Creation of an avocado unambiguous genotype SNP database for germplasm curation and as an aid to breeders

Authors: Kuhn, David; GROH, AMY - Florida International University; RAHAMAN, JORDAN - Florida International University; Freeman, Barbara - Barbie; ARPAIA, MARY LU - University Of California; VAN DEN BERG, NOELANI - University Of Pretoria; ABEYSECARA, NILWALA - University Of California; MANOSALVA, PATRICIA - University Of California; CHAMBERS, ALLAN - University Of Florida

Submitted to: Tree Genetics and Genomes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/18/2019
Publication Date: 8/27/2019
Citation: Kuhn, D.N., Groh, A.M., Rahaman, J., Freeman, B.L., Arpaia, M., Van Den Berg, N., Abeysecara, N., Manosalva, P., Chambers, A.H. 2019. Creation of an avocado unambiguous genotype SNP database for germplasm curation and as an aid to breeders. Tree Genetics and Genomes. 15: 71. https://doi.org/10.1007/s11295-019-1374-1.
DOI: https://doi.org/10.1007/s11295-019-1374-1

Interpretive Summary: Tree breeding is a difficult and time-consuming endeavor. To improve the efficiency of tree breeding, breeders search for some type of marker that will help them identify potentially improved trees at the seedling stage. We have developed many thousands of DNA markers for avocado and begun the association of traits with those markers to aid both breeders and producers. This paper describes the genotyping of 1461avocado trees with 377 SNP markers. Because of the size of the dataset (~580,000 genotypes), a simple visual method has been developed to allow breeders and other interested researchers to analyze the data using only common spreadsheet functions rather than having to develop programming scripts in Perl, Python or R. By using this database along with genotype data of newly developed hybrids or farmers’ selection, breeders can easily determine if a tree in their program is the result of self-pollination, is misidentified/mislabeled, and even identify the paternal parent in some cases. The information presented in this paper is of importance to avocado research scientists, breeders and producers.

Technical Abstract: Avocado (Persea americana) is an important tropical and subtropical fruit tree crop. Traditional tree breeding programs face the challenges of long generation times 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. A total of 1,524 accessions were genotyped with 384 SNPs creating the largest SNP genotype database for avocado. These accessions correspond to four extensive germplasm collections, two housed in Florida and two in California. In addition, hybrids and selections from two rootstock breeding programs (University of California Riverside and Westfalia Technological Services-University of Pretoria ) and 32 accessions of commercially produced clonal rootstocks of Toro Canyon have been genotyped. Genotype data were analyzed using an affinity propagation method to define 155 groups. Using a simple visual method, no more than 30 SNPs are needed to distinguish a single cultivar of interest from all other cultivars in the dataset enabling the accurate identification of important commercial cultivars. The 384 SNP markers provided accurate genotype data for accessions from different Persea species as well as half-siblings. Therefore, the majority of the genetic diversity of the avocado germplasm and related species that were genotyped has been captured. A simple visual method can also be used to identify self-pollinated individuals among the half-siblings of known maternal parents, and, in some cases, to infer likely candidates for the paternal parent. Finally, the dataset is unambiguous so that breeders can determine the genetic diversity of their breeding stock to optimize avocado breeding and selection programs by identifying outcrossed individuals at the seedling stage, thus increasing the efficiency of avocado genetic improvement.