Productivity-reated traits

SNP Markers Associated with Wheat Traits Related to Grain Productivity

Common wheat SNP markers identified in whole-genome association and QTL analysis linked with thousand grain weight (TGW), grain number per ear (GNE) and grain weight per ear (GWE).
This page summarizes the results obtained in our lab.

Traits

Thousand grain weight (TGW) is the total mass of 1,000 wheat grains, expressed in grams. It is a major yield component reflecting average individual grain weight (Pask et al., 2012).

Thousand grain weight

Marker	Chr	Position in IWGSC v1.0	Allele	Allele effect (d)	p-value
BobWhite_rep_c51612_864	2D	77132627	T	2	0.001
RAC875_rep_c69194_867	2D	580971342	T	2	0.001
BS00021968_51	5A	677631865	G	3.56	0.001
Excalibur_c1954_930	5A	680503202	A	3.56	0.001
wsnp_Ex_rep_c101526_86881496	2A	70985070	T	3.08*	0.001
Excalibur_c41125_360	2A	713444629	A	3.3	0.001
BS00022395_51	Un	318960136	G	1.5	0.001
RFL_Contig3621_947	4A	742335447	T	1.5	0.001
AX-94422048	5A	622380065	C	2.57	0.001
CAP7_c4064_162	5A	689916879	T	2.57	0.001
BS00081871_51	2B	12076560	A	-1.52	0.001
AX-94391750	2B	32963435	A	-1.52	0.001
Kukri_c18722_56	4B	649603249	A	2.03	0.001
Kukri_c33550_601	4B	656902657	G	2.03	0.001
AX-95124335	2D	52232863	A	3.23*	0.001
wsnp_BE444144D_Ta_1_1	2D	80730867	T	2.79	0.001
Kukri_c64744_698	4D		C	2.19	0.001
BS00099053_51	4D	3612555	T	2.19	0.001
RAC875_rep_c72023_267	5D	341565439	A	0.57	0.001
wsnp_Ex_rep_c67164_65655648	5D	107584042	G	0.57	0.001
RAC875_rep_c113120_326	2A	675896397	A	2.86	0.001
JD_c15758_288	5A	595373154	C	2.32	0.001
Ex_c6479_750	5A	611649825	G	2.32	0.001
Kukri_rep_c104648_106	6A	33954815	C	3.61	0.001
Excalibur_c41490_397	6A	524313277	C	3.61	0.001
BS00022276_51	2D	29454272	T	3.67	0.001
BS00022459_51	3A	697454068	T	0.2	0.001
BS00081475_51	3A	701891072	T	0.2	0.001

* Mean of 2017 and 2018 allele effect values

Grain number per ear (GNE) is the total number of grains produced by an individual wheat ear (spike). It is a major yield component determined by spikelet development, floret fertility, and successful grain set. (Pask et al., 2012; Wang et al., 2008).

Grain number per ear

Marker	Chr	Position IWGSC v1.0	Allele	Allele effect (d)	p-values
wsnp_Ex_c539_1072859	4A	597688011	A	2.31	0.001
RAC875_c42756_168	4A	495799905	T	2.31	0.001
Tdurum_contig71499_211	5A	570933960	G	-1.55	0.001
Excalibur_c79344_151	5A	575700038	G	-1.55	0.001
Ex_c101666_634	7B	24060479	T	2.075*	0.001
BS00010616_51	7B	63569824	T	2.075*	0.001
RAC875_c35819_165	4A	649808983	A	3.88	0.001
Tdurum_contig15586_563	4A	684514499	C	3.88	0.001
RFL_Contig4336_184	4A	627815349	G	3.77	0.001
Excalibur_c32735_603	4A	584799733	C	3.77	0.001
Ra_c9427_300	7A	78434149	T	-3.65	0.001
wsnp_Ku_c6065_10682531	7A	109843375	C	-3.65	0.001
Tdurum_contig25432_1377	5B	19439455	A	-2.19	0.001
RAC875_c8661_692	5B	26848461	G	-2.19	0.001
Tdurum_contig569_263	6B	704793345	A	0.44	0.001
wsnp_Ku_c43368_50890819	6B	679243223	T	0.44	0.001
RAC875_c95150_286	4A	685939363	A	4.39	0.001
BobWhite_c10610_1096	4A	686382438	G	4.39	0.001
wsnp_CAP12_c1503_764765	2D	35683548	G	4.53	0.001
Excalibur_c30328_713	2D	596912158	C	4.53	0.001
Kukri_rep_c73094_348	5D	278625685	C	-3.04	0.001
wsnp_Ex_rep_c67164_65655648	5D	107584042	T	-3.04	0.001
Excalibur_c21688_724	6D	464943892	A	-2.74	0.001
BS00003697_51	6D	455251609	C	-2.74	0.001
Tdurum_contig27887_55	2A	156366698	C	-2.52	0.001
BobWhite_c28819_733	2A	556987776	C	-2.52	0.001
BS00021718_51	2D	83854119	C	3.53	0.001
tplb0021e03_713	2D	609775907	G	3.53	0.001

* Mean of 2017 and 2018 allele effect values

Grain weight per ear

Grain weight per ear (GWE) is the total mass of grains produced by an individual wheat ear (spike), expressed in grams. It is a yield-related trait reflecting the combined contribution of grain number per ear and individual grain weight (Romero et al. (2013); Wheat Crop Ontology).

Marker	Chr	Position IWGSC v1.0	Allele	Allele effect (d)	p-values
CAP7_c1467_220	3A	1381332	G	0.14	0.001
Ex_c5168_849	6D	461925085	G	0.14	0.001
BS00064039_51	3A	574016420	T	0.12	0.001
wsnp_Ku_c44716_51926415	3A	600007677	A	0.12	0.001
wsnp_Ex_c10751_17505459	2A	716903314	C	-0.01	0.001
BobWhite_c16923_64	2A	719470627	T	-0.01	0.001
RAC875_c94519_448	4A	600904620	C	0.1	0.001
Excalibur_c32735_603	4A	584799733	C	0.1	0.001
BS00010339_51	4A	583953306	G	0.11	0.001
RAC875_c42756_168	4A	495799905	T	0.11	0.001
IAAV717	2B	592585054	G	-0.01	0.001
wsnp_Ex_c14595_22634031	2B	158644755	C	-0.01	0.001
Tdurum_contig25432_1377	5B	19439455	A	-0.06	0.001
RAC875_c8661_692	5B	26848461	G	-0.06	0.001
Ex_c101666_634	7B	24060479	T	0.1	0.001
GENE-4333_211	7B	113626628	A	0.1	0.001
Kukri_rep_c104865_57	5D	562121917	C	0.14	0.001
tplb0030a05_2386	5D	544698237	G	0.14	0.001
RFL_Contig4336_184	4A	627815349	G	0.18	0.001
D_F5XZDLF02G9H4M_286	4A	650602048	G	0.18	0.001
AX-94525876	7A	31879084	A	-0.12	0.001
BS00102773_51	7A	65328329	T	-0.12	0.001
wsnp_CAP12_c1503_764765	2D	35683548	G	0.23	0.001
Excalibur_c30328_713	2D	596912158	C	0.24*	0.001
BS00022276_51	2D	29454272	T	0.22	0.001
AX-95124335	2D	52232863	A	0.22	0.001
BS00021718_51	2D	83854119	C	0.25	0.001

* Mean of 2017 and 2018 allele effect values

Articles providing more information about the presented markers

This work was funded by
RSF, project № 21-76-30003
Budjetary Progect FWNR-2024-0009

ORCID 0000-0002-3725-8596

ResearchGate

Contacts:
Antonina Kiseleva, PhD

Google Scholar

Institute of Cytology and Genetics
Siberian Branch of Russian Academy of Sciences

Department of Plant Molecular Genetics
(Prof. Elena Salina)

Laboratory of Genetic Basis of Grain Crops Breeding