Genotyping-by-sequencing of pear (Pyrus spp.) accessions unravel novel patterns of

genetic diversity and selection footprints

Satish Kumar1*, Chris Kirk2, Cecilia Deng3, Claudia Wiedow2, Mareike Knaebel2, Lester

Brewer4

1The New Zealand Institute for Plant & Food Research Limited, Hawkes Bay Research

Centre, Havelock North, New Zealand.

2Palmerston North Research Centre, Palmerston North, New Zealand.

3Mount Albert Research Centre, Auckland, New Zealand.

4Motueka Research Centre, Motueka, New Zealand.

Corresponding author:

Satish Kumar: satish.kumar@plantandfood.co.nz

This supplementary materials file contains four supplementary figures S1-S5, followed by one supplementary table, S1.

Supplementary Figure S1. Fruit shape index assessment by assigning a numerical score to

different fruit shapes.

Supplementary Figure S2. Genome-wide distribution of population differentiation (Fst) between the three pairs of genetic groups (AS-EU; AS-HY; EU-HY). AS: Asian; EU: European; HY: Hybrid. Scaffold-level averages are shown. Vertical dotted line separates different linkage groups.

0

0.2

0.4

0.6

0.8

1

F st

Position on genome

AS-EU EU-HY AS-HY

171615141312111098654321

Supplementary Figure S3. Manhattan plots of the -log10( p) values for various fruit phenotypes (FF: fruit firmness; TA: titratable acidity; Shape: Shape index; RUS: skin russet cover; SCU: scuffing; COL: over-colour coverage; BIT: skin bitterness) from a genome-wide scan against position on each of 17 linkage groups (represented by different colours).

Supplementary Figure S4. Quantile-quantile plots for various fruit phenotypes (FF: fruit firmness; TA: titratable acidity; Shape; RUS: skin russet cover; SCU: scuffing; COL: over-colour coverage; BIT: skin bitterness) from a genome-wide scan

FF TA Shape RUS

SCUCOL BIT

Supplementary Figure S5. Flanking sequences of the largest-effect SNP loci listed in Table

3.S398.0_140201

ATAGGATTTAGTTTCTTTTTGATGTCCCCATGGATTATTTGTTTAGGGTAAACGAATTTTTCTTCAGTGAGATTGGCTATTTCTTTGCTTCTTGATGGATAATGGGTTTAGGTCTTACCAGTTAAATACAATCATGCACGTGTTGTTTTCATACGGCGGATAAATTAGACGGACAAGGATCCTCTTCGGATTCTCTTTGT[C/T]AGGGGATCCAGAAGATTAATCAATCGTGTTTGTTCATCGTACATCGTGCAGTTTGTTTTCATTAGGTACTATTTATATTCAATTTTAAATATAAAATTTAAAATAATTTCGAACCGCACGATATACGACGAACAGACACAATTGATTGGTCCCCGAATTCCCACAAAGAGGATCTGGAGAGGATCCTACTCCAAATTAGAS155.0_757109

TCAATCGAGTCCTCCCTTCCAGTGTAGAGTTGTAAGCCAAGCTTCTGTTTTGTCTTTGCCTGGAGGGGGTGTCGAGGATCCTCCTTGTAAGAGGGCTAGGCCTAGGTTGGTTCCAATTAGGTATTTCGGCCTGATGTTCAACCTTCAACTTGTTTACTTCCTCAAGGAGTTGTAGGACAAAGGGGTCCTGAGTGGAGTTA[G/A]GTACTGCTGGATCCTTCTTCCGTAAGTCTCCATCTCCTCTTGGAAGTAGGAAAACTTGGTCAAGGGCATGAGATTTTTCTTTAGACTCACCATACTGACTTCCAGGACGAGCCTGTCGAAACGCCCCCGAGTCCCCCGTACCTTCATATTCCTCTAAGACATGTCGCTCATTCCCTAGATTGGCAATTGGCTTGGGGCATS71.0_485233

AGGATCGAGCTTTTGGCTGATGCCATTGATCCGAACTTAAGTACTTGGGTACATACTATTCTATCGTATTTGCATCTTATGCTACTACTAGACTGAATATGAATCATTGTTTAAGATGCTGCATCTAAAAATGTGCAATCCGGATTCTTGAATATGTGATTTTTGCATGAATTTCAGATTACGGAAAAGAAGTACATTTG[C/T]TTGTATGGCGGAGAAGACATAGAGTGGATCCGAAACTTCACGAAGGCTGCAAGAAACGTGGCTGTTGAAGCCAACATTCAGTTGGAAATGCTATATGTGGGGCGGAGCAAGCCTAAGGAGACCGTGGTGAAGAACATCATGAACATCATCCAAGCTGAGAAGCTAAGCCACATCCTTGACTTGAACCTCATTTGGTTCTTS149.0_728797

GTGTCTATTGGGCGTTTTAAGTAGACACTGCTAGCTTTAATTGAAAAAAGGGGTTTTTTTTTTTTTTTTTTACAAAAAGTGGGGGACTTTGGTTTCAAGTCGGGTCCATTTTGTTTTAAAACTAGGTCCACCATTCTTTTAGATAACACATAAGCTTAGACTCAGGAGGATCCTCAATGCTCCTATGGATCATTTAATCA[C/T]ATATGTTCATCGTATATTGTGAGGTCAGAAATTATTGAAATTTTTTTATTTAAAATTAAATATAAATAGTACCTGACAAAAACTGACCGAACGATATACGATAAACGAATATGATTGGAAGATCTCCAGATCCTCACAAAATGGATCCGGCAAGGATCCTTTCTCAGCTTAGACAACCTTGCAAAACTAATAAAAAGAGTS83.0_565142

TAACAAATCTTTGTCGTGATAGATCGATCCGTTCTTTATTCATTAATTAATCATTGATTTGAAAGTATTAATATGCGTAAAGTTGGCATCTCCTGCGTAATCTATTGATTATAGATTTTAGGTCTCCAAACATGAGAGAGGATCCTCGCTAGATTCTCTTTGTGATGAGGATTCTGGGGATCCTCCAGTCACATCCGTTC[A/G]TCGTACATCGTGCGGTCAATTTTCGTCAGGTACTGTTTATATTCAATTTTAAATAAAAAAATTTACAATGATTTATGACCGCACGATGTACGATGAACATATGTGATTTAAGGATCCCCGAAAATCTCACAAAGAGGATCCGTCGAGGATCCTCACTCTCCAAACATATCTGGAGTGGCCAAAGTAAAGTTTAATTAGGTS895.0_79244

TTTCAATTGACAAATTATCTATATATATAGGGTGTCTCTACATTTTCATTTAACCTCCCTTCTCCATCACCAACCAATAAAAAACACACATTACATCAAACAACTAGTTATTGGACCATATTTTAAATGGATTTGGATCCCATCTAGATCTAAATTGTGGGAATCGTAGGGATCCTCACATCTTAACCATTCTTCGTGCA[T/C]CGTGGTGTCAGAACATTTGACTTTTTTATTTAAAATTAAACACAAATAGTACCTGACGAAAACTGACCGCACGATATACGATGAACGGTTAGAATGTGAGGATCCCTAAGATTCCGCCAAAGTGGATCCATAAAGGATCCTCTTCCATTTTCAATTACTTCTAGAGTAGTGTAACATAGCCCTATAGTCTAATCTACATT

Supplementary Table S1. List of accessions and their Pyrus species group.

CULTIVAR / Selection Species CULTIVAR / Selection Species

CANGXILI P. pyrifolia P. calleryana 2 P. calleryanaCAPTAIN HARDY P. pyrifolia Pyrus pashia 1 P. pashiaCHIKUSUI P. pyrifolia 3189 P. communisCHOJU P. pyrifolia 2-301 P. communisCHOJURO P. pyrifolia 6/23/94 P. communisDAN BAE P. pyrifolia 6-31-100 P. communisDAN BAE P. pyrifolia 6-31-68 P. communisDOITSU P. pyrifolia ANGELYS P. communisGION P. pyrifolia AURORA P. communisGOLD NIJISSEIKI P. pyrifolia AUTUMN BERGAM P. communisHAKKO P. pyrifolia BEURRE BOSC P. communisHEISHI P. pyrifolia BEURRE CAPIAMONT P. communisHOKUSEI P. pyrifolia BEURRE EASTER P. communisHOUGETSU P. pyrifolia BEURRE HARDY P. communisIMAMURA AKI P. pyrifolia BEURRE HARDY P. communisNIITAKA P. pyrifolia BROWN BEURRE P. communisP01 P. pyrifolia BUTIRRA PRECOCE MORRETINI P. communisP02 P. pyrifolia BUTIRRA ROSATA MORRETINI P. communisP03 P. pyrifolia CALIFORNIA P. communisP04 P. pyrifolia CARMEN P. communisP05 P. pyrifolia CASCADE P. communisP06 P. pyrifolia COLETTE P. communisP07 P. pyrifolia CONCORDE P. communisP08 P. pyrifolia CRIMSON GEM COMICE P. communisP09 P. pyrifolia D'INCONTINUE P. communisP10 P. pyrifolia DOYENNE DU COMICE P. communisP11 P. pyrifolia ELDORADO P. communisSEIGYOKI P. pyrifolia ELIZABETH COLE P. communisSHINGO P. pyrifolia FERTILITY P. communisSHINKO P. pyrifolia FLEMISH BEAUTY P. communisSHINSUI P. pyrifolia FLORIDA HOME P. communisSUISEI P. pyrifolia GLEAU MORCEAU P. communisTAMA P. pyrifolia GOLDEN RUSSET BOSC P. communisWASEAKA P. pyrifolia GORHAM P. communisYASATO P. pyrifolia GRAND CHAMPION P. communisB01 P. bretschneideri HARROW DELIGHT P. communisB02 P. bretschneideri HIGHLAND P. communisB03 P. bretschneideri HOWELL P. communisPINGGUOLI P. bretschneideri HW606 (HAROVIN SUNDOWN) P. communisQIYUESU P. bretschneideri JUMBO (STARKS) P. communisTSULI P. bretschneideri JUPP P. communisXINYALI P. bretschneideri LOUISE BON DE JERSEY P. communisXUEHUALI P. bretschneideri MADAME BALLET P. communisYALI P. bretschneideri MARGEURITE MARRILAT P. communisP. betulaefolia 1 P. betulaefolia MAX RED BARTLETT P. communisP. calleryana 1 P. calleryana MERTON PRIDE P. communis

(contd)

CULTIVAR / Selection Species CULTIVAR / Selection Species

MODERS P. communis RED SENSATION BARTLETT P. communisMOONGLOW P. communis REIMER RED P. communisNELLIE P. communis ROGUE RED P. communisNEW YORK P. communis ROSEMARIE P. communisNOUVEAU POITER P. communis RUBY P. communisOLD HOME P. communis RX359 P. communisOTTAWA-291 P. communis RX529 P. communisOVID P. communis RX810 P. communisC01 P. communis SIERRA P. communisC02 P. communis SILVERBELL P. communisC03 P. communis STARKING DELICIOUS P. communisC04 P. communis STARKRIMSON P. communisC05 P. communis SUPER COMICE P. communisC06 P. communis SWISS BARTLETT P. communisC07 P. communis TAYLORS GOLD P. communisC08 P. communis TENN P. communisC09 P. communis TN09-46 P. communisC10 P. communis TOSCA P. communisC11 P. communis US307 P. communisC12 P. communis US56112/46 P. communisC13 P. communis UVEDALES ST GERMAINE P. communisC14 P. communis VELVETINE P. communisC15 P. communis WINTER NELIS P. communisC16 P. communis WORDEN SECKLE P. communisC17 P. communis CRISPIE HybridC18 P. communis HWA HONG HybridC19 P. communis MAXIE HybridC20 P. communis H01 HybridC21 P. communis H02 HybridC22 P. communis H03 HybridC23 P. communis H04 HybridC24 P. communis H05 HybridC25 P. communis H06 HybridC26 P. communis H07 HybridC27 P. communis H08 HybridP327-57 P. communis H09 HybridPACKHAM'S TRIUMPH P. communis H10 HybridPASSA CRASSANA P. communis H11 HybridPATTEN P. communis H12 HybridPEAMY P. communis H13 HybridPIERRE CORNEILLE P. communis H14 HybridPRESIDENT D'OSMOND P. communis H15 HybridPRESIDENT HERON P. communis H16 HybridPRINCESS P. communis H17 HybridPT AV-63-2076 P. communis H18 HybridRED ANJOU P. communis H19 Hybrid

(contd)

CULTIVAR / Selection Species

H20 Hybrid

H21 HybridH22 HybridH23 HybridH24 HybridH25 HybridH26 HybridH27 HybridH28 HybridH29 HybridH30 HybridH31 HybridH32 HybridH33 HybridH34 HybridH35 HybridH36 HybridH37 HybridH38 HybridH39 HybridH40 HybridH41 HybridH42 HybridH43 HybridH44 HybridH45 HybridH46 HybridH47 HybridH48 HybridH49 HybridH50 HybridH51 Hybrid