Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Talavera A

PROVIDER: S-EPMC6934854 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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

Talavera Alicia A Soorni Aboozar A Bombarely Aureliano A Matas Antonio J AJ Hormaza Jose I JI

Scientific reports 20191227 1

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 program ...[more]

PMID: 31882769

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Project description: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 (h2) 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.

Project description:BackgroundDiscovering 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.ResultsOur 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.ConclusionsA 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.

Project description:Avocado (Persea americana (Mill.)), an important commercial fruit, is severely affected by Phytophthora Root Rot in areas where the pathogen is prevalent. However, advances in molecular research are hindered by the lack of a high-throughput transient transformation system in this non-model plant. In this study, a proof-of-concept is demonstrated by the successful application of Agrobacterium rhizogenes-mediated plant transformation to produce composite avocado plants. Two ex vitro strategies were assessed on two avocado genotypes (Itzamna and A0.74): In the first approach, 8-week-old etiolated seedlings were scarred with a sterile hacksaw blade at the base of the shoot, and in the second, inch-long incisions were made at the base of the shoot (20-week-old non-etiolated plants) with a sterile blade to remove the cortical tissue. The scarred/wounded shoot surfaces were treated with A. rhizogenes strains (K599 or ARqua1) transformed with or without binary plant transformation vectors pRedRootII (DsRed1 marker), pBYR2e1-GFP (GFP- green fluorescence protein marker) or pBINUbiGUSint (GUS- beta-glucuronidase marker) with and without rooting hormone (Dip 'N' Grow) application. The treated shoot regions were air-layered with sterile moist cocopeat to induce root formation. Results showed that hormone application significantly increased root induction, while Agrobacterium-only treatments resulted in very few roots. Combination treatments of hormone+Agrobacterium (-/+ plasmids) showed no significant difference. Only the ARqua1(+plasmid):A0.74 combination resulted in root transformants, with hormone+ARqua1(+pBINUbiGUSint) being the most effective treatment with ~17 and 25% composite plants resulting from strategy-1 and strategy-2, respectively. GUS- and GFP-expressing roots accounted for less than 4 and ~11%, respectively, of the total roots/treatment/avocado genotype. The average number of transgenic roots on the composite plants was less than one per plant in all treatments. PCR and Southern analysis further confirmed the transgenic nature of the roots expressing the screenable marker genes. Transgenic roots showed hyper-branching compared to the wild-type roots but this had no impact on Phytophthora cinnamomi infection. There was no difference in pathogen load 7-days-post inoculation between transformed and control roots. Strategy-2 involving A0.74:ARqua1 combination was the best ex vitro approach in producing composite avocado plants. The approach followed in this proof-of-concept study needs further optimisation involving multiple avocado genotypes and A. rhizogenes strains to achieve enhanced root transformation efficiencies, which would then serve as an effective high-throughput tool in the functional screening of host and pathogen genes to improve our understanding of the avocado-P. cinnamomi interaction.

Project description:Lipids in avocados have been widely studied due to their nutritional value and several reported bioactivities. Aliphatic acetogenins are a relevant component of the avocado lipidome and have been tested for several potential food and pharma industries applications. This work followed the evolution of avocado fatty acids (FAs) and aliphatic acetogenins during seed germination and leaf growth. Oil extracts of embryonic axes, cotyledons, and leaves from seedlings and trees were divided to analyze free acetylated acetogenins (AcO-acetogenins), and free FAs. Embryonic axes from germinating seeds contained the highest amount of AcO-acetogenins and FAs; this tissue also accumulated the most diverse FA profile with up to 22 detected moieties. Leaves presented the highest variations in AcO-acetogenin profiles during development, although leaves from seedlings accumulated the simplest FA profile with only 10 different FAs. Remarkably, AcO-acetogenins represented half of the carbons allocated to lipids in grown leaves, while embryonic axes and cotyledons always contained more carbons within FAs during germination. Thus, we hypothesized the use of the AcO-acetogenin acyl chain for energy production toward β-oxidation. Also, α-linolenic and docosahexaenoic acids (DHAs) were proposed as close AcO-acetogenin intermediaries based on a correlation network generated using all these data. Another part of the oil extract was fractionated into different lipid classes before transesterification to profile FAs and acetogenins bound to lipids. Acetogenin backbones were identified for the first time in triglycerides from cotyledons and mainly in polar lipids (which include phospholipids) in all developing avocado tissues analyzed. Seed tissues accumulated preferentially polar lipids during germination, while triglycerides were consumed in cotyledons. Seedling leaves contained minute amounts of triglycerides, and polar lipids increased as they developed. Results from this work suggest acetogenins might be part of the energy and signaling metabolisms, and possibly of membrane structures, underlining the yet to establish role(s) of these unusual lipids in the avocado plant physiology.

Dataset Information

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

Publications

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

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