Genome-Wide SNP discovery and genomic characterization in avocado (Persea americana Mill.)

Abstract

Modern crop breeding is based on the use of genetically and phenotypically diverse plant material and, consequently, a proper understanding of population structure and genetic diversity is essential for the effective development of breeding programs. An example is avocado, a woody perennial fruit crop native to Mesoamerica with an increasing popularity worldwide. Despite its commercial success, there are important gaps in the molecular tools available to support on-going avocado breeding programs. In order to fill this gap, in this study, an avocado ‘Hass’ draft assembly was developed and used as reference to study 71 avocado accessions which represent the three traditionally recognized avocado horticultural races or subspecies (Mexican, Guatemalan and West Indian). An average of 5.72 M reads per individual and a total of 7,108 single nucleotide polymorphism (SNP) markers were produced for the 71 accessions analyzed. These molecular markers were used in a study of genetic diversity and population structure. The results broadly separate the accessions studied according to their botanical race in four main groups: Mexican, Guatemalan, West Indian and an additional group of Guatemalan × Mexican hybrids. The high number of SNP markers developed in this study will be a useful genomic resource for the avocado community.

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

“…The 'tropical' lowland ecotype (West Indian) is grown in genuinely tropical countries and warm subtropical regions [5]. These three ecotypes have been distinguished and identified based on genetic and morphological differences [6]. Avocado flowering exhibits a unique 'protogynous dichogamy' opening behavior, which favors cross-pollination, and sterility barriers do not exist between or among the three ecotypes [7].…”

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

“…Previous genetic characterizations providing tangential signals of horticultural races have used targeted genes (Chen et al, 2009), cpDNA (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, 2019c;Rubinstein et al, 2019;Talavera et al, 2019), in some cases using gene-bank accessions, like from the Venezuelan germplasm bank (INIA-CENIAP) (Ferrer-Pereira et al, 2017), the National Germplasm Repository (SHRS ARS USDA) in Miami (Kuhn et al, 2019a;Kuhn et al, 2019b), 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;Cañas-Gutiérrez et al, 2019;Cañas-Gutierrez et al, 2019). However, modern genomic tools have not only reinforced race substructure (Rendón-Anaya et al, 2019;Talavera et al, 2019), but also provided evidence for the hybrid origin of commercially important varieties such as Mexican/Guatemalan 'Hass' avocado (Rendón-Anaya 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;Cañas-Gutiérrez et al, 2019;Cañas-Gutierrez et al, 2019). However, modern genomic tools have not only reinforced race substructure (Rendón-Anaya et al, 2019;Talavera et al, 2019), but also provided evidence for the hybrid origin of commercially important varieties such as Mexican/Guatemalan 'Hass' avocado (Rendón-Anaya et al, 2019). Our characterization has further highlighted the admixed origin of seedling rootstocks currently used at commercial orchards in the northwest Andes.…”

Data_Sheet_9.PDF

“…(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, 2015Cañas-Gutierrez et al, 2019). However, modern genomic tools not only have enlightened race substructure (Rendón-Anaya et al, 2019; Talavera et al, 2019) but also provided evidence for the hybrid origin of commercially important varieties such as Mexican/Guatemalan "Hass" avocado (Rendón-Anaya et al, 2019).…”