Chromosomal passports provide new insights into diffusion of emmer wheat

Abstract

Emmer wheat, Triticum dicoccon schrank (syn. T. dicoccum (schrank) schÜbl.), is one of the earliest domesticated crops, harboring a wide range of genetic diversity and agronomically valuable traits. The crop, however, is currently largely neglected. We provide a wealth of karyotypic information from a comprehensive collection of emmer wheat and related taxa. In addition to C-banding polymorphisms, we identified 43 variants of chromosomal rearrangements in T. dicoccon; among them 26 (60.4%) were novel. The T7A:5B translocation was most abundant in Western Europe and the Mediterranean. The plant genetic resources investigated here might become important in the future for wheat improvement. Based on cluster analysis four major karyotypic groups were discriminated within the T. dicoccon genepool, each harboring characteristic C-banding patterns and translocation spectra: the balkan, asian, european and ethiopian groups. We postulate four major diffusion routes of the crop and discuss their migration out of the Fertile Crescent considering latest archaeobotanical findings.

Fig 1. Generalized idiogram of wheat A and B genome chromosomes.

A and B—wheat genomes; 1–7—homoeologous groups; S and L—short and long arm of a chromosome, respectively. Large permanent C-bands are shown as solid blocks; polymorphic C-bands are shown as shaded blocks; small inconsistent C-bands are indicated by dashed lines. Positions of C-bands are numbered at the right-hand side of each chromosome. The 112 C-bands considered in “chromosomal passports” are shown in red; 38 C-bands most essential for discrimination of karyotypic groups are indicated with *.

Fig 2. Main karyotypic groups/types distinguished among T. dicoccon accessions on the basis of visual analysis of C-banding patterns.

Left side—A-genome chromosomes, right side—B-genome chromosomes; 1–7—homoeologous groups. Chromosomal groups: Balkan, European, Asian, Ethiopian (PI 94664, Saudi Arabia); chromosomal types: Bal (PI 434996, Montenegro), Vol (k-30728, Nizhny Novgorod); WEM-1 type prevailing in European-Mediterranean emmer lines with 7A:5B translocation (k-1730, Germany); WEM-2 (PI 352332, Belgium); WEM-Sp (PI 275998, Spain); Trc (k-14937, Georgia); Irn (TA10540, Iran), Mor (k-22246, Morocco). Small red arrows indicate positions of small group-specific bands; large red arrows show the positions of C-bands with an enlarged size or group-specific supernumerary C-bands; blue arrows indicate group-specific bands with a decreased size (small arrow) or the positions of bands that are missing in the group-specific chromosome variant (large arrow). Large black arrows show the breakpoint position in region-specific translocation variants: T7AS.7AL-5BS and T5BL.5BS-7AL—rearranged chromosomes formed as a result of the T7A:5B translocation; T4AS:1BL and T1BS:4AL—rearranged chromosomes formed as a result of the T4A:1B translocation; T1AS.1AL-6AS and T6AL.6AS-1AL—rearranged chromosomes formed as a result of the T1A:6A translocation; T4BS:6BL and T6BS:4BL—rearranged chromosomes formed as a result of the T4B:6B-1 translocation (see S3 and S4 Tables).

Fig 3. Diversity of chromosomal rearrangements and translocation lineages identified in domesticated emmer.

Translocation types are designated according to S3 and S4 Tables. Translocation variants described in previous papers [35,46] are shown in red and novel translocation variants found in this study are indicated in blue. Red arrows define translocation lineages, i.e. a series of related translocations occurring one after another. A detailed description of all translocation variants is given in S3 and S4 Tables.

Fig 4. Embedding of 545 emmer wheat accessions into three dimensions by non-metric multidimensional scaling (NMDS).

NMDS is based on the Hamming distance calculated on the C-banding patterns (S2 Table). Each point represents a single accession. The four colors blue, red, green and orange are based on k-medoids and represent the European, Balkan, Asian, and Ethiopian, respectively. Additionally, black is used for Dicoccoides and other taxa.

Fig 5. Distribution of karyotypic groups and possible migration routes of domesticated emmer.

One dot corresponds to one line studied. The dots are colored according to k-medoids cluster position (see S1 Table). Square dots designate lines carrying the T7A:5B and round dots designate lines lacking the 7A:5B. Solid lines designate migration routes supported by our data, while dashed lines designate hypothetical migration routes, which were not confirmed in our study. Thick lines correspond to major migration routes, thin lines to secondary migration routes; 1a —possible migration route of Balkan emmer from Anatolia to the Balkans; 1b —possible migration route of Vol emmer from the Balkans to the Volga region; 4a —possible migration route of Ethiopian emmer from Zagros to Ethiopia via the Arabian trading route and to India by maritime route; 4b —possible migration route of Ethiopian emmer from Zagros through India and Oman to Ethiopia.