Highest Polymorphism Information Content Value Research Articles

English

The objectives of the study included the detection of genetic variation of 21 autosomal short tandem repeats (STRs) loci from random unrelated individuals in the middle and South Arab people of Iraq, the Forensic efficiency parameters of the autosomal 21 genetic loci using power plex21® kit and to evaluate the importance of these loci for forensic genetic purposes and the possibility to use the new kit in routine practical work. FTA® Technology was utilized to extract DNA from blood collected on FTA™ paper. Twenty one (21) STR loci including D3S1358, D13S317, PentaE, D16S539, D18S51, D2S1338, CSF1PO, Penta D, THO1, vWA, D21S11, D7S820, TPOX, D8S1179, FGA, D1S1656, D5S818, D6S1043, D12S391, D19S433 and Amelogenin were amplified by using power plex21® kit. PCR products were detected by genetic analyzer 3130xL then, the data processed and analyzed by PowerStatsV1.2 software. Several statistical parameters of genetic and forensic efficiencies based on allelic frequencies have been estimated. This includes the observed heterozygosity (Ho), expected heterozygosity (He), paternity index (PI), random match probability (RMP), power of discrimination (PD), chance of exclusion (CE), polymorphic information content (PIC) and P-value. The power of discrimination values for autosomal tested loci was from 75 to 96% therefore those loci can be safely used to establish a DNA-based database for Iraq population for identifical purpose. The high PIC values of the selected markers confirm their usefulness for genetic polymorphism studies and linkage mapping programs in human as well. The mean heterozygosity observed, expected and mean PIC values across the 20 loci were 0.79, 0.83 and 0.81, respectively indicating high gene diversity. A total of nine off-ladder alleles and one tri-allelic pattern were detected in this study. Key words: Autosomal STR, Iraq, off ladder, statistical parameters, tri-allelic pattern.

Evaluation of microsatellite loci from libraries derived from the wild diploid 'Calcutta 4' and 'Ouro' banana cultivars.

Microsatellite markers have been widely used in the quantification of genetic variability and for genetic breeding in Musa spp. The objective of the present study was to evaluate the discriminatory power of microsatellite markers derived from 'Calcutta 4' and 'Ouro' genomic libraries, and to analyze the genetic variability among 30 banana accessions. Thirty-eight markers were used: 15 from the 'Ouro' library and 23 from the 'Calcutta 4' library. Genetic diversity was evaluated by considering SSR markers as both dominant markers because of the presence of triploid accessions, and co-dominant markers. For the dominant analysis, polymorphism information content (PIC) values for 44 polymorphic markers ranged from 0.063 to 0.533, with a mean value of 0.24. A dendrogram analysis separated the BGB-Banana accessions into 4 groups: the 'Ouro' and 'Muísa Tia' accessions were the most dissimilar (93% dissimilarity), while the most similar accessions were 'Pacovan' and 'Walha'. The mean genetic distance between samples was 0.74. For the analysis considering SSR markers as co-dominants, using only diploid accessions, two groups were separated based on their genome contents (A and B). The PIC values for the markers from the 'Calcutta 4' library varied from 0.4836 to 0.7886, whereas those from the 'Ouro' library ranged from 0.3800 to 0.7521. Given the high PIC values, the markers from both the libraries showed high discriminatory power, and can therefore be widely applied for analysis of genetic diversity, population structures, and linkage mapping in Musa spp.

Novel polymorphic microsatellite markers for Bellamya and their application in population genetics of three species.

Bellamya is a widely distributed freshwater snail genus in China; however, its genetic diversity is completely unknown. Sixty-five novel microsatellite loci were isolated and characterized from a microsatellite-enriched library of Bellamya aeruginosa genomic DNA. Most of the 65 loci were successfully amplified. We found high polymorphic information content values for these loci, ranging from 0.235 to 0.892. There were 3 to 12 alleles per locus, and the HE and HO varied from 0.425 to 0.953 and 0.026 to 1.000, respectively. Fifteen loci deviated significantly from Hardy-Weinberg equilibrium after Bonferroni's correction. All 65 SSR markers were tested in an additional five Bellamya species, and 96.9% of the 325 locus/taxon combinations tested resulted in cross-species amplification. Seven polymorphic microsatellite markers were randomly selected for comparison among nine populations of three species. All populations had moderate to high genetic diversity. In genetic distance-based cluster analysis, the populations of B. aeruginosa and B. dispiralis formed species-based clusters, whereas populations of B. angularia did not. The three examined Bellamya species could be differentiated using SSR markers. These microsatellite loci should be useful for genetic diversity analysis, analysis of phylogenetic relationship, and species delimitation of Bellamya.

Spectrum of β-Globin Gene Mutations and β-Thalassemia Haplotype Analysis among the Iranian Azeri Turkish Population

Background: A variety of mutations influencing gene transcription, translation, or mRNA processing have been identified in β-thalassemia. Several studies demonstrated a nonrandom linkage of particular RFLP haplotypes with specific β-thalassemia mutations. Linkage analysis using β-globin haplotypes is a valuable tool for indirect mutation detection. Our aim was to determine the spectrum and frequency of β-thalassemia mutations among Northwestern Iranians (Azeri Turkish population) along with determining the heterozygosity and polymorphism information content (PIC) value for seven β-globin markers. Method: We investigated spectrum of β-thalassemia mutations via ARMS-PCR technique followed by sequencing technique. Also β-globin gene cluster haplotypes was determined by PCR-RFLP technique on DNA samples of the patients and his (her) parents or siblings. Result: We detected 36 different mutations among 554 non-identical mutant chromosomes. The most frequent mutation was IVSII-1 (G>A) (23.6%), followed by IVSI-110 (G>A) (11.9%) and CD8 (-AA) (10.5%). Of the various β- globin gene cluster haplotypes, haplotypes I and IV were found to be most common among normal (21.36%) and mutant (15.76%) chromosomes, respectively. The highest observed heterozygosity (48%) was found for the HindIII Gγ and HindII 5'ψs polymorphic sites, whereas the highest expected heterozygosity (50%) was predicted for the HindIII Gγ and HindII sites, which also had the highest PIC value of 0.37. Conclusion: The current study implies mutational heterogeneity among investigated population. Haplotype study results (heterozygosity and PIC), clarifies β-globin markers usefulness for tracking mutant alleles as a complementary method to confirm the genotype in prenatal diagnosis (PND) among investigated population.

Physiological and Molecular Characterization of Faba bean (Vicia fabaL.) Genotypes for Adaptation to Drought Stress

AbstractFaba bean (Vicia fabaL.) is one of the most important and drought sensitive grain legumes. Drought stress is thus one of major constraints in global faba bean production. In this study, twenty local and exotic faba bean genotypes were characterized on physiological and molecular basis. Seeds of faba bean genotypes (six per pot) were sown in poly venyl chloride pots. After seedling emergence, soil moisture was maintained at 100%, 50% and 25% of field capacity designated as well watered, moderate drought and severe drought, respectively. Drought stress significantly influenced the leaf area, leaf temperature, stomatal conductance, relative leaf water contents, grain yield and water‐use efficiency. Faba bean genotypes also differed for the leaf area, leaf temperature, relative leaf water contents, grain yield and water‐use efficiency. Faba bean genotypes Kamline and L.4 were better equipped to curtail water loss, maintain tissue water status, produce stable grain yield and had better water‐use efficiency under mild and severe drought stress, and may be used in breeding programmes. Amplified fragment length polymorphism markers showed high potential in detecting polymorphism and estimating genetic diversity among faba bean genotypes. Unweighted pair group method with arithmetic mean cluster analysis of the genotypes illustrated considerable association between molecular diversity, genetic background and geographic origin. In crux, high polymorphic rate and polymorphism information content values, together with the low genetic similarity observed among tested genotypes suggests a high level of heterogeneity, which may be used in breeding programmes to assemble different drought tolerance mechanisms in one genotype.

English

A set of 36 polymorphic simple sequence repeat (SSR) primers well distributed on all the 12 rice chromo-somes have been used to assess the genetic diversity among the rice varieties. A total of 98 alleles were detected with an average of 2.78 alleles per locus across 39 genotypes.  The number of alleles varied from two to four of these SSR loci. Among the primers, RM 401, RM 20A, RM 536, RM 7575 and RM 5862 produced maximum number of alleles (4). Out of the 98 alleles, 86 were polymorphic and this exhibited 87.76% polymorphism. SSR marker analysis differentiated the genotypes into two distinct groups. The polymorphism information content (PIC) value of the markers ranged between 0.28 and 0.50 with a mean value of 0.45. The highest PIC value (0.50) was observed for ten primers that is, RM 2, RM 24, RM 411, RM 104, RM 266, RM 125, RM 4674, RM 247, RM 3476 and RM 3351 while the lowest was 0.28 for RM 29. The genetic similarity coefficients for 39 genotypes obtained with SSR markers ranged from 23.8 to 78.4%.   Key words: Rice, genetic diversity, simple sequence repeat (SSR) markers.

English

The aim of this study was of twofold. One was to determine the genetic structure of Iraq population and the second objective of the study was to evaluate the importance of these loci for forensic genetic purposes. FTA® Technology (FTA™ paper DNA extraction) utilized to extract DNA. Twenty (20) STR loci and Amelogenin), including D3S1358, D13S317, Penta E, D16S539, D18S51, D2S1338, CSF1PO, Penta D, THO1, vWA, D21S11, D7S820, TPOX, D8S1179, FGA, D2S1338, D5S818, D6S1043, D12S391, D19S433 and Amelogenin amplified by using power plex21® kit. Polymerase chain reaction (PCR) products detected by genetic analyzer 3730xL then data analyzed by PowerStatsV1.2. Based on the allelic frequencies, several statistical parameters of genetic and forensic efficiency have been estimated. This includes the homozygosity and heterozygosity, effective number of alleles (n), the polymorphism information content (PIC), the power of discrimination (DP) and the power of exclusion (PE). The power of discrimination values for all tested loci was from 75 to 96%; therefore, those loci can be safely used to establish a DNA-based database for Iraq population. The high PIC values of the selected markers confirm their usefulness for genetic polymorphism studies and linkage mapping programs in human as well. The mean heterozygosity observed, is expected to have mean PIC values across the 20 loci which were 0.77, 0.81 and 0.78, respectively, indicating high gene diversity.   Key words:  Autosomal STR, genetic variation, Iraq, statistical parameters.

Genetic diversity and genetic relationships of japonica rice varieties in Northeast Asia based on SSR markers

Genetic diversity and the relationship among nine japonica rice groups consisting of 288 landraces and varieties in different geographical origins of Northeast Asia (China, Japan, Korea, Democratic People's Republic of Korea) and the Russian Far East district of the Russian Federation were evaluated with 154 simple sequence repeat (SSR) markers. A total of 823 alleles were detected. The observed allele numbers (Na) per locus, Nei's gene diversity (He) and the polymorphism information content (PIC) ranged from 2 to 9, 0.061 to 0.869 and 0.060 to 0.856, with an average of 5.344, 0.624 and 0.586, respectively. Five SSR loci, RM1350, RM1369, RM257, RM336 and RM1374, provided the highest PIC values and are potential for exploring the genetic diversity of rice cultivars in Northeast Asia. Molecular variance analysis showed that a significant difference existed both among groups (91.6%) and within each group (8.4%). The low genetic variation within each group indicated that the gene pool is narrow and alien genetic variation should be introduced into the rice breeding program in Northeast Asia. Based on the He and PIC values, the nine groups were ranked in a descending order: Heilongjiang landraces, Jilin landraces, Japanese improved varieties, Heilongjiang improved varieties, Russian Far East district of the Russian Federation improved varieties, Liaoning improved varieties, Jilin improved varieties, Korean improved varieties and Democratic People's Republic of Korea improved varieties. The nine groups were further divided into three subgroups and the 288 varieties into five clusters. This study provided information for parent selection in order to broaden the gene pool of the japonica rice germplasm in Northeast Asia.

Genetic diversity of DNA microsatellite for Tibetan Yak

To assess the genetic diversity and relationship of the Tibetan yak breeds. The genetic diversity and phylogenies of a total of 480 individual from 11 Tibetan yak groups were analyzed using PCR and multiplex gel electrophoresis of silver staining technology with eight pairs of microsatellite markers.The result showed that these markers were highly polymorphic loci with rich genetic diversity in the Tibetan yak populations.The average polymorphic information content (PIC) in 11 groups of yak were higher than 0.5. The highest HEL13 was 0.8496, and the lowest TGLA57 was 0.7349. Among them, the PICof Dingqing yak was minimum (0.7505), indicating that the group is relatively pure.Sangri Yak had the highest PIC value (0.7949) indicating greater genetic variationwithinthe groups. Among the 11 groups examined, the order of heterozygosity size wasSangri(0.8193)>Jiangda(0.8190)>Sangsang(0.8157)>Baqing(0.8150)>Kangbu(0.8123)> Jiali(0.8087)>Gongbujiangda(0.8054)>Sibu(0.8041)>Leiwuqi(0.8033)>Pali(0.8031)>Dingqing(0.7831). The groups from eastern Tibet had grater genetic diversity than those from Western Tibet, which indicate that Tibet may be one of the cradles of the yak.According to the genetic distance, the cluster relationship constructed with UPGMA and NJ methods showed that 11 yak groups in Tibet could be divided into three forms. In summary,Tibet yak has abundant genetic diversity and the selected microsatellite markers can be used to evaluategenetic diversity of Tibetan yak.

Genetic diversity studies and identification of SSR markers associated with Fusarium wilt (Fusarium udum) resistance in cultivated pigeonpea (Cajanus cajan)

Genetic diversity and identification of simple sequence repeat markers correlated with Fusarium wilt resistance was performed in a set of 36 elite cultivated pigeonpea genotypes differing in levels of resistance to Fusarium wilt. Twenty-four polymorphic sequence repeat markers were screened across these genotypes, and amplified a total of 59 alleles with an average high polymorphic information content value of 0.52. Cluster analysis, done by UPGMA and PCA, grouped the 36 pigeonpea genotypes into two main clusters according to their Fusarium wilt reaction. Based on the Kruskal-Wallis ANOVA and simple regression analysis, six simple sequence repeat markers were found to be significantly associated with Fusarium wilt resistance. The phenotypic variation explained by these markers ranged from 23.7 to 56.4%. The present study helps in finding out feasibility of prescreened SSR markers to be used in genetic diversity analysis and their potential association with disease resistance.

AFLP based genetic relationship and population structure analysis of Canna—An ornamental plant

Genetic relationships among 42 cultivars of Canna were determined by using amplified fragment length polymorphism (AFLP) marker. A total of 1607 DNA fragments was produced with 25 AFLP primer combinations and out of which 1491 (92.78%) were found polymorphic and 116 (7.22%) monomorphic. The number of polymorphic fragments varied from 33 (E-ACA/M-CAA) to 86 (E-ACT/M-CAA) with an average of 59.6 per primer combination and percent polymorphism varied from 81.7% (E-AAG/M-CAA) to 100% (E-ACC/M-CTT) with an average of 92.8% per primer combination. The polymorphism information content (PIC) value ranged from 0.24 to 0.35 with an average of 0.30 per fragment and the highest PIC value (0.35) was noticed for primer combination E-AAG/M-CAC followed by E-ACT/M-CTA, E-ACA/M-CAA, E-AAG/M-CAA (0.34). Marker index (MI) and resolving power (RP) varied from 11.22 to 26.66 and 17.10 to 40.00 respectively. Jaccard's similarity coefficient varied from 0.33 to 0.72 with an average of 0.49±0.03. The maximum genetic similarities (72%) were noticed between the cultivar NBC_1 and NBC_2; NBC_16 and NBC_19 followed by NBC_19 and NBC_30 (70%). Based upon genetic similarity coefficient the cultivars NBC_43, NBC_24, NBC_38, NBC_22, NBC_29 and NBC_36 were found to be most divergent among all the cultivars. The UPGMA clustering revealed four major groups accommodating 93% cultivars and three cultivars each of different species i.e. C. argentina (NBC_24), C. latifolia (NBC_43) and C. generalis (NBC_13) did not grouped with any clusters. Model based clustering obtained from STRUCTURE analysis also reveals similar pattern of grouping.

Elucidation of Genetic Relationships in the Genus Cajanus Using Random Amplified Polymorphic DNA Marker Analysis

In this present investigation, a total of 27 RAPD primers were used to elucidate the genetic relationships between cultivated Cajanus cajan cultivars and 10 allied species of primary, secondary and tertiary gene pool, including C. cajanifolius, C. scarabaeoides, C. platycarpus, C. albicans, C. volubilis, C. sericeus, C. acutifolius, C. lineatus, C. lanceolatus and C. reticulates. All primers showed polymorphism at species level and produced 215 unequivocal polymorphic bands, with an average of 7.96 bands per primer. These polymorphic primers exhibited variation with regard to average band informativeness, resolving power, and showed high polymorphism information content value. No single primer was able to distinguish between all the two cultivars of C. cajan and ten allied species of Cajanus, but several species specific amplified fragments were observed. The pair wise Jaccard’s similarity coefficient values revealed high level of inter-specific genetic variation in the genus Cajanus. Cluster analysis exhibited the grouping of two C. cajan accessions with C. cajanifolius in one cluster, while except C. platycarpus, all the nine wild Cajanus species belonging to the secondary and tertiary gene pool form another cluster. The present analysis more or less agreed with the sectional classification of the genus Cajanus, and it has been hypothesized that cultivated pigeonpea has evolved through multi-genomic interaction through C. cajanifolius, and it has experienced minor genomic reorganization during its divergence. Again, identification of species specific amplification pattern substantiated the utility of RAPD markers on selection of suitable species to transfer the desirable trait into cultivated C. cajan, through marker aided breeding for its genetic augmentation, and also for the effective management of genetic resources of C. cajan.

Phylogenetic relationships of chrysanthemums in Korea based on novel SSR markers

Chrysanthemums are well known for their esthetic and medicinal values. Characterization of chrysanthemums is vital for their conservation and management as well as for understanding their genetic relationships. We found 12 simple sequence repeat markers (SSRs) of 100 designed primers to be polymorphic. These novel SSR markers were used to evaluate 95 accessions of chrysanthemums (3 indigenous and 92 cultivated accessions). Two hundred alleles were identified, with an average of 16.7 alleles per locus. KNUCRY-77 gave the highest polymorphic information content value (0.879), while KNUCRY-10 gave the lowest (0.218). Similar patterns of grouping were observed with a distance-based dendrogram developed using PowerMarker and model-based clustering with Structure. Three clusters with some admixtures were identified by model-based clustering. These newly developed SSR markers will be useful for further studies of chrysanthemums, such as taxonomy and marker-assisted selection breeding.

10.5937/ratpov50-4344 = Molecular evaluation of genetic variability in tomato (Lycopersicon esculentum mill.) genotypes by microsatellite markers

The objective of this research was to assess genetic diversity using eight microsatellite markers in 30 tomato genotypes from the collection of the Institute of Field and Vegetable Crops in Novi Sad. The SSR markers were selected from publicly available data and Solanaceae Genome Network database. Genotypes were grouped into three clusters, using Ward's hierarchical clustering method and Euclidean distance measure. Markers SSR248, TMS9, TMS42 and SSR111 had very high PIC (Polymorphism information content) values and can be recommended for the future studies.

Genetic diversity study of indigenous cattle (Gir and Kankrej) population of Rajasthan using microsatellite markers

The genetic diversity study of native Gir and Kankrej (Bos indicus) cattle populations were evaluated using nine microsatellite markers (ETH-225, CSRM-60, HEL-9, INRA-005, ETH-10, HAUT-24, BM1818, ILSTS-002 and ILSTS-006) suggested by FAO (ISAG). A total of 60 cattle were sampled from different places of local Rajasthan region. For each, 30 individuals were sampled. The mean number of observed and effective alleles in Kankrej were high (5.222 and 3.714) comparatively and the average expected heterozygosity values (0.5403) indicated high diversity in the Kankrej population than Gir (0.4520). High polymorphism information content (PIC) values observed for most of the markers with an average of 0.5116 are indicative of high polymorphism of these markers in Kankrej breed than in Gir (0.4202), which showed high informativeness of all the microsatellite markers in Kankrej breed. Three microsatellites markers (HAUT24, BM1818 AND ILSTS006) did not show amplification in both breeds. INRA005 was the only markers amplified in Kankrej. The allele diversity (mean observed number of alleles was 6.11; mean effective number of alleles was 5.187) and gene diversity (0.2771) values implied a substantial amount of genetic variability in both populations. Reasonably high PIC values observed for most of the markers, with an average PIC value of 0.5116 across all the loci implied that this set of microsatellite are very informative for evaluation of genetic diversity in both the breeds. This informativeness of microsatellite markers showed it can be used for various applications like, conservation, disease diagnosis and polymorphism in different populations. Key words : Genetic diversity, polymorphism information content (PIC), heterozygosity, polymorphism, marker.

Evaluation of genetic diversity in rice using simple sequence repeats (SSR) markers

The genetic diversity of 64 rice genotypes using 20 SSR primers on chromosome number 7-12 was investigated. DNA was extracted by modified cetyl trimethyl ammonium bromide (CTAB) method. The banding pattern was recorded in the form of 0-1 data sheet which was analyzed using unweighted pair group method with arithmetic mean (UPGMA) based on Jaccard's similarity coefficient. The results revealed that out of twenty, eight primers showed distinct polymorphism, indicating the robust nature of microsatellites in revealing polymorphism. The cluster analysis showed higher level of genetic variation among the genotypes. Similarity coefficients ranged from 0.40 to 0.96. The dendrogram revealed 8 major distinct clusters. Higher range of similarity values for related genotypes using simple sequence repeats (SSR) provides greater confidence for the assessment of genetic diversity and relationships. The polymorphism information content (PIC) value for the SSR loci ranged from 0.36 to 0.98. Higher PIC values were associated with higher level of polymorphism. The information obtained from the DNA fingerprinting studies helps to distinctly identify and characterize the various genotypes. Such information can be used in background selections during backcross breeding programs. Key words: Genetic diversity, simple sequence repeats (SSR) marker, dendrogram.

Assessment of in silico BAC-based simple sequence repeat (SSR) marker development for tomato (Solanum lycopersicum L.)

Tomato landraces are less sensitive to environmental stresses and grown mainly under rain fed conditions. They are still grown in small farms due to quality and special demand of consumers. These landraces are valuable sources of genetic traits, and plant breeders can use breeding programs for crop improvement. One of the primary needs of the crop improvement is the estimation of genetic diversity. Development of microsatellite simple sequence repeat (SSR) markers from map-referenced bacterial artificial chromosomes (BAC) clones is a very effective means of targeting markers to marker scarce positions in the genome. This study was aimed at developing a set of functional SSR markers via in silico analysis of publicly available tomato DNA sequences. As a result, 17 SSR markers were developed and tested on one tomato commercial cultivar and eight local landraces. 12 loci (27 alleles) were scored and showed 100% polymorphic patterns. The calculated polymorphism information content (PIC) values for the SSR markers developed ranged from 0.62 to 0.97 (mean 0.89). The SSR motifs CT(26) AT(27) and TTC(6) TTA(4) had the highest PIC value (0.97), while CAA(5)A(8) had the lowest PIC value (0.62). According to tomato expressed sequence tag (EST) analysis, some of these developed SSR markers, such as mono and di-nucleotide are related to some genes. The T(16) motif is related to hydroxyproline-rich glycoprotein, which is a family protein from Arabidopsis thaliana . On the other hand, the SSR with tri-nucleotide repeat motif AAC(4)A(11) was related to a putative homologous protein to A7Q2S4 from Vitis vinifera . Keywords: Tomato landraces, in silico simple sequence repeat (SSR) markers, DNA markers, genetic diversity

Development of 18 microsatellite loci for the freshwater snail Bellamya aeruginosa (Mollusca, Gastropoda)

Although it is a major freshwater gastropod species, genetic diversity of Bellamya aeruginosa was completely unknown. Eighteen microsatellite loci were isolated and characterized from (AC)(15)-enriched genomic libraries of the freshwater snail B. aeruginosa. Most of the 18 loci were successfully amplified and high polymorphic information content values were found, ranging from 0.244 to 0.792 (mean 0.541). The number of alleles per locus ranged from 5 to 13 (mean 8.8), the expected heterozygosity varied from 0.347 to 0.950 (mean 0.815) and the observed heterozygosity varied from 0.087 to 0.782 (mean 0.431). Eight loci showed significant deviation from Hardy-Weinberg equilibrium after Bonferroni's correction and no significant genotypic linkage disequilibrium was detected between most locus pairs, except for TXH79-TXH97 and TXH113-TXH121. These 18 polymorphic microsatellite loci should be useful for population genetics analysis and species identification of Bellamya.

Genetic diversity assessment of sesame core collection in China by phenotype and molecular markers and extraction of a mini-core collection

BackgroundSesame (Sesamum indicum L.) is one of the four major oil crops in China. A sesame core collection (CC) was established in China in 2000, but no complete study on its genetic diversity has been carried out at either the phenotypic or molecular level. To provide technical guidance, a theoretical basis for further collection, effective protection, reasonable application, and a complete analysis of sesame genetic resources, a genetic diversity assessment of the sesame CC in China was conducted using phenotypic and molecular data and by extracting a sesame mini-core collection (MC).ResultsResults from a genetic diversity assessment of sesame CC in China were significantly inconsistent at the phenotypic and molecular levels. A Mantel test revealed the insignificant correlation between phenotype and molecular marker information (r = 0.0043, t = 0.1320, P = 0.5525). The Shannon-Weaver diversity index (I) and Nei genetic diversity index (h) were higher (I = 0.9537, h = 0.5490) when calculated using phenotypic data from the CC than when using molecular data (I = 0.3467, h = 0.2218). A mini-core collection (MC) containing 184 accessions was extracted based on both phenotypic and molecular data, with a low mean difference percentage (MD, 1.64%), low variance difference percentage (VD, 22.58%), large variable rate of coefficient of variance (VR, 114.86%), and large coincidence rate of range (CR, 95.76%). For molecular data, the diversity indices and the polymorphism information content (PIC) for the MC were significantly higher than for the CC. Compared to an alternative random sampling strategy, the advantages of capturing genetic diversity and validation by extracting a MC using an advanced maximization strategy were proven.ConclusionsThis study provides a comprehensive characterization of the phenotypic and molecular genetic diversities of the sesame CC in China. A MC was extracted using both phenotypic and molecular data. Low MD% and VD%, and large VR% and CR% suggested that the MC provides a good representation of the genetic diversity of the original CC. The MC was more genetically diverse with higher diversity indices and a higher PIC value than the CC. A MC may aid in reasonably and efficiently selecting materials for sesame breeding and for genotypic biological studies, and may also be used as a population for association mapping in sesame.

Malt Genotypic Screening of Polymorphism Information Content (PIC) of PCR-based Marker in Barley, Based on Physiological Traits

Brewing genotypes were described by polymorphism information content (PIC) of 22 SSR markers in barley (Hordeum vulgare L.), associated with malt quality. Notably, the values of diastatic power set ranged from 5.53 to 24.13 U/Kg in these samples, suitable to assess the relative importance of biochemical components of malt variations and genetic characteristics. Cluster analysis revealed a significant correlation between eco-geographic origin and SSR marker clustering, resolving the accessions into four subgroups. Moreover, SSRs with higher PIC values and higher average number of alleles per marker in the population with higher values of diastatic power were found to be an efficient utility for distinguishing brewing genotypes in barley. These results possibly indicated that SSRs linked to brewing traits could be very useful for application in monitoring malt traits, evaluating genetic diversity, and determining the sampled eco-geographic origins in barley.