Text S2_Supporting Information
Co-location and co-linearity analysis of NCCR heading date QTLs
A co-location analysis of QTL supporting intervals (QTL CIs) in the NCCR map with previously
reported QTL and meta-QTL for heading date (HD) and a wheat-grasses gene-content co-linearity
analysis in the same QTL CIs was carried out and is reported here. The analysis takes advantage of the
availability within NCCR of QTL map information based on SNP developed from transcribed genes.
Such type of SNPs are more informative in terms of synteny analysis (as extensively reported in
Maccaferri et al. 2014). The QTLs were QHd.ubo-2A, QHd.ubo-2B and QHd.ubo-7A.2. The same loci
appear also to influence maturity date, as highlighted by the detection of QMd.ubo-2A.1, QMd.ubo2B.1 and QMd.ubo-7A.2 QTLs (See Table 4 in main text). Besides the relevance of these QTLs for the
determinism of phenology, we considered the QTLs as case studies to demonstrate that the CI
resolution of QTL analysis and the use of transcript-associated SNPs, coupled with barleyBrachypodium-rice co-linearity analysis, allowed us to define the gene space harboring the QTL causal
genes to intervals containing less than one hundred genes in all three cases.
Comparisons with previously reported HD QTLs approximately co-mapping with PPD and FT
loci in hexaploid and tetraploid wheat was difficult because of differences in marker systems (i.e.,
SNPs vs simple sequence repeats and hybridization-based markers derived from genomic clones).
Therefore, the comparison of confidence intervals across maps was carried out based on normalized
genetic distances, relative to the total chromosome length, assuming nearly complete genome coverage
in both the tetraploid NCCR SNP-based map and the SSR/DArT hexaploid wheat consensus maps
from previously published QTL meta-analyses, such as the SSR consensus map Ta-SSR-2004 (Somers
et al. 2004), and the map used in the meta-QTL analysis reported by Griffiths et al. 2009). CI
boundaries of major PPD- and FT- QTL reported from other maps were first projected on the Ta-SSR2004. In NCCR, the normalized CIs for QHd.ubo-2A and QHd.ubo-2B were comparable to each other
(relative positions of 19.9-23.7 and 14.9-20.3 for IBD-CIM, 3.5-24.7 and 14.9-21.7 for IBS-SMA).
The meta-QTL 1 for HD reported by Griffiths et al. 2009 in chr 2A and corresponding to PPD-A1 was
mapped to a 7.1-32.8 relative position CI. In durum wheat Kofa x Svevo, QHd-2A.2 (Maccaferri et al.
2008) corresponding to PPD-A1 was mapped to a 16.9-22.8 relative position CI (projected on Ta-SSR2004). In chr 2B, the QTL for HD mapped by Bennett et al. (2012), corresponding to PPD-B1, was
mapped to a 19.1-27.1 relative interval. The meta-QTL reported by Hanocq et al. (2007) and the QTL
in durum wheat Kofa x Svevo, chromosome 2B, both centered to the SSR marker gwm148, were
mapped to an interval of 30.0-44.5%. These intervals were very close to the relative intervals of NCCR
QTL.
In NCCR, QHd.ubo-7A.2 was mapped to the relative interval of 20.8-34.5 (the IBS-SMA
included the IBD-CIM interval). This interval is compatible to those reported in Bennett et al. (2012),
equal to 34.7-41.5, in Hanocq et al. (2007), equal to 36.8-51.1, and in Griffitths et al. (2009), with 7A
meta-QTL1 located to an interval of 9.0-19.0 and 7A meta-QTL2 to 33.5-49.03. Bonnin et al. (2008)
mapped TaFT in Courtot x Chinese Spring very close to barc154, whose relative position in the TaSSR-2004 map is 34.5.
Since PPD-1 and TaFT have been cloned (Turner et al. 2005; Yan et al. 2006) the gene-based
SNP feature of the NCCR map was exploited to proof the potential of the map for mapping QTL down
to the candidate gene level. PPD-1 locus was found to contain Ta-PRR73-A1 in wheat, HvPRR37 in
barley, and Bradi1g16490 and Os07g49460 as horthologs in Brachypodium and rice (reviewed by
Higgins et al. 2010). TaFT locus (VRN3 in wheat) was shown to be horthologous of HvFT1-7H in
barley, OsFTL2-Hd3a = Os06g06320 in rice and of Bradi1g48830 in Brachypodium. The genes tagged
by mapped SNPs within the CI of the three QTLs (32, 54 and 26 SNP, respectively) were subjected to
a search for horthologs in barley, Brachypodium and rice in order to define the main conserved
syntenic blocks among grasses in the QTL regions.
As a first step, the ca. 200 bases of the Illumina SNP assay from the wheat 90K Illumina assay
manifest file were associated to unique Triticum turgidum transcript contigs using BLASTN and the
database stored in (http://wheat.pw.usda.gov/GG2/WheatTranscriptome/, Krasileva et al. 2013). The
Triticum turgidum transcript contigs were used to retrieve the corresponding orthologs in barley,
Brachypodium and rice genomes using the bidirectional best hit approach implemented in ChromoWIZ
software, a tool for co-linearity analysis in grass genomes (http://pgsb.helmholtz-muenchen.de/cgibin/db2/chromowiz, Nussbaumer et al. 2014). The results are reported in File S2.
In case of QHd.ubo-2A, starting from 16 unique Triticum turgidum transcripts for which at least
one grass orthologs were identified among barley, Brachypodium and rice (File S2), the number of
orthologs retrieved with the BBH method were 12, 15 and 11 for barley, Brachypodium and rice,
respectively. The IBD-CIM CI pointed out a strong conservation of co-linearity between wheat and
barley, with a unique barley genomic bin of 10 Mb size in chromosome 2H (the third from the top of
chromosome), containing 76 genes, and a more fragmented correspondence with Brachypodium and
rice, with three main distinct syntenic blocks in Brachypodium (chromosome 1, 3 and 5), and rice
chromosome 7 and chromosome 2. Besides of the unique clearly defined barley bin, the PPD-1 causal
gene was clearly confined within a six SNP array including the syntenic block in Brachypodium from
Bradi1g16470 to Bradi1g16590 and in rice (from Os07g49480 to Os07g49300) that spanned the
causal locus (Bradi1g16490 = Os07g49460).
The synteny relationships were less defined for QHd.ubo-2B, which mapped in a chromosome
position orthologous to QHd.ubo-2A. In the case of QHd.ubo-2B, the CI spanned a wider interval
(14.08 cM) with a lower density of mapped SNPs as compared to the corresponding chromosome
region in chromosome 2A. This was probably a consequence of the less defined founder SNP
molecular haplotype patterns in the region. Based on the six transcript mapped in the QHd.ubo-2B CI,
four barley genomic bins were tagged, of which two in chromosome 2H (including the bin identified
for QHd.ubo-2A), one in chromosome 1H and one in chromosome 5H, for a total of 260 genes. The
region was therefore much wider than that pointed out for QHd.ubo-2A. Moreover, the QTL peak and
CI identified based on IBD-CIM and IBS-SIM were not coincident, with the CI for IBD-CIM more
accurate than that resulted from IBS-SIM, based on the chromosome interval harboring the causal gene
Bradi1g16490 (File S2).
The QHd.ubo-7A.2 CI included 8 transcript that clearly identified barley bin fifth in chromosome
7H including 62 genes, among which the causal FT gene (Bradi1g48830 = Os06g06320). The
candidate region was also clearly identified by gene the co-linearity in Brachypodium and in rice.
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