Skip to main content

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