Polymorphism Information Content Values Research Articles

Genetic diversity studies between Ipomoea wild species and cultivated sweet potato (Ipomoea batatas (L.) Lam.) using SSR markers

Sweet potato (Ipomoea batatas (L.) Lam) is one of the major tuber crops in Asian countries, including India, yet the interrelationship and genetic variability among the cultivar and its crop wild relatives remain obscure. The wild relatives of sweet potato represent a vital source of untapped genetic diversity in the breeding programs. In this study, a set of 12 Simple Sequence Repeats (SSR) markers were utilized to understand the extent of genetic diversity and relationship within and between 20 sweet potato accessions, 23 wild Ipomoea species and two Merremia species for utilization in breeding programmes. The SSR primers produced 84 polymorphic alleles within the range of 105-393 bp, collectively showing an average polymorphism of 94.5%. The average Polymorphic Information Content (PIC) value of 0.67 showed that all the primers were polymorphic in nature. Similarity coefficient based dendrogram and Principal Component Analysis (PCA) scatter plot clearly differentiated all the cultivars and wild species. The cluster dendrogram analysis revealed the close relationship of cultivars with I. triloba and I. trifida at a similarity index of 0.75. Our analysis showed a high degree of genetic variability within and between hexaploid sweet potato and diploid wild species, whereas lower within the cultivars, which shows that there is a high level of genetic diversity exists within the Ipomoea species for its utilization in breeding programs. Thus, the two wild species, I. trifida and I. triloba could be used in hybridization for improvement of sweet potato through ploidy manipulation.

Development and characterization of novel EST-SSR markers for Gentiana straminea Maxim., a traditional Tibetan herb in China and cross-amplification in related species

Abstract Gentiana straminea Maxim. (Gentianaceae) is an important traditional Tibetan herb that is mainly distributed on the Qinghai-Tibetan Plateau. Despite its agricultural and pharmacological importance, there remains a paucity of microsatellite markers, particularly expressed sequence tag-simple sequence repeat (EST-SSR) markers, available for this local endemic species. In this study, based on previous Illumina transcriptome data of G. straminea, a total of 96 EST-SSR markers were initially designed and tested. Thirty-two of 96 loci (33.33%) were successfully amplified and verified for validation. Among them, 10 were polymorphic and had clear bands. The polymorphism information content values were 0.09–0.799, the number of alleles per locus ranged from 3 to 14, and the levels of observed and expected heterozygosity were 0.078–0.722 and 0.238–0.884, respectively, which suggested a high level of information. Moreover, cross-amplification was successful for 10 loci in two other related species, Gentiana macrophylla Pallas and Gentiana dahurica Fischer. These EST-SSR markers provide a valuable tool for investigating the genetic diversity related to quantitative traits and population genetic studies on G. straminea and related species in sect. Cruciata Gaudin.

Phenotypic characterization and analysis of genetic diversity between commercial crossbred and indigenous chickens from three different agro-ecological zones using DArT-Seq technology.

Indigenous and were used to study genetic diversity and population structure analyses. Polymorphism information content (PIC) values ranged from 0.0 to 0.5, with 21,285 SNP markers (35%) being in the lowest PIC value range (0 to 0.15) while 13,511 (commercial chickens have developed unique adaptations to their environments, which may include nutrition, pathogens, and thermal stress. Besides, environmental pressures and artificial selection have generated significant genome-wide divergence in chickens, as those selection pressures contribute a considerable evolutionary force to phenotypic and genotypic differentiation. Herein, we determined genomic diversity of indigenous chickens from semi-deciduous rainforest (SDR), coastal savannah (CS) and Guinea savannah (GS) agro-ecological zones (AEZs) in Ghana and commercial crossbreds (CC) reared at the Kwame Nkrumah University of Science and Technology (KNUST). We generated SNP markers from 82 chickens (62 indigenous chicken ecotypes and 26 commercial crossbred ecotype) using DArT-Seq technology. A total of 85,396 SNP markers were generated and after filtering the data, 58,353 markers 21%) were in the highest PIC value range (0.45 to 0.50). The CC were more genetically diverse than the indigenous birds, with the highest expected heterozygosity value of 0.220. Between the commercial crossbreds population and the indigenous ecotypes, pairwise FST values were estimated to be 0.105 between CS, 0.096 between SDF, and 0.133 between GS. Furthermore, PCA analysis showed that the CC, SDF and GS chickens clustered together and are genetically distant from the commercial crossbred. We herein show that chickens from the AEZs studied can be considered as one population. However, due the abundance of agro-byproducts in the SDR compared to the CS and GS, chickens from the SDR AEZ had better growth compared to their counterparts. It is suggested that the genetic diversity within the local ecotypes could form the basis for genetic improvement.

Genetic structure and molecular analysis of the species of the genus Artemisia L. (Asteraceae) distributed in Azerbaijan

In this study, the phylogenetic relationships and genetic structure of 10 collected genotypes of Artemisia szowitziana (Besser) Grossh and Artemisia fragrans Willd. species from different regions of Azerbaijan were investigated using RAPD primers. A total of 94 amplicons were amplified using selected RAPD primers. Among them 3 band with OPA-02 primers and 12 band with OPW-17 primers were amplified. The highest polymorphism among the investigated RAPD markers was 100, 90.91 and 90%, which has been obtained by OPW-17, OPT-19, and OPT-20 primers, respectively. However, the calculated average value of polymorphism was as high as 72.79% based on 10 different RAPD markers. The average PIC (Polymorphism Information Content) value (0.864) has indicated the rich genetic diversity among the studied samples. The cluster analyses by using Jaccard similarity index and UPGMA method classified all Artemisia L. samples into 6 major groups. Principal Component Analysis (PCA) justified 74.22% of the total variance. Based on the results obtained, it has been observed that there is a wide range of diversity in the molecular level between the population of Artemisia szowitziana (1-2 and 4-6 samples) and Artemisia fragrans (3, 5, 7 and 8, 9, 10 samples) and between population of the Artemisia species in Azerbaijan.

Development and utilization of genome-wide InDel markers in Sorghum [Sorghum bicolor (L.) Moench

Sorghum (Sorghum bicolor L. Moench) has become an increasingly valuable crop for food, feed, and especially bioenergy feedstock production, which makes the crop extremely attractive for studying genomics and genetic diversity. Molecular markers and genomics play essential roles in sorghum breeding. The rapid development of next-generation sequencing technology has facilitated the identification of genome-wide insertion-deletion (InDel) polymorphisms, enabling the efficient construction of InDel markers that are suitable for user-friendly PCR. This study was conducted with the objective of discovering and developing InDel markers using double digest restriction site-associated DNA sequencing (ddRAD-Seq) data. A total of 19,226 InDels distributed across 10 chromosomes in the sorghum genome was identified. Of those, deletions constituted 65.7% while the remain was insertions. A comprehensive analysis of all the chromosomes revealed a total of 80 InDel sites with a minimum length of 10 bp. For a good conversion of the InDel regions to beneficial molecular markers, specific primers were designed for the amplification of 47 InDel regions that were selected for further investigation. A diverse panel of sorghum consisting of 16 accessions served a source for the developed InDel markers validation. Of the 47 InDel markers, 14 were tested across 16 sorghum accessions and were demonstrated their helpfulness for marker-assisted selection in sorghum. The polymorphic information content (PIC) values of the 16 markers varied between 0.11 and 0.38, with an average of 0.28. The findings of this study indicated that the identification of InDels and the development of molecular markers for sorghum were accomplished using the ddRAD-Seq data.

Genetic variability analysis of tomato varieties using rapd markers under heat stress

Heat stress threatens agricultural and food security by reducing yield and causing plant death. The use of intra-genetic diversity in heat stress responses is a potential avenue for harnessing tolerance to climate change circumstances. This study investigated the genetic diversity of twelve tomato genotypes in Bangladesh, focusing on their suitability for summer cultivation using seven Random Amplified Polymorphic DNA (RAPD) markers. The banding patterns obtained from the PCR results were used to identify genetic differences between individuals. The RAPD markers were found to show their effectiveness in discriminating the studied lines through the computation of average Polymorphism Information Content (PIC) values, particularly focusing on dominant markers with PIC values ranging from 0 to 0.5, emphasizing the informative nature of the employed primers. Cluster analysis grouped several genotypes with possible common ancestry. Overall, BARI Hybrid Tomato 4, BARI Hybrid Tomato 8, A12, D13, and RHS1 emerged as promising candidates for further genetic research and breeding programs, particularly in the context of heat-stress conditions during summer tomato cultivation in Bangladesh. Bangladesh J. Bot. 53(1): 91-100, 2024 (March)

Genetic diversity of Sinapis arvensis L. (wild mustard) in Türkiye determined by microsatellite markers

Wild mustard (Sinapis arvensis L.) is a self-fertilizing weed species that exerts negative impacts on wheat production and herbicides are intensively used to manage it. Cross-fertilization may lead to genetic differentiation in this species. Therefore, this study investigated genetic diversity among wild mustard populations collected from wheat fields across various regions in Türkiye. Genetic variation was evaluated using 5 simple sequence repeat (SSR) markers in populations collected from 30 different locations. Populations were analyzed using UPGMA (unweighted pair group method with arithmetic mean) and principal component analysis (PCA). The mean genetic diversity (GD) and polymorphism information content (PIC) values were 0.752 and 0.844, respectively. High genetic variability was recorded among populations within geographic locations. The populations were categorized into two major groups by UPGMA. There was no apparent geographic isolation among tested populations, which displayed a high degree of variability. The primary source of this variability is thought to be the adaptability of wild mustard seeds dispersed through various methods across diverse locations. Despite being a predominantly self-pollinating species, wild mustard may also employ some cross-pollination mechanisms. In conclusion, SSR markers proved useful in determining genetic diversity in outcrossing species, especially where no prior genotypic information is available. The study suggests that genetic diversity is maintained in wild mustard populations even with rotational farming practices and intensive use of herbicides.

Development of Novel Genomewide Simple Sequence Repeat Markers for Acer truncatum Bunge and Assessment of Their Transferability to Other Closely Related Species

Acer truncatum Bunge is a versatile woody tree species with high economic and medicinal value in the production of bioactive substances and unsaturated fatty acids (especially nervonic acid). However, the exploitation and evaluation of A. truncatum germplasm resources are limited owing to a lack of sound molecular marker systems. In this study, a large set of genomewide simple sequence repeat (SSR) markers of A. truncatum was developed based on its whole-genome sequences. A total of 462,331 SSR loci were identified in the genome sequences, 99.3% (459,193) of which were located on 13 chromosomes. The chromosome length was significantly positively correlated with the number of SSR loci on the chromosome (r = 0.977, p < 0.001). The (A/T)n, (AT/TA)n, and (AAT/ATT/TAA/TTA/TAT/ATA)n were the most frequent motifs for mono-, di-, and trinucleotide repeat motifs, respectively, showing A/T-base bias. After BLASTN and electronic polymerase chain reaction (PCR) analyses, 199,990 loci with specific physical positions were screened. Most of the SSR loci were located in the intergenic regions and fewest in the coding sequences (CDSs). The frequency of loci with tri- and hexanucleotide repeat motifs was the highest in the CDSs, potentially serving to maintain the stability of gene function and structure. In randomly selected 105 SSR markers, 82 (78.1%) showed allelic polymorphism, with polymorphism information content (PIC) values of 0.032–0.926 (0.481 on average). The SSRs in the noncoding regions exhibited significantly higher PIC values than those in the CDSs. The transferability of the 105 markers was 48.6%–59.0% to seven other Acer species. The large set of valid SSR markers provides a powerful tool for studies on population genetics, conservation genetics, linkage mapping, comparative genomics, and marker-assisted breeding of the genus Acer.

Genetic Diversity in Katchaikatty Sheep based on Microsatellites Polymorphism

Background: Sheep is one of the important species of livestock in India contributing to meat production. India has 44 distinct breeds of sheep, out of which 10 are found in Tamil Nadu. The present study describes the molecular characterization of recently registered breed of sheep - Katchaikatty sheep, genetic variability and genetic structure of the population by microsatellite marker analyses. Methods: DNA from 50 unrelated Katchaikatty sheep was amplified with 25 FAO recommended fluorescent tagged ovine-specific microsatellite markers and genotyped on an automated Genetic Analyzer. In each locus, observed (no) and effective number of microsatellite alleles (ne), allele frequencies, observed (Ho) and expected (He) heterozygosity and heterozygosity deficit estimate (FIS), polymorphism information content (PIC) and Chi-square (χ2) test for Hardy-Weinberg equilibrium (HWE) were assessed. Mode-shift analyses were performed. Result: The study revealed a total of 144 alleles across all the loci. The number of alleles at each locus varied from one to 10 with a mean of 5.76 alleles. The PIC values in the microsatellite loci ranged from 0.34 (OarAE129) to 0.83 (OarFCB48) with an average of 0.59, which showed a high genetic polymorphism. Six out of 25 microsatellite loci studied were in Hardy-Weinberg equilibrium and 19/25 loci showed positive FIS values. The overall mean observed and expected heterozygosity were 0.50 and 0.65 respectively and the estimates elucidated a substantial genetic variability in Katchaikatty sheep population. Mode shift analysis revealed a normal L-shaped curve, describing that the Katchaikatty population had not experienced any genetic bottleneck and remained in mutation-drift equilibrium.

Molecular characterization of Turkish hazelnut cultivars and genotypes using SSR markers

This study defines the genetic characterization of 16 hazelnut varieties and 64 genotypes. SSR method was used in molecular characterization studies. 18 SSR primers were used. In the SSR method, 118 bands were obtained, and 115 were polymorphic. The similarity coefficient in overall genotypes were between 0.12 and 0.98 in SSR andthe polymorphism rate of the primer pairs used was calculated as 98.0%. The lowest polymorphism information content value (0.542) was obtained from the CAC- C 028 locus, and the highest polymorphism information content value (0.987) was obtained from the CAC- B 113 locus. The average polymorphism information content value was 0.786. The total discrimination power values of SSR loci were determined as 17.98; the lowest (0.748) discrimination power value was obtained from the CAC- B 020 locus, while the highest (1.404) discrimination power value was obtained from the CAC- A 024 b locus. The genotypes’clustering positions across the dendograms were essentially correlated with their geographic origins. This result shows that genetic origin plays an important role in terms of classification of genotypes in hazelnut.

Assessing the Genetic Variation of Swarna rice (Oryza sativa L.) Cultivars using SSR marker

Swarna rice cultivars (Indian cultivar) are widely grown in the northern part of Bangladesh because of their higher yield, drought tolerance, higher quality of grain and good plant appearance. Therefore, a study was conducted to observe genetic diversity among eight Swarna cultivars grown in Bangladesh. The genetic diversity of the cultivars was assessed by one hundred SSR (simple sequence repeat) markers. Among these, forty-four primers were polymorphic. In total, 188 alleles from eight rice genotypes with an average of 4.27 alleles per locus were identified. Allele numbers varied from 2 to 11. The average polymorphism information content (PIC) was 0.533, with a range of 0.195 to 0.889. The most suitable markers found were RM149, RM232, and RM3421, which provided the highest PIC value of 0.889. Genetic dissimilarity coefficient values between pairs indicated that the Guti Swarna and Nepali Swarna cultivars along with the Guti Swarna and Deshi Guti Swarna cultivars were the most genetically distant (0.818) cultivars whereas the Nepali Swarna and Nironjon Swarna cultivars were the closest (0.091). A dendrogram constructed based on polymorphism indicated five major groups. It was observed that the Guti Swarna and Sumon Swarna cultivars formed two different solitary groups, I and II whereas the Nepali Swarna and Nironjon Swarna formed group III, the Lal Swarna and Swarna5 constructed group IV, and the Deshi Guti Swarna and Tiger Indian Swarna were in group V. Our findings may help in designing appropriate cross combinations for further improvement of Swarna cultivars.

Population genetic variation and geographic distribution of suitable areas of Coptis species in China.

The rhizomes of Coptis plants have been used in traditional Chinese medicine over 2000 years. Due to increasing market demand, the overexploitation of wild populations, habitat degradation and indiscriminate artificial cultivation of Coptis species have severely damaged the native germplasms of species in China. Genome-wide simple-sequence repeat (SSR) markers were developed using the genomic data of C. chinensis. Population genetic diversity and structure of 345 Coptis accessions collected from 32 different populations were performed based on these SSRs. The distribution of suitable areas for three taxa in China was predicted and the effects of environmental variables on genetic diversity in relation to different population distributions were further analyzed. 22 primer pairs were selected as clear, stable, and polymorphic SSR markers. These had an average of 16.41 alleles and an average polymorphism information content (PIC) value of 0.664. In the neighbor-joining (N-J) clustering analysis, the 345 individuals clustered into three groups, with C. chinensis, C. chinensis var. brevisepala and C. teeta being clearly separated. All C. chinensis accessions were further divided into four subgroups in the population structure analysis. The predicted distributions of suitable areas and the environmental variables shaping these distributions varied considerably among the three species. Overall, the amount of solar radiation, precipitation and altitude were the most important environmental variables influencing the distribution and genetic variation of three species. The findings will provide key information to guide the conservation of genetic resources and construction of a core reserve for species.

Identification of polymorphic markers for germplasm conservation of three precious Chinese palace goldfish using whole-genome sequencing.

China was the first country in the world to breed goldfish and has generated many unique goldfish varieties, including the most aristocratic Chinese palace goldfish. Due to the lack of scientific research on Chinese palace goldfish, their selection and breeding are mainly carried out through traditional hybridization, leading to serious inbreeding and the degradation of germplasm resources. To this end, whole-genome resequencing was performed to understand the genetic variation among three different varieties (eggpompons, goosehead, and tigerhead) from nine core conserved populations in China. A total of 15 polymorphic SSRs were developed for population genetics, and all tested populations were considered moderately polymorphic with an average polymorphism information content value of 0.4943. Genetic diversity in different varieties showed that all conserved populations were well protected with the potential for continued exploitation. This study provides reliable molecular tools and a basis for designing conservation and management programs in Chinese palace goldfish.

Genetic variation among Brassica rapa subsp. rapa genotypes growing in Malatya/Türkiye

AbstractIn this study, the genetic variation of 18 Brassica rapa subsp. rapa genotypes grown in Malatya was determined using the inter simple sequence repeat - polymerase chain reaciton (ISSR-PCR). Using nine ISSR primers, a total of 73 bands were obtained and the polymorphism rate was 91.78%. The mean polymorphism information content value was determined as 0.3319. The mean gene diversity (H) value was determined as 0.4276. The mean major allele frequency value was determined as 0.6531. Similarity index values were determined to be between 0.0928 and 1.0924. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram consisted of two groups. Principal component analysis analysis and UPGMA dendrogram were compatible. In addition, the groups in the phylogenetic trees were partially compatible with geographical distribution. Our results suggest that ISSR-PCR analysis is a suitable approach for breeding Brassica rapa subsp. rapa genotypes and developing different cultivars.

Genetic diversity of maize resources revealed by different molecular markers

AbstractMaize (Zea mays L.) is the third most important cereal crop in the world because of its nutritional value and industrial benefits. Molecular markers are used mainly by the breeders to study the genetic variability of genotypes and its application in the breeding process. Two types of molecular markers, 10 random amplified polymorphic DNA (RAPD) primers and 10 start codon target (SCoT) primers, were assayed to determine the genetic diversity of 25 Slovak maize lines and 25 maize cultivars. A high level of polymorphism was found with both RAPD and SCoT markers, which was confirmed by high average polymorphism information content (PIC) values using both techniques. The efficiency of individual marker techniques in the detection of genotype diversity can be compared by calculating the marker index (MI), detecting diversity index (DDI), discriminating power, resolving power (RP) and other indices. A higher MI (11.788), DDI (2.358) and RP (53.08) value was achieved by the SCoT technique compared to the RAPD method. Three joint dendrograms and PCoA plots constructed based on RAPD, SCoT and both methods combined confirmed the unambiguous separation of maize lines and cultivars from each other. The results obtained from the RAPD and SCoT analysis can be used for the selection of potentially suitable biological sources for further marker-assisted breeding.

Assessment of phenotypic and genotypic diversity in rice for salinity tolerance at reproductive stage

Soil salinity has turned out to be an important global concern, which affects tenable rice production in many agricultural countries like Bangladesh. A cross was made between Binadhan-7 with FL-478 for developing salt tolerant advance lines to assess phenotypic and genotypic diversity in rice for salinity tolerance. Twenty advance rice lines (Binadhan-7/FL-478) along with check varieties were screened for salinity tolerance at reproductive stage using sea site saline water having electrical conductivity (EC) 10 dS m-1. Among the twenty rice lines, seven lines were tolerant, three were moderately tolerant, six were susceptible, four were highly susceptible on the basis of phenotypic evaluation. Seven simple sequence repeat (SSR) markers linked with salt tolerance quantitative trait loci were used for investigation of salt tolerant rice lines. The result revealed that an average number of 6.286 alleles per locus were detected, with polymorphism information content (PIC) values ranging from 0.672 (RM490) to 0.838 (RM562). The highest gene diversity value (0.812) was found in RM562 and the lowest (0.684) was in RM490. A dendrogram constructed from the genetic distance of the genotypes produced four distinct clusters of twenty rice genotypes. Considering both phenotypic and genotypic observation, seven genotypes viz., Binadhan-10, FL-478, SL-51, SL-56, SL-77, EFSD-59 and IZSD-45 were identified as salt-tolerant; on the other hand, EFSD-21, SL-28, SL-32, SL-10, BRRI dhan28, and Binadhan-7 were identified as salt-susceptible. The identified salt-tolerant rice genotypes could be used in the improvement of rice breeding programs. Bangladesh J. Nuclear Agric, 37(2): 1-18, 2023

Analysis of seven populations of cultured redclaw crayfish, Cherax quadricarinatus, using newly developed microsatellite markers

Cherax quadricarinatus, also known as the redclaw crayfish, is native to northern Australia and southern Papua New Guinea and is an important freshwater aquaculture species in many countries. Studying the genetic structure of the current cultured population can improve the breeding plan for redclaw crayfish to better manage the hybridization and germplasm bank and promote their rational utilization; however, microsatellite resources for redclaw crayfish remain insufficient. The purpose of this study was to analyze the genetic diversity of different redclaw crayfish populations in China. After screening 18 pairs of microsatellite markers from redclaw crayfish transcriptome data, 240 samples from seven main breeding areas (Changsha, Guangzhou, Haikou, Huzhou, Jiangmen, Wuxi, and Zhanjiang) were evaluated and detected using these microsatellite markers. In total, 97 alleles were detected, of which the minimum number was two and the maximum number was twelve. The observed heterozygosity ranged from 0.258 to 0.807, with an average of 0.559, and the expected heterozygosity ranged from 0.288 to 0.815, with an average value of 0.558. The polymorphic information content values of seven populations ranged from 0.268 to 0.791, with an average of 0.511. Moreover, pairwise genetic differentiation within the population was between 0.007 and 0.031. The UPGMA clustering results showed that the Zhanjiang population stands alone on a branch, but the genetic variation between branches is very small. Meanwhile, STRUCTURE analysis further revealed that the genetic backgrounds of each population are essentially identical, with no noticeable genetic differentiation arising from geographic differences. These results provide a basic assessment of the genetic diversity of the main cultured populations of redclaw crayfish and a molecular foundation for future genetic monitoring and selective breeding research.

Genetic variability of maize (Zea mays) germplasm from Iran: genotyping with a maize 600K SNP array and genome-wide scanning for selection signatures

Context Maize (Zea mays L.) is one of the most economically important plants of the cereal family; it has value as human food, livestock feed, and as a component of industrial products. Aims This study focused on genetic diversity and existence of genetic divergence among promising maize inbred lines in Iran. Methods A commercial maize 600K SNP (single-nucleotide polymorphism) array was used to inspect genetic variability among 93 maize inbred lines. Key results The rate of transition mutation was twice as high as transversion mutation, and the density of detected SNPs was greater close to telomere regions of maize chromosomes. Considering the fluctuation of observed, expected and total heterozygosity and fixation index values across maize chromosomes, as well as polymorphism information content values, there is a high level of genetic variability among the studied maize panel. In addition, discriminant analysis of the principal components revealed four subpopulations in which the subpopulation ‘Line’ was distinct from other subpopulations and had no genomic overlap with them. Selection signature analysis revealed 177 regions harbouring 75 genes that differentiate among subgroups. Detected genes had a role in the mitogen-activated protein kinase signalling pathway, spliceosome, protein processing in endoplasmic reticulum, and hormone signal transduction. Conclusions We conclude that remarkable genetic diversity and differentiation exists among the studied maize subpopulations. The most differentiated SNPs among the subpopulations were associated with important biological processing genes and pathways. Implications The findings provide valuable insights for future maize breeding programs through exploitation of heterosis, as well as marker-assisted selection.

Assessment of Molecular Diversity and Population Structure of Pakistani Mulberry Accessions Using Retrotransposon-Based DNA Markers

Both morphological and molecular markers have been extensively used to evaluate genetic diversity; however, molecular markers are considered more reliable and can lead to improved reproductive efficiency. This study utilized inter-primer binding site (iPBS) markers to examine the genetic diversity and population structure of thirty mulberry accessions from the districts of Sahiwal and Faisalabad, Pakistan. These mulberry accessions belonged to three species: Morus nigra (n = 13), Morus alba (n = 12), and Morus rubra (n = 5). The use of nine iPBS primers in this study provided a comprehensive understanding of genetic diversity among the selected mulberry accessions. Nine iPBS primers were used in the study and generated 431 bands with allelic frequencies ranging from 21 to 75 and band sizes from 200 to 1500 base pairs. The primer 2230 showed the highest polymorphic information content (PIC) value of 0.47 and the highest Shannon’s information index (I = 0.53). The Morus nigra accessions had the highest levels of expected heterozygosity (He = 0.30), unbiased expected heterozygosity (µHe = 0.33), and Shannon’s information index (I = 0.45). The molecular variance analysis (AMOVA) revealed a high degree of genetic variation, as estimated by the pairwise PhiPT value of 0.21, which was significant at the p < 0.001 *** level. The neighbor joining tree, principal coordinate analysis, and structure analysis grouped the 30 mulberry accessions into four main clusters. The distinct grouping of accessions SWLS14, SWLS6, FSDS30, and SWLS7 validated their notable genetic distinctiveness. Overall, these findings contribute valuable insights into the genetic landscape of mulberry accessions, which are essential for conservation and breeding strategies.

Integrated Discriminant Evaluation of Molecular Genetic Markers and Genetic Diversity Parameters of Endangered Balearic Dog Breeds.

The genetic diversity analysis of six dog breeds, including Ca de Bestiar (CB), Ca de Bou (CBOU), Podenco Ibicenco (PI), Ca Rater (CR), Ca Mè (CM), and Ca de Conills (CC), reveals insightful findings. CB showcases the highest mean number of alleles (6.17) and heterozygosity values, with significant deviations from Hardy-Weinberg equilibrium (HWE) observed in five markers, indicating high intra-racial genetic diversity (average observed heterozygosity (Ho) = 0.754, expected heterozygosity (He) = 0.761). In contrast, CBOU presents the lowest mean number of alleles (5.05) and heterozygosity values, coupled with moderate polymorphic information content (PIC) values and a moderate level of intra-racial genetic diversity (average Ho = 0.313, He = 0.394). PI demonstrates moderate genetic diversity with an average of 5.75 alleles and highly informative PIC values, while CR displays robust genetic diversity with an average of 6.61 alleles and deviations from equilibrium, indicating potential risks of inbreeding (average Ho = 0.563, He = 0.658). CM exhibits moderate genetic diversity and deviations from equilibrium, similar to CBOU, with an average of 6.5 alleles and moderate PIC values (average Ho = 0.598, He = 0.676). Conversely, CC shows a wider range of allelic diversity and deviations from equilibrium (average Ho = 0.611, He = 0.706), suggesting a more diverse genetic background. Inter-racial analysis underscores distinct genetic differentiation between breeds, emphasizing the importance of informed breeding decisions and proactive genetic management strategies to preserve diversity, promote breed health, and ensure long-term sustainability across all breeds studied.