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

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 and application of molecular markers. A total of 1524 individuals were genotyped with 384 SNPs creating the largest SNP genotype database for avocado. These individuals correspond to four extensive germplasm collections including two housed in Florida and two in California. In addition, hybrids and selections from two rootstock breeding programs have been genotyped. Genotype data were analyzed using an affinity propagation method to define 155 groups. The 384 SNP markers provided accurate genotype data for individuals 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, this dataset is unambiguous so 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.

Molecular Markers and a Quality Trait Evaluation for Assessing the Genetic Diversity of Avocado Landraces from China

“…Avocado (Persea americana Mill. ), which is a member of the family Lauraceae of the order Laurales, is one of the most economically important subtropical/tropical fruit crops worldwide [1][2][3]. Avocado is a highly diverse species with local variations that have resulted in various ecological races [4].…”

Inheritance of Rootstock Effects in Avocado (Persea americana Mill.) cv. Hass

“…Previous genetic characterizations providing tangential signals of horticultural races have used targeted genes ( Chen et al, 2009 ), chloroplast DNA ( Ge et al, 2019 ), SSR ( Alcaraz and Hormaza, 2007 ; Ferrer-Pereira et al, 2017 ; Boza et al, 2018 ; Sánchez-González et al, 2020 ), and SNP markers ( Kuhn et al, 2019b ; Rubinstein et al, 2019 ; Talavera et al, 2019 ), in some cases using gene-bank accessions, such as from the Venezuelan germplasm bank—Instituto Nacional de Investigaciones Agrícolas–Centro Nacional de Investigaciones Agropecuarias ( Ferrer-Pereira et al, 2017 ), the National Germplasm Repository (United States Department of Agriculture—Agricultural Research Service Subtropical Horticultural Research Station) in Miami ( Kuhn et al, 2019a ,b), and the Spanish germplasm bank ( Talavera et al, 2019 ). Despite some of these analyses captured all three races ( Talavera et al, 2019 ), others exhibited mixed and inconclusive population structure ( Cañas-Gutiérrez et al, 2015 , 2019 ; Cañas-Gutierrez et al, 2019 ).…”

Advances in Understanding Defense Mechanisms in Persea americana Against Phytophthora cinnamomi

“…Another study identified 5,050 SNPs and used them to construct a high-density linkage map for avocado ( Kuhn et al, 2019b ). This allowed the authors to estimate genetic diversity in germplasm collections, determine parentage and identify mislabeled or self-pollinated individuals ( Kuhn et al, 2019a ).…”