Ganoderma boninense is a basidiomycete pathogen of African oil palm (Elaeis guineensis) and the causal agent of basal stem rot (BSR) disease, which is the most destructive fungal disease of oil palm in Southeast Asia. The disease is fatal for infected palms and can result in 50 to 80% losses in oil yields because of a reduction in productive life span and a yield decline of infected oil palms. In this study, G. boninense isolates collected from different locations and planting blocks with different palm ages were molecularly characterized using microsatellite genotyping. Results showed high pathogen genetic diversity (He = 0.67 to 0.74) among planting blocks and between oil palm estates. Two nearby planting blocks with similar planting ages (i.e., 1999 and 2001) had a similar percentage of BSR incidence (>20%) but showed distinct Ganoderma genetic structure as detected using STRUCTURE. Similar results were obtained from another trial site where planting blocks differing in planting age but located only less than 1 km apart showed a diverse genetic background. The pathogen genetic admixture of the oldest planting (>30% BSR incidence) differed significantly from the younger planting (1.8 to 2.8% BSR incidence, breeding trial block), suggesting that the host-pathogen genotype interaction may impact the Ganoderma genetic variation over time. The genetic structure of G. boninense, as revealed in this study, implies positive selection resulting from the pathogen genetic variation, host-pathogen interaction, and possible introductions of novel genetic variants (through spores) from adjacent plantings. These findings offer new insights into the genetic changes of G. boninense over time. The information is essential to design disease management strategies and breeding for BSR resistance in oil palm.

Adopting disease-tolerant grapevines is an efficient option to implement a smarter management strategy limiting the environmental impacts linked to pesticide use. However, little is known on their production of fruit metabolites regarding expected future climate fluctuations, such as increased water shortage. Moreover, previous studies about how water deficit impacts grape composition, lack accuracy due to imprecise timing of fruit sampling. In this study, we phenotyped six new fungus-tolerant genotypes exposed to varying water status in field-grown conditions. The accumulation of water, main cations, primary and secondary metabolites were precisely monitored at the arrest of phloem unloading in fruits, which was targeted at the whole cluster level. The goal was to decipher the effects of both genotype and water deficit on the allocation of carbon into soluble sugars, organic acids, amino acids and anthocyanins. The results revealed that the effect of decreased water availability was specific to each berry component. While fruit sugar concentration remained relatively unaffected, the malic/tartaric acid balance varied based on differences among genotypes. Despite showing contrasted strategies on carbon allocation into berry metabolites, all genotypes reduced fruit yield and the amount of compounds of interest per plant under water deficit, with the extent of reduction being genotype-dependent and correlated with the response of berry volume to plant water status. This first set of data provides information to help reasoning the adaptation of these varieties according to the expected risks of drought and the possibilities of mitigating them through irrigation.

UNASSIGNED: Continuous cropping affected the stability of soil enzyme activity and the structural characteristics of microbial community. Owing to challenges in the study of complex rhizosphere microbial communities, the composition and function of these microbial communities in farmland ecosystems remain elusive. Here, we studied the microbial communities of the rhizosphere of wine grapes with different years of continuous cropping and investigated their relationships with soil enzyme activity.
UNASSIGNED: Metagenomic sequencing was conducted on the rhizosphere soils from one uncultivated wasteland and four vineyards with varying durations of continuous cropping.
UNASSIGNED: The predominant microbial were bacteria (98.39%), followed by archaea (1.15%) and eukaryotes (0.45%). Continuous cropping caused a significant increase in the relative abundance of Rhizobiales and Micrococcales but a marked decrease in Solirubrobacterales. At the genus level, 75, 88, 65, 132, and 128 microbial genera were unique to uncultivated wasteland, 5, 10, 15, and 20 years of continuous cropping, respectively. The relative abundance of genes with signal transduction function was the highest. The activity of all enzymes measured in this study peaked at 5 years of continuous cropping, and then decreased with 10 to 15 year of continuous cropping, but increased at 20 years again. In addition, soil enzyme activity, especially of alkaline phosphatase was significantly correlated with the diversity of the dominant microorganisms at the genus level. Moreover, the coupled enzyme activities had a greater impact on the diversity of the microbial community than that of individual enzymes.
UNASSIGNED: Our findings reveal the composition and function of the soil microbial communities and enzymes activity in response to changes in cropping years, which has important implications for overcoming continuous cropping obstacles and optimizing land use.

Wheatgrass (Th. intermedium) has been traditionally used in wheat breeding for obtaining wheat-wheatgrass hybrids and varieties with introgressions of new genes for economically valuable traits. However, in the 1980s in the United States wheatgrass was selected from among perennial plant species as having promise for domestication and the development of dual-purpose varieties for grain (as an alternative to perennial wheat) and hay. The result of this work was the creation of the wheatgrass varieties Kernza (The Land Institute, Kansas) and MN-Clearwater (University of Minnesota, Minnesota). In Omsk State Agrarian University, the variety Sova was developed by mass selection of the most winter-hardy biotypes with their subsequent combination from the population of wheatgrass obtained from The Land Institute. The average grain yield of the variety Sova is 9.2 dt/ha, green mass is 210.0 dt/ ha, and hay is 71.0 dt/ha. Wheatgrass is a crop with a large production potential, benef icial environmental properties, and valuable grain for functional food. Many publications show the advantages of growing the Kernza variety compared to annual crops in reducing groundwater nitrate contamination, increasing soil carbon sequestration, and reducing energy and economic costs. However, breeding programs for domestication of perennial crops are very limited in Russia. This paper presents an overview of main tasks faced by breeders, aimed at enhancing the yield and cultivating wheatgrass eff iciency as a perennial grain and fodder crop. To address them, both traditional and modern biotechnological and molecular cytogenetic approaches are used. The most important task is to transfer target genes of Th. intermedium to modern wheat varieties and decrease the level of chromatin carrying undesirable genes of the wild relative. The f irst consensus map of wheatgrass containing 10,029 markers was obtained, which is important for searching for genes and their introgressions to the wheat genome. The results of research on the nutritional and technological properties of wheatgrass grain for the development of food products as well as the differences in the quality of wheatgrass grain and wheat grain are presented.
Пырей средний (Th. intermedium) традиционно применялся в селекции пшеницы для получения пшенично-пырейных гибридов и сортов с интрогрессиями новых генов хозяйственно ценных признаков. Однако в 1980-х гг. в США из множества многолетних видов растений пырей был выбран для доместикации с целью создания сортов двойного направления использования – на зерно (альтернатива многолетней пшенице) и сено. В результате были выведены сорта пырея Kеrnza (The Land Institute, Канзас) и MN-Clearwater (Миннесотский университет, Миннесота). В Омском ГАУ из популяции Th. intermedium, полученной из The Land Institute, массовым отбором наиболее зимостойких биотипов с последующим их объединением создан сорт Сова. Средняя урожайность зерна сорта Сова составляет 9.2 ц/га, зеленой массы – 210.0 ц/га, сена – 71.0 ц/ га. Пырей средний – культура с большим производственным потенциалом, полезными экологическими свойствами и ценным зерном для функционального питания. Во многих публикациях показаны преимущества возделывания сорта Kеrnza по сравнению с однолетними культурами: сокращение стока нитратов в грунтовые воды, увеличение секвестрации почвенного углерода, снижение энергетических и экономических затрат. Однако в России селекционные программы, направленные на доместикацию многолетних культур, весьма ограниченны. В настоящем обзоре рассматриваются основные задачи, стоящие перед селекцией и направленные на повышение урожайности зерна и эффективности возделывания пырея среднего в качестве много- летней зерновой и кормовой культуры. Для их решения используются как традиционные, так и современные биотехнологические и молекулярно-цитогенетические подходы. Важнейшей задачей считается передача це- левых генов Th. intermedium в современные сорта пшеницы и сокращение дозы хроматина, несущего гены нежелательных признаков дикорастущего сородича. Получена первая консенсусная генетическая карта пы- рея среднего, содержащая 10 029 маркеров и представляющая интерес для поиска ценных генов и их интро- дукции в геном пшеницы. Представлены результаты исследований по оценке питательных и технологических свойств зерна пырея и полученных из него продуктов питания в сравнении с пшеницей.

Copper (Cu), as an essential element, is added to animal feed to stimulate growth and prevent disease. The forage crop alfalfa (Medicago sativa L.) produced during Cu phytoextraction may be considered a biofortified crop to substitute the Cu feed additives for livestock production, beneficially alleviating Cu contamination in soils and reducing its input into agriculture systems. To assess this, alfalfa was grown in three similar soils with different Cu levels, i.e., 11, 439 and 779 mg kg-1 for uncontaminated soil (A), moderately Cu-contaminated soil (B) and highly Cu-contaminated soil (C), respectively. EDDS (Ethylenediamine-N,N\'-disuccinic acid) was applied to the soils seven days before the first cutting at four rates (0, 0.5, 2 and 5 mmol kg-1) to enhance bioavailable Cu uptake. Alfalfa grew well in soils A and B but not in the highly Cu-contaminated soil. After applying EDDS, a significant biomass reduction of the first cutting shoot was only observed with 5 mmol kg-1 EDDS in the highly Cu-contaminated soil, with a 45% (P < 0.05) decrease when compared to the control. Alfalfa grown in the three soils gradually wilted after the first cutting with 5 mmol kg-1 EDDS, and Cu concentrations in the first cutting shoot were augmented strongly, by 250% (P < 0.05), 3500% (P < 0.05) and 6700% (P < 0.05) compared to the controls, respectively. Cu concentrations in alfalfa shoots were found to be higher in this study than in some fodder plants and further augmented in soils with higher Cu levels and with EDDS application. These findings suggest that alfalfa grown on clean soils or soils with up to 450 mg Cu kg-1 (with appropriate EDDS dosages) has the potential to be considered as a partial Cu supplementation for livestock. This research laid the foundation for the integration between Cu-phytoextraction and Cu-biofortification for livestock.

Endosulfan was widely used as an insecticide in the agricultural sector before its environmental persistence was fully understood. Although its fate and transport in the environment have been studied, the effects of historic endosulfan residues in soil and its bioaccumulation in crops are not well understood. This knowledge gap was addressed by investigating the dissipation and bioaccumulation of endosulfan in ginseng as a perennial crop in fresh and aged endosulfan-contaminated fields. In addition, the effect of granular biochar (GBC) treatment on the bioaccumulation factor (BAF) of endosulfan residue in ginseng was assessed. The 50% dissipation time (DT50) of the total endosulfan was over 770 days in both the fresh and aged soils under mulching conditions. This was at least twofold greater than the reported (6- > 200 days) in arable soil. Among the endosulfan congeners, the main contributor to the soil residue was endosulfan sulfate, as observed from 150 days after treatment. The BAF for the 2-year-old ginseng was similar in the fresh (1.682-2.055) and aged (1.372-2.570) soils, whereas the BAF for the 3-year-old ginseng in the aged soil (1.087-1.137) was lower than that in the fresh soil (1.771-2.387). The treatment with 0.3 wt% GBC extended the DT50 of endosulfan in soil; however, this could successfully suppress endosulfan uptake, and reduced the BAFs by 66.5-67.7% in the freshly contaminated soil and 32.3-41.4% in the aged soil. Thus, this adsorbent treatment could be an effective, financially viable, and sustainable option to protect human health by reducing plant uptake of endosulfan from contaminated soils.

In agricultural soils, nitrate (NO3-) is the major nitrogen (N) nutrient for plants, but few studies have analyzed molecular and biochemical responses involved in its acquisition by grapevine roots. In viticulture, considering grafting, NO3- acquisition is strictly dependent on rootstock. To improve the knowledge about N nutrition in grapevine, this study analyzed biochemical and proteomic changes induced by, NO3- availability, in a hydroponic system, in the roots of M4, a recently selected grapevine rootstock. The evaluation of biochemical parameters, such as NO3-, sugar and amino acid contents in roots, and the abundance of nitrate reductase, allowed us to define the time course of the metabolic adaptations to NO3- supply. On the basis of these results, the proteomic analysis was conducted by comparing the root profiles in N-starved plants and after 30 h of NO3- resupply. The analysis quantified 461 proteins, 26% of which differed in abundance between conditions. Overall, this approach highlighted, together with an increased N assimilatory metabolism, a concomitant rise in the oxidative pentose phosphate pathway and glycolysis, needed to fulfill the redox power and carbon skeleton demands, respectively. Moreover, a wide modulation of protein and amino acid metabolisms and changes of proteins involved in root development were observed. Finally, some results open new questions about the importance of redox-related post-translational modifications and of NO3- availability in modulating the dialog between root and rhizosphere.

During plant domestication, traits can be subject to a variety of types of selection, ranging from strong directional selection for traits such as seed or fruit size to diversifying selection for traits like color or flavor. These types of selection interact with other evolutionary processes including genetic bottlenecks and interspecific gene flow to generate different levels of genetic diversity across the genome and at target genes in domesticated lineages, but little is known about the impacts of these processes in perennial fruit crops.
We used sequence capture by hybridization to examine patterns of diversity at a suite of candidate domestication and anonymous background genes in domesticated apple (Malus ×domestica) in comparison to its wild relatives Malus sieversii and Malus orientalis.
We found no change in average diversity at these candidate domestication genes across the three species. However, a subset of the genes did exhibit patterns of very high or very low diversity in M. ×domestica compared to its progenitor, M. sieversii. Of the genes with characterized function, the low-diversity genes mainly contributed to fruit quality traits like color and flavor, predicted to be under conscious, directional selection relatively late in the domestication process, while the high-diversity genes included a variety of functions.
Overall, these results are consistent with predictions based on the likely timing and nature of selection during domestication and open new avenues for understanding genes with high diversity in a perennial crop compared to its wild relatives.

The biorefinery technology aiming at protein extraction is rising and identification of suitable plant biomass input with valuable protein compounds for extraction is needed. Forage crops have been evaluated by the Cornell Net Carbohydrate and Protein System (CNCPS), and the result used as proxy of extractable protein in a biorefinery process. This serves as a helpful link between crop production and refinery output; however, the method has never been validated. Such validation is the main aim of this study. Five forage species-white clover, red clover, lucerne, perennial ryegrass, and tall fescue-were cut at four dates during spring and processed in a lab-scale refinery (screw press and subsequent protein precipitation from the green juice). The pulp fraction and the precipitated protein concentrate were both CNCPS analyzed to follow the initial crude protein (CP) plant input into these two fractions. Total recovery in concentrate was highest for the legumes, which points to an advantage of these species in protein extraction setups. High recovery of B1 and B2 (50% or higher for the grasses) in the pulp demonstrated a large proportion of soluble protein ending up in the fibrous pulp and shed light on the reason behind high feed quality of the pulp fraction. In conclusion, the existing tentative assumption of extractable protein being equal to CNCPS fractions of B1 and B2 and partly B3 was shown to be too simplified. The presented findings can improve crop species screening in terms of expected extractable protein yield.

Perennial crops have some advantages over annuals in soil erosion prevention, lower labor and water requirements, carbon sequestration, and maintenance of thriving soil ecosystems. Rhizome, a kind of root-like underground stem, is a critical component of perenniality, which allows many grass species to survive through harsh environment. Identification of rhizome-regulating genes will contribute to the development of perennial crops. There have been no reports on the cloning of such genes until now, which bring urgency for identification of genes controlling rhizomatousness. Using rhizomatous Oryza longistaminata and rhizome-free cultivated rice as male and female parents, respectively, genetic populations were developed to identify genes regulating rhizome. Both entire population genotyping and selective genotyping mapping methods were adopted to detect rhizome-regulating quantitative trait loci (QTL) in 4 years. Results showed that multiple genes regulated development of rhizomes, with over 10 loci related to rhizome growth. At last, five major-effect loci were identified including qRED1.2, qRED3.1, qRED3.3, qRED4.1, and qRED4.2. It has been found that the individual plant with well-developed rhizomes carried at least three major-effect loci and a certain number of minor-effect loci. Both major-effect and minor-effect loci worked together to control rhizome growth, while no one could work alone. These results will provide new understanding of genetic regulation on rhizome growth and reference to the subsequent gene isolation in rice. And the related research methods and results in this study will contribute to the research on rhizome of other species.