Simple Sequence Repeat Markers Markers Research Articles

INTEGRATION OF NOVEL SSR MARKERS INTO THE LENTIL (Lens culinaris Medik.) GENOME

The development of Simple Sequence Repeat markers (SSRs) for lentil has played a pivotal role in enhancing the comprehension of the lentil genome through genetic mapping. The study aimed to determine the relative positions of newly developed microsatellites to the lentil genome using an F7-derived Recombinant Inbred Lines population (RIL) of 71 individuals developed from a cross between Eston and PI320937. Molecular analysis was performed with 100 newly developed lentil SSR markers and a linkage map was constructed using MapMaker/EXP 3.0b and MapChart 2.2 software. Among the 100 SSR markers, 12 markers exhibited polymorphism, 54 markers were identified as monomorphic, and 34 markers remained unamplified. While 10 out of the 12 polymorphic markers successfully integrated into two linkage groups, covering a cumulative length of 19.2cM, two markers remained unlinked. Linkage group-1, comprised of 8 markers, spanned 4.8cM, and linkage group-2 extended over a length of 14.4cM with two markers. Despite only partially representing 2 out of the 7 chromosomes in the lentil genome, this map holds promise for future mapping studies. Through the addition of markers, it could facilitate marker-assisted selection and the identification of QTLs associated with specific agronomic traits.

Assessment of Genetic Diversity in Corchorus olitorius Accessions by Simple Sequence Repeat Markers (SSR)

Indigenous leafy vegetables such as Corchorus olitorius (jew’s mallow) have potential in contributing to food security as they can provide important nutritional requirements needed for human nourishment. However, in Botswana, this plant is not yet domesticated and its utilization is minimal due to lack of knowledge. To have the crop fully domesticated it is important to document important information on the available landraces and wild species. One of the important information is understanding the variation among the available genotypes as this will help not only in domestication but also in breeding purposes. Thus this study aimed to assess the genetic diversity of 49 accessions of jews mallow collected in Botswana and other African countries. Simple sequence repeats (SSR) markers were used to characterize fourty nine accessions. The results revealed that, out of 49 SSR primer pairs used, 46 showed scorable polymorphism by producing clear amplified products. The average polymorphic loci rate was 82.44% with the lowest rate (33.33%) detected in MJM-536 and the highest was 100% recorded by 27 of the primers. The polymorphism information content (PIC) potential ranged from 0.398 for MJM-475 primer to 0.979 for the primer MJM-623 with an average of 0.719. With the Shannon diversity index, an average of 3.626 was recorded under the studied accessions and this confirmed a very high diversity. In addition, a dendrogram was generated to illustrate the genetic diversity and possible relationships among the 49 Corchorus olitorius accessions using the unweighted pair group method (UPGM) with arithmetic means. This UPGM cluster analysis distinctively divided the accessions into five (5) groups at a cophenetic correlation coefficient 0.977. The total number of accessions per cluster varied from one group to the other. These results reinforced the effectiveness of the SSR markers in discriminating individuals within species even within a narrow genetic background.

Association Analysis for Some Biochemical Traits in Wild Relatives of Wheat under Drought Stress Conditions.

In the present study, we estimated genetic diversity and population structure in 186 accessions of Triticum and Aegilops species using 24 simple sequence repeat markers (SSR). Furthermore, an association analysis was performed for antioxidant activities, including guaiacol peroxidase (GPX), ascorbate peroxidase (APX), peroxidase (POX), catalase (CAT), and dry matter (DM) under two control and drought stress conditions. Our findings showed that drought treatment significantly decreased DM, whereas activities of all antioxidant enzymes were increased compared to the control conditions. The results of correlation analysis indicated that, under drought stress conditions, all biochemical traits had a positive and significant association with each other and with dry matter. In the molecular section, the results of the analysis of molecular variance (AMOVA) indicated that the molecular variation within species is more than within them. The dendrogram obtained by cluster analysis showed that grouping the investigated accessions was in accordance with their genomic constitutions. The results of association analysis revealed 8 and 9 significant marker–trait associations (MTA) under control and drought stress conditions, respectively. Among identified MTAs, two associations were simultaneously found in both growing conditions. Moreover, several SSR markers were associated with multiple traits across both conditions. In conclusion, our results could provide worthwhile information regarding marker-assisted selection for the activity of antioxidant enzymes in future breeding programs.

Simple sequence repeat marker development and diversity analysis in buffalograss

AbstractBuffalograss [Buchloë dactyloides (Nutt.) Engelm. syn. Bouteloua dactyloides (Nutt.) Columbus] is a stoloniferous low input turfgrass species native to the central Great Plains of the United States. Several molecular marker techniques have been used to compare relationships among elite buffalograss germplasm, but most rely on random amplification, are transferred from other species, or are developed from limited DNA sequence information. The objectives of this study were to develop buffalograss derived simple sequence repeat markers (SSRs) from buffalograss sequence data using an in‐silico bioinformatics pipeline and use high resolution melt analysis to screen the SSRs based on their melt profiles on buffalograss cultivars and germplasm. Transcriptomes from buffalograss cultivars ‘378’ and ‘Prestige’ were mined for SSRs using the MIcroSAtellite tool. There were 259 conserved SSRs that were polymorphic between 378 and Prestige. Of those, 96 were tested by HRM on a panel of eight genotypes and 24 were selected for producing melt profiles that could distinguish the genotypes. The selected reactions produced 356 distinct melt profiles when tested on a panel of 96 genotypes, including 88 buffalograss germplasm selections, six buffalograss cultivars, and two blue grama [Bouteloua gracilis (H. B. K.) Lag. ex Steud.] selections, with melt profile frequencies ranging from 0.01 to 0.97. A subset of 86 melt profiles segregating among the blue grama and elite buffalograss cultivars distinguished each genotype. The buffalograss‐specific SSR markers presented here will be useful to study buffalograss genetic diversity, line purity maintenance, and for marker supported plant breeding strategies.

Two Indigenous Berberis Species From Spain Were Confirmed as Alternate Hosts of the Yellow Rust Fungus Puccinia striiformis f. sp. tritici.

Puccinia striiformis f. sp. tritici, which causes yellow (or stripe) rust on wheat, is a macrocyclic and heteroecious fungus. In this study, we investigated whether Berberis vulgaris subsp. seroi and B. vulgaris subsp. australis, which are indigenous in Spain, may serve as alternate hosts for P. striiformis f. sp. tritici. Wheat leaves bearing telia of an isolate of P. striiformis f. sp. tritici were harvested and used to inoculate plants of both barberry subspecies. Pycnia were observed on the adaxial side of the leaves from 10 days after inoculation (dai). Following successful fertilization, aecia were observed on the abaxial side of the leaves from 16 dai. At 27 dai, barberry leaves bearing aecia were detached and used to inoculate susceptible wheat seedlings of cultivar Morocco. Uredinia were observed on wheat seedlings from 12 days after aeciospore exposure. Eighty-three single lesions were recovered from individual wheat leaves, of which 43 were genotyped using 19 P. striiformis f. sp. tritici simple sequence repeat markers (SSR). In total, 19 multilocus genotypes (MLGs) were identified among the 43 progeny isolates. The SSR genotyping confirmed that all 43 isolates were derived from the parental isolate. Seven heterozygous SSR markers showed segregation among the progenies, whereas none of the 12 homozygous markers resulted in segregation. These results demonstrated that B. vulgaris subspp. seroi and australis can serve as alternate hosts for P. striiformis f. sp. tritici, which may result in novel virulence combinations that can have a detrimental impact on wheat production. Although P. striiformis f. sp. tritici has not been detected on these barberry species in nature, this study highlights the importance of rust surveillance in barberry areas where suitable conditions for completion of the sexual life cycle may be present.

Genetic characterization of the orphan crop tef [Eragrostis tef (Zucc.) Trotter] accessions using simple sequence repeat markers

Tef is the most important and well adapted cereal crop in Ethiopia and grows better than other cereals both in biotic and abiotic stress conditions. In this study 93 tef accessions representative of various agro-ecologies of Ethiopia along with four improved varieties, one local check and six wild relatives were studied. The materials were genotyped with 12 simple sequence repeat markers (SSRs) to investigate the extent and structure of the genetic diversity of tef. A total of 152 alleles were detected indicating high polymorphism in the studied accessions. The number of alleles per polymorphic loci ranged from seven for CNLT 538 to 29 for CNLT150 with an average of 12.67. High average polymorphic information content (0.82) and average expected heterozygosity (0.86) also signifies the suitability and efficiency of SSR markers to discriminate among tef genotypes. Cluster, principal coordinate and structure analyses grouped the 98 tef genotypes and six wild relatives into four distinct classes. The groupings showed no special pattern despite the different regions of origins for the accessions; however, the five wild relatives were grouped together. The analysis of molecular variance and fixation index showed low genetic differentiation and high gene flow between regions revealing that much of the variability was attributed to within populations variation. Generally, the present study showed that there is high genetic variability with unstructured genetic pattern among the studied tef genotypes which implies the vitality of conserved tef germplasms at Ethiopian Biodiversity Institute and the impact of the seed exchange system on tef breeding activities in Ethiopia.

Molecular screening of Zymoseptoria tritici resistance genes in wheat (Triticum aestivum L.) using tightly linked simple sequence repeat markers

Septoria tritici blotch is becoming the major bottleneck to wheat production throughout the world including Ethiopia. Resistance breeding is currently seen as the best strategy, durable, economical and environmentally friendly method to control the disease. Nowadays, molecular marker technology is widely used in plant breeding program to promote the speed and efficiency of resistance breeding. So far, several Septoria resistant genes and tightly linked simple sequence repeat markers (SSR) have been identified in wheat. These markers can serve as chromosomal land mark in hunting the resistance genes in diverse breeding materials. However, in Ethiopia, the application of molecular tools in resistance breeding is greatly missing. Therefore, the present study was aimed at searching for Septoria resistant genes (Stb genes) in 180 bread wheat genotypes using 16 tightly linked SSR markers. The result revealed greater degree of genetic variability among the tested genotypes for Stb genes. The genetic frequency of the resistance genes ranged from 6.67% (Stb 8 gene) to 96.1% for stb13 gene. Three wheat genotypes (G21, G63, and G64) possessed the maximum (13) Septoria resistance genes. While 14 of the genotypes were found to have 12 Stb genes. Four genotypes were found to have the minimum (four) Stb genes. The study identified 17 wheat genotypes harboring 12 to 13 Septoria resistance genes. The information is very relevant for breeders in developing broad spectrum and/or durable resistant cultivars through gene pyramiding, and for fast track release of the resistant genotypes to contribute to food and nutritional security in Ethiopia.

Molecular screening of traditional rice varieties using tsv1-linked simple sequence repeat markers

AbstractGenebanks offer vast amounts of traditional germplasm with potential sources of novel genes against biotic and abiotic stresses. In order to utilize the germplasm in rice breeding programmes, there should be a fast screening approach such as the use of molecular markers. Thus, the current study aimed to evaluate the use of tsv1 resistance-linked simple sequence repeat markers (SSR) for the preliminary screening of Philippine traditional rice germplasm against rice tungro spherical virus (RTSV). The tsv1 resistance-linked SSR markers consisted of two to four repeat motifs with 5–24 base repeats. Expected sizes ranged from 123 to 465 base pairs (bp) with polymorphism information content ranging from 0.23 to 0.73. Genetic analysis showed six major clusters at 50%: Clusters A, B and C had individual accessions, Cluster D had three accessions, Cluster E had 55 and Cluster F had 42 accessions. The study showed the germplasm with alleles linked to tsv1 but should be validated in the future with induced screening. In general, the material consisted of selected germplasm showing the presence of alleles linked to the tsv1 gene. These rice accessions could be a source of resistance to RTSV following further validation. Furthermore, molecular markers provide a useful tool to accelerate the screening of genetic resources for biotic and abiotic stress tolerance.

Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris).

Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA and include both dry bean and snap beans for the fresh and processing markets. Through population structure, principal components analyses, cluster analysis, and discriminant analysis of principal components (DAPC), Andean and Mesoamerican genotypes as well as most American commercial type classes could be distinguished. The genetic relationship among the commercial cultivars revealed by the SSR markers was generally in agreement with known pedigree data. The Mesoamerican cultivars were separated into three major groups—black, small white, and navy accessions clustered together in a distinct group, while great northern and pinto clustered in another group, showing mixed origin. The Andean cultivars were distributed in two different groups. The kidney market classes formed a single group, while the green bean accessions were distributed between the Andean and Mesoamerican groups, showing inter-gene pool genetic admixture. For a subset of 24 SSR markers, we compared and contrasted the genetic diversity of the commercial cultivars with those of wild and domesticated landrace accessions of common bean. An overall reduction in genetic diversity was observed in both gene pools, Andean and Mesoamerican, from wild to landraces to advanced cultivars. The limited diversity in the commercial cultivars suggests that an important goal of bean breeding programs should be to broaden the cultivated gene pool, particularly the genetic diversity of specific commercial classes, using the genetic variability present in common bean landraces.

Genetic variation in Hydrangea macrophylla (Thunb.) Ser. in Russia based on simple sequence repeat markers

Genetic diversity and genetic relationships among 39 accessions of Hydrangea macrophylla (Thunb.) Ser. were analyzed using 38 previously developed simple sequence repeat markers (SSRs). A total of 38 polymorphic primers representing 166 bands with an average of 4.53 polymorphic bands per primer were selected. The number of alleles detected per locus ranged from two to eight with a total of 163 alleles amplified. The size of the amplified fragments ranged from 70 to180 base pairs. The effective multiallelic markers with high level of heterozygosity (more than 0.7) and effective number of alleles (more than 3.5) were identified. In this study nine SSR markers showed clear polymorphisms. The dendrogram grouped all hybrids in three major clusters, and two of these clusters included only mophead cultivars. The lacecap cultivars clustered more closely to each other. The results of this research could be used in breeding programs of H. macrophylla.

Identification of Sitobion avenae F. Resistance and Genetic Diversity of Wheat Landraces from Qinling Mountains, China

The aphid Sitobion avenae F. is one of the most harmful pests of wheat growth in the world. A primary field screening test was carried out to evaluate the S. avenae resistance of 527 wheat landraces from Shaanxi. The results indicated that 25 accessions (4.74%) were resistant to S. avenae in the three consecutive seasons, of which accession S849 was highly resistant, and seven accessions were moderately resistant. The majority of S. avenae resistant accessions come from Qinling Mountains. Then, the genetic variability of a set of 33 accessions (25 S. avenae resistant and 8 S. avenae susceptible) originating from Qinling Mountains have been assessed by 20 morphological traits and 99 simple sequence repeat markers (SSRs). Morphological traits and SSRs displayed a high level of genetic diversity within 33 accessions. The clustering of the accessions based on morphological traits and SSR markers showed significant discrepancy according to the geographical distribution, resistance to S. avenae and species of accessions. The highly and moderately resistant landrace accessions were collected from the middle and the east part of Qinling Mountains with similar morphology characters, for example slender leaves with wax, lower leaf area, and high ear density. These S. avenae resistant landraces can be used in wheat aphid resistance breeding as valuable resources.

Research Article Large-scale development, characterization, and cross-amplification of EST–SSR markers in Chinese chive

Chinese chive (Allium tuberosum Rottler ex Spr.) is an important vegetable crop. However, genetic and breeding studies of the species have been restricted by the lack of simple sequence repeat markers (SSRs). In the present study, a total of 2553 Chinese chive SSRs were developed from the species’ transcriptome, with 626, 643, and 536 of the makers located in coding sequences, 5' untranslated regions and 3' untranslated region, respectively. The annotation of SSR-containing expressed sequence tags revealed that the transcripts were enriched for several Gene Ontology (GO) categories, including ‘protein binding’, ‘regulation of transcription’, and ‘integral to membrane’. Among the 2,553 SSRs, di- and tri-nucleotide repeat motifs were the most abundant (52.3 and 45.6%, respectively), and AC/GT and GAA/TTC were the most frequent di- and tri-nucleotide motifs, respectively. PCR amplification, using 100 SSR primer pairs, revealed that 94% of the markers were of good quality and that 83-88 of the makers could be amplified in six other Allium species. This suggests that the markers had high cross-species transferability. The substantial number of SSRs developed will provide a valuable resource for future genetic and breeding studies in Chinese chive

Genetic diversity of Sudanese pearl millet (Pennisetum glaucum (L.) R. Br.) landraces as revealed by SSR markers, and relationship between genetic and agro-morphological diversity

Landraces are considered as storehouses of valuable genetic diversity. Understanding the structure of this diversity and identification of distinct clusters with complementary traits is an important goal for a sustained and successful pearl millet breeding program. In this study a collection of 214 pearl millet accessions from different geographical regions of Sudan, and 11 accessions from West Africa, were assessed for their genetic diversity using 30 simple sequence repeat markers (SSRs) and evaluated for 15 agro-morphological traits. The diversity of the studied pearl millet landraces was demonstrated by a large number (400) of detected SSR alleles. The average polymorphic information content (PIC), gene diversity and observed heterozygosity of the 30 SSRs were 0.77, 0.82 and 0.72 respectively. A total of seven phylogenic groups with variable sizes were identified. Low correlation was observed between the agro-morphological matrix and the genetic matrix (r = 0.20). The average PIC values obtained across the seven linkage groups varied significantly. Weak genetic differentiations were observed among the geographical regions, suggesting a high seed and pollen-mediated gene flow among the regions. Analysis of molecular variance revealed that the variation of pearl millet accessions within the regions was much higher than among the regions. The large divergence observed among the landraces of this study is promising for developing new cultivars and for development of heterotic groups which can be used to develop population and hybrid varieties with higher degrees of heterozygosity and therefore hybrid vigor and stability, as well as to intensify yield production in the harsh production environments of Sudan.

English

Cassava genotypes were assessed at genomic DNA level to estimate the genetic diversity within and between them using 36 simple sequence repeat markers (SSR). One hundred and forty-seven (147) F1 progenies derived from crosses amongst the parental genotypes were used to determine the association between three SSR markers and beta-carotene content in cassava. For the diversity study, a total of 131 alleles with an average of 3.7 alleles per locus were found. One yellow fleshed root genotype clustered with a white fleshed root genotype indicating similarity in their genetic background. Three SSR markers were used to screen the parental genotypes and their 147 progenies for a beta-carotene gene. The yellow fleshed root parents and 141 of the F1 progenies had SSR alleles associated with the presence of beta-carotene gene. The SSR markers identified for beta carotene at CIAT appeared linked to the trait as found in the parents, but evaluation in the progenies indicated that each marker did not account for high phenotypic variance individually. Marker NS 717 (allele 206) accounted for 20% beta carotene content and SSRY 301 (allele 331) accounted for 17%. There are minor QTLs that could probably be involved in beta carotene expression. The markers evaluated therefore do not sufficiently account for beta-carotene expression in the F1 progenies.   Key words: Cassava, simple sequence repeat (SSR), pro-vitamin A, diversity, validation.&nbsp

Genetic characterisation and fine mapping of a chlorophyll-deficient mutant (BnaC.ygl) in Brassica napus

A chlorophyll-deficient mutant with yellow-green leaves of Brassica napus was obtained by treatment with the chemical mutagen ethyl methanesulfonate. Compared with the wild type at seedling stage, the mutant displayed decreased total chlorophyll content, less granal stacks and granal membranes. Genetic analysis confirmed that the mutant phenotype was controlled by a recessive gene, which was designated as BnaC.ygl. Mapping of the gene was subsequently conducted in two populations with yellow-green leaves (population IBC8 and IIBC4, which comprised 3,472 and 5,288 individuals, respectively). Analysis on the public simple sequence repeat markers (SSR) showed that four SSR markers linked to BnaC.YGL gene displayed polymorphism. Based on the information of these SSR markers, the BnaC.YGL gene was mapped to the linkage group N17. From a survey of amplified fragment length polymorphism (AFLP), 15 of 47 AFLP markers were successfully converted into sequence characterised amplified region (SCAR) markers. BnY5 and CB10534, the closest flanking markers, were 0.32 and 0.03 cM away from the BnaC.YGL gene, respectively. And in the two populations, 18 makers cosegregated with BnaC.YGL. BLAST analysis revealed that the sequences of the makers displayed highly conserved homology with C06 of B. oleracea. The collinearity of makers to makers on N17 and on C06 showed that there might be an inversion occurring on the N17 group. These results are expected to accelerate the process of cloning the BnaC.YGL gene and facilitate the understanding of the biological processes of chloroplast development in Brassica napus.

Phylogenetic relationships of chrysanthemums in Korea based on novel SSR markers

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

Assessing genetic variability in male sterile and low fertile citrus cultivars utilizing simple sequence repeat markers (SSRs)

Understanding phylogenetic relationships and genetic diversity in citrus are important in clarifying genetic relationships, characterizing germplasm and the registration of new cultivars. In this study, the genetic diversity of 28 accessions of citrus including male sterile, sterile, low fertile and fertile cultivars were investigated using eight pairs of simple sequence repeat markers (SSR) markers, which in total, 54 polymorphic alleles with an average of 4.2 alleles per primer were detected. The lowest number of alleles was observed in TAA27, CTT01, CCSM18 and ATC09 loci with only three alleles and the highest number of alleles was observed in TAA15 locus with eight alleles. Polymorphic information content (PIC) values changed from 0.34 (AG14) to 0.90 (CCSM18). Genetic similarities among accessions were calculated according to Jaccard similarity index and used to construct a dendrogram based on the unweighted pair group method using arithmetic averages (UPGMA) which put the 28 samples into four major groups (A, B, C and D). The cultivars of male sterile satsuma mandarin were clustered into group A; those of orange, grapefruit and Page (a complex hybrid) into group B; mandarin cultivars into group C; and lemon Lisbon into group D. Genetic analysis of sterile and low fertile citrus, provide useful information for further breeding programs, collection, preservation and utilization. Key words : Male sterility, genetic diversity, SSR markers, citrus.

MICROSATELLITE MARKERS DISTINGUISH HAWAIIAN OHELO FROM OTHER VACCINIUM L. SECTION MYRTILLUS SPECIES

The US Department of Agriculture, Agricultural Research Service, National Clonal Germplasm Repository, Corvallis, collection of Vaccinium L. contains >1700 accessions representing 66 species from 33 countries. About 377 accessions belong to 10 species of Vaccinium section Myrtillus. This section is restricted to the Northern Hemisphere where its primary center of diversity occurs around the Pacific Rim in high elevations from Alaska to Guatemala and in mountains of Japan, Kurile, Sakhalin, and Hawaiian Islands, and Russian Siberia. The first objective of this study was to use microsatellite or simple sequence repeat markers (SSR) previously isolated from domestic blueberry, to uniquely identify three clones of Ohelo berry, V. reticulatum, selected for their ornamental qualities. The second objective was to evaluate the SSR markers for cross-transference to other species within Section Myrtillus including: two genotypes from another endemic Hawaiian species, V. calycinum; 17 representatives from seven North American species (V. caespitosum, V. deliciosum, V. membranaceum, V. myrtillus, V. ovalifolium, V. parvifolium, and V. scoparium), and in two accessions of V. praestans from Sakahlin Island, Russian Federation and one genotype from Hokaido, Japan. As many as eighteen microsatellite markers cross-amplified and appeared polymorphic in most of the genotypes evaluated. The three V. reticulatum genotypes were uniquely identified with eight SSR primer pairs. UPGMA clustering based on nine microsatellite primer pairs clearly separated the Hawaiian taxa and grouped V. praestans together. Two accessions of V. myrtillus (V myrt 1684-1, V myrt 1684-3) collected from within the Kalmiopsis Wilderness of southern Oregon had identical fingerprints indicating a clonal relationship. Conserved primers that amplify what appear to be single loci SSRs are recommended for population genetic analyses in diploid Vaccinium section Myrtillus taxa including V. calycinum, V. reticulatum, V. scoparium and V. praestans. SSR-based analysis indicated high diversity in other taxa of section Myrtillus and the need for a larger amount of accessions from each species, additional markers or sequence-based markers, for taxonomic resolution.

Construction of an integrated consensus map of the apple genome based on four mapping populations

An integrated consensus genetic map for apple was constructed on the basis of segregation data from four genetically connected crosses (C1 = Discovery × TN10-8, C2 = Fiesta × Discovery, C3 = Discovery × Prima, C4 = Durello di Forli × Fiesta) with a total of 676 individuals using CarthaGene® software. First, integrated female–male maps were built for each population using common female–male simple sequence repeat markers (SSRs). Then, common SSRs over populations were used for the consensus map integration. The integrated consensus map consists of 1,046 markers, of which 159 are SSR markers, distributed over 17 linkage groups reflecting the basic chromosome number of apple. The total length of the integrated consensus map was 1,032 cM with a mean distance between adjacent loci of 1.1 cM. Markers were proportionally distributed over the 17 linkage groups (χ 2 = 16.53, df = 16, p = 0.41). A non-uniform marker distribution was observed within all of the linkage groups (LGs). Clustering of markers at the same position (within a 1-cM window) was observed throughout LGs and consisted predominantly of only two to three linked markers. The four integrated female–male maps showed a very good colinearity in marker order for their common markers, except for only two (CH01h01, CH05g03) and three (CH05a02z, NZ02b01, Lap-1) markers on LG17 and LG15, respectively. This integrated consensus map provides a framework for performing quantitative trait locus (QTL) detection in a multi-population design and evaluating the genetic background effect on QTL expression.

GENETIC LINKAGE MAPS OF JAPANESE AND EUROPEAN PEARS ALIGNED TO THE APPLE CONSENSUS MAP

Genetic linkage maps of the Japanese pear (Pyrus pyrifolia Nakai) cultivar `Housui? and the European pear (Pyrus communis L.) cultivar `Bartlett? were constructed based on Amplified Fragment Length Polymorphism markers (AFLPs), Simple Sequence Repeat markers (SSRs) (from pear, apple and Prunus), isozymes, and phenotypic traits by using their F1 progenies. The map of the female parent `Bartlett? consisted of 256 loci including 178 AFLPs, 76 SSRs (32 pear, 39 apple, 5 Prunus SSRs), 1 isozyme and a self-incompatibility locus on 19 linkage groups over a total length of 1020 cM. The map of `Housui? contained 180 loci including 110 AFLPs, 64 SSRs (29 pear, 29 apple, 6 Prunus SSRs), 2 phenotypic traits and 4 other markers on 20 linkage groups encompassing a genetic distance of 995 cM. These 2 pear maps were aligned using 37 co-dominant markers that showed segregating alleles in both parents. Out of 80 tested SSR markers developed from apple, more than four-fifth could produce discrete amplified fragments in pear. Thirty-eight apple SSR markers showed 39 segregating loci in the linkage map of `Bartlett?, while 27 markers produced 29 loci in `Housui?. All pear linkage groups could be successfully aligned to the apple consensus map by at least 1 apple SSRs, suggesting that positions and linkages of SSR loci were well conserved between pear and apple. The self-incompatibility locus (S locus) was mapped to linkage group 17 in Japanese and European pears as well as apple. Our results are the first major effort in comparative mapping of pear and apple