Discovery of a Novel Leaf Rust (Puccinia recondita) Resistance Gene in Rye (Secale cereale L.) Using Association Genomics

Leaf rust constitutes one of the most important foliar diseases in rye (Secale cereale L.). To discover new sources of resistance, we phenotyped 180 lines belonging to a less well-characterized Gülzow germplasm at three field trial locations in Denmark and Northern Germany in 2018 and 2019. We observed lines with high leaf rust resistance efficacy at all locations in both years. A genome-wide association study using 261,406 informative single-nucleotide polymorphisms revealed two genomic regions associated with resistance on chromosome arms 1RS and 7RS, respectively. The most resistance-associated marker on chromosome arm 1RS physically co-localized with molecular markers delimiting Pr3. In the reference genomes Lo7 and Weining, the genomic region associated with resistance on chromosome arm 7RS contained a large number of nucleotide-binding leucine-rich repeat (NLR) genes. Residing in close proximity to the most resistance-associated marker, we identified a cluster of NLRs exhibiting close protein sequence similarity with the wheat leaf rust Lr1 gene situated on chromosome arm 5DL in wheat, which is syntenic to chromosome arm 7RS in rye. Due to the close proximity to the most resistance-associated marker, our findings suggest that the considered leaf rust R gene, provisionally denoted Pr6, could be a Lr1 ortholog in rye.

Alterations in the Transcriptome of Rye Plants Following the Microdochium nivale Infection: Identification of Resistance/Susceptibility-Related Reactions Based on RNA-Seq Analysis

Microdochium nivale is a progressive and devastating phytopathogen that causes different types of cereal crop and grass diseases that are poorly characterized at the molecular level. Although rye (Secale cereale L.) is one of the most resistant crops to most of the phytopathogens, it is severely damaged by M. nivale. The recent high-quality chromosome-scale assembly of rye genome has improved whole-genome studies of this crop. In the present work, the first transcriptome study of the M. nivale-infected crop plant (rye) with the detailed functional gene classification was carried out, along with the physiological verification of the RNA-Seq data. The results revealed plant reactions that contributed to their resistance or susceptibility to M. nivale. Phytohormone abscisic acid was shown to promote plant tolerance to M. nivale. Flavonoids were proposed to contribute to plant resistance to this pathogen. The upregulation of plant lipase encoding genes and the induction of lipase activity in M. nivale-infected plants revealed in our study were presumed to play an important role in plant susceptibility to the studied phytopathogen. Our work disclosed important aspects of plant-M. nivale interactions, outlined the directions for future studies on poorly characterized plant diseases caused by this phytopathogen, and provided new opportunities to improve cereals breeding and food security strategies.

Field Studies on the Effect of Rye Cover Crop on Soybean Root Disease and Productivity

Cover crops improve soil and water quality in annual cropping systems, but knowledge of their impact on soybean (Glycine max L.) seedling and root diseases is limited. The effects of winter rye cover crops (Secale cereale L.) on soybean population, biomass, root morphology, seedling and root diseases, pathogen incidence, canopy reflectance, and yield were assessed over two years in Iowa and Missouri, USA. Plots without a rye cover crop were compared to plots with early-kill rye and late-kill rye cover crops, which were terminated 34 to 49 days or 5 to 17 days before soybean planting, respectively. Soybean shoot dry weight, root rot severity, and incidence of Fusarium spp. and Pythium spp. on roots were not influenced by the treatments. Soybean grain yield and plant population were reduced in the presence of rye in two site-years, increased in one site-year, and not changed in the remaining site-years. Soybean canopy reflectance was measured at 810 nm and measurements were first made at 70 to 80 days after planting (DAP). At least five measurements were obtained at 7- to 15- day intervals, ending at 120 to 125 DAP. Measurements at approximately 120 to 125 DAP differed by treatments but were not consistently associated with the presence or absence of a rye cover crop. Our field studies suggest that Iowa and Missouri soybean farmers can use winter rye as a cover crop in soybean fields with low seedling disease pressure without increasing the risk of seedling and root diseases or suppressing yield.

Review and analysis of perennial cereal crops at different maturity stages

The article presents an overview of perennial grain crops, gives a comparative characteristic of annual winter wheat and perennial grain crops such as Trititrigia (Trititrigia cziczinii Tsvelev), Thinopyrum intermedium, perennial rye (Secale cereale L) and perennial sorghum (Sorghum x derzhavinii Tzvel.). The study aims to consider the main perennial crops grown in Russia and in the world, to compare their quality indicators, sowing agrotechnical requirements, cultivation conditions, yields, and to justify the choice of perennial crops that meet the needs and climatic conditions of the Rostov region. Presented is the generalized information on the grain quality changes during maturation, ripeness phases of grain crops are considered. Based on the review, the optimal ripeness phases, at which it is advisable to harvest are presented. Literature review showed that in the phase of lactic (мoлoчнaя cпeлocть) and wax maturity (вocкoвaя cпeлocть) wheat grain contains the greatest amount of basic nutrients. It was found that perennial crops have a positive effect on the state of the soil: prevent its erosion and depletion; there is an accumulation of carbon, soil methane CH 4. Comparative characterization of perennial crops with annual crops shows increased protein content - on average 2-3% higher. Also considered are the green mass quality indicators of perennial crops as a source of nutrients in the feed-production technology.

Single- versus Double-Species Cover Crop Effects on Soil Health and Yield in Mississippi Soybean Fields

Conservation management practices can improve soil health while minimizing deleterious effects of agriculture on the environment. However, adoption of these practices, particularly cover crops, is not widespread, as they often reduce crop yields compared to traditional management practices. The purpose of the current study was to determine if a two-species cover crop treatment of rye (Secale cereale L.) and crimson clover (Trifolium incarnatum L.) could increase soil health parameters and maximize soybean (Glycine max L.) yield greater than rye only in tilled and no-till Mississippi field soils. Enhanced microbial biomass and organic matter input from cover crops increased the activities of β-glucosidase, cellobiohydrolase, fluorescein diacetate hydrolysis, N-acetylglucosaminidase, and phosphatase in surface soils. Rye plus clover tended to elicit higher activities than rye only in no-till plots. Both cover crop treatments inhibited soybean yield in tilled plots by 11–25%. These results indicate that tillage exacerbates yield inhibition by cover crops in soybean and that double-species cover crop treatments were more consistent in increasing activities linked to nutrient cycling. Further study examining different combinations of cover crops in no-till systems is necessary to gain a better understanding of how they can be implemented to enhance soil health while maximizing crop yield.

The Relationships between Plant Developmental Traits and Winter Field Survival in Rye (Secale cereale L.)

Overwintering cereals accumulate low temperature tolerance (LTT) during cold acclimation in the autumn. Simultaneously, the plants adjust to the colder season by making developmental changes at the shoot apical meristem. These processes lead to higher winter hardiness in winter rye varieties (Secale cereale L.) adapted to Northern latitudes as compared to other cereal crops. To dissect the winter-hardiness trait in rye, a panel of 96 genotypes of different origins and growth habits was assessed for winter field survival (WFS), LTT, and six developmental traits. Best Linear Unbiased Estimates for WFS determined from five field trials correlated strongly with LTT (r = 0.90, p < 0.001); thus, cold acclimation efficiency was the major contributor to WFS. WFS also correlated strongly (p < 0.001) with final leaf number (r = 0.80), prostrate growth habit (r = 0.61), plant height (r = 0.34), but showed weaker associations with top internode length (r = 0.30, p < 0.01) and days to anthesis (r = 0.25, p < 0.05). The heritability estimates (h2) for WFS-associated traits ranged from 0.45 (prostrate growth habit) to 0.81 (final leaf number) and were overall higher than for WFS (h2 = 0.48). All developmental traits associated with WFS and LTT are postulated to be regulated by phytohormone levels at shoot apical meristem.

A ddRADseq Survey of the Genetic Diversity of Rye (Secale cereale L.) Landraces from the Western Alps Reveals the Progressive Reduction of the Local Gene Pool

Rye (Secale cereale L.) has been at the basis of agriculture for centuries in most mountainous and northern areas of Eurasia, because it is more resistant than other cereals to low temperatures and poor soils. Rye deserves to be re-evaluated as a source of “environmentally resilient” genes in the future as well, and particularly in a perspective to grow cereals able to withstand global warming. According to recent studies, modern rye varieties have a relatively narrow genetic pool, a condition that is worsening in the most recent breeding processes. The preservation of local landraces as unique sources of genetic diversity has therefore become important, in order to preserve the genetic heritage of rye. In this study, genetic diversity of rye landraces collected in a sector of the Italian Alps particularly suited to traditional agriculture was investigated using the ddRADseq technique. A few landraces still managed with family farming turned out to be genetically distant from the commercial varieties currently in use, highlighting that the phenomenon of homogenization of the local genetic pool can be still circumvented. Ex situ conservation of genetically divergent landraces is a valid tool to avoid the dissipation of an as yet unexplored genetic potential.

Wheat and Cereal Rye Inter-Row Living Mulches Interfere with Early Season Weeds in Soybean

Rapid growth of cool-season weeds in the spring exacerbates weed interference during early soybean (Glycine max (L.) Merr.) establishment in northern climates. This study tested the utility of spring-seeded inter-row living mulches in soybean for early season weed suppression using volunteer canola (Brassica napus L.) as a representative model weed species. The effects of the presence or absence of spring wheat (Triticum aestivum L.) or winter cereal rye (Secale cereale L.) living mulches (mulch type) that had been seeded simultaneously with soybean grown using 38 or 76 cm row spacing (spatial arrangement) and the presence or absence of herbicides used for mid-season mulch termination (herbicide regime) were evaluated in three environments in Manitoba, Canada, in 2013 and 2014. Soybean yield was similar in the presence and absence of the living mulches. In the environment that received the lowest precipitation (Carman 2013), the mulches terminated with post-emergence glyphosate resulted in a 55% greater soybean yield compared to the mulches that remained live throughout the growing season. Inter-row mulches that had been living or terminated mid-season reduced volunteer canola seed production by about one-third (up to 9000 seeds m−2). This study demonstrates the utility of wheat or cereal rye inter-row living mulches for enhanced interference with weeds during early soybean establishment.