Haplotype-resolved genome assembly and genome-wide association study identifies the candidate gene closely related to sugar content and tuber yield in Solanum tuberosum

Abstract

As an important noncereal food crop grown worldwide, the genetic improvement of potato in tuber yield and quality is largely constrained due to the lacking of a high-quality reference genome and understanding of the regulatory mechanism underlying the formation of superior alleles. Here, a chromosome-scale haplotype-resolved genome assembled from an anther-cultured progeny of ‘Ningshu 15’, a tetraploid variety featured by its high starch content and drought resistance was presented. The assembled genome size was 1.653 Gb, with a contig N50 of approximately 1.4 Mb and a scaffold N50 of 61 Mb. The long terminal repeat assembly index score of the two identified haplotypes of ‘Ningshu 15’ was 11.62 and 11.94, respectively. Comparative genomic analysis revealed that positive selection occurred in gene families related to starch, sucrose, fructose and mannose metabolism, and carotenoid biosynthesis. Further genome-wide association study in 141 accessions identified a total number of 53 quantitative trait loci related to fructose, glucose, and sucrose content. Among them, a tonoplast sugar transporter encoding gene, StTST2, closely associated with glucose content was identified. Constitutive expression of StTST2 in potato and Arabidopsis increased the photosynthetic rate, chlorophyll and sugar content, biomass tuber and seed production in transgenic plants. In addition, co-immunoprecipitation assays demonstrated that StTST2 directly interacted with SUT2. Our study provides a high-quality genome assembly and new genetic locus of potato for molecular breeding.

Acknowledgements

This work has been jointly supported by the following grants: the National Natural Science Foundation of China (32260504, 32070344, 32071733, 32371915), the Innovation Foundation of NingXia Academy of Agriculture and Forestry Sciences (NKYG-24-14) and the Mega Crop Breeding Project of Ningxia District-Engineering of New Potato Cultivars.

Author contributions

L.G. and H.X.Z. conceived the original research plans; H.W.Z., L.Z., F.J.N., M.Q.F., X.L., W.J.Y., Z.N.L., Y. Z., G.H.Z., and Z.Q.G. performed the experiments; L.G. and H.X.Z. wrote the manuscript.

Data availability

All the data is available at http://bigd.big.ac.cn/with the BioSample number of SAMC1075593 for the potato genome assembly of N8-4, the accession number of CRA021150 for HIC sequencing data and the accession number of CRA009721 for the whole genome resequencing data of the 141 varieties.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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