Resequencing of sweetpotato germplasm resources reveals key loci associated with multiple agronomic traits

Abstract

Sweetpotato is an important crop that exhibits hexaploidy and high heterozygosity, which limits gene mining for important agronomic traits. Here, 314 sweetpotato germplasm resources were deeply resequenced, and 4,599,509 SNPs and 846,654 InDels were generated, among which 196,124 SNPs were nonsynonymous and 9690 InDels were frameshifted. Based on the Indels, genome-wide marker primers were designed, and 3219 of 40,366 primer pairs were selected to construct the core InDel marker set. The molecular ID of 104 sweetpotato samples verified the availability of these primers. The sweetpotato population structures were then assessed through multiple approaches using SNPs, and diverse approaches demonstrated that population stratification was not obvious for most Chinese germplasm resources. As many as 20 important agronomic traits were evaluated, and a genome-wide association study was conducted on these traits. A total of 19 high-confidence loci were detected in both models. These loci included several candidate genes, such as IbMYB1, IbZEP1, and IbYABBY1, which might be involved in anthocyanin metabolism, carotenoid metabolism, and leaf morphogenesis, respectively. Among them, IbZEP1 and IbYABBY1 were first reported in sweetpotato. The variants in the promoter and the expression levels of IbZEP1 were significantly correlated with flesh color (orange or not orange) in sweetpotato. The expression levels of IbYABBY1 were also correlated with leaf shape. These results will assist in genetic and breeding studies in sweetpotato.

Integrated metabolic and transcriptional analysis reveals the role of carotenoid cleavage dioxygenase 4 (IbCCD4) in carotenoid accumulation in sweetpotato tuberous roots

“…However, the amplitudes of expression vary significantly among them. The underlying mechanisms for balance between biosyntheses and catabolism of carotenoids may involve both gene regulation and carotenoid metabolism, and also may be genotypespecific because the sweetpotato genome exhibits hexaploidy and high heterozygosity [48].…”

A comprehensive overview of omics-based approaches to enhance biotic and abiotic stress tolerance in sweet potato

“…The OutcrossSeq strategy was also applied in sweet potatoes to dissect loci for complex quantitative traits and identify several candidate genes for stress-related agronomic traits in sweet potato [ 23 ]. The re-sequencing of 314 sweet potato germplasm reveals several novel significant loci (Iba_chr02a, Iba_chr05a, Iba_chr06a, Iba_chr07a, Iba_chr10a) associated with stress-tolerance mechanisms related pathways such as carotenoid metabolism and anthocyanin metabolism [ 24 ]. The accessibility of this reference genome information permits its application in different polyploidy crops, and such technologies in sweet potatoes predicted significant progress and sped up the future precision breeding program for abiotic tolerance.…”

Genome-wide association study to identify novel loci and genes for Fusarium root rot resistance in sweet potato using genotyping-by-sequencing

“…Sweet potato, a hexaploid species with 90 chromosomes (2n = 6x = 90), is highly heterozygous, and its genome size is estimated to be approximately 4.8–5.3 pg/2C nucleus ( Ozias-Akins and Jarret, 1994 ; Isobe et al., 2017 ). Sweet potatoes are sometimes cross-incompatible but generally self-incompatible, which limits the construction of genetic populations in this crop ( Yan et al., 2022 ; Xiao et al., 2023 ). Furthermore, diverse genotypes are observed owing to a large number of combinations in F 1 progenies, imposing challenges to genetic mapping and QTL analysis ( Yan et al., 2022 ; Xiao et al., 2023 ).…”

“…Sweet potatoes are sometimes cross-incompatible but generally self-incompatible, which limits the construction of genetic populations in this crop ( Yan et al., 2022 ; Xiao et al., 2023 ). Furthermore, diverse genotypes are observed owing to a large number of combinations in F 1 progenies, imposing challenges to genetic mapping and QTL analysis ( Yan et al., 2022 ; Xiao et al., 2023 ). Studies on Fusarium root rot resistance loci are limited, and further research to clarify the Fusarium root rot resistance mechanism in sweet potatoes is required.…”