Metabolite profiling of yam (Dioscorea spp.) accessions for use in crop improvement programmes

Abstract

IntroductionNinety-seven percent of yam (Dioscorea spp.) production takes place in low income food deficit countries (LIFDCs) and the crop provides 200 calories a day to approximately 300 million people. Therefore, yams are vital for food security. Yams have high-yield potential and high market value potential yet current breeding of yam is hindered by a lack of genomic information and genetic resources. New tools are needed to modernise breeding strategies and unlock the potential of yam to improve livelihood in LIFDCs.ObjectivesMetabolomic screening has been undertaken on a diverse panel of Dioscorea accessions to assess the utility of the approach for advancing breeding strategies in this understudied crop.MethodsPolar and lipophilic extracts from tubers of accessions from the global yam breeding program have been comprehensively profiled via gas chromatography-mass spectrometry.ResultsA visual pathway representation of the measured yam tuber metabolome has been delivered as a resource for biochemical evaluation of yam germplasm. Over 200 compounds were routinely measured in tubers, providing a major advance for the chemo-typing of this crop. Core biochemical redundancy concealed trends that were only elucidated following detailed mining of global metabolomics data. Combined analysis on leaf and tuber material identified a subset of metabolites which allow accurate species classification and highlighted the potential of predicting tuber composition from leaf profiles. Metabolic variation was accession-specific and often localised to compound classes, which will aid trait-targeting for metabolite markers.ConclusionsMetabolomics provides a standalone platform with potential to deliver near-future crop gains for yam. The approach compliments the genetic advancements currently underway and integration with other ‘–omics’ studies will deliver a significant advancement to yam breeding strategies.Electronic supplementary materialThe online version of this article (doi:10.1007/s11306-017-1279-7) contains supplementary material, which is available to authorized users.

Carotenoid profiling of yams: Clarity, comparisons and diversity

“…The profiles of D. dumetorum were most divergent, forming a separate class to the other species and, except for D. rotundata, all species showed monophyletic grouping. At a species level, clustering largely matches the findings of primary metabolite profiles (Price et al 2017). However, clustering of these accessions is not well matched between carotenoid profiles and primary metabolite composition.…”

“…1). Discrimination between D. rotundata and D. cayennensis was not evidenced in measurements of central tuber metabolism (Price et al, 2017) or via genotyping-by-sequencing (GBS) (Girma et al, 2014) and results here support that carotenoid composition can be utilised to provide complementary chemotaxonomic classification. The approach is potentially faster than the detailed morphological classifications or scoring of numerous molecular markers typically required to assess yam diversity (IPGRI & IITA, 1997).…”

“…Tubers were harvested and shipped to the Royal Holloway University of London (RHUL), United Kingdom for further analysis. For standard extractions tubers from three biological replicates per accession were sectioned laterally and longitudinally into 12; and 6 representative sections per tuber frozen in liquid nitrogen (Price, Bhattacharjee, Lopez-Montes, & Fraser, 2017). Sections were freeze-dried (Lyovac GT2, Leybold-Heraeus, Chessington, UK); skin peeled and ground (via a cryogenic mill; SPEX CertiPrep Freezer/Mill 6750, Stanmore, UK) to a homogenous powder prior to extraction.…”

“…Whilst broad metabolomics profiling has been conducted on elite breeding lines (Price et al, 2017), this did not encompass carotenoids, yet most biofortification efforts have focused on enhancing provitamin A activity through increasing the abundance of β-carotene in crops. Since yams are prevalently grown in regions with the highest Vitamin A deficiency, carotenoid screening of breeding lines of this multi-species crop collection provides a basis for improving provitamin A content.…”

Metabolomics in CGIAR Research Program on Roots, Tubers and Bananas (RTB)

“…rotundata, D. alata, D. cayenensis, D. bulbifera and D. dumetorum) commonly used in yam breeding programs was selected. More than 200 compounds were routinely measured in tubers, providing a major advance for the chemotyping of this crop (Price et al 2017). The analysis of leaf and tuber material identified a subset of metabolites which allowed accurate species classification and highlighted the potential of predicting tuber composition from leaf profiles, based on the species classification.…”