Newly developed MAGIC population allows identification of strong associations and candidate genes for anthocyanin pigmentation in eggplant

SummaryMAGIC populations facilitate the genetic dissection of complex quantitative traits in plants and are valuable breeding materials. We report the development of the first eggplant MAGIC population (S3MEGGIC; 8-way), constituted by 420 S3 individuals developed from the intercrossing of seven cultivated eggplant (Solanum melongena) and one wild relative (S. incanum) parents. The S3MEGGIC recombinant population was genotyped with the eggplant 5k probes SPET platform and phenotyped for anthocyanins presence in vegetative plant tissues (PA) and fruit epidermis (FA), and for the light-sensitive anthocyanic pigmentation under the calyx (PUC). The 7,724 filtered high-confidence SNPs confirmed a low residual heterozygosity (6.87%) and a lack of genetic structure in the S3MEGGIC population, including no differentiation among subpopulations carrying cultivated or wild cytoplasm. Inference of haplotype blocks of the nuclear genome revealed an unbalanced representation of founder genomes, suggesting cryptic selection in favour or against specific parental genomes. GWAS analysis for PA, FA and PUC detected strong associations with two MYB genes similar to MYB113 involved in the anthocyanin biosynthesis pathway and with a COP1 gene, which encodes for a photo-regulatory protein and may be responsible for the PUC phenotype. Evidence was found of a duplication of an ancestral MYB113 gene with a translocation from chromosome 10 to chromosome 1. Parental genotypes for the three genes were in agreement with the candidate genes identification performed in the S3MEGGIC population. Our new eggplant MAGIC population is the largest recombinant population in eggplant and is a powerful tool for eggplant genetics and breeding studies.

Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae

Multiparent or synthetic recombinant populations those created by combining distinct isogenic founders to establish a single recombinant background have emerged as a useful tool for dissecting the genetics of complex traits. Synthetic recombinant populations can be used to derive inbred lines in which quantitative traits can be mapped, or the recombinant populations themselves can be sampled for experimental evolution. Especially for the latter application, investigators generally value maximizing genetic variation in a recombinant population; in other words, a population harboring relatively equal contributions of the genetic backgrounds of each isogenic founder strain is a desirable resource. It is well-documented that in evolution experiments initiated from recombinant or outbred ancestral populations, the subsequent adaptation that occurs in evolved populations is driven by standing genetic variation, rather than de novo mutations. Despite the demonstrated importance of initial genetic variation to the adaptive process, little has been done to systematically evaluate methods of constructing a synthetic recombinant population, for creating resources for evolution experiments. Here we seek to address this issue by comparing patterns of genetic variation in different synthetic recombinant populations of Saccharomyces cerevisiae created using one of two combination strategies: pairwise crossing of isogenic strains or simple mixing of strains in equal proportion. We also explore the impact of the varying the number of parental strains used in each strategy. We find that more genetic variation is initially present and subsequently maintained over generations when population construction includes a round of pairwise crossing. We also observe that when using a given crossing strategy, increasing the number of parental strains typically increases genetic diversity. In summary, we suggest that when creating recombinant populations for use in experimental evolution studies, simply mixing founder strains in equal proportion may limit the adaptive potential of that population.

Genetic divergence between half-sibling progenies of kale using different multivariate approaches

ABSTRACT The aim of this study was to evaluate the genetic dissimilarity between half-sibling progenies of kale in order to determine the most divergent progenies and, also, to select potential parents. Thirty-six kale genotypes were evaluated, being thirty-three half-sibling progenies and three commercial cultivars, in a randomized block design with four replicates and six plants per plot. Twenty-eight traits were evaluated in each plant per plot, thirteen quantitative and fifteen qualitative traits. Genetic divergence was studied using MANOVA and canonical variables for quantitative observations. In addition, dendrograms were made for quantitative, qualitative and joint analyses by UPGMA method, using Mahalanobis distance. Genetic divergence was observed between genotypes. Commercial cultivars were more divergent than half-sibling progenies. Among half-sibling progenies, the most divergent ones were P1, P21, P23, P25 and P30. We concluded that half-sibling progenies P1, P23 and P30 can be used as potential parents to compose the recombinant population.

Isoenzyme analysis of Schistosoma haematobium, S. intercalatum and their hybrids and occurrences of natural hybridization in Cameroon

Isoelectric focusing of glucose-6-phosphate dehydrogenase (G6PD) produced clearly identifiable profiles for S. haematobium and S. intercalatum and their hybrids. To provide a more detailed analysis of the interactions of S. haematobium and S. intercalatum in South West Cameroon over the last 12 years, G6PD analyses were carried out on individual schistosomes collected in Kumba in 1990, Loum in 1990, 1999 and 2000 and Barombi Mbo and Barombi Kotto in 1999. Studies were also carried out on the two parental species S. haematobium Barombi Mbo, S. intercalatum Edea and subsequent generations of hybrids resulting from laboratory crosses of the two parental species. The isoenzyme analysis demonstrated that the 1990 isolate from Kumba, was a recombinant of S. intercalatumxS. haematobium, and that 30% of individual schistosomes collected in 1990 in Loum were also recombinants. The remainder gave data indicative of S. haematobium. In 1999, 12.5% of individuals from Loum showed recombination and 10% in 2000. Results from the most recent parasitological survey in October 2000 showed the persistence of the recombinant population in addition to that of S. haematobium. There was also evidence of recombination having taken place in Barombi Kotto but not Barombi Mbo. This study demonstrates how the situation has changed over the last 12 years, and emphasizes the importance of assessing morphological, biological and molecular data together to gain a true picture of the rapidly evolving situation.