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Table 1 Summary of the different metabolomic, transcriptomic and genomic methods and softwares (when information available) used in the cited studies, to improve crop quality

From: Combining metabolomic and transcriptomic approaches to assess and improve crop quality traits

Species Techniques Platforms Reference
Maize Amino acid analysis Amino acid analyzer Deng et al. (2017)
GWAS GEC software
QTL mapping Windows QTL mapping Cartographer V2.5
Maize Primary metabolite profiling GC-TOF–MS Wen et al. (2015)
QTL mapping Windows QTL mapping Cartographer V2.5
Maize Primary metabolite profiling GC-TOF–MS Wen et al. (2018)
GWAS TASSEL3.0 software
Rice Metabolite profiling LC–ESI–MS/MS Chen et al. (2016)
GWAS FaST-LMM program
Bread wheat Metabolite profiling HPLC–MS Peng et al. (2018)
GWAS FaST-LMM program
Rice BCAA analysis LC–ESI–MS/MS Sun et al. (2020)
GWAS FaST-LMM program
Soybean Amino acid analysis NIR spectroscopy Zhang et al. (2018)
GWAS GAPIT, R
Soybean amino acid analysis Amino acid analyzer Qin et al. ( 2019)
GWAS TASSEL 5 software
Potato Metabolite profiling UPLC-Triple-TOF–MS Cho et al. (2016)
Transcriptomics RNA-Seq (Bowtie, DESeq package in R)
Plum Anthocyanin analysis Spectrophotometric determination Fang et al. (2016)
Transcriptomics RNA-Seq (in-house Perl scripts), Trinity for de novo assembly
Pepper Flavonoid profiling UPLC-ESI–MS/MS Liu et al. (2020)
Carotenoid profiling UPLC-APCI-MS/MS
Transcriptomics RNASeq (HISAT2, DeSEQ2 softwares)
Fig Metabolite profiling HPLC–ESI–MS/MS Wang et al. (2017a)
Transcriptomics RNASeq (RSEM software)
Pear Anthocyanin analysis Spectrophotometric determination Wang et al. (2017b)
Transcriptomics RNA-Seq
Pear Metabolite profiling HPLC Zhang et al. (2020)
Transcriptomics RNA-Seq (NGS QC Toolkit, DESeq R package)
Kiwifruit Metabolite profiling UPLC-Triple-TOF–MS Li et al. (2018b)
Transcriptomics RNASeq (iTAK, DESeq R package)
Wild peach Metabolite profiling HPLC–ESI–MS/MS Ying et al. (2019)
Transcriptomics RNA-Seq (TopHat2, cufflinks, cuffcompare packages)
Kiwifruit Anthocyanin and phenolic compounds analysis RP-HPLC Nardozza et al. (2020)
Metabolite profiling HPLC–MS
Transcriptomics RNA-Seq (STAR, DESeq2 R pacakge)
Maize Carotenoid profiling HPLC Azmach et al. (2018)
GWAS TASSEL 4 software
Cassava Total carotenoid content iCheck analytical kit Esuma et al. (2016)
GWAS TASSEL v5.2.9
Maize Carotenoid profiling HPLC Owens et al. (2014)
GWAS Proc MIXED SAS 9.3 software
Chickpea Carotenoid profiling HPLC Rezaei et al. (2019)
QTL mapping IciMapping software
Maize Carotenoid profiling HPLC Xu et al. (2019)
QTL mapping Windows QTL mapping Cartographer 2.5 (Wang
Melon Carotenoid and chlorophyll quantification HPLC Oren et al. (2019)
GWAS TASSEL
Watermelon QTL mapping QTL mappingbim R package Li et al. (2020)
Watermelon Lycopene content HPLC Wang et al. (2019)
QTL mapping IciMapping V3.3 software
Sweetpotato QTL mapping QTL mappingpoly software Gemenet et al. (2020)
Carrot Carotenoid profiling HPLC Ellison et al. (2018)
GWAS TASSEL-GBS version 5.2.26
Banana Carotenoid profiling HPLC Heng et al. (2019)
Proteomics nanolc-MS/MS
Tomato Metabolite profiling LC–ESI–MS/MS Zhu et al. (2018)
Transcriptomics RNA-Seq (RNA-SeQC)
GWAS FaST-LMM program
Sugar profiling High pH ion-exchange chromatography Bauchet et al. (2017)
Organic and amino acid profiling LC–ESI–MS/MS
Volatiles GC–MS
GWAS EMMA algorithm
Carotenoid profiling RP-HPLC Ruggieri et al. (2014)
Ascorbic acid content spectrophotometric determination
GWAS TASSEL v4.0, STRUCTURE 2.3.3
Metabolite profiling GC-TOF–MS Sauvage et al. (2014)
GWAS EMMA algorithm
Volatile profiling GC–MS/SPME–GC–MS Tieman et al. (2017)
GWAS EMMAX, GEC softwares  
QTL mapping EM algorithm  
Primary metabolite profiling GC–MS Ye et al. (2019)
GWAS TASSEL v4.0
Metabolite profiling aH-NMR spectroscopy D’Angelo et al. (2019)
Transcriptomics GeneChip® Tomato arrays (Robin application)
Semi-polar metabolite Profiling HPLC–ESI–MS D’Esposito et al. (2017)
Transcriptomics RNA-Seq (CASAVA, RseQC softwares. TopHat 2.0.6, Cufflinks 2.1.1)
Primary metabolite profiling GC–MS Ye et al. (2017)
GWAS TASSEL v4.0
Genomics Trimmomatic, Megahit Gao et al. (2019)
Transcriptomics RNA-Seq (HISAT2)
Volatile profiling SPME-GC-TOF–MS
Carotenoid profiling HPLC
QTL mapping QTL mapping R package
Volatile profiling SPME–GC–MS Tikunov et al. (2020)
Primary metabolite profiling GC-TOF–MS
Semi-polar secondary metabolite profiling UPLC-MS
QTL mapping mapping GENSTAT software
Volatile profiling GC–MS Alonge et al. (2020)
Transcriptomics RNA-Seq (STAR, HTSeq-count, DESeq2 R package)
Genomics NGMLR, Sniffles, RaGOO
  1. GC: gas chromatography; TOF: time-of-flight; MS: mass spectrometry; LC: liquid chromatography; ESI: electrospray ionization; MS/MS: tandem mass spectrometry; HPLC: high-performance LC; NIR: near-infrared reflectance; UPLC: ultra-performance LC; APCI: atmospheric-pressure chemical ionization; RP-HPLC: reverse-phase HPLC; aH-NMR: proton nuclear magnetic resonance; SPME–GC–MS: solid phase microextraction GC–MS