Neighbor-joining Cluster Analysis Research Articles

Genetic diversity investigation of some Darjeeling Himalayan Rhododendron species based on RAPD method

Ten rare, threatened, and endangered Rhododendron species were collected from different places of altitudinal ranges starting from 2,247 to 3,580 masl. Of Darjeeling Hill. The random amplified polymorphic DNA (RAPD) method was used to measure the degree of the Genetic variation and the interconnection within the species. Out of 19, 6 oligonucleotide primers were chosen based on their performance, for the study. Genetic Similarity Coefficient ranged from 0.45455 to 0.93827 with an average of 79.43% polymorphism. This present study shows a low average level of genetic diversity [Ho = 0.986, Hs = 0.979, Ht = 0.985, I = 3.973, polymorphic information content = 0.2096] in the population of Rhododendron. As well as, a negative value of inbreeding coefficients. The mean inbreeding coefficient (Fst) within subpopulations is 0.006. A RAPD-based dendrogram constructed from Jaccard’s estimates in Free Tree, through the use of neighbor-joining cluster analysis, divided nine (out of ten) Rhododendron species into two main sister groups. The study found that Rhododendron species are at risk of out-crossing depression and require conservation.

Assessing population genetic structure and diversity and their driving factors in Phoebe zhennan populations

BackgroundPhoebe zhennan, commonly known as “golden-thread nanmu,” is one of the most valuable and protected tree species in China. An accurate understanding of the population genetic structure and its environmental factors is of significance for the protection and selection of new P. zhennan varieties.ResultsSixteen nSSR and six cpSSR markers were used to determine the genetic diversity and population structure of P. zhennan and the effect of environmental factors on the genetic structure. The nSSR markers identified a total of 451 number of alleles (Na), while cpSSR markers detected 20 Na. A relative high level of genetic diversity was observed in the P. zhennan population evidenced by high Shannon’s information index (I) of 0.671 and 2.294 based on cpSSR and nSSR datasets. The low value of fixation index (F) observed from the nSSR dataset indicated low breeding within the population. The genetic differentiation was mainly detected within populations (only 28% and 13% of the variance being between populations according to the nSSR and cpSSR datasets). Among them, the HNSZX (H = 0.469) and SCSZZ (I = 1.943) populations exhibited the highest level of genetic diversity, while the HNXXT (H = 0.041) and SCLJS (I = 0.943) populations exhibited the lowest level of genetic diversity. The average genetic differentiation coefficient (Fst) and gene flow (Nm) were 0.022–0.128 and 1.698–11.373, respectively, which indicated a moderate level of genetic differentiation and a high level of gene flow. STRUCTURE, neighbor-joining clustering, and principal coordinate analysis divided 543 individuals into two or three categories based on the nSSR or cpSSR datasets. Four temperature, three precipitation, five chemical, five physical, and one soil texture variable showed significant effects on the genetic structure and distribution of P. zhennan populations. Compared to nSSR, the genetic differentiation among populations based on cpSSR datasets conformed to the geographic isolation model, suggesting that geographic and genetic distances should be considered for further genetic conservation and breeding utilization. The importance of in situ conservation units, such as populations with a high level of genetic diversity, more private alleles, and haplotypes (e.g., population SCGTS, SCYFS, and YNYJX), should be emphasized. Additionally, breeding, along with artificially assisted population regeneration and restoration, should also be carefully planned, taking into account climate and soil properties at the same time.ConclusionsIn conclusion, this study provided genetic background information for the genetic conservation, management, and utilization of P. zhennan.

SeqSNP-Based Targeted GBS Provides Insight into the Genetic Relationships among Global Collections of Brassica rapa ssp. oleifera (Turnip Rape).

Turnip rape is a multi-purpose crop cultivated in temperate regions. Due to its ability to fit into crop rotation systems and its role as a food and feed source, spring-type turnip rape cultivation is on the rise. To improve the crop's productivity and nutritional value, it is essential to understand its genetic diversity. In this study, 188 spring-type accessions were genotyped using SeqSNP, a targeted genotyping-by-sequencing method to determine genetic relationships between various groups and assess the potential effects of mutations within genes regulating major desirable traits. Single nucleotide polymorphism (SNP) alleles at six loci were predicted to have high effects on their corresponding genes' functions, whereas nine loci had country/region-specific alleles. A neighbor-joining cluster analysis revealed three major clusters (I to III). About 72% of cluster-I accessions were of Asian origin, whereas 88.5% of European accessions and all North American accessions were placed in cluster-II or cluster-III. A principal coordinate analysis explained 65.3% of the total genetic variation. An analysis of molecular variance revealed significant differentiation among different groups of accessions. Compared to Asian cultivars, European and North American cultivars share more genetic similarities. Hence, crossbreeding Asian and European cultivars may result in improved cultivars due to desirable allele recombination. Compared to landraces and wild populations, the cultivars had more genetic variation, indicating that breeding had not caused genetic erosion. There were no significant differences between Swedish turnip rape cultivars and the NordGen collection. Hence, crossbreeding with genetically distinct cultivars could enhance the gene pool's genetic diversity and facilitate superior cultivar development.

SSR-BASED ASSESSMENT OF GENETIC DIVERSITY IN TOMATO CULTIVARS AND LINES GROWN IN KAZAKHSTAN

Tomato (Solanum lycopersicum L.) is a versatile crop known for its nutritional value and health benefits, thriving in diverse climates worldwide. Nevertheless, regional variations persist in tomato yield, with Kazakhstan serving as an example of lower productivity in contrast to global averages. Closing this disparity requires comprehensive genetic studies and breeding efforts. This study is focused on the genetic diversity of 49 tomato cultivars and hybrids sourced from Kazakh Research Institute of Fruit and Vegetable Growing (Almaty), employing 10 SSR markers associated with important agronomic traits. SSR genotyping unveiled polymorphisms across 6 markers with variable allele numbers. Genetic diversity metrics highlighted significant genetic diversity within both outdoor and greenhouse tomato cultivars and lines. Bayesian clustering, Neighbor-joining (NJ) clustering, and principal coordinate analysis (PCoA) delineated genetic differentiation between outdoor and greenhouse tomatoes with small admixture, indicating distinct breeding directions for these two types. Highly polymorphic SSRs (PIC > 0.5) associated with essential fruit traits emerge as promising targets for marker-assisted selection (MAS) that can be used to enhance tomato breeding efficiency in Kazakhstan. According to 8 SSRs, 22 out of 30 outdoor accessions and 8 greenhouse tomato accessions were genetically uniform. This study offers comprehensive insights into the genetic diversity and population structure of tomato cultivars and lines in Kazakhstan, laying the foundation for informed breeding endeavors aimed at bolstering yield and resilience in tomato crops.

Genetic diversity and population structure analysis of a diverse panel of pea (Pisum sativum).

Breeding resilient cultivars with increased tolerance to environmental stress and enhanced resistance to pests and diseases demands pre-breeding efforts that include understanding genetic diversity. This study aimed to evaluate the genetic diversity and population structure of 265 pea accessions. The diversity arrays technology (DArT) genotyping method was employed to identify single-nucleotide polymorphisms (SNPs) and silico markers. After stringent filtering, 6966 SNP and 8,454 silico markers were selected for diversity analysis. Genetic diversity was estimated by grouping accessions based on plant material type, geographic origin, growth habit, and seed color. Generally, diversity estimations obtained using SNPs were similar to those estimated using silico markers. The polymorphism information content (PIC) of the SNP markers ranged from 0.0 to 0.5, with a quarter of them displaying PIC values exceeding 0.4, making them highly informative. Analysis based on plant material type revealed narrow observed heterozygosity (Ho = 0.02-0.03) and expected heterozygosity (He = 0.26-0.31), with landrace accessions exhibiting the highest diversity. Geographic origin-based diversity analysis revealed Ho = 0.02-0.03 and He = 0.22 to 0.30, with European accessions showing the greatest diversity. Moreover, private alleles unique to landrace (4) and European (22) accessions were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance revealed a highly significant genetic differentiation among accession groups classified by seed color, growth habit, plant material types, and geographic origin (p < 0.01). Principal coordinate analysis and neighbor-joining cluster analysis revealed weak clustering of accessions at different grouping levels. This study underscores the significance of genetic diversity in pea collections, offering valuable insights for targeted breeding and conservation efforts. By leveraging genomic data and exploring untapped genetic resources, pea breeding programs can be fortified to ensure sustainable plant protein production and address future challenges in agriculture.

Population genetic variation and geographic distribution of suitable areas of Coptis species in China.

The rhizomes of Coptis plants have been used in traditional Chinese medicine over 2000 years. Due to increasing market demand, the overexploitation of wild populations, habitat degradation and indiscriminate artificial cultivation of Coptis species have severely damaged the native germplasms of species in China. Genome-wide simple-sequence repeat (SSR) markers were developed using the genomic data of C. chinensis. Population genetic diversity and structure of 345 Coptis accessions collected from 32 different populations were performed based on these SSRs. The distribution of suitable areas for three taxa in China was predicted and the effects of environmental variables on genetic diversity in relation to different population distributions were further analyzed. 22 primer pairs were selected as clear, stable, and polymorphic SSR markers. These had an average of 16.41 alleles and an average polymorphism information content (PIC) value of 0.664. In the neighbor-joining (N-J) clustering analysis, the 345 individuals clustered into three groups, with C. chinensis, C. chinensis var. brevisepala and C. teeta being clearly separated. All C. chinensis accessions were further divided into four subgroups in the population structure analysis. The predicted distributions of suitable areas and the environmental variables shaping these distributions varied considerably among the three species. Overall, the amount of solar radiation, precipitation and altitude were the most important environmental variables influencing the distribution and genetic variation of three species. The findings will provide key information to guide the conservation of genetic resources and construction of a core reserve for species.

Novel Alleles from Cicer reticulatum L. for Genetic Improvement of Cultivated Chickpeas Identified through Genome Wide Association Analysis.

The availability of wild chickpea (Cicer reticulatum L.) accessions has the potential to be used for the improvement of important traits in cultivated chickpeas. The main objectives of this study were to evaluate the phenotypic and genetic variations of chickpea progeny derived from interspecific crosses between C. arietinum and C. reticulatum, and to establish the association between single nucleotide polymorphism (SNP) markers and a series of important agronomic traits in chickpea. A total of 486 lines derived from interspecific crosses between C. arietinum (CDC Leader) and 20 accessions of C. reticulatum were evaluated at different locations in Saskatchewan, Canada in 2017 and 2018. Significant variations were observed for seed weight per plant, number of seeds per plant, thousand seed weight, and plant biomass. Path coefficient analysis showed significant positive direct effects of the number of seeds per plant, thousand seed weight, and biomass on the total seed weight. Cluster analysis based on the agronomic traits generated six groups that allowed the identification of potential heterotic groups within the interspecific lines for yield improvement and resistance to ascochyta blight disease. Genotyping of the 381 interspecific lines using a modified genotyping by sequencing (tGBS) generated a total of 14,591 SNPs. Neighbour-joining cluster analysis using the SNP data grouped the lines into 20 clusters. The genome wide association analysis identified 51 SNPs that had significant associations with different traits. Several candidate genes associated with early flowering and yield components were identified. The candidate genes and the significant SNP markers associated with different traits have a potential to aid the trait introgression in the breeding program.

Assessing the genetic integrity of sugarcane germplasm in the USDA-ARS National Plant Germplasm System collection using single-dose SNP markers.

The World Collection of Sugarcane and Related Grasses, maintained at the USDA-ARS in Miami, FL, is one of the largest sugarcane germplasm repositories in the world. However, the genetic integrity of the Saccharum spp. germplasm in this collection has not been fully analyzed. In this study, we employed a single-dose SNP panel to genotype 901 sugarcane accessions, representing six Saccharum species and various hybrids. Our analysis uncovered a high rate of clone mislabeling in the collection. Specifically, we identified 86 groups of duplicates, characterized by identical SNP genotypes, which encompassed 211 accessions (23% of the total clones), while 135 groups, constituting 471 clones (52% of the total), exhibited near-identical genotypes. In addition, twenty-seven homonymous groups were detected, which shared the same clone name but differed in SNP genotypes. Hierarchical analysis of population structure partitioned the Saccharum germplasm into five clusters, corresponding to S. barberi, S. sinense, S. officinarum, S. spontaneum and S. robustum/S. edule. An assignment test, based on the five Saccharum species, enabled correcting 141 instances of mislabeled species memberships and inaccuracies. Moreover, we clarified the species membership and parentage of 298 clones that had ambiguous passport records (e.g., 'Saccharum spp', 'unknown', and 'hybrid'). Population structure and genetic diversity in these five species were further supported by Principal Coordinate Analysis and neighbor-joining clustering analysis. Analysis of Molecular Variance revealed that within-species genetic variations accounted for 85% of the total molecular variance, with the remaining 15% attributed to among-species genetic variations. The single-dose SNP markers developed in this study offer a robust tool for characterizing sugarcane germplasm worldwide. These findings have important implications for sugarcane genebank management, germplasm exchange, and crop genetic improvement.

Morpho-physiological traits and SSR markers-based analysis of relationships and genetic diversity among fodder maize landraces in India.

Maize is an excellent fodder crop due to its high biomass, better palatability, succulency, and nutrition. Studies on morpho-physiological and biochemical characterization of fodder maize are limited. The present study aimed to explore the genetic variation in fodder maize landraces for various morpho-physiological traits and estimation of genetic relationship and population structure. The study on 47 fodder maize landraces revealed significant variation for all morpho-physiological traits except leaf-stem ratio. Plant height, stem girth, leaf-width and number of leaves showed positive correlation with green fodder yield. Morpho-physiological traits-based clustering grouped the landraces into three major clusters, whereas neighbour joining cluster and population structure analysis using 40 SSR markers revealed four and five major groups, respectively. Most landraces of Northern Himalaya-Kashmir and Ludhiana fall into a single group, whereas rest groups mainly had landraces from North-Eastern Himalaya. A total of 101 alleles were generated with mean polymorphic information content value of 0.36 and major allele frequency of 0.68. The pair wise genetic dissimilarity between genotypes ranged from 0.21 to 0.67. Mantel test revealed weak but significant correlation between morphological and molecular distance. Biochemical characterisation of superior landraces revealed significant variation for neutral detergent fibre, acid detergent fibre, cellulose and lignin content. Interestingly, significant, and positive correlation of SPAD with lignin content can be explored to bypass the costly affair of invitro quality assessment for digestibility parameters. The study identified superior landraces and demonstrated the use of molecular markers in genetic diversity assessment and grouping of genotypes for fodder maize improvement.

Genetic diversity and population genetic structure in Kadsura coccinea (Schisandraceae), an evergreen woody vine from Hunan, China

ABSTRACT Kadsura coccinea is an evergreen woody vine species indigenous to Southeast Asia and south China with great promise in medicine, food, and ornamental gardening. Its natural resources have decreased dramatically due to irrational fruits and roots harvesting in two decades recently, which may result in heavy erosion of its genetic resources, especially in Hunan Province, China. Here 406 individuals of K. coccinea were collected from 11 natural populations in Hunan Province, and were analyzed for genetic variation using 17 polymorphic microsatellite markers. A total of 163 alleles were amplified with a mean of 9.588 alleles per locus. The mean effective number of alleles per locus, allele richness and the expected heterozygosity of these populations were 2.910, 4.171 and 0.558 on average, respectively, indicating a bit low level of genetic diversity. The among-population differentiation (FST) accounted for 13.63% of the total genetic variation, and analysis of molecular variance also showed 13.38% of genetic variation existed among populations, representing a high genetic differentiation and a bit limited gene flow (Nm = 1.813) among these populations. The results of Bayesian clustering analysis and neighbor-joining clustering analysis showed that populations GD and YZ were specific, and CB and HT were assigned into a cluster. The mantel test demonstrated that the genetic distances revealed by pairwise FST between populations were remarkably correlated to geographic distances. It is the first report on genetic diversity of species in genus Kadsura using molecular markers, and the findings provide fundamental base for genetic resources conservation and breeding of this species.

Assessment of genetic diversity and population structure of Indian common bean accessions using microsatellite markers

AbstractCommon bean (Phaseolus vulgaris L.) is an important crop of family Fabaceae used as a potential source of proteins, fibres and minerals. Thus, characterization of existing germplasm is useful for improvement and conservation. The Indian Himalayan Region harbours plentiful varieties of common bean, but it is nearly unexplored till date. In the present study, physical and genetic diversity of common bean was examined. Fifteen newly designed chloroplast microsatellite (cpSSR) markers were used to assess genetic diversity and population structure in 119 common bean individuals from 20 diverse accessions gathered from Uttarakhand, India. Significantly, positive (p&lt; 0.05) relationship of seed weight was found with seed length (r = 0.813), seed width (r = 0.692) and seed length- width ratio (r = 0.694) using Pearson correlation analysis. A total of 20 alleles were identified using eight cpSSR markers. Mean number of alleles per locus (Na = 1.55), effective allele number (Ne = 1.370), expected heterozygosity (He = 0.213), average polymorphic loci (10.9) and Shannon information index (I = 0.313) were estimated based on cpSSR data. Maximum genetic diversity (He) was recorded in the AKJ/KK/DP/Jhalla/23 accession and minimum in the AKJ/YB/PS/Supi/43 accession. Bayesian-based STRUCTURE evaluation using cpSSR-based information partitioned 20 accessions into two distinct clusters which were also supported by neighbor-joining cluster analysis. These cpSSR markers also demonstrated transferability among other members like Vigna radiata, Macrotyloma uniflorum, Glycine max, Vigna mungo of Fabaceae family, therefore can be used to monitor their genetic heterogeneity. The findings from the study might be valuable to identify elite common bean accessions for production, conservation and future breeding programmes.

Genetic Relationships of 118 Castanea Specific Germplasms and Construction of Their Molecular ID Based on Morphological Characteristics and SSR Markers

To understand the genetic relationships of Castanea species, 16 phenotypic traits were measured, simple sequence repeat (SSR) markers were analyzed, and molecular identity cards (IDs) were constructed for 118 Castanea materials using fluorescent capillary electrophoresis. The coefficient of variation values of the 16 morphological traits of the test materials ranged from 11.11% to 60.38%. A total of 58 alleles were detected using six pairs of SSR core primers, with an average number of 9.7 alleles per locus. The average number of valid alleles per locus was 3.9419 and the proportion of valid alleles was 40.78%. A total of 105 genotypes were detected, and the number of genotypic species that could be amplified per primer pair ranged from 8 to 26. The mean value of the observed heterozygosity was 0.4986. The variation in the He, H, and PIC values was similar; the size of I value was approximately 2.21 times larger, and its mean number of variations was 0.7390, 0.7359, 0.6985, and 1.6015, respectively. The classification of 118 Castanea species was performed using three analytical methods: structure analysis, neighbor-joining (NJ) cluster analysis, and principal coordinate analysis (PCoA), and the results of the three methods were in high agreement. Six pairs of SSR core primers with high polymorphism and strong discriminatory properties were used to identify 118 Castanea plants, and a unique molecular ID card was constructed for each material. These results provide insight into the genetic diversity and population structure of Castanea plants and a theoretical basis for improving the phenomenon of mixed varieties and substandard plants in the Castanea plant market.

High genetic diversity in an endemic and vulnerable species: evidence from Astragalus cyclophyllon (Fabaceae) in Iran

The genus Astragalus L. with about 3000 species is the largest genus of flowering plants. It is also the largest genus in the flora of Iran with more than 850 taxa. Astragalus cyclophyllon Beck is an endemic taxon belonging to Astragalus sect. Incani DC. It occurs scattered in the steppe and semi-steppe areas of the western and central parts of Iran. This species is one of the most important forage taxa of Astragalus. According to IUCN criteria it has been classified as a vulnerable taxon in Iran, as it occurs in habitats intensely used by herders for their livestock. Here we evaluate the genetic diversity of the populations of this species in Iran to see whether genetic diversity is high or if reductions have already happened. For this purpose, sampling was done in all geographical areas with A. cyclophyllon populations in Iran. In total, 80 individuals representing 29 populations were studied using 33 quantitative and qualitative morphological characters and 10 inter-simple sequence repeat (ISSR) primers. ISSR revealed 240 bands which all were polymorphic. Neighbor-joining cluster analysis divided the individuals in four groups, Principal Coordinate Analysis and Bayesian population assignment analysis in Structure resulted in three genetic units. Morphological variation showed no correlation with the molecular data. The mean of Gst and Nm indices are 0.516 and 0.468, respectively, which indicate a very high genetic differentiation and low gene flow between the studied populations. According to these results, we conclude that genetic diversity is high in this species and that, therefore, the major threat for A. cyclophyllon is currently not related to inbreeding depression in populations, but might be due to livestock grazing that could change the population demographic structure by reducing regular establishment of new offspring.

Genetic structure of Spirometra mansoni (Cestoda: Diphyllobothriidae) populations in China revealed by a Target SSR-seq method

BackgroundIn China, the plerocercoid of the cestode Spirometra mansoni is the main causative agent of human and animal sparganosis. However, the population genetic structure of this parasite remains unclear. In this study, we genotyped S. mansoni isolates with the aim to improve current knowledge on the evolution and population diversity of this cestode.MethodsWe first screened 34 perfect simple sequence repeats (SSRs) using all available omic data and then constructed target sequencing technology (Target SSR-seq) based on the Illumina NovaSeq platform. Next, a series of STRUCTURE. clustering, principal component, analysis of molecular variance and TreeMix analyses were performed on 362 worm samples isolated from 12 different hosts in 16 geographical populations of China to identify the genetic structure.ResultsA total of 170 alleles were detected. The whole population could be organized and was found to be derived from the admixture of two ancestral clusters. TreeMix analysis hinted that possible gene flow occurred from Guizhou (GZ) to Sichuan (SC), SC to Jaingxi (JX), SC to Hubei (HB), GZ to Yunnan (YN) and GZ to Jiangsu (JS). Both neighbor-joining clustering and principal coordinate analysis showed that isolates from intermediate hosts tend to cluster together, while parasites from definitive hosts revealed greater genetic differences. Generally, a S. mansoni population was observed to harbor high genetic diversity, moderate genetic differentiation and a little genetic exchange among geographical populations.ConclusionsA Target SSR-seq genotyping method was successfully developed, and an in-depth view of genetic diversity and genetic relationship will have important implications for the prevention and control of sparganosis.Graphical

Real-time PCR assays to detect 10 Shiga toxin subtype (Stx1a, Stx1c, Stx1d, Stx2a, Stx2b, Stx2c, Stx2d, Stx2e, Stx2f, and Stx2g) genes

To develop subtyping methods for Shiga toxin (Stx)1a, Stx1c, Stx1d, Stx2a, Stx2b, Stx2c, Stx2d, Stx2e, Stx2f, and Stx2g genes for epidemiological analyses of Shiga toxin-producing Escherichia coli (STEC), we developed 10 simplex real-time polymerase chain reaction (PCR) assays with reference to 284 valid stx sequences and evaluated their specificity and quantitative accuracy using STEC and non-STEC isolates and recombinant plasmids, respectively. Three stx1 and 5 stx2 subtype genes, except for stx2c and stx2d, were detected with high specificity using STEC isolates. However, some stx2a sequences potentially being close to both Stx2a and Stx2d cluster in neighbor-joining cluster analysis were positive for stx2a and stx2d by real-time PCR. For the stx2c assay, the number of real-time PCR cycles was reduced to avoid unnecessary false-positive results. Based on these considerations, the real-time PCR assays developed here might aid epidemiological investigations of infections or outbreaks caused by STEC harboring any of the stx subtype genes.

NUMERICAL TAXONOMIC STUDY OF SELECTED PLANTS OF ASTERACEAE FAMILY FROM AHMEDABAD DISTRICT, GUJARAT

The article is about the systematic study of 30 species that belongs to 26 genera of Asteraceae family in Ahmedabad District. A total of 52 characters were measured, comprising qualitative and quantitative characters. Characters and character states were determined through examination of both living and herbarium specimens. Numerical taxonomy, also termed as morphometric deals with grouping by numerical methods of taxonomic units into taxa on the basis of their character state. On the basis of UPGMA (Unpaired Group Method off Averaging) clustering, Neighbour joining cluster analysis and a dendrogram was constructed as two clades and other sub clade are recognized. Results obtained from the present study are found congruent with morphological studies showing the significance of numerical analysis for taxonomic relationship in the Asteraceae family

Genetic Variation Among Tropical Maize Inbred Lines from NARS and CGIAR Breeding Programs

The use of molecular markers allows for precise estimates of genetic diversity, which is an important parameter that enables breeders to select parental lines and designing breeding systems. We assessed the level of genetic diversity and population structure in a panel of 151 tropical maize inbred lines using 10,940 SNP (single nucleotide polymorphism) markers generated through the DArTseq genotyping platform. The average gene diversity was 0.39 with expected heterozygosity ranging from 0.00 to 0.84, and a mean of 0.02. Analysis of molecular variance showed that 97% of allelic diversity was attributed to individual inbred lines within the populations while only 3% was distributed among the populations. Both neighbor-joining clustering and STRUCTURE analysis classified the inbred lines into four major groups. The crosses that involve inbred lines from most divergent subgroups are expected to generate maximum heterosis and produce wide variation. The results will be beneficial for breeders to better understand and exploit the genetic diversity available in the set of maize inbred lines we studied.

An initial investigation of dental morphology variation among three southern Naga ethnic groups of Northeast India.

This study examines dental morphology trait prevalence among three southern Naga groups and compares them to 10 ethnic groups from other regions of South Asia to accomplish two objectives: assess the biological relationship of these Tibeto-Burman-speakers to speakers of non-Tibeto-Burman languages in other South Asian regions, and determine which traits distinguish northeast Indians from other South Asians. Dental morphology traits were scored with the Arizona State University Dental Anthropology System. Tooth-trait combinations were evaluated for significant inter-trait correlation and intra-trait correspondence within dental fields. Comparisons were based on simple trait prevalence and with Smith's MMD. Affinities based on the former were accomplished with correspondence analysis and principal components analysis. Affinities based on the latter were undertaken with neighbor-joining cluster analysis and multidimensional scaling. After elimination due to inter-trait correlations and uniform prevalence, biodistances based on the remaining 17 tooth-trait combinations identify significant differences between northeast Indians and other South Asian ethnic groups due to high frequencies of shoveling on the maxillary incisors and Cusp 6 on the mandibular molars coupled with low frequencies of Carabelli's trait and Cusp 5 on UM1 and UM2, respectively. Patterns of biodistances obtained from dental morphology are consilient with those obtained from DNA indicating statistically significant differences between northeast Indians from members of ethnic groups of other regions of South Asia. Researchers should explore the sex-specific patterns. Biodistances should not be limited to "key" teeth within dental fields, for in almost every case traits present on mesial and distal teeth yield non-redundant information.

Genetic diversity and marker trait association for yellow mosaic virus disease ingreen gram, Vigna radiata (L.) Wilczek

Yellow mosaic virus (YMV) disease is known to cause severe damage in green gram in terms of yield loss. As the resistance is often governed by recessive genes, introgression of such resistance faces some difficulty. DNA molecular markers are reported to be effective in this process. However, validation of such markers is important. Here, we have made an attempt to validate DNA markers associated with YMV disease resistance gene from a diverse group of 26 green gram genotypes. A total of 19 molecular markers were used to assess the susceptibility or resistance against YMV disease. Results show that among the amplified 31 alleles, 21 were polymorphic, with a mean of 1.1.0 per locus. The polymorphism information content (PIC) values ranged from 0.32 to 0.80. Only five markers exhibited higher PIC value (&gt;6.0) and were revealed to be polymorphic, suggesting its utility in marker assisted selection for breeding YMV resistant genotypes in greengram. Dice dissimilarity coefficient among the genotypes exhibited a range of 0.07 to 1.0 which show a wide genetic variation among the genotypes for YMV tolerance. Neighbor-joining cluster analysis has grouped 26 green gram genotypes into 4 main clusters which revealed the existence of genetic dissimilarities among the genotypes. The genotypes AUGG 6, VBN (Gg) 2 and CO (Gg) 8 carried the positive alleles for YMV disease resistance and the allele for susceptibility were found in the genotypes AUGG 12, AUGG 15, AUGG 17 and AUGG 19. Single marker analysis indicated that there was correlation between the markers and the disease reaction in the field with exceptions. The findings revealed that the SSR markers CEDG180 and YR4 could be used to screen germplasm in order to discriminate the YMV resistant genotypes from the susceptible genotypes in marker assisted selection.

Genetic Diversity of Juglans mandshurica Populations in Northeast China Based on SSR Markers.

Juglans mandshurica is a native tree species in Northeast China. Due to habitat destruction and human disturbance, its population size has sharply decreased. Currently, information on molecular markers of J. mandshurica is limited and cannot meet the needs of germplasm resource evaluation and molecular marker-assisted breeding of J. mandshurica. Based on transcriptomic data from three tissues (leaves, bark, and fruit pericarp), we developed expressed sequence tag-simple sequence repeats (EST-SSRs) for J. mandshurica, and 15 polymorphic EST-SSR primers were initially selected. The average number of alleles (Na), expected heterozygosity (He), and the polymorphic information content (PIC) at different loci were 18.27, 0.670, and 0.797, respectively. Population genetic diversity analysis revealed that the average Na, He, and Shannon information indices (I) for 15 J. mandshurica populations were 6.993, 0.670, and 1.455, respectively. Among them, population Hunchun exhibited the highest genetic diversity (Na = 7.933, He = 0.723, and I = 1.617), while population Heihe exhibited the lowest genetic diversity (Na = 4.200, He = 0.605, and I = 1.158). STRUCTURE analysis, neighbor-joining method cluster analysis, and principal coordinate analysis showed that the 343 individuals of J. mandshurica from 15 populations were clustered into three categories. Category 1 (green) had 147 individuals from eight populations in Qingyuan, Caohekou, Jian, Ningan, Yongji, Baishishan, Helong, and Maoershan; category 2 (blue) had 81 individuals from three populations in Hulin, Boli, and Sanchazi; and category 3 (red) had 115 individuals from four populations in Heihe, Hunchun, Fangzheng, and Liangshui. Analysis of molecular variance (AMOVA) showed that genetic variations among and within individuals accounted for 16.22% and 21.10% of the total genetic variation, respectively, indicating that genetic variations within populations were greater than genetic variations among populations. The average genetic differentiation coefficient (Fst) and gene flow (Nm) between different populations were 0.109 and 4.063, respectively, implying moderate levels of genetic differentiation and gene flow. Based on the genetic diversity characteristics of different populations, we proposed various genetic conservation strategies for J. mandshurica.