Genetic Diversity Information Research Articles

Genetic Diversity of Local Chili (Capsicum annum L.) from West Sumatra Indonesia Based on Inter Simple Sequences Repeat (ISSR) Markers

Capsicum annum L. is the most widely cultivated species due to its economic importance and health benefits. West Sumatra is one of the largest chili pepper producers in Indonesia, so it has a lot of local chili genetic resources. There is inadequate information on the genetic diversity of local chilies in West Sumatra. The purpose of this research was to analyze the genetic diversity of 23 genotypes of chili pepper from West Sumatra amplified with 10 markers of ISSR. The material used was leaves from 23 genotypes of West Sumatra’s local chili which are collections of the Agriculture Faculty, Andalas University, Padang, West Sumatra. The results showed that ISSR markers (ISSR primer 12, ISSR UBC, and ISSR 3M) had produced 84 polymorphic DNA bands with a total polymorphic percentage of 61.45%. The dendrogram based on 10 ISSR markers showed that the 23 chili genotypes were retrieved into three main groups (I, II, III, IV) with genetic similarity coefficient values ranging from 0.67 to 0.97 or a diversity of features of 0.03–0.33 (30%). Group I consisted of 1 genotype, group II consisted of 3 genotypes, and group III consisted of 14 genotypes. Kopay chili (G20) has a large genetic distance compared to the other genotypes, while Lolai and Gero chilies have a very high similarity. This genetic diversity information can be used as a basis for generating crosses between genotypes in a breeding program. The farther the genetic distance will produce a high population diversity, the greater the chance of getting superior hybrids. Keywords: Capsicum annum, ISSR, local chili, West Sumatra

Study of Genetic Diversity of Aromatic Rice Genotypes Using Random Amplified Polymorphic DNA Markers

The study of genetic variation in aromatic rice is necessary for enhancing and preserving its genetic makeup. In this study, we amplified four Random Amplified Polymorphic DNA (RAPD) markers from the genomes of 11 different aromatic rice genotypes in order to evaluate the genetic variation and relatedness in aromatic rice. The genotypes were collected from different sources- five of which were obtained from the Bangladesh Rice Research Institute, one from the Bangladesh Institute of Nuclear Agriculture, and the remaining five were local genotypes. In RAPD profiling, twenty-seven of the thirty-six bands that were generated by the four primers were polymorphic, resulting in an estimated average polymorphism of 47.22 percent. The average value of the polymorphic information content was 0.309 with a range from 0.165 to 0.456, indicating that the primers were effective to detect genetic diversity between the genotypes. The genetic diversity and Shannon information index across all of the genotypes and primers were 0.176 and 0.260, respectively, which indicated that there was a certain amount of genetic variation in the studied aromatic rice genotypes. Kalizira and Binadhan-9 genotypes had the smallest genetic distance (0.057), while it was the highest (0.406) between the BRRI dhan 34 and BRRI dhan 50. The genotype pairs BRRI dhan 38 vs BRRI dhan 34, BRRI dhan 38 and Kalizira, and Zirakatari and Kalizira had also a higher level (0.365) of genetic distances. The genotypes were grouped into two main clusters in the UPGMA dendrogram. Cluster I included five genotypes: BRRI dhan 34, Basmoti, Atashail, Kalizira, and Binadhan-9. Cluster II included remaining six genotypes: BR5, BRRI dhan 38, BRRI dhan 50, Uknimodhu, BRRI dhan 37, and Zirakatari. Documentation of the genetic variation and relatedness among the aromatic rice genotypes under this investigation could be useful for future research into the development of aromatic rice and related fields. J Bangladesh Agril Univ 22(3): 277-284, 2024

FUT11 expression in gastric cancer: its prognostic significance and role in immune regulation

BackgroundGastric cancer (GC) is a malignant digestive tract tumor with a high recurrence rate and poor prognosis. Fucosylation is important in tumor glycosylation, in which the key enzyme is fucosyltransferase (FUT). FUT11 is a member of the fucosyltransferase family and has been closely associated with the development of multiple cancers. However, the specific relationship between FUT11 and GC prognosis and its molecular mechanism has not been fully studied. This study explored FUT11 expression, clinical correlation, and its role in GC occurrence and development to deepen understanding of its function.MethodsFUT11 expression in 33 cancers was preliminarily analyzed using the Tumor Immunoassay Resource (TIMER2.0) database. FUT11 expression in GC was evaluated using The Cancer Genome Atlas stomach adenocarcinoma (TCGA-STAD) and Gene Expression Profiling Interactive Analysis (GEPIA2) data and verified using the Gene Expression Omnibus (GEO) GSE65801 dataset. Furthermore, we studied the survival prognosis of FUT11 in GC and analyzed its effect on the survival rate of patients with GC using the KM-plotter. We also performed COX regression analysis on TCGA GC clinical data and analyzed FUT11 expression in the pathway using the STRING and LinkedOmics databases. Moreover, the relationship between FUT11 and GC immune infiltration level was examined, and the Kaplan–Meier survival analysis diagram was constructed. The FUT11 genetic variation information was retrieved using cBioPortal, and its drug sensitivity was analyzed using CellMiner. Finally, differential FUT11 expression in GC tissues was verified using immunohistochemistry.ResultsThe data mining and analysis demonstrated that FUT11 expression was abnormally elevated in GC tissues and correlated with poor patient prognosis. The FUT11 expression level was an independent prognostic factor for GC. The difference in FUT11 expression level resulted in different degrees of immune cell infiltration in the patients with GC, which might regulate the tumor microenvironment. FUT11 affected GC development by participating in cancer pathways such as PI3K–AKT, neuroactive ligand–receptor, and MAPK. Immunohistochemical staining revealed that FUT11 was highly expressed in GC.ConclusionsThis study revealed that FUT11 expression is significantly increased in GC tissues. This increase is associated with poor prognosis and might affect immune regulation. FUT11 might have immunological and targeted therapeutic value, providing a new approach to GC treatment.

PRIMITI: A computational approach for accurate prediction of miRNA-target mRNA interaction

Current medical research has been demonstrating the roles of miRNAs in a variety of cellular mechanisms, lending credence to the association between miRNA dysregulation and multiple diseases. Understanding the mechanisms of miRNA is critical for developing effective diagnostic and therapeutic strategies. miRNA-mRNA interactions emerge as the most important mechanism to be understood despite their experimental validation constraints. Accordingly, several computational models have been developed to predict miRNA-mRNA interactions, albeit presenting limited predictive capabilities, poor characterisation of miRNA-mRNA interactions, and low usability. To address these drawbacks, we developed PRIMITI, a PRedictive model for the Identification of novel miRNA-Target mRNA Interactions. PRIMITI is a novel machine learning model that utilises CLIP-seq and expression data to characterise functional target sites in 3’-untranslated regions (3’-UTRs) and predict miRNA-target mRNA repression activity. The model was trained using a reliable negative sample selection approach and the robust extreme gradient boosting (XGBoost) model, which was coupled with newly introduced features, including sequence and genetic variation information. PRIMITI achieved an area under the receiver operating characteristic (ROC) curve (AUC) up to 0.96 for a prediction of functional miRNA-target site binding and 0.96 for a prediction of miRNA-target mRNA repression activity on cross-validation and an independent blind test. Additionally, the model outperformed state-of-the-art methods in recovering miRNA-target repressions in an unseen microarray dataset and in a collection of validated miRNA-mRNA interactions, highlighting its utility for preliminary screening. PRIMITI is available on a reliable, scalable, and user-friendly web server at https://biosig.lab.uq.edu.au/primiti.

Uncovering the genetic diversity in Aedes aegypti insecticide resistance genes through global comparative genomics

Aedes aegypti is vector of many arboviruses including Zika, dengue, yellow fever, West Nile, and Chikungunya. Its control efforts are hampered by widespread insecticide resistance reported in the Americas and Asia, while data from Africa is more limited. Here we use publicly available 729 Ae. aegypti whole-genome sequencing samples from 15 countries, including nine in Africa, to investigate the genetic diversity in four insecticide resistance linked genes: ace-1, GSTe2, rdl and vgsc. Apart from vgsc, the other genes have been less investigated in Ae. aegypti, and almost no genetic diversity information is available. Among the four genes, we identified 1,829 genetic variants including 474 non-synonymous substitutions, some of which have been previously documented, as well as putative copy number variations in GSTe2 and vgsc. Global insecticide resistance phenotypic data demonstrated variable resistance in geographic areas with resistant genotypes. Overall, our work provides the first global catalogue and geographic distribution of known and new amino-acid mutations and duplications that can be used to guide the identification of resistance drivers in Ae. aegypti and thereby support monitoring efforts and strategies for vector control.

Determination of the New SNP g.939A>G of the TYR Gene in Abnormal Coat Color in Bali Cattle

This study aimed to assess the presence of single nucleotide polymorphisms (SNPs) in the exon 1 region of the tyrosinase (TYR) gene in Bali cattle with abnormal coat color. This study analyzed 43 Bali cattle, 26 individuals with typical or standard coat color, and 17 individuals with albinism. The genetic diversity of the TYR gene was determined via direct sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) techniques. The sequence data of the TYR gene were scrutinized using BioEdit and MEGA10 software to detect single nucleotide polymorphisms (SNPs) related to different types of coat color features in Bali cattle. The genetic diversity information was derived from computations performed using PopGen 1.32 software. The results showed that exon 1 of the TYR gene was affected by the new SNP g.939A>G, which is polymorphic in Bali cattle. In conclusion, the SNP c.939A>G can be further analyzed for use as a candidate-assisted selection (MAS) for abnormal coat color in Bali cattle.

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

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

Comparison of Genetic Diversity and Core Locus Information of Abies yuanbaoshanensis Natural Population and Progeny

Comparison of Genetic Diversity and Core Locus Information of Abies yuanbaoshanensis Natural Population and Progeny

Integrative Taxonomy Clarifies the Historical Flaws in the Systematics and Distributions of Two Osteobrama Fishes (Cypriniformes: Cyprinidae) in India

The taxonomy and geographical distributions of Osteobrama species have historically posed challenges to ichthyologists, leading to uncertainties regarding their native ranges. While traditional taxonomy has proven valuable in classification, the utility of an integrated approach is restricted for this particular group due to limitations in combining information from biogeography, morphology, and genetic data. This study addresses the taxonomic puzzle arising from the recent identification of Osteobrama tikarpadaensis in the Mahanadi and Godavari Rivers, casting doubt on the actual distribution and systematics of both O. tikarpadaensis and Osteobrama vigorsii. The research reveals distinctions among specimens resembling O. vigorsii from the Krishna and Godavari riverine systems. Notably, specimens identified as O. vigorsii from the Indian Museum exhibit two pairs of barbels, while those from the Godavari River in this study are identified as O. tikarpadaensis. Inter-species genetic divergence and maximum likelihood phylogeny provide clear delineation between O. vigorsii and O. tikarpadaensis. The study suggests that O. vigorsii may be limited to the Krishna River system in southern India, while O. tikarpadaensis could potentially extend from the Mahanadi River in central India to the Godavari River in southern India. Proposed revision to morphological features for both species, accompanied by revised taxonomic keys, aim to facilitate accurate differentiation among Osteobrama congeners. The data generated by this research provide a resource for future systematic investigations into cyprinids in India and surrounding regions. Further, the genetic diversity information obtained from various riverine systems for Osteobrama species will be instrumental in guiding aquaculture practices and formulating effective conservation action plans.

Genetic Diversity of Bamboo (Yushinia alpina) Borer Larvae in the Mau Forest Complex, Kenya

Bamboo borer larvae have caused major losses of bamboo cover in natural forests and plantations. Lack of information on the fauna of bamboo trees has been cited as the contributing factor to poor management of bamboo stands. Genetic diversity information helps understand the effects of different fauna in guiding management plans. Genetic diversity information has recently become an important tool in conservation science. This paper aimed to determine the genetic diversity of the bamboo borer larvae in the Mau Forest complex in order to generate information that could guide the management and conservation of bamboo trees (Yushinia Alpina) in the Mau Forest Complex. The mitochondrial C oxidase Subunit 1 (COI) of 12 isolates was sequenced and analyzed. A similarity search of the bamboo borer larvae was carried out using the National Center for Biotechnology Information (NCBI) BLAST search to identify the larvae species. The genetic diversity and genetic pairwise distances were determined, and Tajimas D and Nei’s FU Fs statistics were calculated to estimate the population expansion that has occurred. The results showed genetic diversity (haplotype diversity 0.956) in the bamboo borer larvae population of the Mau Forest Complex. The nucleotide diversity (0.283) was found to be low. The similarity search showed that the bamboo borer larvae of Yushinia alpina belonged to four (4) species of noctuid larvae (Lepidoptera). The identity matches to the similar species scored an average of 94%. The Tajimas D (0.374) and FUs Fs (5.547) collectively indicated no rare excess mutations in the population. The results reveal high genetic diversity, which is key in the management of forest species

Systematic exploration of Ziziphus species collection and gene identification influencing physiological traits using genotype-by-sequencing technology.

The Ziziphus genus, belonging to the Rhamnaceae family, holds significant economic, nutritional, and medicinal value. However, much remains to be discovered about its diversity and physical characteristics. Factors such as growth, resilience to changes, disease resistance, and unique features contribute to the quality of Ziziphus species. This study aims to investigate the genomes of 200 genotypes from five Ziziphus species: Ziziphus jujuba (Zj), Ziziphus nummularia (Zm), Ziziphus oxyphylla (Zx), Ziziphus mauritiana (Zm), and the cultivated variety Ziziphus jujube var. jujube, collected from Pakistan and China. Our goal is to identify single nucleotide polymorphisms (SNPs) associated with eight different traits and understand the genetic diversity within the selected Ziziphus species and their genotypes. Using high-quality SNPs obtained through genotype-by-sequencing (GBS), we conducted population structure, phylogenetic, and principal coordinates analyses, identifying a total of 10,945 clean SNPs. These genotypes were categorized into two groups, A and B. Natural Ziziphus variants in Pakistan, specifically Z. jujuba and Z. nummularia, exhibited high levels of genetic diversity and polymorphic information content (PIC) of 0.46 and 0.41, respectively, compared to other species. Furthermore, we identified 15 influential candidate genes that play crucial roles in regulating agronomic traits, such as fruit width and diameter, leaf width, plant height, and stem diameter within this group. This study provides valuable insights that can be utilized in Ziziphus breeding efforts.

Characterization of the complete chloroplast genome of Gastrochilus sinensis (Orchidaceae, Epidendroideae), a beautiful epiphytic orchid from China

Gastrochilus sinensis is a beautiful epiphytic orchid with high ornamental value. In this study, the first complete chloroplast genome sequence of G. sinensis was determined using next-generation sequencing (NGS). The de novo assembled chloroplast genome was 148,020 bp in length, including a pair of inverted repeat regions (IRs; 25,987 bp), a small single-copy region (SSC; 11,045 bp), and a large single-copy region (LSC; 85,001 bp). The chloroplast genome encodes 109 unique genes, including 75 protein-coding genes (PCGs), 30 tRNA genes, and four rRNA genes. The total GC content of the chloroplast genome was 36.8%. The phylogenetic analysis showed a close relationship between G. sinensis and G. formosanus species. The complete chloroplast genome provides fundamental information for genetic diversity and phylogenetic relationships in Gastrochilus.

Genetic diversity, population structure and kinship relationships highlight the environmental influence on Uganda's indigenous goat populations.

Knowledge about genetic diversity and population structure among goat populations is essential for understanding environmental adaptation and fostering efficient utilization, development, and conservation of goat breeds. Uganda's indigenous goats exist in three phenotypic groups: Mubende, Kigezi, and Small East African. However, a limited understanding of their genetic attributes and population structure hinders the development and sustainable utilization of the goats. Using the Goat Illumina 60k chip International Goat Genome Consortium V2, the whole-genome data for 1,021 indigenous goats sourced from 10 agroecological zones in Uganda were analyzed for genetic diversity and population structure. A total of 49,337 (82.6%) single-nucleotide polymorphism markers were aligned to the ARS-1 goat genome and used to assess the genetic diversity, population structure, and kinship relationships of Uganda's indigenous goats. Moderate genetic diversity was observed. The observed and expected heterozygosities were 0.378 and 0.383, the average genetic distance was 0.390, and the average minor allele frequency was 0.30. The average inbreeding coefficient (Fis) was 0.014, and the average fixation index (Fst) was 0.016. Principal component analysis, admixture analysis, and discriminant analysis of principal components grouped the 1,021 goat genotypes into three genetically distinct populations that did not conform to the known phenotypic populations but varied across environmental conditions. Population 1, comprising Mubende (90%) and Kigezi (8.1%) goats, is located in southwest and central Uganda, a warm and humid environment. Population 2, which is 59% Mubende and 49% Small East African goats, is located along the Nile Delta in northwestern Uganda and around the Albertine region, a hot and humid savannah grassland. Population 3, comprising 78.4% Small East African and 21.1% Mubende goats, is found in northeastern to eastern Uganda, a hot and dry Commiphora woodlands. Genetic diversity and population structure information from this study will be a basis for future development, conservation, and sustainable utilization of Uganda's goat genetic resources.

Whole-genome resequencing reveals genetic diversity, differentiation, and selection signatures of yak breeds/populations in southwestern China.

The Sichuan-Yunnan region is the main production area of yaks in southwestern China, with rich genetic resources of Yaks. Nevertheless, there have been limited study on the genetic characteristics of the entire yak populations in Tibet and southwestern China. In this study, we performed whole-genome resequencing to identify genetic variation information in a total of 198 individuals from six yak breeds (populations) in Sichuan (Muli yak, Jinchuan yak, Changtai yak, Maiwa yak), Yunnan (Zhongdian yak), and Tibet (Tibetan yak). The aim was to investigate the whole-genome genetic diversity, population genetic structure, and genome selection signatures. We observed that all six populations exhibit abundant genetic diversity. Except for Tibetan yaks, which showed low nucleotide diversity (0.00104), the remaining yak populations generally displayed high nucleotide diversity (0.00129-0.00153). Population genetic structure analysis revealed that, among the six yak populations, Muli yak exhibited greater differentiation from other yak populations and formed a distinct cluster independently. The Maiwa yak population displayed a complex genetic structure and exhibited gene exchange with Jinchuan and Changtai yaks. Positive selection signals were detected in candidate genes associated with growth (GNB4, HMGA2, TRPS1, and LTBP1), reproduction (PI4KB, DYNC1I1, and GRIP1), immunity (CD200 and IL1RAP), lactation (SNX13 and CPM), hypoxia adaptation (NDUFB6, PRKN, and MRPS9), hair (KRT24, KRT25, and KRT26), meat quality (SUCLG2), digestion and absorption (CLDN1), and pigment deposition (OCA2) using the integrated Pi and F ST methods. This study provides significant insights into understanding the whole-genome genetic characteristics of yak populations in Tibet and southwestern China.

POLYMORPHISM Inter Simple Sequence Repeats (ISSR) PRIMERS FOR GENETIC DIVERSITY FOR POOTI PLANTS (Hopea gregaria)

Pooti (Hopea gregaria) is a medium size tree that can grow up to 35 m from the Dipterocarpaceae family. Since 1998, the International Union for Conservation of Nature (IUCN) has reported the pooti tree as endangered, and the species has a narrow distribution, found only in Southeast Sulawesi. One of the efforts to overcome the rarity of the Pooti plant is through a tree breeding program. However, this tree breeding program will only be successful with the support of genetic diversity information. The study of genetic diversity can be done using a molecular-based approach using Inter Simple Sequence Repeats (ISSR) markers. Samples of Pooti leaves used in the study were taken from Botanical Forest Park Nipa-Nipa (Tahura) and Protected Forest Nanga-Nanga, Kendari City, Southeast Sulawesi Province. A total of 50 samples were extracted using the CTAB (Cetyl Trimethyl Ammonium Bromide) method. Ten types of primers that have been carried out obtained seven primers that can produce bright polymorphic bands and can be continued for study genetic diversity, namely UBC 810, UBC 813, UBC 814, UBC 822, UBC 823, UBC 827, and UBC 830.

Genetic Diversity of Bamboo (Yushinia alpina) Borer Larvae in the Mau Forest Complex, Kenya

Bamboo borer larvae have caused major losses of bamboo cover in natural forests and plantations. Lack of information on the fauna of bamboo trees has been cited as the contributing factor to poor management of bamboo stands. Genetic diversity information helps understand the effects of different fauna in guiding management plans. Genetic diversity information has recently become an important tool in conservation science. This paper aimed to determine the genetic diversity of the bamboo borer larvae in the Mau Forest complex in order to generate information that could guide the management and conservation of bamboo trees (Yushinia Alpina) in the Mau Forest Complex. The mitochondrial C oxidase Subunit 1 (COI) of 12 isolates was sequenced and analyzed. A similarity search of the bamboo borer larvae was carried out using the National Center for Biotechnology Information (NCBI) BLAST search to identify the larvae species. The genetic diversity and genetic pairwise distances were determined, and Tajimas D and Nei’s FU Fs statistics were calculated to estimate the population expansion that has occurred. The results showed genetic diversity (haplotype diversity 0.956) in the bamboo borer larvae population of the Mau Forest Complex. The nucleotide diversity (0.283) was found to be low. The similarity search showed that the bamboo borer larvae of Yushinia alpina belonged to four (4) species of noctuid larvae (Lepidoptera). The identity matches to the similar species scored an average of 94%. The Tajimas D (0.374) and FUs Fs (5.547) collectively indicated no rare excess mutations in the population. The results reveal high genetic diversity, which is key in the management of forest species

Evaluating potential of leaf reflectance spectra to monitor plant genetic variation

Remote sensing of vegetation by spectroscopy is increasingly used to characterize trait distributions in plant communities. How leaves interact with electromagnetic radiation is determined by their structure and contents of pigments, water, and abundant dry matter constituents like lignins, phenolics, and proteins. High-resolution (“hyperspectral”) spectroscopy can characterize trait variation at finer scales, and may help to reveal underlying genetic variation—information important for assessing the potential of populations to adapt to global change. Here, we use a set of 360 inbred genotypes of the wild coyote tobacco Nicotiana attenuata: wild accessions, recombinant inbred lines (RILs), and transgenic lines (TLs) with targeted changes to gene expression, to dissect genetic versus non-genetic influences on variation in leaf spectra across three experiments. We calculated leaf reflectance from hand-held field spectroradiometer measurements covering visible to short-wave infrared wavelengths of electromagnetic radiation (400–2500 nm) using a standard radiation source and backgrounds, resulting in a small and quantifiable measurement uncertainty. Plants were grown in more controlled (glasshouse) or more natural (field) environments, and leaves were measured both on- and off-plant with the measurement set-up thus also in more to less controlled environmental conditions. Entire spectra varied across genotypes and environments. We found that the greatest variance in leaf reflectance was explained by between-experiment and non-genetic between-sample differences, with subtler and more specific variation distinguishing groups of genotypes. The visible spectral region was most variable, distinguishing experimental settings as well as groups of genotypes within experiments, whereas parts of the short-wave infrared may vary more specifically with genotype. Overall, more genetically variable plant populations also showed more varied leaf spectra. We highlight key considerations for the application of field spectroscopy to assess genetic variation in plant populations.

High-density DArTSeq SNP markers revealed wide genetic diversity and structured population in common bean (Phaseolus vulgaris L.) germplasm in Ethiopia

IntroductionCommon bean is one of the widely consumed food security crop in Africa, Asia, and South America. Understanding genetic diversity and population structure is crucial for designing breeding strategies.MaterialsTwo hundred and eighty-nine germplasm were recently collected from different regions of Ethiopia and introduced from CIAT to estimate genetic diversity and population structure using 11,480 DArTSeq SNP markers.ResultsThe overall mean genetic diversity and polymorphic information content (PIC) were 0.38 and 0.30, respectively, suggested the presence of adequate genetic diversity among the genotypes. Among the geographical regions, landraces collected from Oromia showed the highest diversity (0.39) and PIC (0.30). The highest genetic distance was observed between genotypes collected from SNNPR and CIAT (0.49). In addition, genotypes from CIAT were genetically more related to improved varieties than the landraces which could be due to sharing of parents in the improvement process. The analysis of molecular variance revealed that the largest proportion of variation was due to within the population both in geographical region (63.67%) and breeding status (61.3%) based classification. Model-based structure analysis delineated the 289 common bean genotypes into six hypothetical ancestoral populations.ConclusionsThe genotypes were not clustered based on geographical regions and they were not the main drivers for the differentiation. This indicated that selection of the parental lines should be based on systematic assessment of the diversity rather than geographical distance. This article provides new insights into the genetic diversity and population structure of common bean for association studies, designing effective collection and conservation for efficient utilization for the improvement of the crop.

Genetic polymorphism and variability in the Guangdong Hakka, Teochew, and Cantonese groups: A comprehensive analysis of 19 X-STRs.

X chromosomeshort tandem repeat (X-STR) loci are playing an increasingly important role inforensic work, identifying female traces in male contamination and explainingcomplex kinship analyses. In this study, we analyzed thegenetic polymorphism of 19 X-STR loci in the Guangdong Hakka, Teochew and Cantonese groups, respectively, aswell as in the Guangdong Hakka, Teochew andCantonese pooled Han. The genetic diversity and forensic characteristics of the19 X-STRs and 7 linkage groups were investigated, respectively. The experiments showed that the genetic diversity (GD) and polymorphism information content (PIC) in the pooledGuangdong Han ranged from 0.5320 to 0.9234 and 0.4369 to 0.9171, respectively, and the cumulative power of discrimination for males (PDM), power of discrimination for females (PDF) and mean paternity exclusion chance (MEC) were higher than 0.9999999, indicating that the 19 X-STRs had high geneticpolymorphism and discriminatory power. Genetic differences among Chinese Hansubgroups and among different Chinese populations were investigated byphylogenetic reconstruction and principal component analysis (PCA), respectively. Genetic analyses based on neighbor-joining (NJ) tree and principal component analysis plot showed that Cantonese, Teochew and Hakka were closely genetically related, and different populations with closer linguistic components had more genetic affinity. This study adds to the forensic X-STR database and demonstrates the forensic efficiency of 19 X-STRs for the Hakka, Teochewand Cantonese populations in Guangdong, and the pooled Han of Hakka, Teochewand Cantonese people in Guangdong.

High‐throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture

High‐throughput genotyping in estimating genetic resources and detecting pathogens in aquaculture