAGCGT

Candidate marker 11

4.2/10.9

AATTCTATATCTTAGTGATTC[C/A]GTGTAACTTATACTACTAGAGGTAGGTGTGGGATGGCAATTTGACTAGTGAAATGAAGTAAAGTGACTGC

Candidate marker 12

6.8/8.5

AATTCGAACTCATATATGAATACGTGGGCATTCTTTATCAATTGAGTTAGTTGATTATT[A/T]TTTTAATTTCTTAAAAAGTTTTGAGAGCACTT

Candidate marker 13

10.9/11.4

AATTCTGATGTGAAACAACGTGAAAAGAAAGGAGAAAAATCTGTCTTCTGAACAAGAAATGGACA[G/A]ATATCAAAGCTCAGCCAGGAGCATTT

Candidate marker 14

7.42/9.24

AATTCTCTCACAAGCTAATCGACATTCATCTGTATGCTTTGC[T/A]ACAGTAGACTCTAGGACTTTCTCAAGTTCAGTCACTCTATTGCTTAGCT

Candidate marker 15

12.8/14.2

AATTCTCATAATATTTTATAGATCTCATTTAAGAGTTTAAATAGTTAG[G/C]ATAAAGTTTTTTACACATTATTATGATTAGTATTAGTATGTAT

Candidate marker 16

12.0/11.6

AATTCCCCTCAAATTAACACTGTTTCTCGTTTGGGTTCAAGAGCCCTTTGCTTATTGCTTTGAGTTTAAA[G/C]CTCCAAACTTTAAATAGAGTT

Candidate marker 17

14.9/15.6

AATTCCAGAGGATACACATGACACACTACAACATTAGTACCCG[A/G]CAATGCCTCAAAACTGCGGTCTAATATGAAAAAATCGATGTCTTTGTT

Candidate marker 18

13.3/12.5

AATTCACACTCAATCATGTTCTGCAGCTTAAACT[A/G]AAAAAACAATAGGACCTTTTGCTCTTGATAAAATTTCTGATTTAAAAAATGTACAAG

Candidate marker 19

18.9/19.2

AATTCATTCAAGGGTCTTGTCAATCAATTGA[A/C]AAAGATATATGATGAGTTGCAAGCACTTATGCTACTAAGTTCGTTGCTTGAAAACTGGGA

Candidate marker 20

12.9/13.6

AATTCTAGTTTTGTCTTGGTCCTATTGTTTGCTTGATTTTTCAATTCATTACTAAACTATT[C/T]TGACAGTTACTGCATACTATTTGCCTTAAA

Candidate marker 21

16.2/19.2

AATTCTGAAGCAAGTGTATACATTTAAGTTCTAGAAATAGAAAGGATACACTCACGG[G/A]ATGAGATAGCCAAGATAAACTATACATGGAATAT

Candidate marker 22

28.9/26.1

AATTCTAGTTTCTTTTATCTTGTTCTTTTCCCAGAAGATATTACTTGTCTTTAATTTTCTTTTGGGTGGGA[A/G]TGGGAGTGAGGGGAATTAAA

Candidate marker 23

18.7/19.8

AATTCTTTTGTTGATAACCTCAAACAAGATGGCCTAGTGTTAATCATTGGTTAGAACA[C/G]TGAAATTAATTTTTGTTTTTAAGACAACATATA

Candidate marker 24

20.2/19.8

AATTC[T/C]TAATAGGTGTAGTAGGATATATAATAAGAATACTTAAATTACTTAAAAAAGTACATAGATAGATAAATATCACTATTCGACACTCT

Candidate marker 25

14.4/16.6

AATTCTCCGTCTCTCCCCCTTCACCTTGCGGAGCAAAATCCCTCAATAGGTCCCAAGTTGACGAATCATTATCCA[C/T]CGCCGAAATCCTAATT

Candidate marker 26

7.9/7.1

AATTCTCAAGTTAAATATGATGTGGCTAACAGGGTTCACTTCTAGGTCTCGAGGTT[G/A]CTGATGCTGAAAGATCTTATCATACTGAATTGATC

Candidate marker 27

25.1/27.5

AATTCCAAATCTTTAGCTGAAAAGTCAATTAACAACTATCAACATTTTATTCAGTAGAAGTG[C/T]ATAACAGACTAGATATTGGTATTAATAAT

Candidate marker 28

21.4/20.2

AATTCATAACTACTTTGTAATTGATCAAGCTTTTCTTGCTGATCATCATTCTCTTTT[C/T]TCTCTGATTCTCTATGTTGAGTATCAAGAAATAA

Candidate marker 29

14.3/16.0

AATTCAAGCTGCTATCAACTTT[A/G]AAGCTCTCTCCCCACATGCTAACTTGATCAAATGGCTCATATATGCCCATCTTTTTCCCAATGACTAGT

Candidate marker 30

8.9/11.0

AATTCAACAACAAAAAATCATCGTAACGCCAG[T/C]AATCCTCATTGCAACAACTATAATGGCCGCAACCATAATTTAAAATACCGATTTTGTTT

Candidate marker 31

20.5/21.1

AATTCATATTCCACACAGATTTGTTCAACTGTTGAATTTGCTTACATGTCCTGAATCAAAAAGAAGAGAAAAGTTTAGACAC[G/T]ATGCGGTCA

Candidate marker 32

18.4/17.0

AATTCGAAATGGAGAGCAATGTCACTTTCATAAATGGGATAAACAAAATTTCGTTACTTAGTGCAACAGTTGGAATGCC[T/G]GTAATAACAAGC

Candidate marker 33

31.7/31.2

AATTCTGGTGCTGCGACAGAAGTGTTATGCA[A/G]AACTATTAGTCATCCTCTTAAGGTAAAACCTATTATGCTGTTACAAAAGTTCAGCTTGCC

Candidate marker 34

21.9/17.4

AATTCATTACCCTTGACA[A/C]CCTACATGAATTAGTAAAAATAAGTTTAGCCAATTCTAACATGGAACCTGTAGCATATAAAACCAATGTTCTA

Candidate marker 35

27.2/26.1

AATTCAAGCAAATTGGACCATGTGAAATCTGGATACTGTTTTGTCCCATCTTTGACAACAATAGCCTCTGG[T/G]GCTCTCAACACTTTGTCTTC

Candidate marker 36

26.5/28.8

AATTCTGCTAGTGAAGCTGG[A/G]GTTTTTCCTGCACCTGCACATTTTAGACTAGTGCCACATGAACCTGTTTGGCAATTGCCATTGCCACTTTT

Candidate marker 37

25.8/24.8

AATTCTTAGATACTTACAAGGAACAAAATAATTCGGTATATGGTATAAGACCAACACCAACTCAACATTGCACG[G/A]CTACACTAACAGTGATT

Candidate marker 38

32.2/27.6

AATTCAGTGGAATATTTCATGTTCACAAACACATTCGACCATAGCGAGAAAGTGCACCTCTC[T/A]TATTCTATTCATACCTGAATGGTTCTAAG

  1. *Candidate marker numbers were consistent to the candidate makers listed in Table 1.
  2. **The first number was the average coverage depth (x) of the nucleotide from the 10 plants susceptible to anthracnose disease; the second number was the average coverage depth of the nucleotide from the 10 plants resistant to anthracnose.
  3. ***The first nucleotide of each SNP in bracket for each RAD sequence read was from parental plant Unicrop; the second nucleotide of the SNP in bracket for each RAD sequence read was from parental plant Tanjil.
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