Average Polymorphism Information Content Research Articles

Assessment of Genetic Diversity among Intra- and Interspecific Lowland Rice using Morpho-agronomic Traits and SSR Markers

Rice is staple food in many countries of Africa and a major part of the diet in many others. However, Africa’s demand for rice exceeds production with the deficit of 40% being imported. One way to improve Africa’s rice production is through breeding high yielding varieties suitable for the different environment conditions. This study was conducted to assess the genetic variability and stability performance of 48 lowland rice genotypes including 37 interspecific (Oryza glaberrima × Oryza sativa ssp. indica) and 11 intraspecific (O. sativa ssp. indica × O. sativa ssp. indica) in 12 environments in Nigeria, Benin Republic and Togo using Additive Main Effect and Multiplicative Interaction (AMMI) and Genotype+ Genotype x Environment (GGE) biplot models. The combined analysis of variance revealed significant differences (P<0.01) among the genotypes, environments, and genotypes x environment interaction. Both the AMMI and GGE models identified NERICA-L8 and NERICA-LI2 as the best genotypes for cultivation across environments. Ouedeme environments in Benin Republic were the most stable and ideal for rice cultivation, while Ibadan sites were the most unstable. TOG 5681 had the least yield and was the most unstable across seasons. Genetic diversity was analyzed using 22 important morpho-agronomic traits and 50 simple sequence repeat (SSR) markers and the results were subjected to principal components analysis (PCA). The results revealed that the first eight PC axes (PC1–8) accounted for 75.13% of the total variation, while PC1–4 accounted for 50.39% of the total variation among rice genotypes. However, 10 of the 50 SSR markers were polymorphic and generated 49 alleles (average = 4.9 alleles per locus), suggesting moderate to substantial genetic diversity among the rice genotypes. The polymorphic information content (PIC) ranged from 0.24 to 0.65, with an average PIC value of 0.45. Two structured populations were observed which clustered into five heterotic groups and an outgroup, respectively. This suggests that heterosis could be exploited in the next hybridization program by crossing one of the genotypes in any SSR marker-defined cluster, with the rice accession TOG 5681 in cluster I. The results of this study suggest that morpho-agronomic traits should be used to compliment SSR data in rice diversity studies, especially if a few polymorphic SSR markers are to be used.

Assessment of Genetic Diversity among Intra- and Interspecific Lowland Rice using Morpho-agronomic Traits and SSR Markers

Rice is staple food in many countries of Africa and a major part of the diet in many others. However, Africa’s demand for rice exceeds production with the deficit of 40% being imported. One way to improve Africa’s rice production is through breeding high yielding varieties suitable for the different environment conditions. This study was conducted to assess the genetic variability and stability performance of 48 lowland rice genotypes including 37 interspecific (Oryza glaberrima × Oryza sativa ssp. indica) and 11 intraspecific (O. sativa ssp. indica × O. sativa ssp. indica) in 12 environments in Nigeria, Benin Republic and Togo using Additive Main Effect and Multiplicative Interaction (AMMI) and Genotype+ Genotype x Environment (GGE) biplot models. The combined analysis of variance revealed significant differences (P<0.01) among the genotypes, environments, and genotypes x environment interaction. Both the AMMI and GGE models identified NERICA-L8 and NERICA-LI2 as the best genotypes for cultivation across environments. Ouedeme environments in Benin Republic were the most stable and ideal for rice cultivation, while Ibadan sites were the most unstable. TOG 5681 had the least yield and was the most unstable across seasons. Genetic diversity was analyzed using 22 important morpho-agronomic traits and 50 simple sequence repeat (SSR) markers and the results were subjected to principal components analysis (PCA). The results revealed that the first eight PC axes (PC1–8) accounted for 75.13% of the total variation, while PC1–4 accounted for 50.39% of the total variation among rice genotypes. However, 10 of the 50 SSR markers were polymorphic and generated 49 alleles (average = 4.9 alleles per locus), suggesting moderate to substantial genetic diversity among the rice genotypes. The polymorphic information content (PIC) ranged from 0.24 to 0.65, with an average PIC value of 0.45. Two structured populations were observed which clustered into five heterotic groups and an outgroup, respectively. This suggests that heterosis could be exploited in the next hybridization program by crossing one of the genotypes in any SSR marker-defined cluster, with the rice accession TOG 5681 in cluster I. The results of this study suggest that morpho-agronomic traits should be used to compliment SSR data in rice diversity studies, especially if a few polymorphic SSR markers are to be used.

Evaluating molecular and morphological diversity of Phlomis olivieri Benth (Lamiaceae) populations in Iran

ABSTRACT Phlomis olivieri (Lamiaceae) is a medicinal plant that exhibits diverse variations across a multitude of geographical ranges. Here, we studied the genetic diversity of this species according to start codon targeted (SCoT) markers and morphological variability based on 15 morphological traits. Specifically, the genetic diversity was studied among 100 individuals of 10 geographical populations in Iran. The populations were highly variable in almost all morphological traits (P < .01) and the dendrogram showed four main clusters for morphological traits. Out of the 10 primers, five SCoTs produced 93 reproducible bands, of which 92 were polymorphic. Significant values were observed in the average polymorphic information content (0.35), average band informativeness (18.4), resolving power (6.24) and average polymorphism (98.66%). SCoT markers ultimately grouped P. olivieri populations into six main clusters based on the principal component analysis. Using SCoT alleles, the individuals were grouped into eight distinct genetic clusters. The analysis of molecular variance showed a high degree of genetic variation among the populations (71%) and within the populations (29%). The Mantel test revealed a positive correlation between genetic distance and geographical distance. Thus, morphological features and SCoT markers were informative and reliable in revealing diversity among P. olivieri populations.

Morpho-molecular diversity study of rice cultivars in Bangladesh

Rice is one of the frontline cereals in the world and the major cultivated crop in Bangladesh. A total of eleven simple sequence repeats (SSRs) and thirteen sequence-tagged site (STS) markers were used to characterize twenty-four rice cultivars in Bangladesh. Twenty-four markers generated 60 alleles with 2.5 alleles per locus. The average polymorphism information content (PIC) value was 0.40, while the mean value of heterozygosity, gene diversity, and major allele frequency were recorded as 0.10, 0.48 and 0.62, respectively. However, the SSR markers showed more specificity and a higher discrimination power than the STS markers. The cluster analysis displayed four major clusters with a genetic similarity coefficient value of 0.73. The morphological analyses of the grain identified that Binadhan-20 and BRRI dhan34 had the longest and the shortest seed size, respectively, with a variable correlation between the seed length, width and length/width ratio. The phenol reaction test distinguished seven cultivars as japonica and seventeen cultivars as indica or an intermediate type. All these results regarding the phenotypic data and marker information will be useful for parental selection in modern rice breeding programmes.

Genome-Wide Development of Polymorphic Microsatellite Markers and Association Analysis of Major Agronomic Traits in Core Germplasm Resources of Tartary Buckwheat.

Tartary buckwheat (TB; Fagopyrum tataricum Gaertn.) is an important multigrain crop and medicinal plant, but functional genomics and molecular breeding research in this species have been lacking for quite some time. Here, genome-wide screening was performed to develop simple sequence repeat (SSR) markers associated with six major agronomic traits and the rutin contents of 97 core germplasm resources. A total of 40,901 SSR loci were identified; they were uniformly distributed throughout the TB genome, with a mean distance of 11 kb between loci. Based on these loci, 8,089 pairs of SSR primers were designed, and 101 primer pairs for polymorphic SSR loci were used to genotype the 97 core germplasm resources. The polymorphic SSR loci showed high genetic variation in these core germplasm resources, with an average polymorphic information content (PIC) value of 0.48. In addition, multiple SSR markers, such as SXAU8002 [100-grain weight (HGW)] and SXAU8006 [stem diameter (SD)], were found to be associated with agronomic traits in the two environments. Finally, based on gene functional annotation and homology analysis, a candidate gene, FtPinG0007685500, that may affect the node number and SD of the main stem by participating in lignin synthesis was identified. This study reports the mining of genome-wide SSR loci and the development of markers in TB, which can be used for molecular characterization of the germplasm in its gene pool. In addition, the detected markers and candidate genes could be used for marker-assisted breeding and functional gene cloning in TB.

Assessing genetic diversity using the first polymorphic set of EST-SSRs markers and barcoding of Moroccan saffron

Saffron (Crocus sativus L.) is an aromatic and medicinal plant, commonly known as the world's most expensive spice. Understanding its genetic diversity is critical for developing conservation strategies and germplasm management. This study reports the first set of EST-SSRs markers using C. sativus sequencing data available on the National Center for Biotechnology Information (NCBI). A panel of 19 EST-SSRs markers was selected to assess genetic diversity among 14 saffron accessions, mainly from Morocco. Forty-two alleles were detected, the polymorphic loci percentage reached 31.57%, and an average polymorphism information content (PIC) of 0.32 was recorded. DNA sequence polymorphism (DnaSP) analysis of CS/UIZ21 locus (GLT3 gene) identified 9 haplotypes with a haplotype diversity (HD)= 0.848, the average number of nucleotide differences among haplotypes was 2.64 and the nucleotide diversity was Pi= 0.01059. The results indicate that GLT3 barcoding could distinguish between Moroccan, Greek, and French saffron accessions and differentiate Moroccan accessions from each other. We established for the first-time a barcode of Moroccan saffron. Our results demonstrate that EST-SSRs markers and GLT3 barcode are potent tools for evaluating genetic diversity and germplasm analysis, which could be capitalized in future conservation strategies and breeding programs to protect and improve this valuable crop.

The application of microsatellite markers for parentage analysis in selective population of striped catfish (Pangasianodon hypophthalmus)

The research used ten newly developed microsatellites markers set which were assigned offsprings to their parents on the first generation of selection on striped catfish. The result shows: (1) When analysing 50 samples of parents (G0) and 50 samples of offsprings (G1), the PCR ratio was from 98-100%, the allele number (NA) ranged from 5-14 per locus. The average Polymorphic Information Content (PIC) of microsatellites on G0 and G1 were 0.71 and 0.67, respectively. The average observed heterozygosity (HO) and expected heterozygosity (HE) all over loci were 0.73, 0.76, and 0.73, 0.71, respectively. Ten microsatellites are stable and polymorphic that are suitable for parentage analysis. (2) After makers screening, parentage analysis on 50 selective families, the initial set of nine microsatellites (excluded Pahy-02) for parentage analysis was effective with 93.4% of offspring allocated unambiguously to their parental pairs, of which families with the father not having half-sib, 93.0% of offspring was allocated unambiguously to their parental pairs and families with the father having half-sib, 94.0% of offspring allocated unambiguously to their parental pairs. The results show that the maker set with nine microsatellites can be used in parentage analysis for the breeding program on striped catfish.

Evaluation of Genetic Diversity in Three Diospyros Species, Collected from Different Regions in Iran, Using ISSR and SCoT Molecular Markers

ABSTRACT The Diospyros genus contains approximately 400 to 500 species, among which D. kaki is cultivated as the edible persimmon. Knowledge about the genetic diversity of Diospyros genotypes is of high significance for breeding programs. In this research, the genetic diversity of 57 Diospyros genotypes collected from different regions of Iran was evaluated using inter simple sequence repeats (ISSR) and start codon targeted (SCoT) markers. Seven ISSR and 10 SCoT markers produced a total of 42 and 75 fragments with the averages of 6 and 7.5 fragments per primer, respectively. The average polymorphism information content (PIC) for ISSR markers was 0.3 and for SCoT markers was 0.36. The average marker index (MI) for ISSR and SCoT markers were 1.81 and 1.79, respectively. Cluster analysis based on Jaccard’s genetic similarity coefficient and UPGMA method classified 57 Diospyros genotypes into four main groups based on ISSR and SCoT markers. However, the clustering pattern based on the combination of ISSR and SCoT markers data separated the species genotypes better than each marker alone. Accordingly, groups 1 and 2 contained all D. kaki genotypes, both encompassing various subgroups, group 3 included D. lotus and group 4 included D. virginiana genotypes. Genotype distribution visualized with principal coordinate analysis (PCoA) was in accordance with the cluster analysis. Based on our results Iran is a rich source of Diospyrus germplasm, and a combination of ISSR and SCoT markers can be used as an accurate technique for evaluating genetic diversity among the Diospyros genotypes.

Genetic Variability and Population Structure of the Tunisian Sicilo-Sarde Dairy Sheep Breed Inferred from Microsatellites Analysis.

This study analyzed the genetic variability, inbreeding and population structure of the Tunisian–North African dairy sheep breed, the Sicilo-Sarde (SS), created by crossing the Sarda and Comisana dairy breeds. The level of variability in the SS, considered as an endangered breed after a dramatic decrease, was assessed using 17 microsatellite markers by analyzing the two breed populations sampled from their respective cradles: SS of Beja (SSB, n = 27) and SS of Mateur (SSM, n = 25). High levels of genetic diversity in SS were revealed, with a total of 212 alleles, a high mean number of alleles (12.47 ± 4.17) and a high average polymorphism information content (PIC) (0.81 ± 0.10). The observed heterozygosity was considerable in SSB and SSM (0.795 and 0.785, respectively). The inbreeding level measured by the population inbreeding coefficient FIS is higher in the SSM population (0.121) than in the SSB population (0.090). The higher genetic diversity level detected in SSB reflected the effect of new Italian Sarda genes introduced by intra-uterine artificial insemination recently practiced in this population. The Wilcoxon test and the mode-shift distribution indicated that the SS breed is a non-bottlenecked population. The structural analysis reflected the historical miscegenation practiced during the breed creation and highlighted further ancient miscegenation, which could date back to the first waves of sheep introduction to the western Mediterranean region. Microsatellite markers were successfully applied in the assessment of the genetic variability of SS and should be used in monitoring this variability during the application of conservation strategies.

Morphological and microsatellite DNA diversity of Djallonk\xe9 sheep in Guinea-Bissau

BackgroundThe present study aimed at characterizing the Djallonké Sheep (DS), the only local sheep breed raised in Guinea-Bissau. A total of 200 animals were sampled from four regions (Bafatá, Gabú, Oio and Cacheu) and described using 7 visual criteria and 8 measurements. These parameters have been studied by principal components analysis. The genetic diversity and population structure of 92 unrelated animals were studied using 12 microsatellite markers.ResultsThe values of quantitative characters in the Bafatá region were significantly higher than those obtained in the other three regions. A phenotypic diversity of the DS population was observed and three genetic types distinguished: animals with “large traits” in the region of Bafatá, animals with “intermediate traits” in the regions of Gabú and Oio and animals with “small traits” in the Cacheu region. The hair coat colors are dominated by the white color, the shape of the facial head profile is mainly convex and the ears “erected horizontally”. Most of the morphobiometric characteristics were significantly influenced by the “region” and “sex of animals”.The average Polymorphism Information Content (PIC) of 0.65 ± 0.11 supports the use of markers in genetic characterization. Gabú subpopulation had the highest genetic diversity measures (He = 0.716 ± 0.089) while Cacheu DS subpopulation presented the smallest (He = 0.651 ± 0.157). Only Gabú and Bafatá subpopulations presented significant heterozygote deficiency across all loci indicating possible significant inbreeding. Mean values for FIT,FST, FIS and GST statistics across all loci were 0.09, 0.029, 0.063 and 0.043 respectively. The overall genetic differentiation observed between the four DS subpopulations studied was low. Bafatá and Gabú are the most closely related subpopulations (DS = 0.04, genetic identity = 0.96) while Bafatá and Cacheu were the most genetically distant subpopulations (DS = 0.14, genetic identity = 0.87). Using Bayesian approach, the number of K groups that best fit the data is detected between 2 and 3, which is consistent with the morphological analysis and the factorial analysis of correspondence.ConclusionsThe molecular results on DS population of Guinea-Bissau confirmed the ones obtained with morphological analysis. The three genetic types observed phenotypically might be due to a combination of the agro-ecological differences and the management of breeding rather than genetic factors.

Genetic diversity and population structure of rice (Oryza sativa L.) landraces from Kerala, India analyzed through genotyping-by-sequencing.

Researchers stand at the vanguard of advancement and application of next-generation sequencing technology for developing dominant strategies for the sustainable management of genetically diverse crops. We attempt to fill the existing research lacuna in the molecular characterization of potent rice landraces in Kerala. Genotyping-by-sequencing (GBS) was performed on 96 Kerala rice accessions to identify single-nucleotide polymorphisms (SNPs), to examine the genetic diversity, population structure, and to delineate linkage disequilibrium (LD) pattern. GBS identified 5856 high-quality SNPs. The structure analysis indicated three subpopulations with the highest probability for population clustering with significant genetic differentiation, confirmed by principal component analysis. The genome-wide LD decay distance was 772kb, at which the r2 dropped to half its maximum value. The analysis of genetic properties of the identified SNP panel with an average polymorphism information content (PIC) value of 0.22 and a minor allele frequency (MAF) > 0.1 unveiled their efficacy in genome-wide association studies (GWAS). High FST (0.266) and low Nm (0.692) portray a strong genetic differentiation among the rice landraces, complementing the genetic structuring observed in the studied population. Slow LD decay in the rice landraces reflects their self-pollinating behavior and the indirect selection of desired traits by domestication. Moreover, the high LD entails only a minimum number of SNP markers for detecting marker-trait association. The diverse germplasm utilized in this study can be further utilized to disclose genetic variants associated with phenotypic traits and define signatures of selection via GWAS and selective sweep, respectively.

Population differentiation and gene flow of Glaucium flavum (Papaveraceae)

Yellow hornpoppy (Glaucium flavum Crantz.) is a herbaceous plant with gray-green leaves in coastal sands, rocky areas, and heavily eroded soils up to 500 meters above sea level. Glaucium flavum is native to Northern Africa, temperate zones in Western Asia and Europe, and is indigenous to Iran. The plant has been widely recognized for its aporphine-type isoquinoline alkaloids, which are pharmacologically active. Thus, we conducted a combination of morphological and molecular data analysis on such species because of the plant species' relevance. One hundred seven randomly collected plants from 14 natural populations in 5 provinces were evaluated using ISSR markers and morphological traits. The evaluation of molecular variance (AMOVA) demonstrated significant genetic divergence between the examined populations. It indicated that 25% of overall genetic variability was related to intra-population variety, whereas 75% was due to inter-population genetic differentiation. ISSR primers discovered 156 bands, 139 (83 %) of which have been polymorphic, each primer containing an average of 13 bands. The Polymorphic Bands (PPB) Percentage (ISSR-6) varied from 50% to 100%. (ISSR-1, ISSR-4, and ISSR-5). The average polymorphic information content (PIC), Shannon's information indexes (I), and several effective alleles (Ne) were correspondingly 0.39, 0.26, and 1.2.

Analysis of Genetic Diversity and Survey of QTLs for Grain Yield under Drought Stress in Drought Tolerant Rice Landraces Using DTY QTL-linked Markers

Genetic diversity in a set of 60 rice genotypes were analyzed using 27 random and 13 grain yield under drought (DTY) quantitative trait loci (QTLs)-linked simple sequence repeats (SSR) markers. The average gene diversity polymorphism information content were 0.53 and 0.46, respectively. The presence of DTY QTLs for grain yield under drought stress was predicted using peak marker in comparison to the positive checks. The DTY QTL qDTY12.1, amplified by the peak marker RM 28048, was found in 43.3% of genotypes, and qDTY2.2 was detected in only 6.67 % of genotypes using peak marker RM279. Two germplasm accessions, IC389895 and DT 2, possessed maximum number of DTY QTLs and absent is IC525099. Phylogenetic analysis revealed four distinct clusters within the germplasm. Overall, the evaluated genotypes presented a rich source of diversity and contain valuable DTY QTLs which can be utilized in rice genetic enhancement program for drought tolerance.

Investigation of population structure and molecular genetic diversity under coastal agro-ecosystem in rice (Oryza sativa L.)

Molecular markers are useful tools for evaluating genetic diversity and determining cultivar identity. Thirty nine simple sequence repeat (SSR) markers were selected in order to evaluate the genetic diversity in 88 genotypes. A total of 115 alleles were detected in 39 SSR polymorphic markers. The number of alleles per marker ranged from 1 to 5, with an average of 3 alleles per locus. An average polymorphism information content value of 0.5615 was recorded. It ranged from zero (RM431, RM379 and RM262) to 0.6476 (RM324), indicating significant genetic diversity among and within the rice accessions of the present study. The average observed heterozygosity was 0.1136, while the average expected genetic diversity was 0.6105. A dendrogram constructed using the Unweighted Pair Group Method with Arithmetic means (UPGMA), grouped the 88 rice genotypes into three well differentiated major clusters. The structured program without prior information provided support for the existence of three genetically distinct clusters (K=3). Key words: Cluster analysis, SSR marker, Oryza sativa, Rice breeding, Variability.

Marker based genetic variability analysis of rice (Oryza sativa L.) landraces for drought tolerance

Under the present study, assessment of genetic variability of 60 numbers of rice landraces was carried out under morphological and molecular level for selection of promising drought tolerant genotypes under upland ecosystem of North East India. Predominance of additive gene action on characters like leaf rolling index, root: culm ratio, grain yield and other yield contributing traits like plant height came out as effective parameters for selection of drought stress tolerant landraces. Molecular analysis revealed moderate genetic diversity with average Polymorphic Information Content values of 0.44 across the rice landraces. No specific clustering patterns of landraces against some morphological traits numbers of productive tillers per plant, numbers of filled grains per plant etc were found. This signifies the polygenic nature of the quantitative characters and influence of environment on them. Precise correlation between the morphological performance of the landraces and their clustering pattern under molecular analysis was found to be effective in identifying suitable landraces like Chikanswarikabar as a promising parent for future breeding programme and also to formulate efficient strategies for sustainable management of rice landraces under rain fed ecosystem.

Cevizde açık tozlanmış tohumlardan elde edilen genotiplerde fenolojik ve moleküler karakterizasyonun belirlenmesi üzerine bir araştırma

This research was carried out to reveal the phenological and genetic differences between the S-1/1 walnut genotype and its 94 progenies. In the phenological observations made, it was observed that budburst in genotypes took 52 days, leafing 50 days, leaf yellowing 31 days, and defoliation date 27 days. When the mother plant (S-1/1) and the genotypes were compared, it was found that there was a phenological variation of 75.54% in budburst, 73.41% in the leafing, 34.05% in leaf yellowing, and 93.62% in defoliation date, while the average variation was 69.15%. In the dendrogram obtained using phenological data, 2 main and 5 subgroups were obtained. In molecular genetic analyzes, 7 ISSR primers were used to determine genetic variations, as a result, 7 monomorphic and 45 polymorphic bands were obtained, and the rate of polymorphism was found to be 86.53%. The average number of alleles was calculated to be 7.42. In genotypes, the polymorphism information content (PIC) value varied between 0.48 and 0.95, while the average PIC value was calculated to be 0.73. As a result of cluster analysis, it was seen that genotypes were divided into 2 main clusters and 2 subsets. At the end of the study, it was determined that the S-1/1 and its progenies have a significant variation both phenologically and genetically.

Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS).

Olives are one of the most important fruit and woody oil trees cultivated in many parts of the world. Olive oil is a critical component of the Mediterranean diet due to its importance in heart health. Olives are believed to have been brought to the United States from the Mediterranean countries in the 18th century. Despite the increase in demand and production areas, only a few selected olive varieties are grown in most traditional or new growing regions in the US. By understanding the genetic background, new sources of genetic diversity can be incorporated into the olive breeding programs to develop regionally adapted varieties for the US market. This study aimed to explore the genetic diversity and population structure of 90 olive accessions from the USDA repository along with six popular varieties using genotyping-by-sequencing (GBS)-generated SNP markers. After quality filtering, 54,075 SNP markers were retained for the genetic diversity analysis. The average gene diversity (GD) and polymorphic information content (PIC) values of the SNPs were 0.244 and 0.206, respectively, indicating a moderate genetic diversity for the US olive germplasm evaluated in this study. The structure analysis showed that the USDA collection was distributed across seven subpopulations; 63% of the accessions were grouped into an identifiable subpopulation. The phylogenetic and principal coordinate analysis (PCoA) showed that the subpopulations did not align with the geographical origins or climatic zones. An analysis of the molecular variance revealed that the major genetic variation sources were within populations. These findings provide critical information for future olive breeding programs to select genetically distant parents and facilitate future gene identification using genome-wide association studies (GWAS) or a marker-assisted selection (MAS) to develop varieties suited to production in the US.

Development and characterization of novel microsatellite markers in Tilia amurensis Rupr. using next-generation sequencing.

Tilia amurensis (Malvaceae) is a deciduous broad-leaved tree distributed in Korea, China, and Japan. T. amurensis is used as a honey tree and also as a material for furniture, carving, and pulp. This study aimed to develop and characterize novel microsatellite markers using next-generation sequencing (NGS) of T. amurensis. NGS analysis using GS-FLX Titanium obtained 629,273 reads, of which 15,795 contigs were assembled with an average length of 830bp. A total of 4774 microsatellite regions were detected in 3602 of 15,795 contigs. In total, 360 primer sets were designed based on the microsatellite regions. Among them, 15 primer sets were selected as reproducible polymorphic markers and were characterized for three populations of T. amurensis in Korea. The average number of alleles (NA) was 3.5 in Mt. Hambaek (HB), 3.7 in Mt. Odae (OD), and 3.8 in Mt. Sobaek (SB). The average observed heterozygosity (HO) and expected heterozygosity (HE) values were 0.497 and 0.370 in the HB population, 0.470 and 0.372 in the OD population, and 0.524 and 0.410 in the SB population, respectively. The average polymorphic information content (PIC) value of the 15 microsatellite markers was 0.686. The novel microsatellite markers will be useful for further studies on genetic diversity evaluation to conserve the genetic resources and natural populations of T. amurensis.

Evaluation of the genetic diversity of Pinus koraiensis by EST-SSR and its management, utilization and protection

Pinus koraiensis is an important economic species in China. With a gradual decrease in their natural population and the increasing demand for wood, there is an urgent need to collect P. koraiensis germplasm resources and explore their genetic diversity for better management and protection. In this study, 11 pairs of EST-SSR primers were synthesized based on RNA-seq technology. The average polymorphism information content (PIC) was 0.48, which indicated that the primers had good polymorphism. 11 pairs of EST-SSR primers were used to study the genetic diversity in 26 provenances of P. koraiensis. Molecular variance analyses showed that 50% of the variations occurred among the provenances. The average Shannon diversity index (I) was 0.39, which indicated moderate genetic diversity. The observed number of alleles (Na = 41), effective number of alleles (Ne = 2.28), expected heterozygosity (He = 0.47), and Shannon diversity index (I = 0.86) of DST provenance were the maximum, which indicated that the genetic diversity in DST provenance was relatively abundant. The genetic distance was 0.002–1.729. The coefficient of genetic differentiation was 0.010–0.847. Based on genetic structure analyses, through principal coordinate analysis (PCoA) and neighbor-joining method analysis (NJ) 26 provenances were clustered into six categories. The results of this study may provide the reference primers for P. koraiensis and related tree species, and useful genetic information for strategies for improvement, management, and protection of P. koraiensis.

Relationship of Cultivated Grain Amaranth Species and Wild Relative Accessions.

Amaranthus is a genus of C4 dicotyledonous herbaceous plants, and three New World species have been domesticated to produce grain crops with light colored seed which are classified as pseudo-cereals rich in protein and minerals. A core collection of grain amaranths and immediate precursor species has been established, representing the closest related species. The goal of this study was to evaluate the genetic diversity in that collection of cultivated and wild species, using competitive allele single nucleotide polymorphism markers. A secondary objective was to determine the relationships among the three cultivated species and non-domesticated Amaranthus, while a third objective was to evaluate the utility of the markers in detecting diversity in the 276 genotypes. The markers were found to be highly variable with an average polymorphism information content of 0.365. All markers were bi-allelic; and the major allele frequency ranged from 0.388 to 0.871. Population structure analysis of the cultigens revealed the presence of two sub populations. Phylogeny confirmed that the two Mesoamerican species, Amaranthus cruentus and Amaranthus hypochondriacus, were related and distant from the South American species Amaranthus caudatus, which in turn was very closely clustered with Amaranthus quitensis, even though this is considered a weedy relative. The first pair of species were likely to have inter-crossed, while the latter two likely exist in a wild-cultivated hybrid state. In conclusion, the results of this SNP study provided insights on amaranth cultivars and their relationship to wild species, the probable domestication events leading to the cultivars, and possible crop breeding or germplasm conservation strategies.