Genetic differentiation, races and interracial admixture in avocado (Persea americana Mill.), and Persea spp. evaluated using SSR markers

Abstract

Avocado (Persea americana Mill.) is a subtropical domesticated fruit tree indigenous to Mesoamerica. It is a member of the Lauraceae family and is separated into three horticultural races (Guatemalan, Mexican, and West Indian) mainly corresponding to their ecological adaptation, botanical, and physiological traits. Main objectives of this study were to characterize the population structure, genetic diversity, and horticultural race of a total of 354 Persea spp. trees whose origin is as follow: 221 trees [P. americana, (218), P. nubigena (2) and P. krugii (1)] from the USDA-ARS-Subtropical Horticultural Research Station, Miami; 105 trees from the Fairchild Farm [P. americana (104) and P. schiedeana (1)], and 28 trees collected in Mexico [P. schiedeana (23) and P. americana (5)]. The complexity of their interracial admixture; as well as mislabeling frequency was also evaluated. Molecular marker analysis utilizing a set of 55 simple sequence repeat (SSR) markers amplified a total of 869 alleles with a mean number of alleles per locus of 15.8 and average polymorphism information content value of 0.71, indicating a high variability in the allele frequency for the collection. Significant deviations from Hardy–Weinberg equilibrium were identified after Bonferroni correction for a large number of loci (48; 87%) due to the presence of null alleles. The main source of variation for this population was found to be within individuals (66.84%), with 19.30% variation among populations, and 13.86% variation among individuals within populations. Moreover, population specific inbreeding indices (F IS ) were calculated for West Indian, Guatemalan, and Mexican [(0.1918; p value 0.0000), (0.1879; p-value 0.0000), (0.0925; p-value 0.0022)], respectively. Bayesian analysis divided the individual genotypes into groups associated with the Guatemalan, Mexican, West Indian races; interracial admixture; complex hybrids and P. schiedeana species. Also, results of the multivariate clustering method (PCA) and genetic distance analyses calculated among all possible individual combinations within the SSR diversity data agreed with Bayesian or Structure analyses results. The 55 SSRs provided complete resolution of all individuals and the estimated mislabeling error was approximately 0.28%.

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Acknowledgements

The authors are grateful to Drs. Alan W. Meerow, Tomas Ayala-Silva, Eric J. Bishop von Wettberg, James W. Borrone, and Dapeng Zhang for helpful comments and suggestions on the manuscript. This work has been supported by the USDA-ARS-SHRS CRIS project Conservation, Genetic Analyses, and Utilization of Subtropical/tropical Fruit Crops, Sugarcane, and Miscanthus Genetic Resources (Project No. 6038-21000-022-00). We also thank anonymous reviewers for useful comments and suggestions on this publication. Dedication. The authors are extremely grateful for the years of service that Ms. Cecile L. Tondo gave to our research program at USDA-ARS-SHRS. She passed away on April 28, 2016 and is greatly missed. This publication is dedicated to her memory.

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Boza, E.J., Tondo, C.L., Ledesma, N. et al. Genetic differentiation, races and interracial admixture in avocado (Persea americana Mill.), and Persea spp. evaluated using SSR markers. Genet Resour Crop Evol 65, 1195–1215 (2018). https://doi.org/10.1007/s10722-018-0608-7

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Keywords

  • Persea americana
  • Population structure
  • Genetic diversity
  • Genetic differentiation
  • Avocado races
  • Private alleles
  • Persea schiedeana
  • Microsatellites