SSR-based genetic diversity and structure of garlic accessions from Brazil

Author(s)

da Cunha, Camila Pinto ^{[1, 2]} ; Resende, Francisco Vilela ^[3] ; Zucchi, Maria Imaculada ^[4] ; Pinheiro, Jose Baldin ^[1]

Affiliation

^[1] Univ Sao Paulo, Dept Genet, Luiz de Queiroz Coll Agr ESALQ, BR-13418900 Piracicaba, SP - Brazil

^[2] Univ Campinas UNICAMP, Grad Program Genet & Mol Biol, BR-13083862 Campinas, SP - Brazil

^[3] Brazilian Corp Agr Res EMBRAPA Vegetable CNPH, BR-70359970 Brasilia, DF - Brazil

^[4] Sao Paulo Agcy Agribusiness Technol APTA, BR-13400970 Piracicaba, SP - Brazil

• Document type: Journal article
• Source: Genetica; v. 142, n. 5, p. 419-431, OCT 2014.
• Web of Science Citations: 10

Abstract

Garlic is a spice and a medicinal plant; hence, there is an increasing interest in `developing' new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, H-O of 0.5, and H-E of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall F-ST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide. (AU)

• FAPESP's process: 08/02936-5 - Development of library enriched with locus SSRs and agromorphologic and molecular characterization of the Allium sativum L. germoplasm
• Grantee: José Baldin Pinheiro
• Support Opportunities: Regular Research Grants
• FAPESP's process: 09/03577-1 - Microsatellite markers for genetic analysis of GARLIC(Allium sativum L.)GERMPLASM
• Grantee: Camila Pinto da Cunha
• Support Opportunities: Scholarships in Brazil - Master