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Application of genomic tools to avocado (Persea americana) breeding: SNP discovery for genotyping and germplasm characterization

Kuhn, D.N., Livingstone, D.S., Richards, J.H., Manosalva, P., Van den Berg, N., Chambers, A.H.
Scientia horticulturae 2019 v.246 pp. 1-11
Agricultural Research Service, Persea americana, RNA, avocados, breeding programs, chromosome mapping, cultivars, fruit crops, genes, genetic improvement, genetic markers, genetic variation, genomics, genotyping, germplasm, germplasm conservation, germplasm evaluation, human resources, marker-assisted selection, nucleotide sequences, parents, sequence analysis, single nucleotide polymorphism, transcriptome, tree breeding, tropical and subtropical horticulture, Florida
Avocado (Persea americana) is an important tropical and subtropical fruit tree crop. Traditional tree breeding programs face the challenges of long generation time and significant expense in land and personnel resources. Avocado selection and breeding can be more efficient and less expensive through the development of molecular markers for the estimation of germplasm genetic diversity, marker-assisted selection (MAS), and creation of linkage maps. Two important breeding resources, the world's two largest avocado mapping populations and an extensive germplasm collection, are housed at the USDA-ARS Subtropical Horticulture Research Station (SHRS) in Miami, Florida. However, to use these resources to their greatest advantage, many thousands of genetic markers are necessary. Here, we describe the development of the first set of avocado genetic markers based on single-nucleotide polymorphism (SNP) variation in expressed genes. RNA sequencing was used both to build a reference transcriptome from 'Hass', the most widely grown avocado cultivar worldwide, and to identify SNPs by alignment of RNA sequences from the mapping population parents to the ˈHassˈ transcriptome. This study provides a new genomic tool for the avocado community that can be used to assess the genetic diversity of avocado germplasm worldwide and to optimize avocado breeding and selection programs by complementing traditional breeding methods with molecular approaches, thus increasing the efficiency of avocado genetic improvement.