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.

Deep‐sequencing of Solanum commersonii small RNA libraries reveals riboregulators involved in cold stress response

“…; Cho et al . , ), and it has already been exploited to disclose several gene families (D'Amelia et al . , ; Aversano et al .…”

Organellar genome analysis reveals endosymbiotic gene transfers in tomato

“…These species are used as plant models, and their complete nuclear genomes provide insights into many aspects of plant biology [48–50]. The organellar genomes of Solanum have also been studied, and the plastomes of 15 Solanum species have been sequenced [51–57]. These complete plastome sequences increase our understanding of the evolution and phylogenetic relationships of Solanum species.…”

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“…The CP genome of L. chinense is 155,756 bp in length consisting of a large and small singlecopy regions of length 86,595 and 18,209 bp, separated by two inverted repeat regions of 25,476 bp ( Figure 1 and Table 1). The total G+C content is similar to that of other species in the Solanaceae family, which is about 37.8% (Amiryousefi A 2018, Cho et al 2016, Sanchez-Puerta and Abbona 2014, Yang Y. et al 2014. And the G+C contents of the LSC(35.8%) and SSC regions (32.3%)are lower than those of the IR regions (43.1%).…”