Comparison of SNP and SSR Molecular Marker Systems in Sweetpotato (Ipomoea batatas Lam.) Germplasm Analysis and Quantitative Trait Loci Analysis of Anthocyanin Production in Potato (Solanum tuberosum subsp. tuberosum L.) Tubers.
Year: 2019
Type: article
Abstract: CANAL, ADAM MALCOLM.Comparison of SNP and SSR Molecular Marker Systems in Sweetpotato (Ipomoea batatas Lam.) Germplasm Analysis and Quantitative Trait Loci Analysis of Anthocyanin Production in Potato (Solanum tuberosum subsp.tuberosum L.) Tubers (Under the direction of Dr. G. Craig Yencho).The sweetpotato (Ipomoea batatas Lam.) and the potato (Solanum tuberosum subsp.tuberosum L.) have longstanding histories as staple crops, have undergone thousands of years of domestication and cultivation, provide high caloric yield per acre, are dense with essential nutrients, and they are both asexually propagated complex polyploids.Although they have many small differences, both crops serve similar purposes, and from a breeding perspective, similar breeding strategies are used for crop improvement.The studies of the genetic diversity of the sweetpotato breeding germplasm maintained at NCSU and the inheritance of the nutritional anthocyanin pigments produced in a biparental potato mapping population reported herein, were conducted to: 1) increase our understanding of genetic diversity present in the NC State sweetpotato breeding program so that the program can more efficiently harness the diversity to create new varieties; and 2) identify quantitative trait loci (QTL) for anthocyanin production in potato that can be used for marker-assisted breeding of purple-fleshed potatoes for the specialty potato market sector.Maintaining and understanding germplasm diversity is crucial for breeding programs.Sweetpotato is a staple food source for global communities and its complex genetics pose steep challenges for elite cultivar development.We compared simple sequence repeat (SSR) and single nucleotide polymorphisms (SNP) to evaluate the advantages and disadvantages of each marker system for assessing genetic relationships amongst sweetpotato germplasm from different growing regions and breeding programs.Structure cluster analysis, comparison of genetic distance matrices and phylogenetic trees, and principal component analysis were used to assess the population structure predicted by the marker systems.We observed that the 1,312 SNP markers, developed in this study were denser and more evenly distributed throughout the genome, and they characterized the germplasm more effectively compared to the 100 polymorphic bands of the 11 SSR markers.The SSR markers established a population structure of 2 major clades divided into 7 clusters.The SNP markers established a population structure of 3 major clades divided into 8 clusters, with some clones showing genetic admixture.Demand for anthocyanin-rich foods has increased over the past few decades following the increase in literature surrounding the possible health benefits of their antioxidant functionality.With potato being such an important staple crop, breeding for higher anthocyanin content could be a rapid way to include more nutrition in areas that have poor diets.Electrospray ionization-Time of flight/Mass spectrometry (ESI-TOF/MS) and high-performance liquid chromatography (HPLC) were utilized to characterize, identify, and quantify 19 constituent anthocyanin pigments and total monomeric anthocyanin (TMA) concentration in a biparental genetic mapping population in potato, segregating for anthocyanin accumulation.Linkage analysis of SNP markers derived from an Illumina Infinium 8303 Potato Single Nucleotide Polymorphism (SNP) Array was used to build a 1056 cM genetic map of the cross with 12 homologous linkage groups (LG).A total of 36 quantitative trait loci (QTL) were identified for 18 traits associated with anthocyanin and anthocyanidin production in potato.Two QTL were associated with transcript regions that contain key hydroxylase enzymes for the biosynthesis of flavonoids.A third of the putative transcript regions correlated with the QTL contain possible transcription factors.Other putative associated regions were related to stress response, noncoding regions, protein modification enzymes, and sucrose phosphorylation and dephosphorylation enzymes.
Author: Adam Malcolm Canal
Language: English
Subfield: Genetics
Domain: Life Sciences
SDG: Zero hunger
Open Access status: green
OpenAlex ID: W3033115223