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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 F2:3 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
4 Years
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
2 Locations
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 F2:3 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
2 Locations
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
2 Years
10 G. hirsutum 196 F6:8 RILs Cotton SNP 63 k array 5 Years, Fibre strength 63 QTLs Zhang et al. 2017
6 Locations
11 G. hirsutum 196 F6:8 RILs SLAF-seq 11 Environments, Fibre quality 37 QTLs 25 Zhang et al. 2015
6 Locations
12 G. hirsutum 180 RILs Cotton SNP 80 K array 3 Environments Fibre quality 12 116 SNPs, Tan et al. 2018
104 QTLs
13 G. hirsutum 555 RILs and 11 parents GBS 4 Years, Fibre quality 6 071 SNPs, A07 Islam et al. 2016a
2 Locations   86 QTLs
14 G. hirsutum 98 F5:7 RILs GBS 2 Years, Fibre quality and agronomic traits 412 SNPs, 08, 23 Gore et al. 2014
2 Locations 28 QTLs
15 G. hirsutum 419 accessions GBS 12 Environments Fibre related traits 3 665 030 total SNPs, A07, A10, D03, D11 Ma et al. 2018
7 383 unique SNPs
16 G. hirsutum 196 F6:8 RILs SLAF-seq 11 Environments, boll weight 5 521 SNPs, A03, A04 Zhang et al. 2016b
6 Locations 146 QTLs
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
4 QTLs
18 G. hirsutum 1 genotype Amplicon cloning and Sequencing 1 GhMyb8 gene 23 SNPs, Hsu et al. 2008
GhMyb10 gene 44 SNPs
(Fibre quality)
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
3 Locations
21 G. hirsutum 503 accessions Cotton 63 K SNP array 4 Locations, Agronomic traits 324 SNPs, Huang et al. 2017
2 Years 160 QTLs
22 G. hirsutum 355 accessions SLAF-seq 2 Years, Lint percentage 12 SNPs, 02, 08 Su et al. 2016a
2 Locations 2 QTLs
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 F2, 29 QTLs
25 F1
24 G. arboreum 230 accessions, GBS 3 Locations Agronomic traits 17 883 108 SNPs Du et al. 2018
G. herbaceum 13 accessions
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
4 QTLs
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
2 Years 74 QTLs
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
1 282 Salinity SNPs
29 G. hirsutum 277 F2:3 population GBS 3 Environments Salt tolerance 5 178 SNPs, A02, D02, A01, A05, A03, A10, D01 Diouf et al. 2017
66 QTLs
30 G. hirsutum 97 F5:9 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
3 Locations 119 QTLs
34 G. hirsutum 299 accessions SLAF-seq 2 Years Verticillium wilt resistance 85 630 SNPs, A06, A08 Li et al. 2017b
17 unique SNPs
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 F2.3 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
247 QTLs
40 G. hirsutum 355 accessions SLAF-seq 4 Environments Earliness 81 675 SNPs, D01, D03 Su et al. 2016c
11 Favorable SNP alleles
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
2 Locations
42 G. hirsutum 170 F2:3 population GBS 1 Earliness 3 978 SNPs, D03 Li et al. 2017a
47 QTLs
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
11 QTLs
44 G. hirsutum 355 accessions SLAF-seq 2 Locations, Plant architecture traits 93 250 SNPs, D03 Su et al. 2018
3 Years 22 novel SNPs
45 G. hirsutum F2 population dCAPS 1 Short fruiting branch gene 1 SNP locus D07 Zhang et al. 2018a
46 G. hirsutum F2:3 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
G. barbadense 2 accessions
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
G. barbadense
56 G. hirsutum 440 accessions, GBS 1 Haplotype distribution 10 129 SNPs Reddy et al. 2017
G. barbadense 218 accessions