Cytogenetic diversity of SSR motifs within and between Hordeum species carrying the H genome: H. vulgare L. and H. bulbosum L.

Abstract

Non-denaturing FISH (ND-FISH) was used to compare the distribution of four simple sequence repeats (SSRs)-(AG) n , (AAG) n , (ACT) n and (ATC) n -in somatic root tip metaphase spreads of 12 barley (H. vulgare ssp. vulgare) cultivars, seven lines of their wild progenitor H. vulgare ssp. spontaneum, and four lines of their close relative H. bulbosum, to determine whether the range of molecular diversity shown by these highly polymorphic sequences is reflected at the chromosome level. In both, the cultivated and wild barleys, clusters of AG and ATC repeats were invariant. In contrast, clusters of AAG and ACT showed polymorphism. Karyotypes were prepared after the identification of their seven pairs of homologous chromosomes. Variation between these homologues was only observed in one wild accession that showed the segregation of a reciprocal translocation involving chromosomes 5H and 7H. The two subspecies of H. vulgare analysed were no different in terms of their SSRs. Only AAG repeats were found clustered strongly on the chromosomes of all lines of H. bulbosum examined. Wide variation was seen between homologous chromosomes within and across these lines. These results are the first to provide insight into the cytogenetic diversity of SSRs in barley and its closest relatives. Differences in the abundance and distribution of each SSR analysed, between H. vulgare and H. bulbosum, suggest that these species do not share the same H genome, and support the idea that these species are not very closely related. Southern blotting experiments revealed the complex organization of these SSRs, supporting the findings made with ND-FISH.

Chromosomal organization of repetitive DNAs in Hordeum bogdanii and H. brevisubulatum (Poaceae)

“…6). Another distinct difference is exhibited by the dinucleotide AG, which was intensely detected around the centromere in Hordeum vulgare (Hagras et al 2005, Carmona et al 2013a) but was absent in Hordeum bogdanii . Additional differences between Hordeum bogdanii and Hordeum vulgare can be seen in the distribution patterns of AAT, GCC, CAG, 45S rDNA, 5S rDNA and pSc119.2.…”

“…This provided detailed information on the sequence content of barley chromatin and saturated the physical map of all the barley chromosomes (Cuadrado and Jouve 2007a). Later, cytogenetic diversity between Hordeum vulgare and Hordeum bulbosum , was revealed using probes of SSRs, 5S rDNA, 45S rDNA, and 120-bp repeats from Secale cereale Linnaeus, 1753 (Carmona et al 2013a). Karyotypes of the species of the Hordeum marinum complex were determined using several tandem repeats.…”

Next generation sequencing and FISH reveal uneven and nonrandom microsatellite distribution in two grasshopper genomes

“…Moreover, precise chromosomal identification may be based on specific SSR distribution pattern, as is the case in barley where chromosome distribution of (AAG) 5 and (ACT) 5 microsatellite repeats allows easy chromosome identification and detection of structural chromosome rearrangements (e.g., translocations) (Carmona et al 2013). Drosophila is one of the few animals where microsatellites have been profusely analyzed at the chromosomal level Jouve 2007b, 2011;Santos et al 2010).…”

Satellite DNA in Plants: More than Just Rubbish

“…This suggests that satellite arrays undergo rapid evolution through both expansion and shrinkage, resulting in the replacement of the most abundant variant with a different variant [Melters et al, 2013;Zhang et al, 2013b]. Simple sequence repeats are also commonly found forming pericentromeric heterochromatin [Hudakova et al, 2001;Cuadrado and Jouve, 2007;Carmona et al, 2013a;Cuadrado et al, 2013]. In addition to satellite DNA families, centromeric retrotransposons represent an important component of centromeres of a wide range of angiosperm species, implying these families are the key to plant centromere evolution and function .…”