Exploiting Wild Relatives for Genomics-assisted Breeding of Perennial Crops

Advanced Biotechnological Interventions in Mitigating Drought Stress in Plants

This comprehensive article critically analyzes the advanced biotechnological strategies to mitigate plant drought stress. It encompasses an in-depth exploration of the latest developments in plant genomics, proteomics, and metabolomics, shedding light on the complex molecular mechanisms that plants employ to combat drought stress. The study also emphasizes the significant advancements in genetic engineering techniques, particularly CRISPR-Cas9 genome editing, which have revolutionized the creation of drought-resistant crop varieties. Furthermore, the article explores microbial biotechnology's pivotal role, such as plant growth-promoting rhizobacteria (PGPR) and mycorrhizae, in enhancing plant resilience against drought conditions. The integration of these cutting-edge biotechnological interventions with traditional breeding methods is presented as a holistic approach for fortifying crops against drought stress. This integration addresses immediate agricultural needs and contributes significantly to sustainable agriculture, ensuring food security in the face of escalating climate change challenges.

Integrating genomics and genome editing for orphan crop improvement: a bridge between orphan crops and modern agriculture system

Domestication of orphan crops could be explored by editing their genomes. Genome editing has a lot of promise for enhancing agricultural output, and there is a lot of interest in furthering breeding in orphan crops, which are sometimes plagued with unwanted traits that resemble wild cousins. Consequently, applying model crop knowledge to orphan crops allows for the rapid generation of targeted allelic diversity and innovative breeding germplasm. We explain how plant breeders could employ genome editing as a novel platform to accelerate the domestication of semi-domesticated or wild plants, resulting in a more diversified base for future food and fodder supplies. This review emphasizes both the practicality of the strategy and the need to invest in research that advances our understanding of plant genomes, genes, and cellular systems. Planting more of these abandoned orphan crops could help alleviate food scarcities in the challenge of future climate crises.

The East Asian wild apples, Malus baccata (L.) Borkh and Malus hupehensis (Pamp.) Rehder., are additional contributors to the genomes of cultivated European and Chinese varieties

The domestication process in long-lived plant perennials differs dramatically from that of annuals, with a huge amount of genetic exchange between crop and wild populations. Though apple is a major fruit crop grown worldwide, the contribution of wild apple species to the genetic makeup of the cultivated apple genome remains a topic of intense study. We used population genomics approaches to investigate the contributions of several wild apple species to European and Chinese rootstock and dessert genomes, with a focus on the extent of wild-crop gene flow. Population genetic structure inferences revealed that the East Asian wild apples, Malus baccata (L.) Borkh and M. hupehensis (Pamp.), form a single panmictic group, and that the European dessert and rootstock apples form a specific gene pool whereas the Chinese dessert and rootstock apples were a mixture of three wild gene pools, suggesting different evolutionary histories of European and Chinese apple varieties. Coalescent-based inferences and gene flow estimates indicated that M. baccata - M. hupehensis contributed to the genome of both European and Chinese cultivated apples through wild-to-crop introgressions, and not as an initial contributor as previously supposed. We also confirmed the contribution through wild-to-crop introgressions of Malus sylvestris Mill. to the cultivated apple genome. Apple tree domestication is therefore one example in woody perennials that involved gene flow from several wild species from multiple geographical areas. This study provides an example of a complex protracted process of domestication in long-lived plant perennials, and is a starting point for apple breeding programmes.

Multigenic resistance to Xylella fastidiosa in wild grapes (Vitis sps.) and its implications within a changing climate

Xylella fastidiosa is a bacterium that infects crops like grapevines, coffee, almonds, citrus and olives. There is little understanding of the genes that contribute to plant resistance, the genomic architecture of resistance, and the potential role of climate in shaping resistance, in part because major crops like grapevines (Vitis vinifera) are not resistant to the bacterium. Here we study a wild grapevine species, V. arizonica, that segregates for resistance. Using genome-wide association, we identify candidate resistance genes. Resistance-associated kmers are shared with a sister species of V. arizonica but not with more distant species, suggesting that resistance evolved more than once. Finally, resistance is climate dependent, because individuals from low ( < 10 °C) temperature locations in the wettest quarter were typically susceptible to infection, likely reflecting a lack of pathogen pressure in colder climates. In fact, climate is as effective a predictor of resistance phenotypes as some genetic markers. We extend our climate observations to additional crops, predicting that increased pathogen pressure is more likely for grapevines and almonds than some other susceptible crops.

Autochthonous Apple Cultivars from the Campania Region (Southern Italy): Bio-Agronomic and Qualitative Traits

Apple (Malus × domestica Borkh.) is an important fruit crop widely spread in the cold and mild climates of temperate regions in the world, with more than 93 million tons harvested worldwide in 2021. The object of this work was to analyze thirty-one local apple cultivars of the Campania region (Southern Italy) using agronomic, morphological (UPOV descriptors) and physicochemical (solid soluble content, texture, pH and titratable acidity, skin color, Young's modulus and browning index) traits. UPOV descriptors highlighted similarities and differences among apple cultivars with a depth phenotypic characterization. Apple cultivars showed significant differences in fruit weight (31.3-236.02 g) and physicochemical trait ranging from 8.0 to 14.64° Brix for solid soluble content, 2.34-10.38 g malic acid L^-1 for titratable acidity, and 15-40% for browning index. Furthermore, different percentages in apple shape and skin color have been detected. Similarities among the cultivars based on their bio-agronomic and qualitative traits have been evaluated by cluster analyses and principal component analyses. This apple germplasm collection represents an irreplaceable genetic resource with considerable morphological and pomological variabilities among several cultivars. Nowadays, some local cultivars, widespread only in restricted geographical areas, could be reintroduced in cultivation contribution to improving the diversity of our diets and contemporary to preserve knowledge on traditional agricultural systems.

Multiple Leaf Sample Extraction System (MuLES): A tool to improve automated morphometric leaf studies

PREMISE

The measurement of leaf morphometric parameters from digital images can be time-consuming or restrictive when using digital image analysis softwares. The Multiple Leaf Sample Extraction System (MuLES) is a new tool that enables high-throughput leaf shape analysis with minimal user input or prerequisites, such as coding knowledge or image modification.

METHODS AND RESULTS

MuLES uses contrasting pixel color values to distinguish between leaf objects and their background area, eliminating the need for color threshold-based methods or color correction cards typically required in other software methods. The leaf morphometric parameters measured by this software, especially leaf aspect ratio, were able to distinguish between large populations of different accessions for the same species in a high-throughput manner.

CONCLUSIONS

MuLES provides a simple method for the rapid measurement of leaf morphometric parameters in large plant populations from digital images and demonstrates the ability of leaf aspect ratio to distinguish between closely related plant types.

Crop Wild Relatives: A Valuable Source of Tolerance to Various Abiotic Stresses

Global climate change is one of the major constraints limiting plant growth, production, and sustainability worldwide. Moreover, breeding efforts in the past years have focused on improving certain favorable crop traits, leading to genetic bottlenecks. The use of crop wild relatives (CWRs) to expand genetic diversity and improve crop adaptability seems to be a promising and sustainable approach for crop improvement in the context of the ongoing climate challenges. In this review, we present the progress that has been achieved towards CWRs exploitation for enhanced resilience against major abiotic stressors (e.g., water deficiency, increased salinity, and extreme temperatures) in crops of high nutritional and economic value, such as tomato, legumes, and several woody perennial crops. The advances in -omics technologies have facilitated the elucidation of the molecular mechanisms that may underlie abiotic stress tolerance. Comparative analyses of whole genome sequencing (WGS) and transcriptomic profiling (RNA-seq) data between crops and their wild relative counterparts have unraveled important information with respect to the molecular basis of tolerance to abiotic stressors. These studies have uncovered genomic regions, specific stress-responsive genes, gene networks, and biochemical pathways associated with resilience to adverse conditions, such as heat, cold, drought, and salinity, and provide useful tools for the development of molecular markers to be used in breeding programs. CWRs constitute a highly valuable resource of genetic diversity, and by exploiting the full potential of this extended allele pool, new traits conferring abiotic-stress tolerance may be introgressed into cultivated varieties leading to superior and resilient genotypes. Future breeding programs may greatly benefit from CWRs utilization for overcoming crop production challenges arising from extreme environmental conditions.

Soaud S, Huang Q, M. Saleh A, A. S. Abourehab M, Wan L, Cheng GT, Liu J, Ihtisham M, Noor Z, Rouf Mir R, Zhao X, Yan K, Abbas M, Li J. Natural resistance of tomato plants to Tomato yellow leaf curl virus

Tomato yellow leaf curl virus (TYLCV) is one of the most harmful afflictions in the world that affects tomato growth and production. Six regular antagonistic genes (Ty-1, Ty-2, Ty-3, Ty-4, ty-5, and Ty-6) have been transferred from wild germplasms to commercial cultivars as TYLCV protections. With Ty-1 serving as an appropriate source of TYLCV resistance, only Ty-1, Ty-2, and Ty-3 displayed substantial levels of opposition in a few strains. It has been possible to clone three TYLCV opposition genes (Ty-1/Ty-3, Ty-2, and ty-5) that target three antiviral safety mechanisms. However, it significantly impacts obtaining permanent resistance to TYLCV, trying to maintain opposition whenever possible, and spreading opposition globally. Utilizing novel methods, such as using resistance genes and identifying new resistance resources, protects against TYLCV in tomato production. To facilitate the breeders make an informed decision and testing methods for TYLCV blockage, this study highlights the portrayal of typical obstruction genes, common opposition sources, and subatomic indicators. The main goal is to provide a fictitious starting point for the identification and application of resistance genes as well as the maturation of tomato varieties that are TYLCV-resistant.

Unintended Consequences of Plant Domestication

Human selection on wild populations mostly favored a common set of plant traits during domestication. This process of direct selection also altered other independent traits that were not directly perceived or desired during crop domestication and improvement. A deeper knowledge of the inadvertent and undesirable phenotypic effects and their underlying genetic causes can help design strategies to mitigate their effects and improve genetic gain in crop plants. We review different factors explaining the negative consequences of plant domestication at the phenotypic and genomic levels. We further describe the genetic causes of undesirable effects that originate from the selection of favorable alleles during plant domestication. In addition, we propose strategies that could be useful in attenuating such effects for crop improvement. With novel -omics and genome-editing tools, it is relatively approachable to understand and manipulate the genetic and biochemical mechanisms responsible for the undesirable phenotypes in domesticated plants.

Development of a Multi-Criteria Decision-Making Approach for Evaluating the Comprehensive Application of Herbaceous Peony at Low Latitudes

The growing region of herbaceous peony (Paeonia lactiflora) has been severely constrained due to the intensification of global warming and extreme weather events, especially at low latitudes. Assessing and selecting stress-tolerant and high-quality peony germplasm is essential for maintaining the normal growth and application of peonies under adverse conditions. This study proposed a modified multi-criteria decision-making (MCDM) model for assessing peonies adapted to low-latitude climates based on our previous study. This model is low-cost, timesaving and suitable for screening the adapted peony germplasm under hot and humid climates. The evaluation was conducted through the analytic hierarchy process (AHP), three major criteria, including adaptability-related, ornamental feature-related and growth habits-related criteria, and eighteen sub-criteria were proposed and constructed in this study. The model was validated on fifteen herbaceous peonies cultivars from different latitudes. The results showed that 'Meiju', 'Hang Baishao', 'Hongpan Tuojin' and 'Bo Baishao' were assessed as Level I, which have strong growth adaptability and high ornamental values, and were recommended for promotion and application at low latitudes. The reliability and stability of the MCDM model were further confirmed by measuring the chlorophyll fluorescence of the selected adaptive cultivars 'Meiju' and 'Hang Baishao' and one maladaptive cultivar 'Zhuguang'. This study could provide a reference for the introduction, breeding and application of perennials under everchanging unfavorable climatic conditions.

Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabica

Bacteria halo blight (BHB), a coffee plant disease caused by Pseudomonas syringae pv. garcae, has been gaining importance in producing mountain regions and mild temperatures areas as well as in coffee nurseries. Most Coffea arabica cultivars are susceptible to this disease. In contrast, a great source of genetic diversity and resistance to BHB are found in C. arabica Ethiopian accessions. Aiming to identify quantitative trait nucleotides (QTNs) associated with resistance to BHB and the influence of these genomic regions during the domestication of C. arabica, we conducted an analysis of population structure and a Genome-Wide Association Study (GWAS). For this, we used genotyping by sequencing (GBS) and phenotyping for resistance to BHB of a panel with 120 C. arabica Ethiopian accessions from a historical FAO collection, 11 C. arabica cultivars, and the BA-10 genotype. Population structure analysis based on single-nucleotide polymorphisms (SNPs) markers showed that the 132 accessions are divided into 3 clusters: most wild Ethiopian accessions, domesticated Ethiopian accessions, and cultivars. GWAS, using the single-locus model MLM and the multi-locus models mrMLM, FASTmrMLM, FASTmrEMMA, and ISIS EM-BLASSO, identified 11 QTNs associated with resistance to BHB. Among these QTNs, the four with the highest values of association for resistance to BHB are linked to g000 (Chr_0_434_435) and g010741 genes, which are predicted to encode a serine/threonine-kinase protein and a nucleotide binding site leucine-rich repeat (NBS-LRR), respectively. These genes displayed a similar transcriptional downregulation profile in a C. arabica susceptible cultivar and in a C. arabica cultivar with quantitative resistance, when infected with P. syringae pv. garcae. However, peaks of upregulation were observed in a C. arabica cultivar with qualitative resistance, for both genes. Our results provide SNPs that have potential for application in Marker Assisted Selection (MAS) and expand our understanding about the complex genetic control of the resistance to BHB in C. arabica. In addition, the findings contribute to increasing understanding of the C. arabica domestication history.

DNA profiling with the 20K apple SNP array reveals Malus domestica hybridization and admixture in M. sieversii, M. orientalis, and M. sylvestris genebank accessions

The USDA-ARS National Plant Germplasm System (NPGS) apple collection in Geneva, NY, USA maintains accessions of the primary Malus domestica (Suckow) Borkh. progenitor species M. sieversii (Ledeb.) M. Roem., M. orientalis Uglitzk., and M. sylvestris (L.) Mill. Many of these accessions originated from seeds that were collected from wild populations in the species' centers of diversity. Some of these accessions have fruit phenotypes that suggest recent M. domestica hybridization, which if true would represent crop contamination of wild species populations and mislabeled species status of NPGS accessions. Pedigree connections and admixture between M. domestica and its progenitor species can be readily identified with apple SNP array data, despite such arrays not being designed for these purposes. To investigate species purity, most (463 accessions) of the NPGS accessions labeled as these three progenitor species were genotyped using the 20K apple SNP array. DNA profiles obtained were compared with a dataset of more than 5000 unique M. domestica apple cultivars. Only 212 accessions (151 M. sieversii, 26 M. orientalis, and 35 M. sylvestris) were identified as "pure" species representatives because their DNA profiles did not exhibit genotypic signatures of recent hybridization with M. domestica. Twenty-one accessions (17 M. sieversii, 1 M. orientalis, and 3 M. sylvestris) previously labeled as wild species were instead fully M. domestica. Previously unrealized hybridization and admixture between wild species and M. domestica was identified in 230 accessions (215 M. sieversii, 9 M. orientalis, and 6 M. sylvestris). Among these species-mislabeled accessions, 'Alexander', 'Gold Reinette', 'Charlamoff', 'Rosmarina Bianca', and 'King of the Pippins' were the most frequently detected M. domestica parents or grandparents. These results have implications for collection management, including germplasm distribution, and might affect conclusions of previous research focused on these three progenitor species in the NPGS apple collection. Specifically, accessions received from the NPGS for breeding and genomics, genetics, and evolutionary biology research might not be truly representative of their previously assigned species.

Genome–Environment Associations, an Innovative Tool for Studying Heritable Evolutionary Adaptation in Orphan Crops and Wild Relatives

Leveraging innovative tools to speed up prebreeding and discovery of genotypic sources of adaptation from landraces, crop wild relatives, and orphan crops is a key prerequisite to accelerate genetic gain of abiotic stress tolerance in annual crops such as legumes and cereals, many of which are still orphan species despite advances in major row crops. Here, we review a novel, interdisciplinary approach to combine ecological climate data with evolutionary genomics under the paradigm of a new field of study: genome–environment associations (GEAs). We first exemplify how GEA utilizes in situ georeferencing from genotypically characterized, gene bank accessions to pinpoint genomic signatures of natural selection. We later discuss the necessity to update the current GEA models to predict both regional- and local- or micro-habitat–based adaptation with mechanistic ecophysiological climate indices and cutting-edge GWAS-type genetic association models. Furthermore, to account for polygenic evolutionary adaptation, we encourage the community to start gathering genomic estimated adaptive values (GEAVs) for genomic prediction (GP) and multi-dimensional machine learning (ML) models. The latter two should ideally be weighted by de novo GWAS-based GEA estimates and optimized for a scalable marker subset. We end the review by envisioning avenues to make adaptation inferences more robust through the merging of high-resolution data sources, such as environmental remote sensing and summary statistics of the genomic site frequency spectrum, with the epigenetic molecular functionality responsible for plastic inheritance in the wild. Ultimately, we believe that coupling evolutionary adaptive predictions with innovations in ecological genomics such as GEA will help capture hidden genetic adaptations to abiotic stresses based on crop germplasm resources to assist responses to climate change.

“I shall endeavor to find out how nature’s forces act upon one another, and in what manner the geographic environment exerts its influence on animals and plants. In short, I must find out about the harmony in nature” Alexander von Humboldt—Letter to Karl Freiesleben, June 1799.

Advanced Breeding for Biotic Stress Resistance in Poplar

Poplar is one of the most important forest trees because of its high economic value. Thanks to the fast-growing rate, easy vegetative propagation and transformation, and availability of genomic resources, poplar has been considered the model species for forest genetics, genomics, and breeding. Being a field-growing tree, poplar is exposed to environmental threats, including biotic stresses that are becoming more intense and diffused because of global warming. Current poplar farming is mainly based on monocultures of a few elite clones and the expensive and long-term conventional breeding programmes of perennial tree species cannot face current climate-change challenges. Consequently, new tools and methods are necessary to reduce the limits of traditional breeding related to the long generation time and to discover new sources of resistance. Recent advances in genomics, marker-assisted selection, genomic prediction, and genome editing offer powerful tools to efficiently exploit the Populus genetic diversity and allow enabling molecular breeding to support accurate early selection, increasing the efficiency, and reducing the time and costs of poplar breeding, that, in turn, will improve our capacity to face or prevent the emergence of new diseases or pests.

A multi-locus genome-wide association study reveals the genetics underlying muscadine antioxidant in berry skin

Muscadine berries display enhanced nutraceutical value due to the accumulation of distinctive phytochemical constituents with great potential antioxidant activity. Such nutritional and health merits are not only restricted to muscadine, but muscadine berries accumulate higher amounts of bioactive polyphenolics compared with other grape species. For the genetic study of the antioxidant trait in muscadine, a multi-locus genome-wide association study (GWAS) with 350 muscadine genotypes and 1,283 RNase H2 enzyme-dependent amplicon sequencing (rhAmpSeq) markers was performed. Phenotyping was conducted with several antioxidant-related traits, including total phenolic content (TPC), total flavonoid content (TFC), 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical scavenging activity, and FRAP antioxidant assay in muscadine berry skin. The correlation coefficient analysis revealed that the TPC, and DPPH/FRAP activities were significantly correlated. Through the GWAS analysis, 12 QTNs were identified from the four traits, of which six were pleiotropic QTNs. Two pleiotropic QTNs, chr2_14464718 and chr4_16491374, were commonly identified from the TPC and DPPH/FRAP activities. Co-located genes with the two pleiotropic QTNs were isolated, and two candidate genes were identified with transcriptome analysis. UDP-glycosyltransferase and 4-hydroxy-4-methyl-2-oxoglutarate aldolase were the candidate genes that are positively and negatively correlated to the quantitative property of traits, respectively. These results are the first genetic evidence of the quantitative property of antioxidants in muscadine and provide genetic resources for breeding antioxidant-rich cultivars for both Muscadinia and Euvitis species.

Genetic variability for vigor and yield of robusta coffee (Coffea canephora) clones in Ghana

Effectiveness of plant improvement programs, especially in perennial crops like coffee, may be improved by knowing the level of genetic variation which exist within a breeding population coupled with the knowledge of estimates of genetic parameters for key agronomic traits. Thus, this study was conducted to evaluate C. canephora clones for growth (stem diameter, number of laterals and span) and yield traits; estimate genetic parameters of these traits; and determine the phenotypic and genetic associations between these traits to guide future crop improvement efforts. The productivity of 56 coffee clones was assessed from 2012 to 2020 in a clonal experiment planted in a randomized complete block design with three replicates. Each plot consisted of eight plants spaced at 2 × 3 m at the Cocoa Research Institute of Ghana. There were significant (p < 0.001) differences among clones for all the traits assessed. Broad sense heritability was low-to-moderate for all the traits evaluated with the highest (0.34) observed for cumulative yield (CY). Cumulative yield was genetically correlated (p < 0.001) with span and number of laterals (NOL). For the growth traits, NOL was the most strongly associated with CY (r_g = 0.49, p < 0.001). The results revealed that selection based on early years’ yield (MY1) could be as effective as selection based on CY (r_g = 0.87, p < 0.001). Our findings indicate that there is significant genetic variation among the test clones for the parameters assessed and presents a good opportunity for future variety development.

Perennial Cotton Ratoon Cultivation: A Sustainable Method for Cotton Production and Breeding

Cotton production is challenged by high costs with multiple management and material inputs including seed, pesticide, and fertilizer application. The production costs can be decreased and profits can be increased by developing efficient crop management strategies, including perennial cotton ratoon cultivation. This review focuses on the role of ratoon cultivation in cotton productivity and breeding. In areas that are frost-free throughout the year, when the soil temperature is suitable for cotton growth in spring, the buds of survived plants begin to sprout, and so their flowering and fruiting periods are approximately 4-6 weeks earlier than those of sown cotton. Due to the absence of frost damage, the ratoon cotton continues to grow, and the renewed plants can offer a higher yield than cotton sown in the following season. Moreover, ratoon cultivation from the last crop without sowing can help conserve seeds, reduce labor inputs, and reduce soil and water loss. In this review, the preservation of perennial cotton germplasm resources, the classification and genome assignment of perennial species in the cotton gene pools, and effective strategies for the collection, preservation, identification, and utilization of perennial cotton germplasms are discussed. Ratoon cultivation is the main driver of cotton production and breeding, especially to maintain male sterility for the utilization and fixation of heterosis. Ratoon cultivation of cotton is worth adopting because it has succeeded in Brazil, China, and India. Therefore, taking advantages of the warm environment to exploit the indeterminant growth habit of perennial cotton for breeding would be an efficiency-increasing, cost-saving, and eco-friendly approach in frost-free regions. In the future, more attention should be given to ratooning perennial cotton for breeding male-sterile lines.

Development of Superior Fibre Quality Upland Cotton Cultivar Series 'Ravnaq' Using Marker-Assisted Selection

Marker-assisted selection (MAS) helps to shorten breeding time as well as reduce breeding resources and efforts. In our MAS program, we have targeted one of previously reported LD-blocks with its simple sequence repeat (SSR) marker(s), putatively associated with, at least, four different fibre quality QTLs such as fibre length, strength, micronaire and uniformity. In order to transfer targeted QTLs from a donor genotype to a cultivar of choice, we selected G. hirsutum donor genotypes L-141 and LN-1, possessing a fibre quality trait-associated LD-block from the chromosome 7/16. We crossed the donor lines with local elite G. hirsutum cultivars 'Andijan-35' and 'Mekhnat' as recipients. As a result, two segregating populations on LD-block of interest containing fibre QTLs were developed through backcrossing (BC) of F₁ hybrids with their relative recipients (used as recurrent parents) up to five generations. In each BC and segregating BC₁-₅F₁ populations, a transfer of targeted LD-block/QTLs was monitored using a highly polymorphic SSR marker, BNL1604 genotype. The homozygous cultivar genotypes with superior fibre quality and agronomic traits, bearing a targeted LD-block of interest, were individually selected from self-pollinated BC₅F₁ (BC₅F_2-5) population plants using the early-season PCR screening analysis of BNL1604 marker locus and the end-of-season fibre quality parameters. Only improved hybrids with superior fibre quality compared to original recipient parent were used for the next cycle of breeding. We successfully developed two novel MAS-derived cotton cultivars (named as 'Ravnaq-1' and 'Ravnaq-2') of BC₅F₅ generations. Both novel MAS cultivars possessed stronger and longer fibre as well as improved fibre uniformity and micronaire compared to the original recurrent parents, 'Andijan-35' and 'Mekhnat'. Our efforts demonstrated a precise transfer of the same LD-block with, at least, four superior fibre QTLs in the two independent MAS breeding experiments exploiting different parental genotypes. Results exemplify the feasibility of MAS in cotton breeding.

Reproductive biology of wild and domesticated Ensete ventricosum: Further evidence for maintenance of sexual reproductive capacity in a vegetatively propagated perennial crop

Loss of sexual reproductive capacity has been proposed as a syndrome of domestication in vegetatively propagated crops, but there are relatively few examples from agricultural systems. In this study, we compare sexual reproductive capacity in wild (sexual) and domesticated (vegetative) populations of enset (Ensete ventricosum (Welw.) Cheesman), a tropical banana relative and Ethiopian food security crop. We examined floral and seed morphology and germination ecology across 35 wild and domesticated enset. We surveyed variation in floral and seed traits, including seed weight, viability and internal morphology, and germinated seeds across a range of constant and alternating temperature regimes to characterize optimum germination requirements. We report highly consistent floral allometry, seed viability, internal morphology and days to germination in wild and domesticated enset. However, seeds from domesticated plants responded to cooler temperatures with greater diurnal range. Shifts in germination behaviour appear concordant with a climatic envelope shift in the domesticated distribution. Our findings provide evidence that sexual reproductive capacity has been maintained despite long-term near-exclusive vegetative propagation in domesticated enset. Furthermore, certain traits such as germination behaviour and floral morphology may be under continued selection, presumably through rare sexually reproductive events. Compared to sexually propagated crops banked as seeds, vegetative crop diversity is typically conserved in living collections that are more costly and insecure. Improved understanding of sexual propagation in vegetative crops may have applications in germplasm conservation and plant breeding.

As It Stands: The Palouse Wild Cider Apple Breeding Program

Providing hands-on education for the next generation of plant breeders would help maximize effectiveness of future breeding efforts. Such education should include training in introgression of crop wild relative alleles, which can increase genetic diversity while providing cultivar attributes that meet industry and consumer demands in a crop such as cider apple. Incorporation of DNA information in breeding decisions has become more common and is another skill future plant breeders need. The Palouse Wild Cider apple breeding program (PWCabp) was established at Washington State University in early 2014 as a student-run experiential learning opportunity. The objectives of this study were to describe the PWCabp's approaches, outcomes, and student involvement to date that has relied on a systematic operational structure, utilization of wild relatives, and incorporation of DNA information. Students chose the crop (cider apple) and initial target market and stakeholders (backyard growers and hobbyists of the Palouse region). Twelve target attributes were defined including high phenolics and red flesh. Phase one and two field trials were established. Two promising high-bitterness selections were identified and propagated. By running the PWCabp, more than 20 undergraduate and graduate students gained experience in the decisions and operations of a fruit breeding program. PWCabp activities have produced desirable new germplasm via utilization of highly diverse Malus germplasm and trained new plant breeding professionals via experiential learning.

Variability of Phenolic Compound Accumulation and Antioxidant Activity in Wild Plants of Some Rumex Species (Polygonaceae)

Today, more than ever, the search for non-trivial sources of biologically active substances is critical. Plants of the genus Rumex are noteworthy. Plants of this genus stand out for a number of advantages from the dominant plant core of meadow phytocenoses of the temperate climatic zone: a short growing season, an intensive increase in biomass, and undemanding growth conditions. In addition, this plant genus is known as a super-producer of secondary phenolic compounds. The wide distribution and intensive synthesis of biologically active substances make plants from the genus Rumex a promising object for study. Seven species of the genus Rumex (R. acetosa, R. acetosella, R. confertus, R. crispus, R. maritimus, R.obtusifolius, and R. sanguineus) were analyzed. Plants were collected under relatively uniform growing conditions. For subsequent extraction and analysis of phenolic compounds, as well as antioxidant activity, plants leaves were used. R. acetosella, R. crispus, R. maritimus, R. obtusifolius, and R. sanguineus were characterized by a high total content of phenolic compounds (111–131 mg g^–1). The maximum content of flavonoids was found in the leaves of R. maritimus and R. acetosella. At the same time, according to high-performance liquid chromatography with diode-array detection (HPLC-DAD) analysis, derivatives of flavones (apigenin and luteolin) predominated in the leaves of R. acetosella, while in other species, mainly derivatives of flavonols (quercetin and kaempferol) were identified. Plants of R. acetosa, in comparison with other studied species, were characterized by a lower content of the studied groups of phenolic compounds, with the exception of hydroxycinnamic acids, the content of which in this species was comparable to the content of flavonoids. The maximum content of catechins was found in R. sanguineus; proanthocyanidins—in R. sanguineus, R. obtusifolius, and R. crispus; and tannins—in R. obtusifolius. Extracts from R. crispus were characterized by high antioxidant activity, measured by 2,2-diphenyl-1-picrylhydrazyl (DPPH), 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid (ABTS), and ferric reducing antioxidant power (FRAP) assays. In addition, the assessment of the phenolic profile of the plant made it possible to group the plants within the framework of cluster analysis. The distribution pattern in the clusters corresponded to the generally accepted taxonomy, with a characteristic division into subgenera (Acetosa, Acetosella, and Rumex). Thus, the phenolic profile can be considered as an additional instrumental approach when drawing up a systematic hierarchy.

Chromosome-scale haplotype-phased genome assemblies of the male and female lines of wild asparagus (Asparagus kiusianus), a dioecious plant species

Asparagus kiusianus is a disease-resistant dioecious plant species and a wild relative of garden asparagus (Asparagus officinalis). To enhance A. kiusianus genomic resources, advance plant science, and facilitate asparagus breeding, we determined the genome sequences of the male and female lines of A. kiusianus. Genome sequence reads obtained with a linked-read technology were assembled into four haplotype-phased contig sequences (∼1.6 Gb each) for the male and female lines. The contig sequences were aligned onto the chromosome sequences of garden asparagus to construct pseudomolecule sequences. Approximately 55,000 potential protein-encoding genes were predicted in each genome assembly, and ∼70% of the genome sequence was annotated as repetitive. Comparative analysis of the genomes of the two species revealed structural and sequence variants between the two species as well as between the male and female lines of each species. Genes with high sequence similarity with the male-specific sex determinant gene in A. officinalis, MSE1/AoMYB35/AspTDF1, were presented in the genomes of the male line but absent from the female genome assemblies. Overall, the genome sequence assemblies, gene sequences, and structural and sequence variants determined in this study will reveal the genetic mechanisms underlying sexual differentiation in plants, and will accelerate disease-resistance breeding in garden asparagus.

Inheritance of Yield Components and Morphological Traits in Avocado cv. Hass From "Criollo" "Elite Trees" via Half-Sib Seedling Rootstocks

Grafting induces precocity and maintains clonal integrity in fruit tree crops. However, the complex rootstock × scion interaction often precludes understanding how the tree phenotype is shaped, limiting the potential to select optimum rootstocks. Therefore, it is necessary to assess (1) how seedling progenies inherit trait variation from elite 'plus trees', and (2) whether such family superiority may be transferred after grafting to the clonal scion. To bridge this gap, we quantified additive genetic parameters (i.e., narrow sense heritability-h ², and genetic-estimated breeding values-GEBVs) across landraces, "criollo", "plus trees" of the super-food fruit tree crop avocado (Persea americana Mill.), and their open-pollinated (OP) half-sib seedling families. Specifically, we used a genomic best linear unbiased prediction (G-BLUP) model to merge phenotypic characterization of 17 morpho-agronomic traits with genetic screening of 13 highly polymorphic SSR markers in a diverse panel of 104 avocado "criollo" "plus trees." Estimated additive genetic parameters were validated at a 5-year-old common garden trial (i.e., provenance test), in which 22 OP half-sib seedlings from 82 elite "plus trees" served as rootstocks for the cv. Hass clone. Heritability (h ²) scores in the "criollo" "plus trees" ranged from 0.28 to 0.51. The highest h ² values were observed for ribbed petiole and adaxial veins with 0.47 (CI 95%0.2-0.8) and 0.51 (CI 0.2-0.8), respectively. The h ² scores for the agronomic traits ranged from 0.34 (CI 0.2-0.6) to 0.39 (CI 0.2-0.6) for seed weight, fruit weight, and total volume, respectively. When inspecting yield variation across 5-year-old grafted avocado cv. Hass trees with elite OP half-sib seedling rootstocks, the traits total number of fruits and fruits' weight, respectively, exhibited h ² scores of 0.36 (± 0.23) and 0.11 (± 0.09). Our results indicate that elite "criollo" "plus trees" may serve as promissory donors of seedling rootstocks for avocado cv. Hass orchards due to the inheritance of their outstanding trait values. This reinforces the feasibility to leverage natural variation from "plus trees" via OP half-sib seedling rootstock families. By jointly estimating half-sib family effects and rootstock-mediated heritability, this study promises boosting seedling rootstock breeding programs, while better discerning the consequences of grafting in fruit tree crops.

Evolutionary Genetics of Crop-Wild Complexes

Since Darwin's time, the role of crop wild relatives (CWR), landraces, and cultivated genepools in shaping plant diversity and boosting food resources has been a major question [...].

Harnessing Crop Wild Diversity for Climate Change Adaptation

Warming and drought are reducing global crop production with a potential to substantially worsen global malnutrition. As with the green revolution in the last century, plant genetics may offer concrete opportunities to increase yield and crop adaptability. However, the rate at which the threat is happening requires powering new strategies in order to meet the global food demand. In this review, we highlight major recent 'big data' developments from both empirical and theoretical genomics that may speed up the identification, conservation, and breeding of exotic and elite crop varieties with the potential to feed humans. We first emphasize the major bottlenecks to capture and utilize novel sources of variation in abiotic stress (i.e., heat and drought) tolerance. We argue that adaptation of crop wild relatives to dry environments could be informative on how plant phenotypes may react to a drier climate because natural selection has already tested more options than humans ever will. Because isolated pockets of cryptic diversity may still persist in remote semi-arid regions, we encourage new habitat-based population-guided collections for genebanks. We continue discussing how to systematically study abiotic stress tolerance in these crop collections of wild and landraces using geo-referencing and extensive environmental data. By uncovering the genes that underlie the tolerance adaptive trait, natural variation has the potential to be introgressed into elite cultivars. However, unlocking adaptive genetic variation hidden in related wild species and early landraces remains a major challenge for complex traits that, as abiotic stress tolerance, are polygenic (i.e., regulated by many low-effect genes). Therefore, we finish prospecting modern analytical approaches that will serve to overcome this issue. Concretely, genomic prediction, machine learning, and multi-trait gene editing, all offer innovative alternatives to speed up more accurate pre- and breeding efforts toward the increase in crop adaptability and yield, while matching future global food demands in the face of increased heat and drought. In order for these 'big data' approaches to succeed, we advocate for a trans-disciplinary approach with open-source data and long-term funding. The recent developments and perspectives discussed throughout this review ultimately aim to contribute to increased crop adaptability and yield in the face of heat waves and drought events.

Agricultural wilding: rewilding for agricultural landscapes through an increase in wild productive systems

Introducing wild crops and plants complements intentions for improved biodiversity outcomes in agricultural landscapes; and provides opportunity for in-situ conservation of a diverse range of wild plants and crops, and improved connectivity between conserved areas. This opinion article considers definitions and common value of conserving wild crops and plants, and crop wild relatives, in-situ and ex-situ. Rewilding definitions and common uses for policy and practice are described. The Ecological Sensitivity within Human Realities (ESHR) concept was developed to guide human natural-environment interactions in agricultural systems and landscapes for improved functional biodiversity outcomes. It is used to assess possible appropriateness of rewilding for agricultural systems and landscapes. The assessment demonstrates how agricultural systems and landscapes are often excluded, despite appearing a useful term to encourage such conservation efforts. The importance of a more specific term rather than a more specific definition and use of rewilding is suggested. Agricultural wilding is introduced as a more specific term for introducing and conserving wild crops and plants for agricultural purposes, as wild productive systems, useful for policy or other approaches the guide human natural-environment interactions. The conceptual approach to the article provides theoretical suggestions for minimum proportions of wild crops and plants for wild productive systems according to native and non native landscapes. From a conceptual to applied discussion, relevance of agricultural wilding for coffee farming landscapes is explained in some depth, and for an existing biodiversity campaign and an EU agricultural policy, briefly.

Genetic diversity and population structure in Vitis species illustrate phylogeographic patterns in eastern North America

Geographical distribution and diversity of current plant species have been strongly shaped by climatic oscillations during the Quaternary. Analysing the resulting divergence among species and differentiation within species is crucial to understand the evolution of taxa like the Vitis genus, which provides very useful genetic resources for grapevine improvement and might reveal original recolonization patterns due to growth habit and dispersal mode. Here, we studied the genetic structure in natural populations of three species from eastern North America: Vitis aestivalis, V. cinerea and V. riparia using different marker types. Vitis aestivalis and V. cinerea showed higher diversity than V. riparia. The two former species are less differentiated, confirming an earlier divergence of V. riparia. V. aestivalis and V. riparia exhibited different genetic groups on both sides of the Appalachian Mountains that could mirror different recolonization routes from southern refugia. Genetic structure was stronger in V. cinerea, for which two varieties (var. berlandieri and var. cinerea) are morphologically recognized. Our results confirm this distinction and suggest the existence of three other lineages within var. cinerea. These discontinuities appear linked to adaptation of var. berlandieri to dry and limy areas of Texas and partially to the Mississippi River Valley. Rapid range expansions from refugia upon climate warming are also suggested by the low linkage disequilibrium values observed. Furthermore, large variation for downy mildew resistance was observed in the three species. Our findings appeared consistent with the vegetation history of eastern North America.

Tapping Diversity From the Wild: From Sampling to Implementation

The diversity observed among crop wild relatives (CWRs) and their ability to flourish in unfavorable and harsh environments have drawn the attention of plant scientists and breeders for many decades. However, it is also recognized that the benefit gained from using CWRs in breeding is a potential rose between thorns of detrimental genetic variation that is linked to the trait of interest. Despite the increased interest in CWRs, little attention was given so far to the statistical, analytical, and technical considerations that should guide the sampling design, the germplasm characterization, and later its implementation in breeding. Here, we review the entire process of sampling and identifying beneficial genetic variation in CWRs and the challenge of using it in breeding. The ability to detect beneficial genetic variation in CWRs is strongly affected by the sampling design which should be adjusted to the spatial and temporal variation of the target species, the trait of interest, and the analytical approach used. Moreover, linkage disequilibrium is a key factor that constrains the resolution of searching for beneficial alleles along the genome, and later, the ability to deplete linked deleterious genetic variation as a consequence of genetic drag. We also discuss how technological advances in genomics, phenomics, biotechnology, and data science can improve the ability to identify beneficial genetic variation in CWRs and to exploit it in strive for higher-yielding and sustainable crops.

Genomic consequences of apple improvement

The apple (Malus domestica) is one of the world's most commercially important perennial crops and its improvement has been the focus of human effort for thousands of years. Here, we genetically characterise over 1000 apple accessions from the United States Department of Agriculture (USDA) germplasm collection using over 30,000 single-nucleotide polymorphisms (SNPs). We confirm the close genetic relationship between modern apple cultivars and their primary progenitor species, Malus sieversii from Central Asia, and find that cider apples derive more of their ancestry from the European crabapple, Malus sylvestris, than do dessert apples. We determine that most of the USDA collection is a large complex pedigree: over half of the collection is interconnected by a series of first-degree relationships. In addition, 15% of the accessions have a first-degree relationship with one of the top 8 cultivars produced in the USA. With the exception of 'Honeycrisp', the top 8 cultivars are interconnected to each other via pedigree relationships. The cultivars 'Golden Delicious' and 'Red Delicious' were found to have over 60 first-degree relatives, consistent with their repeated use by apple breeders. We detected a signature of intense selection for red skin and provide evidence that breeders also selected for increased firmness. Our results suggest that Americans are eating apples largely from a single family tree and that the apple's future improvement will benefit from increased exploitation of its tremendous natural genetic diversity.

Inheritance of Rootstock Effects in Avocado (Persea americana Mill.) cv. Hass

Grafting is typically utilized to merge adapted seedling rootstocks with highly productive clonal scions. This process implies the interaction of multiple genomes to produce a unique tree phenotype. However, the interconnection of both genotypes obscures individual contributions to phenotypic variation (rootstock-mediated heritability), hampering tree breeding. Therefore, our goal was to quantify the inheritance of seedling rootstock effects on scion traits using avocado (Persea americana Mill.) cv. Hass as a model fruit tree. We characterized 240 diverse rootstocks from 8 avocado cv. Hass orchards with similar management in three regions of the province of Antioquia, northwest Andes of Colombia, using 13 microsatellite markers simple sequence repeats (SSRs). Parallel to this, we recorded 20 phenotypic traits (including morphological, biomass/reproductive, and fruit yield and quality traits) in the scions for 3 years (2015-2017). Relatedness among rootstocks was inferred through the genetic markers and inputted in a "genetic prediction" model to calculate narrow-sense heritabilities (h 2) on scion traits. We used three different randomization tests to highlight traits with consistently significant heritability estimates. This strategy allowed us to capture five traits with significant heritability values that ranged from 0.33 to 0.45 and model fits (r) that oscillated between 0.58 and 0.73 across orchards. The results showed significance in the rootstock effects for four complex harvest and quality traits (i.e., total number of fruits, number of fruits with exportation quality, and number of fruits discarded because of low weight or thrips damage), whereas the only morphological trait that had a significant heritability value was overall trunk height (an emergent property of the rootstock-scion interaction). These findings suggest the inheritance of rootstock effects, beyond root phenotype, on a surprisingly wide spectrum of scion traits in "Hass" avocado. They also reinforce the utility of polymorphic SSRs for relatedness reconstruction and genetic prediction of complex traits. This research is, up to date, the most cohesive evidence of narrow-sense inheritance of rootstock effects in a tropical fruit tree crop. Ultimately, our work highlights the importance of considering the rootstock-scion interaction to broaden the genetic basis of fruit tree breeding programs while enhancing our understanding of the consequences of grafting.

A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds

Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, Indica and Japonica, which result from a combination of natural and human selection. The genetic divergence of these groups reflects the underlying population structure of their wild ancestors, and suggests that a pre-breeding strategy designed to take advantage of existing genetic, geographic and ecological substructure may provide a rational approach to the utilization of crop wild ancestors in plant improvement. Here we describe the coordinated development of six introgression libraries (n = 63 to 81 lines per library) in both Indica (cv. IR64) and Japonica (cv. Cybonnet) backgrounds using three bio-geographically diverse wild donors representing the Oryza rufipogon Species Complex from China, Laos and Indonesia. The final libraries were genotyped using an Infinium 7K rice SNP array (C7AIR) and analyzed under greenhouse conditions for several simply inherited (Mendelian) traits. These six interspecific populations can be used as individual Chromosome Segment Substitution Line libraries and, when considered together, serve as a powerful genetic resource for systematic genetic dissection of agronomic, physiological and developmental traits in rice.

Modern Strategies to Assess and Breed Forest Tree Adaptation to Changing Climate

Studying the genetics of adaptation to new environments in ecologically and industrially important tree species is currently a major research line in the fields of plant science and genetic improvement for tolerance to abiotic stress. Specifically, exploring the genomic basis of local adaptation is imperative for assessing the conditions under which trees will successfully adapt in situ to global climate change. However, this knowledge has scarcely been used in conservation and forest tree improvement because woody perennials face major research limitations such as their outcrossing reproductive systems, long juvenile phase, and huge genome sizes. Therefore, in this review we discuss predictive genomic approaches that promise increasing adaptive selection accuracy and shortening generation intervals. They may also assist the detection of novel allelic variants from tree germplasm, and disclose the genomic potential of adaptation to different environments. For instance, natural populations of tree species invite using tools from the population genomics field to study the signatures of local adaptation. Conventional genetic markers and whole genome sequencing both help identifying genes and markers that diverge between local populations more than expected under neutrality, and that exhibit unique signatures of diversity indicative of "selective sweeps." Ultimately, these efforts inform the conservation and breeding status capable of pivoting forest health, ecosystem services, and sustainable production. Key long-term perspectives include understanding how trees' phylogeographic history may affect the adaptive relevant genetic variation available for adaptation to environmental change. Encouraging "big data" approaches (machine learning-ML) capable of comprehensively merging heterogeneous genomic and ecological datasets is becoming imperative, too.

Global Role of Crop Genomics in the Face of Climate Change

The development of climate change resilient crops is necessary if we are to meet the challenge of feeding the growing world's population. We must be able to increase food production despite the projected decrease in arable land and unpredictable environmental conditions. This review summarizes the technological and conceptual advances that have the potential to transform plant breeding, help overcome the challenges of climate change, and initiate the next plant breeding revolution. Recent developments in genomics in combination with high-throughput and precision phenotyping facilitate the identification of genes controlling critical agronomic traits. The discovery of these genes can now be paired with genome editing techniques to rapidly develop climate change resilient crops, including plants with better biotic and abiotic stress tolerance and enhanced nutritional value. Utilizing the genetic potential of crop wild relatives (CWRs) enables the domestication of new species and the generation of synthetic polyploids. The high-quality crop plant genome assemblies and annotations provide new, exciting research targets, including long non-coding RNAs (lncRNAs) and cis-regulatory regions. Metagenomic studies give insights into plant-microbiome interactions and guide selection of optimal soils for plant cultivation. Together, all these advances will allow breeders to produce improved, resilient crops in relatively short timeframes meeting the demands of the growing population and changing climate.

Extreme heat effects on perennial crops and strategies for sustaining future production

Extreme heat events will challenge agricultural production and raise the risk of food insecurity. California is the largest agricultural producer in the United States, and climate change and extreme heat may significantly affect the state's food production. This paper provides a summary of the current literature on crop responses to extreme heat, with a focus on perennial agriculture in California. We highlight contemporary trends and future projections in heat extremes, and the range of plant responses to extreme heat exposure, noting the variability in plant tolerance and response across season, crop, and cultivar. We also review practices employed to mitigate heat damage and the capacity for those practices to serve as adaptation options in a warmer and drier future. Finally, we discuss current and future research directions aimed at increasing the adaptive capacity of perennial agriculture to the increased heat exposure anticipated with climate change. Collectively, the literature reviewed makes clear the need to understand crop responses and tolerances to heat within the context of climate change and climate extremes in order to sustain crop production, preserve agricultural communities, and bolster food security at local, national, and global scales.

Prospects for the Study and Improvement of Abiotic Stress Tolerance in Date Palms in the Post-genomics Era

Date palm (Phoenix dactylifera L.) is a socio-economically important crop in the Middle East and North Africa and a major contributor to food security in arid regions of the world. P. dactylifera is both drought and salt tolerant, but recent water shortages and increases in groundwater and soil salinity have threatened the continued productivity of the crop. Recent studies of date palm have begun to elucidate the physiological mechanisms of abiotic stress tolerance and the genes and biochemical pathways that control the response to these stresses. Here we review recent studies on tolerance of date palm to salinity and drought stress, the role of the soil and root microbiomes in abiotic stress tolerance, and highlight recent findings of omic-type studies. We present a perspective on future research of abiotic stress in date palm that includes improving existing genome resources, application of genetic mapping to determine the genetic basis of variation in tolerances among cultivars, and adoption of gene-editing technologies to the study of abiotic stress in date palms. Development of necessary resources and application of the proposed methods will provide a foundation for future breeders and genetic engineers aiming to develop more stress-tolerant cultivars of date palm.

Super-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement

The pangenome provides genomic variations in the cultivated gene pool for a given species. However, as the crop's gene pool comprises many species, especially wild relatives with diverse genetic stock, here we suggest using accessions from all available species of a given genus for the development of a more comprehensive and complete pangenome, which we refer to as a super-pangenome. The super-pangenome provides a complete genomic variation repertoire of a genus and offers unprecedented opportunities for crop improvement. This opinion article focuses on recent developments in crop pangenomics, the need for a super-pangenome that should include wild species, and its application for crop improvement.

Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato

BACKGROUND

Continuous storage root formation and bulking (CSRFAB) in sweetpotato is an important trait from agronomic and biological perspectives. Information about the molecular mechanisms underlying CSRFAB traits is lacking.

RESULTS

Here, as a first step toward understanding the genetic basis of CSRFAB in sweetpotato, we performed a genome-wide association study (GWAS) using phenotypic data from four distinct developmental stages and 33,068 single nucleotide polymorphism (SNP) and insertion-deletion (indel) markers. Based on Bonferroni threshold (p-value < 5 × 10- 7), we identified 34 unique SNPs that were significantly associated with the complex trait of CSRFAB at 150 days after planting (DAP) and seven unique SNPs associated with discontinuous storage root formation and bulking (DCSRFAB) at 90 DAP. Importantly, most of the loci associated with these identified SNPs were located within genomic regions (using Ipomoea trifida reference genome) previously reported for quantitative trait loci (QTL) controlling similar traits. Based on these trait-associated SNPs, 12 and seven candidate genes were respectively annotated for CSRFAB and DCSRFAB traits. Congruent with the contrasting and inverse relationship between discontinuous and continuous storage root formation and bulking, a DCSRFAB-associated candidate gene regulates redox signaling, involved in auxin-mediated lateral root formation, while CSRFAB is enriched for genes controlling growth and senescence.

CONCLUSION

Candidate genes identified in this study have potential roles in cell wall remodeling, plant growth, senescence, stress, root development and redox signaling. These findings provide valuable insights into understanding the functional networks to develop strategies for sweetpotato yield improvement. The markers as well as candidate genes identified in this pioneering research for CSRFAB provide important genomic resources for sweetpotato and other root crops.

Fruits of wild and semi-domesticated Diospyros tree species have contrasting phenological, metabolic, and antioxidant activity profiles

BACKGROUND

In contrast to commercial Diospyros species, Mesoamerican fruit-producing species are scarcely known, particularly wild species that might harbor desirable traits suitable for breeding. Thus, metabolomic, chemical, and antioxidant profiles of fruits harvested from cultivated Diospyros digyna and wild Diospyros rekoi trees during consecutive winter seasons were obtained. Fruits were harvested in habitats having marked differences in soil quality, climate, and luminosity.

RESULTS

D. digyna fruits were larger and less acid than D. rekoi fruits, whereas antioxidant activity tended to be higher in D. rekoi fruits. Phenolic, flavonoid, and sugar contents also varied significantly between species. Metabolomic analysis allowed the pre-identification of 519 and 1665 metabolites in negative and positive electrospray ionization (ESI) modes, respectively. Principal component analysis of the positive ESI data explained 51.8% of the variance and indicated clear metabolomic differences between D. rekoi and D. digyna fruits that were confirmed by direct-injection ESI mass spectrometry profiles. Twenty-one discriminating metabolites were detected in fruits of both species; D. digyna fruits differentially accumulated lysophospholipids, whereas discriminating metabolites in D. rekoi fruits were chemically more diverse than those in D. digyna fruits.

CONCLUSION

Domesticated D. digyna fruits have improved physicochemical fruit traits compared with wild D. rekoi fruits, including larger size and lower acidity. The metabolomic and chemical composition of their respective fruits were also significantly different, which in D. rekoi was manifested as a notable season-dependent increase in antioxidant capacity. Therefore, wild D. rekoi can be considered as an important genetic resource for the improvement of commercial Diospyros fruit quality. © 2019 Society of Chemical Industry.

The role of genetics in mainstreaming the production of new and orphan crops to diversify food systems and support human nutrition

Especially in low-income nations, new and orphan crops provide important opportunities to improve diet quality and the sustainability of food production, being rich in nutrients, capable of fitting into multiple niches in production systems, and relatively adapted to low-input conditions. The evolving space for these crops in production systems presents particular genetic improvement requirements that extensive gene pools are able to accommodate. Particular needs for genetic development identified in part with plant breeders relate to three areas of fundamental importance for addressing food production and human demographic trends and associated challenges, namely: facilitating integration into production systems; improving the processability of crop products; and reducing farm labour requirements. Here, we relate diverse involved target genes and crop development techniques. These techniques include transgressive methods that involve defining exemplar crop models for effective new and orphan crop improvement pathways. Research on new and orphan crops not only supports the genetic improvement of these crops, but they serve as important models for understanding crop evolutionary processes more broadly, guiding further major crop evolution. The bridging position of orphan crops between new and major crops provides unique opportunities for investigating genetic approaches for de novo domestications and major crop 'rewildings'.

Benchmarking variant identification tools for plant diversity discovery

BACKGROUND

The ability to accurately and comprehensively identify genomic variations is critical for plant studies utilizing high-throughput sequencing. Most bioinformatics tools for processing next-generation sequencing data were originally developed and tested in human studies, raising questions as to their efficacy for plant research. A detailed evaluation of the entire variant calling pipeline, including alignment, variant calling, variant filtering, and imputation was performed on different programs using both simulated and real plant genomic datasets.

RESULTS

A comparison of SOAP2, Bowtie2, and BWA-MEM found that BWA-MEM was consistently able to align the most reads with high accuracy, whereas Bowtie2 had the highest overall accuracy. Comparative results of GATK HaplotypCaller versus SAMtools mpileup indicated that the choice of variant caller affected precision and recall differentially depending on the levels of diversity, sequence coverage and genome complexity. A cross-reference experiment of S. lycopersicum and S. pennellii reference genomes revealed the inadequacy of single reference genome for variant discovery that includes distantly-related plant individuals. Machine-learning-based variant filtering strategy outperformed the traditional hard-cutoff strategy resulting in higher number of true positive variants and fewer false positive variants. A 2-step imputation method, which utilized a set of high-confidence SNPs as the reference panel, showed up to 60% higher accuracy than direct LD-based imputation.

CONCLUSIONS

Programs in the variant discovery pipeline have different performance on plant genomic dataset. Choice of the programs is subjected to the goal of the study and available resources. This study serves as an important guiding information for plant biologists utilizing next-generation sequencing data for diversity characterization and crop improvement.

A Multifaceted Overview of Apple Tree Domestication

The apple is an iconic tree and a major fruit crop worldwide. It is also a model species for the study of the evolutionary processes and genomic basis underlying the domestication of clonally propagated perennial crops. Multidisciplinary approaches from across Eurasia have documented the pace and process of cultivation of this remarkable crop. While population genetics and genomics have revealed the overall domestication history of apple across Eurasia, untangling the evolutionary processes involved, archeobotany has helped to document the transition from gathering and using apples to the practice of cultivation. Further studies integrating archeogenetic and archeogenomic approaches will bring new insights about key traits involved in apple domestication. Such knowledge has potential to boost innovation in present-day apple breeding.

Genome-Wide Association Studies in Apple Reveal Loci for Aroma Volatiles, Sugar Composition, and Harvest Date

Understanding the genetic architecture of fruit quality traits is crucial to target breeding of apple ( L.) cultivars. We linked genotype and phenotype information by combining genotyping-by-sequencing (GBS) generated single nucleotide polymorphism (SNP) markers with fruit flavor volatile data, sugar and acid content, and historical trait data from a gene bank collection. Using gas chromatography-mass spectrometry (GC-MS) analysis of apple juice samples, we identified 49 fruit volatile organic compounds (VOCs). We found a very variable content of VOCs, especially for the esters, among 149 apple cultivars. We identified convincing associations for the acetate esters especially butyl acetate and hexyl acetate on chromosome 2 in a region of several alcohol acyl-transferases including AAT1. For sucrose content and for fructose and sucrose in percentage of total sugars, we revealed significant SNP associations. Here, we suggest a vacuolar invertase close to significant SNPs for this association as candidate gene. Harvest date was in strong SNP association with a NAC transcription factor gene and sequencing identified two haplotypes associated with harvest date. The study shows that SNP marker characterization of a gene bank collection can be successfully combined with new and historical trait data for association studies. Suggested candidate genes may contribute to an improved understanding of the genetic basis for important traits and simultaneously provide tools for targeted breeding using marker-assisted selection (MAS).

Apple whole genome sequences: recent advances and new prospects

In 2010, a major scientific milestone was achieved for tree fruit crops: publication of the first draft whole genome sequence (WGS) for apple (Malus domestica). This WGS, v1.0, was valuable as the initial reference for sequence information, fine mapping, gene discovery, variant discovery, and tool development. A new, high quality apple WGS, GDDH13 v1.1, was released in 2017 and now serves as the reference genome for apple. Over the past decade, these apple WGSs have had an enormous impact on our understanding of apple biological functioning, trait physiology and inheritance, leading to practical applications for improving this highly valued crop. Causal gene identities for phenotypes of fundamental and practical interest can today be discovered much more rapidly. Genome-wide polymorphisms at high genetic resolution are screened efficiently over hundreds to thousands of individuals with new insights into genetic relationships and pedigrees. High-density genetic maps are constructed efficiently and quantitative trait loci for valuable traits are readily associated with positional candidate genes and/or converted into diagnostic tests for breeders. We understand the species, geographical, and genomic origins of domesticated apple more precisely, as well as its relationship to wild relatives. The WGS has turbo-charged application of these classical research steps to crop improvement and drives innovative methods to achieve more durable, environmentally sound, productive, and consumer-desirable apple production. This review includes examples of basic and practical breakthroughs and challenges in using the apple WGSs. Recommendations for "what's next" focus on necessary upgrades to the genome sequence data pool, as well as for use of the data, to reach new frontiers in genomics-based scientific understanding of apple.

Germplasm Development of Underutilized Temperate U.S. Tree Crops

In the Midwest U.S. dominated corn-soybean landscape, agroforestry systems can be particularly valuable for increasing the provisioning and regulatory capacity of the agricultural landscape. However, these systems have not yet been broadly integrated into the landscape of this region since they are mostly relegated to marginal lands. A growing body of literature suggests a path to increase the adoption of agroforestry in the Midwest U.S. lies in the incorporation of low-input food-producing tree species that provide economic incentives for farmers. Studies of the system-level integration of such approaches have proceeded by using the currently available cultivars and breeding selections of various tree nut and fruit species. While existing varieties and breeding selections provide the opportunity for initial system development and integration, their broad adaptability to the Midwest U.S. and its marginal land-types is unexplored. Thus, a second tier of research includes the genetic improvement and adaptation of tree crop selections to their respective target environments throughout the Midwest U.S. Fortunately, select tree crops of interest are amendable to systematic breeding and have wild relatives that are endemic across the region. In this paper, we discuss the value of these wild relatives for broadening the adaption of cultivated tree crop selections by using the hazelnut as an example species. We present a framework using geospatial tools to define and prioritize target environments for breeding and, in turn, exploiting wild relative germplasm.

Genetic Mapping of the Incompatibility Locus in Olive and Development of a Linked Sequence-Tagged Site Marker

The genetic control of self-incompatibility (SI) has been recently disclosed in olive. Inter-varietal crossing confirmed the presence of only two incompatibility groups (G1 and G2), suggesting a simple Mendelian inheritance of the trait. A double digest restriction associated DNA (ddRAD) sequencing of a biparental population segregating for incompatibility groups has been performed and high-density linkage maps were constructed in order to map the SI locus and identify gene candidates and linked markers. The progeny consisted of a full-sib family of 229 individuals derived from the cross 'Leccino' (G1) × 'Dolce Agogia' (G2) varieties, segregating 1:1 (G1:G2), in accordance with a diallelic self-incompatibility (DSI) model. A total of 16,743 single nucleotide polymorphisms was identified, 7,006 in the female parent 'Leccino' and 9,737 in the male parent 'Dolce Agogia.' Each parental map consisted of 23 linkage groups and showed an unusual large size (5,680 cM in 'Leccino' and 3,538 cM in 'Dolce Agogia'). Recombination was decreased across all linkage groups in pollen mother cells of 'Dolce Agogia,' the parent with higher heterozygosity, compared to megaspore mother cells of 'Leccino,' in a context of a species that showed exceptionally high recombination rates. A subset of 109 adult plants was assigned to either incompatibility group by a stigma test and the diallelic self-incompatibility (DSI) locus was mapped to an interval of 5.4 cM on linkage group 18. This region spanned a size of approximately 300 Kb in the olive genome assembly. We developed a sequence-tagged site marker in the DSI locus and identified five haplotypes in 57 cultivars with known incompatibility group assignment. A combination of two single-nucleotide polymorphisms (SNPs) was sufficient to predict G1 or G2 phenotypes in olive cultivars, enabling early marker-assisted selection of compatible genotypes and allowing for a rapid screening of inter-compatibility among cultivars in order to guarantee effective fertilization and increase olive production. The construction of high-density linkage maps has led to the development of the first functional marker in olive and provided positional candidate genes in the SI locus.

Population structure, relatedness and ploidy levels in an apple gene bank revealed through genotyping-by-sequencing

In recent years, new genome-wide marker systems have provided highly informative alternatives to low density marker systems for evaluating plant populations. To date, most apple germplasm collections have been genotyped using low-density markers such as simple sequence repeats (SSRs), whereas only a few have been explored using high-density genome-wide marker information. We explored the genetic diversity of the Pometum gene bank collection (University of Copenhagen, Denmark) of 349 apple accessions using over 15,000 genome-wide single nucleotide polymorphisms (SNPs) and 15 SSR markers, in order to compare the strength of the two approaches for describing population structure. We found that 119 accessions shared a putative clonal relationship with at least one other accession in the collection, resulting in the identification of 272 (78%) unique accessions. Of these unique accessions, over half (52%) share a first-degree relationship with at least one other accession. There is therefore a high degree of clonal and family relatedness in the Danish apple gene bank. We find significant genetic differentiation between Malus domestica and its supposed primary wild ancestor, M. sieversii, as well as between accessions of Danish origin and all others. Using the GBS approach allowed us to estimate ploidy levels, which were in accordance with flow cytometry results. Overall, we found strong concordance between analyses based on the genome-wide SNPs and the 15 SSR loci. However, we argue that GBS is superior to traditional SSR approaches because it allows detection of a much more detailed population structure and can be further exploited in genome-wide association studies (GWAS). Finally, we compare GBS with SSR for the purpose of identifying clones and pedigree relations in a diverse apple gene bank and discuss the advantages and constraints of the two approaches.