Ecology and Evolution. 2019;1–20.  | 1www.ecolevol.org

1  | INTRODUC TION

Greater yam (Discorea alata L.) is one of the major cultivated yam spe‐cies (Discorea spp.) and the most widely spread among tropical and subtropical regions. The high importance of D. alata for food security has prompted the establishment of several international and national ex situ collections. Due to the limited shelf‐life of stored tuber, yam genetic resources are conserved in vitro or/and in the field. All of these repeated manipulations are time‐consuming and may affect long‐term conservation. Quality control of genotype purity and general collection management is mainly based on morphological

descriptors (IPGRI/IITA, 1997; Mahalakshmi et al., 2007). However, these descriptors are not reliable enough to rationalize ex situ D. alata collection. Indeed, several studies have revealed that morphological variations are not necessarily linked to geographic origin or genetic lineage (Arnau et al., 2017; Lebot, Trilles, Noyer, & Modesto, 1998; Vandenbroucke et al., 2016). Complementary characterization tools are thus required for the conservation and dynamic management of ex situ collections related to germplasm exchange, the development of core collection or identification of future parents for breeding pro‐grams. D. alata is also a polyploid species with ploidy levels of 2n = 2x, 3x, or 4x and a basic chromosome number of x = 20 (Arnau, Némorin,

Received:29August2018  |  Revised:12March2019  |  Accepted:15March2019DOI:10.1002/ece3.5141

O R I G I N A L R E S E A R C H

Development of a cost‐effective single nucleotide polymorphism genotyping array for management of greater yam germplasm collections

Fabien Cormier1,2  | Pierre Mournet2,3 | Sandrine Causse2,3 | Gemma Arnau1,2 | Erick Maledon1,2 | Rose‐Marie Gomez4 | Claudie Pavis4 | Hâna Chair2,3

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.© 2019 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

1CIRAD, UMR AGAP, Petit‐Bourg, France2CIRAD, INRA, Univ Montpellier, Montpellier SupAgro, Montpellier, France3CIRAD, UMR AGAP, Montpellier, France4INRA, UR ASTRO Agrosytèmes Tropicaux, Petit‐Bourg, France

CorrespondenceFabien Cormier, CIRAD, UMR AGAP, Petit‐Bourg, France.Email: fabien.cormier@cirad.fr

Funding informationEuropean Union and Guadeloupe Region

AbstractUsing genome‐wide single nucleotide polymorphism (SNP) discovery in greater yam (Discorea alata L.),4,593goodqualitySNPswere identified in40accessions.Onehundred ninety six of these SNPs were selected to represent the overall dataset and used to design a competitive allele specific PCR array (KASPar). This array was vali‐dated on 141 accessions from the Tropical Plants Biological Resources Centre (CRB‐PT) and CIRAD collections that encompass worldwide D. alata diversity. Overall, 129 SNPs were successfully converted as cost‐effective genotyping tools. The results showed that the ploidy levels of accessions could be accurately estimated using this array. The rate of redundant accessions within the collections was high in agreement with the low genetic diversity of D. alata and its diversification by somatic clone se‐lection. The overall diversity resulting from these 129 polymorphic SNPs was con‐sistent with the findings of previously published studies. This KASPar array will be useful in collection management, ploidy level inference, while complementing accu‐rate agro‐morphological descriptions.

K E Y W O R D S

Dioscorea alata L., ex situ collection, genotyping, KASPar, ploidy, yam

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Maledon, & Abraham, 2009). Ploidy levels detection is consequently a prerequisite for the identification of possible parents as crosses be‐tween the different ploidy levels can fail (Nemorin et al., 2013).

Molecular markers have been used to characterize D. alata di‐versity: random amplified polymorphic DNA (RAPD; Asemota, Ramser, Lopez‐Peralta, Weising, & Kahl, 1996), isoenzymes (Lebot et al., 1998), amplified fragment length polymorphism (AFLP; Malapa, Arnau, Noyer, & Lebot, 2005), simple sequence repeats (SSRs;Siqueira, Marconi, Bonatelli, Zucchi, & Veasey, 2011; Sartie, Asiedu, &Franco,2012;Otoo,Anokye,Asare,&Telleh,2015;Chaïretal.,2016;Arnauetal.,2017),plastidsequences(Chaïretal.,2016),andDiversity Arrays Technology (DArT; Vandenbroucke et al., 2016). These studies generated essential information on the diversity and representativity of the germplasm collections. However, these tools were not tailored for routine collection management. They were found to be either poorly discriminating within D. alata species or they were complex and not cost‐effective to use. Besides the de‐velopment of high‐throughput methods for genome‐wide variant detection, such as genotyping‐by‐sequencing (Davey et al., 2011) paired with cost‐effective SNP assay (Broccanello et al., 2018) as KASPar can lead to the development of appropriate markers for collection management. This approach has been successfully im‐plemented in maize (Semagn et al., 2012), chickpea (Hiremath et al., 2012), Citrus (Garcia‐Lor, Ancillo, Navarro, & Ollitrault, 2013), pigeon pea (Saxena et al., 2014), and Brassica rapa (Su et al., 2018). Regarding the recent release of yam (Dioscorea spp.) genomic resources (Saski, Bhattacharjee,Scheffler,&Asiedu,2015;Tamiruetal.,2017), thedesign of such markers for D. alata collection management would be worthwhile. Indeed, once developed they do not require any specific bioinformatics or wet chemistry skills. The results contain few erro‐neous and missing data and can be easily analyzed and interpreted.

The main objectives of this study were (a) to identify genome‐wide polymorphic SNP markers, (b) to develop a cost‐effective SNP genotyping array using KASPar technology and (c) to test its use as a tool in managing yam ex situ collections.

2  | MATERIAL S AND METHODS

2.1 | Materials

Based on a previous microsatellite markers study (Arnau et al., 2017), a set of 48 accessions representing worldwide D. alata diversity was selected and genotyped to identify polymorphic SNPs and design KASPar markers. Then, for the purpose of validating these markers, 141 landraces from the Tropical Plants Biological Resources Centre (CRB‐PT) and CIRAD ex situ collections maintained in the West French Indies (Guadeloupe) were used.

2.2 | Genotyping‐by‐sequencing (GBS) and SNP discovery

SNP discovery was based on genotyping‐by‐sequencing (GBS). First, DNA extractions were performed with dried leaves from the

48 accessions as described by Risterucci et al. (2009). The genomic DNA quality was checked using agarose gel electrophoresis, and the quantity was estimated using a Nanodrop ND‐1000 spectropho‐tometer (Thermo Scientific, Wilmington, USA). For GBS, a genomic library was prepared using the PstI‐MseI restriction enzymes (New England Biolabs, Hitchin, UK) with a DNA normalized quantity of 200 ng per sample. The procedures published by Elshire et al. (2011) were adapted as described in Cormier et al. (2019).

Digestion and ligation reactions were conducted in the same plate.Digestionwasconductedat37°Cfor2hrandthen65°Cfor20 min to inactivate the enzymes. The ligation reaction was achieved using T4 DNA ligase enzyme (New England Biolabs, Hitchin, UK) at 22°C for 1 hr, and the ligase was then inactivated, prior to sample pooling,byheatingat65°Cfor20min.PooledsampleswerePCR‐amplified in a single tube. Single‐end sequencing was performed on a paired‐end lane of an Illumina HiSeq3000 (at the GeT‐PlaGe plat‐form,Toulouse,France).TheTassel5.2pipeline(Glaubitzetal.,2014)was used for SNP and indel calling. Sequence tags were aligned to D. alata contigs (http://www.ebi.ac.uk/ena/data/view/PRJEB10904) using Bowtie2 v2.2.6 (Langmead & Salzberg, 2012). Accessions with more than 70% missing data were removed. Vcf filtering was per‐formed using Vcftools 0.1.14 (Danecek et al., 2011; option: ‐‐minDP 8, ‐‐maf 0.1, ‐‐max‐missing 0.60, ‐‐max‐alleles 2, ‐‐thin64).

2.3 | KASPar genotyping and allele calling

Polymorphic SNP flanking sequences (60 bp upstream and 60 bp downstream around the variant position) were selected using SNiPlay3 (Dereeper et al., 2011). In order to assess their puta‐tive physical positions, these sequences were then blasted to the D. rotundata reference genome (TDr96_F1 Pseudo_Chromosome: BDMI01000001–BDMI01000021; Tamiru et al., 2017). The physi‐cal position of each SNP was defined using their flanking sequences best hit using a BLAST E‐value threshold of 1e−30 (Basic LocalAlignment Search Tool). Finally, 192 SNPs were selected by form‐ing 192 k‐means cluster based on their relative physical distance (Euclidean distance) and selecting the SNP nearest to the centroid of each cluster using R 3.4.0 (R core team, 2017).

The 192 SNPs were converted into a KASPar assay at LGC ge‐nomics where the primer design and wet chemistry was conducted (Middlesex, UK) on a validation panel of 141 landraces from the CRB‐PT and CIRAD ex situ collections. From raw fluorescence data, allele calling was performed using LGC Kluster Caller software by defining fluorescence clusters. Some accessions with known ploidy level were used as reference to identify fluorescence clusters and assess allelic dosage.

2.4 | Diversity analysis

To identify duplicate accessions and compare accessions with dif‐ferent ploidy levels, a matrix of dissimilarity between each accession pair was computed as the percentage of shared alleles based on the allele presence/absence.

     |  3CORMIER Et al.

Then, to refine the kinship assessment, similarities between ac‐cessions with the same ploidy level were computed in the same way but using the allelic dosage. For diploid accessions, genotypes were coded as 0, 1, and 2 where the number represents the number of nonreference allele. Heterozygous genotypes assessed as polyploid during allele calling were converted to 1. Moreover, for triploid ac‐cessions, genotypes were coded as 0, 1, 2, and 3 with allelic dosage scoreas1:1duringallelecallconvertedto1.5.Fortetraploidacces‐sions, genotypes were thus coded as 0, 1, 2, 3, or 4 and no correction was needed.

Diversity analysis was conducted in two steps. During the first step, groups of duplicate accessions (redundancy groups) were de‐fined by grouping accessions having up to one allele mismatch. Then, in the second step, the diversity analysis focused on the similarity between those groups. Clustering based on allele frequencies within redundancy groups followed by a bootstrap approach (pvclust R package, ward.D2, 10,000 boots, AU threshold=0.95; Suzuki &Shimodaira, 2006) was used to identify gene pools. A diversity net‐work between redundancy groups was also drawn using significant kinship detected through genotype permutations (1,000), with a sig‐nificancethresholdof0.05.

3  | RESULTS

3.1 | KASPar assay development and validation

Genotyping‐by‐sequencing (GBS) produced more than 344 mil‐lionreadsresultingin521,918sequencetagsoutofwhich207,810(39.82%) aligned exactly once on D. alata contigs. The remaining readsalignedatmultiple locations(25.18%)ordidnotaligntoanycontig(35%).Fromthesesequencetags,SNPcallingproducedaraw

vcffileof158,695SNPs.Thisrawvcffilewasthenfilteredresultinginadatasetof40accessions(AppendixA),and4,593goodqualitySNPs out of which 3,879 (84%) SNPs were mapped by BLAST on the D. rotundata reference genome. The KASPar assay was then devel‐oped by selecting 192 SNPs representative of SNPs mapped along the D. rotundata reference sequence, and they were tested on 141 accessions.

Among the 192 SNPs, 26 (13%) SNPs failed as they did not pro‐duce any amplification signal. From the remaining 166 SNPs (87%), 129 SNPs (Appendix C) with less than 20% missing data and a minor allelefrequencyofover5%wereretainedashigh‐qualitySNPs.Thisfinal dataset (129 SNPs × 141 accessions) contained an overall miss‐ingdatarateofonly0.5%withamaximumof3%missingdataperaccession.

The 129 validated KASPar SNPs were distributed on all link‐age groups used to construct the D. rotundata reference genome (Figure 1). Their distribution was not homogeneous along chromo‐somes as their position was planned to be representative of that of the initial set of 3,879 mapped SNPs and not equally spaced.

3.2 | Assessment of ploidy levels

In our D. alata validation panel, three ploidy levels (2x, 3x and 4x) coexisted (Appendix B). Thus, the KASPar assay could theoretically produce a maximum of seven types of fluorescence signal (Table 1) corresponding to two types of fluorescence signal in homozygous states (2:0 = 3:0 = 4:0; 0:2 = 0:3 = 0:4), the fluorescence signal of mixed and balanced allelic dosages (1:1 for diploids or 2:2 for tetra‐ploids) and the four types of fluorescence signal corresponding to the different possible unbalanced allelic dosages at heterozygotic loci (“polyploid‐like” in Table 1) of triploids and tetraploids (1:3; 1:2; 2:1;

F I G U R E 1   Location of KASPar SNPs on the D. rotundata reference genome (Tamiru et al., 2017). The 21 linkage group are aligned from left to right. Black dots, failed or bad quality SNPs; red dots, the 129 validated SNPs

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3:1). In our case, due to insufficient fluorescence resolution, it was not possible to distinguish fluorescence signals of the 1:3 tetraploid allelic dosage from the 1:2 triploid allelic dosage, or the 2:1 triploid allelic dosage from the 3:1 tetraploid allelic dosage. Consequently, a maximum of five types of fluorescence signals were identified. Overall, five, four, three, and two allelic dosages were detected for 64(50%),41(32%),19(15%),and5(4%)SNPs,respectively,becausesome allelic dosages were not present in the validation panel or they were cofounded.

However, the overall allele call and allelic dosage assess‐ment quality were good. Indeed, the ratio of genotypes scored as

“polyploid‐like” on overall heterozygous genotypes by accession was low(0.09±0.05)fordiploidsandhighfortriploids(0.83±0.05).Inaddition, the three distributions of this ratio corresponding to the three ploidy levels did almost not overlap (Figure 2).

We were thus not able to differentiate all allelic dosage from each other when looking at one SNP. However, ploidy level could be deduced when taking all the KASPar array into account and consid‐ering the proportion of genotypes scored as “polyploid‐like” per ac‐cession. This KASPar assay thus differentiated the accession ploidy level and allowed us to assign it for 12 accessions originally of un‐known ploidy. Nine were set as diploid and three as triploid.

F I G U R E 2   Distribution of the percentage of polypoid‐like genotypes (1:3, 1:2, 2:1, and 3:1 allelic dosage) on overall heterozygous genotypes by ploidy level (red, diploid; green, triploid; blue, tetraploid)

TA B L E 1   Summary of genotype, allelic composition and fluorescence signalsType of

genotype Ploidy

Allelic Type of fluorescence signal

Dosage Composition Theo. Obs.

Diploid‐like Diploid 0:2 X:X 1 1

1:1 X:Y 4 3

2:0 Y:Y 7 5

Triploid 0:3 X:X:X 1 1

3:0 Y:Y:Y 7 5

Tetraploid 0:4 X:X:X:X 1 1

2:2 X:X:Y:Y 4 3

4:0 Y:Y:Y:Y 7 5

Polyploid‐like Triploid 1:2 X:X:Y 3 2

2:1 X:Y:Y 5 4

Tetraploid 1:3 X:X:X:Y 2 2

3:1 X:Y:Y:Y 6 4

     |  5CORMIER Et al.

3.3 | Diversity analysis

Overall, 141 accessions from CRB‐PT and CIRAD ex situ collections in Guadeloupe were used to validate the KASPar assay (96 diploids, 36 triploids, and nine tetraploids including accessions with known and deduced ploidy level).

The allele presence and/or absence was used to assess the sim‐ilarity between accessions and thus to identify duplicate accessions

(Figure 3). Indeed, by defining redundancy groups, we ended up with 43 nonredundant groups each containing one to 24 accessions.

These groups of genetically similar accessions were partially ex‐pected based on the accession vernacular names. For example, the second biggest group (redundancy group 6, Appendix B) was com‐posed of 18 accessions, five of which had a name related to “Saint Vincent.” The third biggest group contained 14 accessions, four of which had a name related to “Pacala.”.

F I G U R E 3   Dendrogram of dissimilarity between 141 D. alata accessions (red, diploid; green, triploid; blue, tetraploid)

F I G U R E 4   Distribution of similarity between all accession pairs by ploidy (red, diploid; green, triploid; blue, tetraploid)

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The main group of redundant accessions was composed of 24 triploids collected at several distant locations (Caribbean islands, New Caledonia and Madagascar). This group consisted of 67% (24/36) of the triploid accessions present in the CRB‐PT and CIRAD collections.

More generally, redundancy groups only consisted of accessions with the same ploidy level (Figure 4). Moreover, similarities within triploids or within tetraploids were higher than within diploids.

The diversity analysis was based on these 43 redundancy groups to avoid bias. After clustering, the bootstrap procedure detected five significant gene pools, named “cluster” here, rep‐resented in the kinship network (Figure 5).Only one (cluster C,Figure5)consistedofaccessionsfromthethreeploidylevels.Thiscluster encompassed accessions from the Caribbean and Pacific re‐gions. Clusters A, B, and D contained triploids from the Caribbean and Madagascar, tetraploids from the Pacific and diploids from the Caribbean,respectively(Figure5,AppendixB).ClusterEwasthebiggest one, with 21 nonredundant diploid accessions originat‐ing from India, Nigeria, Côte d'Ivoire, the Caribbean and Pacific (Figure5,AppendixB).

Genotype permutations and network analysis gave a more de‐tailed view of kinship between redundancy groups and Clusters. This approach revealed a low number of significant links between the di‐versityclustersDorEandtheothers(Figure5)revealingthattheseclusters could consist of original genepools.

4  | DISCUSSION

4.1 | Assessment of allelic dosage and detection of ploidy levels

KASPar technology is based on competitive allele‐specific am‐plification followed by allele‐specific fluorescence assessment

(Semagn, Babu, Hearne, & Olsen, 2014). Detection of allelic dos‐age in polyploid species is thus possible (Cuenca, Aleza, Navarro, & Ollitrault, 2013). However, several parameters may influence the fluorescence, such as the DNA quality or primer specificity, and consequently the ability to discriminate fluorescence signals and the allelic dosage. In our case, we were able to discriminate five types of fluorescence signal. At heterozygous loci, fluorescence signals were a mixture of two types of allelic‐specific fluorescence. Fluorescence signals should also be balanced for diploids which have a balanced allelic dosage (1:1) at heterozygous loci. Diploids should therefore theoretically have no genotypes assessed as “polyploid‐like.” Conversely, triploids should theoretically have only genotypes assessed as “polyploid‐like” at heterozygous loci. A balanced allelic dosage is impossible for triploids. Our results showed that 91±5% and 83±5% of heterozygous genotypeswere correctly called for diploids and triploids, respectively. Regarding the recent explosion of genotyping related to next‐gen‐eration sequencing, bioinformatics tools have been developed to accurately determine dosages (e.g., GBS2ploidy; Gompert & Mock, 2017). However, this requires deep sequencing and usually an as‐sumption of ploidy levels present in the dataset (Bourke, Voorrips, Visser, & Maliepaard, 2018).

Application in collection management may nevertheless not re‐quire allelic dosage assessment at each locus. Our aim was thus to develop a tool for estimating ploidy levels and not variations in copy number. Moreover, the results showed that ploidy levels for each accession can be accurately deduced from the percentage of “polyp‐oid‐like” genotypes on overall heterozygous genotypes. Regarding the overlapping distributions of this ratio (Figure 2), the only risk is to confuse triploids and tetraploids estimated at 3%. Consequently, ploidy level assessment is possible and fairly accurate for D. alata using the KASPar assay developed in this study.

F I G U R E 5   Network of kinship for the 43 D. alata redundancy groups based on significant similarity (p<0.05,edge‐weightedspring‐embedded layout). Nodes shape and letter, cluster of diversity identified by a bootstrap procedure; red nodes, diploids; green nodes, triploids; blue nodes, tetraploids; edge colors, similarity from gray (0.64) to black (1)

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4.2 | Identification of duplicate accessions

The dataset included 129 SNPs validated on 141 accessions corre‐sponding to 43 unique redundancy groups. The resuming of the 141 accessions to 43 unique redundancy groups was related to the nar‐row D. alata genetic diversity, above all in polyploid germplasm (i.e., triploids and tetraploids) already identified in previous studies. For example, using DarT markers, a low varietal richness was revealed by Vandenbroucke et al. (2016), who studied 80 landraces from six different Vanuatu islands and differentiated only seven unique genotypes. Using isozyme markers, Lebot et al. (1998) studied 269 worldwide distributed cultivars and concluded that the genetic di‐versity of the most widespread cultivars was narrow.

Regarding the accession vernacular names, redundant acces‐sions were expected in our sample. Some of these redundancy groups contained accessions detected in duplicate, while they could be differentiated by morphological characterization. For example, redundancy group five (including Lupias, Malalagi, or Malankon) ex‐hibited diversity in tuber shape and tuber flesh color in agreement with previous genetic diversity studies that already pooled these ac‐cessions together and highlighted this intragroup variability in tubers (Arnauetal.,2017;Malapaetal.,2005).

Morphological variability within a redundancy cluster mostly arises via D. alata clonal reproduction and farmers' selection of new morphotypes resulting from somatic mutations (Lebot et al., 1998; Malapaet al., 2005;Vandenbrouckeet al., 2016). Small geneticorepigenetic variations are commonly selected to create new diversity in horticultural crops such as yam as reviewed by Krishna et al. (2016).

The ability of KASPar assay developed in this study to differen‐tiate duplicates in collections from genetically close accessions was related: (a) to the low number of studied loci (129), but also (b) to the D. alata diversification process (i.e., selection of somaclonal mutants) and (c) the presence of real duplicates within collections. This tool is thus efficient for attributing accessions to a genetic lineage (e.g., germplasm exchange), but a good complementary agro‐morpholog‐ical and ecophysiological characterization of collections should also be done to completely differentiate somaclonal mutant clones from duplicates (e.g., identification of promising genitors for breeding programs).

4.3 | Diversity and collection management

The CRB‐PT collection has been shown to be representative of worldwide D. alata diversity (Arnau et al., 2017). A subset of this ex situ collection has been genotyped in this study. However, all diver‐sity groups identified by Arnau et al. (2017) were present (except one containing five very similar Indian accessions). Our validation panel was thus representative of the worldwide D. alata diversity. Moreover, a good correlation was obtained between the findings of the previous study of worldwide D. alata diversity of Arnau et al. (2017) and the gene pools identified in this study (Appendix B). We can thus hypothesize that the 129 SNPs KASPar array developed for D. alata allow us to accurately assess genetic diversity and the

findings may be transferable to other collections. Moreover, this genotyping tool is a robust method: (a) to assess complementarity/redundancy between the different collections, (b) to identify under represented genetic groups, and (c) to plan future collects to fill gaps in collections.

5  | CONCLUSION

This is the first SNP array designed for D. alata and validated on a sub‐set of accessions representative of worldwide D. alata diversity. This tool will allow users to estimate accession ploidy levels and genetic lineages. The results showed a good correlation between the diversity assessed by this KASPar array and the findings of previous studies. This KASPar array is a robust and cost‐effective tool for diversity assess‐ment and collections management. Regarding the importance of veg‐etative reproduction and somaclonal selection in D. alata, it is a good tool to complement agro‐morphological description in collections.

ACKNOWLEDG MENTS

This study was financially supported by the European Union and Guadeloupe Region (Programme Opérationnel FEDER—Guadeloupe—Conseil Régional 2014–2017). The authors would like to thank Suzia Gélabale, Marie‐Claire Gravillon, Jean‐Luc Irep, David Lange, and Elie Nudol for their involvement in CRB‐PT and CIRAD in vitro and field collections conservation. Finally, we are grateful to Patrick Ollitrault for his valuable discussion and to David Manley for English proofing.

CONFLIC T OF INTERE S T

The authors declare that they have no conflict of interest.

AUTHOR CONTRIBUTIONS

C.P., F.C., H.C., and P.M. designed the study. C.P., F.C., E.M., G.A., and R‐M.G. contributed to collecting materials and sample prepara‐tion. P.M. and S.C. developed GBS protocol, carried out DNA ex‐traction, and GBS library preparation. H.C. and P.M. performed SNP discovery. F.C. and H.C. designed the KASPar assay and performed its analysis. C.P., F.C., and H.C. wrote the manuscript with the input of all authors.

DATA ACCE SSIBILIT Y

Plant materials may be requested at the CRB‐PT of Guadeloupe http://intertrop.antilles.inra.fr/Portail/accessions/find/11. KASPar primers sequence is available in Appendix B.

ORCID

Fabien Cormier https://orcid.org/0000‐0002‐7283‐4616

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APPENDIX A

TA B L E A 1   Description of the 40 D. alata accessions used to detect polymorphic SNP

Collection Code Name Origin Ploidy

CRB‐PT PT‐IG‐00002 Pakutrany Nlle Caledonie

PT‐IG‐00006 Fénakué Puerto Rico 2

PT‐IG‐00010 Divin 1 Guadeloupe 2

PT‐IG‐00020 DA 26 Guyane Fr 3

PT‐IG‐00338 HYB 30 Guadeloupe

PT‐IG‐00350 Pacala Guadeloupe 2

PT‐IG‐00029 Plimbite Haïti 2

PT‐IG‐00033 Pyramide Puerto Rico 2

PT‐IG‐00046 Sea 190 Puerto Rico 2

PT‐IG‐00053 Kokoéta Nlle Calédonie 2

PT‐IG‐00686 Roujol 4

PT‐IG‐00687 INRA C 143

PT‐IG‐00688 INRAAL56

PT‐IG‐00690 INRA AL 18

PT‐IG‐00692 INRAX154 Guadeloupe

PT‐IG‐00693 INRA X 17 Guadeloupe

PT‐IG‐00694 Dou 4

PT‐IG‐00695 INRA X 142 Guadeloupe

PT‐IG‐00696 Ciradienne 4

PT‐IG‐00697 TiViolet 4

PT‐IG‐00698 Malalagi Vanuatu 2

PT‐IG‐00702 Manlankon Vanuatu 2

PT‐IG‐00689 Nureangdan Vanuatu 3

PT‐IG‐00077 Kinabayo Puerto Rico 2

PT‐IG‐00078 Toro Haïti 3

(Continues)

APPENDIX B

Collection Code Name Origin Ploidy

Cirad Vu 024a Tépuva Vanuatu 2

Vu528a Tacharamivar 2

Vu564a Mendrovar Vanuatu 2

Vu567a Homb Vanuatu 2

Vu754a Intejegan Vanuatu 4

Vu 231a Tagabé Vanuatu 4

Ovy taty Madagascar

Vu 247a n.a Vanuatu 2

Vu 401a Basa Vanuatu 2

Kabusa 2

74F 2

42F 2

61F 2

14M 2

H4x200 4

TA B L E A 1 (Continued)

TA B L E B 1   Description of the 141 D. alata used as the KASPar assay validation panel

Collection Code Ploidya  Div. Clust.b  Redund. Grpc  Accession name Origin SSRd 

PT‐IG‐00087 3 A 26 65 Martinique XII

PT‐IG‐00070 3 A 26 66 Martinique XII

PT‐IG‐00090 3 A 26 Caillade 1 Haïti XII

PT‐IG‐00020 3 A 26 DA 26 French Guyana XII

PT‐IG‐00037 3 A 26 DA 27 French Guyana XII

PT‐IG‐00022 3 A 26 De agua Puerto Rico XII

PT‐IG‐00061 3 A 26 Igname d eau Martinique XII

PT‐IG‐00550 3 A 26 Montpellier XII

PT‐IG‐00075 3 A 26 Renta Yam Jamaica XII

PT‐IG‐00072 3 A 26 Sassa 1 Martinique XII

PT‐IG‐00063 3 A 26 Sassa 2 Martinique

PT‐IG‐00088 3 A 26 St Martin Martinique XII

PT‐IG‐00034 3 A 26 Sweet yam Jamaica XII

PT‐IG‐00557 3 A 26 Tahiti couleuvre Guadeloupe XII

PT‐IG‐00068 3 A 26 Tahiti cultivé Guadeloupe XII

PT‐IG‐00069 3 A 26 Tahiti French Guadeloupe XII

PT‐IG‐00018 3 A 26 Tahiti messien Guadeloupe

PT‐IG‐00064 3 A 26 Tana New Caledonia XII

PT‐IG‐00021 3 A 26 Telemaque Martinique XII

PT‐IG‐00044 3 A 26 Ti Joseph 1 Haïti XII

PT‐IG‐00078 3 A 26 Toro Haïti XII

CT257_CIV 3 A 26 OvyTaty AmbalaKindresy‐Ambohimasoa

Madagascar

CT258_CIV 3 A 26 OvyTaty Amboasary‐Ambohimasoa Madagascar

(Continues)

     |  11CORMIER Et al.

Collection Code Ploidya  Div. Clust.b  Redund. Grpc  Accession name Origin SSRd 

PT‐IG‐00685 3 A 26 Sainte Anne

PT‐IG‐00030 3 A 33 67 Martinique XII

PT‐IG‐00558 4 B 3 Wabé New Caledonia XVIII

Vu472a 4 B 3 Toufi Tetea Vanuatu XVIII

Vu231a 4 B 3 Vanuatu XVIII

Vu750a 4 B 3 Wanorak Vanuatu

Vu534a 4 B 3 Bisoro Vanuatu XVIII

Vu754a 4 B 30 Noulelcae Vanuatu XVI

Vu408a 4 B 31 Manioc Vanuatu

PT‐IG‐00039 2 C 2 Americano Dominican Republic VII

PT‐IG‐00023 2 C 2 Florido Puerto Rico

PT‐IG‐00553 2 C 2 Pro 1 VII

PT‐IG‐00095 2 C 2 SEA 144 Puerto Rico IV

PT‐IG‐00555 2 C 2 SRT 29 VII

PT‐IG‐00041 2 C 2 St Domingue Dominican Republic VII

Vu401a 2 C 2 Basa Vanuatu VII

CT256 2 C 2

PT‐IG‐00009 4 C 12 Nouméa New Caledonia XVI

Vu247a 2 C 14 Vanuatu

Vu528a 2 C 16 Sinoua Vanuatu

PT‐IG‐00025 3 C 22 Goana New Caledonia XIII

PT‐IG‐00002 3 C 22 Pakutrany New Caledonia XIII

Vu699a 3 C 22 Tumas Vanuatu

Vu461a 3 C 22 Tumas Vanuatu XIII

Vu755a 4 C 24 Nepelev Vanuatu

PT‐IG‐00014 2 C 37 Divin 2 Guadeloupe

PT‐IG‐00006 2 C 37 Fénakué Puerto Rico

PT‐IG‐00053 2 C 37 Kokoéta New Caledonia

PT‐IG‐00559 2 C 39 Wassa New Caledonia

PT‐IG‐00001 2 D 7 64 Martinique

PT‐IG‐00010 2 D 7 Divin 1 Guadeloupe

PT‐IG‐00568 2 D 25 77 Martinique IV

PT‐IG‐00092 2 D 34 Caplaou Puerto Rico

PT‐IG‐00561 2 D 42 H 23

PT‐IG‐00562 2 D 42 H50

74F 2 E 4 India

PT‐IG‐00049 2 E 5 Cinq Puerto Rico III

PT‐IG‐00027 2 E 5 Lupias New Caledonia III

PT‐IG‐00046 2 E 5 Sea 190 Puerto Rico III

Vu590a 2 E 5 Vanuatu III

Vu423a 2 E 5 Manlankon Vanuatu III

Vu639a 2 E 5 Malalagi Vanuatu III

Vu024a 2 E 5 Ptris Vanuatu III

PT‐IG‐00065 2 E 6 DA 28 French Guyana IV

TA B L E B 1 (Continued)

(Continues)

12  |     CORMIER Et al.

Collection Code Ploidya  Div. Clust.b  Redund. Grpc  Accession name Origin SSRd 

PT‐IG‐00093 2 E 6 DA 32

PT‐IG‐00395 2 E 6 Fafadro bis IV

PT‐IG‐00060 2 E 6 Grand Etang Guadeloupe IV

PT‐IG‐00051 2 E 6 Morado Cuba IV

PT‐IG‐00073 2 E 6 Purple Lisbon Puerto Rico IV

PT‐IG‐00333 2 E 6 Sainte Catherine Guadeloupe IV

PT‐IG‐00052 2 E 6 Smooth Statia Puerto Rico IV

PT‐IG‐00024 2 E 6 St Vincent blanc 1 Martinique IV

PT‐IG‐00036 2 E 6 St Vincent blanc 2 Martinique IV

PT‐IG‐00556 2 E 6 St Vincent mart. Guadeloupe IV

PT‐IG‐00045 2 E 6 St Vincent Violet Martinique IV

PT‐IG‐00016 2 E 6 St Vincent Yam St. Lucia IV

PT‐IG‐00374 2 E 6 Ti Joseph Haïti IV

PT‐IG‐00067 2 E 6 Wénéféla bis New Caledonia IV

Vu487a 2 E 6 Teroosi Vanuatu VI

770 2 E 6

PT‐IG‐00623 2 E 6

PT‐IG‐00396 2 E 8 A 24

PT‐IG‐00071 2 E 10 72 Martinique VIII

PT‐IG‐00055 2 E 10 76 Martinique VIII

PT‐IG‐00089 2 E 10 Asmhore

PT‐IG‐00058 2 E 10 Bété Bété Côte d'Ivoire VIII

PT‐IG‐00091 2 E 10 Campêche 2

PT‐IG‐00546 2 E 10 Jardin Haitien VIII

PT‐IG‐00547 2 E 10 Kourou 1 French Guyana VIII

PT‐IG‐00548 2 E 10 Kourou 2 French Guyana VIII

PT‐IG‐00350 2 E 10 Pacala Guadeloupe VIII

PT‐IG‐00551 2 E 10 Pacala cacao French Guyana VIII

PT‐IG‐00552 2 E 10 Pacala Guyane French Guyana VIII

PT‐IG‐00017 2 E 10 Pacala station Guadeloupe VIII

PT‐IG‐00554 2 E 10 SRT 24 VIII

19 2 E 10

PT‐IG‐00057 2 E 11 Vino Purple forme Puerto Rico

61F 2 E 15 India

PT‐IG‐00019 2 E 19 Gordito New Caledonia IX

PT‐IG‐00047 2 E 20 Buet New Caledonia

PT‐IG‐00029 2 E 20 Plimbite Haïti

PT‐IG‐00048 2 E 21 Bacala 1 Haïti

PT‐IG‐00413 2 E 21 St Vincent St. Vincent

Cuba6 2 E 23 Cuba

PT‐IG‐00542 2 E 27 AL 10 I

PT‐IG‐00042 2 E 27 Brazzo Fuerte Puerto Rico I

PT‐IG‐00038 2 E 27 Brésil 1 I

PT‐IG‐00564 2 E 27 KL 10 I

PT‐IG‐00565 2 E 27 KL 21

TA B L E B 1 (Continued)

(Continues)

     |  13CORMIER Et al.

Collection Code Ploidya  Div. Clust.b  Redund. Grpc  Accession name Origin SSRd 

PT‐IG‐00566 2 E 27 KL 40 I

PT‐IG‐00054 2 E 27 MP116H56 I

PT‐IG‐00033 2 E 27 Pyramide Puerto Rico I

PT‐IG‐00074 2 E 28 Oriental Barbados II

14M 2 E 29 India

PT‐IG‐00077 2 E 32 Kinabayo Puerto Rico II

PT‐IG‐00085 2 E 35 St Sauveur Guadeloupe

PT‐IG‐00560 2 E 35 Yamjamaïque

PT‐IG‐00543 2 E 36 Cross lisbon

PT‐IG‐00392 2 E 38 A 13

PT‐IG‐00398 2 E 38 A 2

PT‐IG‐00563 2 E 40 Sc.c 1.1

PT‐IG‐00008 2 E 41 AIA445 Nigeria

PT‐IG‐00015 2 E 43 Igname rouge Guadeloupe X

Vu703a 3 F 1 Nawanurunkimanga Vanuatu

PT‐IG‐00544 3 F 9 Cuello largo Puerto Rico XV

PT‐IG‐00026 3 F 9 Féo Puerto Rico XV

Vu696a 3 F 9 Nowateknempian Vanuatu XV

PT‐IG‐00076 3 F 13 Bélep New Caledonia XIV

Vu735a 3 F 13 Noplon Vanuatu XIV

Vu760a 3 F 13 Nureangdan Vanuatu XIV

PT‐IG‐00397 2 F 17 SEA 119, Toki

Vu613a 2 F 17 Peter Vanuatu VI

Vu589a 2 F 17 Makila Vanuatu XI

VU590a 2 F 18 Vanuatu III

Vu554a 2 F 18 Nourembor Vanuatu VI

Vu567a 2 F 18 Letsletsbolos Vanuatu IV

Vu564a 2 F 18 Makila Vanuatu VI

Vu026a 2 F 18 Dammasis Vanuatu VIaIn italic, ploidy detected using the percentage of polyploid genotype type on overall heterozygous loci. bGroup of diversity from diversity analysis cGroup of similarity used to select nonredundant accessions. Genotypes in the same group have a maximum of one allele mismatch). dCluster of diver‐sity identified by SSR in Arnau et al. (2017).

TA B L E B 1 (Continued)

14  |     CORMIER Et al.

APP

END

IX C

TAB

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789

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6617

7831

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3002

321

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3817

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9468

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S1_1

4901

3038

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2903

3873

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S1_54908604

52

3194

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S1_220358774

43

562364

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S1_2

9434

7489

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3182257

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1349

6700

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S1_123502462

53

1221

1409

2E−46

ATAG

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AA

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TTTG

AGTG

AGA

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1298

6600

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1247

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1880

8497

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S1_40517926

54

2442

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AGTC

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AGC

TT

S1_3

4169

0721

34

4172

027

7E−46

TTG

TGC

ATTC

CTC

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CAT

CTC

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GA

ACTG

CAG

CCTG

CCC

ACTC

CAT

CCTC

CCAT

GC

T[A

/G]

CTC

TTG

TGA

ACC

ATC

TCA

ACC

ACTC

TTC

TTC

TTTC

TCTC

TCTC

TTTC

TCTC

TGTT

GTC

TC

(Con

tinue

s)

     |  15CORMIER Et al.

SNP_

ID#

Fluo

.type

Chr.

Pos.

E‐va

lue

Sequ

ence

S1_94822591

54

6518043

4E−37

TCTG

ATG

ATCG

TGC

TTC

TCTC

ATC

AA

ATG

TTAG

ATG

TTG

TTC

TAAC

TCTT

CA

AGC

AAT

CA

[G/A

]G

AAC

TTAT

TTG

CTA

CTA

TGAG

TTG

TGAC

TTAT

TGTT

GC

TGG

TCAC

TGG

ATAC

TGC

AGG

TC

S1_223059854

54

9590872

4E−49

GTT

GC

TGCC

AGC

AAT

CAT

GAG

ACC

ATTA

TGAG

CTA

TGTT

GAT

GG

ATG

GTG

AGG

TTCG

GG

A[C

/T]

GTC

TGTG

GAT

AAG

CTG

TAAC

TGC

AGG

CAG

GC

TACC

TACC

ATTG

GAG

AA

AAT

TGG

CCAG

CT

S3_1940455

44

1160

2024

4E−49

ATG

CCTG

AAT

CTG

GAG

GAC

AAG

CTA

CTG

CAG

TGTG

TCA

AGA

AAT

AGAC

ATAC

TTG

AAG

AG[A

/C]

ATTA

TGA

ATC

AGA

ACAG

TTCC

AGG

CCG

GTA

ATG

TTG

AGTT

CAT

GC

TTTC

TGTT

CCTT

TCT

S2_59089982

44

1302

2373

2E−47

CTC

AAT

AAT

GG

TGG

ACA

AAT

GTG

CCTT

CTA

ATTC

AGA

AA

AA

AA

ATG

TCTA

CTA

ATTA

CCT[

C/G

]TC

CAG

CTC

TGTC

ATTT

ACTT

GTT

ATAG

GAT

GAC

ATA

ATTG

ATG

ACTC

TGC

AGAG

GAT

GAT

S1_29508975

54

13956140

8E−52

TAG

TGAG

CAG

TTG

AGAT

CAT

TAAC

GAG

CAT

AGA

AGA

ACTC

ACTG

CAG

AAG

CCAC

AA

AGCC

[A/T

]G

AAG

TCA

ATG

GAG

TTTC

TATG

GA

ACAT

AAT

GAC

GAG

GA

ATTG

GG

AAC

ACTA

TATT

GC

ACT

S1_7

8099

239

44

1900

9721

2E−33

CAG

GTT

TTC

TTTT

CA

ATTG

CA

AGAG

ACAT

CA

AGC

AA

AGG

CTT

GC

AGA

AAC

CGAT

ACC

AA

A[C

/G]

CTG

AGG

TAG

TATG

CTT

ATC

ATTT

GTG

ATA

AAT

TCAG

TAA

ACC

TGC

AGG

CA

ATTA

GTA

ATG

S1_9

8182

899

54

25059970

2E−47

TGTG

CAC

AAT

GC

TATG

ACC

ACAC

ATAT

GG

TTTC

AA

ACAG

ACA

AGG

AAC

AGA

ATC

AAC

AGA

[T/C

]AC

ACTA

CTT

ACAG

TGAC

AAG

CTC

CGAT

ATC

AGTT

GCG

CAG

ACA

ACCC

TGTT

TTC

TGC

AGC

S1_1

3376

874

34

25692581

2E−40

CTT

GAT

ATG

TCTG

TATT

GG

GTG

TCAT

TTC

TGC

AGTA

TTAT

TTG

GTC

CGC

AA

AGG

TAA

ATC

[A/G

]AT

AGA

AAT

TGG

CGTC

ATTT

AGC

AAT

ATC

TAA

ACTG

TATT

TGA

ATTT

GTA

GTT

CGAG

CAT

T

S1_50863270

54

27382503

2E−54

GTG

GC

TCTC

AA

AGAC

TGAG

GA

AGTG

CGTG

AAG

ATAG

GG

CTC

ATTG

GG

GTA

CCA

ATAT

AAC

[T/C

]G

GTG

ATAT

TTAT

GG

TCAG

GG

TTG

GAT

CAG

TGA

AAT

GTA

TGG

ATAT

TCAT

TTG

GTG

CTG

CA

S1_3

0240

813

55

4418552

4E−43

TCAG

AGAG

TGAG

TCAC

ATA

AA

AAT

AAG

ATTC

ATG

TTG

CAT

TGTG

ATG

CCCC

CTG

ATTC

TT[A

/C]

TTAC

TTG

CCCC

CA

AAC

GAT

AAG

GAC

ATC

TTTT

CTG

AA

AAC

TGC

AGAG

CCTA

AGG

AA

ATTA

S1_284257251

55

8809

466

2E−41

AAT

TTTC

TGAT

CTG

AGTA

TTG

GTC

AAC

AAG

AAT

CCA

ACAT

AA

AAC

TCA

AGTA

AA

ATG

CAG

[T/C

]A

AAT

TAC

AAT

TGTT

ACAT

AAT

TGTT

TCTC

CAC

ATA

ACTT

GC

TAAT

AAT

TATT

TCTG

CAG

A

S1_1

7201

3713

25

15915339

5E−48

AAC

GC

ATG

ATAC

TCA

ATG

TGTT

GTT

ACTA

ATTG

AAT

CTC

AAT

TAAT

ATG

ACC

TGC

AGTT

G[C

/T]

TTG

AAT

TTTC

ATG

CTA

TGTT

TGTA

AGG

CCTC

TAG

TGTT

GCC

AA

AAC

CTC

AGAC

ATC

TTCG

S2_46046547

55

18636385

5E−54

CAC

TGC

AGG

GG

CTG

CTT

CCTT

GAT

GAT

GA

ACCC

AA

AGA

ACTC

TATT

TCTC

AA

ATA

AAG

CG[C

/A]

TTC

ATTG

GA

AAG

AA

ATTC

TCTG

ACCC

GG

AGC

TTC

AGTC

TGAC

TTG

CAG

TTAT

TTCC

TTTT

S1_161404508

45

19741536

5E−42

TGC

TAAT

CA

AA

ACTG

ATG

CCTC

TGC

AGG

GAC

CA

AGTT

GAT

CAT

TGA

AAG

AAT

CAG

GG

ATT[

A/C

]TC

ACTT

TCTA

TCAC

CTG

TAG

AGTA

CTG

CAT

GTA

CAT

AAG

TCAC

CAT

GA

AA

AGC

ACCG

GG

C

S1_86749745

55

2078

4276

1E−48

CCC

TTC

TGAT

ATTT

GC

TTG

GAG

TTG

AGAT

GTC

TGTT

GA

ACTT

TAG

CTG

GA

AAT

TTTA

CAG

[T/C

]C

AAC

TCTA

TGA

ATTG

TGTT

TTC

TGAT

TCAT

ACG

CAC

ATTT

GTG

ATTT

TGTG

CCTG

CAG

AG

S1_3

4943

0697

55

2288

8769

8E−52

TCC

ATCC

TGG

GA

AGC

ACTG

GC

AAT

GG

TTG

ATTT

CGG

TAG

GCC

AAG

ATTT

GG

AGCC

CA

AGC

[G/A

]AC

ATC

TCTA

ACCC

AAT

CGG

AAT

GC

ATC

TGC

AGG

GC

AGG

AA

AGC

AGTC

CAT

TTTC

CAG

CTC

S3_43353096

55

24048351

8E−52

TGAT

GG

GG

GG

AA

ATA

ACCC

AA

ACTG

GTG

GAG

TTC

TATC

AGC

AAC

ATG

AAG

CCA

ACTG

CAG

[G/C

]AG

ATG

AA

ACC

TCTC

TTC

TTTA

TCC

TTTT

CCAT

CTT

CTT

CAC

CTC

TCTT

CCAT

CAC

TAC

TC

S1_51060666

35

26180154

1E−42

GA

AGG

AAG

GC

AGC

AGCC

TTTC

AA

ACC

TGC

AGAT

GA

AGTC

GCC

ACG

TCTT

TTG

AA

AAT

TGC

[A/T

]A

ACCC

AGCC

AAT

TTTG

CAG

CTG

CTA

GTT

TATA

GG

TAAT

GAT

AGAT

AGTT

ATC

TAG

GC

TAT

S1_1

2639

6048

55

27405531

4E−49

CA

ACTC

TGTC

GTA

GG

AA

AAG

AA

ACTG

ACCC

GTC

CAT

GAT

CA

ACA

AA

ACAG

AAT

TTTA

GAG

[G/A

]A

ATG

CCA

AGG

CAC

TTC

TTC

TCA

AGG

TTTT

CTA

ATTC

TGTT

CTT

GAG

GG

TGG

CTT

GTC

TCT

TAB

LE C

1 (C

ontin

ued)

(Con

tinue

s)

16  |     CORMIER Et al.

SNP_

ID#

Fluo

.type

Chr.

Pos.

E‐va

lue

Sequ

ence

S1_189523417

35

30765836

4E−49

TTTA

AAG

CTT

GTG

ACAG

CGAG

TTTG

AAG

ACC

TCTG

CTG

CAG

GC

ATG

CAT

CCAG

CTT

GCG

C[A

/G]

GC

AGG

AAC

AGC

TAC

ACCG

GC

TGTT

ACTG

CCG

TGG

CGC

TTTC

ACTC

AGTG

GAC

TGA

AA

ACA

S1_210690510

55

31577924

2E−53

ATC

ACC

TGTC

ATTC

TTAG

CAT

ACG

CTG

ACAG

CAT

CCAG

CA

ATA

AGCC

ATG

ATG

CTG

GG

CA

[A/T

]G

ATTC

CCA

AGG

ACTG

GAT

CGC

TTG

AA

ACTG

CTC

TTTA

CTC

TCAT

CTA

CA

AGCC

CTG

CAG

A

S1_1

9916

4936

56

10295314

1E−37

ATTA

TTAT

TATT

ATTA

TTTC

TTC

TTC

TGC

AGTA

ACG

GG

TCAC

ATTG

CTT

GG

AAG

AAG

TTG

[T/C

]TG

GAG

CTT

GA

AAC

GC

AA

ATA

ATG

ATAC

GA

ACAC

AGCC

TCAG

CA

ATG

CAC

GAT

TAC

TCG

CT

S1_282211588

56

17925427

2E−40

CAC

TTTG

CAC

AAT

TATC

TGC

TGTA

GA

ATG

TTC

TATT

TGTT

AA

ACC

TGC

AGAT

TAG

GA

AAT

[C/T

]C

TAA

ATTC

TATC

TGC

TGTT

ATG

AAG

TCC

TGG

TAG

TATG

TAC

AAG

CAG

GTT

GAT

TATA

CAT

S1_1

1600

6917

46

21845952

8E−52

TTG

TCA

AGG

AAC

GAT

CCC

TTC

ACC

TCC

TCG

GAG

AAG

AAT

CGCC

CGA

ACAC

ACG

AGAG

ATG

[G/C

]AT

ATG

GCC

GG

AAC

CTG

CAG

AGG

AGA

AAG

CGA

AGCC

CTA

ACCC

TGAG

GTG

CTT

CAG

CAC

AG

S1_45761963

56

27083504

1E−50

TTTT

ATC

ATG

AAC

CGAT

CAT

CCTG

AGAC

AGG

TAG

AAG

AAG

CTC

CCAC

TCTT

CCC

AGG

GG

A[G

/A]

GAT

AAT

TCCC

TCA

AAG

CAT

CAC

TTCC

ACAG

ATCG

TCA

ACAT

ATA

ATC

TGC

AGC

ATC

AAC

C

S1_289563297

36

3121

0760

2E−53

AAT

GA

ACC

ATAT

CAT

AAT

CA

ACTA

GAT

GTG

AA

AA

AAG

AAT

ATTT

GC

ACA

ACTG

CAG

GTG

G[A

/G]

CAG

GA

AAC

CA

AGG

GG

CTA

AAT

AGAC

ACAC

CTC

ATG

ACC

TAG

TTTC

ACAC

CCAT

CTC

CTG

T

S1_2

1028

4742

56

3202

2412

1E−50

AA

AAG

ACCC

AAG

GA

AAT

GAC

ACAG

CAG

AAC

CAT

TGTC

CCAT

TGG

ACAT

TTTC

AAC

TAC

AT[T

/G]

CA

AAC

TGC

AGC

ATA

AA

AAC

CA

AGAT

TTAT

ATC

ACAT

ATCC

ACAC

TAG

TTC

AAT

GA

AAC

AA

S1_2

4404

1680

57

8912

694E−49

ATC

AA

AAC

ATCG

CTC

TCTG

CAG

CCA

AAT

CAC

AGAC

GTT

AGAG

AA

ATAT

TTAT

AGG

CGAG

T[G

/A]

ATG

GCC

TTG

TTG

TTC

TAG

AAT

GG

TAC

AAG

ATTG

TGC

AGCC

AA

AGG

CTT

CGAG

TCG

TTTT

G

S4_1

8312

473

731

8074

85E−48

GAC

AA

ACC

AGA

AAT

CTT

TCC

TTTC

CAT

TAAG

GA

AGC

AA

ATCC

ACC

AAG

GAG

AAC

TGC

AGT[

T/A

]G

CCC

AA

ATG

AAT

CCG

AGG

GC

TCCC

AA

ACC

ACTG

GC

TGCC

TTTT

CA

AGG

ATTG

CCA

AGCG

A

S1_156520859

47

1036

7143

8E−52

TCTT

TTAC

TGAT

ATA

AAG

AGAC

TACC

AGA

ATCC

ATTT

GTA

TGTT

GG

TTA

ATC

TGC

AGAC

A[C

/T]

TGA

AAC

TCTA

TTG

TTG

TTAT

AA

ACTT

TCCG

AGC

TTCC

CA

AGAG

CAT

AAC

ATAC

ATG

AAC

A

S1_1

0990

7043

37

15658966

2E−53

AGG

AGA

AA

AA

ATTC

ATG

TGAT

GTC

CTC

CAT

ATC

TCAG

CCTC

GTC

TCG

GG

TGG

TCA

AAT

GA

[A/G

]AC

TGC

AGC

AAG

TATT

GG

GAC

AAT

TGC

AAG

AAT

AGAC

ATG

GAT

GG

CAC

TCTC

AAT

GTG

AGT

S1_365833705

37

17541018

1E−50

ACAC

ATC

TTC

ACC

ATTC

AAT

CAC

TTTC

ATCC

AAC

TGC

AGC

AAC

GTC

TCA

ACA

AGAT

CTC

C[C

/A]

TGAG

CTA

GG

TATC

ATC

AAT

TTTC

TAC

AAG

CA

ATC

TGC

ATTG

GA

AAG

TGAT

CAT

GG

ACCG

A

S1_215375978

57

1782

8247

4E−49

TGC

TGTG

CTC

ACG

CCG

ATG

GAT

ACTG

TGA

AGC

AGCG

GC

TGC

AGC

TTG

AGAG

TAG

TCCG

TA[C

/T]

AGAG

GG

GTG

GG

TGAT

TGTG

TGAG

GAG

AGTG

ATG

AGG

GA

AGAG

GG

GG

TGCG

TGCG

TTTT

AT

S1_5956960

58

1990

861

5E−35

AGAT

AAG

CAC

TTTG

TATC

TTG

CTA

TTTT

TGTT

GC

TCTT

TATT

ATTG

ATG

TGC

AAC

AAT

GT[

C/T

]CC

CA

ACA

ACC

ACAC

ACAC

ACAC

ACAC

ACAC

AAT

TTTG

TATT

TTTA

TGTT

AGC

TAC

TTC

AT

S1_142832546

58

4073

006

4E−49

AAC

TAAC

ATG

AAT

TTTG

GC

TCA

ATG

ATAT

AAG

ATTA

ACA

ACA

AA

AAC

GTT

TTTG

CTG

CAG

[G/A

]G

TTC

TTG

AAC

AAG

TTTG

ATG

AA

ATC

ACA

AA

ATG

GAT

ATTG

AA

AGTT

TGTA

AGA

ATG

TTAT

S1_1

0292

6938

38

5771893

3E−50

AAT

CTT

TGAT

GAC

AA

AGC

TGC

AGC

TTC

TTTT

CAT

GC

AA

AAC

AAT

AA

AA

AGTA

TACC

GG

AT[C

/T]

TGAT

GTG

ATAT

GG

GAT

GAT

CAG

ATC

ACTA

TAC

TGA

AA

ATG

AA

ACC

TGTG

CCAG

CTT

CTC

T

S1_2

9231

327

58

6476

874

1E−48

TCC

AGC

AA

ATAG

GTG

GG

GA

ACAT

CAT

ACA

ACG

GG

CAC

GG

AAT

GTT

CAT

CGA

AA

ATG

CAC

C[C

/T]

GC

TAAC

ATCG

TGG

CCA

AAG

CTA

TGG

AA

AAC

ATTG

CA

ATAG

AA

AGTA

TAAC

CTG

CAG

CTG

A

S3_54678463

58

7748

403

4E−56

TCA

AGAG

CTT

CA

AGA

AGAG

GA

AAG

AAG

GAT

AAT

AAG

TGA

AAT

ATC

AGAG

TTAG

AGTG

TGG

[G/A

]AG

ACC

TGC

AGA

AGA

ACA

AAG

AGTT

TGTG

TTAC

TGA

AAT

GAT

GG

ATTG

TGTT

ATTG

ATCC

A

TAB

LE C

1 (C

ontin

ued)

(Con

tinue

s)

     |  17CORMIER Et al.

SNP_

ID#

Fluo

.type

Chr.

Pos.

E‐va

lue

Sequ

ence

S1_2

0823

6889

28

9479

207

4E−49

AGG

AAG

GA

AAG

AGA

AAG

AAG

TTTC

TGC

TGC

AGTC

TCAG

CCCC

TTC

TTCG

AAT

TCTT

CTT

G[T

/C]

AGTT

TATC

AAC

AAT

CAC

TCA

ATC

ATAC

GG

TGAC

AAT

GCC

ACTC

TTC

AA

ATA

ACTC

AGC

AT

S1_169356495

58

1213

3164

8E−52

ATAC

AGA

AAT

TATC

AGTG

TAAT

ATAT

TAC

AGA

AGTA

GA

ATG

CTT

CAT

CAC

CAG

AAT

CTG

A[T

/A]

TTTA

TATG

AA

AAC

ACAC

TGAC

CTC

TTG

ATG

AAG

AAT

TAG

GC

AA

AAC

AGG

GAG

TCTG

CAG

A

S3_35309770

58

19352521

2E−47

CAT

TTCC

AA

ATTT

CAG

AA

AAT

AA

ATCG

GTT

TCC

ATA

AGAT

TTG

AGG

TAC

AA

ATAG

TTTC

C[A

/G]

CA

AAG

GAG

GTT

TATC

TGAT

ACA

ACAC

TGC

AGC

TTG

AAT

ATG

GTA

AAT

AAC

TAG

TCTC

ACA

S1_235419648

48

23125222

5E−48

GA

ACTT

CAG

AA

ATTG

TTAT

ACG

CTG

CAG

ATTG

CCC

AA

AAT

GA

AGC

ATTC

ATTA

GAC

ATA

A[C

/T]

TGAT

CCC

ATA

AAT

CAG

CCC

AGC

TTC

TTTT

ATG

TTG

TAC

ATA

AA

AGTT

CA

ATTA

GC

AAG

AT

S2_30875426

38

27554786

1E−43

TTC

ATG

TTTG

GA

AGAT

CTA

ATG

TCA

ATTT

AGAT

GTC

ATAT

GG

TTTA

GTT

TTG

TATT

AGTA

[C/G

]TT

TATG

TTG

TATT

ATTC

CA

ATAT

AAT

CCA

ATAT

CAT

ATC

TGC

AAT

TCTG

CAG

CAG

GTC

TT

S1_71285261

49

1039

396

2E−53

AGAG

AAT

GTC

CGG

ATA

AAT

CCTC

AGAG

AAG

ACTC

CAC

CTT

CGC

AAG

GTG

CCC

AGC

TCG

CA

[C/A

]G

GCC

ATG

AAG

AAC

TCG

AGC

TCTG

TGG

GG

TTAC

GG

CTG

CAG

CTC

AGG

CCAT

GCC

CCAT

CTT

S1_352413390

49

3168

774

2E−53

CTT

TCTT

GG

CA

AAC

AGTT

CTG

CAG

TAG

ATTT

GA

AGTC

AGC

TTC

TTC

TAC

AAG

TCTA

CCA

A[A

/G]

AGAG

GAT

TCC

AAG

TCAG

TGA

ATG

GAT

ATG

ATC

AAT

TTG

CAT

GAC

TGC

TTG

AA

AAG

TCG

GG

S1_58454213

59

3570970

2E−53

TGTC

CTG

TGG

CCTC

ATCG

AGG

AGCC

ATTT

CTC

TAG

CAT

TGAT

AGAG

GAG

GG

TTG

TTAT

GG

[C/T

]TC

TCA

ACTC

TCTC

CTT

CCC

TTC

AGA

ATC

ACC

ATTG

AAG

ATTG

CTG

ATTC

TGC

AGAT

GAT

T

S2_9856110

59

5066064

1E−50

TGG

AA

AAT

TAG

GTA

TCCC

AGTT

ACC

ATG

GA

AAT

CGC

TAG

TGAT

CTG

CTT

GAT

AGG

CA

AGG

[T/C

]CC

AAT

TTAC

AGAG

AGG

ATAC

TGCC

GTG

TTCG

TTAG

CCA

ATC

TGG

AGA

AAC

TGC

AGAT

ACC

S1_157448006

59

7773

168

2E−46

TTTA

ACTT

TTG

AA

AGG

CTG

CAG

GG

TATG

AA

ATC

ACAG

GCC

CCG

AGCC

TGC

TAAT

GTA

GAT

[C/T

]AT

GG

TGA

AGA

AGC

TGC

ATC

TGAG

GAT

GA

AGAG

GA

ATC

TTAT

GAT

GG

ACAT

GAT

GC

AGAT

G

S3_1

4699

960

59

1477

1343

1E−43

AAC

TAA

AAG

CA

AAC

CA

AA

AAT

AA

ATTC

CTC

TGCC

GTT

AA

ATA

ACC

TGC

AGA

AA

AA

AAT

AG[C

/A]

GA

AAT

GTG

ACA

AGG

AGA

ATAT

TTAC

ATAC

CTT

CGCC

TCC

ATG

ACAC

TTC

TTTC

AGAG

TTC

S2_58843160

59

17855377

5E−54

CA

ATTC

ATTT

CAG

GC

ATA

ATG

TTAT

CA

AGTA

ATG

CAT

ATTC

TACC

AGA

AAT

GA

ACTT

TAT[

G/A

]TG

GA

ACAT

CAT

TCTT

GAC

ATTT

GA

AGA

ACTG

CAG

TTG

ATTA

CA

AGTG

AAT

TGC

TTAT

AAC

S1_108505610

59

2313

8342

1E−48

GG

AA

AAT

ATCC

AA

AA

AGC

AAT

AA

AAG

CTG

CA

ATG

GAC

GC

AGCC

AAT

GCC

GC

TGTT

TCAC

A[A

/G]

TCG

AAG

GC

ATTC

TGCC

TAAG

CCG

CGTC

GAT

GTG

GG

TCTA

GAC

ACC

ACTG

CAG

TTCG

AGA

A

S1_9

6409

136

410

2736

969E−45

TGA

AGTT

TGAT

GAT

TCA

ATTT

ACC

AAT

GAT

TTTC

ATG

CAC

AGG

AGTA

TATC

TGAG

AAT

AA

[C/T

]G

AGC

AA

AAT

GAT

GC

AGAG

GTT

ACTT

CAG

CA

AGA

AAT

GC

TGC

AGAG

AAG

GAT

GTG

ACC

AAG

S1_75907479

510

1295979

8E−52

AAT

GTC

TTG

ACAG

AAG

CCAT

GA

AA

AAG

CTC

CAC

AA

AAT

AAG

TCC

AA

ATTG

AGAT

TGG

AGA

[G/A

]C

ATAC

TCTC

CAC

TGC

AGC

AAG

TCTG

TACC

CTG

TCTA

TGTG

ACTG

CTG

GAG

GG

GC

TCTT

GC

S3_1

7911

820

310

2220

748

8E−39

AGTA

GTT

TCTG

AAC

TGG

TAC

TTTG

ATC

AAT

ACC

TGC

AGAG

TTAG

TAG

CAG

TAG

CA

ATA

AG[C

/T]

GAG

GAG

ACC

TCA

ATAT

CTT

GC

ACAT

GAT

CAC

TCAC

CGA

AA

ATG

GA

ACAT

TATC

AGC

ATG

A

S1_2

8203

2037

410

5002351

7E−40

GAT

TTAC

AGG

ACA

ATTA

CAT

TTC

AGAT

TTCC

ATA

ATG

ATG

GTA

ACTA

CA

AGA

ATAT

TATT

[C/A

]TG

TAAG

CAC

CAT

GAT

ACTT

GTA

TCC

ATTA

CAT

GC

ATTG

AAT

CA

AA

AGA

ACTG

CAG

TTTT

A

S2_6

6969

333

210

5976818

2E−52

TTTA

ACTG

TATT

GG

CAG

TGTC

TGC

AGAC

AGAG

CTA

CGTC

TAG

CA

AAG

TGAG

CA

ACTC

ATC

[A/G

]TC

TGA

AAC

AAC

TCC

AAT

CTG

TAA

AAC

AGAG

CA

AGTC

ACAG

AA

AAT

TTAT

ACC

AAG

ATA

AG

TAB

LE C

1 (C

ontin

ued)

(Con

tinue

s)

18  |     CORMIER Et al.

SNP_

ID#

Fluo

.type

Chr.

Pos.

E‐va

lue

Sequ

ence

S2_53836832

310

1047

7461

5E−48

GA

ACAC

TTTC

CTG

GAT

TGA

AA

ATTA

TTTC

TGC

TGC

AGAT

CAT

CGTT

TCTT

TGG

CAC

CAC

A[C

/A]

CCTT

TTTC

TAAT

AA

AAT

ATTC

TTG

AGC

TCTT

TCTC

ATC

TTTG

AGAT

GTG

AA

ACAT

CTA

AC

S1_2

1668

183

410

16038685

2E−53

AGC

TGC

AGA

AAT

TAC

ATC

AAG

GAT

GG

ATC

TCAG

AGC

TTCC

AAC

CTG

CAT

AAC

ATC

TCAT

C[G

/A]

ATTG

CA

ATG

TCAT

CA

ACTG

GA

AGG

TGCC

CTA

TGAT

CCC

TGCC

ACG

GTT

GAT

CTC

TCC

TCT

S1_333790152

511

2622759

4E−56

TGC

TTTG

AA

AGG

CCAG

CAT

GAT

CTT

TTTT

CTA

TTTT

GTG

TTC

TTG

CA

ATG

AGTT

CTG

TCT[

A/T

]AC

ATTG

CTG

ATTT

TTG

TTC

TTG

TGC

AGTC

TGC

AGTA

GAT

TTTG

ATG

ATA

AA

ACC

AGTT

GG

S1_238131512

211

1444

7426

1E−43

AA

ATAT

CGAG

ATG

AAT

TTC

TGG

GA

ACA

AGCC

TGC

AGTT

AGTT

TGAG

GAT

GTG

TTTG

GA

AT[A

/T]

AGTG

ATC

AA

ATG

GC

ATTT

GAG

AAG

CAT

AGTA

TGTA

ATTT

TTCC

GTA

AA

AA

ATG

ATC

AAG

A

S1_3

8918

393

312

17162245

2E−46

AAT

CCC

ATC

AA

ATTT

GTC

TTTC

AA

ATTT

CTG

AAT

TTTT

TCCC

CTA

TCCC

AA

AA

AAT

TCAG

[C/G

]CC

ATC

AAG

AA

AAT

ATG

AGG

CA

AAG

CAT

AA

AAC

TGC

AGC

ATA

ATC

TCTA

TTAG

ATC

TCAT

C

S1_102041015

412

2432

7364

3E−45

GC

AGTA

TAC

AAC

TTC

ATTA

CCAT

GTT

AGAC

CAG

CA

AAT

CTC

AGTC

TGAT

TTC

TTCC

TAG

C[T

/C]

AAC

ACAC

ACAC

ACAC

ACAC

ACA

AA

AGA

AA

ACTT

CA

ATC

TCTG

TTTG

TTTT

CTG

AGTG

CAT

S1_65460849

413

1824

700

1E−42

GC

ATC

TGC

TAG

TTC

AA

AAT

AA

AAG

GC

AAG

CAT

GG

TATC

ACTA

ATAC

TGC

AGA

AA

AAT

GAT

[A/G

]G

TGC

ATA

AAT

ATC

TAAT

GG

GA

AAT

GAT

GC

AGCG

AAG

ATC

AAT

AAC

TTAG

AAT

GA

AAT

TCA

S2_23695000

513

8252985

8E−52

TAC

ATC

TGG

GG

GAC

TGC

AGAG

CTT

TGAG

CAT

CCAC

TGA

ACC

TGG

TGA

AAC

CAG

TGCC

CAG

[G/A

]G

TTG

ACAG

CA

AAG

GG

CA

AGTA

TGTG

GTG

CCA

ATTT

CA

AAG

TTG

ATG

CCC

AAG

CTA

AGA

AG

S1_2

7991

0017

513

27313051

2E−53

GG

CAG

CTT

CCAG

GG

CTC

GG

GAG

CTA

CCA

AGAT

GG

AGTT

TGC

TATC

CAC

GG

ATTT

GTT

CCA

[C/T

]G

AAT

CTG

TAG

CTC

CAT

CGTA

TACC

CTG

AGCC

TGC

AGCC

GTC

TCTG

CAG

TCC

AGAG

CAT

AA

S1_297529258

314

3933

202

7E−46

CTT

ATC

TATG

GCC

AGG

TTC

ATC

AAC

ATAT

AAG

GC

TTC

AAT

GG

TCTC

AA

ATTT

CAT

CGG

TG[A

/C]

TGC

TTC

TGC

TGTG

TGTA

CTT

TTAC

TTG

TCAC

TTAC

GCC

AA

AGTA

ACTG

CAG

CCTG

CAG

GT

S1_252699764

514

1239

1182

4E−49

ACTA

CTG

AAT

AA

ATG

GA

ATC

AAC

TTTA

TTTG

CTG

CAG

TTG

GAC

TAG

CCTA

AGAG

GA

ACTA

[A/T

]G

TGG

CTT

TGG

AAG

AGTG

TTG

ATAC

TTG

GG

ATTT

TATA

TCA

ATG

TGTG

AA

AAT

CAG

TGAC

T

S1_64347285

514

1286

8762

1E−50

GG

ATC

AA

AGTT

CTC

AGAG

ATTA

TTG

ATTT

TGAG

AAG

TCA

AGAT

ATG

CAT

CA

AAT

CCG

TGG

[T/G

]TG

ATC

TCTA

CTG

CAG

CAT

TTAC

CAT

CCC

TTTC

ATG

TCA

ATTG

ACC

AGAG

AGG

TGTC

AGAT

S1_108652759

414

1373

6821

3E−45

GAG

GTA

ATC

TGTG

ACTT

GTC

CAT

ATTA

CTG

CAG

AAC

AGC

AAT

TTAT

TGC

TGAT

CTT

GG

AC[T

/C]

ACTG

ATAT

CCAG

CTT

TCCC

CAG

ATTA

TGTC

ATAT

TGC

ACCC

AGC

AA

ACC

AGTA

CA

ATTT

A

S2_6

8074

878

515

3206

196E−47

CAC

CAC

CAT

CAC

ATCC

GC

ACC

ATTG

TTG

TCC

ACC

TTTG

AAC

CCAG

TGTG

CCTG

AGA

AGG

A[C

/T]

ACC

TGC

AAC

ATAT

CCG

GTG

ATG

ACTT

CTG

GA

AAG

TTG

CCTG

CAG

GG

CAG

ATTA

ATA

AA

AT

S2_15031349

415

2754888

3E−50

TAAG

AGA

AA

AAT

AGC

TTAC

ATTA

TCTG

TGTC

GAC

CTC

TGAT

ATA

ATC

TCTT

TGAT

TGTA

G[T

/C]

GG

CAT

CGCC

CAT

TCCG

TATT

TCTC

CAT

GG

CTG

ATTC

CA

ACTC

ATC

TCTT

GTG

ATAT

AGC

T

S1_3

6116

8697

515

3199245

2E−54

ATTA

CTA

AGAT

GC

AAT

TTAT

AA

ACAT

ATC

TGC

AGTT

CAT

TGC

TCTT

GA

AAT

CTC

TGC

ACA

[A/G

]G

CAG

AAG

AAG

TTG

AGAT

TTCC

GTA

AA

AA

AGCC

TGA

AA

ATG

GTG

GTA

GTG

CTT

CAG

AAG

AG

S1_4

2812

024

515

3456280

8E−52

GA

ACAT

TTTA

TAG

TACC

TCA

AGG

GG

AGTG

CCTT

TAC

TGTC

AAG

AGG

AAG

GG

GA

ACAC

CA

A[C

/T]

TCCG

CAT

CCTC

TCG

GA

AAT

CTG

AAG

CAG

CTA

GG

CCTG

TCAT

CA

ATG

GC

TGC

TGC

AGTA

GC

S1_31917523

515

3839

679

2E−54

TTTA

CAT

CTA

TTG

AAC

TCTC

TGC

AGG

TTG

AAT

CTG

AA

ATAT

TTTG

CTT

GC

ATG

GTG

GTT

T[G

/A]

TCCC

CTT

CTA

TTG

AGAC

CCTT

GAT

AAC

ATAC

GC

AAT

TTTG

ATCG

TGTT

CA

AGAG

GTT

CCT

S1_1

6064

479

515

5173749

1E−50

GC

TCAG

AAG

AGC

TCC

ATAT

GTA

AGTT

GG

TTC

TGG

ACTA

CCTC

CGG

GAG

ACTA

TTG

AAG

TA[A

/T]

CTC

TCTG

CAG

CAT

CTA

CCCC

CTT

GAC

TTTG

GAT

ATA

AGAT

CTA

TTCG

TATT

GC

ATG

GG

TC

TAB

LE C

1 (C

ontin

ued)

(Con

tinue

s)

     |  19CORMIER Et al.

SNP_

ID#

Fluo

.type

Chr.

Pos.

E‐va

lue

Sequ

ence

S1_1

1614

8629

415

6642

827

8E−52

GC

AGG

AAT

ACA

AGAG

TATT

GCC

AGA

ATG

AGG

CTG

GTA

CAT

ATTA

GCC

AAT

CTC

CGA

ATCC

[A/G

]AG

TCAT

TTTA

CAG

TTC

TTG

TACG

TTC

AAT

TCC

AA

AAT

CAC

CTG

AGG

AAT

CAT

ACAG

TGAT

S1_359692995

415

8357684

4E−49

GTG

GC

TGTC

TAAT

TTG

CAG

TAC

TGC

AGA

AGTA

AAT

ATG

AA

AA

AAC

ATG

AA

ATG

ATA

ATC

A[C

/T]

AAT

TCAT

TGAC

TAAC

CTG

TGC

AGAT

CTA

GA

ATAG

TAG

ATG

TAG

GAG

CGAT

TCAC

TTC

ATC

S1_2

9018

1714

415

9566725

2E−54

TCC

TCG

TATG

GG

GCC

CA

AGAG

GG

AAC

TCA

AGTT

TGC

TCTG

GA

ATCC

TTTT

GG

GAT

GG

GA

A[G

/A]

AGC

AGTG

CTG

AAG

ATC

TGC

AGA

AGG

TTG

CTG

CAG

ATC

TCAG

GTC

TTCC

ATTT

GG

AAG

CA

A

S1_2

8232

3032

416

4930

222

4E−49

ACTT

GG

GAT

TGTG

ATG

ATC

AGTG

TGTC

ACTA

TTTT

GTG

CTT

ATG

TCC

TTTG

TCA

AAG

AA

A[C

/T]

CGTA

ATAG

TTC

TGAT

TCA

AA

AAC

AA

ATC

AA

ACTG

CAG

GTA

TTG

CTT

TCAT

TTG

GAT

TTG

A

S1_2

6291

4420

416

8184285

4E−49

AGC

AGC

ACTG

TCAG

CA

AGA

AA

ACTA

TAA

ACC

TGC

AGAC

GAG

AAT

ATA

ACTA

ACAT

CAC

CA

[T/A

]G

AGAC

TTC

AA

AAC

AAC

AAT

TTTA

GTC

AAC

AAG

GTT

CA

AGA

AA

ACAG

AAC

AAG

ACC

TTG

CA

S2_6

3978

772

516

1407

9687

2E−53

AA

ATAC

TGG

TCAT

AA

ATAT

TAG

ATC

ACAC

ATAT

GTG

CCAG

TGTG

GTC

AAC

AGAT

AAT

GCG

[C/T

]TG

CTG

CAG

TAA

AAG

AA

AGA

ACTT

CAG

CAG

TGTG

GC

TAAC

AGAC

CTA

TTG

TAAC

ACTA

GC

A

S2_42975314

516

1909

9744

5E−54

CTG

GG

CCAC

GAG

GG

GAG

GG

CTG

GTG

AA

AAC

TGAC

TGG

AAT

AA

AGC

TCCC

TTC

ACAG

CCTC

[G/A

]TA

CCG

AA

ACTT

CAC

TGC

TGAT

GC

TTG

TGTT

TGG

TCAT

CTG

GCG

CCTC

AAG

CTG

CAG

ATC

A

S1_349651036

416

22229815

5E−54

GC

TTTG

GA

AGAT

AA

AAT

TCA

ATCG

AA

AGTC

AGA

AGA

AGC

AAG

CA

AAT

TAC

ACA

ATTC

GTC

[T/A

]G

CTG

CAG

TTCG

TCC

TCTA

GTT

CAT

CCAC

AGG

CCC

TTG

GAT

ATG

ACA

ACTC

CCTT

CCAG

GA

S1_131821504

417

1114

8474

6E−41

ATC

ACTA

GTA

CA

ATG

CA

ACAT

GAC

AA

AAC

CTG

AAG

TGC

TATA

CA

AGTG

ACTG

CTT

ATTT

C[A

/G]

AAC

AGG

ACA

AAT

CTG

AAG

CAT

AGC

TTG

TAAT

ACTT

CTG

CAG

AA

AA

ATA

ATG

GC

AA

AGTT

T

S1_305511589

517

13065352

5E−48

TGAT

GTG

TAG

ATAT

GAG

TGG

AAC

TGAT

TTTT

ATA

ACTT

TATT

ACA

AAG

CAT

TATT

TTTT

A[T

/G]

CCAT

CTA

ATG

TTC

TGC

AGAT

TAG

GTG

GAT

GC

ATTT

TTTT

TAAT

AAT

TTTT

TTAG

CA

ATTT

S1_1

6237

7692

417

14256863

2E−53

ACAG

AAG

AGA

AAG

CTT

GAT

GAG

ATG

TATG

ATC

AGTT

GAG

AA

ATG

AGTA

TGAG

TCAG

TGA

A[G

/A]

CGAT

CAG

CTA

TAC

AAC

CTG

CAG

GC

AAC

TTC

TTCC

AA

AGAG

CTG

ACCC

AGAC

TTG

TTTT

CA

S1_7095019

517

1848

1610

3E−44

CAC

GG

GTG

AGCC

ATC

AGTA

GTA

CCTG

ATG

CCA

ATG

TTG

AA

ACC

ATCG

AAT

TCCC

TTTC

AC[C

/T]

GAC

TGC

AGG

TATA

CGAC

CTA

TAG

AA

AGG

TTG

CGG

AAT

TAG

TGAC

TAC

TTTT

TTTT

TTTG

T

S1_164752250

517

19197258

1E−50

CGTT

CA

ACAG

CA

AAC

TGC

AGAG

AAC

ATC

AAT

CAG

ATG

ATCG

GAG

CGAG

CTC

ATC

AGC

AGA

[T/G

]A

AAG

CA

ATTG

ATG

ATTG

TGTT

TCAG

GTT

TTG

ATCC

AAG

CAT

CAG

TGAG

GAC

CTG

TTCC

AG

S1_1

0443

0414

418

7027

601

6E−47

GG

TAC

ACAC

TGC

AGAC

CTG

GAG

TCTT

TGTT

CCC

TCTT

ATA

ACAT

GAG

AGC

TTG

TTC

TTC

T[T/

G]

GTC

ATAT

ACTT

GC

TGA

AGC

TTTT

GC

AAC

TCTT

TTTA

CAT

CTG

AAG

CCA

ATTT

CTT

TACC

C

S2_2

3048

737

418

1490

2976

8E−52

TGAT

TATG

CTC

GCC

ATTT

CTT

GTC

CTG

CTG

CAG

TAG

AAT

GC

TTG

GCC

TGTC

TTAT

GA

ATC

[C/A

]A

AGAG

AGG

CTA

CAT

TGG

TTTG

GAG

TAC

TATG

GC

AGG

ACAG

TGAG

CAT

CA

AGAT

TTTG

CCT

S1_259660238

318

1860

9390

8E−52

TTG

TAG

GC

ATC

AAT

CTC

CA

AGA

AAT

CAT

TATC

TATT

TGAT

GG

TGTA

AGTT

CTT

GTT

GAG

G[C

/T]

TGAT

AAC

TGC

TGC

AGCC

TTC

TCTT

AGTT

GA

AGC

ATA

ACC

TTTT

TTTC

TATT

TTCC

CTT

TT

S1_1

7036

7846

518

2149

9070

8E−52

CCAT

GTC

TCG

GCC

TGC

AA

ACAT

TGG

ATAC

CA

AGA

ATTA

TAAG

AA

ATG

GA

AGTG

AAC

GG

AT[G

/A]

CGAT

GG

TGA

AA

ACAT

TTC

AGTA

CCTG

AA

ACTC

TGC

AGTA

AGC

ACTC

TTC

TGA

ATG

AGTT

C

S1_31156518

519

1787

283

2E−53

AGG

ACG

TCC

ACAC

TTG

ATAG

TGTT

TCC

ATTT

GC

ATC

ATG

TTC

ATTC

CAC

ATG

AAT

GCC

TC[T

/C]

GG

AGAC

ATG

TAG

TTC

AGTG

TGCC

AAC

CTG

CAG

TTTA

GTA

ACAT

GA

AAT

GAC

ATAC

TAC

AA

S4_1

7661

015

1929

1231

82E−41

TTC

AGAT

GG

ATC

AGTC

GTA

GAT

TGAG

CTT

TGA

ATC

TCTG

AAC

AAG

GAG

CAT

GAC

GC

ATAG

[G/T

]A

AGCG

GA

AGC

AGG

AAC

AGG

AGA

AGG

GA

AAC

ATG

ATC

TGC

AGC

TGC

AGC

ACC

ATC

ATA

AGA

TAB

LE C

1 (C

ontin

ued)

(Con

tinue

s)

20  |     CORMIER Et al.

SNP_

ID#

Fluo

.type

Chr.

Pos.

E‐va

lue

Sequ

ence

S1_130386685

519

3858772

2E−54

AGAG

TTG

ATTA

TAAT

TTTA

TGAT

CAC

ATA

ATA

ATTG

AAC

AA

AA

ACTG

CAG

AA

ACA

ATAC

C[A

/G]

GC

TAAG

TCAT

TCAG

CAC

CA

AAT

TATT

TAG

AGG

TAAG

TTTT

GAT

TACC

TTC

AAC

TTTC

AAG

S1_6

6878

388

419

4662

624

6E−47

AAT

TGTG

ACAT

CAG

CAG

CA

ATA

AA

ATTT

TTG

AA

AA

ACC

ACCG

CCC

AA

AA

AAT

TTAT

CA

AA

[A/G

]A

AA

ATTA

TCAC

TGTC

TTG

TGTC

AA

ACAT

CAT

CAC

CA

ACTC

CA

AAC

CCAT

ACTG

CAG

AA

AA

S1_4

8170

206

419

8029

141

3E−50

ATTA

TAC

AA

ACTG

ACA

AAC

GTA

TTC

TATA

TCA

AA

ATTG

AAT

TAC

AGG

AGAG

ATTG

GTA

GG

[A/T

]CG

TAA

AGAT

CCA

AAC

ATAG

AA

ATC

AAG

ATG

TTAG

AAG

GAT

ATG

ATAG

AA

ACA

ACTG

CAG

A

S1_85054393

419

9504285

1E−50

CAC

ATC

TGTT

TTC

TTCC

TTG

AGAT

TTC

TAC

AAT

ACA

ACC

TGAG

AAG

TTC

TGCC

AA

AA

ATT[

G/A

]TC

TCTT

TGCG

GG

GTA

AA

ATAT

TTTT

CTC

TCC

ATAG

GAG

TGAC

AAC

AAT

ATC

TGC

AGG

CTT

S1_1

6428

287

520

725184

8E−52

CA

ACG

TAC

TGC

AGAC

CCTG

TCA

AA

ATG

CCAT

GA

ATAG

GTT

ATTA

TAG

TTAT

GA

ACAT

CTC

[G/A

]TC

AA

ACA

AAG

ATTT

GC

AAC

CA

ATG

GTA

TGAG

CAT

TCAG

ATTT

CA

AGAC

TGTC

CA

AA

AA

AC

S1_4

3488

339

520

2904

117

1E−50

GAC

AA

AGTC

ATC

AAG

TAAT

TGCC

TTC

TCAT

GAC

AGAT

AA

ATC

TGAC

TGC

AGG

GAT

GTG

CC[G

/A]

AGC

TTAT

AAG

GCC

AAT

TAG

ACAG

CAT

AA

AAC

AA

ATAG

AA

ATG

CTG

GTC

ATTG

AGAC

AAT

G

S1_114295977

420

6774

493

1E−48

GC

TTG

GC

ATG

TTTA

TGAT

GAG

TATT

CCTT

TTG

ATAG

CAG

TAA

AA

ATAG

TAC

TTAT

TGG

CT[

A/G

]AC

TTG

AA

AGAT

CTA

GA

AGAT

TGG

TTG

GAC

TGC

AGTT

ATAT

TTTT

CTC

TAG

CTC

AGC

TAG

G

S1_30976509

320

8500327

2E−54

ATTG

TTTG

GC

TCC

ATC

AAT

ATAG

GA

AGAT

ATC

TAAG

GAG

TTAC

TGAC

TTG

TAAT

ATG

GA

A[C

/T]

CAT

AAC

TGAC

AAT

ATAG

CTT

CA

ACAT

GAT

GTA

CTT

ACTT

CGTG

AAT

GCC

TGC

AGAG

GAG

G

S5_17384653

520

8742

611

1E−36

TTA

ACC

ATTA

AA

ATTT

ATTT

ACA

ATG

TAA

AAT

TTCC

ACAG

AGAG

TAG

GTT

CTG

TAAT

CTC

[C/A

]G

ATTT

TCTT

CGAC

AA

AAT

CAG

CGG

ATTC

ATTC

TTTA

TTC

TGTT

TATT

GTG

CTC

TGC

AGC

T

S1_160073245

420

9514825

1E−42

TTCC

GCC

TGAT

GC

TTTA

ACAT

ATA

AA

AAG

CTG

CAG

ATG

CAG

AA

ACTA

AAT

ATC

TGAC

ATG

[A/G

]TC

AAT

AGTT

AGAT

TATG

ACTT

TCAG

CTT

GTA

GAT

TACC

AAT

TACC

AGAC

CAC

CAT

AA

AGC

S2_4

6633

476

320

9808

073

1E−50

AGAT

CAT

GTC

GTG

AA

AAT

ACC

TTC

AGAT

CCTT

CTC

CTC

CTC

CCCC

GTT

TCCC

TCG

CGTC

C[T

/A]

CCA

AAT

TCG

CCTT

TCC

TTCC

TCC

ACC

ACC

TCCG

CCTC

CGCC

TATG

ATG

AGC

AGC

AGTG

GA

S1_231563096

520

9944570

4E−49

GTT

GAG

TTTC

AGAG

TTTC

TGC

AGC

TCCC

TTTG

CAG

TAG

TTAG

GC

AGTA

ACCC

ATC

ACC

TG[A

/G]

AA

AGC

ATAT

CGG

TTTC

GAT

ACTG

TATG

AAC

TTCC

ACA

AGA

ACAG

CCC

TGCC

ATTG

CTC

CA

S1_6

0794

376

520

10523563

7E−46

TTC

AAT

ACTT

GTT

GTC

ATTA

TAAC

ATC

AGAG

ATTG

CA

ATTC

CTT

CAT

GAT

GCC

ACTG

CAG

[G/C

]AT

CCCC

ATAT

GG

ACAG

CTG

GTT

TCAG

TTG

TCAT

TATC

CTA

TTG

CAC

TCA

AAT

CTT

GA

AAT

S1_1

9966

6449

521

2404

744E−49

AGTT

CCAC

TCAT

AA

AAC

CAG

TTC

TCTA

CCC

AAG

CGG

TAG

CAC

GA

ATTC

CTC

AAC

AA

AAT

T[A

/G]

TAG

AAT

TTCC

ACTT

TGTT

CTC

CGG

AAG

CAT

TGCC

ATTG

GTG

GTG

CTG

CAG

TTAC

TCC

ATA

S1_257000706

221

928527

2E−54

TAC

AA

AAT

GAG

ATG

GTT

CAC

AAG

CTG

AAG

AAC

AA

ACC

TCAT

CTG

CAG

TAA

AA

AGA

AGA

AC[A

/G]

TCAC

TGTG

CCTC

AA

AA

AA

AGTT

CA

AGAG

CTC

TCTG

TTG

TTG

AGG

CAG

CCC

AAG

CA

AA

AGA

S1_1

7109

0323

521

2104

297

1E−50

CGAG

GG

AAG

GAG

AAT

GTG

GAG

CTA

CTG

ATTG

CAG

ATAT

ACTT

ATTG

GTT

CAG

CAG

ACTA

C[G

/A]

TCC

ATC

ATG

ACCC

CTA

TAAT

ACAT

TGTT

CTG

CAG

GC

AAT

ATC

AGTG

TTC

TTCC

TAG

GAC

C

S1_25663258

321

2772

381

8E−33

TGTG

AA

AAT

TTG

GC

TGTT

TTG

CTG

CAG

TTTC

ATC

ATAT

TGC

AA

ACTA

ATAT

TATA

AAC

TC[A

/T]

AA

AAG

TTTT

GTC

CAC

TATA

GA

ACTA

GTG

TCAG

CAT

CA

ATTT

CCA

ATAT

TAG

CCAG

GC

TAA

S1_371159620

421

3932

249

1E−50

GTC

TGC

AGG

GG

AGG

TCA

AAC

TCG

AGC

AGG

TTTC

GC

ATC

AAT

GAG

TGTA

GC

ACC

TTTA

TCA

[C/T

]C

AGC

ATTT

ATTC

CGG

CTG

CTG

CCG

CCAC

CAC

TCAT

GTT

GG

ACTG

CAT

CCA

ACA

ATCC

TGA

TAB

LE C

1 (C

ontin

ued)