Principal components analysis--K-means transposon element based foxtail millet core collection selection method

Genetic Diversity Maximization as a Strategy for Resilient Forest Ecosystems: A Case Study on Norway Spruce

Norway spruce, economically and ecologically one of the most important European forest tree species, rapidly declines due to massive bark beetle outbreaks across many countries. As a prerequisite of ecosystem stability facing climate changes of uncertain predictions, the reforestation management promoting locally adapted resources of broad genetic diversity should be prioritized, especially in nature conservation areas. In our case study carried out in the national park, Krkonoše Mountains (the Giant Mountains, the Czech Republic), we demonstrated a tree breeding strategy aiming at maximizing genetic diversity. More than four hundred unique Norway spruce accessions were genotyped on 15 microsatellite loci (Ne = 5.764, I = 1.713 and He = 0.685). Two core collection selection approaches were proposed to establish a new deployment population providing local gene sources of high genetic diversity. Namely, the Core Hunter selection algorithm, with average entry-to-nearest-entry distance (EN) optimization, was applied to identify the most diverse core collection set with the highest genetic diversity parameters obtained for 57 selected individuals (Ne = 6.507, I = 1.807, and He = 0.731). The latter core collection method proposed is innovative, based on choosing appropriate genotypes from a clustered heatmap. For simplicity, we demonstrated the principle of selection strategy on a reduced dataset. It is vital to promote panmixia of a newly established production population from a core collection to complete the conservation breeding effort. Thus, we demonstrated the utilization of the Optimum Neighborhood Algorithm (ONA) deployment that outperformed other deployment algorithms, especially in the case of balanced clone representation and uneven shapes of planting plots. We believe that the case study presented can be generalized and considered as a guideline for analogical tree breeding intentions.

Core Hunter 3: flexible core subset selection

Background

Core collections provide genebank curators and plant breeders a way to reduce size of their collections and populations, while minimizing impact on genetic diversity and allele frequency. Many methods have been proposed to generate core collections, often using distance metrics to quantify the similarity of two accessions, based on genetic marker data or phenotypic traits. Core Hunter is a multi-purpose core subset selection tool that uses local search algorithms to generate subsets relying on one or more metrics, including several distance metrics and allelic richness.

Results

In version 3 of Core Hunter (CH3) we have incorporated two new, improved methods for summarizing distances to quantify diversity or representativeness of the core collection. A comparison of CH3 and Core Hunter 2 (CH2) showed that these new metrics can be effectively optimized with less complex algorithms, as compared to those used in CH2. CH3 is more effective at maximizing the improved diversity metric than CH2, still ensures a high average and minimum distance, and is faster for large datasets. Using CH3, a simple stochastic hill-climber is able to find highly diverse core collections, and the more advanced parallel tempering algorithm further increases the quality of the core and further reduces variability across independent samples. We also evaluate the ability of CH3 to simultaneously maximize diversity, and either representativeness or allelic richness, and compare the results with those of the GDOpt and SimEli methods. CH3 can sample equally representative cores as GDOpt, which was specifically designed for this purpose, and is able to construct cores that are simultaneously more diverse, and either are more representative or have higher allelic richness, than those obtained by SimEli.

Conclusions

In version 3, Core Hunter has been updated to include two new core subset selection metrics that construct cores for representativeness or diversity, with improved performance. It combines and outperforms the strengths of other methods, as it (simultaneously) optimizes a variety of metrics. In addition, CH3 is an improvement over CH2, with the option to use genetic marker data or phenotypic traits, or both, and improved speed. Core Hunter 3 is freely available on http://www.corehunter.org.

Genetic Structure and Selection of a Core Collection for Long Term Conservation of Avocado in Mexico

Mexico, as the center of origin of avocado (Persea americama Mill.), harbors a wide genetic diversity of this species, whose identification may provide the grounds to not only understand its unique population structure and domestication history, but also inform the efforts aimed at its conservation. Although molecular characterization of cultivated avocado germplasm has been studied by several research groups, this had not been the case in Mexico. In order to elucidate the genetic structure of avocado in Mexico and the sustainable use of its genetic resources, 318 avocado accessions conserved in the germplasm collection in the National Avocado Genebank were analyzed using 28 markers [9 expressed sequence tag-Simple Sequence Repeats (SSRs) and 19 genomic SSRs]. Deviation from Hardy Weinberg Equilibrium and high inter-locus linkage disequilibrium were observed especially in drymifolia, and guatemalensis. Total averages of the observed and expected heterozygosity were 0.59 and 0.75, respectively. Although clear genetic differentiation was not observed among 3 botanical races: americana, drymifolia, and guatemalensis, the analyzed Mexican population can be classified into two groups that correspond to two different ecological regions. We developed a core-collection by K-means clustering method. The selected 36 individuals as core-collection successfully represented more than 80% of total alleles and showed heterozygosity values equal to or higher than those of the original collection, despite its constituting slightly more than 10% of the latter. Accessions selected as members of the core collection have now become candidates to be introduced in cryopreservation implying a minimum loss of genetic diversity and a back-up for existing field collections of such important genetic resources.