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On the genome constitution and evolution of intermediate wheatgrass (Thinopyrum intermedium: Poaceae, Triticeae).

ABSTRACT: BACKGROUND: The wheat tribe Triticeae (Poaceae) is a diverse group of grasses representing a textbook example of reticulate evolution. Apart from globally important grain crops, there are also wild grasses which are of great practical value. Allohexaploid intermediate wheatgrass, Thinopyrum intermedium (2n = 6x = 42), possesses many desirable agronomic traits that make it an invaluable source of genetic material useful in wheat improvement. Although the identification of its genomic components has been the object of considerable investigation, the complete genomic constitution and its potential variability are still being unravelled. To identify the genomic constitution of this allohexaploid, four accessions of intermediate wheatgrass from its native area were analysed by sequencing of chloroplast trnL-F and partial nuclear GBSSI, and genomic in situ hybridization. RESULTS: The results confirmed the allopolyploid origin of Thinopyrum intermedium and revealed new aspects in its genomic composition. Genomic heterogeneity suggests a more complex origin of the species than would be expected if it originated through allohexaploidy alone. While Pseudoroegneria is the most probable maternal parent of the accessions analysed, nuclear GBSSI sequences suggested the contribution of distinct lineages corresponding to the following present-day genera: Pseudoroegneria, Dasypyrum, Taeniatherum, Aegilops and Thinopyrum. Two subgenomes of the hexaploid have most probably been contributed by Pseudoroegneria and Dasypyrum, but the identity of the third subgenome remains unresolved satisfactorily. Possibly it is of hybridogenous origin, with contributions from Thinopyrum and Aegilops. Surprising diversity of GBSSI copies corresponding to a Dasypyrum-like progenitor indicates either multiple contributions from different sources close to Dasypyrum and maintenance of divergent copies or the presence of divergent paralogs, or a combination of both. Taeniatherum-like GBSSI copies are most probably pseudogenic, and the mode of their acquisition by Th. intermedium remains unclear. CONCLUSIONS: Hybridization has played a key role in the evolution of the Triticeae. Transfer of genetic material via extensive interspecific hybridization and/or introgression could have enriched the species' gene pools significantly. We have shown that the genomic heterogeneity of intermediate wheatgrass is higher than has been previously assumed, which is of particular concern to wheat breeders, who frequently use it as a source of desirable traits in wheat improvement.

SUBMITTER: Mahelka V

PROVIDER: S-EPMC3123223 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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On the genome constitution and evolution of intermediate wheatgrass (Thinopyrum intermedium: Poaceae, Triticeae).

Mahelka Václav V Kopecký David D Paštová Ladislava L

BMC evolutionary biology 20110518

<h4>Background</h4>The wheat tribe Triticeae (Poaceae) is a diverse group of grasses representing a textbook example of reticulate evolution. Apart from globally important grain crops, there are also wild grasses which are of great practical value. Allohexaploid intermediate wheatgrass, Thinopyrum intermedium (2n = 6x = 42), possesses many desirable agronomic traits that make it an invaluable source of genetic material useful in wheat improvement. Although the identification of its genomic compo ...[more]

PMID: 21592357

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Project description:BackgroundIntermediate wheatgrass (IWG) is a novel perennial grain crop currently undergoing domestication. It offers important ecosystem benefits while producing grain suitable for human consumption. Several aspects of plant biology and genetic control are yet to be studied in this new crop. To understand trait behavior and genetic characterization of kernel color in IWG breeding germplasm from the University of Minnesota was evaluated for the CIELAB components (L*, a*, b*) and visual differences. Trait values were used in a genome-wide association scan to reveal genomic regions controlling IWG's kernel color. The usability of genomic prediction in predicting kernel color traits was also evaluated using a four-fold cross validation method.ResultsA wide phenotypic variation was observed for all four kernel color traits with pairwise trait correlations ranging from - 0.85 to 0.27. Medium to high estimates of broad sense trait heritabilities were observed and ranged from 0.41 to 0.78. A genome-wide association scan with single SNP markers detected 20 significant marker-trait associations in 9 chromosomes and 23 associations in 10 chromosomes using multi-allelic haplotype blocks. Four of the 20 significant SNP markers and six of the 23 significant haplotype blocks were common between two or more traits. Evaluation of genomic prediction of kernel color traits revealed the visual score to have highest mean predictive ability (r2 = 0.53); r2 for the CIELAB traits ranged from 0.29-0.33. A search for candidate genes led to detection of seven IWG genes in strong alignment with MYB36 transcription factors from other cereal crops of the Triticeae tribe. Three of these seven IWG genes had moderate similarities with R-A1, R-B1, and R-D1, the three genes that control grain color in wheat.ConclusionsWe characterized the distribution of kernel color in IWG for the first time, which revealed a broad phenotypic diversity in an elite breeding germplasm. Identification of genetic loci controlling the trait and a proof-of-concept that genomic selection might be useful in selecting genotypes of interest could help accelerate the breeding of this novel crop towards specific end-use.

Project description:Fluorescence in situ hybridization was used in Thinopyrum ponticum, a decaploid species, and its related diploid species, to investigate the distribution of the 18S-5.8S-26S rDNA. The distribution of rDNA was similar in all three diploid species (Th. bessarabicum, Th. elongatum and Pseudoroegneria stipifolia). Two pairs of loci were observed in each somatic cell at metaphase and interphase. One pair was located near the terminal end and the other in the interstitial regions of the short arms of one pair of chromosomes. However, all of the major loci in Th. ponticum were located on the terminal end of the short arms of chromosomes, and one chromosome had only one major locus. The maximum number of major loci detected on metaphase spreads was 20, which was the sum of that of its progenitors. The interstitial loci that exist in the possible diploid genome donor species were probably 'lost' during the evolutionary process of the decaploid species. A number of minor loci were also detected on whole regions of two pairs of homologous chromosomes. These results suggested that the position of rDNA loci in the Triticeae might be changeable rather than fixed. Positional changes of 18S-5.8S-26S rDNA loci between Th. ponticum and its candidate genome donors indicate that it is almost impossible to find a genome in the polyploid species that is completely identical to that of its diploid donors. The possible evolutionary significance of the distribution of the rDNA is also discussed. Internal transcribed spacer (ITS) regions of nuclear DNA in Th. ponticum were investigated by PCR amplification and sequencing. The sequence data from five positive clones selected at random, together with restriction site analysis, indicated that the ITS repeated units are nearly homogeneous in this autoallodecapolypoid species. Combined with in situ hybridization results, the data led to the conclusion that the ITS region has experienced interlocus as well as intralocus concerted evolution. Phylogenetic analyses showed that the sequences from Th. ponticum have concerted to the E genome repeat type.

Dataset Information

On the genome constitution and evolution of intermediate wheatgrass (Thinopyrum intermedium: Poaceae, Triticeae).

Publications

On the genome constitution and evolution of intermediate wheatgrass (Thinopyrum intermedium: Poaceae, Triticeae).

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