Average Effective Number Of Alleles Research Articles

Microsatellite marker-based analysis of the genetic diversity and population structure of three Arnebiae Radix in western China

Arnebiae Radix is an important medicinal and perennial herb found in Western China, particularly in the Xinjiang region. However, the assessment, utilization and conservation of Arnebiae Radix resources are still unexplored. In this study, we evaluated the genetic diversity of three Arnebiae Radix populations across 47 regions (Ae = 16, Ag = 16, Ad = 15) in Xinjiang, China, using inter-simple sequence repeat (ISSR) molecular markers. In total, 48 alleles were amplified by six pairs of primers screened with ISSR markers. The average number of effective alleles (Ne) was 1.5770. The percentage of interspecific genetic polymorphisms in A. guttata (Ag = 89.58 %) was greater than that in A. euchroma. and A. decumbens (Ae = Ad = 87.50 %). Intraspecific genetic polymorphisms, Bo Le (BL) population of A. euchroma exhibited the highest percentage of polymorphic bands (PPB% =58.33 %, Na = 1.313, Ne = 1.467, I = 0.0.366, H = 0.255), which indicated high genetic diversity. In contrast, the Tuo Li (TL) population of A. guttata had the lowest values for these parameters (PPB% =0.00 %, Na = 0.313, Ne = 1,000, I = 0.000, H = 0.000). The Arnebiae Radix germplasms were classified into two major groups (I and II) based on UPGMA cluster analysis (Fig. 8a) and principal coordinate analysis (PCOA). In addition, A. decumbens is placed in a separate category due to its high differentiation coefficient. The AMOVA and genetic differentiation coefficient results indicated that the genetic variation in Arnebiae Radix was predominantly due to intrapopulation differences (78 %). Additionally, the gene flow index (Nm) between populations was 2.4128, which further indicated that the genetic diversity of Arnebiae Radix was greater at the intrapopulation level. The destruction of the ecological environment leads to the continuous reduction and degradation of the genetic diversity of Arnebiae Radix germplasm resources. In this study, we used ISSR molecular markers to analyze the genetic diversity and relatedness of Arnebiae Radix, which revealed the genetic relationship of Arnebiae Radix germplasm resources at the molecular level and provided a scientific basis for future research on selecting and breeding good varieties, evaluating the quality of Arnebiae Radix, and conserving and utilizing its resources.

Genetic background of lily germplasm resources based on SSR markers

To study the genetic background of lily (Lilium spp.) germplasm resources, and accurately evaluate and select excellent germplasm for genetic improvement of lily, we analyzed the genetic background of 62 lily germplasm accessions from 11 provinces of China by using simple sequence repeat (SSR) molecular markers. The results showed that 15 out of 83 pairs of lily SSR primers were polymorphic. A total of 157 allelic loci were amplified, with the number of alleles per locus ranging from 5 to 19 and the average number of effective alleles per locus being 4.162 8. The average observed heterozygosity and expected heterozygosity were 0.228 2 and 0.694 1, respectively. The average polymorphic information content was 0.678 8. The average Nei's diversity index and Shannon's information index were 0.694 1 and 1.594 9, respectively, indicating that the tested lily germplasm had high genetic diversity. The 62 germplasm accessions were classified into 5 groups by the unweighted pair group method with arithmetic mean (UPGMA) and into 3 groups by the principal component analysis. The two analyses revealed a geographic correlation among different groups. The majority of lily germplasm accessions from the same source tended to cluster together. The population structure analysis classified the lily accessions into 4 populations and 1 mixed population. The above results provide a theoretical basis and genetic resources for the precise identification and breeding of lily germplasm resources.

Genetic variability and population divergence of Rhododendron platypodum Diels in China in the context of conservation

Genetic diversity in endangered species is of special significance in the face of escalating global climate change and alarming biodiversity declines. Rhododendron platypodum Diels, an endangered species endemic to China, is distinguished by its restricted geographical range. This study aimed to explore genetic diversity and differentiation among its populations, gathering samples from all four distribution sites: Jinfo Mountain (JFM), Zhaoyun Mountain (ZYM), Baima Mountain (BMM), and Mao’er Mountain (MEM). We employed 18 pairs of Simple Sequence Repeat (SSR) primers to ascertain the genetic diversity and structural characteristics of these samples and further utilized 19 phenotypic data points to corroborate the differentiation observed among the populations. These primers detected 52 alleles, with the average number of observed alleles (Na) being 2.89, the average number of effective alleles (Ne) being 2.12, the average observed heterozygosity (Ho) being 0.57, and the expected heterozygosity (He) being 0.50. This array of data demonstrates the efficacy of the primers in reflecting R. platypodum’s genetic diversity. SSR-based genetic analysis of the populations yielded Ho, He, and Shannon index (I) values ranging from 0.47 to 0.65, 0.36 to 0.46, and 0.53 to 0.69, respectively. Notably, the ZYM population emerged as the most genetically diverse. Further analysis, incorporating molecular variance, principal component analysis, UPGMA cluster analysis, and structure analysis, highlighted significant genetic differentiation between the Chongqing (BMM, JFM, ZYM) and Guangxi (MEM) populations. Morphological data analysis corroborated these findings. Additionally, marked genetic and morphological distinctions were evident among the three Chongqing populations (BMM, JFM, and ZYM). This suggests that, despite the observed regional differentiation, R. platypodum’s overall genetic diversity is relatively constrained compared to other species within the Rhododendron genus. Consequently, R. platypodum conservation hinges critically on preserving its genetic diversity and protecting its distinct populations.

Performance of a 74-Microhaplotype Assay in Kinship Analyses.

Microhaplotypes (MHs) consisting of multiple SNPs and indels on short stretches of DNA are new and interesting loci for forensic genetic investigations. In this study, we analysed 74 previously defined MHs in two of the populations that our laboratory provides with forensic genetic services, Danes and Greenlanders. In addition to the 229 SNPs that originally made up the 74 MHs, 66 SNPs and 3 indels were identified in the two populations, and 45 of these variants were included in new definitions of the MHs, whereas 24 SNPs were considered rare and of little value for case work. The average effective number of alleles (Ae) was 3.2, 3.0, and 2.6 in Danes, West Greenlanders, and East Greenlanders, respectively. High levels of linkage disequilibrium were observed in East Greenlanders, which reflects the characteristics of this population that has a small size, and signs of admixture and substructure. Pairwise kinship simulations of full siblings, half-siblings, first cousins, and unrelated individuals were performed using allele frequencies from MHs, STRs and SNPs from Danish and Greenlandic populations. The MH panel outperformed the currently used STR and SNP marker sets and was able to differentiate siblings from unrelated individuals with a 0% false positive rate and a 1.1% false negative rate using an LR threshold of 10,000 in the Danish population. However, the panel was not able to differentiate half-siblings or first cousins from unrelated individuals. The results generated in this study will be used to implement MHs as investigative markers for relationship testing in our laboratory.

Morphological and molecular diversity of eggplant accessions (Solanum melongena L) using Simple Sequence Repeats (SSR) markers

The evaluation of various desirable characteristics in eggplant genotypes has facilitated the efficient process of selecting and improving their traits. Morphological parameters have proven to be valuable in assessing the similarities or differences among different accessions, while molecular data have been used to support the conclusions drawn from the morphological analysis. This study was conducted to evaluate the performance of 42 eggplant genotypes collected from Malaysia, China, and Thailand. Data for growth, yield, and related traits were collected and subjected to analysis of variance (ANOVA) using SAS 9.4. The field trial experiment was designed as a completely randomized block design with three replications. Analysis of variance (ANOVA) showed that the traits under study were highly significant (p ≤ 0.01). MV18 (5.97 kg) and TV17 (5.59 kg) were observed to have high yields per plant. The SSR markers used exhibited moderate average values for the number of alleles (2.53). The major allele frequency displayed a high average value (0.53) and a moderate average number of effective alleles (2.31). Additionally, the observed Shannon's information index, expected heterozygosity, and PIC were high (0.84, 0.54, and 0.45, respectively). 42 accessions were grouped into five major clusters based on similarities using the unweighted pair-group method with arithmetic averages based on similarity matrices UPGMA Dendrogram and the EIGEN module. The findings of this study indicate that the use of simple sequence repeat (SSR) markers can effectively estimate genetic diversity and analyze phylogenetic relationships. Moreover, these markers can assist eggplant breeders in selecting desirable quantitative traits within their breeding program.

ИЗУЧЕНИЕ ПОЛИМОРФИЗМА МИКРОСАТЕЛЛИТНЫХ ЛОКУСОВ ОБРАЗЦОВ ВИНОГРАДА С НЕИДЕНТИФИЦИРОВАННОЙ СОРТОВОЙ ПРИНАДЛЕЖНОСТЬЮ АМПЕЛОГРАФИЧЕСКОЙ КОЛЛЕКЦИИ «МАГАРАЧ» С ИСПОЛЬЗОВАНИЕМ МОЛЕКУЛЯРНЫХ МАРКЕРОВ

The paper presents the results of DNA profiling of 28 grape samples with unidentified varietal affiliation, selected from the Magarach Ampelographic Collection, and provides polymorphism assessment of their microsatellite loci. Genotyping was performed using 9 nuclear (VVMD5, VVMD7, VVMD25, VVMD27, VVMD28, VVMD32, VrZAG62, VrZAG79, VVS2) and 3 chloroplast (ccmp3, ccmp5, ccmp10) SSR markers. For nuclear loci, 105 alleles were identified, the average number of alleles per locus (na) was 11.7; the average effective number of alleles (ne) is 7.23; Shannon information index (I) for the studied batch of samples was 2.13. The highest allele frequency was observed in samples with VVS2133 and VVS2135 (p = 0.250), VVMD5238 (p = 0.232), VVMD7247 (p = 0.232), VVMD25239 (p = 0.250), VVMD27180 (p = 0.232), VVMD28236 (p = 0.143), VVMD32272 (p = 0.304), VrZAG62188 (p = 0.179), VrZAG79251 (p = 0.232) alleles. The average value of actual heterozygosity Heto was 0.8333, expected heterozygosity Hetе was 0.8712. For chloroplast loci, 7 alleles were identified: ccmp3106, ccmp3107, ccmp5104, ccmp5105, ccmp10114, ccmp10115, ccmp10116. Also 4 chlorotypes were identified: A (1 sample), B (9), C (13), D (5). A dendrogram of genetic similarity was constructed using the UPGMA method, which showed the presence of three clusters containing, respectively, 11, 11 and 6 samples. There was a uniform distribution of chlorotypes B and D over three clusters, and chlorotype C – over two clusters. It is concluded that the results can be used to assess the genetic diversity of Magarach Ampelographic Collection.

Analysis of the genetic diversity and population structures of black locust (Robinia pseudoacacia L.) stands in Poland based on simple sequence repeat markers

Abstract Black locust (Robinia pseudoacacia L.) was introduced in Poland over 200 years ago, and its distribution area now covers the whole country, with the highest concentration of occurrence in the western part. Breeding of this species has been started in Poland for about 20 years, albeit on a limited scale, and two selected seed stands, 34 plus trees and two seed orchards have been registered. So far, selection efforts have not been coupled with the recognition of variation in the genetic structure of local populations. To fill the knowledge gap on genetic diversity, we selected the seven qualitatively best populations of R. pseudoacacia for our study. To clarify the origin of the Polish population of R. pseudoacacia, a sample from a seed stand in eastern Germany and from a seed orchard with Hungarian clones from the Oborniki Śląskie Forest District was added. In this study, three microsatellites were used to evaluate genotypes: Rops15, Rops16 and Rops18, with the Rops15 locus (motif AG) showing hypermutability. Moderate or high variability was observed in all microsatellite loci examined, with a total of 27 alleles identified. In all stands, the average observed number of alleles per locus was higher than the average effective number of alleles per locus. Three main clusters have been identified in the genetic structure of the population, one of which is represented by the population from the Regional Directorate of State Forests in Zielona Góra. The second group comprised the populations from Mieszkowice, the populations Pińczów and Wołów, and the population from Germany. The last one included population from Strzelce and Oborniki Śląskie, where the population from Hungary is represented. This may be of great importance for practice. Perhaps it is worth postulating the separation of two seed regions. Under most scenarios, climate change is projected to change the distribution of forest types and tree species in all biomes. It can be assumed that the importance of black locust in times of climate change is likely to increase.

Improving DNA mixtures analysis using compound markers composed of InDels and SNPs screened from the whole genome with next-generation sequencing.

Next-generation sequencing (NGS) allows for better identification of insertion and deletion polymorphisms (InDels) and their combination with adjacent single nucleotide polymorphisms (SNPs) to form compound markers. These markers can improve the polymorphism of microhaplotypes (MHs) within the same length range, and thus, boost the efficiency of DNA mixture analysis. In this study, we screened InDels and SNPs across the whole genome and selected highly polymorphic markers composed of InDels and/or SNPs within 300bp. Further, we successfully developed and evaluated an NGS-based panel comprising 55 loci, of which 24 were composed of both SNPs and InDels. Analysis of 124 unrelated Southern Han Chinese revealed an average effective number of alleles (Ae ) of 7.52 for this panel. The cumulative power of discrimination and cumulative probability of exclusion values of the 55 loci were 1-2.37×10-73 and 1-1.19×10-28 , respectively. Additionally, this panel exhibited high allele detection rates of over 97% in each of the 21 artificial mixtures involving from two to six contributors at different mixing ratios. We used EuroForMix to calculate the likelihood ratio (LR) and evaluate the evidence strength provided by this panel, and it could assess evidence strength with LR, distinguishing real and noncontributors. In conclusion, our panel holds great potential for detecting and analyzing DNA mixtures in forensic applications, with the capability to enhance routine mixture analysis.

Genetic diversity, population structure, and DNA fingerprinting of Ailanthus altissima var. erythrocarpa based on EST-SSR markers

Ailanthus altissima var. erythrocarpa is an A. altissima variety with high economic, ecological and ornamental value, but there have been no reports on the development of SSR primers for it. According to the SSR primer information provided by the transcriptome of A. altissima var. erythrocarpa, 120 individuals with different redness levels were used to screen polymorphic primers. Transcriptomic analysis revealed 10,681 SSR loci, of which mononucleotide repeats were dominant (58.3%), followed by dinucleotide and trinucleotide repeats (16.6%, 15.1%) and pentanucleotide repeats (0.2%). Among 140 pairs of randomly selected primers, nineteen pairs of core primers with high polymorphism were obtained. The average number of alleles (Na), average number of effective alleles (Ne), average Shannon’s diversity index (I), average observed heterozygosity (Ho), average expected heterozygosity (He), fixation index (F) and polymorphic information content (PIC) were 11.623, 4.098, 1.626, 0.516, 0.696, 0.232 and 0.671, respectively. Nineteen EST-SSR markers were used to study the genetic diversity and population structure of A. altissima var. erythrocarpa. The phylogenetic tree, PCoA, and structure analysis all divided the tested resources into two categories, clearly showing the genetic variation between individuals. The population showed high genetic diversity, mainly derived from intraspecific variation. Among nineteen pairs of primers, 4 pairs (p33, p15, p46, p92) could effectively distinguish and be used for fingerprinting of the tested materials. This study is of great significance for genetic diversity analysis and molecular-assisted breeding of A. altissima var. erythrocarpa.

Exploring the Genetic Diversity and Population Structure of Daphnia cucullata Sars, 1862 in Boreal Lakes (Latvian Lakeland) Based on Microsatellites

We have used Daphnia cucullata (Crustacea: Cladocera) as a model organism for the first time in the four deepest Latvian lakes from the Boreal biogeographical region in order to find the genetic diversity of these populations. During the research, we detected the most appropriate microsatellite markers for future genetic studies of Daphnia cucullata populations of lakes Svente, Riča, Dridzis and Geraņimovas-Ilzas in the Boreal biogeographical region. Based on these microsatellite markers, we determined the genetic diversity of these populations. The loci Dgm105 and Dgm101 had the maximum number of alleles and the maximum number of private alleles. The specific locus Dgm105 had five private alleles (62% of all detected alleles), and locus Dgm101 had four private alleles (57% of all detected alleles) in these loci. We determined the observed heterozygosity (Hobs) and the expected heterozygosity (Hexp) level (via Hardy–Weinberg equilibrium), the number of polymorphic loci, the number of detected alleles in each analyzed microsatellite locus, the average number of alleles at the locus (Na), the average effective number of alleles at the locus (Ne), the FST of the population’s genetic differentiation, the genetic distance (D) (following Nei) and the significance (χ2-test) of differences between the levels of observed and expected heterozygosity. It was shown that Daphnia cucullata populations from lakes with a low number of zooplankton taxa (Riča and Geraņimovas-Ilzas) have a higher genetic diversity compared to lakes with a high number of zooplankton taxa (Dridzis and Svente). It was found that Daphnia cucullata populations from lakes Dridzis and Svente have the least genetic distance, and these populations form a single genetic group, as confirmed via clustering.

SSR marker based profiling and population structure analysis in peach (Prunus persica) germplasm

For breeding programmes to be successful and for germplasm conservation, it is essential to characterize and analyze the genetic diversity of available germplasm. The present experiment was conducted at Molecular Biology and Genetic Engineering Laboratory of Uttarakhand Council for Biotechnology, Haldi, Uttarakhand during 2022 to study the molecular profile of 41 peach [Prunus persica (L.) Stokes] accessions using 23 polymorphic SSR markers. The number of alleles detected ranged from 3 to 8 with an average of 4.65 alleles per locus (Na) and a total of 107 alleles were amplified. The average effective number of alleles (Ne) were 2.89 per marker. The SSR marker MA015a produced maximum number of 8 alleles followed by BPPCT 015 and CPPCT14 which produced 7 alleles each. The polymorphic information content (PIC) varied between 0.317–0.836 with a mean value of 0.563. The observed heterozygosity examined was lower (Ho = 0.02) and the expected heterozygosity (He = 0.61) ranged between 0.34 to 0.85. The presence of a higher Shannon’s information index (I) of 1.17 indicates higher diversity in the given set of peach genotypes. Jaccard’s similarity coefficient ranging from 0.533 to 1, indicated a pair-wise relationship among the peach accessions. The cluster dendrogram partitioned the accessions into two main clusters. However, the total accessions were stratified into 3 groups (K=3) based on population structure analysis which was further confirmed by Principal Coordinate Analysis (PCoA). The information generated in the study may have great implications in molecular characterization, fingerprinting and documentation of accessions in the peach improvement programme.

김해 야생차 군락지들의 차나무에 대한 유전적 다양성 분석

This study examined the genetic diversity of 13 tea tree samples to establish a variety discrimination system for the three Gimhae wild tea colonies using ISSR markers and to provide basic data for genetic diversity analysis. Seven primers that showed polymorphic and reproducible results among 100 ISSR universal primers were selected and used to amplify the genomic DNA of the 13 tea trees from three Gimhae wild tea colonies. The results demonstrated that all seven primers generated 117 bands with a 100% polymorphic band ratio. The average observed number of alleles was 2.0. The average effective number of alleles was 1.5323, while the average Nei's gene diversity was 0.3271. The average Shannon's Information index was 0.5001. The genetic similarity among the 13 tea tree samples ranged from 0.4444 to 0.8718, while the genetic distance ranged from 0.1372 to 0.8109. The 13 tea trees in three Gimhae wild colonies displayed a high level of genetic diversity, and the Dongsangdong and Sangdong samples in the three Gimhae wild colonies had a genetic similarity greater than 0.8 with Chinese tea species, indicating a close relationship with Chinese tea. Overall, these findings provide a theoretical basis for preserving and cultivating Gimhae wild tea trees.

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 phylogenetic relationship of Angus herds in Hungary and analyses of their production traits.

This study aims to investigate the genetic structure and characteristics of the Angus cattle population in Hungary. The survey was performed with the assistance of the Hungarian Hereford, Angus, Galloway Association (HHAGA). Genetic parameters of 1,369 animals from 16 Angus herds were analyzed using the genotyping results of 12 microsatellite markers with the aid of PowerMarker, Genalex, GDA-NT2021, and STRUCTURE software. Genotyping of DNA was performed using an automated genetic analyzer. Based on pairwise identity by state values of animals, the Python networkx 2.3 library was used for network analysis of the breed and to identify the central animals. The observed numbers of alleles on the 12 loci under investigation ranged from 11 to 18. The average effective number of alleles was 3.201. The overall expected heterozygosity was 0.659 and the observed heterozygosity was 0.710. Four groups were detected among the 16 Angus herds. The breeders' information validated the grouping results and facilitated the comparison of birth weight, age at first calving, number of calves born and productive lifespan data between the four groups, revealing significant differences. We identified the central animals/herd of the Angus population in Hungary. The match of our group descriptions with the phenotypic data provided by the breeders further underscores the value of cooperation between breeders and researchers. The observation that significant differences in the measured traits occurred among the identified groups paves the way to further enhancement of breeding efficiency. Our findings have the potential to aid the development of new breeding strategies and help breeders keep the Angus populations in Hungary under genetic supervision. Based on our results the efficient use of an upcoming genomic selection can, in some cases, significantly improve birth weight, age at first calving, number of calves born and the productive lifespan of animals.

Genetic Diversity and Core Germplasm Research of 144 Munake Grape Resources Using 22 Pairs of SSR Markers

The Munake grape is a local variety of grape that is widely distributed in Xinjiang, China. This study aims to clarify the genetic structure of the Munake grape population, characterize genetic differentiation and gene flow among populations, gather germplasm, and establish the core germplasm collection. In total, 144 samples were collected from eight geographic populations. Twenty-two SSR markers were used to characterize the genetic diversity as well as the genetic structure of Munake grape germplasm and to establish the core germplasm collection. At each site, the average number of effective alleles (Ne) was 5.019. Overall, genetic diversity was high in the various geographic populations of Munake grapes. Polymorphic information content (PIC) ranged from 0.501 to 0.908, with an average of 0.728. Estimates of genetic differentiation and gene flow indicated that the Artux population had significant genetic differences from the other populations. Screening results indicated that a sampling proportion of 95% of the sample was required to achieve 100% allelic coverage, or a sampling proportion of 65% for 95% allelic coverage. This analysis was based on conventional genetic diversity indicators, with a core germplasm diversity index of 95% coverage. Characterization of the genetic diversity of germplasm from 144 Munake grapes not only provides valuable resources for future genetic mapping and functional genome research, but also facilitates the utilization of core germplasm and molecular breeding of Munake grapes.

Genetic diversity analysis and fingerprints of Chrysanthemum×morifolium based on SSR molecular markers

The present study aims to explore the genetic diversity of germplasm resources of Chrysanthemum×morifolium (hereinafter, C.×morifolium) at the molecular level and to establish a fingerprint database of C.×morifolium varieties. We employed 12 pairs of primers with high levels of polymorphism, clear bands, and high degrees of reproducibility to analyze the SSR molecular markers and genetic diversity of 91 C.×morifolium materials and 14 chrysanthemum- related materials. With regard to constructing the fingerprints of the tested materials, we chose 9 pairs of core primers. The findings revealed that 12 primer pairs detected 104 alleles in 105 samples, ranging from 2 to 26. The average number of observed alleles (Na) per site was 9.25. The average number of effective alleles (Ne) per site was 2.745 6, with its range being 1.276 0 to 4.742 5. Shannon genetic diversity index (I) values ranged between 0.513 3 and 2.239 9 (M=1.209 0). Nei's gene diversity index (H) ranged between 0.216 3 and 0.789 1 (M=0.578 0). The observed heterozygosity (Ho) ranged between 0.223 3 and 0.895 2 (M=0.557 5). The expected heterozygosity (He) ranged between 0.217 4 and 0.793 3 (M=0.580 8). The polymorphism information content (PIC) ranged between 0.211 5 and 0.774 0 (M=0.532 9). The genetic similarity (GS) ranged between 0.228 5 and 1.000 0 (M=0.608 3). Cluster analysis revealed that when the genetic distance (GD) equals to 0.30, the tested materials can be classified into 2 groups. When the GD equals to 0.27, the first group can be divided into 6 subgroups; accordingly, 105 tested materials can be divided into 7 subgroups. The cophenetic correlation test was carried out based on the cluster analysis, and the corresponding results showed that the cluster map correlated with the genetic similarity coefficient (r=0.952 73). According to the results of Structure population analysis, we obtained the optimal population number, with the true number of populations (K) being 3 and the population being divided concerning Q≥0.5. Three subgroups, i.e., Q1, Q2 and Q3, included 34, 33 and 28 germplasms, respectively, and the remaining 10 germplasms were identified as the mixed population. During the experiment, 9 pairs of core primers were screened among the total of 12 for a complete differentiation regarding 105 tested materials, and the fingerprints of 91 C.×morifolium materials and 14 chrysanthemum-related materials were further constructed. Overall, there were significant genetic differences and rich genetic diversity among C.×morifolium materials, which would shed light on the garden application and variety selection fields of C.×morifolium. The fingerprint database of 105 C.×morifolium varieties and chrysanthemum-related species may provide technical support for future research regarding the identification and screening system of C.×morifolium varieties.

Genetic Diversity Analysis and Core Germplasm Collection Construction of Camellia oleifera Based on Fruit Phenotype and SSR Data.

Many Camellia oleifera germplasm resources were collected from Guizhou Province, but the fruit morphological variation and genetic diversity of C. oleifera germplasm resources remain unclear. The genetic diversity of C. oleifera germplasms resources in Guizhou was studied based on fruit traits and simple sequence repeat (SSR) molecular markers to build a core collection. This paper aims to provide a scientific basis for the collection, management, development, and utilization of C. oleifera resources in Guizhou province. The variation coefficients among and within varieties of seven fruit phenotypic traits of C. oleifera ranged from 11.79% to 61.76% and from 8.15% to 42.31%, respectively, showing rich phenotypic variation. Furthermore, 12 SSR markers were used to analyze the genetic diversity. These primers generated 214 polymorphic bands, and the average number was 17.833. The average number of effective alleles (Ne), Shannon's information index (I), observed heterozygosity (Ho), expected heterozygosity (He), polymorphic information content (PIC), and major allele frequency (MAF) were 8.999, 2.301, 0.965, 0.50, 0.836, and 0.238, respectively. The results showed that 12 SSR markers had high polymorphism, and the genetic diversity of 167 C. oleifera germplasm resources was high. Based on SSR molecular marker information and fruit traits clustering, 167 C. oleifera germplasm resources were divided into three groups. When constructing core collections based on fruit traits and molecular marker information, the PowerCore-25 of core collections greatly preserves fruit traits and improves genetic diversity. This paper can provide a reference for the genetic diversity and fruit traits variation of C. camellia germplasm resources in Guizhou Province. It is significant for establishing a core collection, thus promoting germplasm innovation and the development of the oil tea industry in Guizhou.

Application of a custom haplotype caller to analyze sequence-based data of 56 microhaplotypes

Microhaplotypes (microhaps) are recently introduced markers that aim to complement the limitations of conventional forensic markers such as short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). With the potential of microhaps in forensics becoming clearer through massively parallel sequencing (MPS), MPS-based studies on microhaps are being actively reported. However, simpler workflow schemes for the generation and analysis of MPS data are still required to facilitate the practical application of MPS in forensics. In this study, we developed an in-house MPS panel that simultaneously amplifies 56 microhaps and a custom haplotype caller, Visual Microhap. The developed tool works on a web browser and provides four analysis options to extract SNP-based haplotypes from sequence-based data obtained by STRait Razor 3.0. To demonstrate the utility of the MPS panel and data analysis workflow scheme, we also analyzed 56 microhaps of 286 samples from four populations (African-American, Caucasian, Hispanic, and Korean). The average effective number of alleles (Ae) for the four groups was 3.45, ranging from 1.74 to 6.98. Forensic statistical parameters showed that this microhap panel is more powerful than conventional autosomal STRs for human identification. Meanwhile, the 56-plex panel mostly comprised microhaps with high Ae; however, the four populations were grossly distinguishable from each other by cluster analysis. Consequently, the developed in-house MPS panel for 56 microhaps and the adopted workflow using open-source tools can increase the utility of microhap MPS in forensic research and practice.

Exploring genetic diversity and Population structure of five Aegilops species with inter-primer binding site (iPBS) markers.

Turkey is not only a center of origin for wheat, but also contains wild forms of various cereals. Turkey, located in the Fertile Crescent, has conserved its genetic richness to the present day. The aim of the study was to investigate the genetic diversity of 70 wild wheat species, to evaluate the structure of diversity in germplasm and to generate useful data for further breeding programs. Genetic diversity and population structure of 70 wild wheat species (Ae. cylindrica, Ae. geniculata, Ae. triuncialis, T. dicocoides, Ae. columnaris) collected from Eastern and Southeastern Anatolia regions of Turkey were investigated in this study with the use of inter-primer binding site (iPBS) markers. Of 35 iPBS primers used, 11 yielded a total of 61 alleles. Number of alleles per marker varied between 2 (iPBS-2085) and 9 (iPBS-2394) with an average value of 5.55. Polymorphic information content (PIC) values varied between 0.22 and 0.47, with an average value of 0.35. Average number of effective alleles (Ne) was identified as 1.9488, Nei's genetic diversity (H) as 0,4861 and Shannon's information index (I) as 0.6791. Cluster analysis through unweighted pair-group mean average (UPGMA) method revealed that 70 wild wheats were divided into three main clusters. Genetic similarity between the genotypes, calculated with the use of NTSYS-pc software, varied between 19% (YB2 and YB70) and 98% (YB66 and YB67). Principal coordinate analysis (PCoA) revealed that three principal coordinates explained 62.33% of total variation. Moreover, population structure analysis showed that all genotypes formed three sub-populations. Expected heterozygosity values varied between 0.2666 (the first sub-population) and 0.2330 (third sub-population), with an average value of 0.2500. Average population differentiation measurement (Fst) was identified as 0.3716 for the first sub-population, 0.3930 for the second subpopulation and 0.4804 for the third sub-population. Based on present findings population structure of 70 wild wheat genotypes collected from Eastern and Southeastern Anatolia regions of Turkey were successfully characterized with the use of iPBS markers. Present findings suggested that iPBS-retrotransposon markers could reliably be used to elucidate genetic diversity of Aegilops genotypes.

Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of Luculia yunnanensis, an Endangered Species Endemic to Yunnan, Southwestern China.

Luculia yunnanensis (Rubiaceae), an evergreen shrub or small tree, is endemic to China and confined to Nujiang Prefecture, Yunnan Province. This plant is of high ornamental value owing to its attractive pink flowers, sweet fragrance, and long flowering period. Due to the influence of climate change and human factors, the distribution range of L. yunnanensis has exhibited a significant shrinking trend, and it has become a vulnerable species that is in urgent need of conservation and rational utilization research. In this study, the flower transcriptome sequencing of L. yunnanensis was conducted using an Illumina HiSeq platform. We designed and developed a series of EST-SSR primers based on the flower transcriptome data of L. yunnanensis. The results showed that 98,389 unigenes were obtained from the L. yunnanensis flower transcriptome, all of which were aligned with sequences in public databases. Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and GO annotated 31,859, 13,853, 22,684, 10,947, 21,416, 9722, and 23,390 unigenes, respectively. The MISA (Microsatellite) tool was used to identify SSR loci from all unigenes, and a total of 15,384 SSRs were identified. Repeat motifs were given priority with mononucleotides, dinucleotides, and trinucleotides. The 81 primer pairs were synthesized randomly, of which 44 pairs showed effective amplification. A total of 17 primers showed stable amplification, and rich polymorphism was observed in 6 populations. We concluded via genetic diversity analysis that the average effective number of alleles (Ne), Shannon’s information index (I), and polymorphism information content (PIC) were 1.925, 0.837, and 0.403, respectively. In conclusion, 17 EST-SSR primers can be used for subsequent population genetic diversity analysis and molecular-marker-assisted breeding, which is of great significance for formulating resource conservation and utilization strategies for L. yunnanensis.