Genetic Diversity Studies Research Articles

ISSR marker based genetic divergence study for charcoal rot disease resistance triggered by salicyclic acid elicitor in Mungbean (Vigna radiata (L) Wilczek)

ISSR marker based genetic divergence study for charcoal rot disease resistance triggered by salicyclic acid elicitor in Mungbean (Vigna radiata (L) Wilczek)

A reference genome assembly for the continentally distributed ring-necked snake, Diadophis punctatus.

Snakes in the family Colubridae include more than 2,000 currently recognized species, and comprise roughly 75% of the global snake species diversity on Earth. For such a spectacular radiation, colubrid snakes remain poorly understood ecologically and genetically. Two subfamilies, Colubrinae (788 species) and Dipsadinae (833 species), comprise the bulk of colubrid species richness. Dipsadines are a speciose and diverse group of snakes that largely inhabit Central and South America, with a handful of small-body-size genera that have invaded North America. Among them, the ring-necked snake, Diadophis punctatus, has an incredibly broad distribution with 14 subspecies. Given its continental distribution and high degree of variation in coloration, diet, feeding ecology, and behavior, the ring-necked snake is an excellent species for the study of genetic diversity and trait evolution. Within California, six subspecies form a continuously distributed "ring species" around the Central Valley, while a seventh, the regal ring-necked snake, Diadophis punctatus regalis is a disjunct outlier and Species of Special Concern in the state. Here, we report a new reference genome assembly for the San Diego ring-necked snake, D. p. similis, as part of the California Conservation Genomics Project. This assembly comprises a total of 444 scaffolds spanning 1,783 Mb and has a contig N50 of 8.0 Mb, scaffold N50 of 83 Mb, and BUSCO completeness score of 94.5%. This reference genome will be a valuable resource for studies of the taxonomy, conservation, and evolution of the ring-necked snake across its broad, continental distribution.

Morphological Diversity of an Underutilized and Wild Edible Fruit (Cordia) Species in Three Districts of Bastar Region of Chhattisgarh, India

The multipurpose deciduous tree Cordia dichotoma belongs to the family Boraginaceae and it is variously called as Glueberry, Goonda, Lasora and locally as ‘Bohaar’ in Bastar (Chhattisgarh). The diversity in morphological traits in Cordia species were marked and identified at different locations of three districts of Bastar region to assess phenotypic morphological variation and to estimate genotypic and phenotypic variability for various morphological traits of fruits for future use. The quantitative traits like fruit weight, length, and diameter are important quality traits in many horticultural crops are used in genetic diversity studies. The underutilized fruits are advantageous crops being hardy in nature and tolerate extreme climatic conditions and possess high potential to provide nutritional and social benefits. The present investigation is performed for the identification, morphological analysis and diversity exploration with respect to food value of underutilized and wild edible fruit Cordia dichotoma found in the Bastar region of Chhattisgarh. A Total of ten numbers of representative trees of Cordia species from each district were selected for morphological and silvicultural studies. It is found that genotype of Cordia has morphological variations in the region. Two species of Cordia i.e., Cordia obliqua and Cordia dichotoma were taken for the study. This study revealed that source/provenance Jagdalpur and Dantewada had Cordia species with better fruit size than district Kondagaon source, also morphological variations of Cordia species in different sources or provenance with respect to fruit fresh weight, pulp weight, peel weight, pulp and peel ratio revealed that Cordia dichotoma G. Forst has better fruit size and pulp percentage.

Transcriptome Analysis and Novel EST-SSR Marker Development for Pinus tabuliformis Seedlings from Four Provenances

Chinese pine (Pinus tabuliformis) is a conifer species endemic to the temperate, warm temperate, and semi-arid regions of China. It has important ecological and economic values, but lacks suitable molecular markers for genetic studies. In this study, we collected open-pollinated progeny seeds from four provenances: Ningcheng (Nc), Qinyuan (Qy), Weichang (Wc), and Pingquan (Pq). We sequenced the transcriptomes of open-pollinated progeny seedlings from four provenances and annotated 18,244 unigenes. We analyzed the expression of genes involved in the auxin indole-3-acetic acid (IAA), cytokinin (CTK), and gibberellin (GA) signaling pathways among the provenances. Additionally, we detected 2811 expressed sequence tag simple sequence repeat (EST-SSR) loci in 2360 unigenes, with a frequency of 14.83% and an average of one locus per 14,556 base pairs (bp). We developed 10 polymorphic primers from 67 pairs and tested them on 56 samples from the four provenances. These primers exhibited moderate to high polymorphism and distinguished all samples clearly. Our study reveals variation in growth and development among open-pollinated progeny seedlings from different provenances of Chinese pine and provides novel markers for its genetic diversity study and marker-assisted breeding.

Genetic variability and association studies in BC3F1 population of sunflower (Helianthus annuus L.)

Genetic variability and association studies in BC3F1 population of sunflower (Helianthus annuus L.)

Stable nuclear transformation methods for Euglena gracilis and its application to a related Euglenida

Euglenida is a taxonomic group of single-celled flagellates that have a variety of nutrient uptake strategies, making this an excellent model for studying the evolutionary acquisition of secondary chloroplasts. Among Euglenida, Euglena gracilis is the most extensively studied at the biochemical and molecular levels. However, the lack of a widely adopted method of nuclear genome transformation has hindered genetic studies in this organism. Herein, we present a novel nuclear transformation electroporation method that utilizes the 5′ adjacent region sequences of endogenous genes in E. gracilis. We used a NanoLuc reporter to evaluate promoter activity to identify four endogenous promoter candidates with superior luciferase transcriptional activity compared with the activity of the commonly used CaMV 35S promoter in E. gracilis nuclear transformation methods. We used G418 selection to obtain stable E. gracilis transformants harboring the transgene in their genomic DNA. Furthermore, we extended the applicability of our method to Rapaza viridis, a kleptoplastic species in Euglenida. Introduction of the DNA constructs developed for E. gracilis into R. viridis via electroporation generated stable G418-resistant strains exhibiting robust luciferase activity. The introduced promoter sequences functioned effectively, and accurate 5′ end modifications of mRNA were observed in both E. gracilis and R. viridis transformants. These findings demonstrate the broad applicability of our nuclear transformation method across multiple Euglenida species, facilitating molecular biology and genetic diversity studies in this taxonomic group.

Genetic Variability and Correlation Studies in Blackgram (Vigna mungo L. Hepper)

Genetic Variability and Correlation Studies in Blackgram (Vigna mungo L. Hepper)

Genetic Variability and Association Studies ofYield and its Components in Little Millet (Panicum sumatrense L.)

Genetic Variability and Association Studies ofYield and its Components in Little Millet (Panicum sumatrense L.)

High throughput sequencing data reveals the complete mitogenome, abundance, maternal phylogeny, and mitogenomic diversity of Alectoris chukar of Iraq

Alectoris chukar is a wild game bird found in the north of Iraq, near the center of domestication and diversity of species. The mitogenome is one of the most vital resources for comprehensive studies of genetic diversity and molecular evolutionary relationships among avian species. In this study, we used whole genome sequencing raw reads and bioinformatics analysis to sequence and assemble Alectoris chukar's complete mitogenome for the first time. We also studied the maternal lineage and phylogenetic position of Alectoris chukar, as well as some mitogenomic diversity parameters. As a result, the complete mitogenomes with a length ranging from 16686 bp to 16688 bp of four individuals of wild Alectoris chukar were sequenced and assembled. They have a typical avian mitogenome structure with 2 ribosomal RNA (rRNA), 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, and one non-coding control region. Our findings from bioinformatics analysis remarkably demonstrated that copies of the mitogenome are more abundant in liver tissues than in blood and in the liver tissues of females than in males. The results of phylogenetic analysis clustered the studied mitogenomes with Alectoris chukar as a monophyletic clade. Moreover, in comparison to the different genera, Alectoris chukar showed a high level of mitogenomic similarities to the snowcock species of the genus Tetraogallus within the Phasianidae family. However, they were more distant from other partridges. Additionally, a high percentage of mitogenomic pairwise identities within Iraqi Alectoris chukar and high mitogenomic variations compared to Chinese populations were discovered. The number and location of polymorphic sites indicated that the majority of the mitogenome sequences were conserved, with the control region, ND5, and CYTB genes having the most polymorphic sites. Analyses of phylogenetic and mitogenomic diversity revealed that samples of Alectoris chukar from Iraq have a unique maternal lineage and mitogenomic diversity specific to their geographic distribution, suggesting an Alectoris chukar kurdestanica subspecies. The molecular findings presented here provide valuable knowledge and mitogenomic resources into the evolutionary relationships of Alectoris chukar from the Middle East to avian species in the Phasianidae family.
 Key words: DNA sequencing; Mitochondrial genome; Partridges; Phasianidae; Phylogeny

The African Goat Improvement Network: a scientific group empowering smallholder farmers.

The African Goat Improvement Network (AGIN) is a collaborative group of scientists focused on genetic improvement of goats in small holder communities across the African continent. The group emerged from a series of workshops focused on enhancing goat productivity and sustainability. Discussions began in 2011 at the inaugural workshop held in Nairobi, Kenya. The goals of this diverse group were to: improve indigenous goat production in Africa; characterize existing goat populations and to facilitate germplasm preservation where appropriate; and to genomic approaches to better understand adaptation. The long-term goal was to develop cost-effective strategies to apply genomics to improve productivity of small holder farmers without sacrificing adaptation. Genome-wide information on genetic variation enabled genetic diversity studies, facilitated improved germplasm preservation decisions, and provided information necessary to initiate large scale genetic improvement programs. These improvements were partially implemented through a series of community-based breeding programs that engaged and empowered local small farmers, especially women, to promote sustainability of the production system. As with many international collaborative efforts, the AGIN work serves as a platform for human capacity development. This paper chronicles the evolution of the collaborative approach leading to the current AGIN organization and describes how it builds capacity for sustained research and development long after the initial program funds are gone. It is unique in its effectiveness for simultaneous, multi-level capacity building for researchers, students, farmers and communities, and local and regional government officials. The positive impact of AGIN capacity building has been felt by participants from developing, as well as developed country partners.

Stability and Diversity of Elite Lines of Vegetable Cowpea (Vigna unguiculata ssp. unguiculata L.)

Background: The present study was conducted to study the stability and diversity of twenty elite breeding lines of vegetable cowpea developed at ICAR-Indian Institute of Vegetable Research, Varanasi through AMMI analysis and cluster analysis respectively. Methods: All the 20 elite lines were laid out in randomized block design with three replications during three years of sowing viz., Kharif-2018, Kharif- 2019 and Kharif-2021. Each year was considered as onelocation and the dependant variable pod yield per plant was subjected to AMMI analysis for GE interaction study. The mean of all the yield and yield attributes was subjected to cluster analysis for genetic divergence study. Result: AMMI ANOVA showed significant variation for environments (E), genotypes (G) and G×E interactions. The graphical representation of principal component 1 (PC1) vs yield (Y) showed that the genotypes 12,15,11,13,18 were most stable andthe PC1 vs PC2 graph showed that the genotypes 12,11,13,18 were most stable as they were positioned towards the origin. The cluster analysis grouped all the twenty genotypes into four clusters with two genotypes (7,20) in first cluster, five genotypes (17,14,16,8,19) in second cluster, eight genotypes (9,6,1,13,11,12,2,15) in third cluster and five genotypes (5,3,18,4,10) in fourth cluster.

Genetic Diversity and Population Structure of Juniperus seravschanica Kom. Collected in Central Asia.

Juniperus seravschanica Kom. is a species that grows widely in the mountain ranges from Central Asia to Oman. It is an important tree for the formation of shrub-forest massifs in mountainous areas and for draining and fixing soils from middle to high altitudes. A comprehensive study of the species' genetic diversity and population structure is a basic approach to understanding the current status of J. seravschanica resources for the development of future conservation strategies. Samples from 15 populations of J. seravschanica were collected from the mountain ranges of Uzbekistan, Kyrgyzstan, and Kazakhstan. The genetic diversity and population structure of 15 Central Asian populations of J. seravschanica were assessed using 11 polymorphic simple sequence repeat (SSR) markers. Genetic diversity parameters, including the number of alleles (na), the effective number of alleles (ne), Shannon's information index (I), the percentage of polymorphic loci (PPL), Nei's genetic diversity index (Nei), principal coordinate analysis (PCoA), etc., were evaluated. The analysis of 15 J. seravschanica populations based on 11 polymorphic SSRs detected 35 alleles. The average PIC value was 0.432, and the highest value (0.662) was found in the JT_40 marker. Nei's genetic diversity index for the J. seravschanica populations was 0.450, ranging from 0.407 (population 14) to 0.566 (population 4). The analysis of molecular variance (AMOVA) showed that 90.3% of total genetic variation is distributed within the population. Using the alleles of all the populations, the gene flow (Nm) was found to be 4.654. Population structure analysis revealed poor clustering in the studied populations and confirmed our AMOVA results. The output of this work can be efficiently used for the maintenance of the species across the Central Asian region.

Evaluation in Genetic Variation of Krachai by Sequence Related Amplified Polymorphism (SRAP) and Random Amplified Polymorphic DNA (RAPD) Techniques

Krachais are local name of Thai herb which are identified within 2 genera, namely Bosenbergia (white or red krachai) and Kaempferia (black krachai). The rhizome of Bosenbergia rotunda (L.) Mansf. contains major aromatic compounds against COVID19 but its many morphological characteristics such as leaves, stems and rhizome are like other species in same genus or family. In this study, a total of 13 accessions containing 5 samples of B. rotunda, 2 samples of Boesenbergia spp. and 3 samples of Kaempferia parviflora including 3 samples of other species in same family as outgroups were analyzed and clustered using sequence-related amplified polymorphism (SRAP) and random amplified polymorphism DNA (RAPD) markers. The results showed that 8 SRAP primers (M1E1, M1E2, M1E7, M2E10, M3E9, M5E1, M5E2 and M6E10) could generate 79 polymorphism bands with an average of 92.15% whereas a total of 5 RAPD primers (OPY04, OPY02, OPY04, JAT11 and JAT12) could give 64 polymorphisms with 100% as a percentage of the polymorphism band. The PIC of the SRAP marker (0.470) has a higher value than the RAPD marker (0.264). The highest similarity coefficients within genus Boesenbergia of 1.000 and 0.952 were obtained from SRAP and RAPD markers, respectively. The UPGMA dendrogram of SRAP and RAPD information among krachai presented 2 and 4 groups, respectively. The cluster of Boesenbergia was separated from K. parviflora and other species in same family. Furthermore, the results also pointed that Boesenbergia sp. from Phayao is in correct genus and is B. pandurata (Roxb.) Schltr. because of having red leaf while Boesenbergia sp. from Chiang Rai showed confusion between SRAP and RAPD data. It was concluded that SRAP and RAPD have great potential for the study of genetic diversity of Boesenbergia and other species in family Zingiberaceae.

Genetic Variability and Correlation Studies in High-yielding Varieties of Rice (Oryza sativa L.)

Rice is the major staple food crop of India and there is an anticipated high demand due to increasing population. Information on yield contributing traits and the level of heritable variation in these traits is essential for establishing the genotype’s potential for future breeding programmes. The study was conducted to evaluate the variability in yield contributing traits and their correlation in a set of released rice varieties from ICAR – Indian Institute of Rice Research, Hyderabad. The objective of the study was to estimate the genotypic and phenotypic coefficient of variation, heritability and genetic advance of yield and related traits using thirty-two rice cultivars. For all evaluated traits, the phenotypic coefficient of variation was found to be significantly higher than the genotypic coefficient of variance, implying that the expression of these traits is influenced by the environment. High heritability coupled with high genetic advance was observed for panicle weight whereas low heritability coupled with low genetic advance over per cent mean was recorded for productive tiller number. The traits viz., tiller number, productive tiller number, flag leaf width, panicle weight, number of grains per panicle, number of filled grains per panicle and test weight exhibited a positive association, whereas the number of unfilled grains per panicle and plant height exhibited negative association with grain yield.

Genetic Variability and Correlation Studies on Different Hybrid of Bitter Gourd (Momordica charantia L.) in Prayagraj Agroclimatic Condition

An experiment was conducted on Genetic Variability, Heritability and Correlation Studies on 20 hybrids of bitter gourd (Momordica charantia L.) with three replications during Zaid Season of 2022. at the Research Field of Department of Horticulture, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj. They were evaluated for 16 quantitative characters. The results from the present investigation revealed that on the basis of mean performance for days taken to germination (7.00-12.00), Days to 1st Male Flower (26.80 – 30.53 days), Days to 1st Female Flower (31.53 – 35.43 days), Nodes number at which first male flower appears (4.13 – 8.60 nodes), Nodes number at which first female flower appears (6.40 – 15.87 nodes), Days to first fruit picking (40.00 – 48.33 days), Days to last fruit picking (82.33-85.00 days) Fruit Weight (24.60 – 74.94 gm), Number of Fruits per Plant (20.18 – 28.91 fruits), Fruit yield per plant (0.55 – 2.02 kg), Fruit Length (7.83 – 14.13 cm), Fruit diameter (21.28 – 40.51 mm), Yield per Hectare (61.18 – 234.44 q/ha), Vine Length at final Harvest (3.02 – 3.98m), TSS (6.00 – 9.00), Ascorbic acid (79.70 – 84.40 mg/100gm) was found superior in AVT-I 2020 BIGHYB-3 with higher fruit yield per plant and performed better for other desirable traits. This genotype was found superior based on the overall performance of different bitter gourd cultivars for growth and yield in Prayagraj conditions.

Genetic diversity and characterization of Wolbachia endosymbiont in canine filariasis

Canine filariasis is caused by nematodes from the family Onchocercidae, which is transmitted by arthropod vectors. The disease is commonly found in Southeast Asia and exists worldwide. Some filarial nematodes are associated with intracellular bacteria of the genus Wolbachia, which plays an important role in embryogenesis, molting, and the long-term survival of adult worms. This study aims to characterize Wolbachia sp. and determine the association between Wolbachia and canine filarial nematode species in Thailand. A total of 46 dog blood samples that were naturally infected with filarial nematodes were obtained to identify filarial nematode species by Giemsa stained under a light microscope and confirmed using the molecular technique. In order to characterize Wolbachia sp., the nested PCR assay targeting the 16S rRNA gene showed that all samples of Dirofilaria immitis and fifteen samples of Candidatus Dirofilaria hongkongensis were grouped into Wolbachia supergroup C. In addition, all samples of Brugia spp. and five samples of Candidatus Dirofilaria hongkongensis were classified into Wolbachia supergroup D. The genetic diversity analysis conducted using the 16S rRNA gene revealed a similar result when analyzed through phylogenetic tree analysis. This is the first genetic diversity study of Wolbachia of Candidatus Dirofilaria hongkongensis in infected dogs in Thailand.

Genome-Wide Association Studies of Salt-Tolerance-Related Traits in Rice at the Seedling Stage Using InDel Markers Developed by the Genome Re-Sequencing of Japonica Rice Accessions

Japonica-specific markers are crucial for the analysis of genetic diversity, population structure, evolutionary traits, and genome-wide association study (GWAS) of japonica germplasm accessions. This study developed 402 insertion–deletion (InDel) polymorphic markers based on the re-sequencing of four japonica rice landraces and three japonica rice cultivars. These InDel markers were uniformly distributed across 12 rice chromosomes with high polymorphism and good amplification specificity. The average density of InDel markers on each chromosome was 0.95 Mb per locus. On the basis of these InDel markers, genetic diversity analyses and GWASs for 12 salt-tolerance-related traits were performed using 182 japonica rice accessions. In total, 1204 allelic variants were detected, with an average of 3.00 alleles and 2.10 effective alleles per locus. Based on population structure analysis, 182 japonica rice accessions were divided into four subgroups. The GWAS analyses revealed a total of 14 salt-tolerance-related InDels, which were located on chromosomes 1–5, 9, 10, and 12. Twenty-eight allelic loci were identified, explaining 6.83% to 11.22% of the phenotypic variance. Haplotype analysis detected six InDel markers associated with salt-tolerance-related traits that were significantly different (p < 0.05) or highly significantly different (p < 0.01) among different haplotypes. These markers can be utilized for the molecular identification of salt-tolerant rice germplasm accessions.

Genetic variability and stability analysis of chili in three environments

Chili is an important vegetable crop consumed by most Indonesian people. Chili production is affected by the limited varieties and low adaptability to growing in different environments. This study aimed to identify the variability of 22 chili pepper on morphology, the genotype x environment interaction, and the stability of 10 chili pepper genotypes in 3 different environments. The study was conducted from July 2020 to February 2022 in Sleman DIY, Bogor, and Blitar. The experimental design used a single-factor randomized complete block design, each consisting of three replicates. The genotypes evaluated were HCR 17-003, HCR 17-004, HCR 17-007, HCR 17-008, HCR17-012, HCR 17-013, HCR 17-014, HCR 17-017, F7-1, F7-2, F7-3, Ca011, Ca013, Ca020, Ca021, Cf002, Cf005, Cf007, Cf010, Cf015, Bonita, and Loblita. Ten genotypes were evaluated in stability analysis, i.e., PKHT A, PKHT B, Bara, Genie, Centil, PKHT C, PKHT D, Bonita, Sona, and Tunduk. The biplot analysis for genetic diversity study showed a total diversity was 40.5% for the two main components. The genotype x environment interaction had a significant effect on productivity. PKHT C and Sona were identified as stable based on the Francis-Kannenberg method. PKHT C, Sona, PKHT B, and Bonita were stable based on the Wricke method. PKHT A and Bonita were stable based on Finlay-Wilkilson methods. PKHT B, PKHT C, Sona, and Bonita were identified as stable based on the AMMI method. The genotype which is stable based on all stability methods was PKHT C.
 Keywords: AMMI; GxE interaction; parametric stability; variety.

Application of High-Resolution Melting and DNA Barcoding for Discrimination and Taxonomy Definition of Rocket Salad (Diplotaxis spp.) Species.

Nuclear and cytoplasmic DNA barcoding regions are useful for plant identification, breeding, and phylogenesis. In this study, the genetic diversity of 17 Diplotaxis species, was investigated with 5 barcode markers. The allelic variation was based on the sequences of chloroplast DNA markers including the spacer between trnL and trnF and tRNA-Phe gene (trnL-F), the rubisco (rbcl), the maturase K (matk), as well as the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA. A highly polymorphic marker (HRM500) derived from a comparison of cytoplasmic genome sequences in Brassicaceae, was also included. Subsequently, a real-time PCR method coupled with HRM analysis was implemented to better resolve taxonomic relationships and identify assays suitable for species identification. Integration of the five barcode regions revealed a grouping of the species according to the common chromosomal set number. Clusters including species with n = 11 (D. duveryrieriana or cretacea, D. tenuifolia, D. simplex and D. acris), n = 8 (D. ibicensis, D. brevisiliqua and D. ilorcitana), and n = 9 (D. brachycarpa, D. virgata, D. assurgens, and D. berthautii) chromosomes were identified. Both phylogenetic analysis and the genetic structure of the collection identified D. siifolia as the most distant species. Previous studies emphasized this species' extremely high glucosinolate content, particularly for glucobrassicin. High-resolution melting analysis showed specific curve patterns useful for the discrimination of the species, thus determining ITS1 as the best barcode for fingerprinting. Findings demonstrate that the approach used in this study is effective for taxa investigations and genetic diversity studies.

Principal Component Analysis and Genetic Divergence Studies for Yield and Yield-Related Trait of Groundnut (Arachis hypogaea L.) Genotypes at Pawe North Western Ethiopia

A study was conducted on sixty-four (64) groundnut genotypes at Pawe northwestern part of Ethiopia. And the analysis of variance revealed the existence of significant variation among the tested groundnut genotypes. Cluster analysis showed the existence of five (5) divergent groups and the maximum inter-cluster distance was observed between cluster (II) and cluster (V) D2=1419.77 and the shortest inter-cluster squared distance was found between cluster (I) and Cluster (III) D2=247.23. The first four principal components for (PCs) accounted for 70.03% of the total variation. Overall, the results of the current study depicted the presence of sufficient genetic diversity existed among tested groundnut genotypes for further use in breeding programs. However, a one-season experiment will not realize variability because quantitative traits are polygenic and highly influenced by the environment. So, further experiments must be conducted over location and seasons.