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.
Adoption of cover crops has the potential to increase agricultural sustainability in the US and beyond. In 2017, a survey was conducted with Nebraska stakeholders in an attempt to evaluate current ...cover crop management strategies adopted in soybean (Glycine max L. Merr.), field corn (Zea mays L.), and seed corn production. Eighty-two Nebraska stakeholders answered the survey, of which 80% identified themselves as growers. Eighty-seven percent of respondents manage cover crops, and the average cover crop ha planted on a per farm basis is 32%. The primary method of establishing cover crops following soybeans and field corn is drilling. In seed corn, interseeding is the main seeding strategy for cover crop establishment. Cereal rye (Secale cereale L.) appeared as the most adopted cover crop species (either alone or in mixtures with radish Raphanus sativus L. or hairy vetch Vicia villosa Roth). Over 95% of respondents utilize herbicides for cover crop termination in the spring before crop planting. Glyphosate is used by 100% of survey respondents that use herbicides for cover crop termination. The major observed impacts of incorporating cover crops into a production system according to survey respondents are reduced soil erosion and weed suppression. According to 93% of respondents, cover crops improve weed control by suppressing winter and/or summer annual weed species. The biggest challenge reported by cover crop adopters is planting and establishing a decent stand before winter. According to the results of this survey, there are different management strategies, positive outcomes, and challenges that accompany cover crop adoption in Nebraska. These results will help growers, agronomists, and researchers better guide cover crop adoption, management, and future research and education needs in Nebraska and beyond.
•Grapevine mycorrhizal field inoculation through donor plants is an effective method.•Inoculation promoted the establishment of new mycorrhizal taxa in vine roots.•Inoculated cover crops enhanced ...vine’s photosynthetic efficiency after a heat wave.•Inoculation helped vines to partially compensate water competition with cover crops.
Grapevines are highly dependent on arbuscular mycorrhizal fungi (AMF) for normal growth and development. However, vineyard soils may have low AMF abundance and diversity due to conventional soil management practices that are detrimental for these fungi. In this context, the establishment of AMF-inoculated cover crops can be a highly convenient strategy to reestablish soil mycorrhizal potential, as it combines the advantages of a vigorous inoculum source coming from mycorrhizal donor plants with the overall benefits of green covers for grape quality, microbial diversity and soil health. In this work, the potential benefits of Funneliformis mosseae-inoculated under-vine cover crops on grapevine growth, physiology and production were compared to those derived from 1) the establishment of non-inoculated under-vine cover crops, and 2) conventional herbicide-based weed control in the under-vine space. In addition, grapevine root AMF community composition was analyzed to assess if the introduction of a non-native AMF species induced changes on resident mycorrhizal community assemblies and to unveil potential variations in AMF diversity associated to herbicide replacement by green covers. Results indicated that under-vine cover crops, inoculated or not, led to a general vigor decrease in grapevines, probably due to competition between the two species. However, after a heat wave that occurred at harvest time in the second year of the experiment, grapevines growing in plots with inoculated cover crops had the highest photochemical reflectance indices and net photosynthesis rates, and partially compensated production losses due to berry sunburn. Root mycorrhizal community analysis by the end of the experiment revealed that the inoculated F. mosseae isolate colonized grapevine roots from inoculated plots, while it was absent in the other ones. Moreover, inoculation of this AMF did not lead to a replacement of native root AMF communities, but allowed further colonization by other resident Glomeraceae and non-Glomeraceae AMF taxa. Overall, the work herein demonstrates that the introduction of F. mosseae through donor plants is a suitable field inoculation method for grapevines and can help them to better withstand heat waves.
To meet the increasing need for bioenergy several raw materials have to be considered for the production of e.g. bioethanol and biogas. In this study, three lignocellulosic raw materials were ...studied, i.e. (1) winter rye straw (
Secale cereale L), (2) oilseed rape straw (
Brassica napus L.) and (3) faba bean straw (
Viciafaba L.). Their composition with regard to cellulose, hemicellulose, lignin, extractives and ash was evaluated, as well as their potential as raw materials for ethanol and biogas production. The materials were pretreated by wet oxidation using parameters previously found to be optimal for pretreatment of corn stover (195
°C, 15
min, 2
g
l
−1 Na
2CO
3 and 12
bar oxygen). It was shown that pretreatment was necessary for ethanol production from all raw materials and gave increased biogas yield from winter rye straw. Neither biogas productivity nor yield from oilseed rape straw or faba bean straw was significantly affected by pretreatment. Ethanol was produced by the yeast
Saccharomyces cerevisiae during simultaneous enzymatic hydrolysis of the solid material after wet oxidation with yields of 66%, 70% and 52% of theoretical for winter rye, oilseed rape and faba bean straw, respectively. Methane was produced with yields of 0.36, 0.42 and 0.44
l
g
−1 volatile solids for winter rye, oilseed rape and faba bean straw, respectively, without pretreatment of the materials. However, biogas productivity was low and it took over 50 days to reach the final yield. It could be concluded that all three materials are possible raw materials for either biogas or ethanol production; however, improvement of biogas productivity or ethanol yield is necessary before an economical process can be achieved.
Yield physiology of asparagus (Asparagus officinalis L.) is strongly influenced by biotic factors such as crown and root rot caused by Fusarium spp. and by abiotic conditions such as precipitation or ...temperatures, duration of each harvest, and field management practices. Asparagus yields are linked to the availability of soluble carbohydrates (CHO) in the storage root system which is considered a key factor in asparagus productivity. The aim of this study was to quantify the impacts of the long-term application of a range of potential Best Management Practices (BMPs) on yield and storage root carbohydrate content in green asparagus in a long-term field trial. The trial was established in 2016 with the asparagus ‘Gijnlim’ variety. Commercial yields were collected in 2018, 2019 and 2020. Root carbohydrate content was determined in 2019 and 2020. BMPs included (1) companion crops - Rye (Secale cereale L.), Mustard (Sinapis alba L.), (2) interrow surface mulch applications of either straw mulch or PAS 100 compost (Publicly available specification) in combination with shallow soil disturbance (SSD), (3) the conventional practice and modifications of the conventional tillage practice by applying SSD or not applying SSD and (4) a zero-tillage option. Annual re-ridging (R) and not ridging (NR) were applied to BMP options 1–3. SSD had no significant impact on asparagus yields while annual re-ridging negatively affected total yields of treatments with bare soil interrows, which were managed without SSD. Conventional practice was associated with a 22% yield reduction and ∼€4250 ha−1 annual loss in potential revenue as compared to the Zero-tillage treatment. Companion cropping with mustard did not have a significant impact on asparagus yields. Rye without annual re-ridging was however associated with yield reductions of > 20% as compared to the Conventional practice. PAS 100 Compost applied in asparagus interrows (at 25 t ha−1 per year) in combination with SSD without annual re-ridging resulted in improvements to yields of 20%, 10% and 34% in 2018, 2019 and 2020, respectively, as compared to the Conventional practice. No correlation was observed between storage root soluble carbohydrate content and asparagus yields. The results of this study confirmed that asparagus yield, and thus total farm income can be significantly improved through implementation of several of the BMPs investigated.
•Compost application combined with shallow soil disturbance increases asparagus yields.•Zero-tillage led to increased asparagus yield as compared with Conventional practice.•Root soluble carbohydrate content is not linked to asparagus yield.
The breeding of winter rye for adaptability is an important factor in increasing yield and stabilizing gross grain yields. The research was conducted in 2018–2023 in the central agroclimatic zone of ...the Kirov region. Thirteen cultivars of winter rye (Secale cereale L. var. vulgare Koern.) of the mid-late maturity group of different breeding periods (‘Falenskaya 4’ as standard) were studied in the nursery of competitive variety testing. Based on the “yield” trait, the parameters of the general adaptive ability of the cultivar (GAAi), stability (σ2SAAi), breeding value of the genotype, and responsiveness of the genotype to changes in environmental conditions (bi) were determined using the method of A. V. Kilchevsky and L. V. Khotyleva. The "year" factor had the greatest influence on the “yield” trait (the influence of factor h x 2 = 60 %). With high winter hardiness (4.7 points) and plant regeneration (89 %), the yield of winter rye is associated with the amount of precipitation during the resumption of vegetation in April (r = -0.92), as well as during the period “seedlings-autumn tillering” and the “earing” phase (r = 0.55). According to the yield, the ‘Grafinya’ (5.09 t/ha) and ‘Lika’ (5.07 t/ha) cultivars were distinguished with a significant increase to the standard of 0.40 t/ha and 0.38 t/ha, respectively (LSD 05 = 0.24 t/ha). The ‘Grafinya’, ‘Lika’, ‘Batist’, and ‘Perepel’ cultivars had a high general adaptive ability (GAA i = 0.23–0.51). Cultivars of late breeding periods were characterized by a higher general adaptive ability (GAA i = 0.09–0.51) compared to previously created cultivars (GAAi = -0.61…0.01). The cultivars ‘Vyatka 2’,’Kiprez’, ‘Kirovskaya 89’, ‘Sadko’, ‘Grafinya’, ‘Batist’, ‘Rushnik’, ‘Perepel’ were distinguished by high stability of the "yield" trait (σ2SAA = 0.50–0.73). The lowest stability indicators were found in the cultivars ‘Flora’, ‘Lika’, ‘Talitsa’ (σ 2 SAA = 1.13–1.35). The cultivars ‘Flora’, ‘Lika’, ‘Talitsa’, ‘Falenskaya 4’, ‘Perepel’, ‘Rushnik’ were highly responsive to improving growing conditions (b i = 1.1–1.4). The cultivar ‘Grafinya’ combined high yield and stability (selection value of the genotype 2.9).
The study was aimed at the evaluation of the impact of drought stress on the efficiency of the photosynthetic apparatus of rye inbred line GULbw, evaluated based on measurements of chlorophyll ...fluorescence and gas exchange parameters, water balance, assimilation pigments and morphological characters, and by the analysis of the relationship between these parameters. The experiment was performed on the rye inbred line GULbw (original name: Gülzow 661-67, accession numbers: GueR 412; R 1599), obtained from the gene bank of The Federal ex situ Gene Bank for Agricultural and Horticultural Crop Species of The Leibniz Institute of Plant Genetics and Crop Plant Research Gatersleben. Because of drought, the PSII (photosystem PS II) performance index was reduced, and the decrease tendency of the PI (overall performance index of PSII) value intensified with the length of the stress period. The tested rye line did not exhibit any considerable variability of the maximum quantum efficiency of the PS II (Fv/Fm). Significant differences in the intensity of transpiration, stomatal conductance, and substomatal concentration of CO2 was determined on day 18 of drought. A significant positive value of the correlation coefficient r was found between PLSN, LSW, LSGN, LSGW, and E, gs, ci.
Triticum aestivum L. lines introgressed with alien chromosomes create a new genetic background that changes the gene expression of both wheat and donor chromosomes. The genes involved in meiosis ...regulation are localized on wheat chromosome 3B. The purpose of the present study was to investigate the effect of wheat chromosome 3B substituted with homoeologous rye chromosome 3R on meiosis regulation in disomically substituted wheat line 3R(3B). Employing immunostaining with antibodies against microtubule protein, α-tubulin, and the centromerespecific histone (CENH3), as well as FISH, we analyzed microtubule cytoskeleton dynamics and wheat and rye 3R chromosomes behavior in 3R(3B) (Triticum aestivum L. variety Saratovskaya 29 × Secale cereale L. variety Onokhoiskaya) meiosis. The results revealed a set of abnormalities in the microtubule dynamics and chromosome behavior in both first and second divisions. A feature of metaphase I in 3R(3B) was a decrease in the chiasmata number compared with variety Saratovskaya 29, 34.9 ± 0.62 and 41.92 ± 0.38, respectively. Rye homologs 3R in 13.18 % of meiocytes did not form bivalents. Chromosomes were characterized by varying degrees of compaction; 53.33 ± 14.62 cells lacked a metaphase plate. Disturbances were found in microtubule nucleation at the bivalent kinetochores and in their convergence at the spindle division poles. An important feature of meiosis was the asynchronous chromosome behavior in the second division and dyads at the telophase II in 8–13 % of meiocytes, depending on the anther studied. Considering the 3R(3B) meiotic phenotype, chromosome 3B contains the genes involved in the regulation of meiotic division, and substituting 3B3B chromosomes with rye 3R3R does not compensate for their absence.
The study was carried out in the conditions of Kirov region in 2019–2023. Against provocative and infectious backgrounds of snow mold, root rot, ergot, powdery mildew, leaf and stem rust, the ...immunological state and yield of 15 varieties of winter rye created over a 73-year period were studied. Taking into account the breeding methods, the source material used and the year of creation, they were conditionally distributed over five successive periods of breeding and variety change: I – Vyatka 2, Kirovskaya 89; II – Falenskaya 4, Snezhana, Rushnik; III – Flora, Grafinya, Batist; IV – Lika, Talitsa; V – Symphoniya, Garmoniya, Graphit, Graphit FP, Perepel. When recording diseases, well-known methods were used. Research has shown that as a result of breeding, on artificial infectious backgrounds newly created varieties showed a decrease in the development of root rot (Flora, Perepel, Garmoniya – degree of damage 14.6, 15.5 and 15.0 %) and ergot (Flora, Grafinya, Batist, Lika, Symphoniya, Graphit FP, Garmoniya – damage 11.4...15.9 %), grain contamination with sclerotia – 0.38...1.84 %. In varieties of the I period of breeding the degree of root rot infection was 18.8 %, ergot infection – 31.7 %. There is no progress in breeding for resistance to powdery mildew and rust types. The most productive varieties are Lika and Batist (769.3 and 738.7 g/m
2
), which significantly exceed the Falenskaya 4 standard (578.8 g/m
2
). A close and significant dependence (p ≥ 095) was revealed between the yield of winter rye varieties and regrowth of plants after snow mold infection (r = 0.693...0.830) as well as grain contamination with sclerotia (r = -0.531...-0.712). The relationship between the yield of winter rye and the development of other studied diseases is insignificant and weak. Considering the high harmfulness of snow mold and ergot in the research region, it is necessary to continue to carry out breeding improvement of varieties for these characteristics, as well as to increase resistance to powdery mildew and types of rust.
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