Summary
We report on a whole‐genome draft sequence of rye (Secale cereale L.). Rye is a diploid Triticeae species closely related to wheat and barley, and an important crop for food and feed in ...Central and Eastern Europe. Through whole‐genome shotgun sequencing of the 7.9‐Gbp genome of the winter rye inbred line Lo7 we obtained a de novo assembly represented by 1.29 million scaffolds covering a total length of 2.8 Gbp. Our reference sequence represents nearly the entire low‐copy portion of the rye genome. This genome assembly was used to predict 27 784 rye gene models based on homology to sequenced grass genomes. Through resequencing of 10 rye inbred lines and one accession of the wild relative S. vavilovii, we discovered more than 90 million single nucleotide variants and short insertions/deletions in the rye genome. From these variants, we developed the high‐density Rye600k genotyping array with 600 843 markers, which enabled anchoring the sequence contigs along a high‐density genetic map and establishing a synteny‐based virtual gene order. Genotyping data were used to characterize the diversity of rye breeding pools and genetic resources, and to obtain a genome‐wide map of selection signals differentiating the divergent gene pools. This rye whole‐genome sequence closes a gap in Triticeae genome research, and will be highly valuable for comparative genomics, functional studies and genome‐based breeding in rye.
Significance statement
Rye is a diploid Triticeae species closely related to wheat and barley. Here we present a draft genome and a high‐density genotyping array that will facilitate genome‐based research in rye and comparative genomics in Triticeae.
Rye (Secale cereale L.) is the most widely used related species in wheat genetic breeding, and the introduction of its chromosome fragments into the wheat genome through distant hybridization is ...essential for enriching the genetic diversity of wheat. Rapid and accurate detection of rye chromatin in the wheat genome is important for distant hybridization. Simple sequence repeats (SSRs) are widely distributed in the genome, and SSRs of different species often exhibit species-specific characteristics.BACKGROUNDRye (Secale cereale L.) is the most widely used related species in wheat genetic breeding, and the introduction of its chromosome fragments into the wheat genome through distant hybridization is essential for enriching the genetic diversity of wheat. Rapid and accurate detection of rye chromatin in the wheat genome is important for distant hybridization. Simple sequence repeats (SSRs) are widely distributed in the genome, and SSRs of different species often exhibit species-specific characteristics.In this study, genome-wide SSRs in rye were identified, and their characteristics were outlined. A total of 997,027 SSRs were selected, with a density of 115.97 SSRs/Mb on average. There was no significant difference in the number of SSRs on each chromosome. The number of SSRs on 2R was the highest (15.29%), and the number of SSRs on 1R was the lowest (13.02%). The number of SSRs on each chromosome is significantly correlated with chromosome length. The types of SSR motifs were abundant, and each type of SSR was distributed on 7 chromosomes of rye. The numbers of mononucleotide simple sequence repeats (MNRs), dinucleotide simple sequence repeats (DNRs), and trinucleotide simple sequence repeats (TNRs) were the greatest, accounting for 46.90%, 18.37%, and 22.64% of the total number, respectively. Among the MNRs, the number of G/C repeats and the number of 10 bp motifs were the greatest, accounting for 26.24% and 31.32% of the MNRs, respectively. Based on the SSR sequences, a total of 657 pairs of primers were designed. The PCR results showed that 119 pairs of these primers were rye-specific and could effectively detect rye chromatin in the wheat genome. Moreover, 86 pairs of the primers could also detect one or more specific rye chromosomes.RESULTSIn this study, genome-wide SSRs in rye were identified, and their characteristics were outlined. A total of 997,027 SSRs were selected, with a density of 115.97 SSRs/Mb on average. There was no significant difference in the number of SSRs on each chromosome. The number of SSRs on 2R was the highest (15.29%), and the number of SSRs on 1R was the lowest (13.02%). The number of SSRs on each chromosome is significantly correlated with chromosome length. The types of SSR motifs were abundant, and each type of SSR was distributed on 7 chromosomes of rye. The numbers of mononucleotide simple sequence repeats (MNRs), dinucleotide simple sequence repeats (DNRs), and trinucleotide simple sequence repeats (TNRs) were the greatest, accounting for 46.90%, 18.37%, and 22.64% of the total number, respectively. Among the MNRs, the number of G/C repeats and the number of 10 bp motifs were the greatest, accounting for 26.24% and 31.32% of the MNRs, respectively. Based on the SSR sequences, a total of 657 pairs of primers were designed. The PCR results showed that 119 pairs of these primers were rye-specific and could effectively detect rye chromatin in the wheat genome. Moreover, 86 pairs of the primers could also detect one or more specific rye chromosomes.These results lay a foundation for both genomic evolution studies of rye and molecular breeding in wheat.CONCLUSIONThese results lay a foundation for both genomic evolution studies of rye and molecular breeding in wheat.
BACKGROUND AND AIMS: Most plant scientists, in contrast to animal scientists, study only half the organism, namely above-ground stems, leaves, flowers and fruits, and neglect below-ground roots. Yet ...all acknowledge roots are important for anchorage, water and nutrient uptake, and presumably components of yield. This paper investigates the relationship between domestication, and the root systems of landraces, and the parents of early, mid- and late green-revolution bread wheat cultivars. It compares the root system of bread wheat and 'Veery'-type wheat containing the 1RS translocation from rye. METHODS: Wheat germplasm was grown in large pots in sand culture in replicated experiments. This allowed roots to be washed free to study root characters. KEY RESULTS: The three bread wheat parents of early green-revolution wheats have root biomass less than two-thirds the mean of some landrace wheats. Crossing early green-revolution wheat to an F₂ of 'Norin 10' and 'Brevor', further reduced root biomass in mid-generation semi-dwarf and dwarf wheats. Later-generation semi-dwarf wheats show genetic variation for root biomass, but some exhibit further reduction in root size. This is so for some California and UK wheats. The wheat-rye translocation in 'Kavkaz' for the short arm of chromosome 1 (1RS) increased root biomass and branching in cultivars that contained it. CONCLUSIONS: Root size of modern cultivars is small compared with that of landraces. Their root system may be too small for optimum uptake of water and nutrients and maximum grain yield. Optimum root size for grain yield has not been investigated in wheat or most crop plants. Use of 1RS and similar alien translocations may increase root biomass and grain yield significantly in irrigated and rain-fed conditions. Root characters may be integrated into components of yield analysis in wheat. Plant breeders may need to select directly for root characters.
The introduction and spread of rye Seabra, Luís; Teira-Brión, Andrés; López-Dóriga, Inés ...
PloS one,
05/2023, Letnik:
18, Številka:
5
Journal Article
Recenzirano
Some of the earliest Western European macroremains of rye (Secale cereale) have been recently recovered in Northwest Iberia. However, the chronological and cultural contexts of these remains have not ...been yet exhaustively analysed. To address this gap of research, previous and unpublished assemblages have been reviewed and analysed through an analytical set of methods: biometry, radiocarbon dates and integrating the remains of rye in the broad archaeobotanical record of the region. Results show the earliest macroremains of rye in the Iberian Peninsula date to a period between the 3.sup.rd century and the first half of the 1.sup.st century BCE. Rye was usually found in assemblages dominated by spelt and other cereals, in whose fields it was likely acting as a weed. There is no record of rye for about the two following centuries, after which it is probably reintroduced, now as a crop. It is found in several sites from the 3.sup.rd -4.sup.th centuries CE onwards, suggesting it is a staple crop as in other regions in Europe. Significant differences in grain size are only recorded in a 10.sup.th -11.sup.th century settlement, suggesting few changes in grain morphometry before Medieval times.
ABSTRACT
This comprehensive review examined the intricate relationship between climate change and rye (Secale cereale L.) production, focusing on the multifaceted challenges and opportunities posed ...by changing environmental conditions. Rye is a versatile cereal crop cultivated in temperate regions and is known for its resilience and adaptability to adverse growing conditions. However, as global temperatures and atmospheric CO2 concentrations rise, the effects of climate change on rye growth, yield and grain quality become increasingly apparent. In this review, we summarised the recent research findings on various aspects of rye production and quality under climate change, focusing on factors such as temperature (e.g., increasing temperature) resilience, and viability of rye production in the face of ongoing climate challenges, altered rainfall patterns (changing rainfall distributions with decreasing rainfall in the spring and early summer months as well as heavy rainfall events), biotic stress, agronomic practices and greenhouse gas emissions. Exploring the dynamic interplay among climate change, soil quality, biotic stressors and plant–microbe interactions reveals insights into the response of rye to environmental changes. These interactions shape the complex dynamics that influence the adaptation of rye to evolving environmental conditions. Implications for food security, agricultural sustainability and future research directions are also discussed, highlighting the urgent need for adaptive strategies to ensure the resilience and viability of rye production in the face of ongoing climate challenges.
Cover crops (CCs) are recognised as valuable for weed management, while fallow soil between cash crop seasons likely increases weed presence. Weeds may offer similar ecosystem services as CCs, ...although they pose a risk of seedbank buildup. This study evaluated the impact of two winter CC systems (3-year triticale cultivation, TRIT; and a 3-year succession of rye, clover, and mustard, RCM) compared to weedy fallow (WF) on weed seedbank size and composition in a 3-year ‘maize (Zea mays L.)–maize–soybean (Glycine max (L.) Merr)’ crop succession. After 3 years, seed density of spring/summer weeds reduced in all treatments, potentially stemming from herbicide use during cash crop seasons and tillage operations. Triticale had the lowest seedbank density (9,487 seeds m−²) and higher diversity (Shannon Index 6.9) compared to WF (28,543 seeds m-² and 4.1, respectively). Furthermore, stochastic analysis revealed a lower risk of enlarging weed seedbanks in TRIT compared to WF (for seed densities above 900 seeds m−2). Moreover, management practices (CCs, cash crop sowing, termination/harvest) synchronised with weed seed production and germination likely contributed to the decreasing seed density of species including Portulaca oleracea and Chenopodium album, which were reduced by 90 and 80 %, respectively, by the study’s end. Over three years, autumn/winter and indifferent weed seed densities increased 4.2 times more in WF and RCM (22,638 seeds m−²) than in TRIT. This may be due to the varying growth rates among CC species in RCM, whereas TRIT consistently established rapidly, potentially outcompeting weeds until termination. Fallow periods between cash crops may increase weed species linked to that season and future crop–weed interference in varied crop rotations. Introducing CCs can mitigate this effect, although the choice of CC species may influence the extent of the impact.
•Cover crops alter weed community in 3-year maize-maize-soybean succession.•‘Weedy fallow' increases risk of weed competition in subsequent crops.•Different CCs species might have different effects on weeds.•Weedy fallow did not necessarily mean a more diverse weed community.
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 alpha-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 alpha-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 alpha-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.
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