Highest Polymorphism Information Content Value Research Articles

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.

Validation of <i>SalTol</i> Linked Markers and Haplotype Diversity on Chromosome 1 of Rice

To determine the usefulness of SSR markers associated with a major QTL for salinity tolerance designated as collection of 115 diverse rice genotypes was phenotyped and genotyped using tightly linked DNA markers. These markers include five SSRs, RM1287, RM8094, RM3412, RM493 and RM140, and two EST markers, CP6224 and CP03970, on chromosome 1. Among the seven markers, the highest number of alleles (15) was found in RM8094, followed by 10 in RM187, RM3412 and RM493. The polymorphic information content (PIC) values ranged from 0.54 to 0.89. The highest PIC value (0.89) was found for RM8094, followed by RM493 and RM3412 (0.81) and RM1287 and RM140 (0.77). The marker RM8094 was useful for discriminating between tolerant and susceptible genotypes and therefore may be useful for marker-assisted selection. Seven haplotypes were identified among the 115 genotypes using the haplotype of IR66946-3R-178-1-1 (FL478) – the most widely used tolerant parent – which was used as a reference haplotype. Four genotypes had the same haplotype as FL478 and Pokkali-1. Of the seven different Pokkali seed sources tested, Pokkali-1 (IRGC 8948) contributed the SalTol region on the chromosome 1 segment of FL478. Genotypes from the haplotypes (in comparison with FL478) 1, 2 and 5 may be important for selecting alternative tolerant parents.

Genetic diversity in blast resistance of Bhutan rice landraces

With an objective to evaluate the Bhutan rice (Oryza sativa L.) landraces for genetic diversity in blast resistance, 402 accessions viz. 352 landraces, a differential set of 32 R gene lines and 18 modern cultivars were field-evaluated in three blast ‘hotspot’ sites followed by genetic analysis of the 352 landraces with 27 microsatellite markers. Across the sites, 19 landraces (5.4%) exhibited complete resistance with zero disease score and 203 (58%) and 163 (46%) landraces showed high partial resistance for early leaf and panicle blast, respectively, with disease score of four to six. Field evaluation for leaf and panicle blast at three experimental sites in Bhutan showed best cultivar discrimination in early leaf blast at the tillering stage (heritability, h2 = 0.32) and in the panicle blast at maturity (h2 = 0.44). Subdivision of the genetic variation into cultivar groups revealed the most variation for blast severity within the 352 landraces with h2 of 0.31 and 0.46 for early leaf and panicle blast, respectively. Cluster analysis of the landraces revealed two distinct rice cultivar groups, which separated at dissimilarity of 0.84 according to origin of the cultivars from low, mid and high altitude zones in Bhutan. All microsatellites were polymorphic with two to 21 different alleles per marker and a high polymorphic information content value of 0.61. The identified blast resistant landraces were genetically diverse originating from different rice cultivation zones. Further investigation of the resistant and partial resistant material may reveal specific blast resistance genes, which could be useful to mitigate blast incidence in rice-producing countries.

Isolation and characterization of polymorphic microsatellites loci in the freshwater snail Bellamya aeruginosa (Mollusca, Gastropoda)

As one of the major freshwater gastropod species, genetic diversity analysis of Bellamya was totally blank. Fifteen microsatellites loci were isolated and characterized from the freshwater snail Bellamya aeruginosa (Reeve, 1863). Most of the 15 loci had successful amplification and high polymorphic information content value (PIC), which ranged from 0.3174 to 0.8886 (average 0.7074). Allele number per locus ranged from 5 to 12 (average 8.4), the expected heterozygosity (HE) and observed heterozygosity (HO) varied from 0.6674 to 0.9073 and 0.0714 to 0.9130 with an average of 0.7985 and 0.6779, respectively. Six loci showed significant deviation from Hardy–Weinberg equilibrium (HWE) after Bonferroni correction (P < 0.0034) and no significant genotypic linkage disequilibrium was detected between most of locus pair, except for eight locus pairs. These fifteen polymorphic microsatellites loci would be precious for population genetics analysis and species identification of Bellamya.

Morpho-agronomic and simple sequence repeat-based diversity in colored rice (Oryza sativa L.) germplasm from peninsular India

Knowledge of the genetic diversity in the germplasm accessions is important for the efficient germplasm management. We studied 45 colored rice accessions, which had been earlier collected from peninsular India. The accessions were evaluated at two diverse locations for 12 morpho-agronomic traits and genotyped using 50 simple sequence repeat (SSR) markers. Significant genotypic variability was observed for all morpho-agronomic traits studied. Dendrogram and principal component analysis based on morpho-agronomic traits separated the accessions into three clusters. The first two principal components accounted for 82% of the total variation. The most discriminatory traits were number of grains per panicle, biomass yield, and days to flowering and maturity. The SSR analysis revealed high polymorphic information content value of 0.84. Though, Mantel test did not show a significant correlation, yet the classification based on phenotyping and genotyping data showed good agreement for the expression of morpho-agronomic traits in the formation of clusters. Five accessions had high concentration (> 100 μg/g) of Fe and one of Zn. Our study revealed the presence of large genetic variation among the colored rice accessions evaluated and moderate agreement between morpho-agronomic and SSR–based classifications and of these with geographic diversity.

Potentiality of evenly distributed hypervariable microsatellite markers in marker-assisted breeding of rice

With 4 figures and 1 table Abstract To provide ready-to-use markers for background selection in marker-assisted breeding of rice, we have extracted 840 hypervariable microsatellite markers (hvRMs) evenly distributed in the genome from 18 828 Class I simple sequence repeats. These hvRMs were grouped into bins of 5-Mb intervals with 5–8 bins depending on the chromosome length. In each bin, 10 hvRMs were selected based on their microsatellite repeat number and type. Of 840, a representative of 36 hvRMs were selected and its polymorphic information content (PIC) was estimated by amplifying 24 diverse rice cultivars. The findings revealed that hvRMs show high PIC values and more alleles when compared to the 25 randomly chosen microsatellite markers. The informative hvRMs developed for background selection across cultivars in this study along with the already established molecular markers tightly linked to the genes of agronomic value could be of value for the development of a ‘MAS kit’ for speeding up the efforts of plant breeders for targeted crop improvement.

Comparative Analysis of Genetic Diversity and Structure in Rice Using ILP and SSR Markers

Genetic diversity of 36 rice entries from the United States Department of Agriculture (USDA) rice collection was assessed using 103 ILP (intron length polymorphism) and 54 SSR (simple sequence repeats) markers. A total of 236 and 332 alleles were detected by the ILP and SSR markers, respectively. On average, the SSR markers produced higher polymorphism information content value and number of alleles than the ILP markers. Whereas the Nei's genetic distance measured using the SSR markers was much higher than that measured using the ILP markers. Mantel's test indicated that there was a statistically significant correlation ( r=0.827, P<0.001) between the two marker systems. UPGMA clustering based on the ILP and SSR markers resulted in consensus dendrograms. The cophenetic correlation coefficient ( r=0.918, 0.878 and 0.924, P<0.001 for the ILP, SSR and combined markers, respectively) showed a highly accurate dendrogram represented the genetic distance among these entries. The 36 entries were divided into four groups. Four African Oryza glaberrima accessions were clustered within a distinct group (I), and the remaining entries were separated into three groups (II, III and IV). All the entries could be also clustered into two main groups: One was composed of III and IV, considered as indica group, and the other was composed of I ( O. glaberrima) and II (japonica-like). Model-based cluster analysis revealed that the japonica-like group maintained very pure ancestry while the indica group shared mixed ancestry, especially for group III, which had seven admixtures sharing from 19.5% to 30.0% of ancestry with group IV (based on SSR markers). It is suggested that ILP and SSR markers could be very useful for the genetic study and breeding in rice.

Variety identification and genetic relationships of mungbean and blackgram in Thailand based on morphological characters and ISSR analysis

Genetic diversity and relatedness were measured in 17 mungbean (Vigna radiata (L.) Wilczek) and 5 blackgram (Vigna mungo (L.) Hepper) genotypes by means of inter-simple sequence repeat (ISSR) analysis and morphological characters. Unweighted pair-group method arithmetic average (UPGMA) analysis of 19 morpho-agronomic characters showed clear separation of the genotypes into 3 major groups; cluster I containing 15 Thai cultivated mungbean varieties and breeding lines, cluster III containing 4 Thai cultivated blackgram varieties, and cluster II containing a mungbean wild relative (subspecies sublobata), a blackgram wild relative (subspecies silvestris) together with an Indian mungbean landrace. Pair wise coefficients of genetic similarity between all genotypes ranged from 0.17 to 0.84 with an average of 0.52. In total, 341 ISSR fragments were amplified for the two Vigna species by ISSR analysis using 18 ISSR primers. The polymorphism revealed with the ISSR primers was 90.6%. The number of amplified fragments varied from 9 to 32, with a size range of 200 - 1500 bp. The average numbers of fragments per primer and polymorphic fragments per primer were 18.94 and 17.17, respectively. Polymorphism information content (PIC) values ranged from 0.23 to 0.37 with an average of 0.31 across all the genotypes. Pair wise coefficients of ISSR-based genetic similarity between all genotypes ranged from 0.70 to 0.99 with an average of 0.86, suggesting quite narrow genetic base of mungbean and blackgram in Thailand that might limit continued breeding success. UPGMA analysis based on ISSR exhibited 2 major clusters; cluster I containing all mungbean genotypes and cluster II containing all blackgram genotypes. It appeared that ISSR was more effective for classification at the species level although no clear separation at the subspecies level was found. All 22 mungbean and blackgram genotypes can be effectively distinguished by only 6 ISSR primers with the highest PIC values, suggesting the applicability of ISSR analysis for variety identification.

Establishment of DNA Fingerprint ID in Sugarcane Cultivars in Yunnan, China

To well evaluate and use the cultivars, we should identify them scientifically and accurately by DNA molecular markers. In this paper, 27 cultivars developed by two breeding institutes in Yunnan province were analyzed with SSR marker. Eight pairs of core SSR primers selected from about 120 pairs of SSR primers offered by the International Sugarcane Microsatellite Consortium made up the core primers for DNA fingerprint. A total of 129 bands were acquired by PAGE with the core primers, 123 of which were polymorphic bands, accounting for percentage of polymorphic band (PPB) was 95.35%, and the mean value of polymorphism information content (PIC) reached 0.9445; the genetic similarity coefficient of the cultivars was 0.269–0.767. SMC1047HA and MSSCIR21 with high PIC value could be used to distinguish all cultivars, which were the most efficient single primers. The result of evaluating different primer combinations from eight core primers indicated that MSSCIR36/MSSCIR21, MSSCIR16/ MSSCIR36, and MSSCIR36/SMC336BS were very efficient in identifying these Yunnan cultivars, and their similar coefficients were lower than those of other primer combinations. At the same time, three primer combinations were validated with ten main released cultivars. The result showed MSSCIR16/MSSCIR36 was the optimum primer combination, which can be used in con-structing DNA fingerprint ID of cultivars. The DNA fingerprint ID was set up, including serial number of National Nursery of Sugarcane Germplasm Resources (NNSGR), country region code, breeding institute, core primer name and SSR marker data,which not only consists of the important information of cultivars, but also helps researchers to identify cultivars efficiently. At the same time, it can provide reliable scientific evidence for the protection of intellectual property right for these cultivars.

Analysis of phenotypic and microsatellite-based diversity of maize landraces in India, especially from the North East Himalayan region

The maize landraces in the North East Himalayan (NEH) region in India, especially in the Sikkim state, are morphologically highly diverse. The present study provides details of phenotypic and molecular characterization of a set of 48 selected maize landrace accessions, including the 'Sikkim Primitives' which have a unique habit of prolificacy (5-9 ears on a single stalk). Multi-location phenotypic evaluation of these 48 accessions revealed significant genetic variability for grain yield and its components, leading to identification of several promising accessions. Cluster analysis and PCA using nine morpho-agronomic characters clearly separated 'Sikkim Primitives' from the rest of the accessions. PCA revealed two principal components describing 90% of the total variation, with hundred kernel weight, ear length, ear diameter, number of kernels per ear and flowering behaviour forming the most discriminatory traits. The accessions were genotyped using 42 microsatellite or simple sequence repeat (SSR) markers using a 'population bulk DNA fingerprinting strategy', with allele resolution using an automated DNA Sequencer. The study revealed a high mean number of alleles per SSR locus (13.0) and high Polymorphism Information Content (PIC) value of 0.60. The analysis also led to identification of 163 private/unique alleles, differentiating 44 out of 48 accessions. Six highly frequent SSR alleles were detected at different loci (phi014, phi062, phi090, umc1266, umc1367 and umc2250) with individual frequencies >/=0.75. Some of these SSR loci were reported to tag specific genes/QTL for some important traits, indicating that chromosomal regions harboring these SSR alleles were not selectively neutral. Cluster analysis using Rogers' genetic distance also revealed distinct genetic identity of the 'Sikkim Primitives' from the rest of the accessions in India, including Sikkim. Mantel's test revealed significant and positive correlation between the phenotypic and molecular genetic dissimilarity matrices. The study was the first to portray the patterns of phenotypic and molecular diversity in the maize landraces from the NEH region in India.

Variety identification and comparative analysis of genetic diversity in yardlong bean ( Vigna unguiculata spp. sesquipedalis) using morphological characters, SSR and ISSR analysis

Genetic diversity and relatedness of 23 yardlong bean ( Vigna unguiculata spp. sesquipedalis) accessions and 7 accessions of a hybrid between cowpea ( V. unguiculata spp. unguiculata) and yardlong bean (dwarf yardlong bean) in Thailand were estimated using morphological characters, simple sequence repeat (SSR) and inter-simple sequence repeat (ISSR) markers. In addition, two mungbean ( Vigna radiata (L.) Wilczek) and two blackgram ( Vigna mungo (L.) Hepper) accessions were also used as outgroup species for molecular analysis. Five morphological characters were diverse among most accessions. However, five groups of 2–3 accessions could not be distinguished from one another based on these morphological characters alone. Unweighted pair-group arithmetic average (UPGMA) analysis of these characters separated these 30 accessions into 2 major groups; the yardlong bean group and the dwarf yardlong bean group. Eleven of the sixteen SSR primers yielded clear SSRs, ten of which were polymorphic (90.91% polymorphism), detecting a total of 54 alleles with an average of 4.91 alleles per locus. These 10 polymorphic SSR markers successfully distinguished 28 yardlong bean and dwarf yardlong bean accessions. The polymorphic information content (PIC) among genotypes varied from 0.251 to 0.752 with an average of 0.597. Among the 16 ISSR primers used, a total of 312 ISSR fragments were amplified for these three Vigna species, revealing the polymorphism percentage of 91.03%. The average ISSR PIC value (0.197) with the range of 0.137–0.276 was lower than that of SSR. Nevertheless, the average marker index of this multilocus marker was 3.495, which was higher than that of SSR (0.669), owing to the differences in the effective multiplex ratio. In addition, Mantel test cophenetic correlation coefficient was higher for ISSR (0.566) than that of SSR (0.198). These results indicated higher efficiency of ISSR for estimating the levels of genetic diversity and relationships among yardlong beans and dwarf yardlong beans in this study. Pair-wise coefficients of SSR- and ISSR-based genetic similarity among all yardlong bean and dwarf yardlong bean accessions averaged 0.87 and 0.91, respectively, suggesting a narrow genetic base that emphasizes the need to broaden genetic diversity to ensure continued breeding success. Clustering of genotypes within groups was not similar when SSR and ISSR derived dendrograms from UPGMA analysis were compared. It appeared that ISSR was the most effective marker system in determining the genetic variability and relationships among yardlong bean and dwarf yardlong bean accessions and differentiating three Vigna species. In addition, ISSR was also most useful for variety identification since all 30 yardlong beans and dwarf yardlong bean accessions can be effectively distinguished by only four ISSR primers with the highest PIC values.

Genetic Polymorphism of Jeju Horses by Microsatellite DNA Markers in Korea

We determined the genetic diversity and distance between Jeju and Thoroughbred horses by genotyping for 20 microsatellite loci consisting of (TG)n repetitive sequence. The expected heterozygosity ranged from 0.1 to 0.789 in the Jeju horses and from 0.505 to 0.824 in the Thoroughbred horses. Polymorphic information content (PIC) values ranged from 0.09 to 0.709 in the Jeju horses and 0.365 to 0.730 in Thoroughbred horses. There were no significant differences in heterozygosity and PIC values between Jeju and Thoroughbred horsesHowever, LEX035 was estimated relatively high heterozygosity (0.789) and PIC value 0.709) in Jeju horses and LEX050 was respectively 0.824, and 0.730 in the Thoroughbred horses. We may conclude that the genetic differentiation was low between Jeju and Thoroughbred horses. LEX 050, LEX055, LEX059 and LEX 063 could be used as geneticmarkers for differentiating Jeju from Thoroughbred horses.

Gene-based microsatellites for cassava (Manihot esculentaCrantz): prevalence, polymorphisms, and cross-taxa utility

BackgroundCassava (Manihot esculenta Crantz), a starchy root crop grown in tropical and subtropical climates, is the sixth most important crop in the world after wheat, rice, maize, potato and barley. The repertoire of simple sequence repeat (SSR) markers for cassava is limited and warrants a need for a larger number of polymorphic SSRs for germplasm characterization and breeding applications.ResultsA total of 846 putative microsatellites were identified in silico from an 8,577 cassava unigene set with an average density of one SSR every 7 kb. One hundred and ninety-two candidate SSRs were screened for polymorphism among a panel of cassava cultivars from Africa, Latin America and Asia, four wild Manihot species as well as two other important taxa in the Euphorbiaceae, leafy spurge (Euphorbia esula) and castor bean (Ricinus communis). Of 168 markers with clean amplification products, 124 (73.8%) displayed polymorphism based on high resolution agarose gels. Of 85 EST-SSR markers screened, 80 (94.1%) amplified alleles from one or more wild species (M epruinosa, M glaziovii, M brachyandra, M tripartita) whereas 13 (15.3%) amplified alleles from castor bean and 9 (10.6%) amplified alleles from leafy spurge; hence nearly all markers were transferable to wild relatives of M esculenta while only a fraction was transferable to the more distantly related taxa. In a subset of 20 EST-SSRs assessed by fluorescence-based genotyping the number of alleles per locus ranged from 2 to 10 with an average of 4.55 per locus. These markers had a polymorphism information content (PIC) from 0.19 to 0.75 with an average value of 0.55 and showed genetic relationships consistent with existing information on these genotypes.ConclusionA set of 124 new, unique polymorphic EST-SSRs was developed and characterized which extends the repertoire of SSR markers for cultivated cassava and its wild relatives. The markers show high PIC values and therefore will be useful for cultivar identification, taxonomic studies, and genetic mapping. The study further shows that mining ESTs is a highly efficient strategy for polymorphism detection within the cultivated cassava gene pool.

Molecular and Biochemical Characterization of Short Duration Quality Protein Maize

Fifty microsatellite or simple sequence repeat (SSR) markers, spread across the maize genome were used for analyzing a set of 19 elite Quality Protein Maize (QPM) lines, including seventeen lines developed in India and two at CIMMYT, Mexico. Polymorphic profiles for 47 SSR loci have aided in differentiating the QPM inbred lines. The polymorphism information content (PIC) values among the inbreds ranged from 0.06 (umc2229) to 0.70 (umc1071) with an average of 0.45 per primer-pair. The genetic relationships as indicated by the cluster analysis of SSR data were largely in congruence with the known pedigree of the QPM lines. The study resulted in identification of two SSR markers, umc1071 and umc1063 with higher PIC values of 0.70 and 0.64, respectively. The tryptophan content among the genotypes was found to vary considerably. Two genotypes viz., VOL 2 and VOL 8 were found to differ significantly for tryptophan content (0.51% and 0.94%, respectively). Both these QPM genotypes being derived from the same non-QPM parent CM 145, makes them ideal for mapping of modifiers for tryptophan content.

Molecular analysis of cultivated naked barley (Hordeum vulgare L.) from Qinghai-Tibet Plateau in China using SSR markers

Naked barley is widely planted in Qinghai-Tibet Plateau in China and is essential for the daily life of Tibetans in those regions. In this study, the genetic diversity of 64 cultivated naked barley accessions from Qinghai-Tibet Plateau in China was analyzed using 30 mapped SSRs linked with the important traits of barley improvement. A total of 132 alleles were identified at 22 polymorphic SSR loci, with the number of each locus ranging from 2 to 15, the polymorphism information content (PIC) values ranging from 0.16 to 0.91, and with an average of 0.65. Of the selected SSRs, 13 SSR markers with high PIC value were highly efficient for the genetic analysis of Chinese barley. The accessions were divided into five main groups by cluster analysis and could be differentiated from each other. The genetic diversity in the Tibet accessions was slightly higher than in the Sichuan accessions. It is found that there were specific genes linked with the collecting sites. These results indicate the cultivated naked barley from Qinghai-Tibet Plateau in China are highly polymorphic and could be considered as an important resource bank for cultivated naked barley breeding in the future.

Geographical patterns of genetic diversity in cultivated chickpea (Cicer arietinum L.) characterized by amplified fragment length polymorphism

The objective of this study was to evaluate the genetic relationships of 28 chickpea accessions from diverse origin using AFLP markers. On average, 13 polymorphic bands per primer were observed in AFLP analysis. The average polymorphic information content (PIC) was 0.71, ranging from 0.48 to 0.92. The lowest and the highest PIC value were recorded for primer P-GAG/M-GC and P-AT/M-GC, respectively. The average GD, based on Fst values among the 21 accessions was 0.42, ranging from 0.61 to 0.16. From the UPGMA dendrogram, it is discernible that material taken for the analysis can be divided in four clusters. The results indicate that the greatest genetic diversity occurs in Afghanistan, Iran and Lebanon. In many cases, the diversity between individuals of an accession is as great as between individuals of different accessions. Based on DNA markers it is concluded that there are three centers of diversity for chickpea: Pakistan-Afghanistan, Iran-Turkey and Syria-Lebanon. India and Ethiopia, which were previously considered as a secondary center of diversity for chickpea, showed lower diversity than the above regions.

Selections of an Olive Breeding Program Identified by Microsatellite Markers

This work reports on the use of 10 microsatellites for identifying and testing the paternity of the first 17 selections of an olive (Olea europaea L.) breeding program in Córdoba, Spain. The usefulness of the microsatellites was confirmed by the high discrimination power and polymorphism information content values and by the low probability of identity found in the 24 main Spanish cultivars. In the selections from the crosses ‘Picual’ × ‘Arbequina’ and ‘Frantoio’ × Picual, the putative male parent was the expected one. In the individuals coming from putative selfings of Arbequina and Picual and from the putative crosses Frantoio × Arbequina, Arbequina × Frantoio and Picual × Frantoio, the male paternity assigned a priori was wrong. Only three microsatellites were needed to discriminate all the selections and to differentiate them from the 24 main cultivars. The probability of having a seedling with a certain allele combination for the 10 microsatellites was 7.63e‐06, in the case of Arbequina × Picual and the reciprocal cross, and 1.53e‐05 for the cross Frantoio × Picual. A dendrogram generated using the Dice similarity coefficient and the unweighted pair group method with arithmetic mean (UPGMA) agglomeration method showed every selection grouped with one of their two parents.

A high density barley microsatellite consensus map with 775 SSR loci

A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWB(Rec) x OWB(Dom)', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMap 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley.