Detection of adaptive genetic diversity in wild potato populations and its implications in conservation of potato germplasm

Authors: DEL RIO, ALFONSO - University Of Wisconsin; Bamberg, John

Submitted to: American Journal of Plant Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/24/2020
Publication Date: 10/22/2020
Citation: Del Rio, A.H., Bamberg, J.B. 2020. Detection of adaptive genetic diversity in wild potato populations and its implications in conservation of potato germplasm. American Journal of Plant Sciences. 11:1562-1578. https://doi.org/10.4236/ajps.2020.1110113.
DOI: https://doi.org/10.4236/ajps.2020.1110113

Interpretive Summary: Genebanks preserve important crop diversity which can be used to breed for better varieties. To enhance chances of acquiring beneficial diversity, a better understanding of genetic variation at natural habitats is important. To that purpose, DNA markers have been very useful tools. Advances is science and computer methods are helping scientists to expand use of DNA markers. This study investigated the use of adaptive markers, that is, DNA markers potentially associated to selection at natural sites, as another way to characterize potato germplasm for conservation and use. The results showed that 16 adaptive markers were found in a large AFLP marker dataset for populations of S. fendleri from 6 mountain ranges in Arizona, USA. These markers revealed enhanced capacity for identifying coherent geographic structure, and associations with specific environmental variables at habitats. From a practical standpoint, the understanding of mechanisms that shape natural genetic variation could help to predict responses of potato populations to future environmental conditions. This can help genebanks finding populations with good traits since they can be associated to regions with continuous selection for abiotic or biotic stresses.

Technical Abstract: Current advances in genomics are broadening marker applications allowing the identification of markers that reflect genomic regions under selection. Those markers, known as adaptive markers, could unlock additional ways to value, gauge and organize germplasm diversity. In this study we investigated if adaptive marker loci could be identified in a large AFLP marker dataset for populations of wild potato species S. fendleri from six different mountain ranges in southern Arizona, USA. A total of 2094 polymorphic AFLP markers were used to conduct genetic diversity analyses among populations and mountain ranges. To detect adaptive markers, statistics and computational simulations based on Bayesian methods were used to distinguish AFLP marker loci that had departed significantly from frequencies expected under a neutral model of genetic differentiation. Out of 2094 AFLPs, the Bayesian approach identified 16 marker loci that differed significantly from expected frequencies and thus considered to be adaptive. To contrast the genetic diversity information generated with each set of markers, analyses that included all the AFLP markers and only the 16 adaptive markers were conducted. The results showed that both were informative on establishing genetic associations among populations and among mountain ranges. However, adaptive markers were more effective on clustering and discriminating populations. This could indicate that adaptive markers captured genomic variation connected to selection at the natural sites. An additional test to determine if adaptive markers were associated to climate variables found two adaptive marker loci associated to specific climate variables in populations from different regions but with similar environmental structure. This preliminary assessment shows that adaptive genetic diversity could offer an additional way to measure diversity in potato germplasm and to set up options for conservation and research.