Bioscience Methods 2025, Vol.16, No.1, 23-32 http://bioscipublisher.com/index.php/bm 24 2 Sweet Potato Genetics and Genomics: Foundation for Molecular Breeding 2.1 Genomic architecture of sweet potato (hexaploidy and challenges) Sweet potato (Ipomoea batatas) is a hexaploid species, meaning it has six sets of chromosomes. This complex genomic structure poses significant challenges for genetic and genomic studies. The hexaploid nature of sweet potato results in a wide range of meiotic configurations and linkage phases, complicating gene action and genotype data quality (Gemenet et al., 2020). Additionally, the high level of heterozygosity and the presence of multiple homologous chromosomes make it difficult to develop accurate genetic maps and perform genome-wide association studies (Hirakawa et al., 2015; Kim et al., 2017). 2.2 Recent advancements in sweet potato genome sequencing Recent advancements in genome sequencing technologies have significantly improved our understanding of the sweet potato genome. Single-molecule real-time sequencing has enabled the identification of massive full-length cDNAs and alternative splicing events, facilitating comparative and functional genomics studies in sweet potato (Figure 1) (Ding et al., 2019). Moreover, the development of a half haplotype-resolved genome has provided insights into the hexaploidization history of sweet potato, allowing for a more detailed analysis of its genomic structure. These advancements have paved the way for more precise and efficient molecular breeding strategies. Figure 1 Plant materials used in this study and summary of PacBio RS II single-molecule real-time (SMRT) sequencing (Adopted from Ding et al., 2019) Image caption: (A-H) Photos showing the developmental stages and overall morphology of eight tissues in I. batatas used for SMRT sequencing in this study. (A) Young leaves; (B) mature leaves; (C) apical shoots; (D) mature stems; (E) fibrous roots; (F) initiating tuberous roots; (G) expanding tuberous roots; (H) mature tuberous roots. The photos were adopted from our previous report (Ding et al., 2017). Number and length distributions of 220 035 reads in I. batatas (I) and 195,188 reads in I. trifida (J) from different PacBio libraries (fractionated size: 1-2, 2-3, >3 kb); Proportion of different types of PacBio reads in I. batatas (K) and I. trifida (L) (Adopted from Ding et al., 2019)
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