SRAP Markers Research Articles

Genetic diversity and population structure of mahaleb cherry (Prunus mahaleb L.) and sweet cherry (Prunus avium L.) using SRAP markers

Abstract Genetic diversity of 47 Mahaleb cherry genotypes ( Prunus mahaleb L.) and six sweet cherry accessions ( Prunus avium L.) was studied using 13 SRAP primer combinations. The number of polymorphic fragments detected per primer combination ranged from 1 to 10 bands with an average 4.23 bands. Average PIC was 0.42 over all primer combinations. Cluster analysis using UPGMA method and Dice’s coefficient grouped the species into two main clusters with similarity coefficient ranging from 0.16 to 0.93. Sum of first three PCAs could be represented most of (65.64%) the total variation in the original dimensions and confirmed the results of cluster analysis. Based on AMOVA results, the allele numbers among groups and species studied in this research were more than those observed within them. This is the first report of using SRAP marker as a tool for determining genetic variation among and within P. mahaleb and P. avium .

Genetic Diversity of Major Sugar Beet Varieties from Three Regions of China with SRAP Markers

Shortage of sugar beet germlasm resources results in the lag in researches of breeding and molecular biology.It is necessary to analyze the major varieties from three major production regions of China.Eighty-eight primer pairs were used to amplify the genomic DNA from leaves of four types of sugar beet varieties with different economic traits,which contain high yield type;high yield,low sugar and Rhizomania resistant type;standard type;medium yield,high sugar and anti-brown spot type,and 33 of which were obtained to be with availability.Two hundred and forty-one varieties from three major regions of China and nine varieties from abroad were detected with 33 primer pairs of SRAP markers.A total of 719 unambiguous bands were obtained,459 of which were polymorphic.The average ratio of polymorphic bands was 63.8%.Compute over-all mean showed that genetic distance was 0.4165,genetic similarity among varieties was 0.6593,the genetic similarities were 0.7528 among foreign varieties,0.6945 among monogerm varieties,0.6816 among polygerm tetraploid varieties,and 0.6612 among polygerm diploid varieties.A total of 250 varieties were divided into four cluster groups based on cluster analysis by MEGA3.1 (at intercept of 0.2).Each genepool from three major regions of sugar beet production in China showed high level of genetic diversity,of which the Northeast genepool showed the highest.The varieties from China and abroad were classified into two different groups by POPGEN32.This indicated definite difference in the genetic background between foreign and native varieties.

Genetic diversity in rhizosphere soil microbes detected with SRAP markers

Genetic diversity in rhizosphere soil microbes detected with SRAP markers

Use of ISSR, SRAP, and RAPD markers to assess genetic diversity in Turkish melons

The genetic relationships among 63 melon ( Cucumis melo L.) genotypes collected from various regions of Turkey were determined by comparing their molecular ISSR, SRAP, and RAPD markers with those of 19 foreign melon genotypes to investigate the taxonomic relationships and genetic variation of Turkish melon germplasm. Total 162 polymorphic markers (69, 18, and 75 obtained from ISSR, SRAP, and RAPD primers, respectively) were used to define the genetic similarity among the melon genotypes by dendrogram or two and three dimensional scalings. The average similarity (SM coefficient) between any two pairs of accessions examined as estimated by molecular variation was 0.73 ± 0.48. Within-group genetic similarities ranged between 0.46 and 0.96. Related genotypes or genotypes collected from similar regions were partitioned to similar clusters. Southeastern Anatolian genotypes were distinctly apart from group inodorus and group cantalupensis (sweet) genotypes. This reinforced the position of Turkey in the secondary genetic diversity center of melon. The genetic diversity among Turkish genotypes ( H = 0.28 and I = 0.42) was only a little less than that of the world accessions ( H = 0.30 and I = 0.45). On the other hand, the percentage of polymorphic loci among Turkish melon genotypes (90.7%) was even higher than that of the world accessions (87.6%).

An assessment of the cultural capabilities of clonal propagation and molecular characterization of Yucca elephantipes cultivars

This study was conducted to describe an efficient micropropagation protocol suitable for the production of clonally uniform Yucca plants through the shoot tip and lateral bud explants and compare the application and utility of TRAP and SRAP marker techniques for analysis of genetic diversity among six genetically Yucca diverse genotypes. The results indicated that the “Green” cultivar gave the significantly highest average mean value of primary and secondary shoot number (2.02and 3.21 /explant, respectively). Medium protocol B containing MS medium + 0.2 mg/l of NAA+ 4.0 mg/l of BAP significantly gave the highest mean value for shoot multiplication derived from primary and secondary cultures (1.63 and 2.96/explant, respectively). The lateral bud explant derived propagules from the primary and secondary culture was the most effective for shoot multiplication. Molecular markers tools (SRAP and TRAP) analysis were used for detecting polymorphism among six genetically Yucca diverse genotypes. Cluster analysis using SRAP data grouped the 6 Yucca genotypes into two main clusters with Jaccard’s similarity coefficient ranging from 0.40 to 0.64. The dendrogram generated from TRAP data clearly indicated two main clusters with similarity coefficient ranging from 0.40 to 0.92. SRAP and TRAP data were combined to produce a dendrogram and the similarity coefficient among the six Yucca genotypes varied from 0.39 to 0.75.

Genetic diversity in Apium graveolens and related species revealed by SRAP and SSR markers

Genetic diversity is essential to crop improvement. However, lack of molecular markers prevents the understanding of genetic diversity in celery and related species. In this study, SRAP and SSR markers was firstly used to evaluate genetic variation in 68 accessions of Apium graveolens and related species. A total of 888 bands were generated by 40 primer combinations of SRAP and 32 bands were produced by eight SSR markers. Of the 920 bands, 95.1% were polymorphic between A. graveolens and related species, and 49.2% were polymorphic within A. graveolens. Cluster and structure analysis could distinguish local celery, celery, and related species. These results suggested that both SRAP and SSR technologies can be efficiently used to characterize genetic variation and analyze genetic relationship in celery and related species.

Exploitation of SSR, SRAP and CAPS-SNP markers for genetic diversity of Citrus germplasm collection

The present study was to assess informativeness and efficiency of three different molecular markers for genetic diversity among 24 Citrus and its relative species. Sixty one SSR, 33 SRAP and 24 CAPS-SNP markers were used to evaluate the level of polymorphism and discriminating capacity. A total of 596, 656 and 135 polymorphic amplicons were observed in SSR, SRAP and CAPS-SNP markers with average polymorphism information content (PIC) of 0.97, 0.98 and 0.89, respectively. High levels of polymorphism were recorded for SSR and SRAP compared with CAPS-SNP markers. The highest correlations ( r = 0.930) were obtained between SSR and SRAP markers, whereas SSR and CAPS-SNP were poorly correlated ( r = 0.833). Cluster analysis was performed to construct dendrograms using UPGMA. And the dendrogram from SSR data was most congruent with the general dendrogram. These findings provide basis for future efficient use of these molecular markers in the genetic analysis of Citrus and its relatives.

AFLP and SRAP markers linked to the mj gene for root-knot nematode resistance in cucumber

Root-knot nematodes (Meloidogyne spp.) are an important worldwide pest of cucumber (Cucumis sativus L.). Molecular markers linked to the Javanese root-knot nematode (M. javanica) resistance gene mj in cucumber may aid marker assisted selection. One-hundred AFLP (EcoRI-MseI) and 112 SRAP were used to screen resistant and susceptible parents for polymorphisms to develop molecular markers linked to the mj gene. Of the 100 AFLP primers, 92 produced bands and two yielded candidate markers (E-ATT/M-CAA and E-AAC/M-CTG). These two bands were cut off from polyacrylamide gel, cloned and sequenced. Primers designed from the sequences did not yield polymorphic bands between the parents. In addition, the sequences did not contain any restriction site or indel to be used to convert them to CAPS or SCAR markers. The two sequences obtained from polymorphic AFLP markers were used primarily to design D1F, D1R, D17F and D17R primers. SRAP forward and reverse primers were used in combination with these four specific primers to search for polymorphisms between parents. Of the 112 primer combinations 11 yielded polymorphisms between parents. MapMaker Exp 3.0 software was used to analyze the 11 markers. Two markers were identified that flanked the mj gene at distance of 16.3 and 19.3 cM. The results indicated that these markers should be useful to develop molecular markers flanking the mj gene.

Comparative genome mapping among Populus adenopoda, P. alba, P. deltoides, P. euramericana and P. trichocarpa

Among the genus Populus, the sections Populus (white poplar), Aigeiros Duby (black poplar) and Tacamahaca Spach contain many tree species of economical and ecological important properties. Two parental maps for the inter-specific hybrid population of Populus adenopoda × P. alba (two species of Populus section) were constructed based on SSR and SRAP markers by means of a two-way pseudo-test cross mapping strategy. The same set of SSR markers developed from the P. trichocarpa (belonging to Tacamahaca section) genome which were used to construct the maps of P. deltoides and P. euramericana (two species of Aigeiros section) was chosen to analyze the genotype of the experimental population of P. adenopoda × P. alba. Using the mapped SSR markers as allelic bridges, the alignment of the white and black poplar maps to each other and to the P. trichocarpa physical map was conducted. The alignment showed high degree of marker synteny and colinearity and the closer relationship between Aigeiros and Tacamahaca sections than that of Populus and Tacamahaca. Moreover, there was evidence for the chromosomal duplication and inter-chromosomal reorganization involving some poplar linkage groups, suggesting a complicated course of fission or fusion in one of the lineages. A poplar consensus map based on the comparisons could be constructed will be useful in practical applications including marker assisted selection.

Assessing Genetic Structure and Relatedness of Jerusalem Artichoke (<i>Helianthus tuberosus</i> L.) Germplasm with RAPD, ISSR and SRAP Markers

Jerusalem artichoke (Helianthus tuberosus L.) is an old tuber crop with a recently renewed interest in multipurpose improvement, but little effort has been made to characterize its genetic resources. A study was conducted to assess genetic structure and genetic relatedness of 47 diverse Jerusalem artichoke accessions using RAPD, ISSR and SRAP markers. A total of 296 (87.1%) polymorphic bands were detected from 13 RAPD markers; 92 (80%) from six ISSR primers; and 194 (88.6%) for nine combinations of SRAP primers. Five optimal clusters were inferred by the STRUCTURE program from the RAPD or ISSR data, while six optimal clusters were found from the SRAP data or combined marker data. Significant linear relationships between the distance matrices for all pairs of individual accessions were detected for all marker pairs and the estimated correlation coefficient was 0.40 for RAPD-ISSR, 0.53 for RAPD-SRAP, and 0.43 for ISSR-SRAP. Based on the combined data, the neighbor-joining clustering of the 47 accessions matched closely with those inferred from the STRUCTURE program. Three ancestral groups were observed for the Canadian germplasm. Most diverse germplasm harbored in the USA collection. These findings not only reveal the compatible patterns of genetic structure and relatedness inferred with three marker types, but also are useful for managing Jerusalem artichoke germplasm and utilizing diverse germplasm for genetic improvement.

Molecular identification and genetic relationships among coffee species (Coffea L.) inferred from ISSR and SRAP marker analyses

The identification and genetic relationships of 23 coffee species and one coffee-related species Canthium diccocum were studied using ISSR and SRAP markers. The average polymorphism information content of SRAP primers (0.81) was lower than ISSR primers (0.86), whereas the average resolving power of the SRAP primers (9.74) is higher than the ISSR primers (8.64). The genetic similarity among the species ranged from 0.30 to 0.89 using ISSR and 0.11 to 0.90 using SRAP marker systems. Based on marker analysis, all twenty three coffee species were clustered into two major groups. Both the markers amplified species-specific fragments and are useful in genetic diversity analysis of coffee.

Application of SRAP and ISSR Molecular Markers in Genetic Diversity of DaXing’anling Area Wild <i>Auricularia auricula</i>

A genetic diversity analysis was conducted, of 14 wild Auricularia auricula strains and 6 cultivated strains from DaXing'anling region by SRAP and ITS markers. Using PCR-SRAP system, we selected 9 pairs of primers for the wild and cultivated strains respectively, and analyzed their genetic diversity through clustering analysis. The results were as follows: 88 fragments were amplified, and the polymorphic bands were 76. The PIC (polymorphism information content) value of these markers varied from 0.048 to 0.918, averaging 0.599. Kinship of Auricularia auricula strains was determined by analyzing their ITS sequences. The software ClustalX 1.83 and MEGA 4.1 were used to conduct the phylogeny analysis. The results were as follows: ITS 1, 5.8 S, ITS2 had as many genetic loci as 52.1%. Cluster analysis of the two kinds of markers were congruous and there were more genetic diversities in wild strains than in cultivated strains. SRAP and ITS techniques can be used to analyze the genetic diversity in the future study.

QTLS Analysis of Several Traits in Longan

ABSTRACTA big F1 population of ‘FengliduoxDawuyuan’ were created by crossing between a high quality cultivar ‘Fengliduo’ and a large fruit size main cultivar ‘Dawuyuan’. Among the Hybrid population, 94 F1 individuals were randomly chosen and used as the mapping population. Based on the mapping population, a molecular genetic linkage map of longan was constructed with RAPD, ISSR, SRAP and AFLP molecular markers. According to the linkage analysis by JoinMap3.0, the molecular linkage map of ‘Fengliduo’ fell into 20 linkage groups, which contained 184 markers, with an average interval of 6.72 cM and covered a total distance of 1102.8 cM; while the molecular linkage map of ‘Dawuyuan’ fell into 19 linkage groups, which contained 243 markers, with an average interval of 6.02 cM and covered a total distance of 1348.3 cM. The IM method was used to determine QTL associated with some traits in this population. 29 QTLs related to fruit weight, soluble solid content, seed weight, peel weight and edible rate were identified in 20 linkage groups of parents.

Molecular Genetic Map Construction and QTL Analysis for Fruit Maturation Period in Litchi

ABSTRACTA hybrid F1 population of ‘Maguili x Jiaohesanyuehong’ was created by crossing between the very late ripening cultivar ‘Maguili’ as the maternal parent and the very early ripening cultivar ‘Jiaohesanyuehong’ as the paternal parent. Seventy-six randomly chosen F1 individuals were used as the mapping population. SRAP and AFLP molecular marker analysis were carried out with the mapping population and the two parents. Molecular genetic maps for both parents were built. The ‘Maguili’ map contained 179 loci which fell into 16 linkage groups. The coverage of the map was 610.55cM with an average distance of 3.75cM between markers. The ‘Jiaohesanyuehong’ map consisted of 82 loci allocated into 15 linkage groups. The map covered 548.09cM and had a mean distance of 8.18cM between markers. IM method was used to determine QTLs for the fruit maturation period. Five QTLs for fruit maturation period were detected. Two QTLs were on LG ‘JHSYH2’and ‘JHSYH4’ of the paternal map and explained a contribution rate of 34.4% and 70.1% respectively. Three QTLs were on LG ‘MGL2’ and ‘MGL5’, and the contribution rate they can explain was between 38.3% and 65.8%.

A preliminary research of genetic linkage map construction and QTL analysis for growth-related traits in yellow catfish (<I>Pelteobagrus fulvidraco</I>)

Genetic linkage maps of yellow catfish (Pelteobagrus fulvidraco) were constructed using SSR,SRAP and TRAP markers and a pseudo-testcross mapping strategy. A segregating population including 100 progenies was sampled within the first filial generation obtained by artificial fertilization between a male parent and a female parent from wild and breeding populations respectively. Totally,13 SSR,89 SRAP and 26 TRAP markers were used to construct a genetic map. Female map included 16 linkage groups,covering a total of 585.5 cM in length. Male map included 15 linkage groups,covering a total of 752.3 cM in length. Combined map included 5 linkage groups,covering a total of 231.3 cM in length. This map was used to scan the QTL related to growth traits of yellow catfish. One head length QTLs were identified in female map located in LG7,LOD value is 3.2 and accounted for 13 % of phenotypic variation. A body width and a body length QTLs were identified in male map both located in LG1,LOD value is 2.4 and 2.1 respectively,and accounted for 12% and 11% of phenotypic variation respectively. Three QTLs could be considered to apply in marker-assisted selection for growth-related traits breeding of yellow catfish.

A comparative analysis of genetic diversity in medicinal Chrysanthemum morifolium based on morphology, ISSR and SRAP markers

The diversity and genetic relationship among 29 populations of Chrysanthemum morifolium, one of Chrysanthemum indicum and one of Chrysanthemum nankingense from China were analyzed using morphological traits and molecular markers. Twenty morphological traits were scored as well as 182 ISSR marker-fragments, as amplified by 22 primers [the percentage of polymorphic bands (PPB): 81.87%], and 243 SRAP marker-fragments as generated by 26 primer pairs (PPB: 75.72%). Mantel’s test indicated significant correlation (r = 0.624) of morphological trait and SRAP. By contrast, the morphological trait showed low correlation with ISSR (r = 0.246). Cluster analysis showed groupings of the accessions according to all four methods correlated well with their geographic region of origin, and most populations from the south of China were classified into one cluster and most populations from the north of China were classified into another cluster. Finally, an appropriate strategy for conserving the C. morifolium germplasm was proposed.

DNA Fingerprints of 18 Cassava Varieties Based on Sequence-Related Amplified Polymorphism Markers

Thirty-six pairs of polymorphic SRAP markers were used to construct DNA fingerprint of 18 cassava ( Manihot esculenta Crantz) varieties. Among the total 320 amplified bands, 235 (73.4%) were polymorphic with an average of 6.5 bands per primer pair. The unweighted pair-group method with arithmetic average (UPGMA) cluster showed 4 major groups at similarity index of 0.734. Two primer combinations, Me1/Em5 and Me24/Em10, had the highest efficiency to distinguish cassava varieties, which were applicable to develop the DNA fingerprints of the 18 cassava varieties. The amplified bands were converted into binary codes with presence (1) and absence (0), and each variety had a unique 18-digital code. The confident probability of the DNA fingerprint was as high as 99.9996%.

CONSTRUCTION OF GENETIC LINKAGE MAP AND LOCALIZATION OF QTLS FOR POWDERY MILDEW RESISTANCE IN CUCUMBER (CUCUMIS SATIVUS L.)

Based on a population of 188 F 2 family derived from a cross of the cultivar D8 (susceptible to powdery mildew) and JIN5 (resistant to powdery mildew) of cucumber, a genetic linkage map was constructed and mapped QTLs related to the powdery mildew. In this map, a total of 65 markers including ISSR and SRAP markers were clustered into 7 major linkage groups, spanning a total of 831.6 cM, with an average distance of 12.7 cM. The minimum distance of markers intervals is 4.8 cM, and the maximum is 22.3 cM. The association of genetic markers and cucumber powdery mildew resistance was investigated. By using of composite interval-mapping approach, two QTLs associated with powdery mildew resistance were found, which located on the third linkage group, and they explained 7.6 and 13.5% of the trait variation, respectively. The results are useful for the marker assisted selection for the resistance of cucumber powdery mildew.

Genetic diversity of Rehmannia glutinosa cultivars based on sequence-related amplified polymorphism markers

SRAP analytic system was used to assess genetic diversity of Rehmnnia glutinosa. Twenty-three Rehmnnia glutinosa cultivars were screened with 288 primer combinations, of which 13 produced stable and reproducible amplification patterns in three repetitive experiments. Among a total of 338 amplified fragments, 306 (90.5%) were polymorphic, with an average of 23.5 fragments for each primer combination. The percentage of polymorphic bands for each primer combination varied from 58.3 to 100%. The cultivars had a similarity ranging from 0.335 to 0.713 with a mean of 0.518. Shannon's diversity index and expected heterozygosity were 0.3217 and 0.2008, respectively. Based on the cluster, which were conducted on the similarity matrix of SRAP marker data, the cultivars were divided into four groups at the 20 rescaled distance cluster combine. The results demonstrated that SRAP is a stable marker technique for the assessment of genetic diversity of Rehmannia glutinosa cultivars, and that the level of genetic diversity among them from different production areas was relatively high.

Analysis of genetic diversity among indigenous landraces from sesame (Sesamum indicum L.) core collection in China as revealed by SRAP and SSR markers

The molecular genetic diversity of 404 indigenous landraces from sesame core collection in China were evaluated by 11 SRAP and 3 SSR markers, 175 fragments were generated, of which 126 were polymorphic with an average polymorphism rate of 72%. Jaccard’s genetic similarity coefficients (GS=0.7130), Nei’s gene diversity (h=0.2418) and Shannon’s Information index (I=0.3847) were calculated, a dendrogram of the 404 landraces was made, landraces from various zones were distributed throughout the dendrogram, accessions from different agro-ecological zones were indistinguishable by cluster analysis, geographical separation did not generally result in greater genetic distance, a similar pattern was obtained using principal coordinates (PCO) analysis. As to seven agro-ecological zones, the maximum Nei’s gene diversity (h = 0.2613) and Shannon index (I = 0.3980) values in zone VII indicated that they were genetically more diverse than those in other zones, while the least genetically diverse region was zone III (h = 0.1772, I = 0.2858). Nei’s genetic identity and genetic distance among landraces from seven agro-ecological zones were also analyzed, the genetic relationship of seven zones was inferred using the UPGMA method. This study demonstrated that SRAP and SSR markers were appropriate for evaluation of sesame genetic diversities. There existed extensive genetic diverse among indigenous landraces and the abundance of genetic diversity of landraces in different agro-ecological zones was various. Understanding of these characteristics of indigenous landraces in China can provide theoretical foundation for further collection, effective protection and reasonable utilization of these sesame landraces in breeding.