Microsatellite-dense genetic map: towards genome coverage in a tropical maize (Zea mays L.) population

Dense molecular genetic maps are used for an efficient quantitative trait loci (QTL) mapping and in the marker-assisted selection programs. A dense genetic map was generated with 139 microsatellite markers using 256 F2 plants generated by the crossing of two tropical maize inbred lines (L-02-03D and L-20-01F). This map presented 1,858.61 cM in length, where 10 linkage groups were found spanned, with an average interval of 13.47 cM between adjacent markers. Seventy seven percent of the maize genetic mapping bins were covered, which means an increase of 14% coverage in relation to the previous tropical maize maps. The results provide a more detailed and informative genetic map in a tropical maize population representing the first step to make possible the studies of genetic architecture to identify and map QTL and estimate their effects on the variation of quantitative traits, thus allowing the manipulation and use in tropical maize breeding programs.

An enhanced microsatellite map of diploid Fragaria

A total of 45 microsatellites (SSRs) were developed for mapping in Fragaria. They included 31 newly isolated codominant genomic SSRs from F. nubicola and a further 14 SSRs, derived from an expressed sequence tagged library (EST-SSRs) of the cultivated strawberry, F. × ananassa. These, and an additional 64 previously characterised but unmapped SSRs and EST-SSRs, were scored in the diploid Fragaria interspecific F2 mapping population (FV×FN) derived from a cross between F. vesca 815 and F. nubicola 601. The cosegregation data of these 109 SSRs, and of 73 previously mapped molecular markers, were used to elaborate an enhanced linkage map. The map is composed of 182 molecular markers (175 microsatellites, six gene specific markers and one sequence-characterised amplified region) and spans 424 cM over seven linkage groups. The average marker spacing is 2.3 cM/marker and the map now contains just eight gaps longer than 10 cM. The transferability of the new SSR markers to the cultivated strawberry was demonstrated using eight cultivars. Because of the transferable nature of these markers, the map produced will provide a useful reference framework for the development of linkage maps of the cultivated strawberry and for the development of other key resources for Fragaria such as a physical map. In addition, the map now provides a framework upon which to place transferable markers, such as genes of known function, for comparative mapping purposes within Rosaceae.

A genetic linkage map of microsatellite, gene-specific and morphological markers in diploid Fragaria

Diploid Fragaria provide a potential model for genomic studies in the Rosaceae. To develop a genetic linkage map of diploid Fragaria, we scored 78 markers (68 microsatellites, one sequence-characterised amplified region, six gene-specific markers and three morphological traits) in an interspecific F2 population of 94 plants generated from a cross of F.vesca f. semperflorens × F. nubicola. Co-segregation analysis arranged 76 markers into seven discrete linkage groups covering 448 cM, with linkage group sizes ranging from 100.3 cM to 22.9 cM. Marker coverage was generally good; however some clustering of markers was observed on six of the seven linkage groups. Segregation distortion was observed at a high proportion of loci (54%), which could reflect the interspecific nature of the progeny and, in some cases, the self-incompatibility of F. nubicola. Such distortion may also account for some of the marker clustering observed in the map. One of the morphological markers, pale-green leaf (pg) has not previously been mapped in Fragaria and was located to the mid-point of linkage group VI. The transferable nature of the markers used in this study means that the map will be ideal for use as a framework for additional marker incorporation aimed at enhancing and resolving map coverage of the diploid Fragaria genome. The map also provides a sound basis for linkage map transfer to the cultivated octoploid strawberry.

Chloroplast microsatellite markers for the Neotropical orchid genus Epidendrum, and cross-amplification in other Laeliinae species (Orchidaceae)

One of the most significant challenges confronting orchid researchers is the lack of specific molecular markers, mainly for species in the Neotropics. Here we report the first set of specific chloroplast microsatellite primers (cpSSR) developed for Neotropical orchids. In total, nine polymorphic cpSSR loci were isolated and characterized in four species occurring in the Brazilian Atlantic Rainforest: Epidendrum cinnabarinum, E. denticulatum, E. fulgens and E. puniceoluteum. Levels of intraspecific polymorphism were characterized using two populations for each species, with 13-20 individuals each. Allele numbers varied from two to three per locus, while the number of haplotypes ranged from three to six per species. Extensive differentiation among the taxa was detected. All markers were successfully cross-amplified in eight other different genera. These cpSSRs markers will enable novel insights into the evolution of this important Neotropical genus.

Validation of microsatellite markers for assisted selection of soybean genotypes resistant to powdery mildew

Powdery mildew is one of the most serious diseases of soybean and is found in all producing countries. The purpose of this study was to validate microsatellite markers previously identified as associated with resistance to powdery mildew in soybean. The study was conducted in two F, parent populations with contrasting resistance to powdery mildew, In the analysis 10 SSR primers were used for the populations. and tour polymorphic markers were identified for cross I (MGBR95-20937 x IAC-Foscarin 31) and three for cross 2 (MGBR-46 x Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) 48). The Chi-square analysis of the phenotypic evaluation confirmed the expected segregation (3: 1) of a dominant gene related to resistance. The polymorphic markers also segregated as expected (1:2:1). The markers Sat 366 and Sat 393 in the crosses 1 and 2. respectively, located at 9.41 and 12.45 cM from the gene. were considered promising for marker-assisted selection for resistance to powdery mildew in soybean. at a selection efficiency of 92.7% and 60.3% respectively.

Highly polymorphic microsatellite loci in the rice- and maize-infecting fungal pathogen Rhizoctonia solani anastomosis group 1 IA

Ten polymorphic microsatellite loci were isolated and characterized from the rice- and maize-infecting Basidiomycete fungus Rhizoctonia solani anastomosis group AG-1 IA. All loci were polymorphic in two populations from Louisiana in USA and Venezuela. The total number of alleles per locus ranged from four to eight. All 10 loci were also useful for genotyping soybean-infecting R. solani AG-1 isolates from Brazil and USA. One locus, TC06, amplified across two other AG groups representing different species, showing species-specific repeat length polymorphism. This marker suite will be used to determine the global population structure of this important pathogenic fungus.

Development and characterization of 14 microsatellite loci from an enriched genomic library of Eucalyptus camaldulensis Dehnh

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Isolation and characterization of microsatellite loci from the forage species Arachis pintoi (Genus Arachis)

Arachis pintoi is an alternative to forage production in the tropics. Its germplasm comprises more than 150 accessions, that could be used to improve it. Our objective was the isolation and characterization of microsatellite loci in A. pintoi to be used to molecular evaluation of this germplasm and of A. repens (section Caulorrhizae). Seven loci were analyzed using five accessions of A. repens and 20 accessions of A. pintoi. The high variation found makes clear the high potential of this marker in genetic studies in these species. The developed markers showed total transferability to A. repens.

Associations between microsatellite markers and traits related to performance, carcass and organs in chickens

Associations between four microsatellite markers on chromosome 11 and five on chromosome 13 with performance, carcass and organs traits were investigated in chickens using a least-squares approach applied to single-marker analysis. Three hundred and twenty seven F 2 chickens from the EMBRAPA broiler×layer experimental population were evaluated for 16 traits: five related to performance, five to carcass and five to organs, plus the hematocrit. Two significance thresholds were considered: p<0.05 and p<0.0056; the last value resulted from the application of a multiple tests analyses correction. On chromosome 11, six associations (p<0.05) between the genotypes of two markers with four growth related and one carcass trait were found. On chromosome 13, six associations (p<0.05) between marker genotypes and three performance traits, eight associations (p<0.05) between marker genotypes and two carcass traits and eight associations (p<0.05) between marker genotypes and four organs traits were detected. These associations were indications of the presence of quantitative trait loci on these chromosomes, especially on chromosome 13. In this chromosome, the strongest evidence was for body weight at 41 days of age and percentage of carcass because the p-values exceeded the multiple test threshold (p<0.0056), but also for breast percentage and heart weight due to the large number of markers (four) on chromosome 13 associated with each one of these traits. These associations should be further investigated by interval mapping analyses to find QTL positions and to allow the estimation of their effects. © Asian Network for Scientific Information, 2009.

Amplifiability of mitochondrial, microsatellite and amelogenin DNA loci from fecal samples of red brocket deer Mazama americana (Cetartiodactyla, Cervidae)

We tried to amplify mitochondrial, microsatellite and amelogenin loci in DNA from fecal samples of a wild Mazama americana population. Fifty-two deer fecal samples were collected from a 600-ha seasonal semideciduous forest fragment in a subtropical region of Brazil (21°20′, 47°17′W), with the help of a detection dog; then, stored in ethanol and georeferenced. Among these samples 16 were classified as fresh and 36 as non-fresh. DNA was extracted using the QIAamp® DNA Stool Mini Kit. Mitochondrial loci were amplified in 49 of the 52 samples. Five microsatellite loci were amplified by PCR; success in amplification varied according to locus size and sample age. Successful amplifications were achieved in 10/16 of the fresh and in 13/36 of the non-fresh samples; a negative correlation (R = -0.82) was found between successful amplification and locus size. Amplification of the amelogenin locus was successful in 22 of the 52 samples. The difficulty of amplifying nuclear loci in DNA samples extractedfrom feces collected in the field was evident. Some methodological improvements, including collecting fresh samples, selecting primers for shorter loci and quantifying the extracted DNA by real-time PCR, are suggested to increase amplification success in future studies. © FUNPEC-RP.

Isolation and characterization of microsatellite loci for the mud-dauber wasp Trypoxylon (Trypargilum) albitarse (Hymenoptera: Crabronidae)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic variability and efficiency of DNA microsatellite markers for paternity testing in horse breeds from the Brazilian Marajó archipelago

In this study, 15 microsatellite DNA loci used in comparative tests by the International Society for Animal Genetics were applied to the evaluation of genetic diversity and management, and the efficiency of paternity testing in Marajoara horses and Puruca ponies from the Marajó Archipelago. Based on the genotyping of 93 animals, mean allelic diversity was estimated as 9.14 and 7.00 for the Marajoara and Puruca breeds, respectively. While these values are similar to those recorded in most European breeds, mean levels of heterozygosity were much lower (Marajoara 49%, Puruca 40%), probably as a result of high levels of inbreeding in the Marajó populations. The mean informative polymorphic content of this 15-marker system was over 50% in both breeds, and was slightly higher in the Marajoara horses. The discriminative power and exclusion probabilities derived from this system were over 99% for both populations, emphasizing the efficacy of these markers for paternity testing and genetic management in the two breeds.

Development and characterization of microsatellite loci of microglanis cottoides (siluriformes: pseudopimelodidae) and cross-species amplification

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Paternity identification in sugarcane polycrosses by using microsatellite markers

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Microsatellite markers for Bokermannohyla species (Anura, Hylidae) from the Brazilian Cerrado and Atlantic Forest domains

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)