A comparative study of population genetic structure reveals patterns consistent with selection at functional microsatellites in common sunflower

Microsatellites have long been considered non-functional, neutrally evolving regions of the genome. Recent findings suggest that they can function as drivers of rapid adaptive evolution. Previous work on common sunflower identified 479 transcribed microsatellites where allele length significantly correlates with gene expression (eSTRs) in a stepwise manner. Here, a population genetic approach is used to test whether eSTR allele length variation is under selection. Genotypic variation among and within populations at 13 eSTRs was compared with that at 19 anonymous microsatellites in 672 individuals from 17 natural populations of sunflower from across a cline running from Saskatchewan to Oklahoma. Expected heterozygosity, allelic richness, and allelic diversity were significantly lower at eSTRs, a pattern consistent with higher relative rates of purifying selection. Further, an analysis of variation in microsatellite allele lengths (lnRV), and heterozygosities (lnRH), indicate recent selective sweeps at the eSTRs. Mean microsatellite allele lengths at four eSTRs within populations are significantly correlated with latitude consistent with the predictions of the tuning knob model which predicts stepwise relationships between microsatellite allele length and phenotypes. This finding suggests that shorter or longer alleles at eSTRs may be favored in climatic extremes. Collectively, our results imply that eSTRs are likely under selection and that they may be playing a role in facilitating local adaptation across a well-defined cline in the common sunflower.

Multivariate analysis of five chicken breed in Indonesia based on microsatellite allele frequency

<p class="MDPI17abstract"><strong>Objective: </strong>This study tries to examine several multivariate methods in classifying genetic diversity using microsatellite allele frequency data.</p><p class="MDPI17abstract"><strong>Methods: </strong>This study used microsatellite allele frequency data from White Leghorn (n = 48), Kampung (n = 48), Pelung (n = 24), Sentul (n = 24), and Black Kedu (n = 25) from Indonesian Research Institute for Animal Production. Allele frequency data were analyzed by the Neighbor-Joining (NJ) method using the POPTREE2 program. The data was also analyzed by the Principal Component Analysis (PCA), Correspondence Analysis (CA), and Hierarchical Clustering on Principal Components (HCPC) methods using the factoextra and FactoMineR packages in the R 4.0.0 program.<strong></strong></p><p class="MDPI17abstract"><strong>Results: </strong>Correspondence Analysis (CA) found Sentul is more closer to Black Kedu. However, based on NJ, PCA, and HCPC showed Sentul is closer to Kampung. Based on the value of Dimension 1, Correspondence Analysis (80.7%) can explain greater variation than PCA (58.9%). However, CA method generated different results compared to NJ, PCA, and HCPC. NJ, PCA, and HCPC found four chicken clusters, namely cluster 1 (White Leghorn), cluster 2 (Pelung), cluster 3 (Black Kedu), and cluster 4 (Kampung and Sentul).<strong></strong></p><p class="MDPI17abstract"><strong>Conclusions: </strong>In conclusion, HCPC is a better multivariate method for analyzing allele frequency data than PCA and CA. HCPC can be used to analyze allele frequency data better than PCA, because HCPC is a combination of methods from hierarchical clustering and principal components.</p>

Transcribed microsatellite allele lengths are often correlated with gene expression levels in natural sunflower populations

ABSTRACTMicrosatellites are common in most species. While an adaptive role for these highly mutable regions has been considered, little is known concerning their contribution towards phenotypic variation. We used populations of the common sunflower (Helianthus annuus) at two latitudes to quantify the effect of microsatellite allele length on phenotype at the level of gene expression. We conducted a common garden experiment with seed collected from sunflower populations in Kansas and Oklahoma followed by an RNA-Seq experiment on 95 individuals. The effect of microsatellite allele length on gene expression was assessed across 3325 microsatellites that could be consistently scored. Our study revealed 479 microsatellites at which allele length significantly correlates with gene expression (eSTRs). When irregular allele sizes not conforming to the motif length were removed, the number of eSTRs rose to 2379. The percentage of variation in gene expression explained by eSTRs ranged from 1–86% when controlling for population and allele-by-population interaction effects at the 479 eSTRs. Of these, 70.4% are in untranslated regions (UTRs). A Gene Ontology (GO) analysis revealed that eSTRs are significantly enriched for GO terms associated with cis- and trans-regulatory processes. These findings suggest that a substantial number of transcribed microsatellites can influence gene expression.

Dead or just asleep? Variance of microsatellite allele distributions in the human Y-chromosome.

Several different methods confirm that a number of micro-satellites on the human Y-chromosome have allele distributions with different variances in different haplogroups, after adjusting for coalescent times. This can be demonstrated through both heteroscedasticity tests and by poor correlation of the variance vectors in different subclades. The most convincing demonstration however is the complete inactivity of some markers in certain subclades – “microsatellite death”, while they are still active in companion subclades. Many microsatellites have declined in activity as they proceed down through descendant subclades. This appears to confirm the theory of microsatellite life cycles, in which point mutations cause a steady decay in activity. However, the changes are too fast to be caused by point mutations alone, and slippage events may be implicated. The rich microsatellite terrain exposed in our large single-haplotype samples provides new opportunities for genotyping and analysis.

The role of avpr1a microsatellite length on reproductive success of female Microtus ochrogaster

Vasopressin and its’ interactions with the vasopressin 1a receptor (V1aR) are important in the formation of social attachments and parental behavior in male mammals but there also is evidence that vasopressin is involved in maternal behavior in female mammals. Laboratory studies have shown that female rats with greater expression of V1aR in particular brain regions display more maternal behavior than those with less V1aR expression. Previous data showed that variation in neural V1aR expression in males of several species of rodents was influenced by the length of microsatellite DNA within the regulatory region of gene (avpr1a) encoding V1aR. In male prairie voles (Microtus ochrogaster), the neural expression of V1aR differs between individuals with longer versus shorter avpr1a microsatellites. Males with longer avpr1a microsatellites had greater V1aR expression in particular brain regions, spent more time with their female social partner, and licked and groomed pups more than males with shorter avpr1a microsatellite lengths. If avpr1a microsatellite length is correlated with V1aR expression in females in a similar fashion to that in male prairie voles, females with longer avpr1a microsatellites should have greater reproductive success since maternal care should be critical for offspring survival. In addition, female prairie voles may benefit by living with males that have longer avpr1a microsatellites due to increased male presence at the nest and paternal care. We tested these predictions with prairie voles from semi-natural populations. Females that had summed avpr1a microsatellite allele lengths greater than the median produced more litters and total offspring than females with summed avpr1a lengths less than the median. Females with summed avpr1a microsatellite allele lengths greater than the median also produced offspring sired by more males. The avpr1a length of male social and genetic partners did not influence female reproductive success. This is the first field study showing a relationship between avpr1a microsatellite allele length and female reproductive success in any species.