Genome-Wide Association Study of Rice Diversity Panel Reveals New QTLs for Tolerance to Water Deficit Under the Egyptian Conditions

Ghazy, Mohamed I.; EL-Naem, Sabry A.; Hefeina, Ahmed G.; Sallam, Ahmed; Eltaher, Shamseldeen

doi:10.1186/s12284-024-00703-1

Rice

Table 7 The gene ID, gene name coding protein and the biological process for the 16 SNPs

From: Genome-Wide Association Study of Rice Diversity Panel Reveals New QTLs for Tolerance to Water Deficit Under the Egyptian Conditions

Year	Stress	Trait	SNP ID	Gene ID	Gene Name	Protein coding	Biological process
2021	WD	NPP/NTP	SNP-3.1410415	Os03g0124300	FER	Receptor-like protein kinase FERONIA-like	Response To Water Deprivation
2022	WD	NPP/NTP	SNP-3.1410415	Os03g0124300	FER	Receptor-like protein kinase FERONIA-like	Response To Water Deprivation
2021	WD	PH	SNP-3.8751808	Os03g0265300	PXN	Peroxisomal Transport	Primary and secondary metabolism, development, and responses to abiotic and biotic stresses
2022	WD	PH	SNP-3.8751808	Os03g0265300	PXN	Peroxisomal Transport
2021	WD	SET%	SNP-4.16583620	Os04g0348300	CDC5	Pre-mRNA splicing factor component CDC5L/Cef1	Regulation Of Protein Localization
2022	WD	SET%	SNP-4.16583620	Os04g0348300	CDC5	Pre-mRNA splicing factor component CDC5L/Cef1	Regulation Of Protein Localization
2021	WD	PL	SNP-4.33316160	Os04g0653200	OSCAX3	Calcium/proton exchanger	Ion Transport
2022	WD	PL	SNP-4.33316160	Os04g0653200	OSCAX3	Calcium/proton exchanger	Ion Transport
2021	WD	NDH	SNP-10.19624308	Os10g0510400	AdoMet	Putative S-adenosyl-L-methionine-dependent methyltransferase	Response To Water Deprivation
2022	WD	NDH	SNP-10.19624308	Os10g0510400	AdoMet		Response To Water Deprivation
2021	WD	NPP/NTP	SNP-11.20345396	Os11g0549620	PAP3	Purple acid phosphatase	Response To Water Deprivation
2022	WD	NPP/NTP	SNP-11.20345396	Os11g0549620	PAP3	Purple acid phosphatase	Response To Water Deprivation
2021	N	SET%	SNP-2.24141959	Os02g0612800	BIP135	Sister chromatid cohesion protein Pds5	Mitotic Sister Chromatid Cohesion
2022	N	SET%	SNP-2.24141959	Os02g0612800	BIP135	Sister chromatid cohesion protein Pds5	Mitotic Sister Chromatid Cohesion
2021	N	PL	SNP-3.15006885	Os03g0379500	RPS9	Ribosomal protein S4/S9	Positive Regulation of Translational Fidelity
2022	N	PL	SNP-3.15006885	Os03g0379500	RPS9	Ribosomal protein S4/S9	Positive Regulation of Translational Fidelity
2021	N	FLA	SNP-3.27988841	Os03g0698300	MTs	Transmembrane Transporter Activity	Water and nutrient movement and improving tolerance mechanisms against numerous abiotic stresses Regulation Of Developmental Growth
2022	N	FLA	SNP-3.27988841	Os03g0698300	MTs	Transmembrane Transporter Activity
2021	N	FLA	SNP-3.27992294	Os03g0698350	ADCK	ADCK1-like domain
2022	N	FLA	SNP-3.27992294	Os03g0698350	ADCK	ADCK1-like domain
2021	N	FLA	SNP-3.28018218	Os03g0698900	ACER	Alkaline ceramidase, plant	Important functions in plant growth and stress responses
2022	N	FLA	SNP-3.28018218	Os03g0698900	ACER	Alkaline ceramidase, plant	Important functions in plant growth and stress responses
2021	N	FLA	SNP-3.28135195	Os03g0701000	emb2734	Importin beta family	Nucleocytoplasmic transport receptors
2022	N	FLA	SNP-3.28135195	Os03g0701000	emb2734	Importin beta family	Nucleocytoplasmic transport receptors
2021	N	FLA	SNP-3.28220322	Os03g0702500	UGT91D2	UDP-glucuronosyl/UDP-glucosyltransferase	Role in conferring drought tolerance
2022	N	FLA	SNP-3.28220322	Os03g0702500	UGT91D2	UDP-glucuronosyl/UDP-glucosyltransferase	Role in conferring drought tolerance
2021	N	PH	SNP-6.3158894	Os06g0162700	MYB98	SANT/Myb domain	Regulation of a plant-specific developmental program
2022	N	PH	SNP-6.3158894	Os06g0162700	MYB98	SANT/Myb domain	Regulation of a plant-specific developmental program
2021	N	NPP/NTP	SNP-6.422802	Os06g0106500	PLCP	Papain-like cysteine peptidase superfamily	Protein proteolysis and involved in numerous physiological processes
2022	N	NPP/NTP	SNP-6.422802	Os06g0106500	PLCP	Papain-like cysteine peptidase superfamily
2021	N	SET%	SNP-6.682168	Os06g0112100	BSPA	Catalytic Activity	Nucleoside Metabolic Process
2022	N	SET%	SNP-6.682168	Os06g0112100	BSPA	Catalytic Activity	Nucleoside Metabolic Process

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