Carotenoids gene markers for sweetpotato (Ipomoea batatas L. Lam): applications in genetic mapping, diversity evaluation and cross-species transference

Abstract

Carotenoids play essential biological roles in plants, and genes involved in the carotenoid biosynthesis pathway are evolutionarily conserved. Orange sweetpotato is an important source of β-carotene, a precursor of vitamin A. In spite of this, only a few research studies have focussed on the molecular aspects of carotenoid genes regarding their specific sequence and structure. In this study, we used published carotenoid gene sequences from Ipomoea and other species for "exon-primed intron-crossing" approaches. Fifteen pairs of primers representing six carotenoid genes were designed for different introns, eleven of which amplified scorable and reproducible alleles. The sequence of PCR products showed high homology to the original ones. Moreover, the structure and sequence of the introns and exons from five carotenoid structural genes were partially defined. Intron length polymorphism and intron single nucleotide polymorphisms were detected in amplified sequences. Marker dosages and allelic segregations were analysed in a mapping population. The developed markers were evaluated in a set of Ipomoeas batatas accessions so as to analyse genetic diversity and conservation applicability. Using CG strategy combined with EPIC-PCR technique, we developed carotenoid gene markers in sweetpotato. We reported the first set of polymorphic Candidate Gene markers for I. batatas, and demonstrated transferability in seven wild Ipomoea species. We described the sequence and structure of carotenoid genes and introduced new information about genomic constitution and allele dosage.

Linkage Analysis and Haplotype Phasing in Experimental Autopolyploid Populations with High Ploidy Level Using Hidden Markov Models

“…Despite advances in genetic studies in autotetraploids, (Mather 1936; Fisher 1943, 1947; Hackett et al 2001; Luo et al 2004, 2006; Wu et al 2004; Leach et al 2010; Li et al 2010; Hackett et al 2013; Xu et al 2013; Rehmsmeier 2013; Zheng et al 2016), there is still a shortage of statistical methods to address organisms with higher ploidy levels, such as sweet potato (Kriegner et al 2003; Arizio et al 2014; Shirasawa et al 2017), sugarcane (Wang et al 2010; Garcia et al 2013), some ornamental flowers and forage crops (reviewed in (Soltis et al 2014b)). In this work, we denote as high-level autopolyploids those autopolyploid organisms with ploidy level greater than four.…”

Simple Sequence Repeat Marker Analysis of Genetic Diversity among Progeny of a Biparental Mapping Population of Sweetpotato

“…The recalcitrance in polymorphisms of EST-SSR markers in sweetpotato could be solved by developing markers from within the intron regions of candidate genes that show more polymorphism instead of ESTs as more sweetpotato genomics tools are developed. Sweetpotato SSR markers developed from introns of candidate carotenoid genes of Ipomoea and other species showed high levels of polymorphism and across species transferability (Arizio et al, 2014).…”

Carotenoid analysis of sweetpotatoIpomoea batatasand functional identification of its lycopene β- and ε-cyclase genes

“…Although sweetpotato is highly important as a valuable source of carotenoids including β-carotene, very little research has been done on molecular biological aspects of its carotenoid biosynthesis [6,7,9]. 'White Star' (WS) and W71, producing white-and orange-fleshed tubers, respectively, are important sweetpotato cultivars, since they are amenable to Agrobacterium-mediated transformation ( [13,14] and our unpublished results).…”

“…For people of South-east Asia and Africa, this crop is the main source of β-carotene [7]. Sweetpotato is a hexaploid species (2n = 6x = 90) that has a basic chromosome number of 15, and genetic studies on this species are exhausting, since it is difficult to generate seeds and to evaluate the effects of polyploidy on the genome [8,9]. Its tubers exhibit various colors such as white, yellow, orange, and purple among different cultivars, and all species include β-carotene as well as other carotenoids, while orange-fleshed lines were shown to contain β-carotene as the predominant carotenoid [2,4,5,10,11].…”