Tracing the geographic origins of major avocado cultivars

Comprehensive genetic diversity and genome-wide association studies revealed the genetic basis of avocado fruit quality traits

Introduction

Avocado (Persea americana) is a highly nutritious fruit gaining worldwide popularity. However, its cultivation is currently reliant on a limited number of cultivars with restricted genetic diversity. This study aims to investigate the genetic diversity and population structure of avocado germplasm and identify genetic loci associated with key fruit quality traits that influence customer preference.

Methods

A diversity panel of 110 avocado accessions was analyzed using 4,706 high-quality single nucleotide polymorphisms (SNPs). Genetic diversity and population structure were analyzed using pairwise FST, AMOVA, admixture analysis, and phylogenetic analysis. Genome-wide association studies (GWAS) were conducted targeting nine fruit quality traits using two models: General Linear Model (GLM) with Principal Component Analysis (PCA) and Mixed Linear Model (MLM) with PCA and kinship (PCA + K).

Results

The analysis revealed three distinct populations corresponding to the three avocado ecotypes: Guatemalan, West Indian, and Mexican. Phylogenetic analysis indicated a closer relationship between the Guatemalan and West Indian races compared to the Mexican race in our Florida germplasm collection. GWAS led to identification of 12 markers within 11 genomic regions significantly associated with fruit quality traits such as fruit color, shape, taste, and skin texture. These markers explained between 14.84% to 43.96% of the phenotypic variance, with an average of 24.63%. Annotation of these genomic regions unveiled candidate genes potentially responsible for controlling these traits.

Discussion

The findings enhance our understanding of genetic diversity and population structure in avocado germplasm. The identified genetic loci provide valuable insights into the genetic basis of fruit quality traits, aiding breeding programs in developing improved avocado cultivars. Marker-assisted selection can accelerate the development of new varieties, promoting a more diverse and resilient avocado market.

Nyomora A, Joseph CO, Sangu EM, Hormaza JI. Growth and Fruit morphometric characteristics of local avocado germplasm (Persea americana Mill.) grown in northern Tanzania

Tanzania has a diverse agroecological area suitable for growing tropical fruits, including avocados. In Northern Tanzania, avocados have been growing under variable soil and altitudinal characteristics for over 100 years, allowing the naturalisation of this crop in this region. However, the region's avocado germplasm is uncharacterised, thus impeding the selection of elite genotypes for increased value and breeding programmes. This study examined the growth and fruit morphometric characteristics of avocado populations grown under variable soil pH and altitude in six districts in the Tanga, Kilimanjaro and Arusha regions. Variations in growth and fruit morphometric characteristics were compared using a one-way analysis of variance (ANOVA). Pearson product-moment correlations (r) were used to evaluate the relationship between studied growth and fruit morphometric traits. A linear mixed-effects model (LMM) was used to assess the influence of the soil pH, altitude, tree height, canopy diameter, and trunk diameter on fruit length, fruit diameter, pulp thickness, and seed diameter. Principal Component Analysis (PCA) was used to depict the extent of the racial admixtures in the avocado germplasm in the Northern regions of Tanzania. The results revealed a significant variation in growth and fruit morphometric characteristics (p < 0.05). The Korogwe population had the highest tree height, while the Karatu had the lowest. Tree height was positively correlated with the trunk diameter (r = 0.63, p < 0.001. There was a positive correlation between fruit length and pulp thickness (r = 0.51, p < 0.001), fruit diameter and pulp thickness (r = 0.47, p < 0.001), and fruit length and fruit diameter (r = 0.36, p < 0.001). The fruit diameter was positively correlated with the seed diameter (r = 0.61, p < 0.001). There was a significant but weak association between fruit length and trunk diameter (-0.01), fruit length and canopy diameter (0.15), and between seed diameter and tree height (2.95e-2). These findings highlight the influence of individual tree genetic makeup on the variation in growth and fruit morphometric characteristics. The morphometric trait correlations may prove valuable in field measurements, especially when resources are limited. The study further indicates the presence of all avocado races within the local germplasm, highlighting its high diversity. Remarkably, the observed admixture of variant races implies gene flow among studied avocado populations, possibly facilitated by sharing seedlings among farmers or seed disposal through avocado fruit trading. Further study is needed, particularly in quantifying the above-ground biomass of local avocados in northern Tanzania, potentially contributing to carbon credit initiatives for fruit crops..

Diamonds in the not-so-rough: Wild relative diversity hidden in crop genomes

Crop production is becoming an increasing challenge as the global population grows and the climate changes. Modern cultivated crop species are selected for productivity under optimal growth environments and have often lost genetic variants that could allow them to adapt to diverse, and now rapidly changing, environments. These genetic variants are often present in their closest wild relatives, but so are less desirable traits. How to preserve and effectively utilize the rich genetic resources that crop wild relatives offer while avoiding detrimental variants and maladaptive genetic contributions is a central challenge for ongoing crop improvement. This Essay explores this challenge and potential paths that could lead to a solution.

Multiple domestication events explain the origin of Gossypium hirsutum landraces in Mexico

Several Mesoamerican crops constitute wild-to-domesticated complexes generated by multiple initial domestication events, and continuous gene flow among crop populations and between these populations and their wild relatives. It has been suggested that the domestication of cotton (Gossypium hirsutum) started in the northwest of the Yucatán Peninsula, from where it spread to other regions inside and outside of Mexico. We tested this hypothesis by assembling chloroplast genomes of 23 wild, landraces, and breeding lines (transgene-introgressed and conventional). The phylogenetic analysis showed that the evolutionary history of cotton in Mexico involves multiple events of introgression and genetic divergence. From this, we conclude that Mexican landraces arose from multiple wild populations. Our results also revealed that their structural and functional chloroplast organizations had been preserved. However, genetic diversity decreases as a consequence of domestication, mainly in transgene-introgressed (TI) individuals (π = 0.00020, 0.00001, 0.00016, 0, and 0, of wild, TI-wild, landraces, TI-landraces, and breeding lines, respectively). We identified homologous regions that differentiate wild from domesticated plants and indicate a relationship among the samples. A decrease in genetic diversity associated with transgene introgression in cotton was identified for the first time, and our outcomes are therefore relevant to both biosecurity and agrobiodiversity conservation.

Insights into the domestication of avocado and potential genetic contributors to heterodichogamy

The domestication history of the avocado (Persea americana) remains unclear. We created a reference genome from the Gwen varietal, which is closely related to the economically dominant Hass varietal. Our genome assembly had an N50 of 3.37 megabases, a BUSCO score of 91%, and was scaffolded with a genetic map, producing 12 pseudo-chromosomes with 49,450 genes. We used the Gwen genome as a reference to investigate population genomics, based on a sample of 34 resequenced accessions that represented the 3 botanical groups of P. americana. Our analyses were consistent with 3 separate domestication events; we estimated that the Mexican group diverged from the Lowland (formerly known as "West Indian") and Guatemalan groups >1 million years ago. We also identified putative targets of selective sweeps in domestication events; within the Guatemalan group, putative candidate genes were enriched for fruit development and ripening. We also investigated divergence between heterodichogamous flowering types, providing preliminary evidence for potential candidate genes involved in pollination and floral development.

Antibiotics Resistant Pattern of Bacteria Isolated from Spoiled Avocado Fruit Sold in Sokoto Metropolis

Consuming fruit contaminated with bacteria remains a crucial route of foodborne infection in developing countries and creates a severe public health burden. The research aimed to determine the antibiotic-resistant pattern of bacteria associated with the spoilage of Avocado pear (Persea americana) sold in the Sokoto metropolis. Twenty spoilt avocado fruits were obtained from market three in Sokoto Metropolis. The bacteriological analysis was carried out using the pour plate method. The antibiotic resistance pattern was determined using the Kirby-Bauer disk diffusion method. A total of five species of bacteria were isolated and identified in this study. The mean and standard error of total viable bacterial counts of avocado samples across three different locations ranged from 4.20±5.77 to 8.43±33.49 (x 104CFU/g). A total of 19 bacterial isolates were identified from avocado samples. Staphylococcus aureus had the highest frequency of occurrence, 16 (29.2%), while Klebsiella sp. had the lowest frequency of occurrence, 7 (12.7%). Among all antibiotics tested against bacterial species, Escherichia coli isolates were found to have 10 (91%) and 9 (82%) resistance against ciprofloxacin and streptomycin, respectively. Pseudomonas sp. was found to be 100% resistant to chloramphenicol and Septrin (cotrimoxazole). However, S. aureus was found to have 12 (72%) resistance to pefloxacin. Similarly, Klebsiella spp. were found to be 7 (100%) resistant to Septrin. Isolation of these bacterial species, especially E. coli from avocado samples analyzed, is of public health significance, especially the presence of antibiotic resistance species.

Structural Disparity of Avocado Rootstocks In Vitro for Rooting and Acclimation Success

Improving clonal rootstock propagation of avocado has been a major industry/research challenge globally for many decades. Tissue culture has been a focus for clonal propagation with substantial advancements in recent years. In the process of tissue culture, avocado rootstocks display differences in rooting and acclimation capacity. Such differences may relate to the specific structural characteristics of the rootstock. This study aimed to investigate the structural difference during tissue culture in two rootstocks ‘Reed’ and ‘Velvick’, with differing rooting and acclimation capacity. Histological investigations were carried out of stem vasculature, leaves and roots of tissue cultured plantlets. Quantitative parameters; stomatal index, stomatal density, trichome density, vein-islet density and vein termination density were also analysed. Prominent fascicular cambium and fewer phloem fibres in stems positively correlated with rooting capacity. Acclimation success positively correlated to the presence of fully differentiated secondary xylem in root. Presence of smaller epidermal cells, high stomatal density and reduced vein termination density was associated with reduced acclimation success. These findings will support optimisation strategies for micropropagation of not only difficult-to-root and difficult-to-acclimate avocado rootstocks, but also, other woody perennials experiencing similar problems.

Prolonged on-tree maturation vs. cold storage of Hass avocado fruit: Changes in metabolites of bioactive interest at edible ripeness

When the recipient of the product is relatively distant from the production area, it is necessary to use cold storage and controlled humidity to transport the avocado fruits. One of the main advantages of local avocado consumption lies on the possibility of prolonging on-tree maturation; this could foreseeably modify the metabolic profile of the fruit that reaches the consumer. In this work, the effect of prolonged on tree maturation (during different time intervals) on the final composition of avocado fruit (at edible ripeness) was evaluated and compared with the impact of the same periods after prolonged cold storage. The quantitative evolution of nine bioactive metabolites (7 phenolic compounds, pantothenic and abscisic acids) over 40 days (10-days intervals) was studied by using a solid-liquid extraction protocol and a LC-MS methodology. The results were discussed both considering the quantitative evolution of each individual compound and the sum of all of them.

Tropical bee species abundance differs within a narrow elevational gradient

Insect pollination is among the most essential ecosystem services for humanity. Globally, bees are the most effective pollinators, and tropical bees are also important for maintaining tropical biodiversity. Despite their invaluable pollination service, basic distributional patterns of tropical bees along elevation gradients are globally scarce. Here, we surveyed bees at 100 m elevation intervals from 800 to 1100 m elevation in Costa Rica to test if bee abundance, community composition and crop visitor assemblages differed by elevation. We found that 18 of 24 bee species spanning three tribes that represented the most abundantly collected bee species showed abundance differences by elevation, even within this narrow elevational gradient. Bee assemblages at the two crop species tested, avocado and squash, showed community dissimilarity between high and low elevations, and elevation was a significant factor in explaining bee community composition along the gradient. Stingless bees (Tribe Meliponini) were important visitors to both crop species, but there was a more diverse assemblage of bees visiting avocado compared to squash. Our findings suggest that successful conservation of tropical montane bee communities and pollination services will require knowledge of which elevations support the highest numbers of each species, rather than species full altitudinal ranges.

Implications of the foliar phytochemical diversity of the avocado crop Persea americana cv. Hass in its susceptibility to pests and pathogens

Phytochemical diversity (PD) can be considered as a defensive trait; it can operate through single plant secondary metabolites or usually as complex mixtures of them. We tested the more diversity-better defense hypothesis correlating the leaf plant secondary metabolites (PSMs) with the incidence of plant enemies on Hass avocado trees. We expected a negative correlation between the occurrence of plant enemies and PD metrics. Also, as intraspecific PSMs polymorphisms in plant populations are common, we studied the incidence of plant enemies on Hass avocado trees representing chemical variants (chemotypes). We expected a differential incidence of plant enemies among trees grouped by their mono and sesquiterpene + phenylpropanoid chemotypes. We analyzed foliar hexane extracts from 236 trees in 17 orchards by gas chromatography and for the incidence of red mite, thrips, whitefly, avocado branch borer, fruit rot, scab, and peduncle collar blight. The predicted negative correlation between the plant enemies’ incidence and the phytochemical metrics did not occur. To determine the relationship between enemy incidence and chemotypes we grouped the trees by cluster analysis using a matrix of PSMs in each tree. Most trees were grouped under four out of 23 chemotypes. Branch borers attacked trees of low-frequency chemotypes more frequently than trees with common chemotypes. The incidence of five plant enemies was different among the predominant chemotypes. The hypothesis of more diversity-better defense was not supported by the correlations between the phytochemical diversity and the incidence of pests and pathogens in Hass avocado orchards. Based on our results, we hypothesize that phytochemical diversity function as a defensive trait relies more on differentiation among individuals in a population than on the sole increase of chemical diversity. Also, the differential incidence of pests and pathogens on trees classified by their foliar chemotypes implies that these susceptibility or resistance markers represent potential useful tools for Hass avocado orchard pest management.

Cryopreservation of Woody Crops: The Avocado Case

Recent development and implementation of crop cryopreservation protocols has increased the capacity to maintain recalcitrant seeded germplasm collections via cryopreserved in vitro material. To preserve the greatest possible plant genetic resources globally for future food security and breeding programs, it is essential to integrate in situ and ex situ conservation methods into a cohesive conservation plan. In vitro storage using tissue culture and cryopreservation techniques offers promising complementary tools that can be used to promote this approach. These techniques can be employed for crops difficult or impossible to maintain in seed banks for long-term conservation. This includes woody perennial plants, recalcitrant seed crops or crops with no seeds at all and vegetatively or clonally propagated crops where seeds are not true-to-type. Many of the world's most important crops for food, nutrition and livelihoods, are vegetatively propagated or have recalcitrant seeds. This review will look at ex situ conservation, namely field repositories and in vitro storage for some of these economically important crops, focusing on conservation strategies for avocado. To date, cultivar-specific multiplication protocols have been established for maintaining multiple avocado cultivars in tissue culture. Cryopreservation of avocado somatic embryos and somatic embryogenesis have been successful. In addition, a shoot-tip cryopreservation protocol has been developed for cryo-storage and regeneration of true-to-type clonal avocado plants.

Research Progress in Plant Molecular Systematics of Lauraceae

Simple Summary

Lauraceae, as an angiosperm group with high ecological and economic value, has been widely studied. With the development of science and technology, the research of Lauraceae has changed from morphology to molecular systematics. Our paper reviewed the molecular phylogeny of Lauraceae in recent years. From the aspects of gene fragments, chloroplast genome and DNA barcodes, we mainly discussed the establishment of Cinnamomeae in the ‘Core Lauraceae’ and the tribal controversial genera (Actinodaphne, Sassafras, Caryodaphnopsis, Neocinnamomum and Cassytha). We think that the whole genome and inflorescence characteristics are the breakthrough to solve the tribal problem of Lauraceae. Using reliable molecular and morphological evidence to reconstruct the phylogenetic relationship of Lauraceae will provide an important theoretical basis for the rational utilization of Lauraceae resources, the development of potential resources and the protection of rare plants.

Abstract

Lauraceae is a large family of woody plants with high ecological and economic value. The tribal and generic division and phylogenetic relationship of Lauraceae have long been controversial. Based on morphological and molecular evidence, phylogenetic relationships within the Cinnamomeae, Laureae and Perseeae tribes, also called ‘the Core Lauraceae’, have arisen particular attention. In this review, we comprehensively collated the literatures on the phylogeny of Lauraceae published in recent years and summarized progress made in molecular systematic researches employing gene fragments, chloroplast genomes and DNA barcodings analyses. We clarified the phylogenetic relationships and main controversies of ‘the Core Lauraceae’, the systemic position of fuzzy genera (Neocinnamomum, Caryodaphnopsis and Cassytha) and the development of chloroplast genome and DNA barcodes. We further suggested and proposed the whole genome analysis and different inflorescence types would be possible to provide more information for further research on phylogenetic relationships and taxonomy of Lauraceae.

Two Oleosins Expressed in the Mesocarp of Native Mexican Avocado, Key Genes in the Oil Content

Intracellular lipid droplets (LD) provide the oil storage mechanism of plants. They are found within seeds as individual structures, even under conditions of cold stress and dehydration, due to the protein that covers them. This protein, called oleosin, is found exclusively in plants and has been widely studied in seeds. Avocado fruits (Persea americana Mill.) are rich in oil, which is stored in the mesocarp, not in the seeds. The presence of oleosin in the mesocarp tissue of avocadoes has been reported, but its physiological role is still unknown. In this study, we identify two genes that code for oleosin in the mesocarp of the native Mexican avocado. These sequences are very different from those of seed oleosins. Both genes are expressed during fruit ripening, while one, PaOle1, has the highest expression in the green fruit stage. The protein of PaOle1 is stable during the fruit ripening process and covers all the mesocarp LDs. The expression of PaOle1 gene and protein is organ specific to avocado mesocarp. Among avocadoes varieties oleosin abundance is directly related to oil content.

The Effects of Avocado Waste and Its Functional Compounds in Animal Models on Dyslipidemia Parameters

Ischemic heart disease and stroke are two main causes of death that have prevailed for more than 15 years. Dyslipidemia and its parameters like hypercholesterolemia, hypertriglyceridemia, increase in low-density cholesterol, and a reduction of high-density cholesterol have been related with heart disease and risk of stroke. Approaches to improve the health and specifically reduce the risk of heart disease, such as medications and dietary interventions have been effective, but there are other potential sources of biological compounds that could have an effect due to their antioxidant properties. Avocado is a commonly consumed fruit especially its pulp, while the peel, seed, and leaf are usually discarded as waste. Some researchers have reported antioxidant, hepatoprotective, gastroprotective, lipid-lowering, and hypoglycemic effects in these wastes. In this review article, we have summarized the current evidence on the effect of biological compounds from avocado waste on dyslipidemia parameters in preclinical models. Also, we have included the compound extracted and the extraction method from the selected articles.

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.

Phenolic Compounds in Mesoamerican Fruits-Characterization, Health Potential and Processing with Innovative Technologies

Diets rich in phenolic compounds have been associated to reducing the risk of metabolic syndrome and its derived disorders. Fruits are healthy components of the human diet because of their vitamin, mineral, fiber and phenolic profile. However, they have a short shelf-life which is limited by microbiological growth and enzymatic activity. Innovative preservation methods such as high hydrostatic pressure, pulsed electric fields, ultrasound, microwave, cold plasma and ultraviolet light have become popular for the processing of fruits because they can preserve nutritional quality. In this review, the phenolic profile and health potential of 38 Mesoamerican fruits were assessed. Phenolic compounds were classified based on their contribution to the diet as flavonoids, phenolic acids, tannin, lignins and stilbenoids. Due to this composition, fruits showed a wide range of bioactivities which included anti-inflammatory, anti-diabetic, anti-hypertensive and anti-obesity activities, among others. Phenolic content in fruits submitted to innovative food processing technologies depended on parameters such as enzymatic activity, antioxidant capacity, microstructure integrity and cell viability. Innovative technologies could increase phenolic content while assuring microbiological safety by (i) promoting the release of bound phenolic compounds during processing and (ii) inducing the synthesis of phenolic compounds by activation of phenylpropanoid pathway during storage.

Mitigation of the Adverse Effects of the El Niño (El Niño, La Niña) Southern Oscillation (ENSO) Phenomenon and the Most Important Diseases in Avocado cv. Hass Crops

Areas cultivated with Hass avocado crops in Colombia have growth rapidly. One of the major limitations is the avocado wilt complex disease (AWC) caused by biotic and abiotic factors which have increased under the El Niño southern oscillation ENSO phenomenon (El Niño, La Niña). The objective of this study was to evaluate different strategies for mitigating the adverse effects associated with the ENSO phenomenon and AWC in avocado crops. We evaluated native materials, mulches, and parameters associated with the production of seedlings and planting practices in the field. The response variables tested were plant development, incidence, severity, mortality, and microbial dynamics, among others. The results indicated that native genotypes of Persea americana had different levels of adaptability to drought and flooding conditions. These genotypes also showed some degree of resistance to Phytophthora cinnamomi and Verticillium sp. infection with several degrees of rootstock-scion incompatibility with the Hass cultivar. In addition, mulch reduced the variability of soil moisture and temperature in the soil profile. Adequate selection of genotypes and new tools for planting have decreased the susceptibility to adverse effects associated with the ENSO phenomenon and the incidence and mortality caused by diseases under drought and flooding conditions. This work presents alternatives to mitigate adverse effects of climate variability in avocado crops under tropical conditions.

Avocado crops as a floral resource for native bees of Chile

Background

Chile is the second largest avocado producer in the world. However, there have been few studies on interactions between native bees and avocado pollination in a Chilean environment. The flowering period of avocado is very sensitive to temperature fluctuations and so environmental conditions, particularly cool temperatures, can have a strong influence on its floral behaviour. Thus, we aimed to determine whether temperature also influences bee visitation rates to avocado flowers or if this was due to the number of available flowers. Moreover, we proposed to verify the attractiveness of avocado flowers to native bees and compare flower handling time and type of floral resource collected between managed and native bees.

Methods

An avocado orchard of “Hass” cultivar located in the Mediterranean region of Chile was studied during the flowering season of 2016. The frequency of exotic and native bee species in flowers, floral phenology, and environmental temperature were analysed, and the foraging behaviours of exotic and native bee species in avocado flowers compared.

Results

Five Chilean native and two exotic species were recorded visiting avocado flowers at the studied orchard. The bees generally sought nectar rather than pollen. The European honeybee (Apis mellifera) was the most frequent flower visitor, followed by the native species Colletes cyanescens and Cadeguala occidentalis. There was a strong positive correlation between temperature and number of visits, but no significant correlation between number of open flowers and number of visits.

Conclusions

Native Chilean bees visited avocado flowers and some of them were frequent floral visitors. They generally sought for nectar rather than pollen and were as fast as honeybees handling avocado flowers. The environmental temperature plays a key role in the frequency of bees in avocado flowers. The warmer weather is related to the higher number of bees visits to avocado flowers.

Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)

Modern crop breeding is based on the use of genetically and phenotypically diverse plant material and, consequently, a proper understanding of population structure and genetic diversity is essential for the effective development of breeding programs. An example is avocado, a woody perennial fruit crop native to Mesoamerica with an increasing popularity worldwide. Despite its commercial success, there are important gaps in the molecular tools available to support on-going avocado breeding programs. In order to fill this gap, in this study, an avocado 'Hass' draft assembly was developed and used as reference to study 71 avocado accessions which represent the three traditionally recognized avocado horticultural races or subspecies (Mexican, Guatemalan and West Indian). An average of 5.72 M reads per individual and a total of 7,108 single nucleotide polymorphism (SNP) markers were produced for the 71 accessions analyzed. These molecular markers were used in a study of genetic diversity and population structure. The results broadly separate the accessions studied according to their botanical race in four main groups: Mexican, Guatemalan, West Indian and an additional group of Guatemalan × Mexican hybrids. The high number of SNP markers developed in this study will be a useful genomic resource for the avocado community.

Vegetable butters and oils in skin wound healing: Scientific evidence for new opportunities in dermatology

The use of vegetable butters and oils shows promising results in the treatment of skin wounds, as they have an effective impact on the phases of the wound-healing process through their antimicrobial, anti-inflammatory, and antioxidative activities and by promoting cell proliferation, increasing collagen synthesis, stimulating dermal reconstruction, and repairing the skin's lipid barrier function. In this article, in vitro and in vivo studies of argan (Argania spinosa), avocado (Persea americana), black cumin (Nigella sativa), calophyllum (Calophyllum inophyllum), coconut (Cocos nucifera), cranberry (Vaccinium macrocarpon), grape (Vitis vinifera), green coffee (Coffea arabica), lentisk (Pistacia lentiscus), linseed (Linum usitatissimum), lucuma (Pouteria lucuma), mango (Mangifera indica), olive (Olea europaea), pomegranate (Punica granatum), pumpkin (Cucurbita pepo), rapeseed (Brassica napus), sea buckthorn (Hippophae rhamnoides), and sunflower (Helianthus annuus) oils were reviewed. In many cases, vegetable oils proved to be more effective than synthetic wound-healing compounds used as controls. The fatty-acid components of vegetable oils are assumed to play a major role in the wound-healing process, in particular polyunsaturated fatty acids such as linoleic acid. Evidence shows that oils with a higher linoleic to oleic acid ratio are more effective for lipid barrier repair. However, in depth studies are needed to gain knowledge about vegetable oils' effects on the skin and vice versa.

The avocado genome informs deep angiosperm phylogeny, highlights introgressive hybridization, and reveals pathogen-influenced gene space adaptation

The avocado is a nutritious, economically important fruit species that occupies an unresolved position near the earliest evolutionary branchings of flowering plants. Our nuclear genome sequences of Mexican and Hass variety avocados inform ancient evolutionary relationships and genome doublings and the admixed nature of Hass and provide a look at how pathogen interactions have shaped the avocado’s more recent genomic evolutionary history.

The avocado, Persea americana, is a fruit crop of immense importance to Mexican agriculture with an increasing demand worldwide. Avocado lies in the anciently diverged magnoliid clade of angiosperms, which has a controversial phylogenetic position relative to eudicots and monocots. We sequenced the nuclear genomes of the Mexican avocado race, P. americana var. drymifolia, and the most commercially popular hybrid cultivar, Hass, and anchored the latter to chromosomes using a genetic map. Resequencing of Guatemalan and West Indian varieties revealed that ∼39% of the Hass genome represents Guatemalan source regions introgressed into a Mexican race background. Some introgressed blocks are extremely large, consistent with the recent origin of the cultivar. The avocado lineage experienced 2 lineage-specific polyploidy events during its evolutionary history. Although gene-tree/species-tree phylogenomic results are inconclusive, syntenic ortholog distances to other species place avocado as sister to the enormous monocot and eudicot lineages combined. Duplicate genes descending from polyploidy augmented the transcription factor diversity of avocado, while tandem duplicates enhanced the secondary metabolism of the species. Phenylpropanoid biosynthesis, known to be elicited by Colletotrichum (anthracnose) pathogen infection in avocado, is one enriched function among tandems. Furthermore, transcriptome data show that tandem duplicates are significantly up- and down-regulated in response to anthracnose infection, whereas polyploid duplicates are not, supporting the general view that collections of tandem duplicates contribute evolutionarily recent “tuning knobs” in the genome adaptive landscapes of given species.

Neuroprotective Effects of Methanolic Extract of Avocado Persea americana (var. Colinred) Peel on Paraquat-Induced Locomotor Impairment, Lipid Peroxidation and Shortage of Life Span in Transgenic knockdown Parkin Drosophila melanogaster

Parkinson's disease (PD) is a progressive neurodegenerative disorder associated with oxidative stress. Therefore, finding new antioxidant sources might be beneficial for its treatment. Avocado Persea americana is a fruit widely cultivated in tropical and subtropical climates worldwide. Although avocado by-products in the form of peel, seed coat and seeds are currently of no commercial use, they constitute a natural source of bioactive compounds. Methanolic (80%) extract obtained from lyophilized ground peels, seed coats, and seeds of the avocado Hass, Fuerte, Reed and Colinred varieties were analyzed for their total phenolic content (TPC) and their correlations with antioxidant capacity (AC) were assessed by ABTS, FRAP, and ORAC assays. For all varieties, the var. Colinred peel shows the highest TPC and AC. Further analysis showed that the var. Colinred peel presented major phenolic compounds B-type procyanidins and epicatechin according to HPLC-MS. The antioxidant effect of peel extract was evaluated upon in vivo oxidative stress (OS) model. We show for the first time that the peel extract can protect and/or prevent transgenic parkinDrosophila melanogaster fly against paraquat-induced OS, movement impairment and lipid peroxidation, as model of PD. Our findings offer an exceptional opportunity to test natural disease-modifying substances from avocado's by-products.

Genetic diversity of avocado (Persea americana Mill.) germplasm using pooled sequencing

Background

Discovering a genome-wide set of avocado (Persea americana Mill.) single nucleotide polymorphisms and characterizing the diversity of germplasm collection is a powerful tool for breeding. However, discovery is a costly process, due to loss of loci that are proven to be non-informative when genotyping the germplasm.

Results

Our study on a collection of 100 accessions comprised the three race types, Guatemalan, Mexican, and West Indian. To increase the chances of discovering polymorphic loci, three pools of genomic DNA, one from each race, were sequenced and the reads were aligned to a reference transcriptome. In total, 507,917 polymorphic loci were identified in the entire collection. Of these, 345,617 were observed in all three pools, 117,692 in two pools, 44,552 in one of the pools, and only 56 (0.0001%) were homozygous in the three pools but for different alleles. The polymorphic loci were validated using 192 randomly selected SNPs by genotyping the accessions within each pool. The sensitivity of polymorphic locus prediction ranged from 0.77 to 0.94. The correlation between the allele frequency estimated from the pooled sequences and actual allele frequency from genotype calling of individual accessions was r = 0.8. A subset of 109 SNPs were then used to evaluate the genetic relationships among avocado accessions and the genetic diversity of the collection. The three races were distinctly clustered by projecting the genetic variation on a PCA plot. As expected, by estimating the kinship coefficient for all the accessions, many of the cultivars from the California breeding program were closely related to each other, especially, the Hass-like ones. The green-skin avocados, e.g., ‘Bacon’, ‘Zutano’, ‘Ettinger’ and ‘Fuerte’ were also closely related to each other.

Conclusions

A framework for SNP discovery and genetically characterizing of a breeder‘s accessions was described. Sequencing pools of gDNA is a cost-effective approach to create a genome-wide stock of polymorphic loci for a breeding program. Reassessing the botanical and the genetic knowledge about the germplasm accessions is valuable for future breeding. Kinship analysis may be used as a first step in finding a parental candidates in a parentage analyses.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5672-7) contains supplementary material, which is available to authorized users.

Transcriptome Sequencing of Different Avocado Ecotypes: de novo Transcriptome Assembly, Annotation, Identification and Validation of EST-SSR Markers

Avocado (Persea americana Mill.) could be considered as an important tropical and subtropical woody oil crop with high economic and nutritional value. Despite the importance of this species, genomic information is currently unavailable for avocado and closely related congeners. In this study, we generated more than 216 million clean reads from different avocado ecotypes using Illumina HiSeq high-throughput sequencing technology. The high-quality reads were assembled into 154,310 unigenes with an average length of 922 bp. A total of 55,558 simple sequence repeat (SSR) loci detected among the 43,270 SSR-containing unigene sequences were used to develop 74,580 expressed sequence tag (EST)-SSR markers. From these markers, a subset of 100 EST-SSR markers was randomly chosen to identify polymorphic EST-SSR markers in 28 avocado accessions. Sixteen EST-SSR markers with moderate to high polymorphism levels were detected, with polymorphism information contents ranging from 0.33 to 0.84 and averaging 0.63. These 16 polymorphic EST-SSRs could clearly and effectively distinguish the 28 avocado accessions. In summary, our study is the first presentation of transcriptome data of different avocado ecotypes and comprehensive study on the development and analysis of a set of EST-SSR markers in avocado. The application of next-generation sequencing techniques for SSR development is a potentially powerful tool for genetic studies.

Genome-Wide Assessment of Avocado Germplasm Determined from Specific Length Amplified Fragment Sequencing and Transcriptomes: Population Structure, Genetic Diversity, Identification, and Application of Race-Specific Markers

Genomic data is a powerful tool. However, the phylogenetic relationships among different ecological races of avocado remain unclear. Here, we used the results from specific length amplified fragment sequencing (SLAF-seq) and transcriptome data to infer the population structure and genetic diversity of 21 avocado cultivars and reconstructed the phylogeny of three ecological races and two interracial hybrids. The results of the three analyses performed (unweighted pair-group methods with arithmetic means (UPGMA) cluster, Principal coordinate analysis (PCoA), and STRUCTURE) based on single nucleotide polymorphisms (SNPs) from SLAF-seq all indicated the existence of two populations based on botanical race: Mexican–Guatemalan and West Indian genotype populations. Our results based on SNPs from SLAF-seq indicated that the Mexican and Guatemalan races were more closely related to each other than either was to the West Indian race, which also was confirmed in the UPGMA cluster results based on SNPs from transcriptomic data. SNPs from SLAF-seq provided strong evidence that the Guatemalan, Mexican, and Guatemalan × Mexican hybrid accession possessed higher genetic diversity than the West Indian races and Guatemalan × West Indian hybrid accessions. Six race-specific Kompetitive allele specific PCR (KASP) markers based on SNPs from SLAF-seq were then developed and validated.

Spatial Distribution of Bactrocera dorsalis and Thaumatotibia leucotreta in Smallholder Avocado Orchards along Altitudinal Gradient of Taita Hills and Mount Kilimanjaro

Avocado (Persea americana) fruits are an important source of income and a nutritious food for small-scale growers and other stakeholders involved in farming along the Afrotropical highlands of Taita Hills and Mount Kilimanjaro in Kenya and Tanzania, respectively. Avocado fruits are infested by several insect pests, namely the Asian invasive fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), and the false codling moth, Thaumatotibia leucotreta Meyrick (Lepidoptera: Tortricidae). However, there is inadequate information on the distribution patterns of these pests in small-scale avocado cropping systems in the East African highlands. This study was initiated to generate a spatial distribution map of B. dorsalis and T. leucotreta in avocado orchards at Taita Hills and Mount Kilimanjaro in Kenya and Tanzania, respectively. The two pests were monitored by using their respective parapheromone lures for two years between August 2012 and July 2014. Fruit damage was assessed by computing the proportion of infested fruits for B. dorsalis, whereas the damage score was used for T. leucotreta. Our results indicated that the mean number of B. dorsalis per trap per day differed significantly across elevation, being highest in lowland zone for both Taita Hills (15.90) and Mount Kilimanjaro (24.45). Similarly, the percentage infestation of ground collected fruits by B. dorsalis varied with altitude, being lowest at highlands above 1500 m.a.s.l. (0.66% and 0.83% for Taita Hills and Mount Kilimanjaro, respectively). Conversely, the mean number of T. leucotreta did not vary with altitude in either study area. However, the damage score for T. leucotreta infestation was significantly lower in the highlands of both transects (7.0% and11.1% for Taita Hills and Mount Kilimanjaro, respectively). These findings describe spatial trends that are important in formulating strategies aimed at suppressing the populations of B. dorsalis and T. leucotreta in East African avocado cropping systems.

A Mesoamerican origin of cherimoya (Annona cherimola Mill.): Implications for the conservation of plant genetic resources

Knowledge on the structure and distribution of genetic diversity is a key aspect to plan and execute an efficient conservation and utilization of the genetic resources of any crop as well as for determining historical demographic inferences. In this work, a large data set of 1,765 accessions of cherimoya (Annona cherimola Mill, Annonaceae), an underutilized fruit tree crop native to the Neotropics and used as a food source by pre-Columbian cultures, was collected from six different countries across the American continent and amplified with nine highly informative microsatellite markers. The structure analyses, fine representation of the genetic diversity and an ABC approach suggest a Mesoamerican origin of the crop, contrary to previous reports, with clear implications for the dispersion of plant germplasm between Central and South America in pre-Columbian times. These results together with the potential distribution of the species in a climatic change context using two different climate models provide new insights for the history and conservation of extant genetic resources of cherimoya that can be applied to other currently underutilized woody perennial crops.

Genetic Structure and Selection of a Core Collection for Long Term Conservation of Avocado in Mexico

Mexico, as the center of origin of avocado (Persea americama Mill.), harbors a wide genetic diversity of this species, whose identification may provide the grounds to not only understand its unique population structure and domestication history, but also inform the efforts aimed at its conservation. Although molecular characterization of cultivated avocado germplasm has been studied by several research groups, this had not been the case in Mexico. In order to elucidate the genetic structure of avocado in Mexico and the sustainable use of its genetic resources, 318 avocado accessions conserved in the germplasm collection in the National Avocado Genebank were analyzed using 28 markers [9 expressed sequence tag-Simple Sequence Repeats (SSRs) and 19 genomic SSRs]. Deviation from Hardy Weinberg Equilibrium and high inter-locus linkage disequilibrium were observed especially in drymifolia, and guatemalensis. Total averages of the observed and expected heterozygosity were 0.59 and 0.75, respectively. Although clear genetic differentiation was not observed among 3 botanical races: americana, drymifolia, and guatemalensis, the analyzed Mexican population can be classified into two groups that correspond to two different ecological regions. We developed a core-collection by K-means clustering method. The selected 36 individuals as core-collection successfully represented more than 80% of total alleles and showed heterozygosity values equal to or higher than those of the original collection, despite its constituting slightly more than 10% of the latter. Accessions selected as members of the core collection have now become candidates to be introduced in cryopreservation implying a minimum loss of genetic diversity and a back-up for existing field collections of such important genetic resources.

Genome-wide view of genetic diversity reveals paths of selection and cultivar differentiation in peach domestication

Domestication and cultivar differentiation are requisite processes for establishing cultivated crops. These processes inherently involve substantial changes in population structure, including those from artificial selection of key genes. In this study, accessions of peach (Prunus persica) and its wild relatives were analysed genome-wide to identify changes in genetic structures and gene selections associated with their differentiation. Analysis of genome-wide informative single-nucleotide polymorphism loci revealed distinct changes in genetic structures and delineations among domesticated peach and its wild relatives and among peach landraces and modern fruit (F) and modern ornamental (O-A) cultivars. Indications of distinct changes in linkage disequilibrium extension/decay and of strong population bottlenecks or inbreeding were identified. Site frequency spectrum- and extended haplotype homozygosity-based evaluation of genome-wide genetic diversities supported selective sweeps distinguishing the domesticated peach from its wild relatives and each F/O-A cluster from the landrace clusters. The regions with strong selective sweeps harboured promising candidates for genes subjected to selection. Further sequence-based evaluation further defined the candidates and revealed their characteristics. All results suggest opportunities for identifying critical genes associated with each differentiation by analysing genome-wide genetic diversity in currently established populations. This approach obviates the special development of genetic populations, which is particularly difficult for long-lived tree crops.

Genomics and the Contrasting Dynamics of Annual and Perennial Domestication

Plant domestication modifies a wild species genetically for human use. Among thousands of domesticated plants, a major distinction is the difference between annual and perennial life cycles. The domestication of perennials is expected to follow different processes than annuals, with distinct genetic outcomes. Here we examine domestication from a population genetics perspective, with a focus on three issues: genetic bottlenecks during domestication, introgression as a source of local adaptation, and genetic load. These three issues have been studied nominally in major annual crops but even less extensively in perennials. Here we highlight lessons from annual plants, motivations to study these issues in perennial plants, and new approaches that may lead to further progress.

Resequencing data indicate a modest effect of domestication on diversity in barley: a cultigen with multiple origins

The levels of diversity and extent of linkage disequilibrium in cultivated species are largely determined by diversity in their wild progenitors. We report a comparison of nucleotide sequence diversity in wild and cultivated barley (Hordeum vulgare ssp. spontaneum and ssp. vulgare) at 7 nuclear loci totaling 9296bp, using sequence from Hordeum bulbosum to infer the ancestral state of mutations. The sample includes 36 accessions of cultivated barley, including 23 landraces (cultivated forms not subject to modern breeding) and 13 cultivated lines and genetic stocks compared to either 25 or 45 accessions of wild barley for the same loci. Estimates of nucleotide sequence diversity indicate that landraces retain >80% of the diversity in wild barley. The primary population structure in wild barley, which divides the species into eastern and western populations, is reflected in significant differentiation at all loci in wild accessions and at 3 of 7 loci in landraces. "Oriental" landraces have slightly higher diversity than "Occidental" landraces. Genetic assignment suggests more admixture from Occidental landraces into Oriental landraces than the converse, which may explain this difference. Based on θπ for silent sites, modern western cultivars have ~73% of the diversity found in landraces and ~71% of the diversity in wild barley.

Tracing the geographic origins of weedy Ipomoea purpurea in the southeastern United States

Ipomoea purpurea (common morning glory) is an annual vine native to Mexico that is well known for its large, showy flowers. Humans have spread morning glories worldwide, owing to the horticultural appeal of morning glory flowers. Ipomoea purpurea is an opportunistic colonizer of disturbed habitats including roadside and agricultural settings, and it is now regarded as a noxious weed in the Southeastern US. Naturalized populations in the Southeastern United States are highly polymorphic for a number of flower color morphs, unlike native Mexican populations that are typically monomorphic for the purple color morph. Although I. purpurea was introduced into the United States from Mexico, little is known about the specific geographic origins of US populations relative to the Mexican source. We use resequencing data from 11 loci and 30 I. purpurea accessions collected from the native range of the species in Central and Southern Mexico and 8 accessions from the Southeastern United States to infer likely geographic origins in Mexico. Based on genetic assignment analysis, haplotype composition, and the degree of shared polymorphism, I. purpurea samples from the Southeastern United States are genetically most similar to samples from the Valley of Mexico and Veracruz State. This supports earlier speculation that I. purpurea in the Southeastern United States was likely to have been introduced by European colonists from sources in Central Mexico.

Nucleotide sequence diversity of floral pigment genes in Mexican populations of Ipomoea purpurea (morning glory) accord with a neutral model of evolution

The common morning glory (Ipomoea purpurea) is an annual vine native to Central and Southern Mexico. The genetics of flower color polymorphisms and interactions with the biotic environment have been extensively studied in I. purpurea and in its sister species I. nil. In this study, we examine nucleotide sequence polymorphism in 11 loci, 9 of which are known to participate in a pathway that produces floral pigments. A sample of 30 I. purpurea accessions from the native range of Central and Southern Mexico comprise the data, along with one accession from each of the two sister species I. alba and I. nil. We observe moderate levels of nucleotide sequence polymorphism of ~1%. The ratio of recombination to mutation parameter estimates (ρ/θ) of ~2.5 appears consistent with a mixed-mating system. Ipomoea resequencing data from these genic regions are noteworthy in providing a good fit to the standard neutral model of molecular evolution. The derived silent site frequency spectrum is very close to that predicted by coalescent simulations of a drift-mutation process, and Tajima's D values are not significantly different from expectations under neutrality.

New insight into the history of domesticated apple: secondary contribution of the European wild apple to the genome of cultivated varieties

The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species.

Avocado (Persea americana Mill.) phenolics, in vitro antioxidant and antimicrobial activities, and inhibition of lipid and protein oxidation in porcine patties

The first aim of the present work (study 1) was to analyze ethyl acetate, 70% acetone, and 70% methanol extracts of the peel, pulp, and seed from two avocado (Persea americana Mill.) varieties, namely, 'Hass' and 'Fuerte', for their phenolic composition and their in vitro antioxidant activity using the CUPRAC, DPPH, and ABTS assays. Their antimicrobial potential was also studied. Peels and seeds had higher amounts of phenolics and a more intense in vitro antioxidant potential than the pulp. Peels and seeds were rich in catechins, procyanidins, and hydroxycinnamic acids, whereas the pulp was particularly rich in hydroxybenzoic and hydroxycinnamic acids and procyanidins. The total phenolic content and antioxidant potential of avocado phenolics was affected by the extracting solvent and avocado variety. The avocado materials also displayed moderate antimicrobial effects against Gram-positive bacteria. Taking a step forward (study 2), extracts (70% acetone) from avocado peels and seeds were tested as inhibitors of oxidative reactions in meat patties. Avocado extracts protected meat lipids and proteins against oxidation with the effect on lipids being dependent on the avocado variety.

Historical divergence and gene flow in the genus Zea

Gene flow plays a fundamental role in plant evolutionary history, yet its role in population divergence--and ultimately speciation--remains poorly understood. We investigated gene flow and the modalities of divergence in the domesticated Zea mays ssp. mays and three wild Zea taxa using sequence polymorphism data from 26 nuclear loci. We described diversity across loci and assessed evidence for adaptive and purifying selection at nonsynonymous sites. For each of three divergence events in the history of these taxa, we used approximate Bayesian simulation to estimate population sizes and divergence times and explicitly compare among alternative models of divergence. Our estimates of divergence times are surprisingly consistent with previous data from other markers and suggest rapid diversification of lineages within Zea in the last approximately 150,000 years. We found widespread evidence of historical gene flow, including evidence for divergence in the face of gene flow. We speculate that cultivated maize may serve as a bridge for gene flow among otherwise allopatric wild taxa.