Average Polymorphism Information Content Research Articles

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

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

Genetic structure analysis and genetic fingerprinting of pomegranate cultivars (Punica granatum L.) by using SCoT molecular markers

AbstractGenetic diversity and genetic relatedness among 50 genotypes from eight countries, including Iran, Afghanistan, Turkmenistan, Syria, Lebanon, India, Yemen, and the United States located in two continents of Asia and the America, were assessed using SCoT markers. A total of 213 bands were produced; 100% of them were polymorphic; the average polymorphism information content (PIC) was 0.39. The mean Nei's gene diversity and Shannon's index were 0.33 and 0.49, respectively. Analysis of molecular variance suggested significant genetic differences within pomegranate populations. 99% of variance occurs within the populations, whereas 1% of the variation was recorded among the populations of pomegranate. Cluster analysis using SCoT markers able to group genotypes based on their geographical origins. Based on cluster analysis, the genotypes studied were divided into two main groups. The first group included most Asian genotypes, while American genotypes along with some Asian genotypes were in the second group. In the first group, Iranian genotypes were grouped with genotypes from Afghanistan and India. In the second group, the genotypes belonging to the America were in the same group as most of the genotypes of Turkmenistan. According to the present study, SCoT markers can be used to evaluate genetic diversity, identification and DNA fingerprinting pomegranate genotypes of different origins. This information can be used in breeding programs and the management of pomegranate collections.

Molecular genetics and phenotypic assessment of foxtail millet (Setaria italica (L.) P. Beauv.) landraces revealed remarkable variability of morpho-physiological, yield, and yield-related traits.

Foxtail millet (Setaria italica (L.) P. Beauv.) is highly valued for nutritional traits, stress tolerance and sustainability in resource-poor dryland agriculture. However, the low productivity of this crop in semi-arid regions of Southern India, is further threatened by climate stress. Landraces are valuable genetic resources, regionally adapted in form of novel alleles that are responsible for cope up the adverse conditions used by local farmers. In recent years, there is an erosion of genetic diversity. We have hypothesized that plant genetic resources collected from the semi-arid climatic zone would serve as a source of novel alleles for the development of climate resilience foxtail millet lines with enhanced yield. Keeping in view, there is an urgent need for conservation of genetic resources. To explore the genetic diversity, to identify superior genotypes and novel alleles, we collected a heterogeneous mixture of foxtail millet landraces from farmer fields. In an extensive multi-year study, we developed twenty genetically fixed foxtail millet landraces by single seed descent method. These landraces characterized along with four released cultivars with agro-morphological, physiological, yield and yield-related traits assessed genetic diversity and population structure. The landraces showed significant diversity in all the studied traits. We identified landraces S3G5, Red, Black and S1C1 that showed outstanding grain yield with earlier flowering, and maturity as compared to released cultivars. Diversity analysis using 67 simple sequence repeat microsatellite and other markers detected 127 alleles including 11 rare alleles, averaging 1.89 alleles per locus, expected heterozygosity of 0.26 and an average polymorphism information content of 0.23, collectively indicating a moderate genetic diversity in the landrace populations. Euclidean Ward's clustering, based on the molecular markers, principal coordinate analysis and structure analysis concordantly distinguished the genotypes into two to three sub-populations. A significant phenotypic and genotypic diversity observed in the landraces indicates a diverse gene pool that can be utilized for sustainable foxtail millet crop improvement.

Development of Diagnostic Markers and Applied for Genetic Diversity Study and Population Structure of Bipolaris sorokiniana Associated with Leaf Blight Complex of Wheat

Bipolaris sorokiniana, a key pathogenic fungus in the wheat leaf blight complex, was the subject of research that resulted in the development of fifty-five polymorphic microsatellite markers. These markers were then used to examine genetic diversity and population structure in Indian geographical regions. The simple sequence repeat (SSR) like trinucleotides, dinucleotides, and tetranucleotides accounted for 43.37% (1256), 23.86% (691), and 16.54% (479) of the 2896 microsatellite repeats, respectively. There were 109 alleles produced by these loci overall, averaging 2.36 alleles per microsatellite marker. The average polymorphism information content value was 0.3451, with values ranging from 0.1319 to 0.5932. The loci's Shannon diversity varied from 0.2712 to 1.2415. These 36 isolates were divided into two main groups using population structure analysis and unweighted neighbour joining. The groupings were not based on where the isolates came from geographically. Only 7% of the overall variation was found to be between populations, according to an analysis of molecular variance. The high amount of gene flow estimate (NM = 3.261 per generation) among populations demonstrated low genetic differentiation in the entire populations (FST = 0.071). The findings indicate that genetic diversity is often minimal. In order to examine the genetic diversity and population structure of the B. sorokiniana populations, the recently produced microsatellite markers will be helpful. This study's findings may serve as a foundation for developing improved management plans for the leaf blight complex and spot blotch of wheat diseases in India.

Comparative Genetic Diversity Assessment and Marker–Trait Association Using Two DNA Marker Systems in Rice (Oryza sativa L.)

In this paper, the genetic diversities of 12 rice genotypes (Oryza sativa L.), representing Indica, Japonica, and Indica–Japonica varieties, were assessed using twelve ISSR and five SSR markers. In addition, the rice genotypes were evaluated for 11 agro-morphological traits in a two-year trial. Association mapping was performed to detect any association between the DNA markers and the agro-morphological traits. An association analysis was conducted considering the relative kinship among the genotypes and accounting for the population structure using the unified mixed-model approach to avoid possible false-positive associations. Seventy-three alleles were collectively produced by ISSRs and SSRs, with an average of 6.3 and 2.8 alleles per locus, respectively. Both marker systems were informative, and the average polymorphism information content (PIC) was 0.222 and 0.352 for ISSRs and SSRs, respectively. The average expected heterozygosity (Hexp) was 0.264 for ISSRs compared to 0.457 for SSRs. After using the false discovery rate (FDR) method, the association analysis revealed a total of 12 significant marker–trait associations with six agro-morphological traits, including the no. of unfiled grains panicle−1, panicle length, panicle weight, the no. of panicles plant−1, the no. of tillers plant−1, and 1000-grain weight. ISSRs showed seven significant associations with five markers, while SSRs showed three significant associations with three markers. The phenotypic variance (R2) explained by each marker ranged between 29.2% for the ISSR marker HB11 (associated with 1000-grain weight) and 49.3% for the ISSR marker HB8 (associated with the no. of tillers plant−1). The identified marker–trait associations reported herein may improve the expected gain of future molecular-based rice-breeding programs, particularly those designed for improving grain-related or harvest-related traits.

Genetic diversity and population structure assessment of Western Canadian barley cooperative trials.

Studying the population structure and genetic diversity of historical datasets is a proposed use for association analysis. This is particularly important when the dataset contains traits that are time-consuming or costly to measure. A set of 96 elite barley genotypes, developed from eight breeding programs of the Western Canadian Cooperative Trials were used in the current study. Genetic diversity, allelic variation, and linkage disequilibrium (LD) were investigated using 5063 high-quality SNP markers via the Illumina 9K Barley Infinium iSelect SNP assay. The distribution of SNPs markers across the barley genome ranged from 449 markers on chromosome 1H to 1111 markers on chromosome 5H. The average polymorphism information content (PIC) per locus was 0.275 and ranged from 0.094 to 0.375. Bayesian clustering in STRUCTURE and principal coordinate analysis revealed that the populations are differentiated primarily due to the different breeding program origins and ear-row type into five subpopulations. Analysis of molecular variance based on PhiPT values suggested that high values of genetic diversity were observed within populations and accounted for 90% of the total variance. Subpopulation 5 exhibited the most diversity with the highest values of the diversity indices, which represent the breeding program gene pool of AFC, AAFRD, AU, and BARI. With increasing genetic distance, the LD values, expressed as r2, declined to below the critical r2 = 0.18 after 3.91 cM, and the same pattern was observed on each chromosome. Our results identified an important pattern of genetic diversity among the Canadian barley panel that was proposed to be representative of target breeding programs and may have important implications for association mapping in the future. This highlight, that efforts to identify novel variability underlying this diversity may present practical breeding opportunities to develop new barley genotypes.

Genetic diversity and breed identification of Chinese and Vietnamese local chicken breeds based on microsatellite analysis.

South Asia and Southeast Asia are the origins of domestic chickens and are rich in poultry genetic resources, resulting in many unique local chicken breeds. However, with the rapid intensification of poultry farming worldwide, many local chicken breeds are threatened with extinction. In response to China's "One Belt, One Road" policy, it is imperative to strengthen the conservation and breeding of local chicken breeds in China and Vietnam. This study characterized 18 microsatellite molecular genetic markers to analyze the genetic diversity of 21 local chicken populations in southern China (Yunnan and Guangxi Provinces) and Vietnam, breed identification tags for microsatellite loci were constructed. The results showed that a total of 377 alleles were detected in all breeds, and the most alleles (44) and the highest polymorphic information content (0.7820) were detected at the LEI0094 locus. The average polymorphic information content (PIC) content of the whole population was 0.65, indicating moderate polymorphism. The genetic diversity of the whole population was rich, except for two loci MCW0111 and MCW0016, that showed heterozygote excess at microsatellite loci, and the population had high genetic differentiation. The Vietnamese breeds showed low pairwise fixation coefficient (FST) and Nei's standard genetic distance (DS) between them. According to the neighbor-joining dendrogram constructed by DS and the analysis of population genetic structure using the structure program, Longshengfeng chicken, Yunlong dwarf chicken, Tengchong white chicken, Xiayan chicken, and Daweishan mini chicken are similar, and Xishuangbanna game fowl, Wuding chicken, and Lanping silky chicken are similar to Yanjin black-bone chicken. In addition, excluding Dongtao chicken, other Vietnamese breeds are clustered together, indicating that the southern chicken breeds are closely related and have experienced better breeding. Overall, the whole population is rich in genetic resources, and the chicken breeds in the three regions are genetically close because of geographical factors and human activities. Dongtao chicken in Vietnamese, Chinese Yunnan local chicken breeds (Gallus gallus spadiceus), and red jungle fowl chickens (Gallus gallus) may have the same origin. We also constructed unique microsatellite molecular markers for 20 cultivars using 15 microsatellite loci. This study provides valuable insights to facilitate breed identification, improve cultivar protection, and new germplasm construction.

Genetic Diversity and Population Structure Analysis of Barley Landraces from Shanghai Region Using Genotyping-by-Sequencing

Barley (Hordeum vulgare L.) is an important economic crop for food, feed and industrial raw materials. In the present research, 112 barley landraces from the Shanghai region were genotyped using genotyping-by-sequencing (GBS), and the genetic diversity and population structure were analyzed. The results showed that 210,268 Single Nucleotide Polymorphisms (SNPs) were present in total, and the average poly-morphism information content (PIC) was 0.1642. Genetic diversity and population structure analyses suggested that these barley landraces were differentiated and could be divided into three sub-groups, with morphological traits of row-type and adherence of the hulls the main distinguishing factors between groups. Genotypes with similar or duplicated names were also investigated according to their genetic backgrounds and seed appearances. This study provided valuable information on barley landraces from the Shanghai region, and showed that all these barley landraces should be protected and used for future breeding programs.

Screening of Ginkgo Individuals with Superior Growth Structural Characteristics in Different Genetic Groups Using Terrestrial Laser Scanning (TLS) Data.

With the concept of sustainable management of plantations, individual trees with excellent characteristics in plantations have received attention from breeders. To improve and maintain long-term productivity, accurate and high-throughput access to phenotypic characteristics is essential when establishing breeding strategies. Meanwhile, genetic diversity is also an important issue that must be considered, especially for plantations without seed source information. This study was carried out in a ginkgo timber plantation. We used simple sequence repeat (SSR) markers for genetic background analysis and high-density terrestrial laser scanning for growth structural characteristic extraction, aiming to provide a possibility of applying remote sensing approaches for forest breeding. First, we analyzed the genetic diversity and population structure, and grouped individual trees according to the genetic distance. Then, the growth structural characteristics (height, diameter at breast height, crown width, crown area, crown volume, height to living crown, trunk volume, biomass of all components) were extracted. Finally, individual trees in each group were comprehensively evaluated and the best-performing ones were selected. Results illustrate that terrestrial laser scanning (TLS) point cloud data can provide nondestructive estimates of the growth structural characteristics at fine scale. From the ginkgo plantation containing high genetic diversity (average polymorphism information content index was 0.719) and high variation in growth structural characteristics (coefficient of variation ranged from 21.822% to 85.477%), 11 excellent individual trees with superior growth were determined. Our study guides the scientific management of plantations and also provides a potential for applying remote sensing technologies to accelerate forest breeding.

English

Fungal diseases are one of the major causes of losses on wheat yield in the world. Recent studies on plant defense mechanisms have highlighted the role of amino acids and total polyphenols in disease tolerance. Thus, with the objective of identifying on the basis of morphological and physiological variables the high-performance wheat accessions in high and low altitude, we characterized sixteen wheat accessions via quantification of polyphenols (TPP) and amino acids (AA) and identified fungal diseases affecting wheat in Centre Cameroon. Using the set of the three hexaploid wheat cultivars where the 11 microsatellite markers data was available, a total of 29 alleles were detected among cultivars and the number of alleles per locus ranged from 2 to 3 with an average of 2.64. Gene diversity ranged from 0.44 to 0.67 with an average of 0.59, increasing with the number of alleles. Microsatellites markers used had an average Polymorphic Information Content (PIC) value of 0.50, indicating that these markers are useful and will make a contribution to the studies in hexaploid wheat. The assessment of wheat plant to disease tolerance permitted to identify Septoria, Fusarium wilt; tanned spot and powdery mildew in high and low altitude. Analyzes of TPP and AA have made it possible to discriminate accessions that are tolerant to diseases. Hence, accession Atilla 1 was highly tolerant and had high levels of TPP (3.5 ± 0.36 μg/mg) and AA (40.1 ± 1.21 μg/mg) while the accession Sup 152 highly susceptible to disease had low levels (2.3 ± 0.1 and 2.1 ± 0.36 μg/mg, respectively). This study will contribute to the extension of wheat in areas where conditions similar to the study sites will be localized.   Key words: Amino acids, bread wheat, high and low altitude, fungal diseases, polyphenols.

EST-SSR Markers' Development Based on RNA-Sequencing and Their Application in Population Genetic Structure and Diversity Analysis of Eleusine indica in China.

Goosegrass (Eleusine indica) is one of the worst agricultural weeds in China. Molecular markers were developed for genetic diversity and population structure analyses. In this study, we identified 8391 expressed sequence tag-simple sequence repeat (EST-SSR) markers from the de novo assembled unigenes of E. indica. Mononucleotides were the most abundant type of repeats (3591, 42.79%), followed by trinucleotides (3162, 37.68%). The most dominant mononucleotide and trinucleotide repeat motifs were A/T (3406, 40.59%) and AAT/ATT (103, 1.5%), respectively. Fourteen pairs of EST-SSR primers were verified and used to analyze the genetic diversity and population structure of 59 goosegrass populations. A total of 49 alleles were amplified, with the number of alleles (Na) ranging from two to eleven per locus, and the effective number of alleles (Ne) ranged from 1.07 to 4.53. The average polymorphic information content (PIC) was 0.36. Genetic structure analysis (K = 2) and principal coordinate analysis divided 59 E. indica populations into two groups in a manner similar to the unweighted pair-group method (Dice genetic similarity coefficient = 0.700). This study developed a set of EST-SSR markers in E. indica and successfully analyzed the diversity and population genetic structures of 59 E. indica populations in China.

Genetic Diversity Study of Melon Native Landraces Using ISSR Markers in Kurdistan Region of Iraq

Considering the ancient cultivation of various numbers of melons, it seems that there is a valuable and rich gene pool of melon in Kifri city of Kurdistan region of Iraq. In this research, the genetic diversity of 15 indigenous melons of Kifri and 7 non-native melons was analyzed using inter simple sequence repeat (ISSR) markers. A total of 6 primers were used to amplify parts of the genomic DNA of the samples. Genomic DNA was extracted using Salting out method, and polyacrylamide gel was used to separate DNA fragments. In this study, 65 bands were scored and 34 bands had polymorphisms. To evaluate the genetic similarity between the samples, cluster analysis was used using the Jaccard similarity coefficient with the UPGMA method. The average genetic distance between the samples using the Jaccard similarity coefficient was 0.74, and the average polymorphic information content (PIC) was 0.78. The primer (AC)8 G had the highest PIC (0.93). Cluster analysis indicated wide range of diversity across the genotypes used. These genotypes have high diversity which could be used in breeding programs.

Evaluating genetic diversity of geographically diverse populations of Embelia ribes Burm f., a highly medicinal woody liana from the Western Ghats of India, using random amplified polymorphic DNA (RAPD) and intersimple sequence repeats (ISSR) markers.

Embelia ribes Burm f. (Primulaceae) is a medicinal and vulnerable woody liana distributed throughout India. Embelin, a well-recognized active phytoconstituents in berries, is commonly used in ayurvedic formulations. Due to over-exploitation, the status of the plant is vulnerable. Previous studies on this species mainly focused on its phytochemical analysis, which led to overexploitation and loss of the germplasm. In the present study, 20 RAPD and 18 ISSR markers were employed to assess genetic divergence in 40 genotypes of E. ribes collected from different parts of the Western Ghats of India. In RAPD analysis, all 40 accessions with 20 RAPD primers amplified 282 fragments, with 83.91% average polymorphism and with an average of 14.10 bands per primer. The size of amplicons varied from 200 to 2500bp. While, ISSR primers produced 203 fragments of which 161 were polymorphic with an average of 11.28 bands per primer with 73.25% average polymorphism. The size of amplicons ranges from 200 to 2500bp. RAPD and ISSR markers were also assessed by calculating polymorphic information content (PIC) to discriminate the genotypes; the average PIC value for RAPD, ISSR, and combined RAPD + ISSR markers obtained was more than 0.50 suggesting the informativeness of markers. UPGMA analysis based on Jaccard's similarity coefficient for RAPD, ISSR, and RAPD + ISSR data reveals that 40 accessions of E. ribes were depicted in four clusters. The clustering pattern of all individuals in PCoA analysis agreed with the UPGMA dendrograms, which further confirms the genetic relationships explained by cluster analysis. AMOVA analysis of RAPD, ISSR, and combined marker system revealed variation within the population, ranging from 41 to 44%, and among the population, it ranged from 56 to 59%. The present study provides an optimized method for evaluating the genetic diversity of Embelia ribes using RAPD and ISSR markers which are useful for further sustainable utilization and conservation of natural populations in the Western Ghats of India.

Genetic Characterization and Population Structure of Pea (Pisum sativum L.) by Molecular Markers against Rust (Uromyces viciae-fabae) in Newly Developed Genotypes

The understanding of the genetic diversity of germplasm of any crop is necessary for genetic improvement. Pea (Pisum sativum L.) is a very important legume crop that provides protein and several essential vitamins, carbohydrates, and minerals. The genetic diversity and population structure of pea germplasm consisted of 115 entries of Australian accessions and 4 entries of Indian varieties used as checks with varying responses and severities of rust, which were analysed using 31 polymorphic SSR (Simple Sequence Repeats) markers. The combination of the markers revealed that 78 alleles were present at 32 loci. It was also observed that each marker had three alleles with an average PIC (Polymorphic Information Content) value of 0.272. The population structure analysis showed the genetic differentiation of the entries. The model-based population structure grouped the entries into three sub-populations of SP1, SP2, and SP3 having 37, 35, and 32 entries, respectively with 15 entries as admixtures. AMOVA (Analysis of Molecular Variance) disclosed that there was 56% variation among the individuals and 20% within the population. A mean fixation index (Fst) of 0.240 among the pea entries exhibited relatively significant variation in population. This study provides basic information to select parental lines for developing rust resistant varieties to meet the ultimate goal of sustainable agriculture.

CGIAR Barley Breeding Toolbox: A diversity panel to facilitate breeding and genomic research in the developing world.

Breeding programs in developing countries still cannot afford the new genotyping technologies, hindering their research. We aimed to assemble an Association Mapping panel to serve as CGIAR Barley Breeding Toolbox (CBBT), especially for the Developing World. The germplasm had to be representative of the one grown in the Developing World; with high genetic variability and be of public domain. For it, we genotyped with the Infinium iSelect 50K chip, a Global Barley Panel (GBP) of 530 genotypes representing a wide range of row-types, end-uses, growth habits, geographical origins and environments. 40,342 markers were polymorphic with an average polymorphism information content of 0.35 and 66% of them exceeding 0.25. The analysis of the population structure identified 8 subpopulations mostly linked to geographical origin, four of them with significant ICARDA origin. The 16 allele combinations at 4 major flowering genes (HvVRN-H3, HvPPD-H1, HvVRN-H1 and HvCEN) explained 11.07% genetic variation and were linked to the geographic origins of the lines. ICARDA material showed the widest diversity as revealed by the highest number of polymorphic loci (99.76% of all polymorphic SNPs in GBP), number of private alleles and the fact that ICARDA lines were present in all 8 subpopulations and carried all 16 allelic combinations. Due to their genetic diversity and their representativity of the germplasm adapted to the Developing World, ICARDA-derived lines and cultivated landraces were pre-selected to form the CBBT. Using the Mean of Transformed Kinships method, we assembled a panel capturing most of the allelic diversity in the GBP. The CBBT (N=250) preserves good balance between row-types and good representation of both phenology allelic combinations and subpopulations of the GBP. The CBBT and its genotypic data is available to researchers worldwide as a collaborative tool to underpin the genetic mechanisms of traits of interest for barley cultivation.

Characterization of guava (Psidium guajava L.) germplasm through morphological traits and SCoT markers

ABSTRACT Traditional breeding programmes have been limited to the selection and introduction of genotypes with promising agronomic characteristics, but studies focused on genetic diversity in the low hills of the North West(NW) Himalayas have not been conducted, which is very important for the identification of potential parents for breeding programmes in guava. In the present study, six best performing guava cultivars/hybrids were characterised using morphological descriptors and SCoT markers. Broad phenotypic variability among the guava cultivars/hybrids was detected using morphological descriptors. A set of 36 SCoT markers were used for polymorphism, out of which 31(86.1%) markers showed polymorphism, indicating high genetic variability in the guava cultivars/hybrids. During the analysis, 291 polymorphic amplicons were obtained, ranging from four to 19, with an average of 9.4 amplicons per primer and average polymorphic information content of 0.47.The UPGMA classified hybrids and cultivars into two groups. Based on morphological and molecular performance, L-49(Sardar) was ranked as the most promising cultivar for the low hills of NW Himalayan conditions. Morphological descriptors along with SCoT markers proved efficient in detecting the levels of genetic variability among the collections maintained in the field. These results can be used as an additional source of exploitation in guava breeding programmes.

Development of the maize 5.5K loci panel for genomic prediction through genotyping by target sequencing.

Genotyping platforms are important for genetic research and molecular breeding. In this study, a low-density genotyping platform containing 5.5K SNP markers was successfully developed in maize using genotyping by target sequencing (GBTS) technology with capture-in-solution. Two maize populations (Pop1 and Pop2) were used to validate the GBTS panel for genetic and molecular breeding studies. Pop1 comprised 942 hybrids derived from 250 inbred lines and four testers, and Pop2 contained 540 hybrids which were generated from 123 new-developed inbred lines and eight testers. The genetic analyses showed that the average polymorphic information content and genetic diversity values ranged from 0.27 to 0.38 in both populations using all filtered genotyping data. The mean missing rate was 1.23% across populations. The Structure and UPGMA tree analyses revealed similar genetic divergences (76-89%) in both populations. Genomic prediction analyses showed that the prediction accuracy of reproducing kernel Hilbert space (RKHS) was slightly lower than that of genomic best linear unbiased prediction (GBLUP) and three Bayesian methods for general combining ability of grain yield per plant and three yield-related traits in both populations, whereas RKHS with additive effects showed superior advantages over the other four methods in Pop1. In Pop1, the GBLUP and three Bayesian methods with additive-dominance model improved the prediction accuracies by 4.89-134.52% for the four traits in comparison to the additive model. In Pop2, the inclusion of dominance did not improve the accuracy in most cases. In general, low accuracies (0.33-0.43) were achieved for general combing ability of the four traits in Pop1, whereas moderate-to-high accuracies (0.52-0.65) were observed in Pop2. For hybrid performance prediction, the accuracies were moderate to high (0.51-0.75) for the four traits in both populations using the additive-dominance model. This study suggests a reliable genotyping platform that can be implemented in genomic selection-assisted breeding to accelerate maize new cultivar development and improvement.

Assessment of Genetic Diversity among Wild Ruta chalepensis L. from the North of Jordan

Ruta chalepensis, known as Fringed Rue, is a small shrub of the Rutaceae family. To date, there is no record of its natural distribution across Jordan, a country located in the eastern part of the Mediterranean basin, and there are no previous studies on its genetic diversity in the region. Therefore, this study was conducted to assess the genetic diversity of R. chalepensis in the northern parts of Jordan using morphological trait and amplified fragment length polymorphism (AFLP) analyses. For the morphological traits, the analysis of variance indicated that there were significant differences between the identified populations. The Shannon diversity indices showed relatively high values, indicating the existence of a high variability among the identified populations. The principal component analysis explained 82% of the variation between the collected plants, and a clear separation of the collected individuals from the Jarash-A, Jarash-B and Ajloun-B populations from the rest of the populations was observed. The heatmap clustering was in general agreement with the results of the principal component analysis, with the plant height, rachis length and plant width considered as the discriminative traits. The AFLP analysis using eight different primer combinations generated 59 polymorphic bands, with an average polymorphism information content value of 0.32. The phylogenetic analysis identified three main clusters, with the first cluster including 65% of the individuals collected from the Jarash and Ajloun provinces, with a clear separation of the Jarash-B population. The AMOVA revealed that the genetic variation between the populations contributed 30% of the total genetic variation, while the variation within the populations explained 70%. In conclusion, morphological traits and molecular markers were used successfully to assess the genetic diversity among wild R. chalepensis from the north of Jordan, and such data can be used for future conservation plans and utilization purposes.

Genetic diversity and population structure of Saccharomyces cerevisiae isolated from Turkish sourdough by iPBS-retrotransposons markers.

Molecular DNA markers are valuable tools for analyzing genetic variation among yeast from different populations to reveal the genetically different autochthonous strains. In this study, we employed inter-primer binding site (iPBS) retrotransposon polymorphism to assess the genetic variation and population structure of 96 Saccharomyces cerevisiae isolates from four different regions in Turkey. The nine selected iPBS primers amplified 102 reproducible and scorable bands, of which 95.10% were polymorphic with an average of 10.78 polymorphic fragments per primer. The average polymorphism information content and the resolving power were 0.26-3.58, respectively. Analysis of molecular variance (AMOVA) revealed significant (P < 0.001) genetic differences within populations (88%) and between populations (12%). The unweighted pair group mean with arithmetic (UPGMA) dendrogram grouped 96 S. cerevisiae strains into two main clusters, where the highest probability of the data elucidating the population structure was obtained at ΔK = 2. There was not an obvious genetic discrimination of the populations according to geographical regions on UPGMA, supported by principal coordinate analysis. However, the individuals of the closer provinces in each population were more likely to group together or closely. The results indicate that iPBS polymorphism is a useful tool to reveal the genetically diverse autochthonous S. cerevisiae strains that may be important for the production of sourdough or baked goods.

Genetic diversity and population structure of the USDA collection of Brassica juncea L.

The success of plant biofuels relies on finding inexpensive feedstocks that do not compete with food crops and can be cultivated economically in diverse geographical regions and agricultural production systems. Brassica juncea L. is a native crop of the western and central Asia, is considered a good biodiesel candidate due to its high oil content with high unsaturated fatty acids that can be refined into biofuels that equal petroleum-based fuels characteristics. To build genomic resources for B.juncea, a diversity panel consisting of 340 of accessions, were collected from 22 countries and stored at the USDA repository, and were genotyped to explore genetic diversity, relatedness, and population structure. A total of 99030 high-quality single nucleotide polymorphisms (SNP) markers were identified using genotyping-by-sequencing (GBS) technology. Those SNP were distributed over the 18 chromosomes with an average of 5000 SNP per chromosome, an average polymorphism information content (PIC) value of 0.23 and an expected heterozygosity (He) value of 0.281 indicating the genetic diversity within the USDA collection of B. juncea. Population structure and principal components analyses (PCA) based on identified SNPs revealed five distinct subpopulations, with the largest subpopulation containing accessions traced back to Pakistan and India. Analysis of molecular variance (AMOVA) revealed that 40% of the variation in USDA collection was among the five subpopulations, while 49% of the variation was due to the variation among accessions used in the analysis. High fixation index (FST) among distinguished subpopulations indicates a wide genetic diversity and high genetic differentiation among subpopulations. The results explored the genetic diversity in the USDA collection of B. juncea that could be used to genetically improve the crop. This information and accessions provide tools to enhance genetic gain in B. juncea breeding programs through genome-wide association analysis studies (GWAS) and marker-assisted selection (MAS) approaches.