Evaluation Of Genetic Diversity Research Articles

Genetic diversity and genetic structure evaluation of cultivated Chinese wolfberry (Lycium barbarum) based on microsatellite population genetics

A total of 178 Chinese wolfberry individuals from 17 populations were detected by 7 pairs of SSR primers to evaluate genetic diversity and structure, using software GenALEx 6.5,NTSYS,STRUCTURE, the effects of cultivation on genetic diversity and structure were clarified aiming to find the strategies for genetic management and sustainable use. The results showed that the genetic diversity of cultivated Chinese wolfberry was low. The average number of alleles N_A, expected heterozygosity H_E, observed heterozygosity H_O, and Shannon's information index H' was 3.9, 0.443 7, 0.556 6, 0.788 1, respectively. STRUCTURE, UPGMA clustering and PCA test indicated that Chinese wolfberry varieties were severely intermixed but no differentiation among varieties. Mantel test showed no significant correlation between genetic distance and geographic distance. AMOVA analysis showed that genetic variation mainly occurred among individuals within the population(84.58%, P<0.001), and there was almost no genetic differentiation between varieties(3.63%, P<0.001) and between populations(11.79%, P<0.001). The cultivation has caused a significant decline in the genetic diversity of Chinese wolfberry, which may cause inbreeding decline. New germplasm resources should be sought from the wild to improve the existing cultivars. On the other hand, there are obvious homogenization and germplasm intermixing between cultivated varieties and populations. Meanwhile, Chinese wolfberry cultivars should be purified and prevented from flowing into the wild population, in case of causing pollution of the wild germplasm.

Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection

BackgroundThe United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) sorghum core collection contains 3011 accessions randomly selected from 77 countries. Genomic and phenotypic characterization of this core collection is necessary to encourage and facilitate its utilization in breeding programs and to improve conservation efforts. In this study, we examined the genome sequences of 318 accessions belonging to the NPGS Sudan sorghum core set, and characterized their agronomic traits and anthracnose resistance response.ResultsWe identified 183,144 single nucleotide polymorphisms (SNPs) located within or in proximity of 25,124 annotated genes using the genotyping-by-sequencing (GBS) approach. The core collection was genetically highly diverse, with an average pairwise genetic distance of 0.76 among accessions. Population structure and cluster analysis revealed five ancestral populations within the Sudan core set, with moderate to high level of genetic differentiation. In total, 171 accessions (54%) were assigned to one of these populations, which covered 96% of the total genomic variation. Genome scan based on Tajima’s D values revealed two populations under balancing selection. Phenotypic analysis showed differences in agronomic traits among the populations, suggesting that these populations belong to different ecogeographical regions. A total of 55 accessions were resistant to anthracnose; these accessions could represent multiple resistance sources. Genome-wide association study based on fixed and random model Circulating Probability (farmCPU) identified genomic regions associated with plant height, flowering time, panicle length and diameter, and anthracnose resistance response. Integrated analysis of the Sudan core set and sorghum association panel indicated that a large portion of the genetic variation in the Sudan core set might be present in breeding programs but remains unexploited within some clusters of accessions.ConclusionsThe NPGS Sudan core collection comprises genetically and phenotypically diverse germplasm with multiple anthracnose resistance sources. Population genomic analysis could be used to improve screening efforts and identify the most valuable germplasm for breeding programs. The new GBS data set generated in this study represents a novel genomic resource for plant breeders interested in mining the genetic diversity of the NPGS sorghum collection.

Evaluation of Genetic Diversity in Antiaris toxicaria Lesch. from Sacred Groves of the Western Ghats, India

Antiaris toxicaria Lesch. is a deciduous tree belongs to the family Moraceae, is native to the Old World tropics. It is an important industrial forest plant for its veneer, plywood and medicinal values. In the present study, genetic diversity of different populations of A. toxicaria collected from sacred groves of the Western Ghats, India has been evaluated. Thirteen RAPD and ten ISSR primers produced a total of 175 and 143 reproducible bands, respectively. RPI 10 of RAPD primers used showed maximum (0.49) polymorphic information content (PIC), while UBC 809 (0.37) exhibits maximum PIC among ISSR primers. Nei’s genetic similarity showed that pairwise similarity coefficients ranged from 0.460 to 0.832 in RAPD analysis, whereas 0.550–0.842 in ISSR analysis. Understanding the genetic diversity among natural A. toxicaria populations will be useful for effective long-term conservation.

Evaluation of genetic diversity within asparagus germplasm based on morphological traits and ISSR markers.

Asparagus officinalis L. is a dioecious perennial plant globally known for its fine flavor and high nutritional value. An evaluation of genetic diversity in 46 asparagus accessions was carried out based on morphological and inter-simple sequence repeat (ISSR) markers. The result show that the coefficient of variation for 20 morphological characteristics is between 12.45 and 62.22%. Factor analysis revealed that nine factors explained 83.37% of the total variance. At Euclidean distance of 135.7, 46 accessions were divided into two clusters. Genetic similarity coefficient (GSC) based on ISSR data ranged from 0.60 to 0.97, suggesting a relatively abundant genetic base. Furthermore, the 46 asparagus accessions could also be grouped into three major clusters at a GSC of 0.74. And there is no significant relation between the two marker systems using the Mantel test. Clustering based on morphological traits compared with that based on ISSR data was not consistent, however, some common groupings were observed between two dendrograms. Therefore the results elucidated asparagus germplasm genetic background and determined hybrid parents, which will facilitate optimal application of asparagus germplasm resources and provide additional data for genetic improvement.

The Role of Molecular Tools in Genetic Diversity Conservation of Indigenous Chicken Production, Tanzania: Short Communication

Molecular techniques refers to methods used in molecular biology, biochemistry, genetics and biophysics which involve manipulation and analysis of DNA and RNA. Molecular techniques can also be used in biology to study genetic diversity and variation. Genetic diversity refers to the total number of genetic characteristics in the genetic makeup of a species. It shows similarity and variation that exist between breeds of the same species. Genetic diversity serves as a way for populations to adapt to changing environment. An increase loss of genetic diversity has been observed in most of agricultural species and particularly chicken genetic resources are considered to be the most threatened. Selective breeding by humans have led to the creation of many breeds characterized by high productivity, leading to the displacement of local breeds and posing a threat to the survival of many native breeds. Genetic resources are the building blocks for chicken development. The relevance of genetic diversity conservation in chicken production cannot be overemphasized because genes play a great role in formation of breeds and species. With recent advances in molecular technology, a number of techniques for in-depth genome analysis and evaluation of genetic variation in different breeds of chicken have been developed.

Evaluation of Genetic Diversity in Korean Fir Cultivars Based on Microsatellite and Cytoplasmic Markers

Korean fir (Abies koreana) has been cultivated for less than 100 years, mainly in the United States and Europe. Using nuclear microsatellite, mitochondrial, and chloroplast markers, we investigated the origin of cultivated korean fir from South Korea (KC group) as well as the United States and United Kingdom (EU group), and compared these samples to published data from wild populations. All genotypes in the EU and KC groups were most closely related to the wild individuals from Mt. Hallasan, the southernmost A. koreana population on Jejudo Island (South Korea). However, the presence of the chloroplast haplotypes clustered with Abies balsamea in two EU cultivars and the higher diversity values of the EU group compared with the wild individuals from Mt. Hallasan infer a certain level of introgression from different species during cultivation. The EU group had a higher inbreeding coefficient and linkage disequilibrium, and a smaller proportion of rare alleles, than the wild populations. This suggests that the genetic characteristics of korean fir cultivars reflect strong artificial selection pressure for desirable horticultural traits and asexual reproduction. Last, this genetic background study suggests that the other wild populations in the Korean peninsula can serve as valuable genetic resources for future breeding.

Evaluation of genetic diversity of durum wheat (Triticum durum desf.) genotypes using inter-simple sequence repeat (ISSR) and caat box-derived polymorphism (CBDP) markers

Evaluation of genetic diversity is the key principal for plant breeding, providing an opportunity to discover novel characters and alleles for breeders. In the present study, 69 durum wheat genotypes were investigated for genetic diversity using several CAAT box-derived polymorphism (CBDP) and inter-simple sequence repeat (ISSR) markers. Twelve CBDP and sixteen ISSR primers amplified a total of 115 and 160 polymorphic fragments with a mean of 9.58 and 10 fragments per primer, respectively. CBDP primers showed the higher mean values for informativeness parameters such as polymorphic information content (PIC), resolving power (Rp) and marker index (MI) in comparison with ISSR primers. The results of analysis of molecular variance (AMOVA) indicated that the highest proportion of genetic variance referred within populations. Furthermore, CBDP primers indicated high values for all genetic parameters. Besides, the highest values of genetic parameters including number of observed (Na) and effective alleles (Ne), Shannon?s information index (I) and Nei?s gene diversity (He) were estimated for Iranian durum wheat landraces. Cluster analysis based on each molecular technique classified all durum wheat genotypes into three main groups, so that the results of principal coordinate analysis (PCoA) supported the grouping patterns. As a result, the grouping pattern observed by ISSR primers was clearer than CBDP primers and grouped all samples based on their origins. However, Mantel?s coefficient correlation test illustrated the higher positive correlation (0.54) between both marker techniques. Hence, the use of these markers in combination with each other to evaluate the genetic diversity is recommended.

Evaluation of genetic diversity and blood relationships among first- and second-generation plus trees of Hinoki(Chamaecyparis obtusa)in the Kansai breeding region

Evaluation of genetic diversity and blood relationships among first- and second-generation plus trees of Hinoki(Chamaecyparis obtusa)in the Kansai breeding region

Evaluation of Genetic Diversity in Wild Tachibana Population of Heda, Shizuoka, Using DNA Marker Analysis, and Stable Maintenance of the Population

Evaluation of Genetic Diversity in Wild Tachibana Population of Heda, Shizuoka, Using DNA Marker Analysis, and Stable Maintenance of the Population

Analysis of complete chloroplast genome sequence of Korean landrace Cymbidium goeringii.

The complete chloroplast genome sequence of Korean Cymbidium goeringii acc. smg222 was analyzed. Based on a comparison with Chinese C. goeringii, losses of nine ndh subunits (ndhA, ndhB, ndhC, ndhD, ndhE, ndhF, ndhH, ndhJ, and ndhK), three protein-coding genes (ycf 1-like, ycf 15, and ycf 68), six transfer RNAs, and one conserved open reading frame (orf 42). In addition, 219 InDels (insertion or deletion) and 171 simple sequence repeats were observed. Twenty-Five of which InDel markers have been evaluated, that useful for distinguishing Korean and Chinese Cymbidium associations based on the polymorphisms of chloroplast genomes between Korean Cymbidium goeringii acc. smg222 and Chinese C. goeringii and evaluation of genetic diversity. Finally, the phylogenetic relationships of the 39 Korean and 22 Chinese species was constructed based on the five InDel markers of them and obtained high support, indicating that our data may be useful in resolving relationships in this genus. The information about chloroplast DNA structure and gene variants of C. goeringii acc. smg222 chloroplast genome will provide sufficient phylogenetic information for resolving evolutionary relationships. The molecular markers developed in here will contribute to further research of Cymbidium species and conservation of endemic Cymbidium species.

Genetic variation among common beans cultivars (Phaseolus vulgaris L.) as revealed by morphological, protein and molecular markers

The role of genetic diversity is crucial for future improvements to meet societal demand for food security under a climate change scenario. Morphological, biochemical and molecular analyses have been suggested for the evaluation of genetic diversity in common bean (Phaseolus vulgaris L.) from Egypt. Twelve cultivars were collected from different five geographical isolated locations. These cultivars were evaluated using 20 morphological traits (15 qualitative and 5quantitative). The two cultivars P9 and P14 which were collected from Quesna and New Valley, respectively exhibited partially different morphologically features from other cultivars. The electrophoretic pattern of seed storage proteins indicated 45 different molecular weight bands, ranging from 309.7 kDa to 44.3 kDa with the presence of 4 unique bands and 41 polymorphic bands. ISSR results revealed a high level of polymorphism (69.1%) using six ISSR primers, which produced a total of 117 bands; out of them 85 bands are polymorphic, 25 monomorphic and 7 unique. Cluster analysis using CAP software program based on combined data revealed two groups. The obtained data confirmed that morphological, SDS-protein and ISSR markers are important tools for genetic analysis for common bean and recommended to give accurate results.

Evaluation of the genetic diversity of <i> Huperzia serrate </i> by rapd markers

Huperzia serrata, a valuable pharmaceutical plant distributed in Lao Cai (Northwest Vietnam) and Lam Dong (Central Highlands of Vietnam), is known as pharmaceutical materials for the treatment of Alzheimer’s disease. As a result of over-exploitation and habitat fragmentation, H. serrata has become a threatened plant in Vietnam, China and other countries around the world. For the understanding of population dynamics, adaptation, evolution and conservation of plant species in general and H. serrata in particular, the evaluation of genetic diversity is very important. In this study, a total of sixteen RAPD primers were used for evaluation of the genetic diversity of eight H. serrata samples collected from different locations of Sa Pa and Da Lat. Overall, sixteen markers generated a total of 70 fragments in 8 collected samples of H. serrata. Of seventy generated fragments, 44 were found to be polymorphic. The number of fragments of each primer ranged from 1 to 8 with an average of 4,4 fragments per primer. The OPB20 primer revealed the highest polymorphism, while the OPB15, OPB17 and OPC12 primers gave the lowest. Polymorphism information content (PIC) values varied from 0.5266 to 0.8624 with an average of 0.7182, in which the highest value belonged to OPB11 primer while the OPC10 primer showed the lowest PIC value. The dendrogram created based on RAPD data sheet divided the investigated strain into two major groups corresponding to their habitat: Group I included three Da Lat samples (DL1, DL2, DL3) and Group II consisted of five samples from Sa Pa (SP1, Sp2, SP3, Sp4, and SP5). The results of our study could be useful for the conservation and development of H. serrata.

Association mapping of traits related to leaf blast disease in rice (Oryza sativa L.)

The present research was conducted to validate and verify the association of SSR markers with traits related to leaf blast disease in 121 rice cultivars. Number of spots, number of spore-producing spots, spot size, infection type, infection percentage, and the area under the disease progress curve (AUDPC) were the blast-related traits measured in the rice blast nursery. Evaluation of genetic diversity of markers indicated that RM166 had the highest level of diversity indices including observed number of alleles, effective number of alleles, polymorphism information content (PIC) value, gene diversity, and Shannon’s index. Thus, RM166 is the more valuable marker which can be used in association mapping because of the high opportunity of linkage to valuable disease resistance traits. Association mapping was performed using population structure matrix through the general linear model (GLM) and the mixed linear model (MLM). Based on a structure analysis, three subpopulations were observed in the rice population of this study. Among the set of selected markers, 30 and 29 markers exhibited a significant linkage with traits related to blast disease in GLM and MLM, respectively. RM224 had the most significant relationship with evaluated traits in both GLM and MLM, suggesting that this marker can be used in breeding programs.

Allelic variation in candidate genes associated with wood properties of cultivated poplars (Populus).

Since Populus has veritable value as timber, plywood, pulp, and paper, genomic research should create the sound basis for further breeding toward desirable wood quality attributes. In this study, we addressed the need for a research methodology that initially identifies and then characterize candidate genes encoding enzymes with wood property phenotypic traits, toward the aim of developing a genomics-based breeding technology. On 23 different poplar species/hybrid samples, we successfully amplified 55 primers designed on Populus trichocarpa L. Considering the number of polymorphic sites, out of 73,206 bp, 51 SNPs and 31 indel events were found. Non-synonymous single base mutations could be detected in number of 30, 21 out of 164 sequences were the number of minimum recombination events and 41 significant pairwise comparisons between loci could be detected. Our results provide a roadmap for a future association genetic study between nucleotide diversity and precise evaluation of phenotype.

Evaluation of Genetic Diversity of Agronomic and Morphological Traits of Sesame Genotypes

Evaluation of Genetic Diversity of Agronomic and Morphological Traits of Sesame Genotypes

Detection and application of genome-wide variations in peach for association and genetic relationship analysis

BackgroundPeach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited.ResultsIn this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8386~12,298 structure variants (SVs), 2111~2581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions.ConclusionsThe results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.

Diversidad genética en humanos mediante polimorfismos de inserción de Alu en la población de San Pelayo, Córdoba (Colombia)

This research determined the genetic diversity and population structure in human populations in San Pelayo, based on human Alu polymorphism. The samples were obtained from unrelated adults. The DNA of each sample was extracted using the PROMEGA kit, the markers were amplified by PCR and the amplified ones were subjected to electrophoresis and visualized in a transilluminator. The loci were polymorphic, the allelic frequencies showed heterogeneous values. The Hardy Weinberg test indicated that the population was not in equilibrium. Low heterozygosis and a high fixation index were also detected and the markers used were appropriate for the evaluation of genetic diversity. The population showed low diversity and a high polymorphic level.

Evaluation of the genetic diversity of six Chinese indigenous chickens.

ObjectiveThe extensive breeding of commercial chickens has led to a sharp decrease in the resources of many indigenous chickens, especially the indigenous chickens in the southeastern coastal region, which are on the verge of extinction, and the indigenous chickens in the northwestern region of China, which are also at risk. However, there are few reports on the evaluation of genetic diversity and conservation of genetic resources of indigenous chickens in remote areas in the Northwest of China.MethodsIn the present study, the genetic diversity and phylogenetic relationship of six indigenous chickens from different regions were studied based on variation in mitochondrial DNA control region (D-loop), and the degree of introgression from commercial breeds into these chickens was determined by the amount of haplotype sharing between indigenous and commercial breeds.ResultsTwenty-five polymorphic sites and 25 haplotypes were detected in 206 individuals. Principal component analysis showed that the Jingning chicken had the highest genetic diversity among the six indigenous chickens. According to the degree of introgression, the six indigenous breeds may be involved in haplotype sharing with commercial breeds, and the introgression from commercial chickens into the Haidong chicken is the most serious.ConclusionThe genetic uniqueness of indigenous chickens has been eroded, so it is necessary to consider the protection of their genetic resources. Phylogenetic analysis suggests that the six indigenous chickens have two major matrilineal origins: one from Yunnan or its surrounding areas in China and the other from the Indian subcontinent.

Revelation of genetic diversity and structure of wild Elymus excelsus (Poaceae: Triticeae) collection from western China by SSR markers.

Hosting unique and important plant germplasms, the Qinghai-Tibet Plateau (QTP), as the third pole of the world, and Xinjiang, located in the centre of the Eurasian continent, are major distribution areas of perennial Triticeae grasses, especially the widespread Elymus species. Elymus excelsus Turcz. ex Griseb, a perennial forage grass with strong tolerance to environmental stresses, such as drought, cold and soil impoverishment, can be appropriately used for grassland establishment due to its high seed production. To provide basic information for collection, breeding strategies and utilization of E. excelsus germplasm, microsatellite markers (SSR) were employed in the present study to determine the genetic variation and population structure of 25 wild accessions of E. excelsus from Xinjiang (XJC) and the QTP, including Sichuan (SCC) and Gansu (GSC) of western China. Based on the 159 polymorphic bands amplified by 35 primer pairs developed from three related species, the average values of the polymorphic information content (PIC), marker index (MI), resolving power (Rp), Nei’s genetic diversity (H) and Shannon’s diversity index (I) of each pair of primers were 0.289, 1.348, 1.897, 0.301 and 0.459, respectively, validating that these SSR markers can also be used for the evaluation of genetic diversity of E. excelsus germplasms, and demonstrating the superior versatility of EST-SSR vs. G-SSR. We found a relatively moderate differentiation (Fst = 0.151) among the XJC, SCC and GSC geo-groups, and it is worth noting that, the intra-group genetic diversity of the SCC group (He = 0.197) was greater than that of the GSC (He = 0.176) and XJC (He = 0.148) groups. Both the Unweighted Pair Group Method with Arithmetic (UPGMA) clustering and principal coordinates analysis (PCoA) divided the 25 accessions into three groups, whereas the Bayesian STRUCTURE analysis suggested that E. excelsus accessions fell into four main clusters. Besides, this study suggested that geographical distance and environmental variables (annual mean precipitation and average precipitation in growing seasons), especially for QTP accessions, should be combined to explain the population genetic differentiation among the divergent geographical regions. These data provided comprehensive information about these valuable E. excelsus germplasm resources for the protection and collection of germplasms and for breeding strategies in areas of Xinjiang and QTP in western China.

Fingerprinting the genetic variation and intergeneric hybrid dynamics in the family Asteraceae (genera Helianthus, Echinaceae, Tagetes and Verbesina) using iPBS markers

Transposable elements constitute a large fraction of plant genomes and represent a powerful marker tool for genetic diversity studies. Here, the retrotransposon-based marker method inter primer binding sites (iPBS) was used to assess the genetic variation and intergeneric hybrid dynamics in the family Asteraceae by studying genera Helianthus, Echinaceae, Tagetes, Tithonia and Verbesina. Two selected iPBS primers (2222 and 2224) detected intergeneric polymorphism in the range 44.8% - 93.3% (mean 70%) and 85.7% - 100% (mean 89.5%) respectively. Moreover, iPBS markers allowed the genetic discrimination at within-species level between varieties of H. annuus (35.7% and 19.1%) but also between single cross’s segregating intergeneric hybrids (28.6% and 40%). The inheritance of iPBS markers and the parental genomes respectively in intergeneric hybrids of H. annuus has been manifested by the non-random elimination of markers mainly of origin of wild species and the preferential inheritance of markers unique to H. annuus. Such instability evidences genomic reconstruction involving LTR elements. In conclusion, the iPBS method stands as a reliable approach for the evaluation of genetic diversity of Asteraceae germplasms and perspective for use in the breeding practice of sunflower and related species.