Allopolyploidy origins and genome structure of barley relatives

Unravelling relationships within Hordeum, one of the largest genera of the tribe Triticeae (Hordeae), is difficult, as many taxa, including most of the polyploids, are of hybrid origin. Mapping phylogenetic relationships, Cuadrado et al. investigate origins and interspecific affinities of the allotetraploids Hordeum secalinum and H. capense using molecular karyotyping.

Multiple target in situ hybridizations combining GISH using H. marinum subsp. gussoneanum DNA as a probe (gusDNA) — Multiple target *in situ* hybridizations combining GISH using *H. marinum* subsp. *gussoneanum* DNA as a probe (*gus*DNA), and FISH/ND-FISH to analyse the chromosomal distribution of various tandem repetitive DNA probes as indicated in metaphases/chromosomes of four accessions of *H. secalinum*: (A, B) H231, (C–J) BCC2004, (L, M) H3121 and (N, O) GRA1147. Some panels show merged images to facilitate the visualization of the *in situ* signals (green or pink/red) with respect to 4′,6-diamidino-2-phenylindole (DAPI; blue) staining. (K) Karyotype of BCC004 for pAs1 in *H. secalinum*. Note that chromosomes were chosen from the same metaphase used to construct the karyotypes shown in Fig. 2A. The identity of chromosomes belonging to sub-genome Xa and I are indicated in yellow and white, respectively. Arrows in B, E, M and O point to the pair of chromosomes showing an interstitial pSc119·2 signal. Arrowheads in I, J and N point to polymorphic rDNA loci in *H. secalinum* accessions. Asterisks in C and O illustrate the polymorphism observed for the presence/absence for the probe indicated within accessions. Scale bar in K = 10 μm.

Genomic in situ hybridization distinguishes the subgenomes Xa and I while FISH/ND-FISH determines the distribution of ten repetitive DNA sequences. Identification of each chromosome pair in the six analysed accessions reveals an intricate pattern of homologous and putative homeologous relationships among barley species carrying the Xa genome.

This paper is part of the Annals of Botany Special Issue on Polyploidy in Ecology and Evolution. It will be free access until October 2017, then available only to subscribers until August 2018 when it will be free access again.