A HIGH-DENSITY, SNP-BASED CONSENSUS MAP OF TETRAPLOID WHEAT AS A
BRIDGE TO INTEGRATE DURUM AND BREAD WHEAT GENOMICS AND BREEDING
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Marco Maccaferri , Andrea Ricci , Silvio Salvi , Sara Giulia Milner , Enrico Noli , Pier Luigi
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Martelli , Rita Casadio , Eduard Akhunov , Simone Scalabrin , Vera Vendramin , Karim Ammar ,
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Antonio Blanco , Francesca Desiderio , Assaf Distelfeld , Jorge Dubcovsky , Tzion Fahima , Justin
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Faris , Abraham Korol , Andrea Massi , Anna Mastrangelo , Michele Morgante , Curtis
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Pozniak , Steven Xu , Roberto Tuberosa
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Department of Agricultural Science (DipSA), Viale Fanin 44, University of Bologna, 40127 Bologna, Italy
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Biocomputing Group, Via Selmi 3, University of Bologna, 40126 Bologna, Italy
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Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506
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Istituto di Genomica Applicata, c/o Parco Scientifico e Tecnologico L. Danieli, 33100 Udine, Italy and University of
Udine, Dipartimento di Scienze Agrarie e Ambientali, 33100 Udine, Italy
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CIMMYT Carretera Mexico-Veracruz km 45, 56130 Texcoco, Mexico
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Dipartimento di Biologia e Chimica Agro-forestale ed ambientale, Università di Bari, Aldo Moro, Via Amendola 165/A,
70126 Bari, Italy
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Consiglio per la ricerca e la sperimentazione in agricoltura, Genomics Research Centre, Via San Protaso 302, 29017
Fiorenzuola d'Arda, Italy
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Faculty of Life Sciences, Dept. of Molecular Biology and Ecology of Plants, Tel Aviv University, 69978 Tel Aviv, Israel
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Department of Plant Sciences, University of California, Davis, CA 95616, USA, and Howard Hughes Medical Institute,
Chevy Chase, MD 20815
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Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science
Education, University of Haifa, Mt. Carmel, 31905 Haifa, Israel
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USDA-ARS Cereal Crops Research Unit, NCSL 1605 Albrecht Blvd. N., Fargo, 58102-2765 ND, USA
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Società Produttori Sementi Bologna (PSB), Via Macero 1, 40050 Argelato, Italy
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Consiglio per la ricerca e la sperimentazione in agricoltura, Cereal Research Centre, SS16 km 675, 71122 Foggia, Italy
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Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive,
Saskatoon, SK S7N 5A8, Cana
Supplemental Text 1.
SNP-transcript matches tagging homeologous relationships between chromosome regions in
non-nominal homeologous relationships.
Homeologous relationships between loci affected by the T4A/5A were tagged by 629 homeologous
4A-5B and 4B-5A reference SNP-transcript hits and by 436 hits in reversed directions (5B-4A and
5A-4B). The T7B/4A was tagged by 463 7A-4A + 497 4A-7A hits (Supplemental Table S3).
Based on the detailed BLAST results, the T4A/5A could be defined by homeologous relationships
for
4BL-5AL and 4AL-5BL SNP-transcripts pairs that included 296 non redundant SNPs
(chromosome group 4) and 201 reference transcripts (chromosome group 5) and for the 5AL-4BL
and 5BL-4AL SNP-transcripts pairs, including 433 non redundant SNPs (chromosome group 4)
and 263 reference transcripts (chromosome group 5), respectively.
The involved regions spanned most of the genetic maps of chromosome arms 4AL and 4BL with
the highest density of homeologous relationships in the proximal regions of the chromosomes (86115 cM interval for 4A and 70-124 cM interval for 4B) and a considerable portion of genetic maps
of 5AL and 5BL (70-218 cM and 40-206 cM). The results are detailed in Supplemental Table S5.
As to the second translocation that involved chromosome arm 4AL, i.e. the T7BS/4AL, this event
was clearly defined by the homeologous relationships of 4AL-7AS and 7AS-4AL SNP-transcripts
pairs involving 374 non-redundant SNPs on 4AL and 213 reference transcripts on 7AS and, in the
reversed comparison, 338 non-redundant SNPs on 7AS and 220 reference transcripts on 4AL. The
homeologous relationship was mapped in the 127-175 cM interval (distal end) of chromosome 4AL,
containing the 7BS loci, and from top (distal end) to 60 cM interval of chromosome 7AS, with a
few remaining hits between 60 to 118 cM of chromosome 7AS (Supplemental Table S5). On the
other hand, less defined evidences of the reciprocal translocation were found by inspecting the 4B7B pairs. For the majority of the reference transcripts involved in T4AL/5AL and T7BS/4AL
translocations, the Chinese Spring database missed the corresponding homeologs in the alternative
chromosome of the nominal group and this was considered as supporting evidence for the
robustness of the estimates of chromosome regions subjected to the translocations. In addition, the
wide 4A pericentric inversion of 4AS/4AL was evident by checking the correspondence between
the locations of SNPs tagging group 4 homeologous transcripts (Supplemental Table S5).
Besides the wide T4AL/5AL and T4AL/7BS, non-nominal homeologous relationships were also
identified for sets of tightly linked SNPs mapping to the following chromosome pairs: 5B-7B, 5B2B, 2B-4B, 6B-5B. For these cases, evidences for possible smaller and even multiple translocations
events included the identification of groups of contiguous SNPs mapped within relatively short
distances (from a few cM to 30 cM maximum) that were related to the reference transcripts in the
non-homeologous chromosomes but not to the nominal homeologs (data reported to Supplemental
Table S5). Two small regions in the distal end of chromosome 5AL and 5BL showed complete
homeology to distal ends of chr. 7AS and 7BS region, respectively. The regions were defined by the
199.1-210.1 cM interval at the distal end of chromosome 5A and the 206.2 cM chromosome-end
position of chromosome 5B with 3 and 31 non-redundant SNPs, respectively, corresponding to 3
and 12 transcripts originating from Chinese Spring chromosome arms 7AS and 7BS.
Another small region possibly tagging a local translocation was identified based on the homeology
between chromosome 6AS SNPs located in the 6.6-29.1 cM interval and 5B transcripts, for which
no homology was present in the corresponding 5A transcripts.
Differently from the translocations events reported above, specific chromosome pairs showed
higher-than-average number of hits for SNP-reference transcript pairs mapped to different nominal
homeologous groups that at the same time did not exclude the presence of the corresponding
homeologous transcripts in the nominal homeologous groups of the reference Chinese Spring
database. In the cases of chromosome 1-3 and 1-6 group pairs strong sequence similarity was found
for higher than average SNP-transcript pairs mapped along the complete chromosomes. In the case
of the chr. 1-3 group pairs, 146 and 225 BLAST hits related SNPs of chr. 1B to reference transcripts
of chr. 3A and 3B. Additionally, for the majority of these transcripts, the corresponding homeologs
were identified in the group 3 Chinese Spring transcript collection. Similar observations pertain for
chromosome pairs from group 1-6 (Supplemental Table S6).