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 |