Single‐nucleotide polymorphisms that uniquely identify cultivars of avocado (Persea americana)

Abstract

Premise Progeny of avocado (Persea americana) are highly variable due to high levels of heterozygosity. Breeding programs need molecular resources to allow the assessment of genetic differences and the selection of genotypes. Polymorphisms that uniquely identify different avocado cultivars provide a valuable tool to accelerate avocado research and development, including, for example, genotype selection. Methods A double‐digest restriction site–associated DNA sequencing (ddRADseq) approach was used to screen 10 avocado cultivars for single‐nucleotide polymorphisms (SNPs). The fragments were size selected with Blue Pippin and PCR using universal Illumina primers, and catalog tags were then created with de novo alignment using Stacks software. Catalog tags were tabulated and filtered to identify alleles unique to each cultivar. Results A total of 104 million sequences were collected, and 52 homozygous SNPs were identified that uniquely distinguished nine avocado cultivars. The cultivars Carmen Hass and Hass have a strong genetic similarity and no homozygous SNPs distinguishing these cultivars could be identified; therefore, both cultivars were grouped together. Discussion The resource described here for cultivars of P. americana presents a new and significant molecular resource that can enable targeted genotype selection, paternity analysis, germplasm genotyping, pollination dynamics investigation, and crop improvement.

Outcrossing Rate and Fruit Yield of Hass Avocado Trees Decline at Increasing Distance from a Polliniser Cultivar

“…We extracted DNA from the embryo of each of the ten fruit using methods described previously [29]. Each embryo was genotyped using the Agena MassARRAY platform (Agena Bioscience, San Diego, CA, USA) to assign paternity by amplifying DNA regions with unique single nucleotide polymorphisms (SNPs) that we identified previously from all cultivars in the orchard [46].…”

Boron Effects on Fruit Set, Yield, Quality and Paternity of Hass Avocado

“…Disposable 2.3 mm and 0.1 mm zirconia-silica beads and liquid nitrogen were added to samples prior to shaking on a TissueLyser II system (Qiagen, Hilden, Germany). Multiplex PCR reactions were carried out for each DNA sample to amplify the regions with unique single-nucleotide polymorphisms (SNPs) that were identified from the cultivars, Hass, Shepard and Maluma Hass [37,63]. The cultivars Hass and Carmen Hass share the same DNA sequences in these regions and may be isogenic or nearly so [63].…”

“…Multiplex PCR reactions were carried out for each DNA sample to amplify the regions with unique single-nucleotide polymorphisms (SNPs) that were identified from the cultivars, Hass, Shepard and Maluma Hass [37,63]. The cultivars Hass and Carmen Hass share the same DNA sequences in these regions and may be isogenic or nearly so [63]. High-throughput genotyping to assign paternity to each fruitlet and mature seed was performed via the Agena MassARRAY platform (Agena Bioscience, San Diego, CA, USA) using 28 recently designed assays for avocado [37,63].…”

“…The cultivars Hass and Carmen Hass share the same DNA sequences in these regions and may be isogenic or nearly so [63]. High-throughput genotyping to assign paternity to each fruitlet and mature seed was performed via the Agena MassARRAY platform (Agena Bioscience, San Diego, CA, USA) using 28 recently designed assays for avocado [37,63].…”

Development of Retrotransposon-Based Molecular Markers for Characterization of Persea americana (Avocado) Cultivars and Horticultural Races

“…In the same way that the avocado market has been expanded, so interest in development of new molecular markers has grown during recent decades, especially to unequivocally characterize the best cultivars to improve yield, but also to identify cultivars adapted to specific geoclimatic conditions and for development of molecularassisted breeding programs [2]. In this sense, several publications have addressed the identification of molecular markers in P. americana, involving different classic methods such as Restriction Fragment Length Polymorphism (RFLP) [19,20], Amplified Fragment Length Polymorphism (AFLP) [21][22][23][24], Random Amplified Polymorphic DNA (RAPD) [25], Single Sequence Repeats (SSRs) [26][27][28][29][30][31][32][33][34] or Single Nucleotide Polymorphisms (SNPs) [35][36][37][38][39][40].…”