Genetic Diversity and Population Structure Analysis in Early Generations Maize Inbreds Derived From Local Germplasm of Eastern Himalayan Regions Using Microsatellite Markers

North- Eastern parts of India fall under the Eastern Himalayan region and it is a diversity hotspot of many crops, including maize. Maize is an important traditional cereal crop grown in hill ecology of the region mainly for food, fodder and feed. To tap the potentiality of maize genetic resources in crop improvement programmes, assessment of genetic diversity is a basic requirement. Hence, in the present study, assessment of genetic diversity in thirty early generation maize inbreds developed from different germplasm of NE India was taken up using genome wide distributed fifty two microsatellite markers. The marker analysis revealed a large variation with a total of 189 alleles with an average of 3.63 alleles per marker locus. The allele size ranged from 50 bp ( phi 036 ) to 295 bp ( p 101049 ) which revealed a high level of genetic diversity among the loci. The PIC value ranged from 0.17 ( umc 1622 ) to 0.76 ( umc 1153 ) with an average value of 0.49. The value of expected Heterozygosity (H Exp ) ranged from 0.19 to 0.80 with an average of 0.57, whereas the Observed Heterozygosity (H Obs ) ranged from 0 to 0.89 with a mean of 0.14.The genetic dissimilarity between the genotype pairs ranged from 0.40 to 0.64 with a mean value of 0.57. Cluster analysis resolved the inbreds into three distinct sub-clusters. Similarly, population structure analysis also classified the inbred lines into three-subpopulations. Marker-trait associations showed a total of twelve SSR markers significantly associated with seven agronomic traits. From the present study, wide genetic variability was found among the maize inbreds with high potential to contribute new beneficial and unique alleles in genetic enhancement program of maize in India and particularly, in NE region.

Development and characterization of microsatellite markers for the French endemic Angelica heterocarpa (Apiaceae) and congeneric sympatric species

Objective Angelica heterocarpa (Apiaceae) is a wild endemic French species with special conservation interest in the European Union. It belongs to Angelica complex genus which is widespread throughout the north temperate zone, and is sympatric with other congeneric species. The objective of this work is to develop and characterize microsatellite markers as a new tool for understanding the ecology and evolution of Angelica species complex. Results We identified simple sequence repeat (SSR) regions in a microsatellite‐enriched library from A. heterocarpa and A. sylvestris. All 16 selected SSR regions were found to amplify in these species and were highly polymorphic. Marker transferability was validated in A. razulii and A. archangelica. These markers will help us to better understand the evolutionary dynamic between rare endemics and widespread sister species, and be useful for conservation of the endemic species. Moreover, they can provide new tools for studying the numerous traditional medicinal herbs of the Angelica genus.

Assessment of genetic diversity and phylogenetic relationships in Black Pied cattle in the Novosibirsk Region using microsatellite markers

There are currently over a thousand indigenous cattle breeds well adapted to local habitat conditions thanks to their long history of evolution and breeding. Identification of the genetic variations controlling the adaptation of local cattle breeds for their further introduction into the genome of highly productive global breeds is a matter of great relevance. Studying individual populations of the same breed with the use of microsatellite markers makes it possible to assess their genetic diversity, relationships, and breed improvement potential. Although the Black Pied breed is the most common dairy cattle breed in Russia, there are only a few studies on genetic diversity in local Black Pied populations in some Russian regions. The goal of the present study was to analyze the genetic diversity in Black Pied cattle populations in the Novosibirsk Region and compare them with other Russian populations; to identify significantly divergent populations with a view to preserving them under the programs aimed at maintaining the genetic diversity of the domestic Black Pied breed. DNA samples from 4788 animals of the Black Pied breed from six breeding enterprises in the Novosibirsk Region have been studied using 11 microsatellite markers. No significant differences in genetic variability parameters were found between individual populations. Private alleles have been identified in five out of six populations. Five populations have shown inbreeding coefficient values (FIS) below zero, which indicates heterozygosity excess. The population distribution test, principal component analysis, FST and DEST values, cluster analysis, and phylogenetic analysis have revealed two populations genetically distinct from the others. Essentially, the genetic diversity parameters of the six studied Black Pied cattle populations from the Novosibirsk Region show no significant differences from other Russian populations of the breed. Excess heterozygosity is observed in most breeding enterprises, which is a sign of a low inbreeding rate. To maintain the genetic diversity of the Russian Black Pied cattle, we recommend focusing on the two populations with significant genetic distinctions from the others.

Decoupled evolution of mating biology and social structure in Acromyrmex leaf-cutting ants

Insect societies vary greatly in their social structure, mating biology, and life history. Polygyny, the presence of multiple reproductive queens in a single colony, and polyandry, multiple mating by females, both increase the genetic variability in colonies of eusocial organisms, resulting in potential reproductive conflicts. The co-occurrence of polygyny and polyandry in a single species is rarely observed across eusocial insects, and these traits have been found to be negatively correlated in ants. Acromyrmex leaf-cutting ants are well-suited for investigating the evolution of complex mating strategies because both polygyny and polyandry co-occur in this genus. We used microsatellite markers and parentage inference in five South American Acromyrmex species to study how different selective pressures influence the evolution of polygyny and polyandry. We show that Acromyrmex species exhibit independent variation in mating biology and social structure, and polygyny and polyandry are not necessarily negatively correlated within genera. One species, Acromyrmex lobicornis, displays a significantly lower mating frequency compared to others, while another species, A. lundii, appears to have reverted to obligate monogyny. These variations appear to have a small impact on average intra-colonial relatedness, although the biological significance of such a small effect size is unclear. All species show significant reproductive skew between patrilines, but there was no significant difference in reproductive skew between any of the sampled species. We find that the evolution of social structure and mating biology appear to follow independent evolutionary trajectories in different species. Finally, we discuss the evolutionary implications that mating biology and social structure have on life history evolution in Acromyrmex leaf-cutting ants. Significance statement Many species of eusocial insects have colonies with multiple queens (polygyny), or queens mating with multiple males (polyandry). Both behaviors generate potentially beneficial genetic diversity in ant colonies as well as reproductive conflict. The co-occurrence of both polygyny and polyandry in a single species is only known from few ant species. Leaf-cutting ants have both multi-queen colonies and multiply mated queens, providing a well-suited system for studying the co-evolutionary dynamics between mating behavior and genetic diversity in colonies of eusocial insects. We used microsatellite markers to infer the socio-reproductive behavior in five South American leaf-cutter ant species. We found that variation in genetic diversity in colonies was directly associated with the mating frequencies of queens, but not with the number of queens in a colony. We suggest that multi-queen nesting and mating frequency evolve independently of one another, indicating that behavioral and ecological factors other than genetic diversity contribute to the evolution of complex mating behaviors in leaf-cutting ants.

Analysis of the polymorphism of microsatellite loci in Picea abies (L.) H. Karst. and Picea obovatа Ledeb populations

Процессы генезиса хвойных лесов интенсивно изучаются с использованием методов молекулярного маркирования. Микросателлитные локусы рассматриваются в качестве наиболее полиморфной и воспроизводимой системы кодоминантных молекулярных маркеров. В цели исследования входило установить возможность использования микросателлитных маркеров для определения видовых различий между елью европейской и сибирской (Picea abies и Picea obovatа), а также оценить степень генетической обособленности региональных популяций ели на территории Европейской части РФ. Исследование показало, что использование набора из двенадцати микросателлитных маркеров позволяет разделить выборку елей, собранных с европейской и азиатской частей страны, на два генетических кластера, соответствующих видам Picea abies и Picea obovatа. Проанализированные в исследовании микросателлитные локусы могут быть использованы для оценки генетического разнообразия и географического происхождения ели европейской и сибирской. The processes of genesis of coniferous forests are widely investigating using molecular markers. Many studies are based on the analysis of microsatellite loci, which are acknowledged as the most reproducible and polymorphic co-dominant molecular markers. This study is aimed to establish the possibility of using microsatellite markers to determine differentiation between Norway and Siberian spruce (Picea abies and Picea obovata). Another task of this research was to assess the degree of genetic isolation of regional spruce population in the territory of European part of the Russian Federation. This study shows that using a large number of microsatellite markers allows to divide the sample of spruce collected from European part of Russia and Siberia in two genetic clusters, corresponding to Picea abies and Picea obovata. The microsatellite loci analyzed in the study can be used to assess genetic diversity and geographic origin of spruce trees and determine the origin of wood and planting material of Norway and Siberian spruce.

Rapid Differentiation of Vector Species: Development of Microsatellite Markers for Population Genetics of Biting Midges and a Potential Tool for Species Identification of Culicoides Sonorensis

Background: Proper vector surveillance relies on the ability to identify species of interest accurately and efficiently, though this can be difficult in groups containing cryptic species. Culicoides is a genus of small biting flies responsible for the transmission of numerous pathogens to a multitude of vertebrates. Regarding pathogen transmission, the C. variipennis species complex is of particular interest in North America. Of the six species within this group, only C. sonorensis is a proven vector of bluetongue virus and epizootic hemorrhagic disease virus. Unfortunately, subtle morphological differences, cryptic species, and mitonuclear discordance make species identification in the C. variipennis complex challenging. Recently, a SNP analysis enabled discrimination between the species of this group; however, this demanding approach is not practical for vector surveillance. Methods: The aim of the current study was to develop a reliable and affordable way of differentiating the species within the C. variipennis complex, especially C. sonorensis. Twenty-five putative microsatellite markers were identified using the C. sonorensis genome and tested for amplification within five species of the C. variipennis complex. Machine learning was then used to determine which markers best explain the genetic differentiation between species. This led to the development of a subset of four and seven markers which were also tested for species differentiation.Results: A total of 21 microsatellite markers were successfully amplified in the species tested. Clustering analyses of all of these markers recover the same species-level identification as the previous SNP data. Additionally, the subset of seven markers was equally capable of accurately differentiating the members of the C. variipennis complex as the 21 microsatellite markers. Finally, one microsatellite marker (C508) was found to be species-specific, only amplifying in the vector species C. sonorensis among the samples tested. Conclusions: These microsatellites provide an affordable way in which to differentiate the species of the C. variipennis complex and could lead to a better understanding of the species dynamics within this group. Additionally, after further testing, marker C508 may allow for the identification of C. sonorensis with a single-tube assay, potentially providing a powerful new tool for vector surveillance in North America.

Conservation Genomics Reveals Low Connectivity Among Populations of Threatened Roseate Terns in the Atlantic Basin

While the effects of barriers to dispersal such as population declines, habitat fragmentation, and geographic distance have been well-documented in terrestrial wildlife, factors impeding the dispersal of highly vagile taxa such as seabirds are less well understood. The roseate tern (Sterna dougallii) is a globally distributed seabird species, but populations tend to be both fragmented and small, and the species is declining across most of its range. Within the Atlantic Basin, past work has shown differentiation among roseate terns breeding on different continents, but these results were generated with a limited number of microsatellite markers. Relationships between breeding populations in the Northwestern Atlantic and the Caribbean have never been analyzed. We evaluated population structuring of roseate tern populations in North America and the Azores using both microsatellite markers and single-nucleotide polymorphisms generated through targeted sequencing of Ultra-conserved Elements. For both marker types, we found significant genetic differentiation among all 3 populations and evidence for moderate contemporary unidirectional gene flow from the Caribbean to the Azores, but not among other populations. Within the Caribbean metapopulation, we found high rates of unidirectional migration from the Virgin Islands to Florida, potentially indicative of movement from source population to sink or an artifact of dispersal among other unsampled populations in the Caribbean region. These observations have significance for species persistence in the Atlantic, as our results suggest that loss of genetic diversity within populations is unlikely to be buffered by inflow of new alleles from other breeding populations.

Genetic Diversity and Population Structure in Two Captive Rhesus Monkey (Macaca Mulatta) Populations as Revealed by Microsatellite Markers

Rhesus monkeyss (Macaca mulatta) are extensively used in the field of medical and psychological research as valuable experimental animals. 15 polymorphic chromosome-specific microsatellite markers were used to analyze the genetic diversity and population structure in two captive individuals. A total of 155 alleles were identified, with the number of alleles per locus ranging from 7 to 15, giving an average number of 10.3 alleles per locus. The mean number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were 5.602, 0.7297, 0.8016, and 0.7716, respectively. The populations HS and XJ shared partial common alleles, however, the remaining in XJ were not detected. Structure analysis indicated that two populations belong to three genetic lineages. AMOVA showed that the genetic variance was 91% among individuals, while it was 9% among populations, respectively. The bottleneck effect analysis revealed that the two captive populations were in accordance with mutation-drift equilibrium. In the comparison of the genetic parameters and structure between the HS and XJ, we speculated that the genetic diversity was higher, which may be attributed to the exchange of germplasm resources and the input of new individuals from wild populations.

Genetic Diversity and Population Dynamics of Leptobrachium leishanense (Anura: Megophryidae) as Determined by Tetranucleotide Microsatellite Markers Developed from Its Genome

Persisting declination of amphibians around the world has resulted in the public attaching importance to the conservation of their biodiversity. Genetic data can be greatly helpful in conservation planning and management, especially in species that are small in size and hard to observe. It is essential to perform genetic assessments for the conservation of Leptobrachium leishanense, an endangered toad and receiving secondary protection on the list of state-protected wildlife in China. However, current molecular markers with low reliability and efficiency hinder studies. Here, we sampled 120 adult toes from the population in the Leishan Mountain, 23 of which were used to develop tetranucleotide microsatellite markers based on one reference L. leishanense genome. After primer optimization, stability detection, and polymorphism detection, we obtained 12 satisfactory microsatellite loci. Then, we used these loci to evaluate the genetic diversity and population dynamics of the 120 individuals. Our results show that there is a low degree of inbreeding in the population, and it has a high genetic diversity. Recently, the population has not experienced population bottlenecks, and the estimated effective population size was 424.3. Accordingly, stabilizing genetic diversity will be key to population sustainability. Recovering its habitat and avoiding intentional human use will be useful for conservation of this species.