Table 3 Description of expected MTAs by using the imputed SNPs for seed morphometric traits of Iranian wheat accessions exposed to the well-watered and rain-fed environments.

From: Genome-wide association mapping for wheat morphometric seed traits in Iranian landraces and cultivars under rain-fed and well-watered conditions

No.	Environments	SNP	Sequence	Chromosome	Position	Trait- Index	Transcript ID	Biological process	Molecular process	Cellular component	P-value	QTL reported in previous studies	Identified genes in QTL region in Triticum species
1	Well-watered	rs5540	TGCAGAGAGGAAACGGTGGCCGTGCCTGATATCTCGGCGTTGGCTCTCGCTTTGAGGCTCCTGA	1A	3415	Concavity, Convexity, Perim	TraesCS1A02G008500	-	Acyltransferase activity, transferring groups other than amino-acyl groups	–	0.0000946	27	Gamma gliadin-A1, gamma gliadin-A3, gamma gliadin-A4, and LMW-A2 genes
2		rs14628	TGCAGCACCTCTTTACTGAAGCTAGTGGTACTGCTCGCTGCGTATGATGTGGACCGCCATGGCA	1A	31,851	Rfactor, Roundness, ModRatio	TraesCS1A02G399700	transcription, DNA-templated, regulation of transcription, DNA-templated	DNA binding	Nucleus	0.00000146	28	B3 domain-containing protein Os03g0619600-like (LOC123183123)
3		rs15519	TGCAGCACTCTGCAAGAAAAACGTCAAAGTAAGAACCACCTACCCACATCTGCTCCAATTCAAA	1D	47,767	Feret, Perim,Volume, TKW, CArea, Chull, Area, Circ, PerEquivD, ArEquivD, MBCRadius, ArBBox, EquivEllAr	TraesCS1D02G147800	Lipid biosynthetic process	Iron ion binding, oxidoreductase activity	Integral component of membrane	0.0000297551	29	Very-long-chain aldehyde decarbonylase GL1-5-like (LOC123181004)
4		rs2432	TGCAGAATAAGAATATTAAGTTGATCAACATCCAGATCAACGCGCCCGAGAACAGCCCAAACAC	2B	69,414	Perim.1	TraesCS2B02G491300	Carbohydrate metabolic process, cell wall organization	Polygalacturonase activity	Extracellular region	0.000441697	27	Exopolygalacturonase-like (LOC123042122)
5		rs59777	TGCAGTCTTTCAGAAGTGCAGATGTAAACGTATTGCTATATCAGTGGTTTGAACTACATGGTAA	2D	58,883	Area.2, Perim.2, Feret, Volume, TKW	TraesCS2D02G152500	Protein ubiquitination, positive regulation of protein catabolic process	Protein binding	–	0.0000444241	29,30,31,32	Exopolygalacturonase-like (LOC123042122)
6		rs51999	TGCAGGGTTCTGGTGGCGATGCCGACCGTCGTCGAGAGGTTCGTGGACTGGGCGGTGTTGTGGC	3B	67,127	ArBBox, EquivEllAr, MBCRadius, Perim, Chull, Carea, Area, Circ, PerEquivD, ArEquivD, Perim.1, MaxR, Frete	TraesCS2D02G480600	–	–	Integral component of membrane	0.000248572	27,33	HVA22-like protein i (LOC123103004)
7		rs7487	TGCAGATAAACAGCATCAGCTCAGTTCACGGATCGATCGAGCATGTAAAATGGCGACAAACAGT	4A	61,015	Solidity	TraesCS4A02G186500	l-Arabinose metabolic process	Alpha-l-arabinofuranosidase activity	–	0.000230482	29,34	Alpha-l-arabinofuranosidase 1-like (LOC123086376), transcript variant X2,
8		rs31569	TGCAGCGGATGGCTTCAACGTGCTGATGCCCAGCAACATAGACACAACCATAGCCGAGATCGGA	4A	61,015	Solidity	TraesCS4A02G187400	–	Protein binding	Nucleus	0.000143907	29,33	Protein HEAT STRESS TOLERANT DWD 1-like (LOC123086390)
9		rs52301	TGCAGGTACGAAACACCGAGGTGCTGCTGCTGCTGATGATGAACATTTTCGCTCCCAAAGGCCG	7A	0	ArBBox.2, Area.2, Breadth, Perim.2, MinR, Concavity, Solidity, Convexity	TraesCS7A02G015000	Autophagy, protein transport, COPII vesicle coating	–	Golgi membrane, endoplasmic reticulum	0.000228123	28	Protein transport protein SEC16A homolog (LOC123150363)
10		rs1418	TGCAGAACGAAAAACAGAGCATGTACTCAGTTTCTTATAATAAAAAGCTTCAAATATCATCAGA	4A	152,121	Concavity, Perim	TraesCS4A02G495100	Triterpenoid biosynthetic process	Lanosterol synthase activity, intramolecular transferase activity, beta-amyrin synthase activity	Lipid droplet	0.000313328 0.000179158	35	Cycloartenol Synthase-like (LOC123088646), transcript variant X3
1	Rain-fed	rs61378	TGCAGTGGCAGGAGAAATTCTAACGTTTTGTGGCGTGCGATAGCGAGACTGGCGGGAAAGTACC	1A	75,213	Frete, Perim, Chull, Perim.1, MaxR , MBCRadius	TraesCS1A02G361100	Protein-glycosylation	Glycosyltransferase-activity	Integral-component-of-membrane	0.000660236	27	Glucosamine inositolphosphorylceramide transferase 1
2		rs40522	TGCAGCTTACGTGCTCCACATTGGTACTCTTGCGCTGATAATCATGAACCGCAAACTCTATGCA	1B	45,574	MaxR, Frete, CHull	TraesCS1B02G176000	Cytokinin-metabolic-process	Catalytic-activity,-oxidoreductase-activity,-cytokinin-dehydrogenase-activity,-flavin-adenine-dinucleotide-binding,-FAD-binding	Extracellular-space	0.000485937	28	Cytokinin oxidase/dehydrogenase 8 (CKX8) gene
3		rs39898	TGCAGCTGGGGCTGTAGTGCCCCAGCGAACGCCCCTGGATGCGGCGAGTACCACGGCAGGGCCG	1B	45,574	MaxR, Chull, Frete, Perim	TraesCS1B02G178900	–	Kinase-activity	–	0.000335132	27,28	antifreeze protein Maxi-like (LOC123110907)
4		rs37640	TGCAGCTCGTCATCACCGCTCGCCCGCCCGCGTGGATGCAGAAGTGCTCGAACGCCGTGCGGAA	6A	55,893	TKW	TraesCS1B02G421100	Fatty-acid-biosynthetic-process	Acyltransferase-activity,acyltransferase-activity,-transferring-groups-other-than-aminoacyl-groups	Membrane	0.000503086	27,28,28	3-ketoacyl-CoA synthase 5-like (LOC123128295)
5		rs45754	TGCAGGATTTTTATTCAAGTTTGACGTACTTATTTAGCTATATATCCTGATGAATATGGGAAGT	2A	52,385	Aspect.ratio,Compactness,Concavity,ModRatio,Rfactor,Roundness,Shape,Sphericity	TraesCS2A02G115700		–	Membrane,integral-component-of-membrane	0.0000000503	27	Protein SRC2-like (LOC123184774)
6		rs51900	TGCAGGGTGGGGGCGGAGAAAAAGGAGGAGGGGCGGCCGAGATCGGAAGAGCGGGATCACCGA	2D	28,183	TKW	TraesCS2D02G082900	Vesiclemediated-transport	Protein-binding	Plasma-membrane,-integral-component-of-membrane	0.0000429131	29,27,28,29	Syntaxin-binding protein 5-like (LOC123043515)
7		rs16023	TGCAGCAGAGGTGGTTTGGAGGTTTGGTGGCGGCAGGATTCCCCTCCCGCGGGCGGCTCGGCTC	3B	56,892	TKW	TraesCS3B02G373500	Auxinactivated-signaling-pathwa,-transmembrane-transport,-intracellular-auxin-transport		Membrane,-integral-component-of-membrane	0.0000599241	27,29	Protein PIN-LIKES 6-like (LOC123071203)
8		rs1934	TGCAGAAGCAGTCCATCCCCACCAACCCAGCCAGCGCCGCCGCAACTACTCCTACGAGCGAAGC	3B	114,516	ArBBox,Area,ArEquivD,Carea,Circ,EquivEllAr,MBCRadius,PerEquivD	TraesCS3B02G581600	–	Metal-ion-binding	–	0.000605311	27	PH, RCC1 and FYVE domains-containing protein 1-like (LOC123072730)
9		rs15576	TGCAGCACTGGAAATTCTGGAGATGTGTAGGTCCAGACATAGTTTCTGTCGTCAATCAACTGTC	4A	149,842	Perim, Chull, MBCRadius, MaxR , Frete	TraesCS4A02G494000	–	Protein-binding	–	0.000454063	27	F-box protein At4g00755-like (LOC123083653), transcript variant X3
10		rs15577	TGCAGCACTGGAAATTCTGGAGATGTGTAGGTCCAGACATAGTTTCTGTCGTCAATTAACCGTC	4A	149,842	ArBBox,ArEquivD,Carea,Chull,EquivEllAr,Frete,MaxR,MBCRadius,Perim	TraesCS4A02G494000		Protein-binding	–	0.0000166	27,29	F-box protein At4g00755-like (LOC123083653), transcript variant X3

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Table 3 Description of expected MTAs by using the imputed SNPs for seed morphometric traits of Iranian wheat accessions exposed to the well-watered and rain-fed environments.

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