Introgression Browser: High throughput whole-genome SNP visualization
Aflitos, S.A. ; Sanchez Perez, G.F. ; Ridder, D. de; Fransz, P. ; Schranz, M.E. ; Jong, J.H.S.G.M. de; Peters, S.A. - \ 2015
The Plant Journal 82 (2015)1. - ISSN 0960-7412 - p. 174 - 182.
in-situ hybridization - alien chromosomes - recombination - tomato - markers - thaliana - potato - identification - organization - improvement
Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in chromosome regions where crossover recombinants are rare or not viable. Here, we present the Introgression Browser (IBROWSER), a bioinformatics tool aimed at visualizing introgressions at nucleotide or SNP accuracy. The software selects homozygous SNPs from Variant Call Format (VCF) information and filters out heterozygous SNPs, Multi-Nucleotide Polymorphisms (MNPs) and insertion-deletions (InDels). For data analysis IBROWSER makes use of sliding windows, but if needed it can generate any desired fragmentation pattern through General Feature Format (GFF) information. In an example of tomato (Solanum lycopersicum) accessions we visualize SNP patterns and elucidate both position and boundaries of the introgressions. We also show that our tool is capable of identifying alien DNA in a panel of the closely related S. pimpinellifolium by examining phylogenetic relationships of the introgressed segments in tomato. In a third example, we demonstrate the power of the IBROWSER in a panel of 597 Arabidopsis accessions, detecting the boundaries of a SNP-free region around a polymorphic 1.17 Mbp inverted segment on the short arm of chromosome 4. The architecture and functionality of IBROWSER makes the software appropriate for a broad set of analyses including SNP mining, genome structure analysis, and pedigree analysis. Its functionality, together with the capability to process large data sets and efficient visualization of sequence variation, makes IBROWSER a valuable breeding tool.
Alteration of the genomic composition of Solanum nigrum (+) potato backcross derivatives by somatic hybridisation: selection of fusion hybrids by DNA measurements and GISH
Horsman, K. ; Gavrilenko, T. ; Bergervoet, M. ; Huigen, D.J. ; Tjin Wong Joe, A. ; Jacobsen, E. - \ 2001
Plant Breeding 120 (2001)3. - ISSN 0179-9541 - p. 201 - 207.
infestans mont debary - lycopersicon-esculentum - chromosome-number - alien chromosomes - rflp analysis - tuberosum - brevidens - tomato - identification - resistance
Fusion experiments were performed with a first (BC1-6738) and a second (BC2-9017) generation backcross hybrid of 6x Solanum nigrum (+) 2x potato somatic hybrids with potato cultivars. Because no progeny was obtained from the BC2 genotypes, alternative approaches were sought to overcome the sexual crossing barrier. Five potato genotypes, one of which contains the hygromycin resistance gene, were used in the fusion experiments. All vigorous regenerants were used for the estimation of nuclear DNA content using flow cytometry. Plants with a DNA content higher than that of the BC1-6738 or BC2 genotypes were considered potential somatic hybrids. Forty-nine potential somatic hybrids resulted from fusion experiments with BC1-6738, from which 20 grew vigorously in the greenhouse and flowered. After pollination with several 4x potato cultivars. eight genotypes produced seeded berries and five genotypes gave seedless berries. In addition. Il of these 13 somatic hybrids were selected for genomic in situ hybridization (GISH) analysis to determine their genomic composition. Nine had exactly or approximately the expected number of 36 S. nigrum and 60 potato chromosomes. In one genotype. only 22 instead of 36 S. nigrum chromosomes were found acid one potato chromosome was possibly missing. Only five potential somatic hybrids were detected among the 79 regenerants from BC2-9017 (+) 2x potato Fusion experiments that were analysed by flow cytometry. Two of these hybrids were rather vigorous and did flower, but pollinations with potato have not yet yet any berries.