Mitochondrial genome sequence of tuber-bearing wild potato, Solanum commersonii Dunal

Discovery of a novel mitochondrial DNA molecule associated with tetrad pollen sterility in potato

BACKGROUND

Tetrad sterility in potato is caused by a specific cytoplasm, called TSC_sto, derived from the Mexican wild tetraploid species Solanum stoloniferum. Different S. stoloniferum accessions crossed as females with S. tuberosum resulted in 12 fertile hybrids and 27 sterile hybrids exhibiting tetrad sterility.

RESULTS

Whole-mitochondrial-genome sequencing was performed for two fertile hybrids and three hybrids exhibiting tetrad sterility. Two to seven contigs, with the total assembly lengths ranging from 462,716 to 535,375 bp, were assembled for each hybrid. Unlike for the reference mitochondrial genome (cv. Désirée), two different recombinant-type contigs (RC-I and RC-II) were identified. RC-I featured by the rpl5-ψrps14 gene joined to the nad6 gene, generating a novel intergenic region. Using a PCR marker (P-3), we found that this intergenic region occurred exclusively in interspecific hybrids exhibiting tetrad sterility and in their parental S. stoloniferum accessions. A part of this intergenic sequence was expressed in the pollen. From a large survey in which P-3 was applied to 129 accessions of 27 mostly Mexican wild species, RC-I was found in diploid S. verrucosum and polyploid species. From eight accessions of S. verrucosum used as females, 92 interspecific hybrids were generated, in which only those carrying RC-I exhibited tetrad sterility.

CONCLUSIONS

RC-I was clearly associated with tetrad sterility, and the RC-I-specific intergenic region likely contains a causal factor of tetrad sterility.

Mitochondrial genome recombination in somatic hybrids of Solanum commersonii and S. tuberosum

Interspecific somatic hybridization has been performed in potato breeding experiments to increase plant resistance against biotic and abiotic stress conditions. We analyzed the mitochondrial and plastid genomes and 45S nuclear ribosomal DNA (45S rDNA) for the cultivated potato (S. tuberosum, St), wild potato (S. commersonii, Sc), and their somatic hybrid (StSc). Complex genome components and structure, such as the hybrid form of 45S rDNA in StSc, unique plastome in Sc, and recombinant mitogenome were identified. However, the mitogenome exhibited dynamic multipartite structures in both species as well as in the somatic hybrid. In St, the mitogenome is 756,058 bp and is composed of five subgenomes ranging from 297,014 to 49,171 bp. In Sc, it is 552,103 bp long and is composed of two sub-genomes of 338,427 and 213,676 bp length. StSc has 447,645 bp long mitogenome with two subgenomes of length 398,439 and 49,206 bp. The mitogenome structure exhibited dynamic recombination mediated by tandem repeats; however, it contained highly conserved genes in the three species. Among the 35 protein-coding genes of the StSc mitogenome, 21 were identical for all the three species, and 12 and 2 were unique in Sc and St, respectively. The recombinant mitogenome might be derived from homologous recombination between both species during somatic hybrid development.

Complete mitogenome assemblies from a panel of 13 diverse potato taxa

Mitochondrial DNA is maternally inherited and is shown to affect nuclear–cytoplasmic interactions in potato. Analyzing the mitogenome helps understand the evolutionary relationships and improve breeding programs in potato. We report complete mitogenome sequences from a panel of 13 potato accessions of various taxa. Each mitogenome has three independent circular molecules, except one of the S. bukasovii sample BUK2, which has a single circular molecule. Each mitogenome code for 37 non-redundant protein-coding genes, three rRNAs, 20 tRNAs, and 19 hypothetical open reading frames. Phylogenetic analysis reveals congruency between plastome and mitogenome phylogeny.

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

Among wild species used in potato breeding, Solanum commersonii displays the highest tolerance to low temperatures under both acclimated (ACC) and non-acclimated (NACC) conditions. It is also the first wild potato relative with a known whole genome sequence. Recent studies have shown that abiotic stresses induce changes in the expression of many small non-coding RNA (sncRNA). We determined the small non-coding RNA (sncRNAome) of two clones of S. commersonii contrasting in their cold response phenotypes via smRNAseq. Differential analysis provided evidence that expression of several miRNAs changed in response to cold stress conditions. Conserved miR408a and miR408b changed their expression under NACC conditions, whereas miR156 and miR169 were differentially expressed only under ACC conditions. We also report changes in tasiRNA and secondary siRNA expression under both stress conditions. Our results reveal possible roles of sncRNA in the regulatory networks associated with tolerance to low temperatures and provide useful information for a more strategic use of genomic resources in potato breeding.