Molecular Plant Breeding 2025, Vol.16, No.2, 133-145 http://genbreedpublisher.com/index.php/mpb 134 By leveraging advanced genomic technologies, this study aims to elucidate the genetic mechanisms underlying these traits and provide a foundation for breeding programs to improve sweet potato varieties. The scope of the research includes genetic diversity analysis, gene expression profiling, and the identification of candidate genes associated with high yield and superior nutritional quality. These efforts will contribute to the development of sweet potato cultivars that better meet the nutritional needs and preferences of diverse populations, thereby enhancing global food security and health outcomes. 2 Sweet Potato Genomic Structure 2.1 Description of sweet potato genome characteristics The sweet potato (Ipomoea batatas) genome is highly complex due to its hexaploid nature, which means it contains six sets of chromosomes. This complexity is further compounded by the presence of a large number of single-nucleotide polymorphisms (SNPs) and copy number variations (CNVs). For instance, in a study involving the wild relative Ipomoea trifida, which is considered the diploid ancestor of sweet potato, researchers identified 1 464 173 SNPs and 16 682 CNVs (Hirakawa et al., 2015). The genome assembly of sweet potato has revealed a total length of approximately 296 Gb, with a high degree of heterozygosity and repetitive DNA sequences (Yang et al., 2017). Additionally, the sweet potato genome contains a significant number of protein-coding genes, with estimates ranging from 62 407 to 109 449 putative genes identified in different lines of I. trifida (Hirakawa et al., 2015). 2.2 Polyploidy and its impact on gene expression Polyploidy, the condition of having more than two complete sets of chromosomes, plays a crucial role in the genetic and phenotypic diversity of sweet potato. The hexaploid nature of sweet potato has resulted from two recent whole-genome duplication events, estimated to have occurred approximately 0.8 and 0.5 million years ago (Yang et al., 2017). This polyploidy contributes to the complexity of gene expression regulation, as multiple homologous chromosomes can carry different alleles of the same gene. For example, polyploid QTL-seq has been used to identify SNP clusters linked to important traits such as storage root anthocyanin content in hexaploid sweet potato (Yamakawa et al., 2021). Furthermore, polyploidy can lead to differential gene expression and epigenetic modifications, as observed in other polyploid crops like potato, where whole-genome doubling induced changes in histone modifications and gene expression (Guo et al., 2023). 2.3 Techniques used in sequencing the sweet potato genome Several advanced sequencing techniques have been employed to decode the sweet potato genome. Initially, Illumina HiSeq platform was used for de novo whole-genome sequencing of I. trifida, providing a foundation for understanding the sweet potato genome (Hirakawa et al., 2015). More recently, single-molecule real-time (SMRT) sequencing has been utilized to generate full-length cDNA sequences and identify alternative splicing events, which are crucial for functional genomics studies (Ding et al., 2019). Additionally, a novel haplotyping method based on genome assembly has been developed to produce a half haplotype-resolved genome, offering higher resolution in investigating the complex hexaploid genome of sweet potato (Yang et al., 2017). These techniques, combined with next-generation sequencing (NGS) and third-generation sequencing technologies, have significantly advanced our understanding of the sweet potato genome and its regulatory architecture (Gerard et al., 2018; Kyriakidou et al., 2020). 3 Key Genes Influencing Nutrient Composition 3.1 Carbohydrate metabolism genes Starch synthesis and breakdown in sweet potato are regulated by several key genes. The IbAGPb3 and IbGBSS1-1 genes are involved in starch biosynthesis, with variations in intron length among different germplasms affecting their function (Zhang et al., 2020a). Additionally, the IbSnRK1 gene has been shown to increase starch content and improve starch quality by upregulating genes involved in the starch biosynthesis pathway and enhancing the activities of key enzymes (Ren et al., 2018). The vacuolar invertase gene Ibβfruct2-1 also plays a crucial role in regulating starch content by decreasing starch and increasing glucose content (Zhang et al., 2023).
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