Sequence-related Amplified Polymorphism Markers Research Articles

Sequence-Related Amplified Polymorphism-PCR Analysis for Genetic Diversity in Rhizoctonia solani Populations Infecting Pulse Crops in Different Agro-Ecological Regions of India

A B S T R A C T Rhizoctonia solani is a destructive fungal pathogen infecting wide range of crop plants including pulses causing wet root rot or web blight disease. The present study was aimed to determine the genetic diversity of R. solani populations using Sequence-Related Amplified Polymorphism (SRAP) markers. The SRAP markers were used for genetic diversity analysis of 89 isolates of R. solani belonging to 7 Anastomosis Groups (AGs) isolated from different pulse crops representing 21 states from 16 agro-ecological regions of India. Out of 30 SRAP primer combinations evaluated, 16 combinations provided amplification with 100% polymorphism and the primer combinations Me1/Em1and Me1/Em4 provided the highest number of bands (14). The isolates of R. solani showed high level of genetic variability and grouped into 7 major clusters at 35% genetic similarity by using unweighted pair group method with an arithmetic average analysis. Bootstrap analysis grouped the isolates into five major clusters at 28% genetic similarity and about 95% isolates shared common sub-grouping patterns in both the analysis. The majority of the isolates representing various AGs were grouped together into different sub-clusters. The molecular clusters did not correspond to agro-ecological regions and crops of the origin of the isolates because of the diversity in the hosts and adopt ability of the pathogen under different environmental conditions prevalent in various parts of the country. First time an attempt was made in the present study to determine the genetic variability of the R. solani populations isolated from different pulse crops representing various AGs using SRAP markers.

Mapping of Pi, a gene conferring pink leaf in ornamental kale (Brassica oleracea L. var. acephala DC)

We previously found that pink leaf is conferred by a single semi-dominant gene in ornamental kale. To map this gene, we constructed an F2 segregating population containing 184 individuals by crossing W02–7, a white-leaved inbred line, with P02–9, a pink-leaved inbred line. We screened 297 simple sequence repeat (SSR) and 437 sequence-related amplified polymorphism (SRAP) markers using bulked segregant analysis. We identified one SSR and seven SRAP markers that linked tightly to the pink-leaf (Pi) gene. To obtain more specific genomic markers, we converted six SRAPs to sequence-characterized amplified region (SCAR) markers. We constructed a genetic linkage map of the Pi locus using one SSR and five SCAR markers, spanning a total interval of 15.0 cM. One SSR marker, Ni2C12, and one co-dominant SCAR marker, Boac04, flanked Pi on either side at distances of 0.6 and 2.4 cM, respectively. Based on the reference genome sequence of Brassica oleracea, we positioned Pi on the top of chromosome C3. We also detected that pink hypocotyl co-segregated with pink inner leaf. These markers provide the basis for fine-scale mapping and cloning of Pi, and may be used for marker-assisted selection in ornamental kale breeding programs.

Mapping QTL for bruchid resistance in rice bean (Vigna umbellata)

The damage caused to stored seed by bruchids (Callosobruchus maculatus) is considered to be a major production constraint in rice bean (Vigna umbellata). Breeding for genetically determined resistance is the most environmentally benign and cost-effective means to mitigate the losses to bruchid infestation. Here, a screen of rice bean germplasm identified two sources of resistance, and determined the genetic basis of the resistance using a quantitative trait locus (QTL) mapping approach. The two resistant accessions (LRB238 and JP100304) were each crossed to a common susceptible cultivar (LRB26) to generate F2 mapping populations, one of which (LRB238 × LRB26) was genotyped with a range of Vigna sp. microsatellite assays and by sequence related amplified polymorphism (SRAP) fingerprinting. The resulting linkage map comprised ten linkage groups and covered a genetic distance of 872.1 cM with a mean inter-marker distance of 32.05 cM. The subsequent QTL analysis detected the presence of 11 QTL, distributed over all ten linkage groups, most of which were associated with the % damage caused to the seed. Two major QTL, Cmpd1.5 (flanked by the SRAP markers E2M9-270 and E12M7-311) and Cmpd1.6 (flanked by the SRAP marker E7M10-141 and the microsatellite locus CEDG259) mapped within 11.9 cM and 13.0 cM of the flanking markers, respectively, accounted for, 67.3 and 77.4 % of the variance respectively, for % damaged seeds. A bulked segregation analysis carried out in the JP100304 × LRB26 population revealed that the resistance donor harboured some resistance factors not represented in LRB238.

Deciphering population structure and diversity inLuffa cylindrica(L.) M. Roem. using morphological and sequence-related amplified polymorphism markers

Luffa cylindrica(L.) M. Roem. is an underutilized vegetable and a potential biodiesel crop for future. Its fruits are edible and used as vegetable. To aid in the selection of lines for breeding, genetic variation and structure of ten populations ofL. cylindricawere determined with three morphological characters and 23 sequence-related amplified polymorphism (SRAP) markers. All the three morphological characters were found diverse among 45 accessions. The SRAP primers produced a total of 177 bands, out of which 129 were polymorphic. Informative markers assessed by different measures (polymorphism information content = 0.18, marker index = 1.26, resolving power = 2.87) will direct the selection of primers for cultivar identification inL. cylindrica. Low level of genetic differentiation among populations and higher level within populations (Gst= 0.4073,Nm= 0.7277,He= 0.124,I= 0.20) was detected that might be due to cross-pollinated nature ofL. cylindrica. The clustering pattern obtained through dendrogram and principal coordinate analysis was loosely concordant with the geographical distribution. The Bayesian structure analysis indicated an admixture type of population distribution. The results designate that SRAP and morphological markers are informative for characterization ofL. cylindricaand identification of distinctive cultivars.

Mapping of gene conferring adult-plant resistance to stripe rust in Chinese wheat landrace Baidatou

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a destructive foliar disease of wheat worldwide. Sustainable control of the disease is preferably achieved by deploying stripe rust resistance genes in wheat cultivars. Our previous studies have shown that Baidatou, a Chinese wheat landrace, displayed good adult-plant resistance (APR) to wheat stripe rust in Gansu Province, an epidemic region for stripe rust in China. To elucidate the genetic basis of APR to stripe rust in Baidatou, a cross between Baidatou and Mingxian 169, which is susceptible to all the known Chinese (Pst) races, was performed. Adult plants of F1, F2 and F2:3 generations derived from the cross Mingxian 169/Baidatou were inoculated in the field with the most prevalent Chinese Pst race, CYR33, in Yangling, Shaanxi Province, during 2009–2010 and 2010–2011 crop seasons, respectively. The results showed that the resistance of Baidatou to stripe rust was conferred by a single dominant gene. Six hundred and sixty simple sequence repeat (SSR) markers and 128 sequence-related amplified polymorphism (SRAP) markers were screened for association with the resistance gene to stripe rust using bulked segregant analysis. Four polymorphic SSR markers and two SRAP markers were identified to be linked to the resistance gene. A linkage map was constructed with six molecular markers and the resistance gene. The genetic distance of two flanking SSR markers to the resistance gene, temporarily designated YrBai, was 3.6 and 5.4 cM, respectively. Based on the position of the SSR markers on the wheat chromosome, YrBai was located on chromosome 6DS. According to the rust reaction patterns, SSR marker allele analysis and the pedigree of the Yr genes on chromosome 6D, YrBai is likely to be a novel APR gene against stripe rust. The specificity of the two flanking markers of YrBai was validated in 99 wheat germplasms. The gene and its flanking markers should be useful for developing wheat cultivars with durable resistance.

Sequence-related amplified polymorphism and inter-simple sequence repeat marker-based genetic diversity and nuclear DNA content variation in common vetch (Vicia sativaL.)

Genetic diversity of 30 common vetch (Vicia sativaL.) lines and cultivars obtained from various resources or collected from natural flora of Turkey was evaluated by using 55 sequence-related amplified polymorphism (SRAP) and five inter-simple sequence repeat (ISSR) primer sets, and their nuclear DNA contents were determined by flow cytometer. A total of 188 polymorphic loci were detected, with an average of 3.62 loci per primer. The percentage of polymorphic loci was 82.1%. The polymorphism information content values ranged from 0.12 to 0.96, with an average of 0.63. The genetic distance coefficients were in the range of 0.112–0.627. Cluster analysis revealed that the 27 lines and three cultivars could be divided into two main groups. No polyploidy was detected within any vetch lines tested while significant (P< 0.0001) nuclear DNA content differences were determined. The present study revealed that fast and accurate fingerprinting analysis could be done using SRAP and ISSR markers, which indicated existing significant variation among common vetch lines and cultivars.

Analysis on genetic diversity and genetic relationship of medicinal species in Dipsacus from China by SRAP

The author detected the genetic diversity and genetic relationship within and among eight medicinal species of Dipsacus by the approach of sequence-related amplified polymorphism (SRAP). The associated genetic parameters were calculated by POPGENE 1.31. The Genetic distance was calculated by TREECONW and the systematic diagrams of genetic relationship were clustered by UPG-MA. The results showed that, using 26 primers, a total of 558 bands were produced, of which 539 were polymorphic loci. There was a high level of genetic diversity among species (PPB = 96.59%, Na = 1.9659, Na = 1.3375, H = 0.2143, I = 0.3423). However, genetic diversity was lower within species, the average of genetic parameters was PPB = 6.97%, Na = 1.0697, Na = 1.0311, H = 0.0187, I = 0.0291. The Nei's genetic differentiation coefficient was 0.9126, indicated that most of the genetic variation existed among species. By clustering analysis, different individuals gathered in the same group and the classified result of SRAP marker between traditional modal characters was almost same. The results confirmed that SRAP marker can be used as one of the effective methods to reveal the genetic diversity and relationship among medicinal species of Dipsacus.

Agronomic, nutraceutical and molecular variability of feijoa (Acca sellowiana (O. Berg) Burret) germplasm

During three years of investigations (2011–2013), 12 feijoa (Acca sellowiana (O. Berg) Burret) cultivars fruits were characterised in terms of genetic, physico-chemical, nutraceutical and sensory properties. The physical-chemical, nutritional and sensory features were also correlated with a sequence-related amplified polymorphism (SRAP) analysis to assess the existence of a possible genetic relationships among the 12 cultivars and quality traits. SRAP analysis revealed genetic diversity among the 12 feijoa cultivars, this finding have been confirmed by the pomological, nutraceutical and sensory traits. A high antioxidant activity and a considerable amount of bioactive compounds, especially phenols, flavonoids and ascorbic acid, were detected. A higher level of phenols was detected in Triumph (251±25.9mg GAE/100g FW) and Smith (226.6±9.53mg GAE/100g FW), the latter of which was also richer in ascorbic acid (42.9±0.63mg AA 100g−1FW) and flavonoids (40±0.88mg CTE 100g−1 FW) compared to the remaining cultivars. Cluster analyses and principal component analysis made it possible to establish similarities among the cultivars depending on their quality and sensorial characteristics.The Mantel's correlation coefficient of SRAP marker and morphological-qualitative-sensorial traits was 0.495 reflecting that the SRAP marker-based clustering of feijoa cultivars showed similarity to the dendrogram topologies of the morphological-qualitative-sensorial trait-based clustering, although there were some differences in the positioning of some feijoa cultivars in the clusters. This study indicated that the combination of both SRAP marker and morphological trait analysis is more informative for a refined identification and characterisation of plant varieties.

Genetic diversity and relationships of wild and cultivated Zanthoxylum germplasms based on sequence-related amplified polymorphism (SRAP) markers

The genus Zanthoxylum, belonging to Rutaceae, has a long history of cultivation both for economic and chemical values in China. To effectively conserve and sustainably utilize this genus resource, a study on genetic diversity and relationships of Zanthoxylum germplasms was carried out by employing SRAP markers. We used 16 primer combinations to assess genetic variations and relationships among 175 accessions from eight cultivated provenances, including Shandong, Henan, Shanxi, Shaanxi, Gansu, Sichuan, Guizhou and Yunnan. A total of 145 clear repetitive and intense bands were yielded, and the percentage of polymorphic bands was 100 % for per primer combination, indicating a relatively high diversity among Zanthoxylum germplasms. From a geographic perspective, the highest genetic diversity level was observed within Guizhou provenance (Na = 1.97, Ne = 1.52, H = 0.31, I = 0.46) while Henan provenance had the lowest genetic diversity (Na = 1.68, Ne = 1.45, H = 0.25, I = 0.37). Based on AMOVA results, the abundant genetic variation was mainly caused by variation of intra-provenances (84.96 %), rather than among provenances (15.038 %). The results indicated low genetic differentiation (Gst = 0.133) and high gene flow (Nm = 3.2605) among provenances. The neighbor-joining tree revealed that the 175 accessions could be divided into four groups, and groupings indicated a divergence between the cultivated accessions of Zanthoxylum bungeanum Maxim. and Z. armatum DC. Moreover, three accessions of Z. piperitum DC. var. inerme without prickles introduced from Japan gathered one cluster. Cluster IV is composed of accessions of different geographical origin, including 11 wild species and 10 cultivated accessions of Z. bungeanum. The cluster analysis also reflected a relatively close relationship between the geographical origins and the classification of accessions in cluster I. Structure analysis indicated that collected Zanthoxylum accessions could be divided into two major groups. The information obtained from our research would benefit to make use of Zanthoxylum germplasms and assist the management of a Zanthoxylum germplasms collection.

Assessment of genetic diversity among faba bean genotypes using agro-morphological and molecular markers

Forty faba bean (Vicia faba L.) genotypes were evaluated for their agro-morphological performance and molecular diversity under Central Region of Saudi Arabia conditions during 2010–11 and 2011–12 seasons. Field performance results showed that faba genotypes exhibited a significant amount of variation for their agro-morphological studied parameters. Giza40 recorded the tallest genotype (139.5cm), highest number of seeds per plants (100.8), and the highest seed yield per plant (70.8g). The best performing genotypes were Giza40, FLIP03-014FB, Gazira1 and Goff1. Genetic variability among genotypes was determined using Sequence Related Amplified Polymorphism (SRAP) and Amplified Fragment Length Polymorphism (AFLP) markers. A total of 183 amplified fragments (alleles) and 1758 polymorphic fragments (bands) in SRAP and 202 alleles and 716 bands in AFLP were obtained using six SRAP and four AFLP primer combinations respectively. Polymorphism information content (PIC) values for AFLP and SRAP markers were higher than 0.8, indicating the existence of a considerable amount of genetic diversity among faba tested genotypes. The UPGMA based clustering of faba genotypes was largely based on origin and/or genetic background. Result of cluster analysis based on SRAP showed weak and not significant correlation while, it was highly significant based on AFLP analysis with agro-morphological characters (r=0.01, p>0.54 and r=0.26, p<0.004 respectively). Combined SRAP and AFLP markers proved to be significantly useful for genetic diversity assessment at molecular level. They exhibited high discrimination power, and were able to distinguish the faba bean genotypes with high efficiency and accuracy levels.

Genetic diversity in populations of the endangered medicinal plant Tetrastigma hemsleyanum revealed by ISSR and SRAP markers: implications for conservation

Genetic diversity of 27 Tetrastigma hemsleyanum accessions from wild or cultivated populations was evaluated using SRAP (sequence-related amplified polymorphism) and ISSR (inter-simple sequence repeat) markers. ISSR and SRAP analysis yielded 112 and 66 scorable amplified bands, respectively, of which 85.71 and 77.27 % were polymorphic. ISSR revealed efficiency over SRAP due to high Shannon’s Information Index (I), Nei’s gene diversity (H), and total genetic diversity (Ht). The dendrograms showed clear clustering pattern of geographically distribution. The correlation between the coefficient matrices for the SRAP and ISSR data was high (r = 0.869, P < 0.01). Higher level of genetic similarity was observed in intra-population than in inter-population. The average genetic similarity among cultivated populations were far above that among wild populations, the low level of gene flow, distance isolation, and asexual reproduction were likely related to the low level of differentiation among populations. The promotion of genes exchange will be very beneficial to conserve and utilize the enormous genetic variability contained in the T. hemsleyanum.

Genetic variability in proso millet [Panicum miliaceum] germplasm of Central Himalayan Region based on morpho-physiological traits and molecular markers

Sixteen representative a ccessions of proso millet [Panicum miliaceum] having distinct traits of agronomic importance were collected from altitudinal range of 510–2,695 m asl in the Central Himalayan Region (CHR) of India. Considerable diversity was found in morpho-physiological traits viz., leaf length (16.80–32.00 cm), leaf width (1.7–2.1 cm), plant height (57.00–134.00 cm), days to 50 % flowering (34–54), days to 80 % maturity (111–144), and 1,000 seed weight (0.68–1.86 g). Collected accessions have been evaluated for a battery of biochemical parameters viz., chlorophyll, carotenoids, lipid peroxidation, cellular hydrogen peroxide, activity of nitrate reductase, lipoxygenase, catalase, peroxidase, superoxide dismutase along with super oxide free radical formation, glutathione (total, reduced, and oxidized), glutathione reductase, glutathione S-transferase, ascorbate (total, reduced, and oxidized), monodehydroascorbate reductase, and didehydroascorbate reductase. The sets of 12 genic-SSRs (simple sequence repeats), 54 ISSR (inter simple sequence repeats), and 40 SRAP (sequence related amplified polymorphism) markers were used to study the level of genetic diversity, and Nei’s gene diversity value of 0.20 was obtained with both ISSR and SRAP markers. SRAP markers showed higher average number of polymorphic bands, % polymorphism, polymorphic information content (PIC), and Shannon information index compared to ISSR markers; genic-SSRs showed no allelic variation. Cluster analysis shows close groupings of germplasm based on morpho-physiological traits as well as molecular markers. The diverse germplasm identified based on molecular markers with considerable diversity in morpho-physiological traits may be utilized for development of climate resilient cultivars.

Evaluating genetic diversity and constructing core collections of Chinese Lentinula edodes cultivars using ISSR and SRAP markers.

Genetic diversity among 89 Chinese Lentinula edodes cultivars was analyzed by inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. A 123 out of 126 ISSR loci (97.62%) and 108 out of 129 SRAP loci (83.73%) were polymorphic between two or more strains. A dendrogram constructed by cluster analysis based on the ISSR and SRAP markers separated the L. edodes strains into two major groups, of which group B was further divided into five subgroups. Clustering results also showed a positive correlation with the main agronomic traits of the strains, and that strains with similar traits clustered together into the same groups or subgroups in most cases. The average coefficient of pairwise genetic similarity was 0.820 (range: 0.576-0.988). Compared to the wild strains, Chinese L. edodes cultivars indicated a lower level of genetic diversity. Two preliminary core collections of L. edodes, Core1 and Core2, were established based on the ISSR and SRAP data, respectively. Core1 was constructed by the advanced M (maximization) strategy using the PowerCore version 1.0 software and contained 21 strains, whereas Core2 was created by the allele preferred sampling strategy using the cluster method and contained 18 strains. Both core collections were highly representative of the genetic diversity of the original germplasm, as confirmed by the values of Na (observed number of alleles), Ne (effective number of alleles), H (Nei's gene diversity) and I (Shannon's information index), as well as results of principal coordinate analysis. The loci retention ratio of Core1 (99.61%) was higher than that of Core2 (97.65%). Moreover, Core1 contained strains with more types of agronomic traits than those in Core2. This study builds the basis for further effective protection, management and use of L. edodes germplasm resource.

Genetic diversity and population structure of Eucommia ulmoides Oliver, an endangered medicinal plant in China.

Eucommia ulmoides Oliver, one of the tertiary relict species found only in China, is the only extant species of Eucommiaceae. Using inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers, we studied the genetic diversity and population genetic structure of 187 accessions from 17 E. ulmoides populations throughout its main distribution in China. A total of 65 bands were amplified using eight ISSR primers, of which 50 bands (76.9%) were polymorphic. Meanwhile, another 244 bands were observed using eight SRAP primer combinations and 163 (66.8%) of these were polymorphic. The analysis of molecular variation (AMOVA) indicated that 88.8 and 92.4% of the total variation resided within populations based on ISSR and SRAP analysis, respectively. Moreover, we found that the E. ulmoides populations were clustered into six distinct groups using ISSR and SRAP markers via the unweighted pair-group method (UPGMA). Furthermore, STRUCTURE analysis showed that these 17 populations could be classified into four groups using ISSR markers, but only two groups using SRAP markers. No significant relevancy was observed between genetic and geographic distances among the sampled populations. The results of this study support the view that exchange of seeds among local farmers plays an important role in shaping the present genetic distribution pattern. "Core collection" is suggested for genetic diversity conservation of E. ulmoides in China.

Identification of quantitative trait loci for bolting and flowering times in Chinese kale (Brassica oleracea var. alboglabra) based on SSR and SRAP markers

SUMMARYExpressed sequence tag-simple sequence repeat (EST-SSR), simple sequence repeat (SSR), and sequence-related amplified polymorphism (SRAP) markers were used to construct the first intra-specific genetic linkage map for B. oleracea var. alboglabra. In addition, QTL locations were determined for bolting and flowering traits. A total of 189 polymorphic marker loci were detected in the two parents, with 45 marker loci not located on any linkage group (LG). The remaining 144 loci defined ten LGs and included 69 EST-SSR loci, three SSR loci, and 72 SRAP loci. The length of the map was 1,173.8 cM, the average distance between loci was 8.15 cM, and the proportion of segregation distortion loci was 25.7%. Three QTLs controlling bolting time and two QTLs controlling flowering time were detected in the F2:3 generation, which explained 37.07% and 18.44% of the phenotypic variation, respectively. Two QTLs controlling bolting time and two QTLs controlling flowering time were detected in the F2 generation, which explained 27.90% and 25.59% of the phenotypic variation, respectively. In both generations, QTLs ftB.1 and ftA.1 were located on LG5, and the distance between the two QTLs was only 1.0 cM, suggesting that they could be at an identical locus. These results provide a useful reference for future QTL studies on bolting and flowering time in B. oleracea var. alboglabra, and can be used to identify markers linked to these QTLs for marker-assisted selection in commercial breeding programmes.

Genetic diversity in intraspecific hybrid populations of Eucommia ulmoides Oliver evaluated from ISSR and SRAP molecular marker analysis.

Eucommia ulmoides Oliver, the only extant species of Eucommiaceae, is a second-category state-protected endangered plant in China. Evaluation of genetic diversity among some intraspecific hybrid populations of E. ulmoides Oliver is vital for breeding programs and further conservation of this rare species. We studied the genetic diversity of 130 accessions from 13 E. ulmoides intraspecific hybrid populations using inter-simple sequence related (ISSR) and sequence-related amplified polymorphism (SRAP) markers. Of the 100 ISSR primers and 100 SRAP primer combinations screened, eight ISSRs and eight SRAPs were used to evaluate the level of polymorphism and discriminating capacity. A total number of 65 bands were amplified using eight ISSR primers, in which 50 bands (76.9%) were polymorphic, with an average of 8.1 polymorphic fragments per primer. Alternatively, another 244 bands were observed using eight SRAP primer combinations, and 163 (66.8%) of them were polymorphic, with an average of 30.5 polymorphic fragments per primer. The unweighted pair-group method (UPGMA) analysis showed that these 13 populations could be classified into three groups by the ISSR marker and two groups by the SRAP marker. Principal coordinate analysis using SRAP was completely identical to the UPGMA-based clustering, although this was partly confirmed by the results of UPGMA cluster analysis using the ISSR marker. This study provides insights into the genetic background of E. ulmoides intraspecific hybrids. The progenies of the variations "Huazhong-3", "big fruit", "Yanci", and "smooth bark" present high genetic diversity and offer great potential for E. ulmoides breeding and conservation.

Comparative analysis of genetic diversity among Chinese watermelon germplasmsusing SSR and SRAP markers, and implications for future genetic improvement

The genetic diversity of watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] in China, the world's largest producer of watermelon fruits, has not been examined. Two molecular markers, sequence-related amplified polymorphism (SRAP) and simple sequence repeat (SSR), were used to investigate the genetic variation and genetic relationship among 54 Chinese watermelon accessions, as well as 7 accessions from Africa, the United States, and Japan. SRAP assay generated 312 bands, of which 163 were polymorphic, while SSR assay detected 101 alleles with 87 polymorphic alleles and 114 genotypes. A comparative analysis of the diversity index, effective multiplex ratio, and marker index of the 2 markers showed higher efficiency of SRAP markers in watermelon germplasm fingerprinting. The Mantel test resulted in a high correlation between SRAP and SSR data with a value of $\gamma$ = 0.863, revealing a good fit between the 2 marker systems. Genetic diversity among the accession set was estimated by a construction of dendrograms using SRAP, SSR, or SRAP-SSR combined data. There was clear consistency between the 3 dendrograms on the positioning of most accessions. The study demonstrated that most Chinese cultivated germplasms (CCGs) were clustered independently of their geographical distribution and horticultural classification, and had a narrow genetic base; most CCGs and foreign cultivars had a high genetic closeness and showed similar lineages; and the 4 wild accessions were the most genetically diverse, followed by the small-fruited accessions from northern China and edible-seeded accessions. We concluded that CCGs lacked genetic variation, and we offer a means of introducing new genetic diversity into the watermelon germplasm pool in China, which is essential to maximizing productivity in watermelon.

Diversity and population structure of a dominant deciduous tree based on morphological and genetic data.

Knowledge of the genetic diversity and structure of tree species across their geographic ranges is essential for sustainable use and management of forest ecosystems. Acer grosseri Pax., an economically and ecologically important maple species, is mainly distributed in North China. In this study, the genetic diversity and population differentiation of 24 natural populations of this species were evaluated using sequence-related amplified polymorphism markers and morphological characters. The results show that highly significant differences occurred in 32 morphological traits. The coefficient of variation of 34 characters was 18.19 %. Principal component analysis indicated that 18 of 34 traits explained 60.20 % of the total variance. The phenotypic differentiation coefficient (VST) was 36.06 % for all morphological traits. The Shannon-Wiener index of 34 morphological characters was 6.09, while at the population level, it was 1.77. The percentage of polymorphic bands of all studied A. grosseri populations was 82.14 %. Nei's gene diversity (He) and Shannon's information index (I) were 0.35 and 0.50, respectively. Less genetic differentiation was detected among the natural populations (GST = 0.20, ΦST = 0.10). Twenty-four populations of A. grosseri formed two main clusters, which is consistent with morphological cluster analysis. Principal coordinates analysis and STRUCTURE analysis supported the UPGMA-cluster dendrogram. There was no significant correlation between genetic and geographical distances among populations. Both molecular and morphological data suggested that A. grosseri is rich in genetic diversity. The high level of genetic variation within populations could be affected by the biological characters, mating system and lifespan of A. grosseri, whereas the lower genetic diversity among populations could be caused by effective gene exchange, selective pressure from environmental heterogeneity and the species' geographical range.

Development of AFLP markers associated with zucchini yellow mosaicvirus resistance in cucumber (Cucumis sativus L.)

Zucchini yellow mosaic virus (ZYMV) is one of the most important pathogens that cause significant yield losses in many cucurbit crops including cucumber (Cucumis sativus L). ZYMV resistance in cucumber is inherited by a single recessive gene. The purpose of this study was to identify molecular markers linked to the gene conferring ZYMV resistance in cucumber. We developed a population of 188 F2 plants derived from inbred cucumber lines. Individual F2 plants were self-pollinated to generate F3 populations. Ten randomly selected plants from each F3 population were tested for ZYMV resistance. We used a bulk segregant analysis method to identify putative molecular markers linked to ZYMV resistance. Using bulked DNA samples with parental lines and F1, a total of 170 sequence-related amplified polymorphism (SRAP), 586 simple sequence repeat (SSR), and 308 amplified fragment length polymorphism (AFLP) primer combinations were screened. Neither polymorphic SRAP nor SSR markers were linked with ZYMV resistance. Among the 308 AFLP primer combinations tested, an AFLP marker in the E-ACA/MCA primer combination showed significant association among parental lines, F1, and resistant and susceptible plants. The combination of E-ACA/M-CA was achieved on parental lines, F1, and 188 F2 individuals for confirmation of the marker segregation on the F2 population. We found that the combination of E-ACA/M-CA was linked to the zym locus with 6.91 cM.

Identification of QTLs of resistance to white mold in common bean from multiple markers by using Bayesian analysis.

In this study, we identified simple sequence repeat, ampli-fied fragment length polymorphism, and sequence-related amplified poly-morphism markers linked to quantitative trait loci (QTLs) for resistance to white mold disease in common bean progenies derived from a cross between lines CNFC 9506 and RP-2, evaluated using the oxalic acid test and using Bayesian analysis. DNA was extracted from 186 F₂ plants and their parental lines for molecular analysis. Fifteen experiments were car-ried out for phenotypic analysis, which included 186 F₂:₄ progenies, the F₁ generation, the F₂ generation, and the lines CNFC 9506, RP-2, and G122 as common treatments. A completely randomized experimental design with 3 replications was used in controlled environments. The adjusted means for the F₂:₄ generation were to identify QTLs by Bayesian shrink-age analysis. Significant differences were observed among the progenies for the reaction to white mold. The moving away method under the Bayes-ian approach was effective for identifying QTLs when it was not possible to obtain a genetic map because of low marker density. Using the Wald test, 25 markers identified QTLs for resistance to white mold, as well as 16 simple sequence repeats, 7 amplified fragment length polymorphisms, and 2 sequence-related amplified polymorphisms. The markers BM184, BM211, and PV-gaat001 showed low distances from QTLs related white mold resistance. In addition, these markers showed, signal effects with increasing resistance to white mold and high heritability in the analysis with oxalic acid, and thus, are promising for marker-assisted selection.