Mean Effective Number Of Alleles Research Articles

Genetic diversity and fingerprinting of Elaeagnus angustifolia based on SSR molecular markers

DNA fingerprinting can reveal the genetic diversity of Elaeagnus angustifolia germplasm resources and clarify the source and genetic background of E. angustifolia germplasm, which are the preconditions for the breeding of new varieties, the identification and protection of germplasm resources, and the comprehensive development of the E. angustifolia industry considering both ecological and economic benefits. We employed 11 pairs of primers with high polymorphism, clear bands, and high reproducibility to analyze the genetic diversity of 150 E. angustifolia germplasm accessions from Gansu and Beijing by the simple sequence repeat (SSR) molecular markers. We then employed the unweighted pair-group method with arithmetic means (UPGMA) to perform the cluster analysis based on genetic distance and analyzed the genetic structure of the 150 germplasm accessions based on a Bayesian model in Structure v2.3.3. The genetic diversity analysis revealed the mean number of alleles (Na) of 7.636 4, the mean number of effective alleles (Ne) of 2.832 6, the mean Shannon genetic diversity index (I) of 1.178 1, the mean Nei's gene diversity index (H) of 0.582 1, the mean observed heterozygosity (Ho) of 0.489 9, the mean expected heterozygosity (He) of 0.584 0, the mean polymorphism information content (PIC) of 0.535 4, and the mean genetic similarity (GS) of 0.831 5. These results suggested that the E. angustifolia germplasm resources we studied exhibited significant genetic differences and rich genetic diversity. The cluster analysis revealed that the tested materials can be classified into 3 groups, with the main genetic distance (GD) of 0.422 9. The clustering results were not completely consistent with the geographic origin. The population structure analysis classified the germplasm accessions into 2 populations. We used 8 pairs of primers with high PIC to construct the fingerprints of 150 E. angustifolia germplasm accessions. The present study successfully constructs the DNA fingerprints and clarified the genetic relationship of the E. angustifolia germplasm resources in Gansu and Beijing, providing a theoretical basis for germplasm resource identification, breeding of elite varieties, application in gardening, and molecular-assisted breeding of E. angustifolia.

Assessing the population structure and genetic diversity of wheat germplasm with the iPBS-retrotransposons marker system

Context Wheat (Triticum aestivum L.) is an important crop that provides food to millions of people all over the world. Currently, wheat production is limited due to various biotic and abiotic stresses resulting from uneven patterns of climate change. Therefore, it is very important to develop climate-resilient wheat cultivars. Crop genetic diversity allows the scientific community to identify genetic variations that can be utilised in the development of improved cultivars. Aims This study planned to characterise the wheat germplasm with the iPBS-retrotransposons marker system. Methods A total of 30 iPBS-retrotransposons markers were screened and among these, the 12 most polymorphic markers were selected for further analysis. Key results Molecular characterisation yielded a total of 170 bands, of which 143 were polymorphic. A substantial level of genetic diversity was observed (mean effective number of alleles: 1.37, Shannon’s information index: 0.23, gene diversity: 0.35). Maximum genetic distance was observed in G9 and G60 genotypes. Analysis of molecular variance revealed that most genetic variation (95%) occurred within the populations. The model-based structure algorithm divided the studied germplasm into three populations based on their collection regions. Similarly, the neighbour-joining analysis also divided 70 tested wheat genotypes into three populations, whereas principal coordinate analysis divided the evaluated germplasm into four populations. Conclusions This study confirms the iPBS-retrotransposons as an ideal marker for the genetic diversity assessment studies for any crop, especially for wheat. Implications The results presented here will be helpful for the scientific community in the marker-assisted breeding of wheat.

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 CHARACTERIZATION OF RELICT ENDEMIC LIQUIDAMBAR ORIENTALIS (ALTINGIACEAE) POPULATIONS

Liquidambar orientalis, a relict endemic species, is distributed in the south-west of Turkey. The natural spread areas of the species have been decreasing since the early 1900s. This poses a great threat to the future and genetic diversity of the species. In this study, the genetic diversity of a total of 190 individuals in ten populations was examined with ten polymorphic ISSR primers. Data analysis was performed using POPGENE ver. 1.32 and GenAlEx 6.503 softwares. According to the results of the analysis, a total of 271 loci were identified. For the ten populations, the rate of polymorphic loci ranged from 21.03% to 34.69%. The mean number of observed alleles (Na) and mean number of effective alleles (Ne) were found as 1.98 ± 0.13 and 1.47 ± 24 0.37, respectively. Nei's genetic diversity values (h) ranged from 0.07 ± 0.15 to 0.12 ± 0.18. According to the results of Molecular Analysis of Variance (AMOVA) and POPGENE ver. 1.32 analysis, it was determined that the main contribution to the genetic variance originated from among the populations. In addition, the gene flow level (NM) was found to be low with a value of 0.27 per generation.

Genetic Diversity and Population Structure Analysis of Excellent Sugar Beet (Beta vulgaris L.) Germplasm Resources

This study analyzed the genetic diversity, population structure, and cluster analysis of 129 sugar beet germplasm resources to screen superior germplasms for breeding using the 27 simple sequence repeat (SSR) and 33 pairs of insertion–deletion (InDel) molecular markers. After integrating the phenotypic variation of 16 descriptive and 4 qualitative phenotypic variables, the genetic variation levels of the 129 sugar beet germplasms’ phenotypic traits were analyzed using the principal component analysis (PCA), correlation analysis, and analysis of variance methods. The genetic diversity examination of molecular markers showed a polymorphism information content (PIC) of 0.419–0.773 (mean = 0.610). Moreover, the mean number of effective alleles detected via the SSR and InDel markers was 3.054 and 2.298, respectively. Meanwhile, the PIC ranged from 0.130 to 0.602 (mean = 0.462). The population structure analysis revealed the most appropriate K-value, indicating three populations (K = 3). The genetic distances of the 129 germplasm resources ranged from 0.099 to 0.466 (mean = 0.283). The cluster analysis results demonstrated that the germplasms were grouped into three primary classes. Based on the analysis of variance, the two qualitative features with the highest coefficients of variation were petiole width (16.64%) and length (17.11%). The descriptive trait root length index (1.395) exhibited the greatest genetic diversity. The PCA reduced the 20 phenotypic traits into five principal components, contributing 51.151%. The results of this study provide a theoretical foundation for the future selection and breeding of superior sugar beet germplasm resources.

Parentage verification and genetic diversity of the Arabian and Thoroughbred horse populations in Türkiye using microsatellite analysis.

This study aimed to determine the effectiveness of parentage verification in Arabian and Thoroughbred horses in Türkiye using microsatellite markers. A total of 813 Arabian and 959 Thoroughbred horses were genotyped using a total of 17 microsatellite markers. The mean effective number of alleles was 3,34 and the mean number of alleles was 7,41 in Arabian horses. It was calculated that the mean He and Ho values in Arabian horses were 0,677 and 0,680, respectively. The mean effective number of alleles was 3,55 and the mean number of alleles was 6,59 in Thoroughbred horses. It was calculated that the mean Ho and He values in Thoroughbred horses were 0,697 and 0,684, respectively. When the studied Arabian and Thoroughbred horse populations are considered as a single population, the mean FIT, FST and FIS values were found to be 0,063, 0,074 and, - 0,011, respectively. Also, 4 loci in Arabian horses and 3 loci in Thoroughbred horses significantly deviated from HWE. The mean PIC value was 0,63 in Arabian horses and 0,64 in Thoroughbred horses. As a result; the microsatellites including the most informative 15 and 9 loci had a total value of > 0,9999 (11 and 7 loci > 0,999) in each population for PE - 1 and PE - 3, respectively. It has been concluded that parentage verification and genetic identification can be made successfully in the Arabian and Thoroughbred horse populations by using the microsatellite markers panel.

Genetic diversity and conservation of Siberian apricot (Prunus sibirica L.) based on microsatellite markers

Siberian apricot (Prunus sibirica L.) is a woody tree species of ecological, economic, and social importance. To evaluate the genetic diversity, differentiation, and structure of P. sibirica, we analyzed 176 individuals from 10 natural populations using 14 microsatellite markers. These markers generated 194 alleles in total. The mean number of alleles (13.8571) was higher than the mean number of effective alleles (6.4822). The average expected heterozygosity (0.8292) was higher than the average observed heterozygosity (0.3178). Shannon information index and polymorphism information content were separately 2.0610 and 0.8093, demonstrating the rich genetic diversity of P. sibirica. Analysis of molecular variance revealed that 85% of the genetic variation occurred within populations, with only 15% among them. The genetic differentiation coefficient and gene flow were separately 0.151 and 1.401, indicating a high degree of genetic differentiation. Clustering results showed that a genetic distance coefficient of 0.6 divided the 10 natural populations into two subgroups (subgroups A and B). STRUCTURE and principal coordinate analysis divided the 176 individuals into two subgroups (clusters 1 and 2). Mantel tests revealed that genetic distance was correlated with geographical distance and elevation differences. These findings can contribute to the effective conservation and management of P. sibirica resources.

Genetic diversity and population genetic structure in Kadsura coccinea (Schisandraceae), an evergreen woody vine from Hunan, China

ABSTRACT Kadsura coccinea is an evergreen woody vine species indigenous to Southeast Asia and south China with great promise in medicine, food, and ornamental gardening. Its natural resources have decreased dramatically due to irrational fruits and roots harvesting in two decades recently, which may result in heavy erosion of its genetic resources, especially in Hunan Province, China. Here 406 individuals of K. coccinea were collected from 11 natural populations in Hunan Province, and were analyzed for genetic variation using 17 polymorphic microsatellite markers. A total of 163 alleles were amplified with a mean of 9.588 alleles per locus. The mean effective number of alleles per locus, allele richness and the expected heterozygosity of these populations were 2.910, 4.171 and 0.558 on average, respectively, indicating a bit low level of genetic diversity. The among-population differentiation (FST) accounted for 13.63% of the total genetic variation, and analysis of molecular variance also showed 13.38% of genetic variation existed among populations, representing a high genetic differentiation and a bit limited gene flow (Nm = 1.813) among these populations. The results of Bayesian clustering analysis and neighbor-joining clustering analysis showed that populations GD and YZ were specific, and CB and HT were assigned into a cluster. The mantel test demonstrated that the genetic distances revealed by pairwise FST between populations were remarkably correlated to geographic distances. It is the first report on genetic diversity of species in genus Kadsura using molecular markers, and the findings provide fundamental base for genetic resources conservation and breeding of this species.

Assessment of genetic diversity based on agro-morphological traits and ISSR molecular markers in einkorn wheat (Triticum monococcum ssp. monococcum) landrace populations from Turkey

The aim of this study is to investigate genetic diversity in 48 einkorn (Triticum monococcum L. ssp. monococcum) landraces grown in agricultural areas of Bolu and Kastamonu. Therefore, variation in seven agro-morphological traits was investigated. Agro-morphological traits such as leaf weight (mg), coleoptile length (cm), root number (n), root length (cm), fresh root weight (mg), and dry root weight (mg) were examined by the coefficient of variation, ANOVA, and principal components analysis. The highest coefficient of variation (%) was observed in fresh root weight (FRW = 52.09%), while the lowest was in leaf weight (LW = 8.9%). Principal Component Analysis (PCA) was calculated as 76.93% variation in two main components. For molecular characterization, data obtained with iSSR primers were analyzed with the population genetics analysis program PopGene (ver. 1.32). According to PopGene results, the mean number of alleles, the mean number of effective alleles, and average genetic diversity values were calculated as na = 2, nea = 1.33, and h = 0.13, respectively. Among the agro-morphological traits, germination power, root number, and coleoptile length appeared to be reliable traits. The results show that the use of morphological characters alone for genetic diversity in populations is not sufficient to determine the difference between populations and their genetic structure.

Kazakh national dog breed Tazy: What do we know?

The Tazy or Kazakh National sighthound has been officially recognized as the national heritage of Kazakhstan. Comprehensive genetic studies of genetic diversity and population structure that could be used for selection and conservation of this unique dog breed have not been conducted so far. The aim of this study was to determine the genetic structure of the Tazy using microsatellite and SNP markers and to place the breed in the context of the world sighthound breeds. Our results showed that all 19 microsatellite loci examined were polymorphic. The observed number of alleles in the Tazy population varied from 6 (INU030 locus) to 12 (AHT137, REN169D01, AHTh260, AHT121, and FH2054 loci) with a mean of 9.778 alleles per locus. The mean number of effective alleles was 4.869 and ranged from 3.349 f to 4.841. All markers were highly informative (PIC values greater than 0.5) and ranged from 0.543 (REN247M23 locus) to 0.865 (AHT121 locus). The observed and expected heterozygosities in a total population were 0.748 and 0.769 and ranged from 0.746 to 0.750 and 0.656 to 0.769, respectively. Overall, the results confirmed that the Tazy breed has a high level of genetic diversity, no significant inbreeding, and a specific genetic structure. Three gene pools underlie the genetic diversity of the Tazy breed. SNP analysis using the CanineHD SNP array, which contains more than 170,000 SNP markers, showed that the Tazy breed is distinct from other sighthound breeds and genetically related to ancient eastern sighthound breeds sharing the same branch with the Afghan Hound and the Saluki. The results, together with archeological findings, confirm the ancient origin of the breed. The findings can be used for the conservation and international registration of the Tazy dog breed.

Genetic characterization and diversity assessment in ‘Bhangor’ indigenous swamp buffalo population using heterologous microsatellite markers

‘Bhangor’ newly identified swamp buffalo population from North East Indian, was characterized using microsatellite markers. Genomic DNA was isolated from blood samples of 76 unrelated animals, 15 microsatellite markers (CSSM33, BM1818, CSRM60, HEL13, ILSTS019, ILSTS025, ILSTS028, ILSTS029, ILSTS033, ILSTS036, ILSTS056, ILSTS058, ILSTS061, ILSTS089 and ETH003) were found to be highly polymorphic in the population of the selected markers. A total of 114 alleles were observed, which ranged from 3 in CSRM60 and ILSTS025 locus to 12 in ILSTS056 and ILSTS061. The mean effective number of alleles across all polymorphic loci was found to be 3.76. The overall mean expected heterozygosity and unbiased expected heterozygosity values were 0.67 and 0.68, ranging from 0.067 (ILSTS025) to 0.85 (ILSTS058) and 0.068 (ILSTS025) to 0.86 (ILSTS058), respectively. Within the population, the inbreeding estimates (FIS) ranged between −0.4352 and 0.804, with an average FIS of 0.114 ± 0.033. The outcome for infinite allele model (IAM), two-phase model (TPM) and test for mode shift revealed the absence of any recent bottleneck in the investigated buffalo population. The population was found to be in optimum diversity based on polymorphic microsatellite markers. With fast changing agro-climatic conditions; there is an urgent need to characterize the nondescript livestock populations.

Dissection of genetic diversity present in eggplant populations using simple sequence repeat markers

Eggplant (Solanum melongena L.) is the third most important solanaceous vegetable and most diversified within species spread across the world-geographical area. A study was conducted to assess the genetic diversity among the selected fifty-four eggplant genotypes (sub-categorized into five sub-population) using twenty-three SSR markers. The Analysis of Molecular Variance among the five sub-population of eggplant revealed the existence of 90.67% variation within populations and 9.34% variation among populations. The SSR markers analysis revealed important locus-wise information like mean Observed-Heterozygosity (0.216), mean Expected-Heterozygosity (0.496), Shannon’s Information Index (0.879), mean number of different alleles (3.209), mean number of effective alleles (2.535), Fixation-Index (0.649). Further, Phylogenetic-analysis clearly categorize genetically distinct individuals in which the most diversified clusters was cluster-1 (C1) out of total of five clusters and especially, wild cultivars were grouped into cluster-5 (C5). The obtained results can be used in eggplant breeding and germplasm conservation in a resourceful manner.

Genetic Diversity of Philippine Native Pigs (Sus scrofa L.) from Quezon and Marinduque Based on Morphological and Microsatellite Markers

Nine microsatellite markers recommended by the Food and Agriculture Organization were used to measure the genetic diversity of Quezon and Marinduque native pig populations – with a total of 37 and 40 individuals, respectively. All markers were discovered to be polymorphic, with a mean number of alleles per locus of 10. Marinduque native pigs were found to have a mean effective number of alleles (EA), mean observed heterozygosity (HO), mean expected heterozygosity (HE), and mean polymorphic information content (PIC) of 5.005 ± 0.547, 0.673 ± 0.040, 0.780 ± 0.024, and 0.76 ± 0.03, respectively. By contrast, Quezon native pigs had mean EA, mean HO, mean HE, and mean PIC values of 5.280 ± 0.787, 0.634 ± 0.044, 0.773 ± 0.035, and 0.75 ± 0.04, respectively. Between the two populations, the heterozygosity (HE > HO) and positive values of FIS (0.1714) and FIT (0.1868) indicated a low number of heterozygotes, suggesting the possibility of inbreeding. The test of Hardy-Weinberg equilibrium (HWE) showed that three loci each in the Quezon and Marinduque native pig populations deviated from HWE. Although morphological analysis revealed significant differences in snout shape, head profile, ear type, and all morphometric traits, a low level of genetic differentiation between the two populations was observed (FST = 0.0186; Nei genetic distance = 0.130; Nei unbiased genetic distance = 0.082). Overall, these findings imply that further studies on the genetic improvement and conservation of Philippine native pigs are required for the development of signature pig breeds across the country.

SSR-Based Molecular Identification and Population Structure Analysis for Forage Pea (Pisum sativum var. arvense L.) Landraces.

Plant genetic diversity has a significant role in providing traits that can help meet future challenges, such as the need to adapt crops to changing climatic conditions or outbreaks of disease. Our aim in this study was to evaluate the diversity of 61 forage pea specimens (P. sativum ssp. arvense L.) collected from the northeastern Anatolia region of Turkey using 28 simple sequence repeat (SSR) markers. These primers generated a total of 82 polymorphic bands. The number of observed alleles (Na) per primer varied from 2 to 4 with a mean of 2.89 alleles/locus. The mean value of expected heterozygosity (Exp-Het = 0.50) was higher than the mean value of observed heterozygosity (Obs-Het = 0.22). The mean of polymorphic information content (PIC) was 0.41 with a range of 0.03–0.70. The mean number of effective alleles (Ne) was found to be 2.15, Nei’s expected heterozygosity (H) 0.49, and Shannon’s information index (I) 0.81. Cluster analysis through the unweighted pair-group mean average (UPGMA) method revealed that 61 forage pea landraces were divided into three main clusters. Genetic dissimilarity between the genotypes, calculated with the use of NTSYS-pc software, varied between 0.10 (G30 and G34) and 0.66 (G1 and G32). Principal coordinate analysis (PCoA) revealed that three principal coordinates explained 51.54% of the total variation. Moreover, population structure analysis showed that all genotypes formed three sub-populations. Expected heterozygosity values varied between 0.2669 (the first sub-population) and 0.3223 (third sub-population), with an average value of 0.2924. Average population differentiation measurement (Fst) was identified as 0.2351 for the first sub-population, 0.3838 for the second sub-population, and 0.2506 for the third sub-population. In general, current results suggest that SSR markers could be constantly used to illuminate the genetic diversity of forage pea landraces and can potentially be incorporated into future studies that examine the diversity within a larger collection of forage pea genotypes from diverse regions.

Genetic diversity of Prunus armeniaca L. var. ansu Maxim. germplasm revealed by simple sequence repeat (SSR) markers.

The genetic diversity and genetic structure of P. armeniaca var. ansu were analyzed based on SSR markers. The aim was to provide scientific basis for conservation, efficient utilization, molecular marker assisted breeding and improved variety selection of P. armeniaca var. ansu germplasm resources. The results showed that the level of genetic diversity within the population was high. Among the 30 SSR markers, the mean number of observed alleles was 11.433, the mean number of effective alleles was 4.433, the mean of Shannon information index was 1.670, and the mean of polymorphic information content was 0.670. Among the eight provenances, Tuanjie Township, Xinyuan County, Xinjiang had the highest genetic diversity. The observed alleles, effective alleles, Shannon information index and Nei’s gene diversity index among provenances were higher than those within provenances. Based on Bayesian mathematical modeling and UPGMA cluster analysis, 86 P. armeniaca var. ansu accessions were divided into three subpopulations and four groups, which reflected individual differences in provenances. Subpopulations classified by Bayesian mathematical modeling and groups classified by UPGMA cluster analysis were significantly correlated with geographical provenance (Sig<0.01) and the provenances significantly impacted classification of groups. The provenances played an important role in classification of groups. The genetic distance between Tuanjie Township of Xinyuan County and Alemale Township of Xinyuan County was the smallest, while the genetic relationship between them was the closest and the degree of genetic differentiation was small.

Genetic diversity in populations of Girardinia diversifolia from Nepal Himalaya using ISSR markers

Girardinia diversifolia (Link) Friis from Urticaceae family is a perennial herb, commonly known as the Himalayan giant nettle. It has cultural, medicinal, and economic values among the indigenous peoples and local communities living in the mountains of Nepal and India. Prior knowledge of genetic diversity in plant species may contribute to conservation and sustainable utilization of important genotype. The aim of this study is to assess the genetic diversity within and among different populations of the 45 accessions of G. diversifolia collected from Far-western, Central, and Eastern regions of Nepal. The amplification of genomic deoxyribonucleic acid (DNA) with ten inter-simple sequence repeat (ISSR) primers yielded 131 clear DNA bands, of which 98.09% were found to be polymorphic. The mean effective number of alleles (ne), Nei's gene diversity (h) and Shannon's information index (I) were 1.598, 0.349, and 0.523, respectively. The total genetic diversity Ht (0.350 ± 0.04), low intrapopulation genetic diversity Hs (0.141 ± 0.03) and low estimated gene flow Nm (0.355 ± 0.11) reflected high genetic differentiation among population Gst (0.594 ± 0.08). The analysis of molecular variance among and within five populations of G. diversifolia showed that the value of genetic variation among the population was 60% whereas the value of genetic variation within the population was 40%. The results show that the ISSR markers are informative for the study of genetic diversity, which may help in the conservation and sustainable utilization of G. diversifolia and allied taxa.

Genetic diversity and population structure of Indian willow (Salix tetrasperma Roxb.) with dominant molecular markers along its distribution range in Himalayan region

Indian willow (Salix tetrasperma) is an agriculturally useful tree which occurs over a wide geographic area across South Asia and bears importance. So far, this species has never been studied for molecular genetic diversity. The present study was, therefore, carried out to assess the genetic diversity and population structure analysis using RAPD and ISSR molecular markers in diverse genotypes from five populations covering North India. The mean number of effective alleles, Shannon information index and gene diversity i.e., 1.38 ± 0.013, 0.35 ± 0.010 and 0.23 ± 0.007, respectively were obtained with RAPD + ISSR markers. The analysis of molecular variance generated by RAPD + ISSR revealed a higher genetic variation (87%) within population as compared to that of among population (13%). Nei genetic distance was maximum (0.185) between Jammu and Kashmir and Punjab populations. Significant Mantel correlation (r=0.551,) was obtained between RAPD and ISSR markers. Bayesian clustering pattern obtained through STRUCTURE software showed four gene pools. Based on the genetic information obtained with regards to Indian willow by combining the RAPD and ISSR marker systems, it is proposed that an individual tree be selected within populations rather than among populations for the improvement of economic traits of Indian willow alongwith conservation of entire ecological populations.

Elucidating Genetic Diversity in Apricot (Prunus armeniaca L.) Cultivated in the North-Western Himalayan Provinces of India Using SSR Markers.

Apricot (Prunus armeniaca L.) is an important temperate fruit crop worldwide. The availability of wild apricot germplasm and its characterization through genomic studies can guide us towards its conservation, increasing productivity and nutritional composition. Therefore, in this study, we carried out the genomic characterization of 50 phenotypically variable accessions by using SSR markers in the erstwhile States of Jammu and Kashmir to reveal genetic variability among accessions and their genetic associations. The genetic parameter results revealed that the number of alleles per locus (Na) ranged from 1 to 6 with a mean Na value of 3.89 and the mean effective number of alleles (Ne) per locus 1.882 with a range of 1.22 to 2. Similarly, the polymorphic information content (PIC) values ranged from 0.464 to 0.104. The observed heterozygosity (Ho) (0.547) was found to have higher than expected heterozygosity (He) (0.453) with average heterozygosity of 0.4483. The dendrogram clustered genotypes into three main clades based on their pedigree. The population structure revealed IV sub-populations with all admixtures except the III sub-population, which was mainly formed of exotic cultivars. The average expected heterozygosity (He) and population differentiation within four sub-populations was 1.78 and 0.04, respectively, and explained 95.0% of the total genetic variance in the population. The results revealed that the SSR marker studies could easily decrypt the genetic variability present within the germplasm, which may form the base for the establishment of good gene banks by reducing redundancy of germplasm, selection of parents for any breeding program.

A novel set of short microhaplotypes based on non-binary SNPs for forensic challenging samples.

Short tandem repeats (STRs) are the most widely used genetic markers in forensic application, but they are not ideal genetic markers for the analysis of forensic challenging samples such as highly degraded or unbalanced mixed samples because of their relatively large amplicons and stutter peaks. In this study, we developed a set of short microhaplotypes based on non-binary SNPs with molecular extent sizes no longer than 60 bases and genotyped 100 unrelated individuals from northern Han groups. Our results showed this panel has similar discrimination power to STR kits, as the combined random match probability (CMP) reached 1.396 × 10-22 and mean effective number of alleles (Ae) was 3.59. The cumulative probability of exclusion for duos (CPE-duos) was 0.999919 and the cumulative probability of exclusion for trios (CPE-trios) was 0.9999999987, suggesting this panel could be applied for forensic personal identification and parentage testing independently. Population differentiation in 26 populations from the 1000 Genomes Project indicated this panel could distinguish populations from Africa, East Asia, South Asia, America, and Europe. These microhaplotypes based on non-binary SNPs have short amplicons, good discrimination power, no stutter artifacts, and have great potential in detection of highly degraded and unbalanced mixtures for personal identification, paternity testing, and ancestry inference.

Study on Genetic Relationship of Genus Corylus Resources in Sichuan Province Based on SSR Markers

At least seven domestic wild hazelnut species are distributed in Sichuan province, which is an important distribution area for genus Corylus resources. In this study, nine SSR markers were used to analyze the population genetic diversity and genetic relationships of C. heterophylla var. sutchuenensis, C. yunnanensis, C. ferox, C. mandshurica, and C. avellana. The results showed that the mean number of effective alleles, observed heterozygosity, expected heterozygosity, and Shannon's information index of eleven test populations were 2.772, 0.644, 0.546, and 1.016, respectively, indicating that the population genetic diversity was at a medium level. In addition, the population diversity level of C. heterophylla var. sutchuenensis in Maoxian county and of C. yunnanensis in Luding county were higher than the other populations. Meanwhile, principal coordinate analysis and UPGMA cluster analysis showed that C. mandshurica was closely related with C. avellana, and that C. heterophylla var. sutchuenensis was also closely related with C. yunnanensis. This study was helpful to promote the breeding, protection and utilization of hazelnut germplasm resources in Sichuan province.