The Agropyron cristatum karyotype, chromosome structure and cross-genome homoeology as revealed by fluorescence in situ hybridization with tandem repeats and wheat single-gene probes

Abstract

Key messageFluorescence in situ hybridization with probes for 45 cDNAs and five tandem repeats revealed homoeologous relationships of Agropyron cristatum with wheat. The results will contribute to alien gene introgression in wheat improvement.AbstractCrested wheatgrass (Agropyron cristatum L. Gaertn.) is a wild relative of wheat and a promising source of novel genes for wheat improvement. To date, identification of A. cristatum chromosomes has not been possible, and its molecular karyotype has not been available. Furthermore, homoeologous relationship between the genomes of A. cristatum and wheat has not been determined. To develop chromosome-specific landmarks, A. cristatum genomic DNA was sequenced, and new tandem repeats were discovered. Their distribution on mitotic chromosomes was studied by fluorescence in situ hybridization (FISH), which revealed specific patterns for five repeats in addition to 5S and 45S ribosomal DNA and rye subtelomeric repeats pSc119.2 and pSc200. FISH with one tandem repeat together with 45S rDNA enabled identification of all A. cristatum chromosomes. To analyze the structure and cross-species homoeology of A. cristatum chromosomes with wheat, probes for 45 mapped wheat cDNAs covering all seven chromosome groups were localized by FISH. Thirty-four cDNAs hybridized to homoeologous chromosomes of A. cristatum, nine hybridized to homoeologous and non-homoeologous chromosomes, and two hybridized to unique positions on non-homoeologous chromosomes. FISH using single-gene probes revealed that the wheat-A. cristatum collinearity was distorted, and important structural rearrangements were observed for chromosomes 2P, 4P, 5P, 6P and 7P. Chromosomal inversions were found for pericentric region of 4P and whole chromosome arm 6PL. Furthermore, reciprocal translocations between 2PS and 4PL were detected. These results provide new insights into the genome evolution within Triticeae and will facilitate the use of crested wheatgrass in alien gene introgression into wheat.Electronic supplementary materialThe online version of this article (10.1007/s00122-018-3148-9) contains supplementary material, which is available to authorized users.

Dissecting the Complex Genome of Crested Wheatgrass by Chromosome Flow Sorting

“…Such variation in Parkway was observed previously (Said et al, 2018a), and similar observations have been made in other genotypes of crested wheatgrass (Linc et al, 2017) and other open‐pollinated species such as rye (Szakács and Molnár‐Láng, 2008). The results of flow karyotyping in crested wheatgrass are consistent with our data on chromosome length (Said et al, 2018a). The order of chromosomes from the shortest to the largest (4P, 3P, 1P, 7P, 5P, 6P, and 2P) agrees with the assignment of chromosome groups to Peaks I (1P, 3P, 4P), II (5P, 6P) and III (2P, 7P) on monoparametric (DAPI‐) flow karyotypes.…”

“…Numerous genes providing tolerance to biotic stress (i.e., resistance to barley yellow dwarf virus, wheat streak mosaic virus, yellow rust, leaf rust, stem rust, and powdery mildew) and abiotic stresses (i.e., cold‐, salinity‐ and drought tolerance) as well as genes improving yield were identified in crested wheatgrass (Shukle et al, 1987; Brettell et al, 1988; Littlejohn, 1988; Whelan, 1988; Friebe et al, 1992; Luan et al, 2010; Song et al, 2013; Ceoloni et al, 2015; Ochoa et al, 2015). In the present study, we extended the chromosome‐based approach to the complex P‐genome of crested wheatgrass (Said et al, 2018a) to produce genomic resources for chromosome‐mediated gene transfer into wheat.…”

“…This compares well with the study of Endo et al (2014), in which the size of flow‐sorted wheat chromosomes 1B and 6B were more than seven times longer than chromosomes in mitotic metaphase plates. The hyperexpanded chromosomes of crested wheatgrass will also be useful for the construction of detailed cytological maps using single‐copy FISH (Said et al, 2018a). In fact, the spatial resolution of FISH may be increased further by artificial stretching of flow‐sorted chromosomes.…”

“…However, de novo genome sequencing and assembly is still difficult to implement in Triticeae species with large genomes. Crested wheatgrass has a large and complex P genome estimated to exceed 6 Gbp 1C −1 (Said et al, 2018a), which hampers genomic studies and the development of an effective marker system for introgression breeding programs.…”

Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryegrasses

“…The pipeline uses graph-based clustering and is suitable for the analysis of next generation sequencing data to reconstruct and characterize DNA repeats in a particular species, or to compare DNA repeat composition in different genotypes [22,23,48,49]. The pipeline has been used frequently to reconstruct DNA repeats in diversity studies, to create repeat databases for repeat masking [18,45,47] and to identify tandem organized repeats suitable as probes for molecular cytogenetics [34,51,52].…”