title: In silico identification and experimental validation of insertion-deletion polymorphisms in tomato genome.
abstract: Comparative analysis of the genome sequences of Solanum lycopersicum variety Heinz 1706 and S. pimpinellifolium accession LA 1589 using MUGSY software identified 145 695 insertion-deletion (InDel) polymorphisms. A selected set of 3029 candidate InDels (≥2 bp) across the entire tomato genome were subjected to PCR validation, and 82.4% could be verified. Of 2272 polymorphic InDels between LA 1589 and Heinz 1706, 61.6, 45.2, and 31.6% were polymorphic in 8 accessions of S. pimpinellifolium, 4 accessions of S. lycopersicum var. cerasiforme, and 10 varieties of S. lycopersicum, respectively. Genetic distance was 0.216 in S. pimpinellifolium, 0.202 in S. lycopersicum var. cerasiforme, and 0.108 in S. lycopersicum. The data suggested a reduction of genetic variation from S. pimpinellifolium to S. lycopersicum var. cerasiforme and S. lycopersicum. Cluster analysis showed that the 8 accessions of S. pimpinellifolium were in one group, whereas 4 accessions of S. lycopersicum var. cerasiforme and 10 varieties of S. lycopersicum were in the same group.
authors.affiliation: Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Yang
authors.affiliation: Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China.
authors.forename: Huolin
authors.initials: H
authors.lastname: Shen
authors.affiliation: Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Science, China Agricultural University, No. 2 Yuanmingyuan Xilu, Beijing 100193, China yangwencai@cau.edu.cn.
authors.forename: Wencai
authors.initials: W
authors.lastname: Yang
mesh_terms: D003198:Computer Simulation; D005819:Genetic Markers; D018745:Genome, Plant; D054643:INDEL Mutation; D018551:Solanum lycopersicum / Q000235:genetics*; D011110:Polymorphism, Genetic; D032322:Solanum / Q000235:genetics
chemical_list: D005819:Genetic Markers
keywords: Solanum lycopersicum; genetic variation; insertion–deletion