title: Analysis of BAC-end sequences in common bean (Phaseolus vulgaris L.) towards the development and characterization of long motifs SSRs.
abstract: The increasing volume of genomic data on the Phaseolus vulgaris species have contributed to its importance as a model genetic species and positively affected the investigation of other legumes of scientific and economic value. To expand and gain a more in-depth knowledge of the common bean genome, the ends of a number of bacterial artificial chromosome (BAC) were sequenced, annotated and the presence of repetitive sequences was determined. In total, 52,270 BESs (BAC-end sequences), equivalent to 32 Mbp (~6 %) of the genome, were processed. In total, 3,789 BES-SSRs were identified, with a distribution of one SSR (simple sequence repeat) per 8.36 kbp and 2,000 were suitable for the development of SSRs, of which 194 were evaluated in low-resolution screening. From 40 BES-SSRs based on long motifs SSRs (≥ trinucleotides) analyzed in high-resolution genotyping, 34 showed an equally good amplification for the Andean and for the Mesoamerican genepools, exhibiting an average gene diversity (H E) of 0.490 and 5.59 alleles/locus, of which six classified as Class I showed a H E ≥ 0.7. The PCoA and structure analysis allowed to discriminate the gene pools (K = 2, FST = 0.733). From the 52,270 BESs, 2 % corresponded to transcription factors and 3 % to transposable elements. Putative functions for 24,321 BESs were identified and for 19,363 were assigned functional categories (gene ontology). This study identified highly polymorphic BES-SSRs containing tri- to hexanucleotides motifs and bringing together relevant genetic characteristics useful for breeding programs. Additionally, the BESs were incorporated into the international genome-sequencing project for the common bean.
authors.affiliation: Laboratório de Genética Molecular de Plantas, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa (UFV), Viçosa, MG, Brazil.
authors.forename: Bárbara Salomão de Faria
authors.initials: BS
authors.lastname: Müller
authors.forename: Tetsu
authors.initials: T
authors.lastname: Sakamoto
authors.forename: Ivandilson Pessoa Pinto
authors.initials: IP
authors.lastname: de Menezes
authors.forename: Guilherme Souza
authors.initials: GS
authors.lastname: Prado
authors.forename: Wellington Santos
authors.initials: WS
authors.lastname: Martins
authors.forename: Claudio
authors.initials: C
authors.lastname: Brondani
authors.forename: Everaldo Gonçalves
authors.initials: EG
authors.lastname: de Barros
authors.forename: Rosana Pereira
authors.initials: RP
authors.lastname: Vianello
mesh_terms: D001483:Base Sequence; D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics*; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics; D015698:Genomic Library; D005838:Genotype; D018895:Microsatellite Repeats / Q000235:genetics*; D027805:Phaseolus / Q000235:genetics*; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant