Genetic divergence of rubber tree estimated by multivariate techniques and microsatellite markers

Genetic diversity of 60 Hevea genotypes, consisting of Asiatic, Amazonian, African and IAC clones, and pertaining to the genetic breeding program of the Agronomic Institute (IAC), Brazil, was estimated. Analyses were based on phenotypic multivariate parameters and microsatellites. Five agronomic descriptors were employed in multivariate procedures, such as Standard Euclidian Distance, Tocher clustering and principal component analysis. Genetic variability among the genotypes was estimated with 68 selected polymorphic SSRs, by way of Modified Rogers Genetic Distance and UPGMA clustering. Structure software in a Bayesian approach was used in discriminating among groups. Genetic diversity was estimated through Nei's statistics. The genotypes were clustered into 12 groups according to the Tocher method, while the molecular analysis identified six groups. In the phenotypic and microsatellite analyses, the Amazonian and IAC genotypes were distributed in several groups, whereas the Asiatic were in only a few. Observed heterozygosity ranged from 0.05 to 0.96. Both high total diversity (HT' = 0.58) and high gene differentiation (G st' = 0.61) were observed, and indicated high genetic variation among the 60 genotypes, which may be useful for breeding programs. The analyzed agronomic parameters and SSRs markers were effective in assessing genetic diversity among Hevea genotypes, besides proving to be useful for characterizing genetic variability

Genetic diversity in cultivated carioca common beans based on molecular marker analysis

A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm

Development and application of microsatellites in plant breeding

Molecular markers are powerful tools for analyzing genome diversity within a species, and to evaluate geneticrelationships between individuals and populations. Among them, microsatellites (SSRs) are one of the most important polymorphicmarkers that can be used effectively to distinguish germplasm accessions. These markers present high informative content due totheir codominant inheritance, multiallelism, mendelian pattern and good genome coverage. The enrichment methodology formicrosatellite development has a superior efficiency in plants, especially when performed using biotin-labeled microsatellite oligoprobes and streptavidin-coated magnetic beads. The development of EST-SSR markers has become a fast and relatively inexpensive way butit is limited to species for which this type of database exists. Given the high polymorphism level of microsatellites when compared toother markers, SSRs have been used to study population structure, for genetic diversity analysis, genetic mapping and markerassisted selection

A whole genome DArT assay to assess germplasm collection diversity in common beans

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)A Diversity Arrays Technology (DArT) marker system was applied for the first time to common beans (Phaseolus vulgaris L.) and tested on 89 accessions from the IAC and CIAT common bean breeding programs, as well as on landraces from the FAO collection. Seven frequently used restriction endonucleases were tested in combination with a rare-cutting restriction enzyme, PstI, to evaluate their suitability for DArT technology. Two restriction enzyme combinations (PstI/BstNI and PstI/TaqI) were selected to evaluate polymorphisms and PstI/BstNI, which yielded the most polymorphisms, was used to construct the final array. Genotyping was done by labelling the genomic representations with the fluorescent nucleotides cy3-dUTP and cy5-dUTP. The poly-linker fragment was labelled with 6-FAM and used as a control treatment and standard to determine the amount of DNA spotted on the array for each clone. DArTsoft version 7.3 software was used to analyse, identify and score polymorphic markers. Arrays containing individual fragments from these representations generated DArT fingerprints with a genotype call rate of 97.1% and a scoring reproducibility of at least 99.9%. A total of 2,501 polymorphic markers were found. Neighbour-joining distance matrices were used to create dispersion graphs that distinguished the two major gene pools of common beans and classified the accessions as either Andean or Mesoamerican. A principal coordinate analysis of the DArT marker results explained 82% of the total data variation. These results show that the DArT platform was accurate for studying the genetic diversity of the common bean and efficient for the large-scale detection of polymorphisms. These properties make marker technology a choice for future experiments. This is the first report to describe the use of DArT technology for genotyping the common bean.301181193Fundag (Fundacao de Apoio a Pesquisa Agricola)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Inheritance of growth habit detected by genetic linkage analysis using microsatellites in the common bean (phaseolus vulgaris L.)

The genetic linkage map for the common bean (Phaseolus vulgaris L.) is a valuable tool for breeding programs. Breeders provide new cultivars that meet the requirements of farmers and consumers, such as seed color, seed size, maturity, and growth habit. A genetic study was conducted to examine the genetics behind certain qualitative traits. Growth habit is usually described as a recessive trait inherited by a single gene, and there is no consensus about the position of the locus. The aim of this study was to develop a new genetic linkage map using genic and genomic microsatellite markers and three morphological traits: growth habit, flower color, and pod tip shape. A mapping population consisting of 380 recombinant F10 lines was generated from IAC-UNA × CAL143. A total of 871 microsatellites were screened for polymorphisms among the parents, and a linkage map was obtained with 198 mapped microsatellites. The total map length was 1865.9 cM, and the average distance between markers was 9.4 cM. Flower color and pod tip shape were mapped and segregated at Mendelian ratios, as expected. The segregation ratio and linkage data analyses indicated that the determinacy growth habit was inherited as two independent and dominant genes, and a genetic model is proposed for this trait27549560CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPnão temnão te

Inheritance of growth habit detected by genetic linkage analysis using microsatellites in the common bean (Phaseolus vulgaris L.)

The genetic linkage map for the common bean (Phaseolus vulgaris L.) is a valuable tool for breeding programs. Breeders provide new cultivars that meet the requirements of farmers and consumers, such as seed color, seed size, maturity, and growth habit. A genetic study was conducted to examine the genetics behind certain qualitative traits. Growth habit is usually described as a recessive trait inherited by a single gene, and there is no consensus about the position of the locus. The aim of this study was to develop a new genetic linkage map using genic and genomic microsatellite markers and three morphological traits: growth habit, flower color, and pod tip shape. A mapping population consisting of 380 recombinant F10 lines was generated from IAC-UNA x CAL143. A total of 871 microsatellites were screened for polymorphisms among the parents, and a linkage map was obtained with 198 mapped microsatellites. The total map length was 1865.9 cM, and the average distance between markers was 9.4 cM. Flower color and pod tip shape were mapped and segregated at Mendelian ratios, as expected. The segregation ratio and linkage data analyses indicated that the determinacy growth habit was inherited as two independent and dominant genes, and a genetic model is proposed for this trait.State of Sao Paulo Research Foundation (FAPESP)Brazilian National Council for Scientific and Technological Development (CNPq)FAPES