UPGMA Analysis Research Articles

Molecular Insights into the Reproductive Patterns and Genetic Structure of Wheat Stripe Rust in Ili, Xinjiang.

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a globally significant fungal disease that seriously threatens wheat yield, particularly in China. This study investigates the genetic structure and reproductive patterns of Pst populations in Ili, Xinjiang, using 12 pairs of Simple Sequence Repeat (SSR) molecular markers. Analyses of 79 Pst isolates from either spring or winter wheat areas in Ili revealed three primary genetic clusters, indicating notable differences between populations associated with spring and winter wheat. The STRUCTURE results, complemented by UPGMA and PCoA analyses, highlight significant genetic diversity within these populations, with evidence of genetic recombination and sexual reproduction in certain areas. Pst populations in Ili exhibit a mixed mode of reproduction, predominantly sexual in Qapqal and Xinyuan D and primarily asexual within the spring wheat populations. The gene flow analysis underscores extensive inter-population communication, which facilitates the spread and adaptation of the pathogen across diverse wheat-growing environments. This study marks the first documentation of sexual reproduction in Pst within Xinjiang, providing new insights into its spread and genetic variation. These findings suggest that sexual reproduction may play a role in the regional adaptation and evolution of Pst, impacting future management strategies for wheat stripe rust in Xinjiang and potentially in broader Central Asian contexts.

Exploration of Genetic Variation and Population Structure in Bergenia ciliata for its Conservation Implications.

Bergenia ciliata (Haw.)Sternb. is a perennial medicinal herb distributed in Indian Himalayan Region(IHR). A total of eight populations of B.ciliata were collected from diverse locales of IHR, and 17 EST-SSR markers were used in this study. The present study revealed moderate genetic diversity at the locus level with the mean number of alleles (Na = 7.823), mean number effective of alleles (Ne = 3.375), mean expected heterozygosity (He = 0.570), and meanShannon's diversity index (I = 1.264). The MSR (He = 0.543, I = 1.067) and DRJ populations (He = 0.309, I = 0.519) revealed the highest and lowest genetic diversity at the population level, respectively. AMOVA analysis showed that 81.76% of genetic variation was within populations, 10.55% was among populations, and 7.69% was among the regions. In addition, a moderate to high level of differentiation was found among the populations (FST = 0.182), which could be indicative of low to moderate gene flow (Nm = 0.669) in the B. ciliata populations. UPGMA and PCoA analysis revealed that eight populations could be differentiated into two groups, while the structure analysis of the 96 individuals differentiated into three groups. The Mantel test showed a positive relationship between genetic and geographical distance. The findings of this study will provide the development of conservation and germplasm management strategies for this valuable medicinal species.

Investigation of genetic diversity in lentil genotypes obtain from different countries using SDS-PAGE methodology

Pulses are an important component of the agricultural production system, providing high-quality food to millions of people worldwide. Among pulses, lentil is an annual and self-pollinated crop known to be its high proteins, amino acids, dietary fibers and low fat in the world. In the current study, the characterization of 44 lentil genotypes was performed using SDS-PAGE (Sodium dodecyl sulfate-polyacrylamide gel electrophoresis) technique. The protein bands were scored according to a binary system as the present (1) or absent (0) that ranged 12-20 bands in lentil genotypes. The Jaccard’s coefficient of genetic dissimilarity (GD) was measured, and the mean GD was 0.216. Maximum genetic distance was found as 0.526 between Syria2 with Iraq3 and these genotypes might be recommended for future lentil breeding. AMOVA explored the presence of higher genetic variety within genotypes (83%) than among genotypes (17% variations). STRUCTURE algorithm separated lentil genotypes into two groups mainly on the basis of their geographic. The UPGMA clustering separated lentil genotypes into two main clusters A and B. The PCoA was also conducted to confirm the results of structure and UPGMA analyses. Findigs from the PCoA and structure analyses were in full agreement with those obtained by UPGMA. The results might be useful for researchers worldwide who are interested in lentil breeding.

Using ddRADseq to assess the genetic diversity of in-farm and gene bank cacao resources in the Baracoa region, eastern Cuba, for use and conservation purposes.

The Baracoa region, eastern Cuba, hosts around 80 % of the country cacao (Theobroma cacao L.) plantations. Cacao plants in farms are diverse in origin and propagation, with grafted and hybrid plants being the more common ones. Less frequent are plants from cuttings, TSH progeny, and traditional Cuban cacao. A national cacao gene bank is also present in Baracoa, with 282 accessions either prospected in Cuba or introduced from other countries. A breeding program associated with the gene bank started in the 1990s based on agro-morphological descriptors. The genetic diversity of cacao resources in Baracoa has been poorly described, except for traditional Cuban cacao, affecting the proper development of the breeding program and the cacao planting policies in the region. To assess the population structure and genetic diversity of cacao resources in Baracoa region, we genotyped plants from both cacao gene bank (CG) and cacao farms (CF) applying a new ddRADseq protocol for cacao. After data processing, two SNPs datasets containing 11,425 and 6,481 high-quality SNPs were generated with 238 CG and 135 CF plants, respectively. SNPs were unevenly distributed along the 10 cacao chromosomes and laid mainly in noncoding regions of the genome. Population structure analysis with these SNP datasets identified seven and four genetic groups in CG and CF samples, respectively. Clustering using UPGMA and principal component analysis mostly agree with population structure results. Amelonado was the predominant cacao ancestry, accounting for 49.22 % (CG) and 57.73 % (CF) of the total. Criollo, Contamana, Iquitos, and Nanay ancestries were detected in both CG and CF samples, while Nacional and Marañon backgrounds were only identified in CG. Genetic differentiation among CG (FST ranging from 0.071 to 0.407) was higher than among CF genetic groups (FST: 0.093-0.282). Genetic diversity parameters showed similar values for CG and CF samples. The CG and CF genetic groups with the lowest genetic diversity parameters had the highest proportion of Amelonado ancestry. These results should contribute to reinforcing the ongoing breeding program and updating the planting policies on cacao farms, with an impact on the social and economic life of the region.

Demre Çayı (Antalya) Makrozoobentik Faunası

In this study, it was aimed to determine the benthic macroinvertebrate fauna of Demre Stream in Antalya. Benthic macroinvertebrate samples were taken seasonally from 12 stations determined on Demre Stream between April 2015 and December 2015 and the obtained individuals belonging to Clitellata, Rhabditophora, Gastropoda, Insecta, and Arachnida groups Macroinvertebrate based clustering of stations was calculated by using UPGMA analysis. The lowest similarity was determined between the 3rd and 10th stations, and the highest similarity was between the 8th and 11th stations. Simpson and Shannon-Wiener diversity indices were applied to determine the diversity values of the stations. According to both diversity indices, the highest diversity value was reached at the 5th station, while the lowest diversity value was reached at the 3rd station. This study is the first study to determine the benthic fauna of the Demre Stream and therefore all the groups identified are the first records for the Demre Stream.

DNA variants and population structure of Magelang ducks across generation

Magelang ducks (MD) are Indonesian local ducks and are known as dual-purpose type ducks which have high egg production, duck day production (DDP), and body weight size. Nowadays, the MD is selected to establish the pure line to advance the egg production trait in the Breeding and Rearing Center of Non-Ruminant Animals Banyubiru, Central Java. The mitochondrial DNA (mtDNA) Dloop region, is highly polymorphic and could be used to analyze the population genetics. The present research aims to examine the impacts of continuous selection on population structure and genetic mutations on MD across two generations using the mtDNA D-loop region. Thirty-six blood samples from the second (G2) and third (G3) generations were examined using the sequencing method. The MEGA X and DnaSP software were applied to calculate the genetic diversity, genetic distance, and to generate a phylogenetic tree. The number of haplotypes (H), haplotype diversity (Hd), and Tajima's D are 26, 0.9746, and -1.46, respectively. The Fst value of MD is 0.156. The genetic distance among populations ranges from 0.0000 – 2.097. The UPGMA analysis constructs one clade in a phylogenetic tree between MD, Indonesian local Ducks, Indian Ducks, Vietnamese Ducks, and Chinese Ducks. The study found that the genetic variation and population structure did not significantly change between the second and third generations.

KARAKTERISTIK HABITAT IKAN CUPANG LIAR (WILD BETTA) ENDEMIK SEBAGAI DASAR PENGEMBANGAN POTENSI BUDIDAYA DI KABUPATEN LABUHANBATU RAYA

Wild betta fish has high economic value as one of the ornamental fish commodities in Indonesia. The potential for cultivation development so far has not been maximized so that it still relies on the results of capture from nature. The main key to the development of wild fish farming is actually dependent on food conversion and water quality. Water quality management must adjust to its habitat in nature, however, the study of the physical chemical parameters of wild betta fish waters endemic to Sumatra has not been widely reported. Studies related to habitat characteristics can be used as the basis for aquaculture management in the future. This study aims to analyze the condition of the physical parameters of aquatic chemistry in the natural habitat of wild betta fish in the Regency Labuhanbatu Selatan, Labuhanbatu, and Labuhanbatu Utara. This research is exlorative by observing physical and chemical factors carried out insitu and exitu. The research data is analyzed quantitatively, presented discriptively and discussed based on relevant literature. The results of the main component analysis (Principal Component Analysis) show the main characteristic parameters of wild betta fish habitat in the form of: BOD, COD, DO, conductivity, temperature, and pH. Based on the results of UPGMA analysis, the percentage of similarity of stations 1 and 2 (90.5%) while station 3 (83.6%). It was concluded that the key parameters for wild betta fish farming activities are BOD, COD, DO, conductivity, temperature, and pH and these parameters need to be measured continuously.

Multilocus sequence typing of Candida albicans oral isolates reveals high genetic relatedness of mother-child dyads in early life.

Candida albicans is a pathogenic fungus recently recognized for its role in severe early childhood caries development (S-ECC). C. albicans oral colonization begins at birth, but the extent of the mother's involvement in yeast transmission to their children is unclear, therefore, this study used a prospective mother-infant cohort to investigate the maternal contribution of C. albicans oral colonization in early life. Oral samples were collected from 160 mother-child dyads during pregnancy and from birth to two years of life. We used whole-genome sequencing to obtain the genetic information of C. albicans isolates and examined the genetic relatedness of C. albicans between mothers and their children using Multilocus Sequence Typing. Multivariate statistical methods were used to identify factors associated with C. albicans' acquisition (horizontal and vertical transmissions). Overall, 227 C. albicans oral isolates were obtained from 93 (58.1%) of mother-child pairs. eBURST analysis revealed 16 clonal complexes, and UPGMA analysis identified 6 clades, with clade 1 being the most populated 124 isolates (54.6%). Significantly, 94% of mothers and children with oral C. albicans had highly genetically related strains, highlighting a strong maternal influence on children's C. albicans acquisition. Although factors such as race, ethnicity, delivery method, and feeding behaviors did not show a significant association with C. albicans vertical transmission, the mother's oral hygiene status reflected by plaque index (PI) emerged as a significant factor; Mothers with higher dental plaque accumulation (PI >=2) had a significantly increased risk of vertically transmitting C. albicans to their infants [odds ratio (95% confidence interval) of 8.02 (1.21, 53.24), p=0.03]. Furthermore, Black infants and those who attended daycare had an elevated risk of acquiring C. albicans through horizontal transmission (p <0.01). These findings highlight the substantial role of maternal transmission in the oral acquisition of C. albicans during early life. Incorporating screening for maternal fungal oral carriage and implementing oral health education programs during the perinatal stage may prove valuable in preventing fungal transmission in early infancy.

Genetic Diversity and Its Relationship of Dendrobium (Orchidaceae) Based on Bioactive Compounds and Their Biological Activities: A Meta-Analysis

Information on genetic diversity and its relationship is fundamental for the preservation and improvement of orchid germplasm. For Dendrobium, such information, particularly by a meta-analysis, was limited. The study aimed to assess the genetic diversity and relationships of Dendrobium germplasm based on bioactive compounds, their biological activities, and plant organs by a meta-analysis approach. A total of 51 species of Dendrobium have been collected and identified as producing bioactive compounds, including their biological activities and plant organs (parts). In this case, the highest genetic diversity was shown by polyphenols (H' index = 0.90) as substances, neuroprotective (H' = 0.80) for activity, and the leaf organ with an H' index of 0.89. The UPGMA analysis showed that Dendrobium grouped into seven clusters, where the furthest relationship was presented by D. moschatum and D. catenatum. However, the closest relation was by D. scabrilingue with D. delacourii, including D. snowflake and D. ovatum. Following these parameters, Dendrobium shows unique genetic diversity and relationships. Thus, it is valuable for future preservation and improvement programs of Dendrobium.

Characters evolution of Encyclia (Laeliinae-Orchidaceae) reveals a complex pattern not phylogenetically determined: insights from macro- and micromorphology

Encyclia is the second-largest genus in the neotropical subtribe Laeliinae (Orchidaceae) and has more than 150 species, which are characterized by fairly consistent flower morphology. Its taxonomy and species boundaries, however, seem to be still under debate. In the present study, we first examined the lip micromorphology of 61 species of Encyclia sensu stricto. We correlated our results with external flower morphology and phylogenetic analyses performed on a combined dataset that included both nuclear (ITS, Xdh, PhyC) and plastid markers (ycf1, rpl32, and trnL-trnF). Phylogenetic reconstruction showed that Encyclia sensu stricto species form a coherent, monophyletic group. However, it is difficult to determine the relationships between the different groups within one larger clade. The groups all form distinct lineages that evolved from a common ancestor. The UPGMA cluster analysis for the seven qualitative micromorphological features clearly divides the genus into two main groups, the larger of which is further subdivided into two subgroups. None of these, however, overlap with any of the phylogeographic units distinguished in previously published papers or in presented article. It is worth noting that the groups resulting from the UPGMA analysis cannot be defined by macromorphological features. The pattern of similarities between species, taking into account both macro- and micromorphological features, is eminently mosaic in nature, and only a multifaceted approach can explain this enigmatic group.

Variability of the Moroccan sweet chestnut (Castanea sativa Mill.): Contribution of the morphological parameters and qualitative descriptors of the nut

The areas occupied by the common chestnut tree, Castanea sativa Mill. are continuously declining on an international scale. In Morocco, the chestnut trees are present in a restricted geographical area in the North and remains relatively unknown in the rest of the kingdom. This study represents the first contribution to the characterization and the evaluation of phenotypic similarities among Moroccan populations of Castanea sativa Mill. through univariate and multivariate statistical analysis of quantitative parameters and qualitative descriptors of fruits. The analysis was conducted on 13,455 fruits from 299 trees distributed across 31 populations from three regions. Ten qualitative descriptors were evaluated: nut shape (NSh), nut size (NSz), area of pubescence on upper part (AP), area of hilum (AH), shape of border line of hilum and pericarp (BSh), color of skin (CSk), glossiness (Gl), kernel color (CKr), coat adherence to kernel (CoA), and kernel inner-cavity (KC). In addition, the number of fruits/cupule (N/B), the number of fruits/kilo (N/K), and the average weight of fruits (W) were measured along with 11 quantitative parameters: nut length (NL), nut width (NW), nut thickness (NT), hilum length (HL), hilum width (HW), NL/NW, NT/NL, NT/NW, NW/HL, HW/NT, and HW/HL. The results of statistical analysis conducted on the 24 quantitative and qualitative parameters studied (ANOVA and SNK mean comparison test) demonstrated a very highly significant intra and inter-population variability for all the studied parameters. The correlation matrix analysis of the 12 quantitative parameters reveals a strong correlation between the fruit and hilum measurements, specifically NL, NW, NT, HW, and HL. Principal Component Analysis (PCA) and UPGMA analyses have shown the structuring of the 31 populations subdivided into two groups with subgroups, indicating significant diversity. The overall results highlighted a high genotypic variability of Moroccan populations of the chestnut trees and can be used to develop programs that aim to preserve the existing genetic variability of the chestnut tree and establish an in-situ collection of genetic resources in a geographically restricted area in the North of Morocco.

Investigation of genetic relatedness, antimicrobial resistance, biofilm formation, biofilm-related virulence genes and integron-related genes of Stenotrophomonas maltophilia isolates obtained from bovine milk samples with mastitis

Treatment of infections caused by opportunistic pathogenic Stenotrophomonas maltophilia is complicated by the bacterium's ability to produce biofilms and high antibiotic resistance. This study aimed to investigate the prevalence of genetic relatedness, antimicrobial resistance, biofilm formation, biofilm genes associated with virulence and integron genes among isolates of S. maltophilia recovered from bovine milk with subclinical mastitis. In this study, bacterial identification was performed using conventional methods. While using the smeT gene-based Polymerase Chain Reaction (PCR) to confirm the species-level identification of isolates; PCR was also used to detect virulence and integron genes, too. The quantitative Microplate Test (MP) method was used to determine the phenotypic biofilm production capacity of the isolates. The resistance patterns of the isolates against 9 antibiotics belonging to 9 antimicrobial families were examined using the disk diffusion method. Isolates resistant to at least three drug classes from various antimicrobial drug classes were defined as multi-drug resistant (MDR). The genetic linkage of S. maltophilia isolates was investigated by Enterobacterial Repetitive Intragenic Consensus (ERIC) PCR. The Chi-Square (χ2) test was used to compare the relationship between the biofilm-forming capacity of the isolates with the prevalence of biofilm-associated virulence genes and integron genes with MDR. In the study, a total of 312 milk samples with subclinical mastitis were taken from 27 farms. Ten isolates from five farms were phenotypically and genotypically identified as S. maltophilia. All isolates were resistant to cefepime and imipenem. While 70% of the isolates were MDR; 80% carried one of the integron genes. By the MP test, the phenotypically biofilm-forming capacity identified in isolates was detected at 80%. The prevalence of the studied virulence genes was rpfF 60%, rmlA 70%, spgM and smf1 80%. There was no significant relationship between the biofilm-forming capacity of the isolates with the prevalence of biofilm-associated virulence genes and MDR with integron genes. S. maltophilia isolates were detected simply and quickly, using PCR based on the smeT gene, from bovine milk samples for the first time in Turkey. In the UPGMA analysis performed in the PyElph 1.4 program, a total of 5 genotypes were found, 2 single and 3 multiple according to 18% similarity coefficient. ERIC-PCR can be useful in identifying S. maltophilia isolates with epidemic potential.

MORPHOLOGICAL VARIATION OF GLYPTOTHORAX PLATYPOGON VALENCIENNES, 1840 IN SERAYU RIVER BANJARNEGARA AND RINGIN RIVER SEMARANG CENTRAL JAVA

Glyptothorax platypogon is freshwater fish, it’s potential to be an ornamental fish. Its need to be protected from extinction because population in other areas is till abundance. G. platypogon has reported that it's in Serayu River and based on pre-research observations found in Ringin River, Semarang, Central Java. The differences in the geographic location of the two rivers have the potential for the emergence of morphological variations of G. platypogon. Research on the morphology study of the G. platypogon from the Serayu River in Banjarnegara and the Ringin River has been conducted. This study describe morphological variations and provide information about the phenetic relationship between them. Sampling was carried out at Serayu River and Ringin River by direct observation and collection methods in the Field then continued at the Structure Laboratory of Biology Department State Islamic University Walisongo for observed morphometric and meristic,including 43 characters. Data was analyzed with the Kruskall Wallis test, Mann Whitney U test, PCA (Principal Component Analysis) and UPGMA (Unweighted Pair Group Arithmetic Average Method). The result showed that there were high morphological variations in the Allopatric population in Serayu River and Ringin River and there were low morphological variations in the Sympatric population in Serayu river. There were two clad taxa branching groups from Serayu and Ringin population which show morphological variation. UPGMA analysis and Euclidean distance show the population of Serayu River and Ringin River have a close phenetic relationship.

SSR assisted identification of mango (Mangifera indica L.) hybrids and development of DNA barcodes

The importance of varietal identification has grown dramatically on a global scale, particularly in the context of plant variety protection. To address the same, 100 new hyper-variable mango simple sequence repeats (HMSSRs) markers were screened for polymorphism among 24 mango hybrids bred at ICAR- IARI, New Delhi. Out of which, 89 polymorphic HMSSRs were used for the generation of DNA barcodes of mango hybrids. A total of 1,861 alleles with an amplicon size of 130 to 450 bp have been detected. The average number of alleles was 2.60 per locus, and PIC ranged from 0.04 (HMSSR1382) to 0.72 (HMSSR1289) with an average of 0.39. UPGMA analysis grouped these mango hybrids into two major clusters broadly representing the parental influence in hybrids. Cluster II comprised of 14 hybrids and cluster I had 10 hybrids. Model-based structure analysis revealed two gene pools, and AMOVA indicated that higher molecular variation is due to individuals (82%). The generated allelic variations of these polymorphic markers were translated into DNA barcodes by separating the allele size for each polymorphic HMSSR locus. A total 11 unique and 35 rare alleles from amplified alleles have been observed. Validation of these hybrid-specific alleles was attempted on a set of four tree replicates of the same genotypes grown at different places, of which seven hybrid-specific alleles could be validated in the present study. Overall, the present set of HMSSRs convincingly revealed to be highly informative and useful for future molecular research in mango. Furthermore, identifying hybrid-specific alleles would be highly useful in identifying and protecting mango hybrids.

Identification of Strawberry Wilt Caused by Plectosphaerella cucumerina in China.

Strawberry (Fragaria × ananassa Duch.) is a widely cultivated economic crop in China. In April 2022, an unusual wilt disease was observed on strawberry plants (6 months' old) in Chenzui town, Wuqing district, Tianjin, China (117°1'E, 39°17'N). The incidence across the greenhouses (≈0.34 ha) was approximately 50 to 75%. The first wilt symptoms were observed on the outer leaves, then the whole seedlings wilted and died. The rhizome of the diseased seedlings changed color and became necrotic and rotted. Symptomatic roots were surface disinfected with 75% ethanol for 30 s, washed with sterile distilled water for three times, and then cut into 3 mm2 pieces (four pieces per seedling) and placed on petri dish with potato dextrose agar (PDA) containing 50 mg/L of streptomycin sulfate and incubated at 26℃ in the dark. After 6 days' incubation, hyphal tips of the growing colonies were transferred onto PDA. Eighty-four isolates belong to five fungal species were obtained from 20 diseased root samples based on their morphological characteristics. To confirm their pathogenicity, ten two-month-old healthy seedlings of strawberry (cv Red Face) planted in sterilized nutrient soil, were inoculated by pouring 50 mL of conidial suspension (107 conidia/mL) (Cai et al. 2021). Another ten seedlings poured with sterile distilled water were used as controls. Each treatment was repeated three times in a greenhouse at 25 to 28℃ and 75% relative humidity under a 12-h photoperiod. After 15 days，only seedlings inoculated with Plectosphaerella (an original percentage of 35.71%) exhibited similar symptoms to those of diseased seedlings originally observed in the field. Seedlings had no symptoms in the control and other fungi inoculation treatments. To fulfill the Koch's postulates, Plectosphaerella isolates were reisolated from each inoculated, symptomatic seedling with a percentage of 100%, but were not recovered from any of the control seedlings. The experiments were repeated twice with similar results. The results indicated that the genus Plectosphaerella was the pathogen causing strawberry wilt. Colonies of the genus Plectosphaerella isolates on PDA were white to cream, and then gradually became salmon pink, with few aerial hyphae and slimy surfaces. Colonies produced numerous hyphal coils with conidiophores. Conidia were 4.56 to 10.07 μm × 1.11 to 4.54 μm (avg. 7.10 × 2.56 μm, n=100), septate or aseptate, ellipsoidal, hyaline and smooth. Such morphological characteristics were identical to those of Plectosphaerella spp. (Palm et al. 1995). For species identification, the ITS region and D1/D2 domain of the 28S rRNA gene of representative isolates (CM2, CM3, CM4, CM5 and CM6) were amplified and sequenced with the primer pair ITS1/ITS4 and NL1/NL4, respectively (White et al. 1990; O'Donnell and Gray 1993). By BLASTn analysis, the obtained sequences of ITS amplicon (ON629742, ON629743, ON629744, ON629745, and ON629746) and D1/D2 domain amplicon (OQ519896, OQ519897, OQ519898, OQ519899, and OQ519900) showed 99.14% to 99.81% identity to sequences of P. cucumerina (MW320463.1 and HQ239025.1) in the NCBI database. A multilocus phylogenetic tree performed by the UPGMA analysis showed that the representative isolates were assigned to the group of P. cucumerina. To our knowledge, this is the first report of P. cucumerina causing strawberry wilt worldwide. This disease may induce serious economic losses in strawberry production, thus effective management strategies should be taken.

Traditional Management of Maize in the Sierra Sur, Oaxaca, Maintains Moderate Levels of Genetic Diversity and Low Population Differentiation Among Landraces

Oaxaca is one of the areas of early maize diversification, with 28 to 35 recognized agronomic races. Campesinos (farmers) cultivate at least ten different races in the Los Loxicha region. There is evidence of introgression between them; however, some traditional practices have promoted further differentiation evidenced by the presence of different landraces, clearly recognized by various morphological and phenological characteristics. Therefore, moderate levels of genetic diversity and low levels of population differentiation are expected. Seven communities belonging to two municipalities were selected in 2005. In total, 140 semistructured interviews were administered, inquiring about cultural practices, which included questions about maize seed, ear, and cob management and selection and maize cultivation. Based on interviews and permissions, 30 maize plants from each of 28 fields (milpas) with maize crop belonging to five landraces (Conejo, Hueso, Tablita, Tepecente, and Pinto) were sampled. From the 82 ISSR loci amplified, Hueso and Conejo exhibited the highest and lowest number of loci (70 and 56 loci, respectively); 72% of loci analyzed in the five populations were polymorphic. The Hueso landrace presented the highest percentage of polymorphism (73%) and Conejo the lowest (54%). The expected heterozygosity (HeT) for the five landraces was 0.225 ± 0.032, and the genetic diversity of Nei (HST) was 0.225 ± 0.034. The population differentiation values obtained with GST indicated that Tablita and Hueso were the least differentiated, while the most differentiated were Pinto and Tepecente. STRUCTURE analysis identified two genetically differentiated groups (k = 2), consistent with the length of their agricultural cycle (number of days until flowering). UPGMA analysis showed that milpas belonging to the same landrace and with a specific agricultural cycle length were grouped, regardless of their geographic distribution. These results indicate that traditional management of maize in the Los Loxicha region, particularly as it relates to the selection of ears and seeds and control of the agricultural cycle, maintains a balance between morphological differentiation, moderate levels of genetic diversity and gene flow, and low levels of population differentiation. This has contributed to the high richness and low evenness of agronomic races reported for the mountainous regions of the Sierra Madre del Sur and for Oaxaca.

Genetic Variation of Ceiba pentandra (L.) Gaertn. from Three Populations in West Sumatra, Indonesia Based on RAPD Markers

Ceiba pentandra (L.) Gaertn. is one of the cotton-producing plants. However, there is a population decline in some areas, resulting in a decrease in genetic variation. This study aims to determine intrapopulation and interpopulation genetic variation and genetic differentiation of C. pentandra in three populations in West Sumatra. The research was conducted with the descriptive method using molecular data and sample collection with the survey method. Analysis of genetic variation using RAPD (Random Amplified Polymorphic DNA) markers on 15 individual plants collected from three populations, namely Solok, Pesisir Selatan, and Padang Pariaman. The results showed that primers OPA-01, OPA-02, and OPB-10 could detect polymorphism. The value of intrapopulation genetic variation was highest in the South Coastal population (H = 0.1857) and lowest in the Solok population (H = 0.1228). Interpopulation genetic variation (DST = 0.0326) was lower than intrapopulation genetic variation (Hs = 0.1607), with a low genetic differentiation value (GST = 0.1686) and a high gene flow value (Nm = 2.4660). Cluster analysis showed that the Pesisir Selatan and Solok populations had the farthest genetic distances (0.0580). UPGMA analysis shows that accessions do not cluster specifically based on their population.

Molecular phylogeny of plant pathogenic fungi based on start codon targeted (SCoT) polymorphism.

A number of molecular marker systems have been developed to assess genetic diversity, carry out phylogenetic analysis, and diagnose and discriminate plant pathogenic fungi. The start codon targeted (SCoT) markers system is a novel approach used here to investigate intra and interspecific polymorphisms of phytopathogenic fungi. This study assessed genetic variability between and within 96 isolates of ten fungal species associated with a variety of plant species using 36 SCoT primers. The six primers generated 331 distinct and reproducible banding patterns, of which 322 were polymorphic (97.28%), resulting in 53.67 polymorphic bands per primer. All primers produced informative amplification profiles that distinguished all fungal species. With a resolving power of 10.65, SCoT primer 12 showed the highest polymorphism among species, followed by primer 33 and primer 29. Polymorphic loci (PPL), Nei's diversity index (h), and Shannon index (I) percentages were 6.25, 0.018, and 0.028, respectively. UPGMA analysis separated all isolates based on morphological classification and revealed significant genetic variation among fungal isolates at the intraspecific level. PCoA analysis strongly supported fungal species discrimination and genetic variation. The other parameters of evaluation proved that SCoT markers are at least as effective as other DNA markers. SCoT markers were effective in identifying plant pathogenic fungi and were a powerful tool for estimating genetic variation and population structure of different fungi species.

The SSR Genetic Diversity of Wild Red Fruit Lycium (Lycium barbarum) in Northwest China

Through a comprehensive regional systematic collection, we conducted a genetic diversity analysis of wild red-fruited Lycium resources across the entire northwest region of China. This study provides a valuable genetic basis for germplasm exploration and the selection of new Lycium varieties. Utilizing fluorescence capillary electrophoresis, we carefully screened 16 pairs of SSR primers exhibiting high polymorphism. Subsequently, we inferred the genetic diversity of Lycium germplasm through structure clustering, UPGMA analysis, and molecular AMOVA. The 113 Lycium barbarum samples collected from northwest China exhibited distinct subgroups, namely the Qinghai–Gansu–Ningxia subgroup and the Xinjiang subgroup. These subgroups were clearly distinguishable based on genetic clustering. The genetic diversity within the samples was remarkably rich, as indicated by a mean I value of 1.04, He value of 0.57, and PIC value of 0.73. Notably, the majority of genetic diversity (72.99%) was found within populations, signifying substantial intrapopulation variation. Furthermore, our findings revealed significant genetic differentiation among populations, with a substantial Fst value of 0.27 and gene flow Nm estimated at 0.68. This suggests that the genetic variation levels in northwest Lycium were notably high, primarily driven by pronounced genetic differentiation among populations. Nonetheless, it is important to note that genetic diversity predominantly persists within populations. The observed subpopulation structure of Qinghai–Gansu–Ningxia and Xinjiang regions in northwest China can be primarily attributed to geographical isolation. These geographical barriers have played a pivotal role in shaping the genetic differentiation and structure of Lycium populations in the region. Consequently, our study sheds light on the complex genetic landscape of Northwest Lycium and highlights the significance of considering both within-population diversity and population differentiation in conservation and breeding programs.

STUDI BIOGEOGRAFIS IKAN PUYAU (osteochilus SP) BERBASIS PROFIL PROTEIN DARI DANAU ROWO IJO, SITUS BUKIT BANGKAI

This Bukit Bangkai would like be became a candidate for place evolution rock art heritage unit (PERAHU). In this site, the Rowo Ijo lake as a habitat, where it was found biogeographically, a Puyau fish (Osteochilus sp). Furthermore, the method of precipitation fraction of ammonium sulfate ((NH4)2SO4) with Lowry and SDS-PAGE elaboration was used, as the main method to obtain the protein profile of fish protein. Analysis of kinship relations was carried out using the UPGMA method based on the profile.. Based on the results of the fraction (NH4)2SO4 and Lowry methods, the optimum protein content was obtained, namely 68.93; 116.08; 6.72; 7.96 (mg/ml) in the 70-80% fraction and 4 samples from Banjar Regency 19.17; 16.93; 20.04; and 20.04 mg/mL in the 40-70% fraction, respectively. Based on the results of SDS-PAGE at the optimum level of protein; Puyau Rowo Ijo fish have 64 bands, with a profile of 11 bands on P.1R code, 9 bands on P.2R code, 10 bands on P.3R code and 9 bands on P.4R. For Puyau Banjar fish there are 25 bands with the following profile; each code P.1B and P.2B has 6 bands, while P.3B has 10 bands and P.4B has 3 bands. The types of proteins found were thought to include Actin Protein, Carbonic Anhydrase, Trypsin Inhibitor, -lactalbumin, and Lysozyme. The results of the UPGMA analysis based on the distribution of protein species and weights were that there was related closely to two groups form (clusters) between puyau from the Lake Rowo Ijo and Banjar Regency.