Figure S1. Heterogeneity in pea cultivars VavD265, Melrose, Kazar, and Baccara.
Colored horizontal bars represent markers revealing differences between parental
accessions that served to construct RIL populations and positive control genotypes
from this study. Marker genetic positions are according to the consensus genetic map.
Figure S2. Cluster dendrogram illustrating the genetic dissimilarity between
mapping populations’ parental accessions. All parental accessions are represented
except Sommette. Modified Roger’s distance (Wright 1978) was computed for each
pair of accessions using genotyping data from 32 simple sequence repeat markers and
a Ward hierarchical classification was then performed on the total molecular distance
matrix using the hclust function of the R Stats package (https://www.r-project.org/).
Figure S3. Examples of GenoPlots observed for SNPs from the GenoPea 13.2K
SNP Array. Each sample is represented by a dot. Genotypes are called using their
signal intensity (Norm R) and allele frequency (Norm Theta) relative to canonical
cluster positions. Color codes refer to: red, AA (homozygous); purple, AB
(heterozygous); and blue, BB (homozygous) genotypes. The grey-shaded number
above each GenoPlot refers to the score given for all SNPs showing a similar number
and position of clusters.
Figure S4. Collinearity between individual genetic maps over LGs I, II, III, IV, V,
and VII. Pop6 map was used as a reference: for each pairwise comparison, common
marker positions according to Pop6 map were plotted on the x-axis and common
marker positions on the other map on the y-axis. The 222 SNP markers showing
different LG positions amongst different populations’ maps were not included.
Figure S5. Marker order conservation between the consensus map from this
study and consensus maps developed by Bordat et al. (2011) [A], Duarte et al.
(2014) [B], and Sindhu et al. (2014) [C]. Only common SNP markers with the maps
from Duarte et al. (2014) and Sindhu et al. (2014) were used for comparisons.
Figure S6. Illustration of syntenic relationships between pea and M. truncatula,
C. arietinum, L. japonicus, and G. max. Observed synteny between P. sativum LG
IV and LG VII and M. truncatula chromosomes 4 and 8, respectively, may be specific
to the M. truncatula reference genotype A17 that was reported to bear a reciprocal
translocation involving chromosomes 4 and 8 (Kamphuis et al., 2007). See Table S13
for full information.
Table S1. Passport and phenotypic information related to the pea accessions
composing the SNP detection panel and/or being parents of one or more
mapping populations from this study (blue-shaded).
Table S2. Detailed description of the 15,000 SNP markers selected to develop a
pea SNP genotyping array powered by Illumina Infinium® II technology. For each
SNP, its flanking sequence, its ADT score, its predicted position, and effect, and the
genotyping class to which it belongs for each mapping population are provided. The
comments’ section indicate potential multi-loci markers and those with low-signal
intensity.
Table S3. Links between transcript-derived SNPs from the SNP genotyping array
and currently-available pea sequences and marker resources. The symbols, “¤”,
“§”, or “&”, following EST and nucleotide accession numbers are used to indicate that
these were obtained while using respectively: transcript sequences, SNP-flanking
sequences, or both as BLAST queries. The bracketed “M” following each marker name
from Bordat et al. (2011), Duarte et al. (2014), Leonforte et al. (2013), and Sindhu et
al. (2014) indicates that the marker was successfully mapped in the respective study.
In case of an overlap between the flanking sequence of the SNP marker from the
present study and the flanking sequence of a corresponding SNP from another SNP,
the name of this latter is underlined. When further validation is necessary to confirm
the correspondence between any SNP marker from this study and another marker, the
name of this latter is followed by the following symbols: [?].
Table S4. Number and percentage of SNP markers per population assigned to
each of the marker classes. See also Figure S3.
Table S5. Genotypes of the mapping populations' parental accessions at 9,997
high-quality SNP markers from the GenoPea 13.2K SNP Array. These 9,997
markers have exclusively shown typical GenoPlots for scores 1 (when polymorphic) or
7 (when monomorphic) in all populations. See also Table S2.
Table S6. Parameters used for the construction of the individual and consensus
genetic maps.
Table S7. List of SNP markers among which seeds for the construction of
scaffold maps were selected. Markers’ genetic positions were inferred from
previously-published markers located in the same gene sequences. Seed markers
finally used for the construction of at least one map are underlined. For Pop3 LG VII
and Pop2, seed markers were obtained from individual maps of other populations from
this study. Additional references are provided in Appendix S1.
Table S8. Marker positions on individual genetic maps for all mapping
populations. Only SNP markers from this study are displayed. The SNP class, the
number of individuals having no genotypic data, and the observed Chi-Square value
are provided for each marker of each population. The positions of markers on the
scaffold, framework, and complete maps from all populations are detailed. Note that
the significance levels from the Chi-squared test are only indicated when markers have
a low rate of missing data: 'a' 90 % confidence, 'b' 95 % confidence, 'c' 97,5 %
confidence, and 'd' 99 % confidence.
Table S9. Marker positions on the consensus genetic map. A full description of the
15,352 markers including nucleotide, EST, or protein accession numbers for genebased and protein markers is provided. 'X' symbols under population names indicate
the origin of the genotyping data used to map each marker. Each grey-colored "X"
indicates that the marker is polymorphic in the specific population but the related
genotyping data were masked because of high level of segregation distortion. Markers
showing high levels of segregation distortion in all polymorphic populations (blueshaded marker names) were included for the construction of the consensus map but
were assigned low scores in order not to be positioned neither on the scaffold nor the
framework maps.
Table S10. Annotation of the transcript sequences corresponding to mapped
SNP markers. SNP markers are shown according to their order on the consensus
genetic map. Other markers not originating from the GenoPea 13.2K SNP Array were
kept in order to be used as links with previous studies. The predicted protein function
for each transcript sequence was obtained following Blastx search against pea, M.
truncatula, G. max, and A. thaliana protein sequences. The Expect value (e-value) of
the best match from each species is indicated. Previously-cloned pea genes related to
SNP markers from this study are indicated; those whose genetic positions were, to our
knowledge, not described so far are underlined. Additional references are provided in
Appendix S1.
Table S11. Pea transcript pairs likely originating from the 58-Mya papilionoid
WGD. Only pairs of transcripts where both members contain mapped SNP markers
are listed. SNP positions are according to the consensus genetic map. Predicted
protein functions for the putative ohnologs were deduced from Blastx search against
M. truncatula (Table S10).
Table S12. Pea transcripts possibly arising from local single-gene or segmental
duplication events. Code references starting with "LD" refer to duplicates likely
resulting from local (tandem or proximal) single-gene duplications. Transcripts located
on LG II region where a potential segmental duplication event was identified have code
references starting with the prefix "SD_LG2". "DR_LG3" distinguishes the members of
a resistance gene cluster on the bottom of LG III. Predicted protein functions were
obtained from Blastx of pea transcripts against M. truncatula protein sequences (Table
S10).
Table S13. Putative orthologous genes from pea, M. truncatula, C. arietinum, L.
japonicus, and G. max identified using the INPARANOID algorithm (Remm et al.,
2001). Pea genes were represented by peptide sequences corresponding to the
transcripts from the unigene set (Alves-Carvalho et al., 2015); only those related to
transcripts harbouring mapped SNPs are shown. The peptide sequences for other
plant species were from the following genome assembly versions: C. arietinum CaGA
V1.0, M. truncatula Mt4.0v1, L. japonicus Lj2.5, and G. max Glyma1.1. Best hits
between Pea and M. truncatula, C. arietinum, L. japonicus, or G. max that are not
located in conserved syntenic blocks, suggesting that they are not real orthologs, are
grey-shaded. Two G. max best hits per pea sequence are shown, when possible. M.
truncatula genes from ohnolog-rich regions identified within the M. truncatula genome
are in red.
Appendix S1. Additional references.