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 6 Annotation of genes harbouring the significant trait-associated SNPs across all chromosomes in Iranian wheat accessions exposed to salinity stress

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	R² (%)	Gene ID in wheat	Molecular function	Biological process
rs15925	TGCAGCAGAGAGGCGCGGAAACACGCGATCTCCGCACGCTGGGCCGCCCCAGTGGGCGGCGGTC	ELI	7A	200,599,649-200,608,278	0.25	7.27	TraesCS7A02G230100	antiporter activity, xenobiotic transmembrane transporter activity	transmembrane transport
rs15925	TGCAGCAGAGAGGCGCGGAAACACGCGATCTCCGCACGCTGGGCCGCCCCAGTGGGCGGCGGTC	ELI	7A	200,599,649-200,608,278	0.25	7.27	TraesCS7A02G230100	antiporter activity, xenobiotic transmembrane transporter activity
rs7347	TGCAGAGTTATAGGGAAGAAGAAGAAGGCGTACGTGGAAAAAACGATTCGAGGAGCGCTCCCGT	SPAD	2A	373,418,967-373,421,254	0.31	8.43	TraesCS2A02G249000	electron transfer activity, protein-disulfide reductase activity, glutathione oxidoreductase activity	cell redox homeostasis
rs53540	TGCAGGTCTCGCTAATCGATCCTCGCTTTTTTTTGAGCATCAGTACAGACACAAGCGCTCATAT	SFW	6A	264,830,763-264,834,472	0.31	6.97	TraesCS6A02G192900	protein kinase activity ATP binding	protein phosphorylation
rs35884	TGCAGCTCACGTAGAAGGAGACCCGACCGACAGCGCGATTCGCAAGACAGTCGACGAGCGCTTT	SDW	3B	768,470,821-768,482,837	0.12	9.08	TraesCS3B02G526100	hydrolase activity, hydrolyzing O-glycosyl compounds	carbohydrate metabolic process
rs54146	TGCAGGTGGAAAATGGAATCGCTAGGCCGCCGCCGAGATCGGAAGAGCGGGATCACCGACTGCC	RWC	4A	685,748,621-685,752,222	0.21	10.33	TraesCS4A02G415700	protein binding
rs257	TGCAGAAAAGTAAGAAATTTGAAGGAGTTTTGTTCAATCACCATTTTATTACGTGTCCTCCCGA	RFW	7B	594,048,516-594,116,949	0.10	17.48	TraesCS7B02G339500	protein binding
rs37983	TGCAGCTCTGACCGACTCCGCCTGAAGCCGCCATCGTTGCCACACAGGAGGACGACCTATTATT	RDW	3B	325,816,754-325,873,702	0.18	16.57	TraesCS3B02G227800	protein binding
rs18682	TGCAGCAGTGGTGGTGTGCCCTTGGTCCATGCCATGTTTGTGTGCTCACCCTGTGGTTGTGGTG	RV	1B	688,351,698-688,354,737	0.38	10.14	TraesCS1B02G480700	DNA binding	nucleosome assembly regulation of transcription
rs55629	TGCAGTAAACCAATCAAAATGCATGGAACTCGCAGCGCTGCTCCCGCTTGTTCCCTTCGCCG	SH	3B	193,605,454-193,613,941	0.43	22.64	TraesCS3B02G182700	endoribonuclease activity, producing 5′-phosphomonoesters	tRNA processing, tRNA 3′-trailer cleavage
rs44076	TGCAGGAGATGGAGGGGAGCAGTAGGGGGGTTCTCTGCTCCGCAATCAGGGATCCGAGATCGGA	RH	2D	417,090,322-417,092,425	0.31	5.79	TraesCS2D02G324100	protein binding
rs34693	TGCAGCTACGGCGACGGCGGATGGGGCCTTGTTGGTCACCCCACTGCGCGTCGCAGCGCCTAGG	Chl a	7B	524,991,414-525,003,565	0.18	7.05	TraesCS7B02G289500	DNA binding, DNA clamp loader activity, ATP binding, ATPase	resolution of meiotic recombination intermediates, DNA replication and repair, response to abscisic acid, regulation of chromatin silencing, regulation of histone H3-K9 methylation
rs18445	TGCAGCAGTCAGTTTCCTCCTCCTCGACTCCGACCGCCTTCGTCACCCGAGGCGTCTCTGCGTC	Chl b	6A	580,203,253-580,213,091	0.29	6.21	TraesCS6A02G347900	ionotropic glutamate receptor activity, ligand-gated ion channel activity
rs34693	TGCAGCTACGGCGACGGCGGATGGGGCCTTGTTGGTCACCCCACTGCGCGTCGCAGCGCCTAGG	Total Chl	7B	524,991,414-525,003,565	0.18	7.48	TraesCS7B02G289500	DNA binding, DNA clamp loader activity, ATP binding, ATPase	resolution of meiotic recombination intermediates, DNA replication and repair, response to abscisic acid, regulation of chromatin silencing, regulation of histone H3-K9 methylation
rs59624	TGCAGTCTGGCTGCGATGGTTTCCTCGCTTCCTCCACCTTCTTTAGAAAATAGAGACGGAGGCA	Car	6B	604,212,469-604,220,915	0.31	6.07	TraesCS6B02G343300	catalytic activity, metal ion binding	proteolysis
rs18946	TGCAGCATAGGAAACAGAGAACAAGTTAAGGCTGGTTTTAATGGTGAGTATCATATACTATTAT	protein	3B	521,699,476-521,702,489	0.29	6.2	TraesCS3B02G322400	proton transmembrane transporter activity	ion transport, ATP synthesis coupled proton transport
rs15183	TGCAGCACGGCTCAATCTCCTCCTGGGACAAGATGCGCGACCGTGTTGTCGCCAACTTCTAGGG	proline	1D	220,060,401-220,078,971	0.11	23.21	TraesCS1D02G156100	hydrolase activity, metal ion binding, metalloaminopeptidase activity
rs10254	TGCAGATTGCGCCGCTGGGCGTGCCACACGTGGCGCGCGGCTGCTACGAGAAGGCGACGGCCAT	CAT	3B	790,521,121-790,523,205	0.16	5.1	TraesCS3B02G556500	transferase activity, glycosyltransferase activity, pentosyltransferase activity
rs61179	TGCAGTGGAAGCGGATGGTTGAGGACCTGCTGGCGCTGGGCAAACTCAACAACTGCCTCGCCGT	GPX	1B	28,373,087-28,375,944	0.14	6.23	TraesCS1B02G048300	catalytic activity, ammonia-lyase activity, phenylalanine ammonia-lyase activity	L-phenylalanine catabolic process, cinnamic acid biosynthetic process
rs10192	TGCAGATTGAACCCATCCTATTCTTCTGATTGAATTCATCAGTTAATTAGAAGAAGGGAAATGG	MDA	Un	75,218,183-75,222,714	0.06	7.88	TraesCSU02G083400	ADP binding
rs9791	TGCAGATGTTAGAAAACAGCCCTATACTCAATCAAGATGGCCTCAAATCAAAAAGTGTTCAGCA	MDA	6A	263,871,061-263,911,967	0.14	7.45	TraesCS6A02G192800	GTPase activity GTP binding
rs61025	TGCAGTGCTAGCTGCATGCACGGGGGAGGCGATGCCATGGCATGGCGCGGCACGGGCACGGGCA	Na-s	1B	680,162,318-680,165,052	0.08	8.58	TraesCS1B02G472200	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen
rs3228	TGCAGACACAAACGTCTCGTACCAGTGGAATGTGTAAAGAATAGTTGTTATATATCTTGCCATC	Na-r	4B	621,667,176-621,669,677	0.14	7.26	TraesCS4B02G330600	acyltransferase activity, transferring groups other than amino-acyl groups
rs63185	TGCAGTTCCATATAGCCCAAAGTAATGCGCAAATTCCTATCTGAATATGTTCGGCAATAGCTGG	K-s	Un	67,782,631-67,803,633	0.45	11.67	TraesCSU02G075800	calcium ion binding	photosynthesis
rs63185	TGCAGTTCCATATAGCCCAAAGTAATGCGCAAATTCCTATCTGAATATGTTCGGCAATAGCTGG	K-s	5A	204,996,408-205,013,771	0.45	11.67	TraesCS5A02G109600	calcium ion binding	photosynthesis
rs28569	TGCAGCGACTCCAGCGTGTCCGACTTGTCGCCGTCCGTGGCCGCCGTGGCCGCGCGCACCACCA	K-r	1A	511,009,417-511,015,060	0.44	9.92	TraesCS1A02G320400	potassium ion transmembrane transporter activity	potassium ion transmembrane transport
rs85	TGCAGAAAAATAAAAGTTAGTTATTCGGTTGTAACCGACATAAGCTATCTCTCCAGCACGGCAG	K/Na-s	1B	396,597,678-396,605,441	0.34	8.2	TraesCS1B02G219500	ubiquitin-protein transferase activity, protein binding	protein ubiquitination interstrand cross-link repair
rs30786	TGCAGCGCGGCGATGACCAGGGTGACAAGGTCTCGCGGAGGCAGCGCGAGCGGGCTCCTTCAGG	K/Na-r	Un	74,817,236-74,821,587	0.45	8.7	TraesCSU02G082000	sucrose synthase activity, glycosyltransferase activity	sucrose metabolic process, callose deposition in phloem sieve plate
rs30786	TGCAGCGCGGCGATGACCAGGGTGACAAGGTCTCGCGGAGGCAGCGCGAGCGGGCTCCTTCAGG	K/Na-r	6D	471,917,727-471,921,914	0.45	8.7	TraesCS6D02G403800	sucrose synthase activity, glycosyltransferase activity	sucrose metabolic process

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ISSN: 1471-2229

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