Population genetic structure revealed by a school of the freshwater migratory fish, Brycon hilarii

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A radiation hybrid map of river buffalo (Bubalus bubalis) chromosome 7 and comparative mapping to the cattle and human genomes

A preliminary radiation hybrid (RH) map containing 50 loci on chromosome 7 of the domestic river buffalo Bubalus bubalis (BBU; 2n = 50) was constructed based on a comparative mapping approach. The RH map of BBU7 includes thirty-seven gene markers and thirteen microsatellites. All loci have been previously assigned to Bos taurus (BTA) chromosome BTA6, which is known for its association with several economically important milk production traits in cattle. The map consists of two linkage groups spanning a total length of 627.9 cR(5,000). Comparative analysis of the BBU7 RH 5,000 map with BTA6 in cattle gave new evidence for strong similarity between the two chromosomes over their entire length and exposed minor differences in locus order. Comparison of the BBU7 RH 5,000 map with the Homo sapiens (HSA) genome revealed similarity with a large chromosome segment of HSA4. Comparative analysis of loci in both species revealed more variability than previously known in gene order and several chromosome rearrangements including centromere relocation. The data obtained in our study define the evolutionarily conserved segment on BBU7 and HSA4 to be between 3.5 megabases (Mb) and 115.8 Mb in the HSA4 (genome build 36) DNA sequence. Copyright (c) 2008 S. Karger AG, Basel.

A radiation hybrid map of river buffalo (Bubalus bubalis) chromosome 1 (BBU1)

The largest chromosome in the river buffalo karyotype, BBU1, is a submetacentric chromosome with reported homology between BBU1q and bovine chromosome 1 and between BBU1p and BTA27. We present the first radiation hybrid map of this chromosome containing 69 cattle derived markers including 48 coding genes, 17 microsatellites and four ESTs distributed in two linkage groups spanning a total length of 1330.1 cR(5000). The RH map was constructed based on analysis of a recently developed river buffalo-hamster whole genome radiation hybrid (BBURH5000) panel. The retention frequency of individual markers across the panel ranged from 17.8 to 52.2%. With few exceptions, the order of markers within linkage groups is identical to the order established for corresponding cattle RH maps. The BBU1 map provides a starting point for comparison of gene order rearrangements between river buffalo chromosome 1 and its bovine homologs. Copyright (C) 2007 S. Karger AG, Basel.

Microsatellite loci isolation from river buffalo using enriched partial genomic libraries

The extensive use of buffalo in agriculture, especially in developing countries, begs for genetic resources to evaluate and improve traits important to local and regional economies. Brazil presents the largest water buffalo populations in the New World, with 1 1 million heads including swamp and river types. To design rational breeding strategies for optimum utilization and conservation of available genetic variability in the Brazilian buffalo's population, it is essential to understand their genetic architecture and relationship among various breeds. This depends, in part, on the knowledge of their genetic structure based on molecular markers like microsatellites. In the present study, we developed six enriched partial genomic libraries for river buffalo using selective hybridization methods. Genomic DNA was hybridized with six different arrays of repeat motif, 5' biotinylated - (CA)(15), (CT)(15), (AGG)(8), (GAAA)(8), (GATA)(8), (AAAAC)(8) - and bound to streptavidin coated beads. The cloning process generated a total of 1920 recombinant clones. Up to date, 487 were directly sequenced for the presence of repeats, from which 13 have been positive for presence of repeats as follows: 9 for di-nucleotide repeats, 3 for tri-nucleotide repeats and 1 for tetra-nucleotide repeat. PCR primer pairs for the isolated microsatellites are under construction to determine optimum annealing temperature. These microsatellites will be useful for studies involving phylogenetic relationships, genome mapping and genetic diversity analysis within buffalo populations worldwide.

First radiation hybrid map of the river buffalo X chromosome (BBUX) and comparison with BTAX

We report the first radiation hybrid map of the river buffalo X chromosome generated from a recently constructed river buffalo (Bubalus bubalis) whole-genome radiation hybrid panel (BBURH5000). This map contains a total of 33 cattle-derived markers, including 10 genes, four ESTs and 19 microsatellites. The markers are distributed in two linkage groups: LG1 contains eight markers spanning 125.6 cR, and LG2 contains 25 markers spanning 366.3 cR. LG1 contains six markers in common with bovine sequence assembly BUILD 3.1. With the exception of BMS2152, the order of these markers on our BBUX map is shuffled when compared to the cow X chromosome (Bos taurus; BTAX). From LG2, two markers (AMELX and BL22) map to a more distal portion of BTAX compared to BBUX. In addition, two pairs of LG2 markers exhibit inversions compared to BTAX (ILSTS017 and ATRX; XBM38 and PPEF1). Alternatively, when compared to the most recent bovine RH map (Bov-Gen 3000rads), BL1098 and BMS2227 from LG1 as well as PLS3 and BMS1820 from LG2 showed inverted positions on the BBUX map. These discrepancies in buffalo and cattle maps may reflect evolutionary divergence of the chromosomes or mapping errors in one of the two species. Although the set of mapped markers does not cover the entire X chromosome, this map is a starting point for the construction of a high-resolution map, which is necessary for characterization of small rearrangements that might have occurred between the Bubalus bubalis and Bos taurus X chromosomes.

A first generation whole genome RH map of the river buffalo with comparison to domestic cattle

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

Preliminary radiation hybrid map for river buffalo chromosome 6 and comparison to bovine chromosome 3

We present the first radiation hybrid (RH) map of river buffalo (Bubalus bubalis) chromosome 6 (BBU6) developed with a recently constructed river buffalo whole-genome RH panel (BBURH5000). The preliminary map contains 33 cattle-derived markers, including 12 microsatellites, 19 coding genes and two ESTs, distributed across two linkage groups. Retention frequencies for markers ranged from 14.4% to 40.0%. Most of the marker orders within the linkage groups on BBU6 were consistent with the cattle genome sequence and RH maps. This preliminary RH map is the starting point for comparing gene order between river buffalo and cattle, presenting an opportunity for the examination of micro-rearrangements of these chromosomes. Also, resources for positional candidate cloning in river buffalo are enhanced.

Diversidade genética e tamanho efetivo de duas populações de Myracrodruon urundeuva Fr. All., sob conservação ex situ

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genetic linkage map of chicken chromosome 1 from a Brazilian resource population

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

Identification of haploid maize by flow cytometry, morphological and molecular markers

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Evaluation of nine microsatellite loci and misidentification paternity frequency in a population of Gyr breed bovines

Erros de identificação de paternidade são prejudiciais por reduzir o ganho genético anual e comprometer um programa eficiente de melhoramento genético. O objetivo principal deste trabalho foi avaliar o potencial de uso de nove microssatélites em testes de paternidade e investigar a freqüência de erro de identificação de famílias de um rebanho de animais da raça Gir. No experimento foram utilizadas amostras de sangue de quarenta famílias (touro/ vaca/ bezerro) de animais da raça Gir, Puros de Origem e registrados na Associação Brasileira dos Criadores de Zebu (ABCZ). A maior parte dos microssatélites avaliados neste trabalho são recomendados, para Testes de Paternidade em bovinos, pela Sociedade Internacional de Genética Animal (ISAG). As regiões microssatélites TGLA122, TGLA126, BM1824, BMS2533, SPS115, ETH3, ETH10, ETH225 e POTCHA foram amplificadas por meio da técnica de PCR. Os produtos da amplificação foram separados por eletroforese em gel de poliacrilamida desnaturante. A partir dos dados obtidos foram calculadas as freqüências alélicas, diversidade gênica, conteúdo de polimorfismo informativo e probabilidade de exclusão para cada microssatélite. Também foram calculadas as freqüências genotípicas, heterozigosidade, probabilidade de exclusão combinada e probabilidade de Paternidade nas famílias consideradas. A probabilidade de exclusão combinada para todos os microssatélites estudados foi de 0,9789. Os resultados dos testes de paternidade acusaram erro de identificação em onze das 40 famílias estudadas, ou seja, 27,5% da amostra. A probabilidade de paternidade variou entre 0,8691 e 0,9999, com valor médio de 0,9512.

Development and characterization of polymorphic microsatellite markers for the sweet orange (Citrus sinensis L. Osbeck)

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

Isolation and characterization of microsatellite loci in the woolly mouse opossum, Micoureus paraguayanus (Marsupialia : Didelphimorphia)

Five microsatellite loci were isolated and characterized within the woolly mouse opossum (Micoureus paraguayanus), a Neotropical marsupial, using an enrichment cloning procedure. Between four and seven alleles were detected per locus, with expected heterozygosity ranging from 0.358 to 0.560. These microsatellites should provide useful markers in a variety of genetic analyses to examine parentage, inbreeding, population structure and population dynamics in fragmented forest habitats.

Mapping QTLs on chicken chromosome 1 for performance and carcass traits in a broiler x layer cross

With the objective of mapping quantitative trait loci (QTLs) for performance and carcass traits, an F-2 chicken population was developed by crossing broiler and layer lines. A total of 2063 F-2 chicks in 21 full-sib families were reared as broilers and slaughtered at 42 days of age. Seventeen performance and carcass traits were measured. Parental (F-0) and F-1 individuals were genotyped with 80 microsatellites from chicken chromosome 1 to select informative markers. Thirty-three informative markers were used for selective genotyping of F-2 individuals with extreme phenotypes for body weight at 42 days of age (BW42). Based on the regions identified by selective genotyping, seven full-sib families (649 F-2 chicks) were genotyped with 26 markers. Quantitative trait loci affecting body weight, feed intake, carcass weight, drums and thighs weight and abdominal fat weight were mapped to regions already identified in other populations. Quantitative trait loci for weights of gizzard, liver, lungs, heart and feet, as well as length of intestine, not previously described in the literature were mapped on chromosome 1. This F-2 population can be used to identify novel QTLs and constitutes a new resource for studies of genes related to growth and carcass traits in poultry.

RH maps of bovine chromosomes 15 and 29: conservation of human chromosomes 11 and 5

Comparative mapping data on evolutionary conserved coding sequences and synteny maps between human and cattle are insufficient to define the extent and distribution of conserved segments between these two species, because the order of loci is often rearranged. A 5000-rad cattle whole-genome radiation hybrid (WG-RH) panel was constructed to provide high-resolution comparative maps and also to integrate linkage maps of microsatellites with evolutionary conserved genes and transcripts in a single ordered map. We used the WG-RH panel to construct radiation hybrid maps of bovine Chromosomes (Chrs) 15 and 29 (BTA15 and BTA29), integrating microsatellites from published linkage maps with selected genes. The comprehensive map of BTA15 consists of 24 markers. 13 of which were placed in the framework map. Eleven molecular markers compose the comprehensive map of BTA29. seven of which were placed in the framework map. We identified the homologous regions between bovine Chr 15 (BTA15) and human Chrs 5 and 11 (HSA5 and HSA11), as well as between BTA29 and HSA11, the present study demonstrates that WG-RH mapping is an efficient method for integrating multiple genetic maps into one map and for incorporating monomorphic Type I loci into ordered maps for comparison between species.