Tropentag, September 20 - 22, 2017 in Bonn "Future Agriculture: Social-ecological transitions and bio-cultural shifts"

Genetic Structure in Wild and Cultivated Populations of Inga edulis Mart. (Fabaceae) in Peruvian Amazon

¹Czech University of Life Sciences Prague, Fac. Tropical AgriSciences, Dept. of Crop Sciences and Agroforestry, Czech Republic
²Students for the Living Amazon o.p.s., Czech Republic
³Czech University of Life Sciences Prague, Fac. of Environm. Sciences, Czech Republic
⁴Escola Superior Agrária do Instituto Politécnico de Castelo Barnco, Dept. of Natural Resources and Sustainable Development, Portugal

Abstract

Inga edulis Mart. has been improved through history by human selection focusing on the edible fruit, and, also, to provide shade for other crops. We aimed at comparing wild and cultivated I. edulis populations' genetic structure spanning the Peruvian Amazon. We evaluated a total of 259 trees, 197 cultivated and 62 wild, sampled from 27 populations. For each individual a voucher specimen was kept. The total genomic DNA was extracted for each sample and genotyped with four microsatellite primers.
We identified 71 alleles, with an average of 17.8 alleles per locus. For the 27 populations with at least 5 samples, the average number of alleles was 5.7, the average allelic richness 4.4, the observed heterozygosity 0.59, and the expected heterozygosity 0.69. The heterozygote deficit was non-significant, but the inbreeding coefficient was 0.153. Twelve populations were not in Hardy-Weinberg equilibrium. These populations were distributed randomly across the I. edulis sampled range and across cultivated and wild populations. We compared the wild vs. the cultivated populations, and significant deviation from the null expectation emerged. The allelic richness and the observed heterozygosity were lower in the group of cultivated populations. The level of differentiation among populations was significantly higher in the cultivated compared to the wild populations.
A hierarchical analysis of molecular variance revealed that a majority of the genetic diversity was partitioned within populations (78.8%), 14.3% was partitioned among populations within groups (wild and cultivated) and 6.9% was partitioned between cultivated and wild groups. To further assess the population structure, we estimated the number of genetic clusters (K) and to fractionally assign individuals sampled from cultivated and wild populations to the inferred groups. Due to the weak population structure, we used a “locprior&rdquo model, which incorporated a priori sampling information. Two groups of populations were used as priors, the cultivated and the wild populations. The number of clusters (K) was set at each value from one through twenty-eight, and the simulation was run ten times at each K value to confirm the repeatability of the results. According to the Bayesian structuring results we inferred that the cultivated material in Peruvian Amazon has different origins.

Keywords: DNA, genetic structure, Inga edulis Mart., microsatellite locus, PCR, peruvian Amazon, population

Contact Address: Alexandr Rollo, Czech Univerzity of Life Sciences Prague, Dept. of Crop Sciences and Agroforestry in the Tropics and Subtropics, Kamycka 129, 16521 Prague, Czech Republic, e-mail: rolloftz.czu.cz