Genome-wide QTL and bulked transcriptomic analysis reveals new candidate genes for the control of tuber carotenoid content in potato (Solanum tuberosum L.)

Abstract

Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9. The carotenoid content of edible plant storage organs is a key nutritional and quality trait. Although the structural genes that encode the biosynthetic enzymes are well characterised, much less is known about the factors that determine overall storage organ content. In this study, genome-wide QTL mapping, in concert with an efficient 'genetical genomics' analysis using bulked samples, has been employed to investigate the genetic architecture of potato tuber carotenoid content. Two diploid populations of Solanum tuberosum Group Phureja were genotyped (AFLP, SSR and DArT markers) and analysed for their tuber carotenoid content over two growing seasons. Common to both populations were QTL that explained relatively small proportions of the variation in constituent carotenoids and a major QTL on chromosome 3 explaining up to 71 % of the variation in carotenoid content. In one of the populations (01H15), a second major carotenoid QTL was identified on chromosome 9, explaining up to 20 % of the phenotypic variation. Whereas the major chromosome 3 QTL was likely to be due to an allele of a gene encoding β-carotene hydroxylase, no known carotenoid biosynthetic genes are located in the vicinity of the chromosome 9 QTL. A unique expression profiling strategy using phenotypically distinct bulks comprised individuals with similar carotenoid content provided further support for the QTL mapping to chromosome 9. This study shows the potential of using the potato genome sequence to link genetic maps to data arising from eQTL approaches to enhance the discovery of candidate genes underlying QTLs.

Identification and Expression Analysis of Candidate Genes Involved in Carotenoid Biosynthesis in Chickpea Seeds

“…Various approaches including metabolic and genetic engineering (Welsch et al, 2010; Kumar et al, 2012; Mintz-Oron et al, 2012; Nogueira et al, 2013; Ariizumi et al, 2014), advanced genomics and bioinformatics (Wurtzel et al, 2012), genomic-assisted selection (Campbell et al, 2014; Owens et al, 2014) and transcriptome analysis (Caroca et al, 2013; Frusciante et al, 2014) have been applied for studying carotenogenesis and improvement of carotenoid content in different crops. To develop chickpea cultivars with higher carotenoid concentration, information on the genetic basis of carotenogenesis in chickpea is substantial.…”

Genetic Stocks Used for Potato Genome Sequencing

“…As of March, 2017, the original publication of the DM sequence has been cited more than 500 times, providing a framework for studies of gene families (Charfeddine et al 2015;Gao et al 2016;Ma et al 2016;Schreiber et al 2014;Seo et al 2016;Tang et al 2016;Van Harsselaar et al 2017), a scaffold for alignment of transcriptomic data (Campbell et al 2014;Gong et al 2015;Goyer et al 2015;Liu et al 2015;Morris et al 2014;Tang et al 2014) or a reference genome against which to discover genomic variation (Hardigan et al 2016), to cite just a few. As sequencing platforms improve, the DM assembly will likely be supplanted by that of a more robust commercial potato line.…”

Polyploidy and Plant Breeding

“…The genome sequence provides a new resource to characterize germplasm collections based on allelic variance and for use in potato breeding (Visser et al 2009), because it will simplify both the characterization and deployment of quantitative traits in cultivars. Moreover, it links genetic maps to data arising from expression QTL, which will enhance finding candidates genes underlying QTL, as done for tuber carotenoid content (Campbell et al 2014). An 8303 SNP marker array using potato genome and transcriptome resources was developed and validated to facilitate genome-guided breeding in potato (Felcher et al 2012).…”