Polymorphism Information Content Research Articles

Genetic polymorphism and frequency study at 15 short tandem repeat loci in the North and East Indian populations for use in personal identification and applications in India

Allele frequency is a crucial factor in estimating the weight of evidence (WoE) for an individual’s involvement in a DNA sample. To determine the allele and genotype frequencies within the populations of the northern and eastern states of India, 15 short tandem repeats (STRs) were used, including Penta E, CSF1PO, D18S51, D7S820, D21S11, TH01, D3S1358, Vwa, FGA, TPOX, D8S1179, D16S539, D13S317, Penta D, and D5S818. The study involved 509 randomly selected individuals, analyzed using the PowerPlex 16 System Kit. Various statistical parameters of forensic significance were calculated using Forensic Statistic Analysis Toolbox (FORSTAT) software, including the typical paternity index (TPI), power of exclusion (PE), matching probability (MP), power of discrimination (PD), polymorphism information content (PIC), and observed (Hobs) and expected heterozygosities (Hexp). The analysis revealed a maximum allele frequency of 0.4282 at TPOX, with a minimum frequency of 0.0009 observed at different loci. FGA was found to be the most polymorphic loci among the 15 loci analyzed in the North and East Indian populations. Furthermore, no divergence from the Hardy‐Weinberg equilibrium (HWE) was observed. The results serve as a valuable source of information for establishing a DNA database for North and East Indian populations, providing essential information for population genetics studies and forensic casework in India.

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 analysis of banana using SSR markers

Banana, a crucial fruit crop thriving in tropical and sub-tropical regions, facing a notable challenge of elevated sterility across various cultivated banana genotypes. This sterility issue hampers the cultivation of diverse banana varieties. Therefore, a focused endeavour is crucial to thoroughly investigate the richness of diversity within both wild and cultivated banana genotypes, aiming to preserve it for future utilization. In the present study, 21 Musa genotypes were collected from different places of North-Eastern Region, and conserved in the field gene bank at Department of Horticulture, College of Agriculture, Lembucherra, Tripura during 2015-2022. Molecular characterization and DNA fingerprinting of these banana accessions were performed by employing 16 banana SSR markers. The number of alleles per locus ranged from 15 to 24 with an average 20.375. The expected heterozygosity (He) ranged from 0.564-0.967 with a mean of 0.852, and the polymorphic information content (PIC) varies from 0.638–0.945 (mean = 0.859). Genetic diversity analysis showed dissimilar groups, indicating possibility of involvement of different accuminata and balbisiana types in evaluation of banana in NE region. The outcome of the current study will be useful for des igning banana crops against different stresses

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.

Growth performance and selection signatures revealed by whole-genome resequencing in genetically selected grass carp (Ctenopharyngodon idella)

Grass carp (Ctenopharyngodon idella) is a highly productive freshwater fish species that is widely cultivated worldwide, contributing substantial economic value to the aquaculture industry annually. Recently, a breeding program for grass carp has progressed to the fourth generation (F4) after four consecutive generations of family selection. To further assess the growth performance of the genetically selected grass carp F4, a 90-day consecutive growth comparison experiment was conducted between the selected population and a wild base population. The results showed that the selected grass carp F4 had better growth performance. Whole-genome resequencing of both wild and selected populations of grass carp yielded a total of 4,354,416 high-quality single nucleotide polymorphisms (SNPs). Parameters of genetic diversity including observed heterozygosity (Ho), expected heterozygosity (He), nucleotide diversity (π), and polymorphic information content (PIC) were slightly decreased in the selected population compared to the wild population. The fixation index (Fst) indicated a low level of genetic differentiation (Fst = 0.021). Selection signatures analysis identified a total of 173 candidate selected regions with a cumulative size of 23.75 Mb, and 912 candidate genes including igf-1r, igfbp-2, igfbp-5 and itga6. This study provides valuable insights into the growth performance and the genetic basis of selection signatures in the process of grass carp selective breeding, and offers guidance for future breeding programs.

Development and characterization of 40 InDel markers from the major histocompatibility complex genes of largemouth bass (Micropterus salmoides).

The genetic improvement in growth and food habit domestication of largemouth bass (Micropterus salmoides) have made breakthroughs in past decades, while the relevant work on disease resistance were rarely carried out. Major histocompatibility complex (MHC) genes, which are well known as their numbers and high polymorphisms, have been used as candidate genes to mine disease-resistant-related molecular markers in many species. In present study, we developed and characterized 40 polymorphic and biallelic InDel markers from the major histocompatibility complex genes of largemouth bass. The minor allele frequency, observed heterozygosity, expected heterozygosity and polymorphic information content of these markers ranged from 0.0556 to 0.5000, 0.1111 to 0.6389, 0.1064 to 0.5070, and 0.0994 to 0.3750, respectively. Three loci deviated significantly from Hardy-Weinberg equilibrium, while linkage disequilibrium existed at none of these loci. These InDel markers might provide references for the further correlation analysis and molecular assisted selection of disease resistance in largemouth bass.

Molecular Genetic Diversity of Manioc (Manihot esculenta Crantz) Using Simple Sequence Repeated Markers (SSR) in the Kara Region of Togo

Cassava (Manihot esculenta Crantz), a plant of the future, is one of the main crops with high genetic potential. Therefore, the knowledge of its genetic variability would be of great importance for its effective use in genetic improvement programs. The objective of this work was to characterize the genetic diversity of cassava cultivars present in the Kara region of Togo. Thus, a total of 91 cassava leaf samples collected in the 7 prefectures of the Kara region were analyzed using 7 pairs of SSR microsatellite primers. Fifty-three alleles were detected with an average of 7.57 alleles per locus. The polymorphic information content ranged from 0.63 to 0.83 with an average of 0.74, indicating a high level of marker polymorphism. Molecular analysis of variance revealed that the majority of variability occurred within individuals and accounted for 99 % of the total variation between individuals. Weak genetic differentiation (Fst=0.011) was also observed between populations. The genetic structuring model based on the Neighbour-Joining algorithm method divided the individuals into 6 groups independently of local names. These results indicate the presence of high genetic resource variability in the studied populations. Therefore, it would be important to implement management strategies to better conserve cassava genetic resources and to facilitate the identification of successful cultivars.

Genetic diversity and population structure of Ethiopian basil (Ocimum basilicum L.) accessions using DArTseq markers

In Ethiopia, basil is the most widely used aromatic and medicinal herb. Despite being widely available across the nation and utilized for a variety of purposes for centuries, little is known about the degree of genetic variability in sweet basil. Thus, 62 basil accessions that were collected from various locations in Ethiopia were examined for genetic diversity and population structure, and genome-wide SNPs were created using genotyping by sequencing (GBS). The observed and expected heterozygosis are (0.01–0.02) and (0.13–0.33), respectively. The gene diversity index (GD) ranged from 0.13 to 0.29, with an overall mean of 0.13. Moreover, the polymorphic information content (PIC) varied from 0.23 to 0.37, with an average of 0.37. The Shannon index (I) ranged from 0.01 to 0.41, with an average of 0.12. A total variation of 90 % and 1 % within and among populations, respectively, was revealed using analysis of molecular variance (AMOVA). Furthermore, genetic variation showed a coefficient of gene differentiation of 0.01 and a gene flow value of 2.013 among populations. The 62 basil accessions were divided into two genetic groups according to STRUCTURE analysis, unweighted pair group method (UPGMA), discriminant analysis of principal components (DAPC), and principal coordinate analysis (PCoA). This research confirmed the diversity and population structure of the Ethiopian basil. Therefore, the variation pattern in their genetic diversity can serve as a basis for the selection, breeding, and maintenance of basil in Ethiopia.

Genetic diversity and heritability of tomato parental lines assembled for Ralstonia solanacearum resistance

Bacterial wilt is a disease caused by Ralstonia solanacearum, which affects over 450 plant species and causes significant reduction in crop yields including of tomato (Solanum lycopersicum) worldwide. Developing and identifying tomato genotypes with Ralstonia solanacearum tolerance and high yield potential, presents an opportunity for improvement of crop productivity. The objective of this study was to explore the heritability of tomato resistance against bacterial wilt and the genetic variation within the population for breeding purposes. A breeding population was created by crossing two bacterial wilt-resistant (MT56 and BL333) and three commercially desirable susceptible (Assila, Rambo and Heinz) tomato varieties, using North Carolina Design II, in a screen house at the Makerere University Agricultural Research Institute, Kabanyolo (MUARIK). Results showed that the Area Under Disease Progress Curve was significant (P<0.001), indicating that cumulative disease progress was less in resistant genotypes of segregating generations. Disease severity increased with days after inoculation (DAI), with Heinz showing the highest level of susceptibility. The General Combining Ability for male parent (GCAm) was significant (P< 0.01), and Specific Combining Ability (SCAf×m) and GCAf were significant (P<0.01) for the F2 generation. Broad-sense heritability was higher than the narrow-sense heritability in both F1 and F2 generations, suggesting that non-additive gene action predominately controlled tomato resistance to bacterial wilt infestation. The genetic diversity ranged from 0.5 to 0.6759, with a mean value of 0.5787. Polymorphism Information Content (PIC) varied from 0.375 to 0.6357, with a mean of 0.4888, indicating a high degree of variation. SLM 12-2 was the most polymorphic marker, with a PIC of 0.6357. The Unweighted Pair-Group Method with Arithmetic Average (UPGMA) classified all tomato genotypes into six clusters, namely Clusters 1 and 2 (Susceptible parents), Cluster 3 (Resistant parents), Clusters 4 and 5 (New source of resistance), and Cluster 6 (F1P1×P5).

Investigating growth associated genomic short tandem repeats (STRs) in a resource population generated through molecular breeding of RIR chicken

The long-term selection based on phenotypes causes loss of variation in performance traits and slows down the genetic progress per generation in the population; genomic selection could restore the variability along with faster genetic progress. Genomic short tandem repeats (STRs) in a resource population of RIR chicken were explored investigating randomly selected 114 pedigreed chicks. Alleles separated through 3.4% MetaPhor agarose gel electrophoresis at ten STR loci, and data recorded on growth traits were analyzed. Twenty-six alleles were resolved with frequencies of 0.1140–0.7632 and > 38.60% for the most frequent alleles at ten STR loci. The most frequent genotypes appeared with frequency >21.93% at different loci. Polymorphic information contents ranged from 0.2961 (LEI0079) to 0.6716 (LEI0071). Effective number of alleles ranged from 1.5662 (LEI0079) to 3.5836 (LEI0071). Mean FIS statistics revealed overall 21.78% heterozygosity deficit. Average heterozygosity ranged from 0.3630 (LEI0079) to 0.7241 (LEI0071). Chi-square and G-square test showed the population in Hardy-Weinberg disequilibrium at nine loci. Chick weight was significantly influenced by the factor of sire, and body weight traits by sex and hatch factors of the birds coded with STR-genotypes. ADL0328-BB genotype had the highest chick weight. LEI0068-BC and LEI0071-CC genotypes showed maximum 28-weeks body weight. MCW0010-AA genotype had the potential bearing of the highest body weight records at 16, 32, 36 and 40 weeks of age. MCW0058-CC genotype revealed the same at 24 and 28 weeks of age. The study impacts on marker assisted selection program for genetic improvement of growth traits in poultry.

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.

Comparing genetic differentiation and variation using ISSR and SCoT among Juniper plant markers in Saudi Arabia.

Juniperus, a genus of fragrant evergreen trees in the Cupressaceae family, encompasses up to 67 distinct species distributed globally. Among these, Juniperus procera, also known as the East African pencil cedar or African Juniper, stands out for its notable medicinal properties. Due to the well-recognized therapeutic benefits of Juniper species, assessing genetic diversity is essential for various breeding initiatives. Thus, in this work, six ISSR and six SCoT primers were utilized to evaluate the genetic diversity between 23 Juniper genotypes collected from different locations in Saudi Arabia. 29 out of 103 and 26 out of 105 amplified bands, respectively, were found to be polymorphic markers using the ISSR and SCoT studies. With the help of 120 genotype-specific markers, including 60 for ISSR and 60 for SCoT, several varieties of Juniper were discovered. In addition, the polymorphism information content (PIC) was computed to assess the effectiveness of the markers. The findings of this study highlight the importance of conserving the genetic diversity of Juniperus procera, as it holds immense potential for developing new medicinal products. Additionally, the results provide valuable insights into the genetic structure of Juniper populations in western Saudi Arabia, which can inform future conservation and management efforts. However, all of the techniques utilized to profile the genotypes of Juniper can be regarded as useful techniques for long-term fingerprinting and diagnostic markers.

The genetic diversity of Oncomelania hupensis robertsoni, intermediate hosts of Schistosoma japonicum in hilly regions of China, using microsatellite markers

BackgroundThe elimination of schistosomiasis remains a challenging task, with current measures primarily focused on the monitoring and control of Oncomelania hupensis (O. hupensis) snail, the sole intermediate host of Schistosome japonicum. Given the emerging, re-emerging, and persistent habitats of snails, understanding their genetic diversity might be essential for their successful monitoring and control. The aims of this study were to analyze the genetic diversity of Oncomelania hupensis robertsoni (O. h. robertsoni) using microsatellite DNA markers; and validate the applicability of previously identified microsatellite loci for O. hupensis in hilly regions.MethodsA total of 17 populations of O. h. robertsoni from Yunnan Province in China were selected for analysis of genetic diversity using six microsatellite DNA polymorphic loci (P82, P84, T4-22, T5-11, T5-13, and T6-27).ResultsThe number of alleles among populations ranged from 0 to 19, with an average of 5. The average ranges of expected (He) and observed (Ho) heterozygosity within populations were 0.506 to 0.761 and 0.443 to 0.792, respectively. The average fixation index within the population ranged from – 0.801 to 0.211. The average polymorphic information content (PIC) within the population ranged from 0.411 to 0.757, appearing to be polymorphic for all loci (all PIC > 0.5), except for P28 and P48. A total of 68 loci showed significant deviations from Hardy-Weinberg equilibrium (P < 0.05), and pairwise Fst values ranged from 0.051 to 0.379. The analysis of molecular variance indicated that 88% of the variation occurred within snail populations, whereas 12% occurred among snail populations. Phylogenetic trees and principal coordinate analysis revealed two distinct clusters within the snail population, corresponding to “Yunnan North” and “Yunnan South”.ConclusionsO. h. robertsoni exhibited a relatively high level of genetic differentiation, with variation chiefly existing within snail populations. All snail in this region could be separated into two clusters. The microsatellite loci P82 and P84 might not be suitable for classification studies of O. hupensis in hilly regions. These findings provided important information for the monitoring and control of snail, and for further genetic diversity studies on snail populations.Graphical

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.

Molecular Genetic Diversity of Cassava (Manihot esculenta CRANTZ) in the Maritime Region of Togo using Simple Sequence Repeat (SSR) Markers

Cassava is a plant cultivated for its calorie-rich leaves and tuberous roots. Unfortunately, genetic improvement of cassava is limited by the lack of information on its genetic variability. The objective of the present work was to study the genetic and molecular diversity of cassava cultivars using microsatellite markers (SSR) in the Maritime region of Togo. A total of 95 cassava individuals from 7 cultivars were evaluated using 7 SSRs. The average polymorphic information content was 0.74 and the average number of alleles per locus was 7. The average observed heterozygosity was lower than the expected average heterozygosity for the 7 cultivars, showing positive fixation indices and presence of inbreeding. Molecular analysis of variance revealed greater molecular variation within cultivars (94%). The dendrogram constructed using the Neighbor Joining method resulted in 3 groups. The high genetic diversity observed could be due to the exchange of cuttings by growers. This diversity would be valuable for efficient germplasm management and for effective use of the material in breeding.

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.

Dissecting the Genetic Diversity of USDA Cowpea Germplasm Collection Using Kompetitive Allele Specific PCR-Single Nucleotide Polymorphism Markers.

Cowpea (Vigna unguiculata L. Walp) is an important grain legume crop of the subtropics, particularly in West Africa, where it contributes to the livelihoods of small-scale farmers. Despite being a drought-resilient crop, cowpea production is hampered by insect pests, diseases, parasitic weeds, and various abiotic stresses. Genetic improvement can help overcome these limitations, and exploring diverse cowpea genetic resources is crucial for cowpea breeding. This study evaluated the genetic diversity of 361 cowpea accessions from the USDA core collection for the species using 102 Kompetitive Allele Specific PCR (KASP) single nucleotide polymorphism (SNP) markers. A total of 102 KASP-SNP was validated in the germplasm panel, and 72 showed polymorphism across the germplasm panel. The polymorphism information content (PIC) of all SNPs ranged from 0.1 to 0.37, with an average of 0.29, while the mean observed heterozygosity was 0.52. The population structure revealed three distinct populations that clustered into two major groups after phylogenetic analysis. Analysis of molecular variance (AMOVA) indicated greater genetic variation within populations than among populations. Although cowpea generally has a narrow genetic diversity, the accessions used in this study exhibited considerable variation across geographical regions, sub-species, and improvement status. These results indicated that the selected KASP genotyping assay can provide robust and accurate genotyping data for application in the selection and management of cowpea germplasm in breeding programs and genebanks.

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.