Introduction. This protocol applies to the characterization of genome structure and evolution of M. acuminata and M. balbisiana genomes; construction of physical maps around markers of interest and QTLs; comparative genomic studies with other monocot species; and study of banana streak virus (BSV) integration patterns in banana nuclear genomes. The principle, key advantages, starting plant material, time required and expected results are presented. Materials and methods. This part describes the required materials, and the protocols for isolation and lysis of banana nuclei; high-molecular-weight (HMW) DNA Hind III digestion and pulsed-field gel electrophoresis (PFGE) analysis; large-scale HMW DNA Hind III digestion and ligation to the pINDIGOBAC–5 vector; and analysis of recombinant BAC clones. It mentions the main problems which can occur. Results. The described protocols will enable the efficient construction of BAC libraries from Musa species. These libraries can be used to construct physical maps and select specific genomic regions to be sequenced.

Introduction. The citrus industry is one of the main activities of Brazilian agriculture. Several pests and diseases have threatened citrus culture in recent years. Genetic mapping is one of the most efficient strategies for conducting advanced genetic studies by facilitating plant selection guided by markers. The objective of this study was to construct an integrated genetic map between Citrus sinensis (L.) Osbeck cv. ‘Pêra’ and C. reticulata Blanco cv. ‘Cravo’ using two different types of segregation of markers. Materials and methods. The linkage analyses were conducted with segregation data obtained from 256 RAPD markers in a population of 94 hybrids. Analyses were performed through the software JoinMap, LOD ≥ 6.0, θ ≤ 0.25, and the Kosambi function. Results and discussion. The linked map between the two cultivars had 217 markers defined by 15 linkage groups, covering 527 cM. This map had five linkage groups with common markers of ‘Pêra’ and ‘Cravo’. The inclusion of new markers would increase the number of linkage groups with markers from both parents, thus making their number equal to the haploid chromosome number. The alterations in the order and in the distances among the markers, due to the presence or absence of bridging markers in the linkage map, are discussed.