Comparative chloroplast genomics of sugar beet and wild relatives: insights into photosystem gene regulation and stress tolerance

Official URL: https://dx.doi.org/10.1007/s10142-026-01883-3

Chloroplast genome analyses provide critical insights into plant genetic diversity, evolution, and responses to abiotic stress. In Beta vulgaris L., a major crop contributing approximately 20% of global sugar production, breeding efforts have focused on improving root and sugar yield, including the introgression of traits from wild relatives such as Beta maritima for resistance to Rhizomania, Cercospora leaf spot, and nematodes. Haploid and doubled haploid technologies have further accelerated the development of homozygous lines for hybrid seed production. In this study, chloroplast genomes from ten cultivated and wild Beta genotypes were analyzed to elucidate their structural and functional features. All genomes displayed a typical quadripartite structure with conserved gene content and organization, encoding 113 unique genes related to photosynthesis, ribosomal RNA, and tRNA. Comparative analyses revealed conserved codon usage and identified polymorphisms, including single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs), which serve as valuable genetic markers. SSR analysis detected 44-53 loci per genome, predominantly mononucleotide A/T repeats, while SNP analysis identified 333 A/G transitions and 306-309 C/T transitions across Beta species. Promoter analysis of photosystem genes further revealed a conserved regulatory architecture characterized by plastid-encoded RNA polymerase (PEP) - 10/-35 motifs and nuclear-encoded RNA polymerase (NEP) YRTA-type elements (TATA, TGTA, and CATA). Despite overall conservation, minor SNPs, particularly in B. corolliflora, were observed within promoter regions, indicating subtle regulatory variation. The coexistence of conserved PEP and NEP elements with limited polymorphism suggests a finely tuned transcriptional system that supports stable photosynthetic gene expression while allowing adaptive responses to environmental stress.