title: Complete chloroplast genome sequences of Solanum commersonii and its application to chloroplast genotype in somatic hybrids with Solanum tuberosum.
abstract: Chloroplast genome of Solanum commersonii and S olanum tuberosum were completely sequenced, and Indel markers were successfully applied to distinguish chlorotypes demonstrating the chloroplast genome was randomly distributed during protoplast fusion. Somatic hybridization has been widely employed for the introgression of resistance to several diseases from wild Solanum species to overcome sexual barriers in potato breeding. Solanum commersonii is a major resource used as a parent line in somatic hybridization to improve bacterial wilt resistance in interspecies transfer to cultivated potato (S. tuberosum). Here, we sequenced the complete chloroplast genomes of Lz3.2 (S. commersonii) and S. tuberosum (PT56), which were used to develop fusion products, then compared them with those of five members of the Solanaceae family, S. tuberosum, Capsicum annum, S. lycopersicum, S. bulbocastanum and S. nigrum and Coffea arabica as an out-group. We then developed Indel markers for application in chloroplast genotyping. The complete chloroplast genome of Lz3.2 is composed of 155,525 bp, which is larger than the PT56 genome with 155,296 bp. Gene content, order and orientation of the S. commersonii chloroplast genome were highly conserved with those of other Solanaceae species, and the phylogenetic tree revealed that S. commersonii is located within the same node of S. tuberosum. However, sequence alignment revealed nine Indels between S. commersonii and S. tuberosum in their chloroplast genomes, allowing two Indel markers to be developed. The markers could distinguish the two species and were successfully applied to chloroplast genotyping (chlorotype) in somatic hybrids and their progenies. The results obtained in this study confirmed the random distribution of the chloroplast genome during protoplast fusion and its maternal inheritance and can be applied to select proper plastid genotypes in potato breeding program.
authors.affiliation: Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea.
authors.forename: Kwang-Soo
authors.initials: KS
authors.lastname: Cho
authors.affiliation: Department of Biological Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea.
authors.forename: Kyeong-Sik
authors.initials: KS
authors.lastname: Cheon
authors.affiliation: Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea.
authors.forename: Su-Young
authors.initials: SY
authors.lastname: Hong
authors.affiliation: Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea.
authors.forename: Ji-Hong
authors.initials: JH
authors.lastname: Cho
authors.affiliation: Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea.
authors.forename: Ju-Seong
authors.initials: JS
authors.lastname: Im
authors.affiliation: Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang, 25342, Republic of Korea.
authors.forename: Manjulatha
authors.initials: M
authors.lastname: Mekapogu
authors.affiliation: Phygen Genomics Institute, Baekgoong Plaza 1, Bundang-gu, Seongnam, 13558, Republic of Korea.
authors.forename: Yei-Soo
authors.initials: YS
authors.lastname: Yu
authors.affiliation: Department of Horticulture and Institute of Life and Environment, Daegu University, Gyeongsan, 38453, Republic of Korea. thzoo@daegu.ac.kr.
authors.forename: Tae-Ho
authors.identifier: http://orcid.org/0000-0002-4316-5732
authors.initials: TH
authors.lastname: Park
mesh_terms: D001483:Base Sequence; D003062:Codon / Q000235:genetics; D003433:Crosses, Genetic; D004270:DNA, Circular / Q000235:genetics; D005819:Genetic Markers; D014644:Genetic Variation; D054628:Genome, Chloroplast; D005838:Genotype; D006824:Hybridization, Genetic; D054643:INDEL Mutation / Q000235:genetics; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D032322:Solanum / Q000235:genetics*; D020080:Tandem Repeat Sequences / Q000235:genetics
chemical_list: D003062:Codon; D004270:DNA, Circular; D005819:Genetic Markers
keywords: Chloroplast; Indel marker; Protoplast fusion; Solanum commersonii; Solanum tuberosum