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

Tandem repeat polymorphisms shape local adaptation

Within widespread populations, efficient adaptation to local environmental conditions can be facilitated by abundant quantitative variation supplied by short tandem DNA repeats. The peculiar site-specific mutability of such repeats can provide populations with the functional equivalent of tuning knobs for adaptively adjusting quantitative trait values.

Assessing population structure and morpho-molecular characterization of sunflower (Helianthus annuus L.) for elite germplasm identification

Sunflower (Helianthus annuus L.), known for its adaptability and high yield potential, is vital in global edible oil production. Estimating genetic diversity is a key pre-breeding activity in crop breeding. The current study comprised of 48 genotypes which were assessed for their biometrical traits at department of Oilseeds, Tamil Nadu Agricultural University, during the rainy season of 2022. The lines were subsequently characterised using 103 simple sequence repeat (SSR) markers for molecular diversity analysis. The results indicated that the net nucleotide distances indicated varying genetic divergence, with subpopulations II and V showing the highest (0.056) and I and IV the lowest (0.014). Subpopulation IV exhibited the highest heterozygosity (0.352), while subpopulation III had the lowest heterozygosity and a low Fst (0.173). Principal components analysis (PCA) and hierarchical cluster analysis were employed for assessing the morphological diversity, facilitating genotype grouping and parent selection for breeding programs. The first four components cumulatively accounted for 86.72% of the total variation. Cluster Analysis grouped 48 sunflower genotypes into three clusters based on genetic diversity. COSF 13B stands out for its high head diameter, oil content, seed yield, and oil yield based on mean performance of morphological data. Principal coordinate analysis (PCoA) mirrored the groupings from the Neighbor Joining method, with the first three components explaining 27.24% of the total variation. Molecular data analysis identified five distinct clusters among the germplasm. By integrating morphological and molecular marker data with genetic distance analysis, substantial diversity was revealed with the genotypes RHA 273 and GMU 325 consistently demonstrated high oil yield per plant. The genotypes GMU 477, GMU 450, COSF 13B, RHA 102, CMS 1103B, and RHA GPR 58 have been identified as suitable parents for enhancing oil content in sunflower breeding programs. These findings also aid in selecting SSR markers for genotype characterization and in choosing diverse parents for breeding programs.

Clinal Variation in Short Tandem Repeats Linked to Gene Expression in Sunflower (Helianthus annuus L.)

Short tandem repeat (STR) variation is rarely explored as a contributor to adaptive evolution. An intriguing mechanism involving STRs suggests that STRs function as "tuning knobs" of adaptation whereby stepwise changes in STR allele length have stepwise effects on phenotypes. Previously, we tested the predictions of the "tuning knob" model at the gene expression level by conducting an RNA-Seq experiment on natural populations of common sunflower (Helianthus annuus L.) transecting a well-defined cline from Kansas to Oklahoma. We identified 479 STRs with significant allele length effects on gene expression (eSTRs). In this study, we expanded the range to populations further north and south of the focal populations and used a targeted approach to study the relationship between STR allele length and gene expression in five selected eSTRs. Seeds from 96 individuals from six natural populations of sunflower from Nebraska and Texas were grown in a common garden. The individuals were genotyped at the five eSTRs, and gene expression was quantified with qRT-PCR. Linear regression models identified that eSTR length in comp26672 was significantly correlated with gene expression. Further, the length of comp26672 eSTR was significantly correlated with latitude across the range from Nebraska to Texas. The eSTR locus comp26672 was located in the CHUP1 gene, a gene associated with chloroplast movement in response to light intensity, which suggests a potential adaptive role for the eSTR locus. Collectively, our results from this targeted study show a consistent relationship between allele length and gene expression in some eSTRs across a broad geographical range in sunflower and suggest that some eSTRs may contribute to adaptive traits in common sunflower.

Statistical Genomics Analysis of Simple Sequence Repeats from the Paphiopedilum Malipoense Transcriptome Reveals Control Knob Motifs Modulating Gene Expression

Simple sequence repeats (SSRs) are found in nonrandom distributions in genomes and are thought to impact gene expression. The distribution patterns of 48 295 SSRs of Paphiopedilum malipoense are mined and characterized based on the first full-length transcriptome and comprehensive transcriptome dataset from 12 organs. Statistical genomics analyses are used to investigate how SSRs in transcripts affect gene expression. The results demonstrate the correlations between SSR distributions, characteristics, and expression level. Nine expression-modulating motifs (expMotifs) are identified and a model is proposed to explain the effect of their key features, potency, and gene function on an intra-transcribed region scale. The expMotif-transcribed region combination is the most predominant contributor to the expression-modulating effect of SSRs, and some intra-transcribed regions are critical for this effect. Genes containing the same type of expMotif-SSR elements in the same transcribed region are likely linked in function, regulation, or evolution aspects. This study offers novel evidence to understand how SSRs regulate gene expression and provides potential regulatory elements for plant genetic engineering.

Genetic variation at innate and adaptive immune genes - contrasting patterns of differentiation and local adaptation in a wild gull

Immunogenetic variation in natural vertebrate populations is expected to respond to spatial and temporal fluctuations in pathogen assemblages. While spatial heterogeneity in pathogen-driven selection enhances local immunogenetic adaptations and population divergence, different immune genes may yield contrasting responses to the environment. Here, we investigated population differentiation at the key pathogen recognition genes of the innate and adaptive immune system in a colonial bird species, the black-headed gull Chroicocephalus ridibundus. We assessed genetic variation at three toll-like receptor (TLR) genes (innate immunity) and the major histocompatibility complex (MHC) class I and II genes (adaptive immunity) in gulls from seven colonies scattered across Poland. As expected, we found much greater polymorphism at the MHC than TLRs. Population differentiation at the MHC class II, but not MHC-I, was significantly stronger than at neutral microsatellite loci, suggesting local adaptation. This could reflect spatial variation in the composition of extracellular parasite communities (e.g., helminths), possibly driven by sharp differences in habitat structure between colonies. Despite contrasting patterns of population differentiation, both MHC classes showed similar regimes of diversifying selection. Some significant population differentiation was also observed at TLRs, suggesting that innate immune receptors may respond to fine-scale spatial variation in pathogen pressure, although this pattern could have been enhanced by drift. Our results suggested that local adaptation at the pathogen recognition immune genes can be maintained at relatively small or moderate spatial scales in species with high dispersal potential and they highlighted the complexity of immunogenetic responses of animals to heterogeneous environments.