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ARS Home » Southeast Area » Miami, Florida » Subtropical Horticulture Research » Research » Publications at this Location » Publication #354872
Research Project: Conservation, Evaluation, and Distribution of Sugarcane, Mango, Avocado and Other Subtropical and Tropical Genetic Resources and Associated Data

Location: Subtropical Horticulture Research

Title: Genetic diversity of avocado (Persea Americana Mill.) germplasm using pooled sequences for SNP discovery

Author
item RUBENSTEIN, MOR - Agricultural Research Organization, Volcani Center
item ECHED, RAVIT - Agricultural Research Organization, Volcani Center
item ROZEN, ADA - Agricultural Research Organization, Volcani Center
item ZVIAN, TALI - Agricultural Research Organization, Volcani Center
item OPHIR, RON - Agricultural Research Organization, Volcani Center
item Kuhn, David
item SHERMAN, AMIR - Agricultural Research Organization, Volcani Center

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/8/2019
Publication Date: 5/15/2019
Citation: Rubenstein, M., Eched, R., Rozen, A., Zvian, T., Ophir, R., Kuhn, D.N., Sherman, A. 2019. Genetic diversity of avocado (Persea Americana Mill.) germplasm using pooled sequences for SNP discovery. Scientific Reports. 20:379. https://doi.org/10.1186/s12864-019-5672-7.
DOI: https://doi.org/10.1186/s12864-019-5672-7

Interpretive Summary: Avocado (Persea americana) is an important tropical and subtropical fruit crop. In 2010, worldwide production of avocado was 3 to 3.5 MMT, with over 1 MMT produced in Mexico [1]. In the US, which ranks ninth in worldwide avocado production, California is the largest producer with Florida and Hawaii accounting for smaller percentages of the yearly crop. Here we describe the identification and analysis of single nucleotide polymorphism (SNP) genetic markers to be used to make a genetic map and associate important agronomic traits to individual SNP markers for marker assisted selection (MAS) and germplasm evaluation. Results of SNP genotyping of mapping populations and germplasm collections are important to scientists and breeders worldwide and will lead to the identification of new, improved cultivars of avocado for distribution to growers.

Technical Abstract: Pooled next generation sequencing approach was used for single nucleotide polymorphism (SNP) discovery from a collection of avocado (Persea americana Mill.) trees. The collection of 101 accessions includes the three types of races, Guatemalan, Mexican, and West-Indian. Three pools of gnomic DNA, one from each race, were sequenced to increase the chance for discovery of polymorphic loci. Next generation sequencing reads were aligned to a reference transcripome. The sensitivity of polymorphic-loci prediction ranged from 0.77 to 0.96. The correlation between the pooled allele frequency and the actual allele frequency from genotype calling was r = 0.8. A sample of 192 SNPs was selected to evaluate the relationship among the ARO avocado collection. A combination of the genetic evaluation and the morphological characteristics of the germplasm accessions was used to select a core set from each race which used as a reference to assign the rest of the accessions in the collection to one of the races or as admixed. By identifying SNPs that are identical by descent (IBD) a kinship coefficient was estimated to reveal accessions relatedness in a second degree. We reported here a framework for genetically characterizing of a breeder‘s accessions. The SNP discovery is a cost effective way to enrich polymorphic loci, the classification of the accessions may assist in a future breeding and association studies, and kinship analysis may be used as the first step to find a parental candidate in a parentage analysis.