Haplotype-resolved genome and mapping of freezing tolerance in the wild potato Solanum commersonii.

Solanum commersonii (2n = 2x = 24, 1EBN, Endosperm Balance Number), native to the southern regions of Brazil, Uruguay, and northeastern Argentina, is the first wild potato germplasm collected by botanists and exhibits a remarkable array of traits related to disease resistance and stress tolerance. In this study, we present a high-quality haplotype-resolved genome of S. commersonii. The two identified haplotypes demonstrate chromosome sizes of 706.48 and 711.55 Mb, respectively, with corresponding chromosome anchoring rates of 94.2 and 96.9%. Additionally, the contig N50 lengths are documented at 50.87 and 45.16 Mb. The gene annotation outcomes indicate that the haplotypes encompasses a gene count of 39 799 and 40 078, respectively. The genome contiguity, completeness, and accuracy assessments collectively indicate that the current assembly has produced a high-quality genome of S. commersonii. Evolutionary analysis revealed significant positive selection acting on certain disease resistance genes, stress response genes, and environmentally adaptive genes during the evolutionary process of S. commersonii. These genes may be related to the formation of diverse and superior germplasm resources in the wild potato species S. commersonii. Furthermore, we utilized a hybrid population of S. commersonii and S. verrucosum to conduct the mapping of potato freezing tolerance genes. By combining BSA-seq analysis with traditional QTL mapping, we successfully mapped the potato freezing tolerance genes to a specific region on Chr07, spanning 1.25 Mb, with a phenotypic contribution rate of 18.81%. In short, current research provides a haplotype-resolved reference genome of the diploid wild potato species S. commersonii and establishes a foundation for further cloning and unraveling the mechanisms underlying cold tolerance in potatoes.

Mapping of a novel locus Ra conferring extreme resistance against potato virus A in cultivated potato (Solanum tuberosum L.).

KEY MESSAGE: The Ra extreme resistance against potato virus A was mapped to the upper of chromosome 4 in tetraploid potato. Potato virus A (PVA) is one of the major viruses affecting potato worldwide and can cause serious disease symptoms and yield losses. Previously, we determined that potato cultivar Barbara harbors Rysto (genotype: Ryryryry) and Ra (genotype: Rararara) that each independently confer extreme resistance to PVA. In this study, employing a combination of next-generation sequencing and bulked-segregant analysis, we further located this novel Ra on chromosome 4 using a tetraploid BC1 potato population derived from a Ry-free progeny (Rararararyryryry) of Barbara (RarararaRyryryry) × F58050 (rararararyryryry). Using 29 insertion-deletion (InDel) markers spanning chromosome 4, Ra was delimited by the InDel markers M8-83 and M10-8 within a genetic interval of 1.46 cM, corresponding to a 1.86-Mb genomic region in the potato DM reference genome. The InDel marker M10-8, which is closely linked with the resistance against PVA in the Ry-free segregating populations, was then used to screen 43 selected Rysto-free tetraploid potato breeding clones. The phenotype to PVA was significantly correlated with the present/absent of the marker, albeit with a 9.3% false positive rate and a 14.0% false negative rate. These findings are of importance in furthering the cloning of Ra and employing the marker-assisted selection for PVA resistance.

Genome sequence analysis provides insights into the mode of 2n egg formation in Solanum malmeanum.

KEY MESSAGE: Our genomic investigation confirms the mechanism of 2n eggs formation in S. malmeanum and aid in optimizing the use of wild germplasm. Wild potatoes are a valuable source of agronomic traits. However, substantial reproductive barriers limit gene flow into cultivated species. 2n gametes are instrumental in preventing endosperm abortion caused by genetic imbalances in the endosperm. However, little is known about the molecular mechanisms underlying the formation of 2n gametes. Here, the wild species Solanum malmeanum Bitter (2x, 1EBN, endosperm balance number) was used in inter- and intrapoloid crosses with other Solanum species, with viable seeds being produced only when S. malmeanum was used as the female parent to cross the 2EBN Solanum genus and with the likely involvement of 2n gametes. Subsequently, we substantiated the formation of 2n eggs in S. malmeanum using fluorescence in situ hybridization (FISH) and genomic sequencing technology. Additionally, the transmission rate of maternal heterozygous polymorphism sites was assessed from a genomic perspective to analyze the mode of 2n egg formation in S. malmeanum × S. tuberosum and S. malmeanum × S. chacoense crosses; each cross acquired an average of 31.12% and 22.79% maternal sites, respectively. This confirmed that 2n egg formation in S. malmeanum attributed to second-division restitution (SDR) coupled with the occurrence of exchange events. The high-throughput sequencing technology used in this study has strong advantages over traditional cytological analyses. Furthermore, S. malmeanum, which has a variety of excellent traits not available from present cultivated potato genepool, has received little research attention and has successfully achieved gene flow in cultivated species in the current study. These findings will facilitate the understanding and optimization of wild germplasm utilization in potatoes.

Molecular Marker-Assisted Selection for Frost Tolerance in a Diallel Population of Potato.

A multi-parental population is an innovative tool for mapping large numbers of loci and genetic modifications, particularly where they have been used for breeding and pre-breeding in crops. Frost injury is an environmental stress factor that greatly affects the growth, development, production efficiency, and geographical distribution of crops. No reported study has focused on genetic mapping and molecular marker development using diallel populations of potatoes. In this study, 23 successful cross combinations, obtained by a half diallel cross among 16 parents, including eight frost-tolerant advanced breeding lines and eight cultivars, were used to map the genetic loci for frost tolerance and to create a molecular marker-assisted selection (MAS) system. Three candidate regions related to frost tolerance on chromosomes II, V, and IX were mapped by bulked segregant analysis (BSA). Furthermore, six SNP markers associated with frost tolerance from candidate regions were developed and validated. Above all, a MAS system for the frost tolerance screening of early breeding offspring was established. This study highlights the practical advantages of applying diallel populations to broaden and improve frost-tolerant germplasm resources.

QTL analysis of tuber shape in a diploid potato population.

Tuber shape is one of the most important traits for potato breeding. Since poor or irregular shape increases the difficulty of handling and processing, researching the inheritance of potato tuber shape for potato breeding is highly important. To efficiently identify QTL for tuber shape, a diploid potato population (PM7) was generated by self-pollinated M6 (S. chacoense). A QTL TScha6 for tuber shape was identified by the QTL-seq approach at 50.91-59.93 Mb on chromosome 6 in the potato DM reference genome. To confirm TScha6, four SSR and twenty CAPS markers around the QTL were developed and the TScha6 was narrowed down to an interval of ~ 1.85 Mb. The CAPS marker C6-58.27_665 linked to TScha6 was then used to screen 86 potato cultivars and advanced breeding lines. The tuber length/width (LW) ratio was significantly correlated with the presence/absence of C6-58.27_665, and the correlation coefficient was r = 0.55 (p < 0.01). These results showed that C6-58.27_665 could be applied in marker-assisted selection (MAS) for tuber shape breeding in the future. Our research sets the important stage for the future cloning of the tuber shape gene and utilities of the marker in the breeding program.

Combining genome composition and differential gene expression analyses reveals that SmPGH1 contributes to bacterial wilt resistance in somatic hybrids.

KEY MESSAGE: Clarification of the genome composition of the potato + eggplant somatic hybrids cooperated with transcriptome analysis efficiently identified the eggplant gene SmPGH1 that contributes to bacterial wilt resistance. The cultivated potato is susceptible and lacks resistance to bacterial wilt (BW), a soil-borne disease caused by Ralstonia solanacearum. It also has interspecies incompatibility within Solanaceae plants. Previously, we have successfully conducted the protoplast fusion of potato and eggplant and regenerated somatic hybrids that showing resistance to eggplant BW. For efficient use of these novel germplasm and improve BW resistance of cultivated potato, it is essential to dissect the genetic basis of the resistance to BW obtained from eggplant. The strategy of combining genome composition and transcriptome analysis was established to explore the gene that confers BW resistance to the hybrids. Genome composition of the 90 somatic hybrids was studied using genomic in situ hybridization coupled with 44 selected eggplant-specific SSRs (smSSRs). The analysis revealed a diverse set of genome combinations among the hybrids and showed a possibility of integration of alien genes along with the detection of 7 smSSRs linked to BW resistance (BW-linked SSRs) in the hybrids. Transcriptome comparison between the resistant and susceptible gene pools identified a BW resistance associated gene, smPGH1, which was significantly induced by R. solanacearum in the resistant pool. Remarkably, smPGH1 was co-localized with the BW-linked SSR emh01E15 on eggplant chromosome 9, which was further confirmed that smPGH1 was activated by R. solanacearum only in the resistant hybrids. Taken together, the identified gene smPGH1 and BW-linked SSRs have provided novel genetic resources that will aid in potato breeding for BW resistance.