Analysis Of Molecular Variance Research Articles

Diversity Assessment of Winged Bean [Psophocarpus tetragonolobus (L.) DC.] Accessions from IITA Genebank

The capability of winged bean to support food and nutrition security in sub-Saharan Africa is recurrently being affected by several constraints, which include a lack of genetic improvement. The dearth of adequate information on the level of available genetic diversity in winged bean germplasm has been a major setback in planning appropriate improvement programs. Fifteen winged bean accessions were assessed for genetic diversity using 10 quantitative traits and 10 simple sequence repeat (SSR) markers. The accessions were laid out in RCBD with three replicates for two growing seasons. Leaf samples were obtained from 10 plants representing each accession for SSR marker genotyping. The accessions exhibited significant (p < 0.05) differences for measured traits. Broad-sense heritability estimates varied from 10.31% for days to first plant maturity to 72.67% for pod weight. Pod weight had a positive and significant correlations with pod length (0.53, p < 0.05), pod width (0.70, p < 0.01), and number of seeds per pod (0.64, p < 0.01). However, the number of seeds per pod was negatively correlated with days to maturity (−0.71, p < 0.01). Number of seeds per pod was positively predicted by pod weight, seed thickness, and days to maturity. Cluster analysis delineated the accessions into two distinct groups. Average number of alleles of 4.2, gene diversity of 0.25, and polymorphic information content of 0.22 were recorded. Analysis of molecular variance revealed intra-accession variation of 95% as compared to inter-accession variation of 5%. Two primary genetic groups were identified and only three accessions, namely TPt-6, TPt-126, and TPt-48, showed genetic purity. The results of this study provide the basis for exploiting the existing diversity for winged bean improvement.

Genetic diversity and population structure of Saccharum hybrids.

Sugarcane breeding programs incorporate foreign material to broaden the genetic base, expanding the gene pool. In South America, the Inter-university Network for the Development of the Sugarcane Industry (RIDESA) and Estación Experimental Agroindustrial Obispo Colombres (EEAOC) sugarcane breeding programs from Brazil and Argentina, respectively, have never exchanged materials. In that sense, the knowledge of the genetic diversity and population structure among sugarcane genotypes of both germplasm banks, determined in a reliable way through their molecular profiles, will provide valuable information to select the best parental accessions for crossing aimed at the efficient introgression of desirable alleles. For that, the aim was to determine the genetic diversity and population structure of 96 Saccharum commercial hybrids from RIDESA and EEAOC sugarcane breeding programs by using TRAP, SSR and markers related to disease resistance (e.g. Bru1 and G1). Genetic structure was determined through genetic similarity analysis, analysis of molecular variance (AMOVA), Multidimensional scaling (MDS), and a Bayesian method. Average PIC values were 0.25 and 0.26, Ho values were 0.24 and 0.28, and He values were 0.25 and 0.28, for TRAP and SSR primers, respectively. Genetic similarity, MDS, and analysis of structure revealed that Brazilian and Argentinean genotypes clustered in two groups clearly differentiated, whereas AMOVA suggested that there is more variability within programs than between them. Regarding Bru1 markers, Brazilian genotypes showed high frequency of haplotype 1 (71.4%) whereas Argentinean genotypes showed high frequency of haplotype 4 (80.8%); haplotypes 1 and 4 are indicated for the presence and absence of the brown rust resistance gene (Bru1), respectively. Respecting the G1 marker, most of the evaluated genotypes (60.4%) showed the presence of the fragment, in a similar proportion for genotypes of both programs. In conclusion, the exchange of materials, at least the most diverse genotypes, between RIDESA and EEAOC breeding programs will allow extending the genetic base of their germplasm banks, and the knowledge of genetic diversity will help breeders to better manage crosses, increasing the probability of obtaining more productive varieties.

Genetic Structure and Genetic Diversity of the Endemic Korean Aucha Perch, Coreoperca herzi (Centropomidae), in Korea.

The Korean endemic aucha perch, Coreoperca herzi, belongs to the family Centropomidae. Thus far, studies on C. herzi have focused on mitochondrial genomes, egg development, and early life history, while studies on their genetic diversity or genetic structure are lacking. We investigated these aspects in this study using mitochondrial DNA data. Haplotypes were divided into the Hangang River, Nakdonggang River, Geumgang River, and southwest region water system populations. A translocated population, the Yangyang Namdaechun Stream, was confirmed to have originated from the Hangang River water system population based on haplotype distribution and genetic structure results. The FST of the mitochondrial DNA indicated distinct genetic differentiation in the Hangang, Nakdonggang, Geumgang, and southwest regions. According to COI and analyses, the analysis of molecular variance revealed a higher variance in the four water system groups (98.41%) than in the southwest region water system versus the Hangang River water system (80.27%) groups. This study presents basic data for conservation by providing extensive information on the genetic diversity, genetic structure, and translocation population of C. herzi.

Genetic Diversity and Relationship of Shanlan Upland Rice Were Revealed Based on 214 Upland Rice SSR Markers.

Shanlan upland rice (Oryza sativa L.) is a unique upland rice variety cultivated by the Li nationality for a long time, which has good drought resistance and high utilization value in drought resistance breeding. To explore the origin of Shanlan upland rice and its genetic relationship with upland rice from other geographical sources, 214 upland rice cultivars from Southeast Asia and five provinces (regions) in southern China were used to study genetic diversity by using SSR markers. Twelve SSR primers were screened and 164 alleles (Na) were detected, with the minimum number of alleles being 8 and the maximum number of alleles being 23, with an average of 13.667. The analysis of genetic diversity and analysis of molecular variance (AMOVA) showed that the differences among the materials mainly came from the individuals of upland rice. The results of gene flow and genetic differentiation revealed the relationship between the upland rice populations, and Hainan Shanlan upland rice presumably originated from upland rice in Guangdong province, and some of them were genetically differentiated from Hunan upland rice. It can be indirectly proved that the Li nationality in Hainan is a descendant of the ancient Baiyue ethnic group, which provides circumstantial evidence for the migration history of the Li nationality in Hainan, and also provides basic data for the advanced protection of Shanlan upland rice, and the innovative utilization of germplasm resources.

Molecular insight into genetic differentiation, population structure and banding pattern analysis of Bambara groundnut (Vigna subterranea [L.] Verdc.) linked with inter simple sequence repeats (ISSR).

A set of 44 selected Bambara groundnut (Vigna subterranea [L.] Verdc.) accessions was sampled from 11 distinct populations of four geographical zones to assess the genetic drift, population structure, phylogenetic relationship, and genetic differentiation linked with ISSR primers. The amplification of genomic DNA with 32 ISSR markers detected an average of 97.64% polymorphism while 35.15% and 51.08% polymorphism per population and geographical zone, respectively. Analysis of molecular variance revealed significant variation within population 75% and between population 25% whereas within region 84% and between region 16%. The Bidillali exposed greater number of locally common band i.e., NLCB (≤ 25%) = 25 and NLCB (≤ 50%) = 115 were shown by Cancaraki while the lowest was recorded as NLCB (≤ 25%) = 6 and NLCB (≤ 50%) = 72 for Roko and Maibergo, accordingly. The highest PhiPT value was noted between Roko and Katawa (0.405*) whereas Nei's genetic distance was maximum between Roko and Karu (0.124). Based on Nei's genetic distance, a radial phylogenetic tree was constructed that assembled the entire accessions into 3 major clusters for further confirmation unrooted NJ vs NNet split tree analysis based on uncorrected P distance exposed the similar result. Principal coordinate analysis showed variation as PC1 (15.04%) > PC2 (5.81%). The current study leads to prompting the genetic improvement and future breeding program by maximum utilization and better conservation of existing accessions. The accessions under Cancaraki and Jatau are population documented for future breeding program due to their higher genetic divergence and homozygosity.

Population genetic structure of Dermatophagoides farinae (Acari: Pyroglyphidae) from different geographic populations based on mitochondrial cytochrome b gene

Dermatophagoides farinae (Acari: Pyroglyphidae) has been regarded as an important source of indoor allergens due to its prevalence and close proximity to humans. This study serves as an introductory probe into the population genetic structure of D. farinae, for which a few related studies of population genetic structure are available. In this study, the genetic structure of seven D. farinae populations in China was investigated based on the 372 bp mitochondrial cytochrome b (cytb) gene. A total of 29 haplotypes of the 68 cytb gene sequences were detected. The network diagram could be divided into Branch I (regions north of the Yangtze River: SJZ, CZ, FY and HN) and Branch II (regions south of the Yangtze River: AQ, WX and WH). Analysis of molecular variance (AMOVA) conducted according to the results of the network diagram revealed major genetic differentiation among groups, indicating that a significant genetic structure existed among groups. The results of population genetic structure could be largely attributed to geographical isolation. The existence of gene flow in a few populations may be influenced by grain trade activities. This study may facilitate a better understanding of the population genetic structure of D. farinae and could be utilized as the foundation for the development of efficient management strategies for D. farinae.

Analysis of the Conservation Status, Genetic Diversity and Population Structure of Endangered Ostrya rehderiana Resources Using SSR Markers

Climate change and anthropogenic habitat destruction have led to the extinction of many species. Ostrya rehderiana (Betulaceae) is a typical rare and endangered species, and only five wild individuals have survived. In the 1980s, the offspring of the five wild trees were planted for ex situ conservation and have grown into stable cultivated populations. To protect O. rehderiana resources, the genetic diversity and genetic structure of this species were analysed using SSR markers. A total of 167 alleles were detected among 116 individuals from the only wild population and five cultivated populations at 12 SSR loci. The genetic diversity level of O. rehderiana was He = 0.88. Genetic differentiations occurred among populations (Fst = 0.17), which was also validated via an analysis of molecular variance (AMOVA). The cultivated populations TM1, TM2 and WC showed considerable genetic differences from the wild population WP based on Bayesian clustering analysis, phylogenetic tree reconstruction and principal coordinate analysis (PCoA). The cultivated populations had more genetic diversity than the wild one. It is speculated that novel alleles may have emerged out of natural processes of evolution and adaptation. The cultivated population QY with the most unique alleles has begun to propagate seedlings naturally, and the small population size and geographical isolation may negatively influence the founding of this population. To weaken the effects of bottlenecks and genetic drift, anthropogenic gene flow among populations is necessary. In addition to the wild population, the cultivated population QY and six individuals from populations QY and WC were also found to be important for the conservation of O. rehderiana. The results of this study may guide the development of conservation policies for endangered O. rehderiana.

Genetic diversity in Sickleweed (Falcaria vulgaris) and using stepwise regression to identify marker associated with traits

One of the well-known medicinal plants in the Falcaria genus is Sickleweed. Falcaria species exhibit a high degree of genetic variability, posing challenges in the examination of genetic diversity due to the significant potential for hybridization and introgression among them. Utilizing morphological traits and molecular markers may prove to be a valuable approach in evaluating and harnessing germplasm, considering the current obstacles faced in breeding this medicinal herb. In 2021, fifteen Sickleweed populations were cultivated in pots under field conditions, employing a randomized complete block design with three replications. This aimed to assess genetic diversity and conduct marker-trait association analyses utilizing morpho-physiological characteristics and SSR markers. The Sickleweed populations displayed considerable genetic diversity across all traits. Through cluster analysis of traits and the utilization of the UPGMA method based on the Gower distance matrix, the population was classified into three distinct clusters. Upon examining all genotypes, 52 polymorphic bands were detected, with an average of 8.68 bands per primer. The average expected heterozygosity across all loci was 0.864, while the average PIC was 0.855. Molecular data analysis employing the Jaccard similarity index and UPGMA method revealed the division of Sickleweed populations into two major groups. Furthermore, the results of molecular variance analysis indicated that variation within the population exceeded that between populations. Thirty-two SSR fragments were found to be significantly associated with genomic regions controlling the studied traits, determined through the application of stepwise regression. Selection based on molecular markers offers a rapid method for breeding programs, with the genetic information obtained from these markers playing a crucial role. Therefore, alongside traits, selecting superior genotypes and populations of high value in breeding programs becomes feasible. The findings highlight that certain markers are linked to multiple traits, emphasizing the critical importance of this characteristic in plant breeding for the simultaneous improvement of numerous traits. The study’s insights regarding markers hold potential for application in Sickleweed breeding programs.

Population Structure and Genetic Diversity of Rice (Oryza sativa L.) Germplasm from the Democratic Republic of Congo (DRC) Using DArTseq-Derived Single Nucleotide Polymorphism (SNP)

Understanding the genetic diversity and population structure of rice is crucial for breeding programs, conservation efforts, and the development of sustainable agricultural practices. This study aimed to assess the genetic diversity and population structure of 94 rice (Oryza sativa L.) genotypes from the Democratic Republic of Congo using a set of 8389 high-quality DArTseq-based single nucleotide polymorphism (SNP) markers. The average polymorphic information content (PIC) of the markers was 0.25. About 42.4% of the SNPs had a PIC value between 0.25 and 0.5, which were moderately informative. The ADMIXTURE program was used for structure analysis, which revealed five sub-populations (K = 5), with admixtures. In principal component analysis (PCA), the first three principal components accounted for 36.3% of the total variation. Analysis of molecular variance revealed significant variation between sub-populations (36.09%) and within genotypes (34.04%). The low overall number of migrants (Nm = 0.23) and high fixation index (Fst = 0.52) indicated limited gene flow and significant differentiation between the sub-populations. Observed heterozygosity (Ho = 0.08) was lower than expected heterozygosity (He = 0.14) because of the high inbreeding (Fis = 0.52) nature of rice. A high average Euclidean genetic distance (0.87) revealed the existence of genetic diversity among the 94 genotypes. The significant genetic diversity among the evaluated rice genotypes can be further explored to obtain potentially desirable genes for rice improvement.

Genetic Diversity of Cowpea Parental Lines Assembled for Breeding in Uganda

Cowpea is a grain legume that is commonly grown in Sub-Saharan Africa (SSA) for a variety of uses including food, feed, and soil fertility enhancement through nitrogen fixation. Genetic improvement in cowpea can be accomplished by creating breeding populations from high-performing but genetically diverse parental lines. The goal of this study was to use single nucleotide polymorphic markers (SNPs) to estimate genetic diversity and population stratification among cowpea parental genotypes from five countries. A total of 2,746 SNP markers were used to analyze 62 cowpea genotypes that differed in key characteristics. Only 55% of the SNP markers were polymorphic across the 62 genotypes and met the selection requirement. The gene diversity varied from 0.52 to 0.57 with an average of 0.55, while the polymorphic information content ranged from 0.46 to 0.51 with an average of 0.49, showing that the cowpea parental lines are genetically diverse. The analysis of molecular variance (AMOVA) found high significant (p < 0.001) variation among genotypes and non-significant variation across genotypes depending on country of origin. The cluster analysis for the 62 genotypes using the unweighted pair group procedure with arithmetic mean approach divided the genotypes into two distinct groups. Genotypes from the same geographical regions tended to cluster together and there was a significant level of genetic variation among genotypes from Uganda and Nigeria. The SNP markers utilized in this study were effective at distinguishing genotypes and may be used to estimate the diversity in the cowpea core collection. The genetic diversity in this collection is important for future development of improved varieties of cowpea in Uganda.

Genetic diversity analysis and potential suitable habitat of Chuanminshen violaceum for climate change

To provide a scientific basis for the sustainable development of C. violaceum, we correctly identified the different germplasm resources and obtained excellent germplasm resources. In this study, MaxEnt was used to predict the distribution range of C. violaceum in China under current and future climate scenarios and explain the impact of environmental variables on its distribution. An SRAP (sequence-related amplified polymorphism) molecular marker was used to analyse the genetic diversity of the plant. The results showed the areas of the total, most, moderately and poorly suitable habitats of C. violaceum were 69.93 × 104 km2, 7.77 × 104 km2, 12.68 × 104 km2 and 49.49 × 104 km2, respectively. The most suitable habitat was concentrated in central and eastern Sichuan, and scattered in Chongqing and Hubei. Under SS1–2.6, SSP2–4.5 and SSP5–8.5 scenarios in 2050s and 2090s, the area of the most suitable habitat would decrease by 25.13%–34.88%. The centroid of the most suitable habitat would move to the west by 45.44 km (SSP1–2.6), 42.15 km (SSP2–4.5) and 37.72 km (SSP5–8.5) in the future. Annual precipitation (bio12), minimum temperature of the coldest month (bio6), precipitation of coldest quarter (bio19), temperature annual range (bio7), elevation (El) and mean UV-B of highest month (UV-B3) were identified as the dominant environmental variables related to the distribution of C. violaceum. A total of 374 bands were amplified by 37 primer pairs, of which 283 bands were polymorphic, and the polymorphic percentage was 75.67%. The analysis of molecular variance showed higher percentages of genetic variation within the population. All the accessions could be distinguished by SRAP markers. The cluster analysis results showed that 63 accessions were classified into 7 groups, which were correlated with the geographical distribution of the accessions to some degree. The accessions from Langzhong and Qingbaijiang had higher diversity. These results suggest that strategic transplantation of C. violaceum from particular geographic locations could help make the species more resilient to climate change and slow the contraction of the species' distribution.

Evaluation of the Genetic Diversity of Greek Garlic (Allium sativum L.) Accessions Using DNA Markers and Association with Phenotypic and Chemical Variation

The genetic diversity of 27 garlic accessions (local varieties/landraces) was investigated using five simple sequence repeat (SSR) and six inter-simple sequence repeat (ISSR) markers. The SSR genotyping revealed 26 different alleles, while 84 polymorphic bands were produced using the ISSR markers. The average polymorphism information content (PIC) was 0.471 and 0.465 for the SSR and the ISSR markers, respectively. Compared to ISSRs, SSR markers revealed a higher level of redundancy, indicating potential duplicates among the accessions. The analysis of molecular variance (AMOVA) based on both marker systems showed that most of the molecular diversity was attributable to differences within accessions, rather than among them. UPGMA, STRUCTURE, and Principal Coordinate Analysis (PCoA) based on the SSRs produced similar clustering results, although not in agreement with those produced by the ISSR markers. Fisher’s exact tests and multinomial logistic regression analyses identified significant associations between the chemical compounds, the morphological traits of the bulb, and specific SSR and ISSR loci. Our results provide a molecular basis for understanding the genetic diversity of Greek garlic landraces, which could be useful for the conservation and sustainable management of this crop. Potential markers fostering the selection of genotypes in garlic breeding have also been revealed.

Replicative Study in Performance-Related Genes of Brazilian Elite Soccer Players Highlights Genetic Differences from African Ancestry and Similarities between Professional and U20 Youth Athletes.

Classically, genetic association studies have attempted to assess genetic polymorphisms related to human physiology and physical performance. However, the heterogeneity of some findings drives the research to replicate, validate, and confirmation as essential aspects for ensuring their applicability in sports sciences. Genetic distance matrix and molecular variance analyses may offer an alternative approach to comparing athletes' genomes with those from public databases. Thus, we performed a complete sequencing of 44 genomes from male Brazilian first-division soccer players under 20 years of age (U20_BFDSC). The performance-related SNP genotypes were obtained from players and from the "1000 Genomes" database (European, African, American, East Asian, and South Asian). Surprisingly, U20_BFDSC performance-related genotypes had significantly larger FST levels (p < 0.00001) than African populations, although studies using ancestry markers have shown an important similarity between Brazilian and African populations (12-24%). U20_BFDSC were genetically similar to professional athletes, showing the intense genetic selection pressure likely to occur before this maturation stage. Our study highlighted that performance-related genes might undergo selective pressure due to physical performance and environmental, cognitive, and sociocultural factors. This replicative study suggests that molecular variance and Wright's statistics can yield novel conclusions in exercise science.

Genetic diversity and population structure of Capitulum mitella (Linnaeus, 1767) in Fujian (China) revealed by mtDNA COI sequences.

Background: Capitulum mitella is a widely distributed and ecologically important stalked barnacle that settles extensively on rocky shores. This species contributes to the structural complexity of intertidal habitats and plays a critical role in the marine ecosystem. This study aimed to reveal the genetic diversity and population structure of C. mitella by analyzing the mitochondrial cytochrome oxidase I (COI) gene. Methods: A 683bp fragment of the COI gene was sequenced from 390 individuals sampled from six localities in Fujian, China. Results: A total of 84 distinct haplotypes were identified through the analysis of 82 polymorphic sites, resulting in an average haplotype diversity (h) of 0.660 and nucleotide diversity (π) of 0.00182. Analysis of molecular variance (AMOVA) and pairwise F ST statistics showed no significant population structure. Neutrality tests and mismatch distributions provided evidence of recent population expansion for the species. Conclusions: We suggest that the species' high dispersal ability, and ocean currents coupled with limited physical barriers in the region, contribute to its current phylogeographic structure. These findings enhance our comprehension of the genetic diversity and population structure of C. mitella, providing valuable insights for future conservation efforts.

Conservation Genetics of Clinch Dace Chrosomus sp. cf. saylori

Clinch Dace (Chrosomus sp. cf. saylori) is a newly recognized and yet-undescribed species of minnow with a restricted and fragmented distribution in the upper Tennessee River basin in southwestern Virginia, USA. We collected Clinch Dace from seven streams and observed variations at nine selectively neutral microsatellite DNA loci to infer population genetic processes and identify units for conservation management. Bayesian cluster analysis showed that three of the seven surveyed populations were genetically distinct, while the other four populations showed signs of recent admixture. Estimated effective population sizes and m-ratios were low within most populations, suggesting loss of alleles due to recent genetic drift. Positive FIS values, high average individual inbreeding coefficients, and high degrees of inferred relatedness among individuals suggested that inbreeding is taking place in some populations. FST values were high, and analysis of molecular variance indicated genetic divergence among populations. These indicators suggest that Clinch Dace populations are subject to the genetic processes that are characteristic of small and isolated populations.

Phylogeography of the Asian green mussel, Perna viridis: pronounced regional genetic differentiation is explained by major freshwater input into the Bay of Bengal

The Asian green mussel (AGM), Perna viridis, is a mussel of ecological and economic importance throughout much of the tropical and subtropical regions of Asia, from China and Korea in the east to Oman on the Arabian Peninsula in the west. We collated published DNA sequence data and then analysed 467 bp of cytochrome c oxidase I gene (COI) sequence variation from 649 mussels (576 from SE Asia and 73 from India) to test for regional differentiation. Analysis of molecular variation, a haplotype network and a neighbour-joining tree all revealed significant differentiation between mussels from India and those from SE Asia. We observed a greater number of segregating sites (haplotypes) and private haplotypes than expected for Indian mussels compared to SE Asian mussels, based on the respective sample sizes. Tests of neutrality revealed population expansion or a recent selective sweep for only the mussels from India. We suggest that the differentiation of the Indian from the SE Asian mussels is explained by the pronounced seasonal input of freshwater into the northern Bay of Bengal area, which acts as a (semi-permeable) barrier to gene flow between the two regions (i.e., east versus west of the Bay). This suggestion is based on the oceanography of the region and is consistent with the biogeography and reports of genetic breaks in a range of taxa in this region. Further targetted sampling of AGMs from the east coast of India, Bangladesh and Myanmar is required to test this hypothesis, and additional sampling of AGMs from west of India (e.g., Pakistan, Iran, the Arabian Peninsula) will also be informative. Finally, this study is based on the analysis of a single marker (COI) because this is all that is presently available from published sources but we note that the application of new molecular markers such as single nucleotide polymorphisms to newly collected mussel samples will greatly advance our understanding of the AGM genetic discontinuity and its age, and help test its geographical location and its nature (e.g., a steep/shallow cline or a stepped cline).

Comparative analysis of nine Tilletia indica genomes for the development of novel microsatellite markers for genetic diversity and population structure analysis.

Karnal bunt (KB; Tilletia indica) is the prime quarantine concern for quality wheat production throughout the world. The most effective approach to dealing with this biotic stress is to breed KB-resistant wheat varieties, which warrants a better understanding of T. indica genome architecture. In India, the North Western Plain Zone is the prime hot spot for KB disease, but only limited efforts have been made to decipher T. indica diversity at the genomic level. Microsatellites offer a powerful and robust typing system for the characterization and genetic diversity assessment of plant pathogens. At present, inadequate information is available with respect to the development of genome-derived markers for revealing genetic variability in T. indica populations. In current research, nine complete genome sequences of T. indica (PSWKBGH_1, PSWKBGH_2, PSWKBGD_1_3, RAKB_UP_1, TiK_1, Tik, DAOMC236408, DAOMC236414, and DAOMC236416) that exist in the public domain were explored to know the dynamic distribution of microsatellites. Comparative genome analysis revealed a high level of relative abundance and relative density of microsatellites in the PSWKBGH_1 genome in contrast to other genomes. No significant correlation between microsatellite distribution for GC content and genome size was established. All the genomes showed the dominance of tri-nucleotide motifs, followed by mono-, di-, tetra-, hexa-, and penta-nucleotide motifs. Out of 50 tested markers, 36 showed successful amplification in T. indica isolates and produced 52 different alleles. A PCR assay along with analysis of the polymorphic information content (PIC) revealed 10 markers as neutral and polymorphic loci (PIC 0.37). The identified polymorphic SSR loci grouped a geographically distinct T. indica population of 50 isolates representing seven Indian regions (Jammu, Himachal Pradesh, Punjab, Haryana, Uttarakhand, Uttar Pradesh, and Rajasthan) into four distinct clusters. The results of the analysis of molecular variance identified 94% genetic variation within the population and 6% among the population. Structure analysis also confirmed the existence of four genetically diverse groups containing admixtures of T. indica isolates across populations. In nutshell, the current study was successful in identifying novel, neutral and polymorphic microsatellite markers that will be valuable in offering deep insight into the evolutionary relationship and dynamics of the T. indica population for devising effective KB management strategies in wheat.

The population genetic structure and phylogeographic dispersal of Nodularia breviconcha in the Korean Peninsula based on COI and 16S rRNA genes.

A freshwater mussel, Nodularia breviconcha (Mollusca: Bivalvia: Unionida) is endemic to Korean Peninsula. It has recently been taxonomically reexamined and elevated from a subspecies of N. douglasiae to an independent species. But population genetic studies for the species have rarely been conducted. To explore the population genetic structure of N. breviconcha, the nucleotide sequences of cytochrome oxidase subunit I(COI) and 16S rRNA genes from 135 N. breviconcha individuals, including 52 from this study and 83 from Choi et al. (2020). We found 23 COI and 11 16S rRNA genes haplotypes. Phylogeny, TCS network, Principal coordinates analysis, and spatial analysis of molecular variance performed with COI gene indicated that there are exist three different genetic lineages in the N. breviconcha populations: West lineage, Southwest lineage, and Southeast lineage. According to the time calibrated phylogeny, they are likely to be diverged during the late Miocene (8-6 Ma). Geographical distribution patterns of the three genetic lineages may be related to the formation of Taebaek and Sobaek-Noryeong mountain ranges in the Korean Peninsula occurred during the Miocene (30-10 Ma). The present results of this study will be helpful not only for the conservation, but also for the exploration of the population genetic structure of endemic freshwater mussels in the Korean Peninsula.

Genetic diversity and conservation of Siberian apricot (Prunus sibirica L.) based on microsatellite markers

Siberian apricot (Prunus sibirica L.) is a woody tree species of ecological, economic, and social importance. To evaluate the genetic diversity, differentiation, and structure of P. sibirica, we analyzed 176 individuals from 10 natural populations using 14 microsatellite markers. These markers generated 194 alleles in total. The mean number of alleles (13.8571) was higher than the mean number of effective alleles (6.4822). The average expected heterozygosity (0.8292) was higher than the average observed heterozygosity (0.3178). Shannon information index and polymorphism information content were separately 2.0610 and 0.8093, demonstrating the rich genetic diversity of P. sibirica. Analysis of molecular variance revealed that 85% of the genetic variation occurred within populations, with only 15% among them. The genetic differentiation coefficient and gene flow were separately 0.151 and 1.401, indicating a high degree of genetic differentiation. Clustering results showed that a genetic distance coefficient of 0.6 divided the 10 natural populations into two subgroups (subgroups A and B). STRUCTURE and principal coordinate analysis divided the 176 individuals into two subgroups (clusters 1 and 2). Mantel tests revealed that genetic distance was correlated with geographical distance and elevation differences. These findings can contribute to the effective conservation and management of P. sibirica resources.

Evidence of population expansion and insecticide resistance mechanism in invasive fall armyworm (Spodoptera frugiperda)

BackgroundThe invasive and calamitous polyphagous pest Spodoptera frugiperda or commonly known as fall armyworm (FAW) poses serious menace to the global agricultural production. Owing to the revamped invasion of FAW in 2018 in India, present study was undertaken for precise assessment of its genetic identity and pesticide resistance to aid in pest-management strategies.ResultsTo evaluate the diversity in FAW population across Eastern India, mitochondrial COI sequences were used which revealed a low nucleotide diversity. Analysis of molecular variance indicated significant genetic variation between four global geographical FAW populations with lowest differentiation between India and Africa suggesting a present-day and shared origin of FAW. The study demonstrated existence of two different strains (‘R’ strain and ‘C’ strain) based on COI gene marker. However, discrepancies between COI marker and host plant association of FAW was observed. Characterization of Tpi gene revealed abundance of TpiCa1a followed by TpiCa2b and TpiR1a strains respectively. The FAW population showed higher susceptibility towards chlorantraniliprole and spinetoram than cypermethrin. Insecticide resistance genes depicted marked upregulation although with lot of variance. Chlorantraniliprole resistance ratio (RR) exhibited significant correlation with 1950 (Glutathione S-transferase, GST), 9131 (Cytochrome P450, CYP) and 9360 (CYP) genes, while spinetoram and cypermethrin RR was found to correlate with 1950 (GST) and 9360 (CYP) genes.ConclusionThis study manifests Indian subcontinent as the potential new hotspot for the growth and distribution of FAW population that can be effectively controlled using chlorantraniliprole and spinetoram. This study also adds novel significant information on FAW population across Eastern India for developing a comprehensive pest management approach for S. frugiperda.