Genome-Wide Association Study (GWAS) and genome prediction of seedling salt tolerance in bread wheat (Triticum aestivum L.)

Javid, Saeideh; Bihamta, Mohammad Reza; Omidi, Mansour; Abbasi, Ali Reza; Alipour, Hadi; Ingvarsson, Pär K.

doi:10.1186/s12870-022-03936-8

Table 5 Annotation of genes harbouring the significant trait-associated SNPs across all chromosomes in Iranian wheat accessions exposed to normal conditions

From: Genome-Wide Association Study (GWAS) and genome prediction of seedling salt tolerance in bread wheat (Triticum aestivum L.)

Marker	Sequence	Trait	Ch.	Position (bp)	MAF^a	R² (%)	Gene ID in wheat	Molecular function	Biological process
rs23576	TGCAGCCCCCTCAAAGTCCAACAAAGGAAGCCTGTGTTCAAACATATCATCAGTCTTCACCCGA	ELI	7A	118,145,757-118,159,311	0.09	5.42	TraesCS7A02G161500	protein binding
rs2956	TGCAGAATTCCCATATCTACCACCTGCCAAAAATTCAGCAATATCCGACCGTCAAAACTCCGAG	ELI	6B	689,197,969-689,222,878	0.20	4.94	TraesCS6B02G417300
rs3669	TGCAGACCAAGTCCCTGACCGATTTAATCATTTGAACAAGTTCCTCCCGATTCAGTTAGTCAGG	SPAD	4B	389,114,118-389,118,175	0.47	10.88	TraesCS4B02G178000	channel activity	transmembrane transport
rs17742	TGCAGCAGGAGCTTAACGGGCCCGATCTGGGCCCGAGATCGGAAGAGCGGGATCACCGACTGCC	SFW	6D	384,280,526-384,287,890	0.12	8.25	TraesCS6D02G275200	hydrolase activity, acting on ester bonds D-aminoacyl-tRNA deacylase activity	D-amino acid catabolic process
rs9473	TGCAGATGGCGGCCTTCACAGAGGAGAGGAGTGAGGACACGATGGAGGAGGAGCCGTCGGCCGC	SDW	5B	571,834,531-571,837,033	0.35	10.67	TraesCS5B02G394000	hydrolase activity, hydrolyzing O-glycosyl compounds	carbohydrate metabolic process
rs10128	TGCAGATTCTACGCCGCTGCCTTGCCCATACTGTTATTAAGATTTAGCTCCCGCCTCGTTGCCT	RWC	1B	19,047,105-19,051,706	0.11	8.97	TraesCS1B02G039600	protein kinase activity, protein binding, ATP binding	protein phosphorylation
rs2460	TGCAGAATACAAGAAAACTTGGGTTGGACAGAATGCCCTTCCAACACCTCCAGGTCGAAGTTCC	RFW	2B	777,935,599-777,935,901	0.06	19.32	TraesCS2B02G593100	monooxygenase activity, iron ion binding, oxidoreductase activity, acting on paired donors with incorporation or reduction of molecular oxygen heme binding
rs56706	TGCAGTAGATCAGGTGCTTGTAGCTTGACTGAACGCAATTGAAGTCTTTCCTCATAGTCGGGCT	RFW	2B	653,745,832-653,748,302	0.41	19.26	TraesCS2B02G459300	alternative oxidase activity
rs43005	TGCAGGAATGCTTAGGAGTCCTGGATTACGGGGTTCTCGGGGAGCTGCCCTATGTGTCATGGGC	RDW	6B	22,081,260-22,105,393	0.09	12.94	TraesCS6B02G037600	protein kinase activity, calcium ion binding, ATP binding, polysaccharide binding	protein phosphorylation
rs23154	TGCAGCCCAGGGCATAGGACAGAGGCACCAAGGACCTGGCGAGATGGTGTGCACGAGGCGGGTC	RV	1B	250,982,539-251,056,868	0.39	10.15	TraesCS1B02G153500	oligopeptide transmembrane, transporter activity	transmembrane transport
rs2275	TGCAGAAGGTCTGAATTTGGGTGGCGTGTATGCAGGTACTCGTGCGTACACCTCCACACATGCT	RV	3A	369,616,744-369,620,089	0.39	10.06	TraesCS5B02G203300	protein binding	cell redox homeostasis
rs61560	TGCAGTGGCTGGACGACAAGCTCACCTCGCTCGCCCTCCCCGAACCCGAGATCGGAAGAGCGGG	SH	1B	531,203,778-531,206,255	0.07	22.4	TraesCS1B02G308700	protein binding, zinc ion binding
rs61560	TGCAGTGGCTGGACGACAAGCTCACCTCGCTCGCCCTCCCCGAACCCGAGATCGGAAGAGCGGG	SH	3D	531,365,324-531,367,807	0.07	22.4	TraesCS3D02G418800	protein binding, zinc ion binding
rs61560	TGCAGTGGCTGGACGACAAGCTCACCTCGCTCGCCCTCCCCGAACCCGAGATCGGAAGAGCGGG	SH	3A	665,964,671-665,967,157	0.07	22.4	TraesCS3A02G423500	protein binding, zinc ion binding
rs61560	TGCAGTGGCTGGACGACAAGCTCACCTCGCTCGCCCTCCCCGAACCCGAGATCGGAAGAGCGGG	SH	1A	493,821,133-493,823,736	0.07	22.4	TraesCS1A02G299000	protein binding, zinc ion binding
rs61560	TGCAGTGGCTGGACGACAAGCTCACCTCGCTCGCCCTCCCCGAACCCGAGATCGGAAGAGCGGG	SH	3B	702,690,096-702,692,579	0.07	22.4	TraesCS3B02G459000	protein binding, zinc ion binding
rs61560	TGCAGTGGCTGGACGACAAGCTCACCTCGCTCGCCCTCCCCGAACCCGAGATCGGAAGAGCGGG	SH	1D	391,317,043-391,325,294	0.07	22.4	TraesCS1D02G292300	protein binding, zinc ion binding
rs46112	TGCAGGCACGGCGACTGCGGGCAGCCAAGTTTTTAGTCCCACCTCGCCCGACAGAGCGCGCGAC	RH	6D	85,504,595-85,544,103	0.33	8.06	TraesCS6D02G120400	protein binding
rs27832	TGCAGCGAAACCATACGATGGATGAAAATAGTACATGATGTATCAAATGGAAACTATGCCACGA	Chl a	4A	232,506,122-232,523,385	0.31	6.15	TraesCS4A02G143000	nucleotide binding, iron ion binding, ATP binding, ATPase, ribosomal small subunit binding, metal ion binding, iron-sulfur cluster binding	ribosomal subunit export from nucleus, translational initiation, translational termination
rs31586	TGCAGCGGATTTTTAGTCCCACCTCGCTCCGCTAACAGAGTTTTACCACATTAAATATGTTACT	Chl a	2B	613,205,484-613,234,917	0.09	6.11	TraesCS2B02G426600	serine-type endopeptidase activity, serine-type peptidase activity	proteolysis
rs1928	TGCAGAAGCAGCGGCACCGATAACTTCCTCCATGGGCACGATGTAAGCGGCGGTGCAGAAAGGA	Chl a	1D	317,426,727-317,457,933	0.12	5.98	TraesCS1D02G229300	protein serine/threonine kinase activity, protein binding, kinase activity, protein-containing, complex binding
rs1928	TGCAGAAGCAGCGGCACCGATAACTTCCTCCATGGGCACGATGTAAGCGGCGGTGCAGAAAGGA	Chl a	1B	429,583,237-429,614,696	0.12	5.98	TraesCS1B02G241900	protein serine/threonine kinase activity, protein binding, kinase activity, protein-containing, complex binding
rs40144	TGCAGCTGTACGTGCCTCCACATGTACATGTACCTCTGCCGAGATCGGAAGAGCGGGATCACCG	Chl a	2D	644,092,500-644,096,696	0.17	5.93	TraesCS2D02G584900	protein binding
rs33651	TGCAGCGTGAGCAGGTTGAACAAGGGACAGACAGACAGACATGGCTGCTACACTTACCAAGTGC	Chl a	5B	707,439,895-707,441,048	0.14	5.72	TraesCS5B02G561300	hydrolase activity	cytokinin biosynthetic process
rs24738	TGCAGCCGACCGATAGAATTGATCCAGCCATCACTCTAGGCAGCAAGGTTCTACATCTGTGTGC	Chl b	3A	507,757,264-507,766,229	0.18	6.03	TraesCS3A02G278200	cysteine-type peptidase activity	proteolysis
rs30395	TGCAGCGCCTCCACCACCGACCATGATCTGCGAGGGAGCGTCTTGCTGGTGCTCATTCGATATC	Chl b	5B	703,644,434-703,646,112	0.18	5.59	TraesCS5B02G553700	protein binding
rs30395	TGCAGCGCCTCCACCACCGACCATGATCTGCGAGGGAGCGTCTTGCTGGTGCTCATTCGATATC	Chl b	3B	705,135,930-705,140,149	0.18	5.59	TraesCS3B02G462000	metal ion binding	primary metabolic process cellular macromolecule metabolic process
rs59549	TGCAGTCTGAGAACCTTGAGGACCAGTTGACTGGTTAGGTACTGCCACTTGGCTTCTCATTTGA	Total Chl	6A	6,727,564-6,735,295	0.16	5.74	TraesCS6A02G013700	protein binding
rs53598	TGCAGGTCTGGTGAGTTTGTGCTGGTCATCAGTCATCGCTCGTGCAGACGATACGAGGCTCCTA	Car	1B	677,527,503-677,530,414	0.49	7.23	TraesCS1B02G467800	protein kinase activity, protein binding, ATP binding	protein phosphorylation
rs59088	TGCAGTCGGAGCATCCGATGAAAATCAAATAAATTTGTTTTAGCTTCATACATACTCCAAGCAA	protein	7A	679,052,946-679,060,925	0.15	5.21	TraesCS7A02G488800	protein kinase activity, ATP binding	protein phosphorylation
rs14676	TGCAGCACCTTCCGCCCAATCGCCACCGACTGCTCCTTCCGCCGCCGATTCCGCCGAGATCGGA	proline	7D	607,607,584-607,615,127	0.17	32.55	TraesCS7D02G502100	protein binding
rs3861	TGCAGACCCCTTTCCAGAACAGCCTCCGCGAGGTGCTGGAGGATGAGGAGGGGGTGCCGAGATC	CAT	3A	728,320,620-728,322,996	0.08	6.32	TraesCS3A02G507200	UDP-glycosyltransferase activity, hexosyltransferase activity
rs9866	TGCAGATTACATCAAGGAGGACACCCCCGCCGACGGGCTCGGTGATCTGCCCGCCCAGCCACCG	GPX	1B	313,080,958-313,101,223	0.41	5.85	TraesCS1B02G174400	zinc ion binding
rs9047	TGCAGATGAGGCGGTGGACGATGCGGTCGATGCAGTCCTGGGCGTCGTGCACCAGGCCAAGCAT	MDA	5A	548,503,107-548,507,985	0.07	6.37	TraesCS5A02G344000	ADP binding
rs63113	TGCAGTTCCAAATTGCCCATAACAACGCATACACTCCTACACGAATATGTCTAGCTGTATCGGA	Na-s	5B	108,985,650-108,994,401	0.08	5.37	TraesCS5B02G086000	serine-type carboxypeptidase activity	proteolysis
rs58688	TGCAGTCCGTTTTTAATTTCTGGCCTGGATCAGTTTCTTCCTCTGGATGGCCACGCTTATTTGT	Na-r	2B	692,871,667-692,873,184	0.16	10.13	TraesCS2B02G495900	protein binding
rs60006	TGCAGTGACCACGAGGCGGGGTTTCGGTCGGACGACGACTTCACGTGTCCGAGATCGGAAGAGC	K-s	4D	505,330,644-505,333,517	0.06	7.61	TraesCS4D02G356300	oxidoreductase activity, oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor, fatty-acyl-CoA reductase activity, alcohol-forming fatty acyl-CoA reductase activity	lipid metabolic process
rs10679	TGCAGCAAAAATGCACGCACTCATCAGTGCTGGGTTGTGTTTCATGGGTTTCTTTACCTTTCTT	K-r	3B	75,972,378-75,978,353	0.07	9.49	TraesCS3B02G110100	transferase activity, glycosyltransferase activity, cellulose synthase (UDP-forming) activity, mannan synthase activity	plant-type primary cell wall biogenesis cellulose biosynthetic process cell wall organization plant-type cell wall organization or biogenesis mannosylation
rs37461	TGCAGCTCGGCCAGCTCCGCGAGCAGCGCCGCGTCGGCCGACGACTTGGACATGTCGCCGAGAT	K/Na-s	1B	411,987,863-411,990,884	0.28	5.62	TraesCS1B02G229400	protein kinase activity, protein serine/threonine kinase activity, ATP binding	protein phosphorylation
rs17596	TGCAGCAGCTTCTCGAATACATGGCTAGAGGACGCCACCAAACTGATGAGCTCTGCTGTGAGTG	K/Na-r	6A	430,341,106-430,343,509	0.11	7.91	TraesCS6A02G228200	hydrolase activity, acting on ester bonds

^a MAF Minor allele frequency

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