Genetic Diversity Studies Research Articles

A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila)

Aythya marila is one of the few species of Anatidae, and the only Aythya to live in the circumpolar. However, there is a relative lack of research on genetics of this species. In this study, we reported and assembled the first high-quality chromosome-level genome assembly of A. marila. This genome was assembled using Nanopore long reads, and errors corrected using Illumina short reads, with a final genome size of 1.14 Gb, scaffold N50 of 85.44 Mb, and contig N50 of 32.46 Mb. 106 contigs were clustered and ordered onto 35 chromosomes based on Hi-C data, covering approximately 98.28% of the genome. BUSCO assessment showed that 97.0% of the highly conserved genes in aves_odb10 were present intact in the genome assembly. In addition, a total of 154.94 Mb of repetitive sequences were identified. 15,953 protein-coding genes were predicted in the genome, and 98.96% of genes were functionally annotated. This genome will be a valuable resource for future genetic diversity and genomics studies of A. marila.

황해쑥 품종 구별을 위한 유전체 염기서열 기반 genomic SSR marker 개발

Background: Artemisia argyi is an economically important medicinal plant with in the genus of Artemisia. However, the lack of the molecular markers hinders the understanding of genetic diversity and cultivar discrimination. Therefore, the main objectives of this study were to characterize the SSRs of Artemisia argyi in the reference genome, and to developed polymorphic SSRs for cultivar discrimination and population genetic studies.BRMethods and Results: Novel 100 simple sequence repeat (SSR) markers were designed based on the whole-genome sequence data of Artemisia argyi, and selected 78 polymorphic markers were selected. Upon the assessment of the five accessions with the full set of 78 SSR, the major allele frequency (MAF) ranged from 0.20 to 1, with an average of 0.36. In addition, the number of alleles per locus ranged from 2 to 9 alleles with a mean value of 5.2 alleles per locus. The polymorphism information content (PIC) values ranged from 0.27 to 0.87 with a mean PIC value of 0.69.BRConclusions: The Artemisia argyi alleles were detected in 5 accessions, among them six primers (argyi-gSSR003, argyi-gSSR014, argyi-gSSR035, argyi-gSSR036, argyi-gSSR093, argyigSSR094) produced five cultivar-specific loci, therefore very promising for cultivar identification, genetic diversity and breeding studies in Artemisia argyi.

Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing

BackgroundMoth bean (Vigna aconitifolia) is an underutilized, protein-rich legume that is grown in arid and semi-arid areas of south Asia and is highly resistant to abiotic stresses such as heat and drought. Despite its economic importance, the crop remains unexplored at the genomic level for genetic diversity and trait mapping studies. To date, there is no report of SNP marker discovery and association mapping of any trait in this crop. Therefore, this study aimed to dissect the genetic diversity, population structure and marker-trait association for the flowering trait in a diversity panel of 428 moth bean accessions using genotyping by sequencing (GBS) approach.ResultsA total of 9078 high-quality single nucleotide polymorphisms (SNPs) were discovered by genotyping of 428 moth bean accessions. Model-based structure analysis and PCA grouped the moth bean accessions into two subpopulations. Cluster analysis revealed accessions belonging to the Northwestern region of India had higher variability than accessions from the other regions suggesting that this region represents its center of diversity. AMOVA revealed more variations within individuals (74%) and among the individuals (24%) than among the populations (2%). Marker-trait association analysis using seven multi-locus models including mrMLM, FASTmrEMMA FASTmrEMMA, ISIS EM-BLASSO, MLMM, BLINK and FarmCPU revealed 29 potential genomic regions for the trait days to 50% flowering, which were consistently detected in three or more models. Analysis of the allelic effect of the major genomic regions explaining phenotypic variance of more than 10% and those detected in at least 2 environments showed 4 genomic regions with significant phenotypic effect on this trait. Further, we also analyzed genetic relationships among the Vigna species using SNP markers. The genomic localization of moth bean SNPs on genomes of closely related Vigna species demonstrated that maximum numbers of SNPs were getting localized on Vigna mungo. This suggested that the moth bean is most closely related to V. mungo.ConclusionOur study shows that the north-western regions of India represent the center of diversity of the moth bean. Further, the study revealed flowering-related genomic regions/candidate genes which can be potentially exploited in breeding programs to develop early-maturity moth bean varieties.

Molecular Prevalence and Genetic Diversity Based on Msp1a Gene of Anaplasma ovis in Goats from Türkiye.

Anaplasma ovis is a tick-borne obligated intraerythrocytic bacterium that infects domestic sheep, goats, and wild ruminants. Recently, several studies have been carried out using 16S rRNA and msp4 genes to identify the genetic diversity of A. ovis. Instead of these genes, which are known to be highly stable among heterologous strains, Msp1a, which is accepted as a stable molecular marker to classify A. marginale strains, was used in A. ovis genetic diversity studies. The genetic diversity of A. ovis strains according to the Msp1a gene has not been extensively reported. Therefore, the purpose of this study was to examine the genetic diversity of A. ovis in goats specifically using analysis of the Msp1a gene. Blood samples were taken from the vena jugularis to the EDTA tubes from 293 randomly selected goats (apparently healthy) in the Antalya and Mersin provinces of Mediterranean region of Türkiye. The Msp1a gene of A. ovis was amplified in all DNA samples through the use of PCR, using a specific set of primers named AoMsp1aF and AoMsp1aR. Among the amplified products, well-defined bands with different band sizes were subjected to sequence analysis. The obtained sequence data were converted into amino acid sequences using an online bioinformatics program and the tandem regions were examined. The Msp1a gene of A. ovis was amplified in 46.1% (135 out of 293) of the goats. Through tandem analysis, five distinct tandems (Ao8, Ao18, Tr15-16-17) were identified, and it was found that three of these tandems (Tr15-16-17) were previously unknown and were therefore defined as new tandems. The study also involved examination of ticks from goats. It was observed that the goats in the area were infested with several tick species, including Rhipicephalus bursa (888/1091, 81.4%), R. turanicus (96/1091, 8.8%), Dermacentor raskemensis (92/1091, 8.4%), Hyalomma marginatum (9/1091, 0.8%), and R. sanguineus s.l. (6/1091, 0.5%). This study provides important data for understanding the genetic diversity and evolution of A. ovis based on tandem repeats in the Msp1a protein.

Genetic Diversity and Population Structure Assessed Using Microsatellite (SSR) Markers from Relict Populations of Nuphar pumila (Nymphaeaceae).

The genus Nuphar (Nymphaeaceae) comprises aquatic plant species inhabiting freshwater bodies of the Northern hemisphere temperate regions known as yellow water-lilies. Nuphar lutea and N. pumila are the only representatives in the European continent and present different ecologies: the former is a widespread generalist, while the latter is restricted to northern latitudes or high-altitudes due to its requirements for colder and oligotrophic waters. The Central Europe mountainous areas, the Massif Central (France) and the Cantabrian Mountains (north Iberian Peninsula) harbor relict isolated N. pumila populations endangered by eutrophication and hybridization with N. lutea. We aim to detect hybridization processes in the Massif Central and Cantabrian Mountains populations and compare the genetic diversity of N. pumila in the relict populations of Central Europe by using microsatellite (SSR) markers. No evidence of hybridization was found in the Iberian population, whereas the admixture between N. pumila and N. lutea in the Massif Central populations could be due to hybridization or ancient introgression. Our current knowledge would benefit from genetic diversity studies focusing on both species throughout their distributional range. The Iberian and Massif Central N. pumila populations were genetically distinct, representing two different clusters from other relict populations, with low genetic diversity and a genetic boundary within Central Europe.

Genetic legacy of southern Middle Siberian mountain and foothill populations of Scots pine (Pinus sylvestris L.): Diversity and differentiation

Scots pine (Pinus sylvestris L.) is a widespread and economically important tree species in Eurasia. Southern Siberian, Scots pine mountain and foothills forests are especially valuable natural objects that help to stabilize environmental conditions. Due to the associated impact of natural and anthropogenic factors, the habitats of the species in southern Siberia are constantly shrinking. In this regard, the study of genetic diversity and structure of Scots pine forests in southern Siberia is very relevant. Here, we studied the genetic diversity and structure of eight Scots pine populations located in southern Middle Siberia (Russia). A high level of genetic diversity (HE = 0.518) was detected in the studied populations. No recent bottleneck effect, isolation by distance or isolation-by-environment were detected. Most genetic diversity was found within populations, while only 7% of genetic diversity occurred among populations. Both STRUCTURE analysis and UPGMA clustering showed two genetic groups. Two populations from the Minusink basin and a population from the Western Sayan Mts. formed the first group and the second group was composed of the other populations from Kuznetsk Alatau Mts., Central Tuva basin and Todzha basin. Our findings suggest that the studied Scots pine populations originate from different gene pools. The pattern of genetic diversity revealed by our study may be useful for the elaboration of conservation measures of genetic resources of Scots pine in southern Middle Siberia.

Genetic divergence studies for yield and its component traits in Mung bean (Vigna radiata L. Wilczek)

The present investigation was carried out at Genetics and Plant Breeding (GPB) farm, College of Agriculture, Central Agricultural University, Imphal, Manipur during kharif 2021 using 60 genotypes of Mung bean. Mahalanobis D2 statistics was used to evaluate the diversity. A total of fourteen clusters were formed with maximum number of genotypes in cluster I i.e., 29 genotypes followed by cluster II with 17 genotypes, cluster XII with 3 genotypes, all the remaining clusters were mono genotypic. It was found that the pattern of genotype distribution into different clusters was random and unrelated to geographic diversity. Results on genotype diversity between clusters IV and IX revealed the greatest inter-cluster distances, whereas cluster XII had the greatest intra-cluster distances. The largest cluster mean for seed yield per plant was found in cluster IX. Further, maximum contribution towards divergence was by number of seeds per plant (52.49%) followed by seed yield (17.8%) and days to 50% flowering (7.34%), while minimum by pod length which had shown 0% contribution.

Molecular Marker Based Genetic Diversity Study of Curcuma Caesia Roxb. – A Mini Review

The availability of genetic resource provides an opportunity for plant breeders to develop new cultivars with desirable characteristics and these characteristics encompass various traits preferred by farmers (high yield potential, larger seed size, etc) as well as traits favored by breeders (pests and disease resistance). Genetic resources are also essential for conservation, as they provide a basis for identifying threatened species and developing conservation strategies. Curcuma caesia Roxb. (Zingiberaceae) is an underutilized perennial herb with bluish-black tuberous rhizome having the characteristic of aromatic and medicinal properties. There is an ample genetic diversity of Curcuma plants with medicinal importance around the world. Authentication and ensuring the genuineness of Curcuma are crucial aspects for marker-based analysis. Therefore, genetic variation serves as the base for the identification and characterisation of the plants. Molecular marker technology is widely used in genetic diversity analysis, germplasm resource identification, and molecular marker-assisted breeding technique. Multiple molecular markers have been used for characterization and identification of species for its sustainable utilization and conservation. The molecular investigation, which involves techniques like RAPD, SCAR, ISSR, and AFLP for fingerprinting, plays a crucial role in establishing molecular markers to assess the authenticity and diversity of plant species. Various marker analyses have demonstrated a significant degree of genetic variation among the species and these patterns tend to differ due to environmental influences and genetic factors. This review facilitates a complete information about the molecularassisted genetic diversity study of Curcuma caesia Roxb. (Black turmeric) which may be used as a database while exploring the diversity analysis.

GENETIC DIVERSITY OF MAJOR POLYPHAGOUS SPIDER MITE SPECIES ACROSS HOST PLANTS AND SPATIAL DISTRIBUTION

Different agroecosystems of southern Karnataka sampled for plant associated mites recorded six genera of tetranychid mites viz., Aponychus, Eutetranychus, Oligonychus, Petrobia, Schizotetranychus and Tetranychus. Neutrality test revealed a lowest haplotype diversity (0.993) of T. neocaledonicus population and Tajima’s D and Fu’s Fs test values were negatively significant for T. fijiensis, E. orientalis and S. baltazari populations, indicating the greater expansion of populations. Genetic analysis with ITS2 (rDNA) sequences revealed highest similarity between mite genera Petrobia and Aponychus showing lowest genetic distance of 0.51. Schizotetranychus has sister relationship with Eutetranychus which in turn clustered with Petrobia and Aponychus. Tetranychus and Oligonychus genera with lower genetic distance of 0.60 are clustered together. The study confirmed the clustering of morphologically related genera and lower genetic distances observed between related genera, expressed sister relationship. Molecular phylogenetic analysis of species under genus Oligonychus showed clustering in line with the morphology-based species taxonomic keys, while polyphagous species under the genus Tetranychus did not express form this grouping. Genetic diversity study of ten polyphagous mite species across their host plants and geographical occurrence revealed grouping according to locations in the phylogenetic tree. However, populations of Oligonychus tylus with a narrow host range showed close relationship for host plants than geographical locations which was evident in phylogenetic tree branching.

Correlation and path analysis studies in onion (Allium cepa) genotypes

The present study was carried out at the experimental farm of the Department of Vegetable Sciences, Dr. YashwantSingh Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh during the winter (rabi) season of 2019–20 and 2020–21 to study the genetic variability, correlation and path studies in 30 different genotypes of the onion (Allium cepa L.) crop. All genotypes reflected a wide and significant spectrum of variability for all the traits under study. Genotypes UHF-ONI-13, UHF-ONI-15 and UHF-ONI-16 outperformed other genotypes in terms of yield and other critical horticultural characteristics. The magnitude of phenotypic coefficient of variation was higher than the genotypic coefficient of variation for all the characters. The phenotypic and genotypic coefficients of variability were high for doubles/deformed bulbs, moderate for leaf length, plant height, average bulb weight, bulb yield per plot and per hectare. High heritability along with high to moderate genetic gain was observed for doubles/deformed bulbs, leaf length, plant height, average bulb weight, bulb yield per plot and bulb yield per hectare, which suggested that improvement can be achieved through simple selection. Bulb yield had significant and positive correlation with average bulb weight, equatorial diameter, plant height, polar diameter, days to harvest and days to 50% neck fall. Path analysis showed that bulb weight, equatorial diameter, bulb shape index, neck thickness, total soluble solids, plant height and leaf length had a positive direct effect on bulb yield.

The Prospects of gene introgression from crop wild relatives into cultivated lentil for climate change mitigation.

Crop wild relatives (CWRs), landraces and exotic germplasm are important sources of genetic variability, alien alleles, and useful crop traits that can help mitigate a plethora of abiotic and biotic stresses and crop yield reduction arising due to global climatic changes. In the pulse crop genus Lens, the cultivated varieties have a narrow genetic base due to recurrent selections, genetic bottleneck and linkage drag. The collection and characterization of wild Lens germplasm resources have offered new avenues for the genetic improvement and development of stress-tolerant, climate-resilient lentil varieties with sustainable yield gains to meet future food and nutritional requirements. Most of the lentil breeding traits such as high-yield, adaptation to abiotic stresses and resistance to diseases are quantitative and require the identification of quantitative trait loci (QTLs) for marker assisted selection and breeding. Advances in genetic diversity studies, genome mapping and advanced high-throughput sequencing technologies have helped identify many stress-responsive adaptive genes, quantitative trait loci (QTLs) and other useful crop traits in the CWRs. The recent integration of genomics technologies with plant breeding has resulted in the generation of dense genomic linkage maps, massive global genotyping, large transcriptomic datasets, single nucleotide polymorphisms (SNPs), expressed sequence tags (ESTs) that have advanced lentil genomic research substantially and allowed for the identification of QTLs for marker-assisted selection (MAS) and breeding. Assembly of lentil and its wild species genomes (~4Gbp) opens up newer possibilities for understanding genomic architecture and evolution of this important legume crop. This review highlights the recent strides in the characterization of wild genetic resources for useful alleles, development of high-density genetic maps, high-resolution QTL mapping, genome-wide studies, MAS, genomic selections, new databases and genome assemblies in traditionally bred genus Lens for future crop improvement amidst the impending global climate change.

Kazakh national dog breed Tazy: What do we know?

The Tazy or Kazakh National sighthound has been officially recognized as the national heritage of Kazakhstan. Comprehensive genetic studies of genetic diversity and population structure that could be used for selection and conservation of this unique dog breed have not been conducted so far. The aim of this study was to determine the genetic structure of the Tazy using microsatellite and SNP markers and to place the breed in the context of the world sighthound breeds. Our results showed that all 19 microsatellite loci examined were polymorphic. The observed number of alleles in the Tazy population varied from 6 (INU030 locus) to 12 (AHT137, REN169D01, AHTh260, AHT121, and FH2054 loci) with a mean of 9.778 alleles per locus. The mean number of effective alleles was 4.869 and ranged from 3.349 f to 4.841. All markers were highly informative (PIC values greater than 0.5) and ranged from 0.543 (REN247M23 locus) to 0.865 (AHT121 locus). The observed and expected heterozygosities in a total population were 0.748 and 0.769 and ranged from 0.746 to 0.750 and 0.656 to 0.769, respectively. Overall, the results confirmed that the Tazy breed has a high level of genetic diversity, no significant inbreeding, and a specific genetic structure. Three gene pools underlie the genetic diversity of the Tazy breed. SNP analysis using the CanineHD SNP array, which contains more than 170,000 SNP markers, showed that the Tazy breed is distinct from other sighthound breeds and genetically related to ancient eastern sighthound breeds sharing the same branch with the Afghan Hound and the Saluki. The results, together with archeological findings, confirm the ancient origin of the breed. The findings can be used for the conservation and international registration of the Tazy dog breed.

Genetic variability studies in field pea (Pisum sativum L.) for yield and associated characters

The prime and foremost objective of the study was to estimate the genetic variability for yield and its associated characteristics among the 23 genotypes of field pea and also to engender information regarding genetic parameters like range, mean, phenotypic coefficient of variation (PCV), genotypic coefficient of variation (GCV), heritability and genetic advance as a percentage over means for the18 traits under consideration. It was disclosed from the results of the analysis of variance that there exists a difference among the 23 genotypes for all the 18 traits under consideration. The trait including primary branches per plant, secondary branches per plant, plant height, swelling capacity, swelling index, biological yield per plant, and seed yield recorded high amounts of GCV and PCV. High heritability combined with high genetic advance was documented for the trait’s plant height and seeds per plant, whereas high heritability coupled with low genetic advance, was recorded for the trait’s days to fifty % flowering, days to maturity, primary branches per plant, secondary branches per plant, pod length, 100 seed weight, percent disease incidence and seed yield per plant. The existing variability identified can be further exploited in crop improvement of field pea

Study of genetic variability and diversity analysis in maize (Zea mays L.) by agglomerative hierarchical clustering and principal component analysis

Study of genetic variability and diversity analysis in maize (Zea mays L.) by agglomerative hierarchical clustering and principal component analysis

Genetic variability and character association studies among seed yield and yield component traits in safflower (Carthamus tinctorius L.) genotypes

Genetic variability and character association studies among seed yield and yield component traits in safflower (Carthamus tinctorius L.) genotypes

Genetic Variability Studies for Yield, Nutritional and Cooking Quality Characters in Coloured Rice (Oryza sativa L.)

Genetic Variability Studies for Yield, Nutritional and Cooking Quality Characters in Coloured Rice (Oryza sativa L.)

Avena sterilis L.’in Mikrosatellit İşaretleyicileri ile Genetik Çeşitlilik Analizi

Avena sterilis is an important grassy weed that causes a problem in wheat cultivation areas, and intensive herbicides are used to control it. Genetic diversity study is important to have information how on the effect weed species of the environmental factors and herbicides. The high level of genetic diversity within the species is a guarantee for adaptation to changing environmental conditions. This study was conducted based on complaints of the loss of effectiveness during the chemical control. Analyses were carried out on 27 selected populations collected from wheat cultivation areas in Turkey's Middle Black Sea region. Seventy-seven alleles from microsatellite loci were detected, and the average number of alleles per locus was determined as five using 17 microsatellite primers. The average gene diversity (GD) and polymorphism information content (PIC) values were 0.894 and 0.732, respectively. According to the UPGMA dendrogram generated using Average Linkage, the populations were clustered into two main groups. A high degree of diversity was found among the studied steril oat genotypes, and it is seen that there is no geographical isolation. It is understood that this situation primarily provides adaptation to those geographical areas by transporting weed seeds from other provinces in various ways. According to these findings, issues such as crop rotation, cultural control methods, encouraging the use of certified seeds, and the use of herbicides with different mechanisms of action can be listed among the measures that can be taken to control the high genetic diversity, which is an indicator of herbicide resistance.

Optimization of single-tube nested PCR for the detection of Echinococcus spp.

Echinococcosis is a serious zoonotic life-threatening parasitic disease caused by metacestodes of Echinococcus spp., and appropriate sensitive diagnosis and genotyping techniques are required to detect infections and study the genetic characterization of Echinococcus spp. isolates. In this study, a single-tube nested PCR (STNPCR) method was developed and evaluated for the detection of Echinococcus spp. DNA based on the COI gene. STNPCR was 100 times more sensitive than conventional PCR and showed the same sensitivity to common nested PCR (NPCR); but with a lower risk of cross-contamination. The limit of detection of the developed STNPCR method was estimated to be 10 copies/μL of the recombinant standard plasmids of Echinococcus spp. COI gene. In clinical application, 8 cyst tissue samples and 12 calcification tissue samples were analysed by conventional PCR with outer and inner primers and resulted in 100.00% (8/8) and 8.33% (1/12), 100.00% (8/8) and 16.67% (2/12) positive reactions, respectively, while STNPCR and NPCR were all able to identify the presence of genomic DNA in 100.00% (8/8) and 83.33% (10/12) of the same samples. Due to its high sensitivity combined with the potential for the elimination of cross-contamination, the STNPCR method was suitable for epidemiological investigations and characteristic genetic studies of Echinococcus spp. tissue samples. The STNPCR method can effectively amplify low concentrations of genomic DNA from calcification samples and cyst residues infected with Echinococcus spp. Subsequently, the sequences of positive PCR products were obtained, which were useful for haplotype analysis, genetic diversity, and evolution studies of Echinococcus spp., and understanding of Echinococcus spp. dissemination and transmission among the hosts.

Genetic Diversity Studies in Super-early Pigeonpea [Cajanu cajan (L.) Millsp.

Background: Pigeonpea is an important legume crop in India. The super early genotypes which matures within 100 days have been developed at ICRISAT. They are photo-insensitive, aids in crop intensification and escapes abiotic and biotic stresses. The super early genotypes were exploited for genetic diversity for further improvement of the genotypes. Methods: The study was conducted at International Crop Research Institute for the Semi-Arid Tropics, Patancheru, Telangana during kharif, 2017. The thirty-super early pigeonpea genotypes developed at ICRISAT were subjected for the study of genetic diversity (Mahalanobis D2 method) based on twelve quantitative characters. Result: The 30 super early genotypes were grouped into five clusters. The largest number of genotypes were confined to cluster III (19 genotypes) followed by cluster IV (6 genotypes), cluster I and II (2 genotypes). Cluster V is a solitary cluster with the check MN1.The inter cluster distance was high between the clusters III and IV followed by cluster I and III. The intra cluster distance was highest for the cluster III indicating the presence of variation among the genotypes within the cluster. The highest mean for single plant yield was observed for the cluster III followed by cluster V. The clusters with more inter cluster distance can be used to select parents to be involved in hybridization programmes.

A Set of Highly Polymorphic Microsatellite Markers for Genetic Diversity Studies in the Genus Origanum

This study reports the development of a set of 20 highly polymorphic genomic SSR markers which can be used for both cultivar identification and genetic diversity studies in several Origanum species, including some of the most popular ones like Greek oregano (Origanum vulgare L. ssp. hirtum), common oregano (O. vulgare L. ssp. vulgare), and sweet marjoram (O. majorana L.). Analysis of the polymorphic information content (PIC) showed an average PIC value of 0.75 with a minimum of 0.41 and a maximum of 0.89, where 17 of the markers showed PIC values above 0.73. Comparative analysis of the genetic diversity of eight natural populations of Greek oregano in Bulgaria showed that six of the genomic SSR markers revealed significantly higher portions of genetic diversity in the populations, compared to 12 EST SSR markers used in our previous study. We also compared the performance of the same six genomic SSR markers with the results for eight SRAP primer combinations, which showed that SRAP markers captured more precisely the genetic structure in natural populations. The developed highly polymorphic genomic SSR markers can be successfully applied to evaluation of the genetic diversity in the genus Origanum, based on the expected and observed heterozygosity in the populations as well as for easy identification of breeding lines and cultivars based on unique SSR fingerprints.