Percentage Of Polymorphic Loci Research Articles

Genetic structure and gene flow among populations of willow (Salix species)

The newly developed Salix hybrids were assessed for genetic diversity using ISSR (Inter Simple Sequence Repeats) molecular markers. The results revealed 88.08 polymorphism, 0.53 polymorphism information content, 4.70 effective multiplex ratio, 2.54 marker index, and 7.18 resolving power from the amplified primers. Clones of the Salix matsudana (MAT) population recorded a maximum mean number of effective alleles (1.42), Shannon information index (0.38), gene diversity (0.25), and percentage of polymorphic loci (82.24 %). The AMOVA (Analysis of molecular variance) results revealed a moderate genetic divergence with a genetic variation of 88 per cent within populations and 12 per cent among the populations. The highest value of total diversity (0.28) and gene diversity (0.24) was recorded between S. matsudana (MAT) and S. tetrasperma (TETRA) populations, while there was more gene flow between S. matsudana (MAT) and S. tetrasperma (TETRA) populations (5.86). The clustering pattern obtained through STRUCTURE software showed two main gene pools and a mixture of 6–7 gene pools to confirm the hybrids based on ISSR marker data. S. matsudana and S. tetrasperma clones showed the highest gene diversity due to their proximity from their original locations, resulting in the least amount of gene exchange among populations. Molecular characterization using ISSR markers was extremely useful for studying the genetic diversity among the willow hybrids and high genetic variability should be utilized for breeding purposes in the future.

Genetic diversity of SP1 population of space mutagenized Pueraria montana

To explore the mutagenic effect of the space environment on Pueraria montana and select the elite germplasm with good growth conditions and high isoflavone content, this study observed the agronomic traits, determined the flower isoflavone content, and labeled amplified fragment length polymorphism(AFLP) fluorescent molecular markers of 79 P. montana plants exposed to space mutagenesis(SP1 group) and 10 control plants of P. montana(CK group). Excel 2019, SPSS 25.0, NTSYSpc-2.11F, and Popgen 32 were employed to analyze the genetic diversity and perform the cluster analysis. The results showed that the SP1 group presented changed leaf hairy attitude and flower structure and higher CV and H' of quantitative traits than the CK group. The cluster analysis screened out five plants in the SP1 group. Ten P. montana plants in the SP1 group had higher content of 6″-O-xylosyl-tectoridin and tectoridin in the flowers than the control group, with the total content of both exceeding 11%. After clustering, 9 plants in the SP1 group were separated. Nine pairs of polymorphic primers were screened out frrom 64 pairs of primers. A total of 1 620 polymorphic loci were detected, with the average percentage of polymorphic loci(PPL) of 83.33%. The average Nei's gene diversity index(H) and Shannon's information index(I) were 0.192 2 and 0.305 2, respectively. After clustering, 4 plants in the SP1 group were screened out. According to the above results, plants No. 30, No. 66, and No. 89 in the SP1 group were subjected to greater mutagenic effect by the space environment and presented better growth and higher flower isoflavone content. Moreover, plant No. 30 showed the flower structure variation and flower weight two times of that in the CK group. These plants can be used as key materials for the subsequent experiments.

Genetic Diversity Assessment of Cupressus gigantea W. C. Cheng & L. K. Fu Using Inter-Simple Sequence Repeat Technique

Cupressus gigantea W. C. Cheng & L. K. Fu is an endemic conifer tree species that is distributed widely along the northern portion of the deep gorge of the Yarlung Tsangbo River on the Tibetan Plateau. However, as a key plant species growing on the Tibetan plateau, C. gigantea has since become an endangered species due to habitat loss and degradation, overexploitation, and other factors. It has been listed as a first-grade national protected wild plant species in China. Accordingly, to conserve this plant species, we should obtain more information on its genetic structure. In this study, the genetic diversity and structure among 67 samples were evaluated by the inter-simple sequence repeat (ISSR) technique. Overall, 78 bands were produced with a molecular length of 200 bp to 3100 bp using 10 ISSR primers. The mean values for the average number of alleles (Na), effective number of alleles (Ne), Nei’s gene diversity (H), and Shannon’s information index (I) were 1.529, 1.348, 0.199, and 0.293, respectively. Additionally, the number of polymorphic loci (NPLs) and percentage of polymorphic loci (PPLs) averaged 41.25 and 52.90, respectively. Further, total variation among populations was 14.2%, while that within populations was 85.8%; accordingly, the within-population genetic differentiation was found to be significant (p < 0.001). These results demonstrated that a genetic structure model with K = 3 fitted the data best, which agreed with the unweighted pair group method with arithmetic average (UPGMA) cluster and the principal coordinate analysis (PCoA). These findings are beneficial for ensuring the development and genetic protection of C. gigantea populations in the future.

Assessing the Genetic Diversity of Wild and Commercial Feijoa sellowiana Accessions Using AFLPs

Feijoa sellowiana (O. Berg) is a broadly widespread fruit tree species at a very early stage of domestication. Although appreciated for its flavored berries rich in nutrients and nutraceuticals, and as an ornamental plant, feijoa is still considered an underutilized species and little information is available about its genetic background, cultivar traceability and divergence. This study aimed to investigate, for the first time, the genetic diversity of feijoa through the application of AFLPs. Specifically, twenty cultivars from different countries and six wild types (WTs) from their area of origin (Misiones, Argentina) were analyzed. The AFLPs proved to be informative, revealing the values of the percentage of polymorphic loci (PPB), Nei’s genetic diversity (h), and the Shannon index (I) at 69.36%, 0.27, and 0.43, respectively, consistent with the average of long-lived perennial and outcrossing species. However, despite the limited number of WTs examined, the genetic variability (h) was higher (approximately 37%) within the six samples compared to cultivars. The population structure analysis identified three clusters, with WTs forming a separated cluster (III) as expected. Cultivars were divided into two clusters (I and II), with cluster I exhibiting a closer genetic proximity to WTs compared to cluster II. This finding was further confirmed using the UPGMA dendrogram based on Provesti distances. This work raised awareness of the genetic variability among the feijoa’s widespread cultivars and demonstrated that the limited genetic breeding programs over the last decades resulted in low diversity among them. Moreover, these results confirm the hypothesis that all varieties are derived from a single narrow ancestral population. The potential of this species is considerable and needs to be further investigated to exploit its peculiarities.

Exploring the extents of genetic diversity and population structure of enset [Ensete ventricosum (Welw.) cheesman] from southern Ethiopia using simple sequence repeat markers: Implications for crop improvement and conservation

Enset (Ensete ventricosum) is a multi-use perennial herbaceous crop used as a staple food for over 20 million people in Ethiopia. Despite its high use values, very few studies have been conducted to improve this crop, particularly using molecular marker systems. In this context, the study aimed at evaluating the magnitude of genetic diversity and population structure of enset germplasm collections from four major enset growing zones in southern Ethiopia using 12 simple sequence repeat (SSR) markers. A total of 147 individual leaf samples were collected from the entire enset populations and gave 289 alleles, ranging from 12 to 41 alleles per locus, with a mean of 24.5. The polymorphism information content for each locus varied from 0.86 to 0.95, with a mean of 0.91. The number of effective alleles ranged from 5.13 to 11.79 with a mean of 8.27. The expected and observed heterozygosity showed average values of 0.85 and 0.84, respectively. The greatest genetic distance (1.16) was between Gurage and wild populations, while the shortest (0.37) was between Gurage and Silte. Among the six populations, the wild had the highest percentage of polymorphic loci (100%). AMOVA attributed 89% of the genetic variation to intra-population and only 11% to among populations. The whole set of germplasm indicates low genetic differentiation and high gene flow (Nm). The UPGMA and principal coordinates largely correspond to each other and indicate three major groups. Overall, the information gained from this study would be useful for enset improvements and conservation strategies.

Genetic Diversity of West African Honey Bee (Apis ‎mellifera adansonii Latreille, 1804) from Rural and Urban ‎Areas of ‎Kwara State, North-Central Nigeria

Over one third of the world’s crops– including fruits, vegetables, nuts, spices, and oilseed–‎require insect pollination, and human reliance on ‎pollination services by honey bees (Apis ‎mellifera) to promote these crops continues to rise due to increasing demands from growing ‎human ‎populations. Identifying the effects of urbanization on genetic diversity on this ‎pollinating insect is important in the field of bioscience. This study aimed to investigate genetic diversity of A. mellifera in Kwara State, Nigeria, using the random amplified polymorphic DNA (RAPD) marker. ‎Thirty honey bees ‎were simultaneously collected from both rural and urban regions in ‎Kwara state, Nigeria. Samples were morphologically identified using ‎standard methods, ‎genomic DNA isolated and amplified using five RAPD primers. Data collected were ‎analysed using PyElph, ‎ARLEQUIN, and GeneAlEx version 6.501 software. The results ‎showed that the DNA fragment sizes produced per primer varied from 200 to ‎‎3000 bp. Percentages of polymorphic loci amplified by each primer varied from 17.33 to 33.33%. ‎Analysis of unbiased Nei genetic ‎distance values showed that Agbede (rural) and Adewole ‎‎(urban) showed the highest value of unbiased genetic distance (0.073), while ‎Amoyo ‎‎(rural) to Idofian (urban) exhibited the lowest value (0.027). Dendrogram analysis revealed ‎genetically close relationships among the sampled ‎A. mellifera‎ populations. The low level of genetic ‎polymorphisms observed among the honey bee populations in the two ‎regions ‎indicated that there is genetic relatedness among them. This study concluded that RAPD ‎marker is a useful method for ‎understanding population genetic structure of the African honey ‎bees. These results can be used as baseline information for future genetic ‎diversity ‎assessment of honey bees in Nigeria with larger samples. It is therefore recommended that ‎there is a need to safeguard the genetic ‎diversity of A. mellifera‎ to prevent extinction or ‎gradual loss of diversity‎‎‎.

Genetic variability of wild palms Euterpe precatoria, Euterpe oleracea and Mauritia flexuosa with molecular markers ISSR

Wild palms constitute a group of plants of particular economic importance in the tropics, being a valuable source for obtaining construction materials, fabrics, fuel, food, ornamental and medicinal plants. Despite their economic, social, and environmental importance, the genetic variability existing in wild palms, mainly of the genus Mauritia and Euterpe, is unknown, which limits their potential use and the identification of promising genotypes to be included in recombination programs. The genetic variability of three wild palm species (Euterpe oleracea, Euterpe precatoria, and Mauritia flexuosa) was evaluated using Inter-Simple Sequence Repeat (ISSR) markers. A total of 51 genotypes were analyzed with seven ISSR primers, which generated a total of 153 bands, with a percentage of polymorphic loci of 90.24%. The cluster analysis revealed the formation of six groups at a similarity level of 37%, grouping the palm genotypes by species and geographical origin. Molecular variance analysis revealed that within group variations contributed more to genetic diversity (89%) than between group variations (11%). The average value of Fst was 0.20, demonstrating moderate genetic differentiation. The high genetic variability found in this study indicates the valuable genetic potential present in palm germplasm, which could be used for future improvement programs of the species.

Analysis of Genetic Diversity and Construction of a Core Collection of Ginkgo biloba Germplasm Using EST-SSR Markers

Understanding genetic diversity and population structure is essential for the conservation and utilization of germplasm. Ginkgo biloba L. is a medicinal, edible and ornamental tree species. Detailed knowledge of genetic variability and diversity in different Ginkgo germplasm resources is still scarce. In this study, a total of 173,160 Expressed Sequence Tag Simple Sequences Repeat (EST-SSR) loci were derived from 43,073 Unigenes of the Ginkgo genome. A total of 43,731 pairs of specific primers were designed for the EST-SSR loci, with sequence lengths >20 bp, and 100 of the SSR primers were randomly selected. Among these, 20 EST-SSR markers were verified and used to assess the genetic diversity of 101 Ginkgo individuals collected from different regions. The average values for Shannon’s diversity index (I, 0.993), expected heterozygosity (0.566) and Nei’s genetic diversity index (H, 0.563) indicate a high level of genetic diversity of Ginkgo populations. Based on the EST-SSR markers, a core collection of Ginkgo germplasm comprising 27 genetic resources was constructed. The retention rates of the number of resources, the number of alleles, the number of effective alleles, the I index, the H index and the percentage of polymorphic loci of the constructed core collection are 26.73%, 95.29%, 103.43%, 102.25%, 102.91% and 100.00%, respectively. The molecular markers developed in this study are an effective tool for Ginkgo genetic diversity analysis and will facilitate the future breeding of this species.

Morphometric Characteristics and Genetic Issr Marker Variability in Rhodiola rosea L. (Crassulaceae) in Different Ecological and Geographic Conditions in the Altai Republic.

Rhodiola rosea L. is a vulnerable species in the Altai Republic (AR) and Russia in general. For the first time on the territory of AR, studies of the adaptive capabilities of the species and genetic differentiation using ISSR markers were carried out in seven cenopopulations (CP) of R. rosea in 2018 and 2020. The research was founded on the notion of conducting a comparative analysis of the morphogenetic structure of Rhodiola rosea populations in various ecological and geographical conditions of AR. The aim of this work is to evaluate the variability of morphometric traits of sexually mature living female R. rosea plants and to conduct a comparative analysis of genetic variability in cenopopulations (CP) both under undisturbed conditions and under stressful conditions of anthropogenic impact (grazing). Of the 8 primers used, HB12 turned out to be the most informative. The percentage of polymorphic loci in the populations between 0 and 88%. Two populations, located in favorable conditions at relatively low absolute altitudes (2000 m above sea level) (masl) in the undisturbed habitats of the Katun and Altai reserves of AR, were characterized by higher polymorphism. The share of polymorphic loci reached 80%. According to the analysis of statistical data, the highest values of morphometric parameters of the aerial parts of R. rosea plants and the highest potential seed productivity were also recorded in these habitats. Representatives of two high-mountain CPs (2400-2500 masl) in the Sailyugemsky National Park (SNP) were characterized by the lowest genetic polymorphism. Their genetic structure is the most homogeneous, since we have not found polymorphic loci. Due to spatial isolation, these individuals are reliably genetically differentiated. In addition, individuals of one type were subjected to stressful anthropogenic impact (grazing). Therefore, the smallest sizes and lowest potential seed productivity were recorded. Our research shows that alpine populations of R. rosea in AR, under conditions of anthropogenic stress, need protection for their gene pool.

Exploration of transcriptome SSR markers and its application in genetic diversity assessment of Asarum sieboldii

To explore the genetic diversity of Asarum sieboldii this study developed SSR markers based on transcriptome sequencing results and five populations of A.sieboldii from different regions were used as samples for genetic diversity assessment using software such as GenALEx 6.5, NTSYS 2.1, and Structure 2.3.4. The results showed that 16 SSR markers with high polymorphism and good repeatability were selected from the A.sieboldii transcriptome. Primers designed based on the flanking sequences of these markers successfully amplified 56 polymorphic fragments from 150 individual samples of the five A.sieboldii populations. On average, each primer amplified 3.5 polymorphic fragments, ranging from 2 to 8. The mean values of expected heterozygosity(H_e), Shannon's diversity index(I), Nei's gene diversity index(H), and the polymorphic information content(PIC) were 0.172, 0.281, 0.429, and 0.382, respectively. The mean population differentiation coefficient(F_(ST)) was 0.588, consistent with the analysis of molecular variance(AMOVA) results, which indicated greater genetic variation among A.sieboldii populations(69%) than that within populations(31%). The percentage of polymorphic loci(PPL) ranged from highest to lowest as SNJ>LN>SY>SZ>TB. Principal coordinate analysis(PCoA) and UPGMA clustering analysis further revealed genetic clustering of A.sieboldii individuals based on their geographical distribution, consistent with the results of the structure clustering analysis. In summary, the SSR markers developed from the transcriptome effectively assessed the genetic differentiation and population structure of natural A.sieboldii populations, revealing a relatively low genetic diversity in A.sieboldii, with genetic variation primarily observed at the population level and a correlation between population differentiation and geographic distance.

Large scale genetic landscape and population structure of Ethiopian sesame (Sesamum indicum L.) germplasm revealed through molecular marker analysis

Sesame (Sesamum indicum L.) plays a crucial role in Ethiopian agriculture, serving both subsistence and commercial purposes. However, our understanding of the extensive genetic diversity and population structure of Ethiopian sesame remains limited. To address this knowledge gap, we genotyped 368 Ethiopian sesame germplasms, categorizing into four distinct breeding groups: Accessions, landraces, improved varieties, and wild types, using a comprehensive set of 28 polymorphic markers, including 23 simple sequence repeat (SSR) and five Insertion-Deletion (InDel) markers. These markers ensured robust genomic representation, with at least two markers per linkage group. Our results unveiled substantial genetic diversity, identifying a total of 535 alleles across all accessions. On average, each locus displayed 8.83 alleles, with observed and expected heterozygosity values of 0.30 and 0.36, respectively. Gene Diversity and Polymorphic Information Content (PIC) were recorded at 0.37 and 0.35. The percentage of polymorphic loci varied significantly among breeding groups, ranging from 8.00% to 82.40%, indicating high diversity in accessions (82.4%), moderate diversity in improved varieties (31.20%) and landraces (29.60%), and limited diversity in wild types (8.00). Analysis of Molecular Variance (AMOVA) results emphasized significant genetic differentiation among populations, with substantial diversity (P ​< ​0.001) within each population. Approximately 8% of the entire genetic diversity could be attributed to distinctions among populations, while the larger proportion of genetic diversity (92%) resided within each individual sesame population, showcasing heightened diversity within each group. Our study's findings received support from both Bayesian clustering and Neighbor-joining (NJ) analysis, reaffirming the credibility of our genetic structure insights. Notably, Population structure analysis at its highest Δk value (k ​= ​2) revealed the existence of two primary genetic clusters, further subdivided into four sub-populations at k ​= ​4. Similarly, NJ analysis identified two prominent clusters, each displaying additional sub-clustering. In conclusion, our research provides a comprehensive understanding of genetic groups, subpopulations, and overall diversity within Ethiopian sesame populations. These findings underscore the significant genetic diversity and population structure within Ethiopian sesame germplasm collections. This genetic richness holds promise for breeding and conservation efforts, highlighting the importance of preserving genetic diversity to ensure adaptation to changing environments and meet the needs of farmers and consumers.

Genetic diversity assessment of some Iraqi Sheep breeds using micro satellite DNA markers

To assess genetic diversity among some Iraqi sheep breeds (Karadi, Jaff, and Awassi) randomly selected from three different locations of Sulaimani governorate (Jeshana, Halabjai Shahid and Kirkuk) respectively. A total of 150 blood samples were collected (50 animals per breed from both sexes) using 10 microsatellite markers, 7 were amplified and showed bands. Four primers were polymorphism and three were monomorphism. The results demonstrated that the total fragment number (TFN) for the 7 primes was 14 fragments. The overall polymorphic fragments number (PFN) was 6, the highest PFN found at locus OarJMP29 which had 3 bands, whereas the lowest PFN found at locus HUJ616, OarFCB20 and OarFCB304 which was 1 band. The overall mean percentage of polymorphic loci was 35.71 %. The OarJMP29 locus showed the highest polymorphism which was 100% and the lowest polymorphism was 0.0% for ILSTS5, MAF214, and OarJMP58 loci. In the current study mean value of number of alleles (Na) was 2 and effective number of alleles (Ne) was 1.5214. Nei’s gene diversity and Shannon index are respectively averaged of 0.3296, and 0.5063. The smallest genetic distance recorded between Jaff and Awassi which was 0.0554, while the farthest distance was observed between Karadi and Awassi 0.1168.The results of genetic identity showed that the Jaff and Awassi populations are more genetically alike (0.9461) while the Karadi and the Awassi populations were the least genetically identical (0.8898). The dendrogram tree separated the studied breeds into two clusters, the first one including Jaff and Awassi breeds, and the second cluster includes Karadi breed. Finally, moderate value for both of polymorphism and genetic diversity were observed among the studied sheep breeds, which will help in developing a suitable approach for the genetic improvement, utilization and conservation of Iraqi sheep breeds.

Genetic evaluation of F2 and F3 interspecific hybrids of mung bean (Vigna radiata L. Wilczek) using retrotransposon‐based insertion polymorphism and sequence‐related amplified polymorphism markers

Mung bean (Vigna radiata L. Wilczek) is a self‐pollinating and indispensable pulse crop in Indonesia. While low yield productivity is a major concern, genetic improvement is possible through interspecific hybridization. However, interspecific hybridization is relatively infrequent and produces low recombination exchanges, significantly limiting crop breeding efficiency. Thus, a comprehensive study is needed of the selection and genetic diversity evaluation of progenies in advanced generations derived from interspecific hybridization using a specific molecular marker. This study aims to confirm the heterozygosity in the F2 population and assess the genetic diversity in F3 mung bean populations resulting from interspecific hybridization between the mung bean and common bean. We designed the retrotransposon‐based insertion polymorphism (RBIP) marker by identifying the syntenic regions in the flanking sequences of retrotransposon insertion in common bean and mung bean. The RBIP marker can be applied to distinguish the heterozygote progenies from the homozygote progenies. Six combinations of sequence‐related amplified polymorphism (SRAP) primers were used in the genotyping of F3 mung bean progenies. The SRAP marker showed a high degree of polymorphism of up to 100%, while high genetic variation was observed within the population (71%) of mung bean progenies. The F3.4 population had the greatest number of genotypes and displayed the highest number of effective alleles, private alleles, and percentage of polymorphic loci, suggesting the existence of high genetic diversity within this population. These genetic diversity data are exceptionally critical for future genetic research since it has potentially high yield production. The genomic and marker‐assisted selection studies will support the major goals of the mung bean breeding program.

Genetic diversity of an invasive tree across time and contrasting landscape conditions

Current biodiversity changes mostly result from human land-use changes and terrestrial biological invasions. These disturbances are often intermingled as invasive species often colonize fragmented habitats. No research has yet assessed fragmentation effects on the genetic diversity of invasive plant populations, incorporating both the relative onset of the invasion and habitat fragmentation processes. Here, we estimated the age of all sampled adult tree individuals of Glossy privet (Ligustrum lucidum) and assessed the genetic diversity of invasive populations established before and after the major events of habitat loss and fragmentation in the late 1980′s in Sierras Chicas, central Argentina. When considering all the individuals together within each forest condition, regardless of their relative age, we observed a mild but significant lower allelic richness and percent polymorphic loci in populations growing in fragmented conditions. However, when incorporating the relative age of individuals in the model, fragmentation effects are overridden and become non-significant; that is, both pre- and post-fragmentation individual cohorts show similar levels of genetic diversity in both landscape conditions. Interestingly, younger trees showed higher genetic diversity than older cohorts regardless of landscape condition, implying the occurrence of multiple introduction events since its initial spreading. Our results suggest that bird seed dispersal of this invasive tree species provides high connectivity across the landscape, maintaining and even increasing genetic diversity across time and space.

The Genetic Diversity and Genetic Structure of the Germplasm Resources of the Medicinal Orchid Plant Habenaria dentata.

Habenaria dentata has medicinal and ornamental value, but the number of wild populations is decreasing dramatically. Thus, conducting research on its genetic diversity and structure is necessary to provide a basis for its conservation. This study aimed to explore the genetic diversity of the wild plant H. dentata and protect and optimize its wild resources. The genetic diversity of 133 samples from six wild populations of H. dentata was analyzed using Inter Simple Sequence Repeat molecular markers to provide a scientific basis for the screening of improved germplasm resources. The results showed that the average number of alleles was 1.765, the average number of effective alleles was 1.424, the average Nei's gene diversity index was 0.252, the average Shannon diversity index was 0.381, and the average percentage of polymorphic loci was 76.499%. The variation within the populations was 77.34%, and the variation between the populations was 22.66%. The gene flow was 1.705, which was greater than 1. The results of the cluster analysis showed that the six populations were mainly divided into four clusters and were not classified according to their geographical location. There was no significant correlation between the geographical location and genetic distance between the populations (r = 0.557, p > 0.05). The genetic diversity of H. dentata is high. Among the six wild populations, the genetic diversity of the Mulun population was the highest and this population can be used as a key protection unit. The study on the genetic diversity of H. dentata can not only reveal the reasons for the decrease in the number of individuals in the population to a certain extent, and put forward the protection strategy, but also provide a scientific basis for the breeding of excellent seed resources.

Genetic Diversity and Population Structure of Juniperus seravschanica Kom. Collected in Central Asia.

Juniperus seravschanica Kom. is a species that grows widely in the mountain ranges from Central Asia to Oman. It is an important tree for the formation of shrub-forest massifs in mountainous areas and for draining and fixing soils from middle to high altitudes. A comprehensive study of the species' genetic diversity and population structure is a basic approach to understanding the current status of J. seravschanica resources for the development of future conservation strategies. Samples from 15 populations of J. seravschanica were collected from the mountain ranges of Uzbekistan, Kyrgyzstan, and Kazakhstan. The genetic diversity and population structure of 15 Central Asian populations of J. seravschanica were assessed using 11 polymorphic simple sequence repeat (SSR) markers. Genetic diversity parameters, including the number of alleles (na), the effective number of alleles (ne), Shannon's information index (I), the percentage of polymorphic loci (PPL), Nei's genetic diversity index (Nei), principal coordinate analysis (PCoA), etc., were evaluated. The analysis of 15 J. seravschanica populations based on 11 polymorphic SSRs detected 35 alleles. The average PIC value was 0.432, and the highest value (0.662) was found in the JT_40 marker. Nei's genetic diversity index for the J. seravschanica populations was 0.450, ranging from 0.407 (population 14) to 0.566 (population 4). The analysis of molecular variance (AMOVA) showed that 90.3% of total genetic variation is distributed within the population. Using the alleles of all the populations, the gene flow (Nm) was found to be 4.654. Population structure analysis revealed poor clustering in the studied populations and confirmed our AMOVA results. The output of this work can be efficiently used for the maintenance of the species across the Central Asian region.

Identification of ROH Islands Conserved through Generations in Pigs Belonging to the Nero Lucano Breed.

The recovery of Nero Lucano (NL) pigs in the Basilicata region (Southern Italy) started in 2001 with the collaboration of several public authorities in order to preserve native breeds that can play a significant economic role both due to their remarkable ability to adapt to difficult environments and the value of typical products from their area of origin. In this study, by using the Illumina Porcine SNP60 BeadChip, we compared the genetic structures of NL pigs reared in a single farm in two different periods separated by a time interval corresponding to at least three generations. The results showed an increase in the percentage of polymorphic loci, a decrease in the inbreeding coefficient calculated according to ROH genome coverage (FROH), a reduction in the number of ROH longer than 16 Mb and an increase in ROH with a length between 2 and 4 Mb, highlighting a picture of improved genetic variability. In addition, ROH island analysis in the two groups allowed us to identify five conserved regions, located on chromosomes 1, 4, 8, 14 and 15, containing genes involved in biological processes affecting immune response, reproduction and production traits. Only the conserved ROH island on chromosome 14 contains markers which, according to the literature, are associated with QTLs affecting thoracic vertebra number, teat number, gestation length, age at puberty and mean platelet volume.

SSR and 18S rDNA based molecular profiling of Neopyropia yezoensis (Rhodophyta) in China: insight into genetic impact of laver aquaculture on wild resource

Neopyropia yezoensis is a typical intertidal seaweed and an indispensable species for conservation of seaweed resources. As one of the most important marine vegetables, the cultivation area of N. yezoensis has been largely increasing in the past decade and ranked the second highest among all the farmed seaweeds in China. It remains unknown whether large-scale cultivation of N. yezoensis has a genetic impact on wild populations. In this study, SSR markers and 18S rDNA were applied for diversity and genetic structure analysis of 22 N. yezoensis populations from North China. Twenty-two haplotypes were generated from 352 18S rDNA sequences and only three haplotypes were shared by both cultivated and wild populations. Based on 11 polymorphic SSR markers developed, the average polymorphism of the cultivated N. yezoensis populations was higher than that of the wild populations, with the percentage of polymorphic loci being 90.91% in most cultivated populations. The cultivated populations were clustered separately from the wild ones based on the population phylogenetic tree. This indicates that cultivated N. yezoensis populations are diverse and divergent from wild populations in China. However, there were cultivated individuals mixed with the wild ones based on the individual phylogenetic tree and STRUCTURE analysis. The genetic differentiation between cultivated and wild populations decreased with increasing cultivation time, suggesting a possible long-term and slow process of genetic introgression between cultivated N. yezoensis and the wild resource. The wild populations were grouped into two distinct clades by SSRs, with one distributed around the intersection between the Yellow Sea and the Bohai Sea, where the populations were characterized by a specific 18S rDNA haplotype. These findings provide useful insights into germplasm conservation, genetic breeding and improvement of N. yezoensis farming practices.

MOLECULAR DIVERSITY IN POPULATIONS OF CHILI (CAPSICUM ANNUUM L.)

Chili (Capsicum annuum L.) is a self-pollinated crop, with natural cross-pollination occurring below 4%–5%. It intends to have low heterosis. Developing cross-pollination in chili currently receives much attention to achieve diversity in trait improvement. Double-crossing becomes one of the alternatives to achieving this goal. In this study, three different parental chili genotypes (K, B, and T) gained crossing, with four populations (S2 K, F3 KB, F2 BTKB, and F2 KBBT) developed. Using 11 selected sequence-related amplified polymorphism (SRAP) combination markers that target Open Reading Frame (ORF) regions assessed molecular diversity in these chili populations. Results revealed the possibility of identifying diversity using SRAP markers based on primer profile information. The iMEC analysis showed high values of PIC (0.3381), discriminant power (0.882), and mean polymorphic value (97.88%). The highest similarity emerged between the populations BTKB and KBBT as the reciprocal. Then, the smallest similarity appeared between K and the double cross. Compared with the self-pollinated genotype, SRAP primers discovered that double crosses provided more variation based on Shannon’s index (I) and percentage of polymorphic loci (PPL). The genetic distance denotes maternal inheritance or extraneous involvement in progeny. However, multiple-parent hybridization authenticated the boost in genetic diversity.

Infraspecific genetic diversity and seed fatty acid composition in Sesamum indicum L. populations (Pedaliaceae) in Iran

Sesamum indicum L. of the Pedaliaceae family is considered an economically important oil-bearing plant that has been cultivated for more than 5000 years. In this research, we examined genetic diversity and seed fatty acid composition in 11 Iranian populations of S. indicum. We extracted the nuclear DNA using the CTAB protocol and then amplified the genomes using 10 SCoT molecular primers. For the phytochemical study, the seed fatty acid methyl esters were subjected to a GC apparatus and their composition was determined. The data were then analyzed using PAST, POPGENE, Geno-Dive, and STRUCTURE software. We determined that the percentage of polymorphic loci was 62%. According to the AMOVA test and estimated genetic diversity parameters, high genetic differentiation occurred between the examined populations, which was followed by a low rate of gene flow and Hs. Based on the Nei's genetic distance and Structure analysis, the populations were divided into seven genotype groups. Most identified genotypes had homogeneous genetic structures indicating a limited genetic flow rate. The phytochemical evaluation revealed that a great part of the seed oils was composed of unsaturated fatty acids with linoleic and oleic acids as the main compounds. We detected palmitic acid as the major saturated fatty acid. The populations were divided into four chemotype groups based on the seed oil fatty acids composition. However, the population clustering patterns in the molecular genetic and seed fatty acid analyses were not identical. These results indicated that some environmental parameters strongly affect the seed oil fatty acids composition. We suppose that the populations under study are comprised of several genotypes or cultivars grown in various Iranian locations.