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The influence of Al³⁺ on DNA methylation and sequence changes in the triticale (× Triticosecale Wittmack) genome.

ABSTRACT: Abiotic stressors such as drought, salinity, and exposure to heavy metals can induce epigenetic changes in plants. In this study, liquid chromatography (RP-HPLC), methylation amplified fragment length polymorphisms (metAFLP), and methylation-sensitive amplification polymorphisms (MSAP) analysis was used to investigate the effects of aluminum (Al) stress on DNA methylation levels in the crop species triticale. RP-HPLC, but not metAFLP or MSAP, revealed significant differences in methylation between Al-tolerant (T) and non-tolerant (NT) triticale lines. The direction of methylation change was dependent on phenotype and organ. Al treatment increased the level of global DNA methylation in roots of T lines by approximately 0.6%, whereas demethylation of approximately 1.0% was observed in NT lines. DNA methylation in leaves was not affected by Al stress. The metAFLP and MSAP approaches identified DNA alterations induced by Al³⁺ treatment. The metAFLP technique revealed sequence changes in roots of all analyzed triticale lines and few mutations in leaves. MSAP showed that demethylation of CCGG sites reached approximately 3.97% and 3.75% for T and NT lines, respectively, and was more abundant than de novo methylation, which was observed only in two tolerant lines affected by Al stress. Three of the MSAP fragments showed similarity to genes involved in abiotic stress.

SUBMITTER: Niedziela A

PROVIDER: S-EPMC7902597 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Alloploidization resulting from remote (interspecific or intergeneric) hybridization is one of the main factors in plant evolution, leading to the formation of new species. Triticale (× Triticosecale Wittmack, 1889) is the first artificial species created by crossing wheat (Triticum spp.) and rye (Secale cereale Linnaeus, 1753) and has a great potential as a grain and forage crop. Remote hybridization is a stress factor that causes a rapid reorganization of the parental genomes in hybrid progeny ("genomic shock") and is accompanied by abnormalities in the chromosome set of hybrids. The formation of the hybrid genome and its subsequent stabilization are directly related to the normalization of meiosis and the correct chromosome segregation. The aim of this work was to cytogenetically characterize triticale (× Triticosecale rimpaui Wittmack, 1899, AABBDDRR) obtained by crossing Triticum aestivum Linnaeus, 1753. Triple Dirk D × Secale cereale L. Korotkostebel'naya 69 in F3-F6 generations of hybrids, and to trace the process of genetic stabilization of hybrid genomes. Also, a comparative analysis of the nucleotide sequences of the centromeric histone CENH3 genes was performed in wheat-rye allopolyploids of various ploidy as well as their parental forms. In the hybrid genomes of octoploid triticale an increased expression of the rye CENH3 variants was detected. The octoploid triticale plants contain complete chromosome sets of the parental subgenomes maintaining the chromosome balance and meiotic stability. For three generations the percentage of aneuploids in the progeny of such plants has been gradually decreasing, and they maintain a complete set of the paternal rye chromosomes. However, the emergence of hexaploid and new aneuploid plants in F5 and F6 generations indicates that stabilization of the hybrid genome is not complete yet. This conclusion was confirmed by the analysis of morphological features in hybrid plants: the progeny of one plant having the whole chromosome sets of parental subgenomes showed significant morphological variations in awn length and spike density. Thus, we expect that the results of our karyotyping of octoploid triticales obtained by crossing hexaploid wheat to diploid rye supplemented by comparative analysis of CENH3 sequences will be applicable to targeted breeding of stable octo- and hexaploid hybrids.

Project description:Freezing tolerance of triticale is a major trait contributing to its winter hardiness. The identification of genomic regions - quantitative trait loci (QTL) and molecular markers associated with freezing tolerance in winter hexaploid triticale - was the aim of this study. For that purpose, a new genetic linkage map was developed for the population of 92 doubled haploid lines derived from 'Hewo' × 'Magnat' F1 hybrid. Those lines, together with parents were subjected to freezing tolerance test three times during two winter seasons. Plants were grown and cold-hardened under natural fall/winter conditions and then subjected to freezing in controlled conditions. Freezing tolerance was assessed as the plants recovery (REC), the electrolyte leakage (EL) from leaves and chlorophyll fluorescence parameters (JIP) after freezing. Three consistent QTL for several fluorescence parameters, electrolyte leakage, and the percentage of the survived plants were identified with composite interval mapping (CIM) and single marker analysis (SMA). The first locus Qfr.hm-7A.1 explained 9% of variation of both electrolyte leakage and plants recovery after freezing. Two QTL explaining up to 12% of variation in plants recovery and shared by selected chlorophyll fluorescence parameters were found on 4R and 5R chromosomes. Finally, main locus Qchl.hm-5A.1 was detected for chlorophyll fluorescence parameters that explained up to 19.6% of phenotypic variation. The co-located QTL on chromosomes 7A.1, 4R and 5R, clearly indicated physiological and genetic relationship of the plant survival after freezing with the ability to maintain optimal photochemical activity of the photosystem II and preservation of the cell membranes integrity. The genes located in silico within the identified QTL include those encoding BTR1-like protein, transmembrane helix proteins like potassium channel, and phosphoric ester hydrolase involved in response to osmotic stress as well as proteins involved in the regulation of the gene expression, chloroplast RNA processing, and pyrimidine salvage pathway. Additionally, our results confirm that the JIP test is a valuable tool to evaluate freezing tolerance of triticale under unstable winter environments.

Project description:BackgroundRecent advances in genotyping with high-density markers nowadays enable genome-wide genomic analyses in crops. A detailed characterisation of the population structure and linkage disequilibrium (LD) is essential for the application of genomic approaches and consequently for knowledge-based breeding. In this study we used the triticale-specific DArT array to analyze population structure, genetic diversity, and LD in a worldwide set of 161 winter and spring triticale lines.ResultsThe principal coordinate analysis revealed that the first principal coordinate divides the triticale population into two clusters according to their growth habit. The density distributions of the first ten principal coordinates revealed that several show a distribution indicative of population structure. In addition, we observed relatedness within growth habits which was higher among the spring types than among the winter types. The genome-wide analysis of polymorphic information content (PIC) showed that the PIC is variable among and along chromosomes and that especially the R genome of spring types possesses a reduced genetic diversity. We also found that several chromosomes showed regions of high genetic distance between the two growth habits, indicative of divergent selection. Regarding linkage disequilibrium, the A and B genomes showed a similar LD of 0.24 for closely linked markers and a decay within approximately 12 cM. LD in the R genome was lower with 0.19 and decayed within a shorter map distance of approximately 5 cM. The extent of LD was generally higher for the spring types compared to the winter types. In addition, we observed strong variability of LD along the chromosomes.ConclusionsOur results confirm winter and spring growth habit are the major contributors to population structure in triticale, and a family structure exists in both growth types. The specific patterns of genetic diversity observed within these types, such as the low diversity on some rye chromosomes of spring habits, provide a basis for targeted broadening of the available breeding germplasm. In addition, the genome-wide analysis of the extent and the pattern of LD will assist scientists and breeders alike in the implementation and the interpretation of association mapping in triticale.

Project description:BackgroundTriticale is adapted to a wide range of abiotic stress conditions, is an important high-quality feed stock and produces similar grain yield but more biomass compared to other crops. Modern genomic approaches aimed at enhancing breeding progress in cereals require high-quality genetic linkage maps. Consensus maps are genetic maps that are created by a joint analysis of the data from several segregating populations and different approaches are available for their construction. The phenomenon that alleles at a locus deviate from the Mendelian expectation has been defined as segregation distortion. The study of segregation distortion is of particular interest in doubled haploid (DH) populations due to the selection pressure exerted on the plants during the process of their establishment.ResultsThe final consensus map, constructed out of six segregating populations derived from nine parental lines, incorporated 2555 DArT markers mapped to 2602 loci (1929 unique). The map spanned 2309.9 cM with an average number of 123.9 loci per chromosome and an average marker density of one unique locus every 1.2 cM. The R genome showed the highest marker coverage followed by the B genome and the A genome. In general, locus order was well maintained between the consensus linkage map and the component maps. However, we observed several groups of loci for which the colinearity was slightly uneven. Among the 2602 loci mapped on the consensus map, 886 showed distorted segregation in at least one of the individual mapping populations. In several DH populations derived by androgenesis, we found chromosomes (2B, 3B, 1R, 2R, 4R and 7R) containing regions where markers exhibited a distorted segregation pattern. In addition, we observed evidence for segregation distortion between pairs of loci caused either by a predominance of parental or recombinant genotypes.ConclusionsWe have constructed a reliable, high-density DArT marker consensus genetic linkage map as a basis for genomic approaches in triticale research and breeding, for example for multiple-line cross QTL mapping experiments. The results of our study exemplify the tremendous impact of different DH production techniques on allele frequencies and segregation distortion covering whole chromosomes.

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The influence of Al³⁺ on DNA methylation and sequence changes in the triticale (× Triticosecale Wittmack) genome.

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The influence of Al³⁺ on DNA methylation and sequence changes in the triticale (× Triticosecale Wittmack) genome.