TABLE 3.

The crucial genomics, transcriptomics, metabolomics, and proteomics approaches used in different crops.

Omics approach	Crop	Technology	References
Genomics	Arabidopsis	BAC (bacterial artificial chromosome) by BAC	Kaul et al. (2000)
	Rice	Whole-genome sequencing analysis Genome-wide meta-analysis	Subudhi et al. (2020), Mansuri et al. (2020)
	Barley	BAC by BAC Hierarchical shotgun sequencing Roche/454 pyrosequencing Genome-wide association study	Schulte et al. (2009), Wicker et al. (2009), Mwando et al. (2020)
	Maize	BAC by BAC	Pennisi (2008), Schnable et al. (2009)
	Poplar	Whole-genome shotgun sequencing (WGS)	Tuskan et al. (2006)
	Grape	WGS	Jaillon et al. (2007)
	Papaya	WGS	Ming et al. (2008)
	Sorghum	WGS	Paterson et al. (2009)
	Soybean	WGS	Schmutz et al. (2010)
	Apple	Genome-wide duplication (GWD)	Velasco et al. (2010).
	Potato	WGS	Potato Genome Sequencing Consortium (2011)
	Mango	PAC biosequencing	Singh et al. (2014)
	Peach	WGS	Ahmad et al. (2011)
	Banana	WGS	D’Hont et al., 2012
	Tomato	WGS	https://www.wur.nl/en/show/Sequencing-of-the-tomato-genome.htm
	Cucumber	WGS	Huang et al. (2009).
	Wild strawberries	Roche/454, Illumina/Solexa and Life Technologies/SOLiD platforms, next-generation sequencing (NGS)	Shulaev et al. (2011)
	Musk melon	NGS	Garcia-Mas et al. (2012)
	Watermelon	NGS	Garcia-Mas et al. (2012)
Transcriptomics	Rice	Micro array SAGE (serial analysis of gene expression)	Li et al. (2006), Matsumura et al. (1999)
	Wheat	DNA array	Jauregui et al. (2015)
	Maize	RNA sequencing	Zhao et al. (2019).
	Barley	RT-PCR (real time polymerase chain reaction)	Svensson et al. (2006)
	Arabidopsis	SAGE	Ekman et al. (2003)
	Cassava	ESTs (expression sequence tags)	Suarez et al. (2000)
	Peas	RNA display analysis	Lapopin et al. (1999)
Proteomics	Rice	2D-GE (2-dimension gel electrophoresis) Isobaric Tags for Relative and Absolute Quantitation (iTRAQ)	Zi et al. (2012), Xu et al. (2017), and Lakra et al. (2019)
	Maize	2D-GE iTRAQ	Amara et al. (2012), Luo et al. (2018), and Chen et al. (2019)
	Wheat	2D-PAGE (Polyacrylamide gel electrophoresis) MS/MS (mass spectrometry)	Amiour et al. (2002), Singh et al. (2017)
	Barley		Süle et al. (2004)
	Soyabean	Mass spectrometry	Galant et al. (2012)
	Tomato	2D-PAGE	Afroz et al. (2009)
	Sugar beet	Liquid chromatography-tandem mass spectrometry (LC-MS/MS)	Hajheidari et al. (2005)
	Grape berry	2D-PAGE	Di Carli et al. (2011)
	Peanut	LC-Q-TOF (MS/MS)	Chassaigne et al. (2007)
	Apple	2D electrophoresis and IgE-reactivity. Electrophoresis	Herndl et al. (2007)
	Pear		Pedreschi et al. (2008)
	Peach		Zhang L. et al. (2011)
	Populus	Shotgun MS/MS profiling	Kalluri et al. (2009)
	Stone fruit	2D PAGE	Abdi et al. (2002)
Metabolomics	Rice	GC-MS, NMR (nuclear magnetic resonance)	Gayen et al. (2019), Ma et al. (2018)
	Maize	HNMR, GC-MS	Gavaghan et al. (2011), Zörb et al. (2013)
	Wheat	GC-MS, HPLC, GC-TOF/MS	Guo R. et al. (2015), Borrelli et al. (2018), and Che-Othman et al. (2019)
	Barley	TIC (total ion chromatogram)	Shelden et al. (2016)
	Arabidopsis	RHPLC (high performance liquid chromatography)	Arrivault et al. (2009)
	Tobacco	NMR	Zhang J. et al. (2011)
	Tomato	UHPLC-ESI/QTOF-MS	Rouphael et al. (2018)
	Nitraria	GC-TOF/MS	Ni et al. (2015)
	Lotus	GC-TOF/MS (gas chromatography- time-of-flight mass spectrometry)	Sanchez et al. (2011)
Ionomics	Alfalfa Halophytes Lotus Barley	High-throughput sequencing, element-specific profiling, mass spectrometry, deletion mapping, X-ray fluorescence, neutron activation analysis, DNA microarray, and bulk segregant analysis	Baxter (2009), Becker and Becker (2010), Sanchez et al. (2011), Wu et al. (2013), Huang and Salt (2016), and Arshad et al. (2017)
Phenomics	Rice	PHENOPSIS WIWAM	Granier et al. (2006), Humplík et al. (2015), and Meng et al. (2017)