Average Polymorphism Information Content Value Research Articles

Development of Intragenic InDel Markers From RNA‐Seq Data for Map‐Based Cloning and Marker‐Assisted Selection in Maize (Zea mays L.)

ABSTRACTMaize is one of the most extensively grown and produced crops in the world. Functional molecular markers (FMM) are essential tools for enhancing the efficiency of both breeding and basic research. The transcriptome obtained from high‐throughput sequencing is a valuable resource for developing FMM. In this study, we precisely identified high‐density and highly polymorphic RNA‐derived InDel markers from 368 high‐quality, high read depth maize RNA‐seq datasets using stringent criteria. The nonredundant marker dataset comprised 13,904 InDel markers with a Polymorphism Information Content (PIC) ≥ 0.5 and a principal allelic difference (length difference between the most and second most frequent alleles) ≥ 3 bp, covering 7749 genes. Subsequently, the polymorphism of InDel markers was verified experimentally. Fifty InDel markers were randomly selected, and their average PIC values in 20 maize inbred lines selected from 368 RNA‐seq samples and 20 newly selected maize inbred lines were 0.53 and 0.54, with range intervals of 0.18 to 0.77 and 0.22 to 0.74, respectively. The high density and polymorphism of RNA‐derived InDel markers identified in this study make them effective tools for maize gene cloning, genetic diversity studies, genome‐wide association analysis, and marker‐assisted selection.

Genetic relationships among some old walnuts (Juglans regia L.) genotypes in Iran and selection of superior genotypes

Abstract Walnut (Juglans regia L.) is one of the oldest and most economically important edible nut species due to its high nutritional value. Iran is known as one of the most important centres of the origin and diversity of walnuts worldwide. This research was carried out to determine the genetic relationships of some old walnut genotypes in Iran in order to select superior genotypes and better conserve them. The results of morphological evaluation of the fruits showed that the highest coefficients of variation were related to nut weight, kernel weight, percentage kernel, thickness and weight of the shell, and thickness and weight of the packing tissue in both years. The average morphological traits among the studied genotypes were different, such that the highest nut weights in the first and second years were 15.59 and 14.79 g and the corresponding lowest values were 7.37 and 7.79 g, respectively. The highest and lowest kernel weights were observed in the first years to be 8.09 and 3.80 g and in the second years were 6.94 and 2.65 g, respectively. The highest kernel percentages in the first and second years were 64.97 and 59.79% and the lowest percentages were 39.52 and 27.80% in the first and second years, respectively. Molecular evaluation results showed that the 16 start codon of target (SCoT) primers amplified a total of 166 bands with an average of 10.44 bands per primer. The number of polymorphic bands was changed from 2 to 19 in primers SCoT-19 and SCoT-15. The average polymorphism information content value was 0.30 and the highest amount of this index (0.36) was observed in SCoT-14 and SCoT-19 primers. The results of principal component analysis and analysis of molecular variance indicated the presence of relatively high diversity within the investigated genotypes. The amount of genetic diversity within the investigated regions was 84% and that between areas was 16%. Based on the obtained results, it was concluded that SCoT markers could provide helpful information on the genetic relationships among walnut genotypes, which can be used in future walnut breeding and conservation programmes.

Characterization of some local and commercial bread wheat (Triticum aestivum L.) genotypes with allele-specific DNA markers

Landraces play a significant role as genetic reservoirs in wheat breeding endeavors. Advances in functional marker technology have facilitated early and more precise selection processes. This study involved the characterization of a total of 96 bread wheat genotypes, comprising 76 landraces and 20 registered cultivars, utilizing allele-specific DNA markers targeting various genes including those for gluten strength, yellow rust resistance, stem rust resistance, dwarfism, rye translocation, hardness, and softness. Molecular analysis revealed the presence of 148 alleles, with an average of 21.14 alleles per marker, and an average polymorphic information content (PIC) value of 0.5625. Specific genes such as the rye translocation gene were identified in genotypes 161 and 884, while the hardness gene was found in genotypes 672, 3088, 3384, 3414, and 3541. Stem rust resistance gene was detected in the cultivar Adana-99, yellow rust resistance gene in genotypes 1635 and 2115, and the softness gene in 31 genotypes including the cultivar Masaccio. Based on the dendrogram analysis, genotype 3652 exhibited around 93% genetic similarity with the cultivar Masaccio, while genotypes 2190, 2715, and 2897 showed similarity to genotype 2946. Genotypes 2959 and 2960 and genotypes 3334 and 3359 shared approximately 91% genetic similarity.

Assessment of Genetic Diversity and Relatedness of Local Banana (Musa spp.) Cultivars in Malaysia Using Simple Sequence Repeat (SSR) Markers

Banana (Musa spp.) is an economically important crop widely consumed all over the world. Understanding the genetic diversity and relatedness between various banana cultivars is important to continuously improve its fruit characteristics, nutritional value, and disease resistance. This study aimed to develop a DNA fingerprinting panel using polymorphic simple sequence repeat (SSR) markers for the genetic characterisation of 11 banana cultivars in Malaysia. A total of 10 polymorphic SSR markers were developed into a multiplex PCR reaction and capillary electrophoresis to uniquely profile our collection of banana cultivars. The developed fingerprinting panel successfully amplified a total of 95 alleles, with 6 to 13 alleles per SSR marker. The average SSR marker polymorphic information content (PIC) value is 0.812, indicating the informativeness of the panel. Analysis of molecular variance (AMOVA) shows that 97% of the molecular variance from our banana collection is due to inter-variety genetic diversity, while the remaining 3% is due to intra-variety genetic diversity. A population structure analysis groups our collection of banana varieties according to the presence of at least one M. balbisiana (B) genome in their genetic makeup. The Cavendish variety, however, showed a distinct structure compared to the other cultivars. This SSR fingerprinting panel provides valuable insights into the genetic diversity and relatedness between banana cultivars in Malaysia. It has the potential to assist future banana breeding initiatives and serve as an effective quality control measure for verifying varieties in a tissue culture facility involved in banana planting materials production.

Development and validation of a novel forensic STR multiplex assay for blue (Anthropoides paradiseus), wattled (Bugeranus carunculatus), and grey-crowned crane (Balearica regulorum)

The blue crane (Anthropoides paradiseus), wattled crane (Bugeranus carunculatus), and grey-crowned crane (Balearica regulorum) are species of concern as their populations are declining and they face several threats including habitat loss, disturbance and illegal trade. In South Africa, these species are bred in captivity for trade purposes which is permitted and regulated globally under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). Legal sustainable trade through captive breeding of endangered wildlife species such as cranes has been promoted to counteract the illegal trade of individuals from the wild. Captive breeding independent of wild populations may reduce the harvest pressures on wild bird populations which in turn benefit the recovery of exploited species. This approach is considered to be controversial by some individuals. Although captive breeding of endangered species, for both population sustainability and commercial purposes, is promoted to aid in conserving species, concerns have been raised with regards to breeding facilities being used for laundering of animals. To monitor the legal trade of cranes in South Africa a short tandem repeat (STR) assay following recommendations of the International Society for Forensic Genetics (ISFG) was developed and validated. An STR assay comprising of four multiplexes that include 16 STR markers and two gender determination markers was proven to be highly informative with average polymorphic information content (PIC) values of 0.806, 0.646 and 0.725 for A. paradiseus, B. regulorum and B. carunculatus respectively. In addition, the assay showed sufficient discriminatory power for parentage assignment of closely related individuals in all three species (A. paradiseus: PI = 1.7×10−24, PIsibs = 4.7×10−08, and B. carunculatus: PI = 1.4×10−19, PIsibs = 2.9×10−07 and B. regulorum: PI = 1.7×10−12, PIsibs = 5.0×10−05). Analysis of 251 samples suggested that the validated multiplex assay ensures reliability, reproducibility, and repeatability for applications in forensic case work where illegal trade of offspring is suspected through verifying parentage of captive birds in breeding facilities.

Association study of allelic variation identified at yield contributing loci in rice (Oryza sativa L.)

The knowledge of functionally characterized genes and linked markers that govern grain yield and its related traits were used to unravel the markers/genes that associate with diversity of yield traits in a panel 30 novel rice genotypes comprising of indica, japonica, aromatic, landraces, interspecific crosses (O.glaberrima/O.sativa) etc. The ANOVA showed significant differences (P=<0.001) for all traits among the genotypes. Molecular analysis was done by employing 37 gene-specific markers targeting 24 yield governing genes in rice. Two markers viz., RM223(YLD) on chromosome 8 and GW004(GW2, LOC_Os02g14720) on chromosome 2 were identified as polymorphic. Average PIC (polymorphic information content) value for these primers was 0.37, suggesting the availability of accountable variability at these loci. Cluster analysis grouped the genotypes into three clusters. Marker-trait-association analysis revealed significant association of the marker GW004 with panicle length, plant height and filled grains in rice. Pearson correlation study also supported the molecular associations through significant phenotypic associations for trait pairs plant height and filled grains, panicle length and plant height. The phenotypic variance explained (R2%) by the marker across panicle length, plant height and filled grains was ≥15%, suggesting major role of the locus/gene in controlling respective traits. Thus, GW004 marker could be employed in breeding programs for simultaneous selection of three traits panicle length, plant height and filled grains. From the current study it can be concluded that allelic variation studies using novel genotypes can result in the identification of suitable donors along with trait associated markers for rice yield improvement.

Genetic Diversity and Population Structure of a Large USDA Sesame Collection.

Sesame, Sesamum indicum L., is one of the oldest domesticated crops used for its oil and protein in many parts of the world. To build genomic resources for sesame that could be used to improve sesame productivity and responses to stresses, a USDA sesame germplasm collection of 501 accessions originating from 36 countries was used in this study. The panel was genotyped using genotyping-by-sequencing (GBS) technology to explore its genetic diversity and population structure and the relatedness among its accessions. A total of 24,735 high-quality single-nucleotide polymorphism (SNP) markers were identified over the 13 chromosomes. The marker density was 1900 SNP per chromosome, with an average polymorphism information content (PIC) value of 0.267. The marker polymorphisms and heterozygosity estimators indicated the usefulness of the identified SNPs to be used in future genetic studies and breeding activities. The population structure, principal components analysis (PCA), and unrooted neighbor-joining phylogenetic tree analyses classified two distinct subpopulations, indicating a wide genetic diversity within the USDA sesame collection. Analysis of molecular variance (AMOVA) revealed that 29.5% of the variation in this population was due to subpopulations, while 57.5% of the variation was due to variation among the accessions within the subpopulations. These results showed the degree of differentiation between the two subpopulations as well as within each subpopulation. The high fixation index (FST) between the distinguished subpopulations indicates a wide genetic diversity and high genetic differentiation among and within the identified subpopulations. The linkage disequilibrium (LD) pattern averaged 161 Kbp for the whole sesame genome, while the LD decay ranged from 168 Kbp at chromosome LG09 to 123 Kbp in chromosome LG05. These findings could explain the complications of linkage drag among the traits during selections. The selected accessions and genotyped SNPs provide tools to enhance genetic gain in sesame breeding programs through molecular approaches.

Integrating multilocus genome-wide association studies in chickpea landraces to discern the genetics of drought tolerance

In chickpea breeding, drought is a major concern and a complex trait controlled by several genes. To develop drought-tolerant varieties, it is essential to use the available germplasm and genomic resources. Over the years, the landraces have proven to be a good source for the dissection of genes for different yield and yield-related traits. The present investigation for marker–trait associations (MTAs) and candidate gene identification was conducted by studying 125 chickpea landraces collected from the West Asia and North Africa (WANA) region, along with 4 varieties suitable for irrigated and rainfed environments. This study analyzed 13 physio-morphological traits in 2 consecutive years at two isolated locations (IARI, New Delhi, and Dharwad). A strong correlation coefficient was observed between the trait seed yield (SY) and biological yield (BY) under both conditions. The Drought Susceptibility Index (DSI) ranged from 0.02 to 1.84 and 0.10 to 2.04 at the IARI, New Delhi and Dharwad locations, respectively. The genotypic data of 6,367 single nucleotide polymorphisms (SNPs) distributed across the genome were used for genetic diversity study, population structure, and genome-wide association study (GWAS). The average polymorphic information content (PIC) value observed was 0.25, and the average linkage disequilibrium (LD) decay distance was 152,269 bp across the genome. A total of four subgroups were observed within the population for genotypic data. Fixed and random model Circulating Probability Unification (FarmCPU) was used for the GWAS analysis, which considered both fixed- and random-effect models. A total of 52 significant SNPs were reported in both irrigated and rainfed conditions at low locations; 7 SNPs were associated with more than one trait, which may have pleiotropic effects. Significant SNPs were annotated in the pulse database. The identified genomic region found in or near MTA under rainfed conditions encodes for guard cell hydrogen peroxide-resistant1 (GHR1), late embryogenesis-abundant, E3 ubiquitin-protein ligase, walls are thin1 (WAT1), and beta-galactosidase that are known to be associated with drought tolerance.

Unveiling the genetic structure of pig population in a Himalayan state Uttarakhand through microsatellite and mitochondrial DNA analyses.

This study traced the maternal lineage of the domestic swine populations using mitochondrial DNA control region markers and genetic diversity using microsatellite markers in Uttarakhand, an Indian state situated at the foothills of the world's youngest (geo-dynamically sensitive) mountain system, "the Himalayas". Analysis of 68 maternally unrelated individuals revealed 20 haplotypes. The maternal signature of the Pacific, Southeast Asian, European, and ubiquitously distributed Chinese haplotypes was present in Uttarakhand's domestic pig population. The D3 haplotype reported in wild pigs from North India was also identified in 47 domestic samples. A unique gene pool, UKD (Uttarakhand Domestic), as another lineage specific to this region has been proposed. Genotypes were analyzed, using 13 sets of microsatellite markers. The observed (Ho) and expected (He) heterozygosities were 0.83 ± 0.02 and 0.84 ± 0.01, respectively. The average polymorphic information content value of 0.83 ± 0.01 indicated the high informativeness of the marker. The overall mean FIS value for all the microsatellite markers was low (F = 0.04, P < 0.01). Seven loci deviated from Hardy-Weinberg equilibrium (HWE) at a significant level (p < 0.05). Two clusters were identified, indicating overlapping populations. These results suggested that though belonging to different maternal lineages, the traditional management practices in Uttarakhand have allowed for genetic mixing and the sharing of genetic material among pig populations. It could contribute to increased genetic diversity but might also result in the loss of distinct genetic characteristics or breed purity of the local breeds if not carefully managed.

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.

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.

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)

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.

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 diversity of maize resources revealed by different molecular markers

Maize (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.

Diversity Analysis of 53 Soybean Accessions Introduced from China Based on Morphological Characteristics and SSR Markers

Indonesia still faces challenges in meeting its national soybean demand. Genetic diversity can provide new resources to improve soybean production and quality. Genetic diversity of 53 soybean accessions introduced from China, based on morphological characteristics and 17 SSR markers, was analyzed in this study. Principal component analysis (PCA) conducted on morphological characters produced a total diversity value of 64.67% and identified four main components. Based on phylogenetic analysis and principal coordinate analysis (PCoA) two accessions showed low genetic similarity of 78% (China cult-55 and Mi yang niu mao huang), which indicated that they could be selected as parents for plant breeding programs. In addition, 772 SSR alleles at an average of 45 alleles per locus were detected. The average heterozygosity was 0.83, and the average polymorphic information content (PIC) value was 0.96. All SSR markers showed a PIC value &gt; 0.8, indicating their informativeness in analyzing genetic diversity of soybean. The phylogenetic analysis indicated a genetic similarity of 82% and the accessions were grouped into two main clusters. The phylogenetic analysis depicted that several accessions could be grouped based on the growth type and origin. The results of morphological characterization and molecular markers in the analysis of genetic diversity are beneficial for selecting parental crosses when developing new varieties.

Molecular characterization and diversity analysis of promising tgms lines and high-yieding varieties In rice by using ssr markers

The present investigation was intended to assess the extent of genetic diversity present among the selected genotypes of Oryza sativa (including TGMS lines) using SSR markers. The SSR markers used for the study gave average Polymorphism Information Content (PIC) value of 0.551. The primer RM 9 followed by RM 536 has given maximum PIC value and the primer RM 29 gave the minimum. It was inferred that the primers RM 9 and RM 536 had been the better choices in this study. The lines, TS09 24 and TS09 26 were in the same cluster as they derived from the same parents. The TGMS lines TS 29 and TNAU 27S are in separate cluster from other parents indicating that these lines are highly diversified and their crosses can give improved cultivars. Bangladesh J. Bot. 52(4): 1067-1070, 2023 (December)

Genetic relationship of kasturi mango (Mangifera casturi Kosterm.) from South Kalimantan and Riau based on microsatellite markers

Mangifera casturi Kosterm is one of the endemic fruits from South Kalimantan. It belongs to the genus Mangifera of the Anacardiaceae family. This study aimed to analyze the genetic relationship of Mangifera casturi from South Kalimantan and Riau using microsatellite markers. Fourteen Mangifera casturi accessions were amplified using fourteen microsatellite loci, and the data produced was utilized to evaluate the genetic relationship. DNA amplification using the multiplex PCR method with fluorescence-labeled dyes on the forward primer will be detected using capillary electrophoresis. Forty-two alleles were obtained from the fourteen loci, averaging three per locus. The observed heterozygosity value (Ho) is 0.24, which is lower than the expected heterozygosity value (He), with an average of 0.48. The fourteen-microsatellite fixation index (FIS) loci ranged between –0.876 and 1. The average Polymorphic information content (PIC) value is 0.39, with the highest found in MC58089 loci (0.65), indicating the SSR marker loci are informative for revealing genetic diversity. The phylogenetic analysis using the neighbor-joining method was constructed into four groups. Kasturi mango from Riau is closely related to Pelipisan and Cuban cultivars from South Kalimantan.

Genome Assembly and Microsatellite Marker Development Using Illumina and PacBio Sequencing in the Carex pumila (Cyperaceae) from Korea.

This study is the first to report the characterization of Carex pumila genomic information. Assembly of the genome generated a draft of C. pumila based on PacBio Sequel II and Illumina paired-end sequencing, which was assembled from 2941 contigs with an estimated genome size of 0.346 Gb. The estimate of repeats in the genome was 31.0%, and heterozygosity ranged from 0.426 to 0.441%. The integrity evaluation of the assembly revealed 1481 complete benchmarked universal single-copy orthologs (BUSCO) (91.76%), indicating the high quality of the draft assembly. A total of 23,402 protein-coding genes were successfully predicted and annotated in the protein database. UpsetR plots showed that 7481 orthogroups were shared by all species. The phylogenetic tree showed that C. pumila is a close but distant relative of Ananas comosus. C. pumila had greater contraction (3154) than expansion (392). Among the extended gene families, aquaporins have been found to be enriched. Primers for microsatellite markers determined 30 polymorphic markers out of 100. The average number of alleles amplified by these 30 polymorphic markers was 4 to 12, with an average polymorphism information content (PIC) value of 0.660. In conclusion, our study provides a useful resource for comparative genomics, phylogeny, and future population studies of C. pumila.