Genetic Variation and Sequence Diversity of Starch Biosynthesis and Sucrose Metabolism Genes in Sweet Potato

Abstract

Knowledge of genetic variations can provide clues into the molecular mechanisms regulating key crop traits. Sweet potato (Ipomoea batatas (L.) Lam.) is an important starch-producing crop, but little is known about the genetic variations in starch biosynthesis and sucrose metabolism genes. Here, we used high-throughput sequencing of pooled amplicons of target genes to identify sequence variations in 20 genes encoding key enzymes involved in starch biosynthesis and sucrose metabolism in 507 sweet potato germplasms. After filtering potential variations between gene copies within the genome, we identified 622 potential allelic single nucleotide polymorphisms (SNPs) and 85 insertions/deletions (InDels), including 50 non-synonymous SNPs (nsSNPs) and 12 frameshift InDels. Three nsSNPs were confirmed to be present in eight sweet potato varieties with various starch properties using cleaved amplified polymorphic sequence (CAPS) markers. Gene copy with loss of the fifth intron was detected in IbAGPb3 genes, and loss of multiple introns were observed in IbGBSS1-1 genes and various among germplasms based on intron length polymorphism (ILP) markers. Thus, we identified sequence variations between germplasms in 20 genes involved in starch biosynthesis and sucrose metabolism, and demonstrated the diversity in intron-loss alleles among sweet potato germplasms. These findings provide critical genetic information and useful molecular markers for revealing regulatory mechanism of starch properties.

Engineering Properties of Sweet Potato Starch for Industrial Applications by Biotechnological Techniques including Genome Editing

“…The cassava SSVI protein potentially influences the activities of AGPase, GBSS, and ISA, by forming a protein complex with the key starch biosynthetic enzymes (SSI, SSVI, SBEI, SBEII, ISAI, ISAII, and GBSSI) [37]. SBE catalyzes the formation of branch points by cleaving the α-1,4 linkage in polyglucans and reattaching the chain via β-1,6-glucan linkage [44]. Plants possess two classes of SBE, i.e., SBEI and SBEII, based on biochemical and physicochemical properties.…”

“…Starch contents vary from 4.5 to 31.8% in fresh storage roots of different sweet potato cultivars [17,44,[46][47][48][49]. Sweet potato starch is a mixture of linear or slightly branched amylose and highly branched amylopectin, usually present at 20-30% and 70-80%, respectively [47].…”

“…The amylose/amylopectin ratio is regulated by starch biosynthetic enzymes [38] and genetic variability [82]. The amylose/amylopectin ratios of 507 sweet potato germplasms range from 0.247 to 0.429 [44]. Changing the amylose/amylopectin ratio by altering the amylose content is a practical approach for improving the performance of starch derivative products.…”

Analysis of Crop Genetic and Germplasm Diversity

“…In this research, sequence variations between germplasms were identified in 20 genes involved in starch biosynthesis and sucrose metabolism, demonstrating the diversity in intron-loss alleles among sweet potato germplasms. These findings provide critical genetic information and useful molecular markers for revealing the regulatory mechanism of starch properties [22]. Cowpea is a multiple-purpose, drought-tolerant leguminous pulse crop grown in several dry tropical areas.…”

“…Genetic variation and population structure and phytochemical and molecular diversity were studied in these crops. The variation in a relevant tuber crop, sweet potato (Ipomoea batatas L. Lam) [21,22], was assessed using chloroplast SSR markers and sequence diversity of biosynthesis pathways. In legumes, the genetic diversity in cowpea (Vigna unguiculata (L.) Walp.)…”