Role of SNPs in determining QTLs for major traits in cotton

MAJEED, Sajid; RANA, Iqrar Ahmad; ATIF, Rana Muhammad; ALI, Zulfiqar; HINZE, Lori; AZHAR, Muhammad Tehseen

doi:10.1186/s42397-019-0022-5

Journal of Cotton Research

Table 1 Characterization of reported SNPs/QTLs in cotton for various traits of economic interest, stresses and plant architecture

From: Role of SNPs in determining QTLs for major traits in cotton

No.	Cotton species	Source of genotyping	Genotyping method	No. of Experimental Years/Locations/Environments	Traits	No. of QTLs/QTNs/ SNPs discovered	Chromosomal location of major SNPs/QTLs	Ref.
Yield and fibre quality traits
1	G. hirsutum	188 F₈ RILs	Cotton 63 K SNP array	2 Locations	Fibre quality and yield	71 QTLs, 16 Stable QTLs	05, 09, 10, 14, 19, 20	Li et al. 2016
2	G. hirsutum	277 F_2:3 population	GBS	3 Years	Fibre quality and yield	5 178 SNPs, 110 QTLs	17, 26	Diouf et al. 2018
3	G. hirsutum	231 RILs population	Cotton SNP 80 K array	4 Locations,	Fibre quality and yield	256 QTLs, 57 Stable QTLs	–	Liu et al. 2018
3	G. hirsutum	231 RILs population	Cotton SNP 80 K array	4 Years	Fibre quality and yield	256 QTLs, 57 Stable QTLs	–	Liu et al. 2018
4	G. hirsutum	169 accessions	Cotton SNP 80 K array	2 Years,	Fibre quality traits	342 QTNs	A01, A06, A07, D01, D12, D13	Li et al. 2018a
4	G. hirsutum	169 accessions	Cotton SNP 80 K array	2 Locations	Fibre quality traits	342 QTNs	A01, A06, A07, D01, D12, D13	Li et al. 2018a
5	G. hirsutum	201 accessions	Cotton 63 K SNP array	4 Years,	Fibre quality and yield	23 254 SNPs	24	Handi et al. 2017
				5 Environments,
				3 Locations
6	G. hirsutum	F_2:3 lines	RAD-seq	1	Fibre quality and yield	27 QTLs, 9 366 SNPs	–	Wang et al. 2015b
7	G. hirsutum	178 RILs	RAD-seq	6 Years,	Fibre quality and yield	134 QTLs	–	Wang et al. 2015a
7	G. hirsutum	178 RILs	RAD-seq	2 Locations	Fibre quality and yield	134 QTLs	–	Wang et al. 2015a
8	G. hirsutum	355 accessions	SLAF-seq	4 Environments	Fibre quality traits	33 SNPs	D07	Su et al. 2016b
9	G. hirsutum	180 RILs	SLAF-seq	3 Locations,	Fibre quality	6 254 SNPs, 95 QTLs	–	Ali et al. 2018
9	G. hirsutum	180 RILs	SLAF-seq	2 Years	Fibre quality	6 254 SNPs, 95 QTLs	–	Ali et al. 2018
10	G. hirsutum	196 F_6:8 RILs	Cotton SNP 63 k array	5 Years,	Fibre strength	63 QTLs	–	Zhang et al. 2017
10	G. hirsutum	196 F_6:8 RILs	Cotton SNP 63 k array	6 Locations	Fibre strength	63 QTLs	–	Zhang et al. 2017
11	G. hirsutum	196 F_6:8 RILs	SLAF-seq	11 Environments,	Fibre quality	37 QTLs	25	Zhang et al. 2015
11	G. hirsutum	196 F_6:8 RILs	SLAF-seq	6 Locations	Fibre quality	37 QTLs	25	Zhang et al. 2015
12	G. hirsutum	180 RILs	Cotton SNP 80 K array	3 Environments	Fibre quality	12 116 SNPs,	–	Tan et al. 2018
12	G. hirsutum	180 RILs	Cotton SNP 80 K array	3 Environments	Fibre quality	104 QTLs	–	Tan et al. 2018
13	G. hirsutum	555 RILs and 11 parents	GBS	4 Years,	Fibre quality	6 071 SNPs,	A07	Islam et al. 2016a
13	G. hirsutum	555 RILs and 11 parents	GBS	2 Locations		86 QTLs	A07	Islam et al. 2016a
14	G. hirsutum	98 F_5:7 RILs	GBS	2 Years,	Fibre quality and agronomic traits	412 SNPs,	08, 23	Gore et al. 2014
14	G. hirsutum	98 F_5:7 RILs	GBS	2 Locations	Fibre quality and agronomic traits	28 QTLs	08, 23	Gore et al. 2014
15	G. hirsutum	419 accessions	GBS	12 Environments	Fibre related traits	3 665 030 total SNPs,	A07, A10, D03, D11	Ma et al. 2018
15	G. hirsutum	419 accessions	GBS	12 Environments	Fibre related traits	7 383 unique SNPs	A07, A10, D03, D11	Ma et al. 2018
16	G. hirsutum	196 F_6:8 RILs	SLAF-seq	11 Environments,	boll weight	5 521 SNPs,	A03, A04	Zhang et al. 2016b
16	G. hirsutum	196 F_6:8 RILs	SLAF-seq	6 Locations	boll weight	146 QTLs	A03, A04	Zhang et al. 2016b
17	G. hirsutum	375 F3 lines	Mapping by sequencing (MBS)	1	MD52ne genes (fibre strength and quality)	27 SNPs,	03, 14, 24	Islam et al. 2016b
17	G. hirsutum	375 F3 lines	Mapping by sequencing (MBS)	1	MD52ne genes (fibre strength and quality)	4 QTLs	03, 14, 24	Islam et al. 2016b
18	G. hirsutum	1 genotype	Amplicon cloning and Sequencing	1	GhMyb8 gene	23 SNPs,	–	Hsu et al. 2008
					GhMyb10 gene	44 SNPs
					(Fibre quality)	44 SNPs
19	G. hirsutum	Fibreless mutant line	Transcriptome sequencing	1	Fibre initiation	28 610 SNPs	12, 26	Ma et al. 2016
20	G. hirsutum	277 varieties	Eco-TILLING	3 Years,	Fibre quality and seed traits (GhSus genes)	24 SNPs	16, 19, 25	Zeng et al. 2016
20	G. hirsutum	277 varieties	Eco-TILLING	3 Locations	Fibre quality and seed traits (GhSus genes)	24 SNPs	16, 19, 25	Zeng et al. 2016
21	G. hirsutum	503 accessions	Cotton 63 K SNP array	4 Locations,	Agronomic traits	324 SNPs,	–	Huang et al. 2017
21	G. hirsutum	503 accessions	Cotton 63 K SNP array	2 Years	Agronomic traits	160 QTLs	–	Huang et al. 2017
22	G. hirsutum	355 accessions	SLAF-seq	2 Years,	Lint percentage	12 SNPs,	02, 08	Su et al. 2016a
22	G. hirsutum	355 accessions	SLAF-seq	2 Locations	Lint percentage	2 QTLs	02, 08	Su et al. 2016a
23	G. barbadense	2 genotypes,	Cotton 63 K SNP array	1	Fibre quality and yield	460 SNPs,	05, 06, 23	Kumar et al. 2019
		185 F_2,				29 QTLs
		25 F₁				29 QTLs
24	G. arboreum	230 accessions,	GBS	3 Locations	Agronomic traits	17 883 108 SNPs	–	Du et al. 2018
24	G. herbaceum	13 accessions	GBS	3 Locations	Agronomic traits	17 883 108 SNPs	–	Du et al. 2018
25	G. hirsutum × G. barbadense	146 Backcross inbred lines (BILs)	RNA-Seq	5 Environments	Fibre length	703 SNPs,	05, 11, 12, 21	Li et al. 2017c
25	G. hirsutum × G. barbadense	146 Backcross inbred lines (BILs)	RNA-Seq	5 Environments	Fibre length	4 QTLs	05, 11, 12, 21	Li et al. 2017c
26	G. hirsutum × G. tomentosum	107 BC₅S₅ introgression lines	SLAF-seq	3 Locations,	Fibre quality and yield	3 157 SNPs,	A01, A13, DO6	Keerio et al. 2018
26	G. hirsutum × G. tomentosum	107 BC₅S₅ introgression lines	SLAF-seq	2 Years	Fibre quality and yield	74 QTLs	A01, A13, DO6	Keerio et al. 2018
27	G. hirsutum	2 lines,	Amplicon cloning and Sequencing	1	R2R3-MYB transcription factors	108 SNPs	–	An et al. 2008
	G. tomentosum	1 line,
	G. barbadense	1 line,
	G. mustelinum	1 line,
	G. hirsutum ×	186 RILs
	G. barbadense
Biotic and abiotic stress tolerance
28	G. hirsutum	8 varieties	Cotton SNP 63 K array	1	Salt tolerance	7 087 SNPs,	A04, D01	Wang et al. 2016
28	G. hirsutum	8 varieties	Cotton SNP 63 K array	1	Salt tolerance	1 282 Salinity SNPs	A04, D01	Wang et al. 2016
29	G. hirsutum	277 F_2:3 population	GBS	3 Environments	Salt tolerance	5 178 SNPs,	A02, D02, A01, A05, A03, A10, D01	Diouf et al. 2017
29	G. hirsutum	277 F_2:3 population	GBS	3 Environments	Salt tolerance	66 QTLs	A02, D02, A01, A05, A03, A10, D01	Diouf et al. 2017
30	G. hirsutum	97 F_5:9 RILs	GBS	2 Environments	Drought and salt tolerance	165 QTLs	–	Abdelraheem et al. 2018
31	G. hirsutum × G. tomentosum	BC₂F₂ population	GBS	1	Drought tolerance	10 888 SNPs	23, 25	Magwanga et al. 2018
32	G. arboreum	2 Genotypes,	Amplicon cloning and sequencing	1	MT-sHSP gene	21 SNPs	–	Shaheen et al. 2009
	G. hirsutum	1 genotype,			(Heat stress)
	G. herbaceum	1 genotype,
	G. sturtianum	1 genotype,
	G. aridum	1 genotype,
	G. gossypoides	1 genotype,
	G. laxum	1 genotype,
	G. stocksii	1 genotype
33	G. hirsutum	318 accessions	GBS	3 Years,	Verticillium wilt resistance, Fibre quality and yield	1 871 401 SNPs,	A02, A13, D08	Fang et al. 2017
33	G. hirsutum	318 accessions	GBS	3 Locations	Verticillium wilt resistance, Fibre quality and yield	119 QTLs	A02, A13, D08	Fang et al. 2017
34	G. hirsutum	299 accessions	SLAF-seq	2 Years	Verticillium wilt resistance	85 630 SNPs,	A06, A08	Li et al. 2017b
34	G. hirsutum	299 accessions	SLAF-seq	2 Years	Verticillium wilt resistance	17 unique SNPs	A06, A08	Li et al. 2017b
35	G. hirsutum	120 accessions	Cotton SNP 63 K array	2 Environments	Verticillium wilt resistance	21 171 SNPs,	19	Zhao et al. 2017
						3 cluster QTLs,
						2 Major QTLs
36	G. hirsutum	196 RILs	Cotton SNP 63 K array	4 Years	Verticillium wilt Resistance	119 QTLs	–	Palanga et al. 2017
37	G. hirsutum	F4:5 population of 285 families	Amplicon cloning and Sequencing	1	Xanthomonas axonopodis resistance (Bacterial blight)	4 SNPs	14	Xiao et al. 2010
38	G. hirsutum	364 F_2.3 population	Amplicon cloning and Sequencing	1	Cotton blue disease	4 SNPs	10	Fang et al. 2010
Earliness
39	G. hirsutum	137 RILs	GBS	6 Years	Earliness	6 295 SNPs,	A06, D03	Jia et al. 2016
39	G. hirsutum	137 RILs	GBS	6 Years	Earliness	247 QTLs	A06, D03	Jia et al. 2016
40	G. hirsutum	355 accessions	SLAF-seq	4 Environments	Earliness	81 675 SNPs,	D01, D03	Su et al. 2016c
40	G. hirsutum	355 accessions	SLAF-seq	4 Environments	Earliness	11 Favorable SNP alleles	D01, D03	Su et al. 2016c
41	G. hirsutum	169 accession	Cotton SNP 80 K array	2 Years,	Earliness	49 650 SNPs, 29 Significant SNPs	A06, A07, A08, D01, D02, D09	Li et al. 2018b
41	G. hirsutum	169 accession	Cotton SNP 80 K array	2 Locations	Earliness	49 650 SNPs, 29 Significant SNPs	A06, A07, A08, D01, D02, D09	Li et al. 2018b
42	G. hirsutum	170 F_2:3 population	GBS	1	Earliness	3 978 SNPs,	D03	Li et al. 2017a
42	G. hirsutum	170 F_2:3 population	GBS	1	Earliness	47 QTLs	D03	Li et al. 2017a
Plant architecture and related traits
43	G. hirsutum	121 genotypes	GBS	3 Environments	Plant height and fruit spur branch number	2 620 639 SNPs,	A08, D02	Wen et al. 2019
43	G. hirsutum	121 genotypes	GBS	3 Environments	Plant height and fruit spur branch number	11 QTLs	A08, D02	Wen et al. 2019
44	G. hirsutum	355 accessions	SLAF-seq	2 Locations,	Plant architecture traits	93 250 SNPs,	D03	Su et al. 2018
44	G. hirsutum	355 accessions	SLAF-seq	3 Years	Plant architecture traits	22 novel SNPs	D03	Su et al. 2018
45	G. hirsutum	F₂ population	dCAPS	1	Short fruiting branch gene	1 SNP locus	D07	Zhang et al. 2018a
46	G. hirsutum	F_2:3 lines	GBS	1	Plant height, height of fruiting branch node and number of vegetative shoot	17 QTLs	03, 04, 05, 07, 09, 17, 19, 23, 25	Qi et al. 2017
47	G. hirsutum × G. barbadense	168 F₂ population	GBS	1	Nulliplex-branch gene (gb_nb1)	42 SNPs	16(D07)	Chen et al. 2015
48	G. hirsutum	3 parental lines and their BC₁F₁ population	Amplicon cloning and sequencing	1	Virescent leaf expression	4 SNPs	20	Zhang et al. 2018b
49	G. barbadense	3 genotypes	cDNA library sequencing	2 Locations	Diversity of leaf transcriptomes	> 10 000 SNPs	–	Kottapalli et al. 2016
50	G. hirsutum	395 genotypes	Cotton 63 K SNP array	1	Diversity analysis	38 822 SNPs	02, 13, 15	Hinze et al. 2017
51	G. hirsutum	11 genotypes and their C₅S₆ RILs	GBS	1	Genetic diversity	5 617 SNPs	08, 09	Islam et al. 2015
52	G. hirsutum	2 accessions,	GR-RSC and KASP assays	1	Genetic diversity	151 000 putative SNPs	–	Byers et al. 2012
52	G. barbadense	2 accessions	GR-RSC and KASP assays	1	Genetic diversity	151 000 putative SNPs	–	Byers et al. 2012
53	G. hirsutum	2 genotypes,	GBS	1	Genetic diversity	25 529 SNPs	–	Logan-Young et al. 2015
	G. barbadense	2 genotypes,
	G. herbaceum	1 genotype,
	G. raimondii	1 genotype
54	G. hirsutum × G. barbadense	59 interspecific F₂ individuals	GBS	1	Structural variability	4 999 048 SNPs	–	Wang et al. 2015c
55	G. hirsutum ×	186 RILs	Golden Gate assay	1	–	247 SNPs	–	John et al. 2012
55	G. barbadense	186 RILs	Golden Gate assay	1	–	247 SNPs	–	John et al. 2012
56	G. hirsutum	440 accessions,	GBS	1	Haplotype distribution	10 129 SNPs	–	Reddy et al. 2017
56	G. barbadense	218 accessions	GBS	1	Haplotype distribution	10 129 SNPs	–	Reddy et al. 2017

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