During domestication and subsequent improvement plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future ...targeted broadening of diversity in breeding programmes. Rye (Secale cereale L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection.
Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a relatively narrow diversity of S. sylvestre, very high diversity of S. strictum, and signatures of strong positive selection in S. vavilovii. Within cultivated ryes we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production.
Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In present years, the use of zinc oxide nanoparticles (ZnO‐NPs) has received great attention due to increase in the nutrient accumulation by plants for improving the capability of agronomic Zn ...biofortification. Although, the emergence of polyvinyl chloride (PVC) microplastics (MPs) as pollutants in agricultural soils is increasingly alarming, presenting significant toxic threats to soil ecosystems. The present work studied the impact of different levels of PVC‐MPs, namely 0 (no PVC‐MPs), 2, and 4 mg L−1, along with mercury (Hg) levels of 0 (no Hg), 10, and 25 mg kg−1 in the soil, while concurrently applying with ZnO‐NPs at 0 (no ZnO‐NPs), 50, and 100 μg mL−1 to rye (Secale cereale L.) plants. This study aimed to examine plant growth and biomass, photosynthetic pigments and gas exchange characteristics, oxidative stress indicators, and the response of various antioxidants (enzymatic and non‐enzymatic) and their specific gene expression, proline metabolism, the ascorbic acid–dehydroascorbic acid (AsA–GSH) cycle, and cellular fractionation in the plants. The research outcomes indicated that elevated levels of PVC‐MPs and Hg stress in the soil notably reduced plant growth and biomass, photosynthetic pigments, and gas exchange attributes. However, PVC‐MPs and Hg stress also induced oxidative stress in the roots and shoots of the plants by increasing malondialdehyde (MDA), hydrogen peroxide (H2O2), and electrolyte leakage (EL) which also induced increased compounds of various enzymatic and non‐enzymatic antioxidants, and also the gene expression and sugar content. Furthermore, a significant increase in proline metabolism, the AsA–GSH cycle, and the pigmentation of cellular components was observed. Although, the application of ZnO‐NPs showed a significant increase in plant growth and biomass, gas exchange characteristics, enzymatic and non‐enzymatic compounds, and their gene expression and also decreased oxidative stress. In addition, the application of ZnO‐NPs enhanced cellular fractionation and decreased the proline metabolism and AsA–GSH cycle in S. cereale plants. These results open new insights for sustainable agriculture practices and hold immense promise in addressing the pressing challenges of heavy metal contamination in agricultural soils.
Rye (
Secale cereale
L.) is an important genetic resource for improving the disease resistance of wheat. An increasing number of rye chromosome segments have been transferred into modern wheat ...cultivars via chromatin insertions. In this study, 185 recombinant inbred lines (RILs) derived from a cross between a wheat accession containing rye chromosomes 1RS and 3R and a wheat-breeding founder parent Chuanmai 42 from southwestern China were used to decipher the cytological and genetic effects of 1RS and 3R via fluorescence/genomic in situ hybridization and quantitative trait locus (QTL) analyses. Chromosome centromere breakage and fusion were detected in the RIL population. Additionally, the recombination of chromosomes 1BS and 3D from Chuanmai 42 was completely suppressed by 1RS and 3R in the RIL population. In contrast to chromosome 3D of Chuanmai 42, rye chromosome 3R was significantly associated with white seed coats and decreased yield-related traits, as revealed by QTL and single marker analyses, whereas it had no effect on stripe rust resistance. Rye chromosome 1RS did not affect yield-related traits and it increased the susceptibility of plants to stripe rust. Most of the detected QTLs that positively affected yield-related traits were from Chuanmai 42. The findings of this study suggest that the negative effects of rye-wheat substitutions or translocations, including the suppression of the pyramiding of favorable QTLs on paired wheat chromosomes from different parents and the transfer of disadvantageous alleles to filial generations, should be considered when selecting alien germplasm to enhance wheat-breeding founder parents or to breed new varieties.
Transcription factor (TF) GAMYB, belonging to MYB family (named after the gene of the avian myeloblastosis virus) is a master gibberellin (GA)-induced regulatory protein that is crucial for ...development and germination of cereal grain and involved in anther formation. It activates many genes including high-molecular-weight glutenin and α-amylase gene families. This study presents the first attempt to characterize the rye gene encoding GAMYB in relation to its sequence, polymorphisms, and phenotypic effects.
ScGAMYB was mapped on rye chromosome 3R using high-density Diversity Arrays Technology (DArT)/DArTseq-based maps developed in three mapping populations. The ScGAMYB sequences were identified in RNA-seq libraries of four rye inbred lines. The transcriptome used for the search contained almost 151,000 transcripts with a median contig length of 500 nt. The average amount of total base raw data was approximately 9 GB. Comparative analysis of the ScGAMYB sequence revealed its high level of homology to wheat and barley orthologues. Single nucleotide polymorphisms (SNPs) detected among rye inbred lines allowed the development of allele specific-PCR (AS-PCR) markers for ScGAMYB that might be used to detect this gene in wide genetic stocks of rye and triticale. Segregation of the ScGAMYB alleles showed significant relationship with α-amylase activity (AMY).
The research showed the strong similarity of rye GAMYB sequence to its orthologues in other Graminae and confirmed the position in the genome consistent with the collinearity rule of cereal genomes. Concurrently, the ScGAMYB coding sequence (cds) showed stronger variability (24 SNPs) compared to the analogous region of wheat (5 SNPs) and barley (7 SNPs). The moderate regulatory effect of ScGAMYB on AMY was confirmed, therefore, ScGAMYB was identified as a candidate gene for partial control of α-amylase production in rye grain. The predicted structural protein change in the aa region 362-372, caused by a single SNP (C/G) at the 1100 position in ScGAMYB cds and single aa sequence change (S/C) at the 367 position, is the likely cause of the differences in the effectiveness of ScGAMYB regulatory function associated with AMY. The development of sequence-based, allele-specific (AS) PCR markers could be useful in research and application.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The results of molecular analysis of 45 rye taxa (Secale cereale L.) represented by agricultural varieties originated from Central Europe and the Union of Soviet Socialist Republics (SUN) are ...presented. The genetic diversity of rye cultivars by 6 SSR markers was evaluated. Six specific microsatellite primer pairs produced 58 polymorphic alleles with an average of 9.7 alleles per locus. The number of alleles ranged from 6 (SCM2) to 14 (SCM86). Genetic polymorphism was characterized based on diversity index (DI), probability of identity (PI) and polymorphic information content (PIC). The diversity index (DI) of SSR markers ranged from 0.5478 (SCM2) to 0.887 (SCM86) with an average of 0.778. The lowest value of polymorphic information content was recorded for SCM2 (0.484) and the highest value for SCM86 (0.885) of PIC was detected in SCM86 with an average of 0.760.The dendrogram of genetic similarity was constructed, based on UPGMA algorithm. The hierarchical cluster analysis divided rye genotypes into 4 main clusters. The first cluster of 14 genotypes was subdivided in two subclusters (1a and 1b) where 50% of genotypes were Czechoslovak origin. The second cluster contained four genotypes were three (75%) of them had Czech or Czechoslovak origin. In the third subcluster separated three rye genotypes of different origin. The rest (24) of rye genotypes in the fourth cluster were divided into two subclusters (4a and 4b) where clearly separated group of Polish (4aa) and Czech and Czechoslovak (4ab) genotypes. Two genotypes of 4aa subcluster (Wojcieszyckie and Dankowskie Nowe) from Poland were genetically the closest. In the dendrogram alle genotypes were differentiated and clustering partially reflects geographic origin of studied rye genotypes. In this experiment, SSRs markers proved to be a high informative and usefull tool in genetic diversity research for the distinguishing and characterization of close related varieties.
This work reports four TaqMan real-time PCR assays for authenticity testing of wheat, barley, rye and oat species in food and feed. The method uses three specific primer/probe systems targeting DNA ...fragments from the ITS1 region for the detection of wheat, barley and oats, and a fourth primer/probe system targeting the MIPS gene for rye detection. The real-time PCR systems showed high specificity and sensitivity, achieving relative detection limits ranging from 0.00001 to 0.01% in an experimental flour binary mixture model. The developed technique was further applied at the field level to check the labeling of 270 food and pet food products regarding the presence/absence of wheat, barley, rye and oat cereals. The assay allowed the authentication of foods with different labeling schemes, in which the presence of the targeted cereals was either declared, not declared or declared as possible traces.
•Authenticity testing of wheat, barley, rye and oats by real-time PCR assays.•The method allows sensitive and specific detection of each target cereal.•The applicability of the assay was demonstrated by analyses of commercial foods.•The assay is a useful tool for monitoring food/feed mislabeling.
Under the conditions of the Kirov region in 2020-2022 there were studied 21 varieties of winter rye bred by Russian scientific institutions according to the nature of the relationship in the ...patho-system "Secale cereale L. – Claviceps purpurea (Fr.) Tul.". Under artificial inoculation of flowers with a suspension of the pathogen all the studied varieties were affected by ergot in the range from 3.17 (Graphite FP) to 34.69 % (Saratovskaya 10), with grain contamination with sclerotia – from 0.13 (Graphite FP, Quail) up to 1.87 % (Amber), which indicates their susceptibility to the disease. However, taking into account the signs of "damage by ergot", "contamination of grain with sclerotia" and "yield" for further breeding for ergot resistance, it is possible to recommend varieties Perepel, Lika and Graphite FP (bred by the Federal Agricultural Research Center of the North-East named N. V. Rudnitsky. The influence of the genotype on the biometry of sclerotia has been revealed. This is indirectly evidenced by the significant variability of their parameters in different varieties of rye, which should be taken into account during the mechanical cleaning of grain. Using the Graphite variety as an example, a significant (P ≥ 095) decrease in the grain content and productivity of an ear has been established when more than two sclerotia are formed in it, and four sclerotia form 1000 grains. With an increase in their number to 11 pieces, this pattern remained unchanged, and the harmfulness of ergot reached 64.05 % (ear grain size), 79.60 % (ear productivity) and 46.32 % (grain size). In the process of regression analysis, it has been established that with an increase in infection of the ear by 1-2 sclerotia, the number of grains in the ear decreases by 4.96 pieces, the mass of grain per ear – by 0.26 g, the grain size – by 2.49 g. The similar calculations with a preliminary analysis of the degree of plant damage can be of prognostic value in assessing the potential harmfulness of ergot.
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