<b>Linkage disequilibrium and population structure in <i>Fragaria chiloensis</i> revealed by SSR markers transferred from commercial strawberry

Abstract

ABSTRACT. The Chilean strawberry [Fragaria chiloensis (L.) Mill.] is the maternal progenitor of the commercial strawberry (Fragaria × ananassa Duch.), which is characterized by fruits with high organoleptic quality and is well-suited to areas where drought and salinity represent a constraint on crop growth and productivity. We examined the patterns of linkage disequilibrium, genetic diversity and population structure among 54 accessions of F. chiloensis to understand the genetic basis of this species. We used a core microsatellite marker set (n = 95) from a consensus linkage map of strawberry. A transferability rate of 82.1% (78/95) was found, and 38 markers were selected for this study. The SSR primers produced a total of 259 alleles, which varied between 112 and 342 bp. Lower genetic diversity at the species level (H E = 0.17, Shannon's index = 0.28) was found compared to previous studies of this species. No climatic region pattern for SSR diversity was observed. Structure analysis suggests that the accessions are grouped into three significantly differentiated clusters. Pairwise estimates of φ ST indicated a low degree of differentiation between the three genetic groups (φ ST = 0.023 to 0.06). These groups are in concordance with potential glacial refugia in the region, with many accessions being an admixture of them.Keywords: genetic diversity, microsatellites, Chilean strawberry, marker transferability. Desequilíbrio de ligação e estrutura populacional em Fragaria chiloensis usando marcadores SSR transferidos do morango comercial RESUMO. O morango chileno [Fragaria chiloensis (L.)Mill.] é o progenitor materno do morangueiro comercial (Fragaria × ananassa Duch.), caracterizado por frutos com alta qualidade organoléptica, sendo uma cultura bem adequada para áreas caracterizadas pela seca e a salinidade. Neste trabalho, foram examinados os padrões de desequilíbrio de ligação, diversidade genética e estrutura da populacional em 54 acessos de F. chiloensis, com o intuito de avaliar a base genética da espécie. Utilizou-se um conjunto de marcadores de microssatélites (n = 95) obtidos do mapa de ligação consenso do morango comercial. A taxa de transferibilidade foi de 82,1% (78/95). Dos marcadores transferidos, 38 foram selecionados e usados neste estudo, os quais produziram um total de 259 alelos, que variaram entre 112 e 342 pb. Encontrou-se uma menor diversidade genética ao nível da espécie (H E = 0,17, índice de Shannon = 0,28), em comparação com estudos prévios com a espécie. Não foi observado padrão de região climática para a diversidade genética. A análise da estrutura sugere que os acessos são agrupados em três grupos significativamente diferenciados. As estimativas de pares de φST indicaram baixo grau de diferenciação entre os três grupos genéticos (φST = 0,023 a 0,06). Esses grupos estão em concordância com os potenciais refúgios glaciários na região, sendo muitas adições uma mistura deles.

Genetic Variation and Trait Correlations for Fruit Weight, Firmness and Color Parameters in Wild Accessions of Fragaria chiloensis

“…Previous studies have shown low and moderate levels of genetic diversity among F. chiloensis germplasm collections, which generally depend on the size of the collection and the type of molecular marker used [10,16,17]. a general linear model for each trait were used as the adjusted phenotypes for the Bayesian regression, taking into account the effect of genetic structure [10]. All the statistical analyses were performed using the R package MCMCglmm (version 3.6.1; https://www.r-project.org) [15].…”

“…chiloensis f. chiloensis and f. patagonica were defined as previously reported [7,9]. The analyzed accessions (Table S1) correspond to a subset from the germplasm collection evaluated by Mora et al [2] and Oñate et al [10]. Table S1.…”

“…We compared the genetic model (1) with a null-model (without the genotype effect), and models with DIC differences (delta DIC) >10 were considered to be significantly supported against a null-model. Additionally, in order to examine the existence of pleotropic loci between two correlated traits, thirty-nine SSR markers were assessed [10] (Table S2). These SSR primers yielded a total of 259 alleles, which were analyzed individually according to a Bayesian bi-trait regression (single-locus bi-trait model) [14].…”

“…The probability that a determined locus was associated jointly with two correlated traits (pleiotropic) was evaluated by the probability of the posterior estimates including zero in the Bayesian regression model (probability of Markov chain Monte Carlo; pMCMC). The residuals from a general linear model for each trait were used as the adjusted phenotypes for the Bayesian regression, taking into account the effect of genetic structure [10]. All the statistical analyses were performed using the R package MCMCglmm (version 3.6.1; https://www.r-project.org) [15].…”

“…To date, the color diversity (along with fruit firmness and fresh weight) has not been characterized in a native germplasm collection of F. chiloensis. Thus, with the intention to start domestication and breeding programs that allow the development of F. chiloensis genotypes with higher fruit quality, especially with color variants and a longer postharvest life, the present study aimed to examine the genetic variation and trait correlations for fruit firmness, fresh weight, and color (L*, a*, b*, Hue angle and Chroma parameters) in wild populations of F. chiloensis [2,10] from south-central Chile. Additionally, in order to examine the existence of pleotropic loci between two correlated traits, previously reported cross-species transfer of simple sequence repeats (SSR) markers in F. chiloensis [10] were used and analyzed individually according to a Bayesian bi-trait regression.…”