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The contributions of crop wild relatives (CWR) to food security depend on their conservation and accessibility for use. The United States contains a diverse native flora of CWR, including those of important cereal, fruit, nut, oil, pulse, root and tuber, and vegetable crops, which may be threatened in their natural habitats and underrepresented in plant conservation repositories. To determine conservation priorities for these plants, we developed a national inventory, compiled occurrence information, modeled potential distributions, and conducted threat assessments and conservation gap analyses for 600 native taxa. We found that 7.1% of the taxa may be critically endangered in their natural habitats, 50% may be endangered, and 28% may be vulnerable. We categorized 58.8% of the taxa as of urgent priority for further action, 37% as high priority, and 4.2% as medium priority. Major ex situ conservation gaps were identified for 93.3% of the wild relatives (categorized as urgent or high priority), with 83 taxa absent from conservation repositories, while 93.1% of the plants were equivalently prioritized for further habitat protection. Various taxonomic richness hotspots across the US represent focal regions for further conservation action. Related needs include facilitating greater access to and characterization of these cultural-genetic-natural resources and raising public awareness of their existence, value, and plight.

Genetic engineering based on -mediated transformation has been a desirable tool to manipulate single or multiple genes of existing genotypes of woody fruit crops, for which conventional breeding is a difficult and lengthy process due to heterozygosity, sexual incompatibility, juvenility, or a lack of natural sources. To date, successful transformation has been reported for many fruit crops. We review the major progress in genetic transformation of these fruit crops made in the past 5 years, emphasizing reproducible transformation protocols as well as the strategies that have been tested in fruit crops. While direct transformation of scion cultivars was mostly used for fruit quality improvement, biotic and abiotic tolerance, and functional gene analysis, transgrafting on genetically modified (GM) rootstocks showed a potential to produce non-GM fruit products. More recently, genome editing technology has demonstrated a potential for gene(s) manipulation of several fruit crops. However, substantial efforts are still needed to produce plants from gene-edited cells, for which tremendous challenge remains in the context of either cell's recalcitrance to regeneration or inefficient gene-editing due to their polyploidy. We propose that effective transient transformation and efficient regeneration are the key for future utilization of genome editing technologies for improvement of fruit crops.

Macadamia integrifolia is a representative of the large basal eudicot family Proteaceae and the main progenitor species of the Australian native nut crop macadamia. Since its commercialisation in Hawaii fewer than 100 years ago, global production has expanded rapidly. However, genomic resources are limited in comparison to other horticultural crops. The first draft assembly of M. integrifolia had good coverage of the functional gene space but its high fragmentation has restricted its use in comparative genomics and association studies. Here we have generated an improved assembly of cultivar HAES 741 (4,094 scaffolds, 745 Mb, N50 413 kb) using a combination of Illumina paired and PacBio long read sequences. Scaffolds were anchored to 14 pseudo-chromosomes using seven genetic linkage maps. This assembly has improved contiguity and coverage, with >120 Gb of additional sequence. Following annotation, 34,274 protein-coding genes were predicted, representing 90% of the expected gene content. Our results indicate that the macadamia genome is repetitive and heterozygous. The total repeat content was 55% and genome-wide heterozygosity, estimated by read mapping, was 0.98% or an average of one SNP per 102 bp. This is the first chromosome-scale genome assembly for macadamia and the Proteaceae. It is expected to be a valuable resource for breeding, gene discovery, conservation and evolutionary genomics.

Branch and trunk canker diseases have become prevalent on nut crops in Iran. During 2015 to 2018, extensive field surveys were conducted on 58 almond, 43 pistachio and 80 walnut orchards in Iran to study fungal pathogens associated with symptomatic trees. One hundred and fifty-six representative fungal isolates were selected and identified based on morphological characteristics and by phylogenetic comparison of DNA sequence data. Fungal species found were Collophorina hispanica, Pleurostoma richardsiae, nine species of Phaeoacremonium (namely P. angustius, P. cinereum, P. italicum, P. fraxinopennsylvanicum, P. minimum, P. parasiticum, P. scolyti, P. tuscanum and P. viticola), 11 species of Botryosphaeriaceae (namely Botryosphaeria dothidea, Diplodia gallae, D. mutila, D. seriata, Dothiorella plurivora, Do. sarmentorum, Do. viticola, Lasiodiplodia citricola, L. mahajangana, L. theobromae and Neofusicoccum parvum), four species of Diatrypaceae (namely Cryptosphaeria pullmanensis, Diatrype whitmanensis, Eutypella citricola and E. vitis) and two non-identified Eutypella spp. (Eutypella sp. 1 and Eutypella sp. 2). Some of these species represent new reports in Iran and/or are reported for the first time in their respective hosts. Pathogenicity tests demonstrated that most of these fungi were pathogenic to inoculated almond, pistachio and walnut shoots. Therefore, more importance should be given to fungal trunk pathogens in Iran, and specific management strategies should be included within the nut crops IPM management programs, with the aim of improving their sustainability.

Carya , in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of Carya and its two EA and NA major subclades, the maternal phylogeny of Carya still need to be comprehensively evaluated. The variation of Carya plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes of congeneric Carya species, including the recently rediscovered critically endangered C. poilanei . The overall assessment of plastomes revealed highly conservative in the general structures. Our results indicated that remarkable differences in several plastome features are highly consistent with the EA-NA disjunction and showed the relatively diverse matrilineal sources among EA Carya compared to NA Carya . The maternal phylogenies were conducted with different plastome regions and full-length plastome datasets from 30 plastomes, representing 26 species in six genera of Juglandoideae and Myrica rubra (as root). Six out of seven phylogenetic topologies strongly supported the previously reported relationships among genera of Juglandoideae and the two subclades of EA and NA Carya , but displayed significant incongruencies between species within the EA and NA subclades. The phylogenetic tree generated from full-length plastomes demonstrated the optimal topology and revealed significant geographical maternal relationships among Carya species, especially for EA Carya within overlapping distribution areas. The full-length plastome-based phylogenetic topology also strongly supported the taxonomic status of five controversial species as separate species of Carya . Historical and recent introgressive hybridization and plastid captures might contribute to plastome geographic patterns and inconsistencies between topologies built from different datasets, while incomplete lineage sorting could account for the discordance between maternal topology and the previous nuclear genome data-based phylogeny. Our findings highlight full-length plastomes as an ideal tool for exploring maternal relationships among the subclades of Carya , and potentially in other outcrossing perennial woody plants, for resolving plastome phylogenetic relationships.

Agriculture is the primary source of income for the majority of the Indian farming community. Plantation crops play a significant part in improving the farmers' economic condition. The proposed work aims to develop a system model for prognostic reasoning by analyzing the impact of fertilizer and irrigation on areca nut crop yield, as well as to predict diseases that may affect areca nut palms using data analytics and a formal statistical approach. The dataset is constructed by interacting with the farmers in the Mangaluru region of Karnataka, India. To find the optimal features, the formal statistical test chi-square is applied. The performance of various classifiers, such as Logistic Regression, Nave Bayes, Support Vector Machine, Decision Tree, and Random Forest, is examined during prognostic reasoning. For disease prediction and crop yield, the decision tree outperformed other classifiers with an accuracy of 96% and 95.86%, respectively. The most significant irrigation type and fertilizer for increasing areca nut crop yield are also identified.

1. Whilst most studies reviewing the reliance of global agriculture on insect pollination advocate increasing the 'supply' of pollinators (wild or managed) to improve crop yields, there has been little focus on altering a crop's 'demand' for pollinators. 2. Parthenocarpy (fruit set in the absence of fertilization) is a trait which can increase fruit quantity and quality from pollinator-dependent crops by removing the need for pollination. 3. Here we present a meta-analysis of studies examining the extent and effectiveness of parthenocarpy-promoting techniques (genetic modification, hormone application and selective breeding) currently being used commercially, or experimentally, on pollinator-dependent crops in different test environments (no pollination, hand pollination, open pollination). 4. All techniques significantly increased fruit quantity and quality in 18 pollinator-dependent crop species (not including seed and nut crops as parthenocarpy causes seedlessness). The degree to which plants experienced pollen limitation in the different test environments could not be ascertained, so the absolute effect of parthenocarpy relative to optimal pollination could not be determined. 5. Synthesis and applications. Parthenocarpy has the potential to lower a crop's demand for pollinators, whilst extending current geographic and climatic ranges of production. Thus, growers may wish to use parthenocarpic crop plants, in combination with other environmentally considerate practices, to improve food security and their economic prospects.

is a major pathogen causing twig canker and shoot blight disease on almond crops. Knowledge about the influence of environmental factors on the biology and epidemiology of this pathogen has mainly been obtained on peach, but there is scarce information on almond. Thus, the main objective of this research was to better understand how environmental factors, such as temperature and wetness periods, determine the cycle of this disease on almond crops in Mediterranean conditions. Several experiments were conducted to obtain information about mycelial growth, sporulation, plant infection and lesion development using almond isolates of . Our results showed that the temperature ranges for both α-conidia germination and almond infection are broad and overlap (between 5 and 35°C), potentially allowing infections to occur year-round. Nevertheless, the highest infection of almond plants was observed after 72 h of wetness period, while the lowest occurred after 6 h, explaining why is a prevalent disease in spring and autumn when rain events are more frequent. Mycelial growth of and lesion development were promoted by warm temperatures. The production of mature pycnidia on cankers had lower and narrower temperature requirements, thus suggesting an adaptation to late winter and early spring conditions. Moreover, the optimum temperature for α-conidia production in pycnidia was around 22°C. All this information could be used to develop a mechanistic model for almond twig canker and shoot blight disease management to enhance the timeliness and effectiveness of control strategies, while reducing both economic costs and environmental impacts.

Mating disruption is used to help manage the navel orangeworm on approximately 200,000 ha of tree nut crops. Aerosol dispensers are the most common formulation, and all formulations use an incomplete pheromone blend consisting solely of (Z11,Z13)-hexadecadienal. Profile analysis (examination of capture and males in pheromone traps as a function of spatial density of dispensers) demonstrated a sharp drop of males captured with a very low density of dispensers, and then an approximately linear relationship between 90 and approaching 100% suppression. This near-linear portion of the profile includes both dispenser densities in which crop protection has been demonstrated, and densities in which it is unlikely. Suppression of males in pheromone traps was lost the next night after dispensers were removed, suggesting that the active ingredient was not persistent in the orchard environment. During most of the summer preharvest period, turning the dispensers off 1 or 2 h before the end of the predawn period of sexual activity provides the same amount of suppression of sexual communication as emission throughout the period of sexual activity. This suggests that encountering the pheromone from the mating disruption dispensers had a persistent effect on males. During the autumn postharvest period, only emission prior to midnight suppressed communication on nights on which the temperature fell below 19°C by midnight. These findings and the analysis will help manufacturers refine their offerings for mating disruption for this important California pest, and buyers of mating disruption to assess cost-effectiveness of competing offerings.

Aims Vegetative groundcover and rootstock selection are popular growth control practices for fruit and nut crops. Theoretically, plant potential growth rate should influence competitive effectiveness; however, it is unclear if rootstock vigor alters crop productivity when groundcover is present. Methods In a humid-climate vineyard we grew young grapevines on low- and medium-vigor rootstocks with and without groundcover. Vegetative growth was determined on dormant stems; yield was determined at harvest. Roots were extracted with soil cores and distribution, morphology, and mycorrhizal colonization were determined. Resource competition was assessed by water and nutrient depletion in vines and soil. Results Compared to vines on low-vigor rootstocks, vines on medium-vigor rootstocks exhibited greater reductions in vegetative (40% vs 19%) and reproductive (22% vs 0%) growth by presence of groundcover. Irrespective of rootstock vigor, grapevine root systems coped with competition by increasing specific root length, decreasing absorptive root diameter, and redistributing roots deeper. Competition for nutrients was the apparent main cause of growth reductions with groundcover; however, mechanisms for differential rootstock responses remain unclear. Conclusions This study suggests that in a wet year, young grapevines grafted on low-vigor rootstocks may be more tolerant of groundcover competition than those on medium-vigor rootstocks; however, both rootstocks cope with a similar root response.