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

Authors: KUHN, DAVID; LIVINGSTONE III, D - MARS, INC.; RICHARDS, J - FLORIDA INTERNATIONAL UNIVERSITY; MANOSALVA, PATRICIA - UNIVERSITY OF CALIFORNIA; VAN DEN BERG, NOELANI - UNIVERSITY OF PRETORIA; CHAMBERS, ALAN - UNIVERSITY OF FLORIDA

Submitted to: Scientia Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/5/2018
Publication Date: 2/27/2019
Citation: Kuhn, D.N., Livingstone III, D.S., Richards, J.H., Manosalva, P., Van Den Berg, N., Chambers, A. 2019. Application of genomic tools avocado (Persea americana) breeding: SNP discovery for genotyping and germplasm characterization. Scientia Horticulturae. 246:1-11. https://doi.org/10.1016/j.scienta.2018.10.011.
DOI: https://doi.org/10.1016/j.scienta.2018.10.011

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. 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. Almost all the cultivated avocado acreage in California is the variety 'Hass', currently described as a Mexican x Guatemalan hybrid. Because there are a limited number of cultivars grown in Florida and California, we wanted to evaluate F1 populations of Florida varieties ('Simmonds' and 'Tonnage') and California varieties ('Hass' and 'Bacon') for interesting progeny to develop new commercial avocado varieties and to screen for disease resistance. We also wanted to associate favorable traits with particular regions of the genome (quantitative trait loci, QTL) to facilitate marker assisted selection (MAS). The advantage of MAS is that after a cross, seedlings can be screened with molecular markers for offtypes (non-hybrids) and the presence of favorable alleles, thereby reducing the number of seedlings to plant and raise to maturity for evaluation. This would improve the efficiency of traditional breeding, with its high costs in land and personnel resources. Here we describe the identification and analysis of ~600,000 single nucleotide polymorphism (SNP) genetic markers to be used to make a genetic map and associate important agronomic traits to individual SNP markers for 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 mango for distribution to growers.

Technical Abstract: The USDA-ARS Subtropical Horticulture Research Station (SHRS) houses the two largest avocado mapping populations in the world ('Bacon' x 'Hass' and reciprocal, 'Simmonds' x 'Tonnage' and reciprocal), as well as an extensive germplasm collection. To produce a genetic map and assess genetic diversity in our germplasm collection, thousands of single nucleotide polymorphism (SNP) markers were needed. As avocado is the second most important agricultural crop after citrus in Florida, USA, development of SNP markers will improve avocado breeding through marker-assisted selection (MAS) and through the use of genetically diverse germplasm for crossing with commercial cultivars. Because the avocado genome sequence was not available, SNP discovery using RNA sequencing of leaf and flower tissue of the parents was undertaken. A reference transcriptome from 'Hass', the most widely grown avocado cultivar worldwide, was generated. RNA sequences from the four mapping population parents were mapped onto the reference transcriptome to identify SNPs.