PhD research (2018) presented at Beltwide Cotton Conferences (2019)

1. Dissecting Quantitative Variation Introgressed
into Upland Cotton Using QTL-Stacked
Segregating Populations
1Sameer Khanal, 1Jinesh D. Patel, 1Jeevan Adhikari, 1Rahul Chandnani, 1Zining Wang,
1Sayan Das, 2Nino Brown, 3Don Jones, 2Peng Chee and 1Andrew H. Paterson
1University of Georgia, Athens, GA
2University of Georgia, Tifton, GA
3Cotton Incorporated, Cary, NC
Pic. google images

2. Background of the study
G. tomentosum Maps G. mustelinum Maps
Genetic material used to detect
QTL alleles for improved fiber
quality traits (Wang et al.
2016, 2017)

3. G. tomentosum (Gto) study
Additive PVE% Additive PVE%
qFE11.1 Chr11 pBAM422yE3C CA3093 BC3F2 (TX) -0.66** 6.7
qFE14.1 Chr14 pAR815E3C CA3084, CA3093 BC3F2 (TX) -0.64** 9
CA3084, CA3093 BC3F3 (TX) -0.53* 4.5
qFE21.1 Chr21 G1261aE3C CA3093 BC3F2 (TX) -0.72** 7.8
CA3093 BC3F3 (TX) -0.72* 5.7
qFF05.1 Chr05 pAR1-28E3C CA3084, CA3093 BC3F3 (GA) 0.32** 8.1
qFF07.1 Chr07 G1158bE5C CA3093 BC3F3 (TX) 0.40** 6
qFS15.1e Chr15 A1720xE4R CA3084 BC3F2 (TX) -0.89** 8.3
BC3F2 (TX), BC3F3 (TX) and BC3F3 (GA) indicate BC3F2 at Lubbock (TX), BC3F3 at Lubbock (TX), and BC3F3 at Tifton (GA),
respectively.
* and ** represent the significance with a P-value 0.001 and 0.0001 respectively.
e indicate significant interaction (P<0.001) genotype × environment
PVE, Phenotypic variance explained
Environment
a positive sign (+) of the additive effect indicates that the allele originated from G. hirsutum increases the value of the trait;
negative sign (-) of the additive effect indicates that the allele originated from G. tomentosum increases the value of the trait.
Table 1a
QTL for fiber related-traits in G. hirsutum populations introgressed with G. tomentosum chromosome segments
a
table copied from Zhang et al. (2011)
CA3084 background CA3093 background
Fiber elongation (%)
Fiber fineness (micronaire)
Fiber strength (cN/tex)
QTL Chromosome Nearest marker Background

4. G. mustelinum (Gm) study
QTL Chromosome Flanking markers Populationb
Environment LOD Additive PVE (%) Dominance
Fiber elongation (%)
qELO-1-1 Chr01 MUSS523b-NAU2095 B15 BC3F2 (GA) 3.8 -0.52 14.5 0.03
MUSS523b-NAU2095 BC3F3 (GA) 3 -0.26 9.9 0.14
qELO-11-1 Chr11 BNL3442-MUSS123b B16 BC3F2 (GA) 7.7 -0.80 26.7 -0.20
BNL3442-MUSS123b BC3F3 (GA) 7.4 -0.54 21.2 -0.11
qELO-11-1 Chr11 MUSS123b-NAU3377b B17 BC3F2 (GA) 3 -0.43 8.8 0.23
MUSS123b-NAU3377b BC3F3 (GA) 3.9 -0.36 10.6 -0.04
qELO-21-2 Chr21 NAU3074-BNL1034 B16 BC3F2 (GA) 5.4 -0.71 15 0.15
NAU3074-BNL1034 BC3F3 (GA) 4.1 -0.54 14.2 -0.12
Fiber strength (cN/TEX)
qSTR-25-1 Chr25 BNL3264-BNL4001b B17 BC3F2 (GA) 3.1 -1.39 13.5 -0.37
STS511-BNL3264 BC3F3 (GA) 2.9 -1.67 17.2 -0.79
b
backcross populations with target QTL introgressions
PVE, Phenotypic variance explained
BC3F2 (GA) and BC3F3 (GA) indicate BC3F2 and BC3F3 at Tifton (GA).
a negative sign (-) of the additive effect indicates that the allele originated from G. mustelinum increases the value of the trait.
Table 2a
QTL for fiber related-traits in G. hirsutum populations introgressed with G. mustelinum chromosome segments
a
table provided by Dr. Chee (unpublished)

5. Gto- and Gm-QTL synopsis
Favorable alleles, particularly for fiber elongation and
fiber fineness, were recovered from seemingly
unfavorable parents.
QTLs were mapped to QTL hotspots

6. Together with the fact that:
evolution of efficient spinning
technologies
increased demand for quality fibers
better price premium
competition from synthetic fibers
accessibility to genomic tools
Opportunities and interest in
improving fiber quality has increased

7. PhD research
▪ Dissecting quantitative
variation in fiber quality
traits with QTL-stacked
Gossypium hirsutum
(Upland cotton) genetic
backgrounds
Objective:
To assess the effects of
introgressed QTLs and
their interactions in elite
genetic backgrounds of
Upland cotton

8. Project outline: populations
Phase I: Introducing Gto-QTLs from advanced-
backcross populations to different G. hirsutum
genetic backgrounds
BC3F2/ BC3F3QTL mapping (Zhang et al. 2011)
BC3F3 x Elite Lines- Identify individuals with target QTL
- QTL introgressed lines x elite lines
1. GA2004230
2. DP50
3. R01- 40-08
4. GA2004089
5. Paymaster HS26
6. Acala SJ-4
Actions:
- Four QTL regions were
tagged with SSR markers
- BC3F3 lines screened for
target QTLs
- Gto-QTL x Elite crosses were
made
Additive PVE% Additive PVE%
qFE11.1 Chr11 pBAM422yE3C CA3093 BC3F2 (TX) -0.66** 6.7
qFE14.1 Chr14 pAR815E3C CA3084, CA3093 BC3F2 (TX) -0.64** 9
CA3084, CA3093 BC3F3 (TX) -0.53* 4.5
qFE21.1 Chr21 G1261aE3C CA3093 BC3F2 (TX) -0.72** 7.8
CA3093 BC3F3 (TX) -0.72* 5.7
qFF05.1 Chr05 pAR1-28E3C CA3084, CA3093 BC3F3 (GA) 0.32** 8.1
qFF07.1 Chr07 G1158bE5C CA3093 BC3F3 (TX) 0.40** 6
Environment
Table 1a
QTL for fiber related-traits in G. hirsutum populations introgressed with G. tomentosum chromosome segments
CA3084 background CA3093 background
Fiber elongation (%)
Fiber fineness (micronaire)
Fiber strength (cN/tex)
QTL Chromosome Nearest marker Background
Table Gt-QTL targets List Elite lines

9. Project outline: populations
Phase II: Stacking Gto- and Gm-QTLs in six different
genetic backgrounds of G. hirsutum
BC3F2/ BC3F3QTL mapping (Zhang et al. 2011)
BC3F3 x Elite Lines
F1 (QTL target A) x F1 or BC3F3
- Identify individuals with target QTL
- QTL introgressed lines x elite lines
- Identify individuals with target QTL
- Crosses between different QTL targets
Actions:
- F1s (Gto-QTL x Elite) were
genotyped for target QTLs
- BC3F3 (Gm selections) were
also genotyped for target
QTLs
- Gto- x Gto-QTL crosses were
made in all combinations
- Gto- x Gm-QTL crosses were
made in all combinations
(QTL target B)
QTL Chromosome Flanking markers Populationb
Environment LOD Additive PVE (%) Dominance
Fiber elongation (%)
qELO-1-1 Chr01 MUSS523b-NAU2095 B15 BC3F2 (GA) 3.8 -0.52 14.5 0.03
MUSS523b-NAU2095 BC3F3 (GA) 3 -0.26 9.9 0.14
qELO-11-1 Chr11 BNL3442-MUSS123b B16 BC3F2 (GA) 7.7 -0.80 26.7 -0.20
BNL3442-MUSS123b BC3F3 (GA) 7.4 -0.54 21.2 -0.11
qELO-11-1 Chr11 MUSS123b-NAU3377b B17 BC3F2 (GA) 3 -0.43 8.8 0.23
MUSS123b-NAU3377b BC3F3 (GA) 3.9 -0.36 10.6 -0.04
qELO-21-2 Chr21 NAU3074-BNL1034 B16 BC3F2 (GA) 5.4 -0.71 15 0.15
NAU3074-BNL1034 BC3F3 (GA) 4.1 -0.54 14.2 -0.12
Fiber strength (cN/TEX)
qSTR-25-1 Chr25 BNL3264-BNL4001b B17 BC3F2 (GA) 3.1 -1.39 13.5 -0.37
STS511-BNL3264 BC3F3 (GA) 2.9 -1.67 17.2 -0.79
Table 2a
QTL for fiber related-traits in G. hirsutum populations introgressed with G. mustelinum chromosome segmentsTable Gm-QTL targets

10. Phase III: Identifying QTL stacked lines, targeted
genotyping, and analyzing marker-trait associations
in QTL-stacked F2 populations
Project outline: populations
BC3F2/ BC3F3QTL mapping (Zhang et al. 2011)
BC3F3 x Elite Lines
F1 (QTL A) x F1 (QTL B)
F1
- Identify individuals with target QTL
- QTL introgressed lines x elite lines
QTL mapping population
F2
- Identifying QTL stacked lines
- Self QTL stacked lines
- Identify individuals with target QTL
- Crosses between different QTL targets
Actions:
- Subset of crosses were
screened for QTL stacked
individuals
- QTL stacked lines were selfed
to constitute QTL mapping
populations
- QTL mapping was performed

11. Phase IV: Validating QTL effects by phenotyping
F2:3 progenies of QTL-stacked selections for fiber
quality traits
Project outline: populations
BC3F2/ BC3F3QTL mapping (Zhang et al. 2011)
BC3F3 x Elite Lines
F1 (QTL A) x F1 (QTL B)
F1
- Identify individuals with target QTL
- QTL introgressed lines x elite lines
QTL mapping population
F2
- Identifying QTL stacked lines
- Self QTL stacked lines
- Identify individuals with target QTL
- Crosses between different QTL targets
F2:3QTL validation population
Actions:
- Homozygous QTL
introgressions were identified
- Selectively advanced lines were
planted at 2 locations (Athens,
Tifton; 2 reps/location)
- HVI analysis and statistical
analysis

12. Results: populations
Table Gt-QTL x Gt-QTL crosses Table Gt-QTL x Gm-QTL crosses
Populations Year Background Specifics
a
Size
b
Pop. 01 2013 R01 Gt(14)xGm(25)xGb(01) 46
Pop. 01 2014 R01 Gt(14)xGm(25)xGb(01) 65
Pop. 02 2013 R01 Gt(14)xGm(11/21)xGb(01) 132
Pop. 03 2013 R01 Gt(14)xGm(01)xGb(01) 64
Pop. 03 2014 R01 Gt(14)xGm(01)xGb(01) 58
Pop. 04 2013 R01 Gt(07)xGm(25)xGb(01) 94
Pop. 05 2013 GA30 Gt(14)xGm(21) 62
Pop. 06 2014 GA30 Gt(21)xGm(25) 33
Pop. 07 2013 GA30 Gt(07)xGm(11/21) 105
Pop. 08 2014 GA30 Gt(14)xGm(01) 47
Pop. 09 2014 R01 Gt(07)xGm(11)xGb(01) 34
Pop. 10 2013 GA30 Gt(21)xGm(11) 57
Pop. 11 2013 R01 Gt(21)xGm(25) 75
Pop. 12 2013 R01 Gt(21)xGm(01) 47
Pop. 13 2013 R01 Gt(11)xGm(25) 62
Pop. 14 2013 R01 Gt(11)xGm(21) 33
Pop. 15 2013 GA30 Gt(11)xGm(25) 48
Pop. 16 2013 GA30 Gt(11)xGm(21) 69
Pop. 17 2014 R01 Gt(07)xGm(21) 36
Pop. 18 2013 R01 Gt(07)xGm(01) 96
Pop. 19 2013 GA30 Gt(07)xGm(01) 76
Pop. 20 2013 R01 Gt(11)xGm(01) 60
Pop. 21 2014 GA30 Gt(11)xGm(01) 110
Populations Year Background Specificsa
Sizeb
Pop. 01 2013 R01 Gt(11)xGt(14)xGb(01) 109
Pop. 02 2013 PM26 Gt(11)xGt(21) 98
Pop. 03 2013 GA30 Gt(11)xGt(14) 62
Pop. 04 2013 GA89 Gt(11)xGt(21) 73
Pop. 05 2013 GA30 Gt(11)xGt(21) 77
Pop. 06 2014 R01 Gt(11)xGt(21) 39
Pop. 07 2013 R01 Gt(14)xGt(21)xGb(01) 107
Pop. 08 2013 R01 Gt(07)xGt(14)xGb(01) 97
Pop. 09 2013 R01 Gt(07)xGt(11)xGb(01) 114
Pop. 10 2013 AC4 Gt(07)xGt(14) 68
Pop. 11 2013 GA30 Gt(07)xGt(11) 74
Pop. 12 2013 PM26 Gt(07)xGt(14) 114
Pop. 13 2014 GA30 Gt(07)xGt(21) 48
Pop. 14 2013 DP50 Gt(07)xGt(11) 93
Pop. 15 2014 GA30 Gt(14)xGt(21) 54
Pop. 16 2014 GA30 Gt(07)xGt(14) 33
Pop. 17 2014 GA89 Gt(07)xGt(14) 60
A total of 38 populations were studied for marker-trait
associations in F2 generation

13. Results: Gt-QTL x Gm-QTL
Figure 2. Distribution of micronaire, fiber strength, and fiber elongation in F2 populations. Distribution of
QTL-stacked F2 populations shown above x-axis, while corresponding distribution in control crosses (i.e.,
GA200230 x PD94042 and R01-40-08 x PD94042) juxtaposed below abscissa as inverted bar-charts.

14. Results: Gt-QTL x Gm-QTL
A synopsis of marker-trait association
Four Gm-QTLs
- Two Gm-QTLs (qELO-1-1 & qELO-11-1) - ‘reasonably’ stable - showed
significant QTL effects (increased elongation) in two elite backgrounds
- Gm-QTL qSTR-25-1: effect validated (increased strength) in one
population
- Gm-QTL qELO-21-1 did not show significant effects in segregating
populations
Four Gt-QTLs
- Gt-QTL qFF07.1: decreased fineness in two F2 populations and effect
validated (in F2/F2:3) in one population
- Gt-QTL qFE14.1 effect was also significant in one population
- Gt-QTLs qFE11.1 and qFE21.1 effects were not significant
G. tomentosum QTLs were ‘elusive’ and ‘erratic’

15. Results: Gt-QTL x Gm-QTL
Pop. 08 (2014) GA30 NAU2095c Gh/Gm 0.47 0.33 -0.69 0.001 0.25
Pop. 11 (2013) R01 NAU3074d Gh/Gt 0.14 0.19 -1.41 0.015 0.004 0.15
Fuzz color Gm -0.31 - - 0.013
Pop. 12 (2013) R01 NAU3731c§ Gh/Gt -0.25 0.04 0.15 0.001 0.27
Pop. 15 (2013) GA30 NAU1014d Gt/Gm 0.31 0.05 -0.17 0.007 <.001 0.28
Fuzz color Gm -0.58 - - 0.002
Pop. 18 (2013) R01 NAU2095c† Gh/Gm 0.19 0.00 0.01 0.006 0.12
Pop. 19 (2013) GA30 NAU2432c† Gh/Gt ‡ -0.20 -0.04 -0.19 0.013 0.14
Pop. 21 (2014) GA30 NAU1014d Gh/Gt -0.24 0.30 1.25 0.003 0.10
Fiber Pop. 02 (2013) R01 MUSS123c Gh/Gm 1.07 -0.13 -0.12 0.001 0.09
Strength NAU3377c Gh/Gm 1.43 0.22 0.15 <.001 0.15
(STR) NAU3341c Gh/Gm 1.08 0.00 0.00 <.001 0.10
Pop. 03 (2014) R01 NAU5027c Gh/Gt 0.84 0.14 0.17 0.003 <.001 0.25
NAU2095c Gh/Gm 0.77 -0.05 -0.06 0.004
Pop. 06 (2014) GA30 Fuzz color Gm 2.35 - - 0.006 0.19
Pop. 08 (2014) GA30 NAU2095c Gh/Gm 1.59 -1.36 -0.85 0.002 0.24
Pop. 09 (2014) R01 NAU3053c Gh/Gh 0.79 -2.33 -2.96 0.028 0.004 0.32
NAU3341c Gh/Gm 0.27 2.13 8.00 0.019
Pop. 13 (2013) R01 NAU2565 Gm -1.92 - - <.001 0.16
NAU2679 Gm -1.92 - - <.001 0.16
Fiber Pop. 01 (2014) R01 NAU1014d Gh/Gm 0.34 -0.07 -0.22 0.028 0.008 0.20
Elongation NAU5027c Gh/Gt -0.25 -0.23 0.90 0.030
(ELO) Pop. 02 (2013) R01 MUSS123c Gh/Gm -0.60 0.08 -0.13 <.001 0.19
NAU3377c Gh/Gm -0.67 0.04 -0.06 <.001 0.20
NAU3341c Gh/Gm -0.65 -0.12 0.18 <.001 0.25
Pop. 03 (2013) R01 NAU2095b Gm -0.47 - - 0.050 0.12
Pop. 08 (2014) GA30 NAU2095c Gh/Gm -0.27 0.23 -0.85 0.038 0.14
Pop. 09 (2014) R01 NAU3341c Gh/Gm -1.36 -0.36 0.26 0.002 0.30
NAU3377c† Gh/Gm -0.62 1.17 -1.89 0.036 0.23
MUSS123c† Gh/Gm -0.98 0.43 -0.43 0.013 0.29
Pop. 10 (2013) GA30 NAU3341c Gh/Gm -0.54 0.10 -0.19 <.001 0.22
MUSS123c† Gh/Gm -0.43 0.17 -0.39 0.005 0.21
Pop. 12 (2013) R01 NAU3731c† Gh/Gt 0.33 -0.05 -0.15 0.005 0.32
Pop. 18 (2013) R01 NAU2095c Gh/Gm -0.29 -0.07 0.25 0.011 <.001 0.16
NAU2432c Gh/Gt -0.29 -0.24 0.83 0.006
Pop. 21 (2014) GA30 NAU1014d Gh/Gt 0.15 0.38 2.52 0.019 0.008 0.11
NAU2095c Gh/Gm -0.28 0.02 -0.08 0.051
§ model is also significant when replaced with other diagnostic SSR mapped to the region
† significance reported for contrast between homozygous lines; ‡ Gh allele contributed by PD94042
Fiber elongation
- Gm-QTL qELO-11-1 effect was significant in 3 out of 4 F2 populations
QTL allele increased elongation (r2 = 28-29%)
- Major ‘stable’ QTL that transcends genetic backgrounds
a d d/a Marker Model
Micronaire Pop. 01 (2013) R01 Fuzz color Gm -0.54 - - <.001 0.23
(MIC) Pop. 01 (2014) R01 NAU1014d Gh/Gm 0.27 0.02 -0.08 0.018 0.009 0.19
NAU5027c Gh/Gt 0.13 -0.35 2.76 0.040
Pop. 04 (2013) R01 NAU2432c Gh/Gt -0.16 0.00 -0.03 0.034 <.001 0.16
NAU2238a§ Gm -0.31 - - 0.004
Fuzz color Gm -0.26 - - 0.006
Pop. 06 (2014) GA30 NAU3053c Gh/Gh 0.59 0.14 -0.24 0.004 0.26
Pop. 08 (2014) GA30 NAU2095c Gh/Gm 0.47 0.33 -0.69 0.001 0.25
Pop. 11 (2013) R01 NAU3074d Gh/Gt 0.14 0.19 -1.41 0.015 0.004 0.15
Fuzz color Gm -0.31 - - 0.013
Pop. 12 (2013) R01 NAU3731c§ Gh/Gt -0.25 0.04 0.15 0.001 0.27
Pop. 15 (2013) GA30 NAU1014d Gt/Gm 0.31 0.05 -0.17 0.007 <.001 0.28
Fuzz color Gm -0.58 - - 0.002
Pop. 18 (2013) R01 NAU2095c† Gh/Gm 0.19 0.00 0.01 0.006 0.12
Pop. 19 (2013) GA30 NAU2432c† Gh/Gt ‡ -0.20 -0.04 -0.19 0.013 0.14
Pop. 21 (2014) GA30 NAU1014d Gh/Gt -0.24 0.30 1.25 0.003 0.10
Fiber Pop. 02 (2013) R01 MUSS123c Gh/Gm 1.07 -0.13 -0.12 0.001 0.09
Strength NAU3377c Gh/Gm 1.43 0.22 0.15 <.001 0.15
(STR) NAU3341c Gh/Gm 1.08 0.00 0.00 <.001 0.10
Pop. 03 (2014) R01 NAU5027c Gh/Gt 0.84 0.14 0.17 0.003 <.001 0.25
NAU2095c Gh/Gm 0.77 -0.05 -0.06 0.004
Effect
P > FPopulation Background
Test of Significance
Trait
R
2Locus/interaction Source

16. Results: Gt-QTL x Gm-QTL
Fiber elongation
- Gm-QTL qELO-11-1 effect was significant in 3 out of 4 F2 populations
QTL allele increased elongation (r2 = 28-29%)
- Effect was validated in pop. 02 F2/F2:3 selection
Pop. 02 (R01 background)
Pop. 07 (GA230 background)
Pop. 10 (GA230 background)
Percent improvement
R01-40-08 PD94042
ELO qELO-11-1 234-138 7.60±0.79 28.6 34.3
233-165 7.56±0.78 27.9 33.6
Trait QTL Best lines Value
Best lines from pop. 02

17. Results: Gt-QTL x Gm-QTL
Pop. 08 (2014) GA30 NAU2095c Gh/Gm 0.47 0.33 -0.69 0.001 0.25
Pop. 11 (2013) R01 NAU3074d Gh/Gt 0.14 0.19 -1.41 0.015 0.004 0.15
Fuzz color Gm -0.31 - - 0.013
Pop. 12 (2013) R01 NAU3731c§ Gh/Gt -0.25 0.04 0.15 0.001 0.27
Pop. 15 (2013) GA30 NAU1014d Gt/Gm 0.31 0.05 -0.17 0.007 <.001 0.28
Fuzz color Gm -0.58 - - 0.002
Pop. 18 (2013) R01 NAU2095c† Gh/Gm 0.19 0.00 0.01 0.006 0.12
Pop. 19 (2013) GA30 NAU2432c† Gh/Gt ‡ -0.20 -0.04 -0.19 0.013 0.14
Pop. 21 (2014) GA30 NAU1014d Gh/Gt -0.24 0.30 1.25 0.003 0.10
Fiber Pop. 02 (2013) R01 MUSS123c Gh/Gm 1.07 -0.13 -0.12 0.001 0.09
Strength NAU3377c Gh/Gm 1.43 0.22 0.15 <.001 0.15
(STR) NAU3341c Gh/Gm 1.08 0.00 0.00 <.001 0.10
Pop. 03 (2014) R01 NAU5027c Gh/Gt 0.84 0.14 0.17 0.003 <.001 0.25
NAU2095c Gh/Gm 0.77 -0.05 -0.06 0.004
Pop. 06 (2014) GA30 Fuzz color Gm 2.35 - - 0.006 0.19
Pop. 08 (2014) GA30 NAU2095c Gh/Gm 1.59 -1.36 -0.85 0.002 0.24
Pop. 09 (2014) R01 NAU3053c Gh/Gh 0.79 -2.33 -2.96 0.028 0.004 0.32
NAU3341c Gh/Gm 0.27 2.13 8.00 0.019
Pop. 13 (2013) R01 NAU2565 Gm -1.92 - - <.001 0.16
NAU2679 Gm -1.92 - - <.001 0.16
Fiber Pop. 01 (2014) R01 NAU1014d Gh/Gm 0.34 -0.07 -0.22 0.028 0.008 0.20
Elongation NAU5027c Gh/Gt -0.25 -0.23 0.90 0.030
(ELO) Pop. 02 (2013) R01 MUSS123c Gh/Gm -0.60 0.08 -0.13 <.001 0.19
NAU3377c Gh/Gm -0.67 0.04 -0.06 <.001 0.20
NAU3341c Gh/Gm -0.65 -0.12 0.18 <.001 0.25
Pop. 03 (2013) R01 NAU2095b Gm -0.47 - - 0.050 0.12
Pop. 08 (2014) GA30 NAU2095c Gh/Gm -0.27 0.23 -0.85 0.038 0.14
Pop. 09 (2014) R01 NAU3341c Gh/Gm -1.36 -0.36 0.26 0.002 0.30
NAU3377c† Gh/Gm -0.62 1.17 -1.89 0.036 0.23
MUSS123c† Gh/Gm -0.98 0.43 -0.43 0.013 0.29
Pop. 10 (2013) GA30 NAU3341c Gh/Gm -0.54 0.10 -0.19 <.001 0.22
MUSS123c† Gh/Gm -0.43 0.17 -0.39 0.005 0.21
Pop. 12 (2013) R01 NAU3731c† Gh/Gt 0.33 -0.05 -0.15 0.005 0.32
Pop. 18 (2013) R01 NAU2095c Gh/Gm -0.29 -0.07 0.25 0.011 <.001 0.16
NAU2432c Gh/Gt -0.29 -0.24 0.83 0.006
Pop. 21 (2014) GA30 NAU1014d Gh/Gt 0.15 0.38 2.52 0.019 0.008 0.11
NAU2095c Gh/Gm -0.28 0.02 -0.08 0.051
§ model is also significant when replaced with other diagnostic SSR mapped to the region
† significance reported for contrast between homozygous lines; ‡ Gh allele contributed by PD94042
Fiber elongation
- Gm-QTL qELO-1-1 effect was significant in 4 out of 7 F2 populations
QTL allele increased elongation (r2 = 5-12%)
Minor effect QTL that transcends genetic backgrounds
a d d/a Marker Model
Micronaire Pop. 01 (2013) R01 Fuzz color Gm -0.54 - - <.001 0.23
(MIC) Pop. 01 (2014) R01 NAU1014d Gh/Gm 0.27 0.02 -0.08 0.018 0.009 0.19
NAU5027c Gh/Gt 0.13 -0.35 2.76 0.040
Pop. 04 (2013) R01 NAU2432c Gh/Gt -0.16 0.00 -0.03 0.034 <.001 0.16
NAU2238a§ Gm -0.31 - - 0.004
Fuzz color Gm -0.26 - - 0.006
Pop. 06 (2014) GA30 NAU3053c Gh/Gh 0.59 0.14 -0.24 0.004 0.26
Pop. 08 (2014) GA30 NAU2095c Gh/Gm 0.47 0.33 -0.69 0.001 0.25
Pop. 11 (2013) R01 NAU3074d Gh/Gt 0.14 0.19 -1.41 0.015 0.004 0.15
Fuzz color Gm -0.31 - - 0.013
Pop. 12 (2013) R01 NAU3731c§ Gh/Gt -0.25 0.04 0.15 0.001 0.27
Pop. 15 (2013) GA30 NAU1014d Gt/Gm 0.31 0.05 -0.17 0.007 <.001 0.28
Fuzz color Gm -0.58 - - 0.002
Pop. 18 (2013) R01 NAU2095c† Gh/Gm 0.19 0.00 0.01 0.006 0.12
Pop. 19 (2013) GA30 NAU2432c† Gh/Gt ‡ -0.20 -0.04 -0.19 0.013 0.14
Pop. 21 (2014) GA30 NAU1014d Gh/Gt -0.24 0.30 1.25 0.003 0.10
Fiber Pop. 02 (2013) R01 MUSS123c Gh/Gm 1.07 -0.13 -0.12 0.001 0.09
Strength NAU3377c Gh/Gm 1.43 0.22 0.15 <.001 0.15
(STR) NAU3341c Gh/Gm 1.08 0.00 0.00 <.001 0.10
Pop. 03 (2014) R01 NAU5027c Gh/Gt 0.84 0.14 0.17 0.003 <.001 0.25
NAU2095c Gh/Gm 0.77 -0.05 -0.06 0.004
Effect
P > FPopulation Background
Test of Significance
Trait
R
2Locus/interaction Source

18. Pop. 20 (R01 background)
Results: Gt-QTL x Gm-QTL
Fiber elongation
- Gm-QTL qELO-1-1 effect was significant in 4 out of 7 F2 populations
QTL allele increased elongation (r2 = 5-12%)
- Effect was validated in pop. 12, pop. 18 and pop. 20 F2/F2:3 selection
Pop. 12 (R01 background)
Pop. 18 (R01 background)
Pop. 19 (GA30 background)
R01-40-08 GA2004230 PD94042
ELO qELO-1-1 244-086 8.18±0.93 47.6 44.5
244-174 7.56±0.86 27.9 33.6
Trait QTL Best lines Value
Percent improvement

19. a d d/a Marker Model
Micronaire Pop. 01 (2013) R01 Fuzz color Gm -0.54 - - <.001 0.23
(MIC) Pop. 01 (2014) R01 NAU1014d Gh/Gm 0.27 0.02 -0.08 0.018 0.009 0.19
NAU5027c Gh/Gt 0.13 -0.35 2.76 0.040
Pop. 04 (2013) R01 NAU2432c Gh/Gt -0.16 0.00 -0.03 0.034 <.001 0.16
NAU2238a§ Gm -0.31 - - 0.004
Fuzz color Gm -0.26 - - 0.006
Pop. 06 (2014) GA30 NAU3053c Gh/Gh 0.59 0.14 -0.24 0.004 0.26
Pop. 08 (2014) GA30 NAU2095c Gh/Gm 0.47 0.33 -0.69 0.001 0.25
Pop. 11 (2013) R01 NAU3074d Gh/Gt 0.14 0.19 -1.41 0.015 0.004 0.15
Fuzz color Gm -0.31 - - 0.013
Pop. 12 (2013) R01 NAU3731c§ Gh/Gt -0.25 0.04 0.15 0.001 0.27
Pop. 15 (2013) GA30 NAU1014d Gt/Gm 0.31 0.05 -0.17 0.007 <.001 0.28
Fuzz color Gm -0.58 - - 0.002
Pop. 18 (2013) R01 NAU2095c† Gh/Gm 0.19 0.00 0.01 0.006 0.12
Pop. 19 (2013) GA30 NAU2432c† Gh/Gt ‡ -0.20 -0.04 -0.19 0.013 0.14
Pop. 21 (2014) GA30 NAU1014d Gh/Gt -0.24 0.30 1.25 0.003 0.10
Fiber Pop. 02 (2013) R01 MUSS123c Gh/Gm 1.07 -0.13 -0.12 0.001 0.09
Strength NAU3377c Gh/Gm 1.43 0.22 0.15 <.001 0.15
(STR) NAU3341c Gh/Gm 1.08 0.00 0.00 <.001 0.10
Pop. 03 (2014) R01 NAU5027c Gh/Gt 0.84 0.14 0.17 0.003 <.001 0.25
NAU2095c Gh/Gm 0.77 -0.05 -0.06 0.004
Pop. 06 (2014) GA30 Fuzz color Gm 2.35 - - 0.006 0.19
Effect
P > FPopulation Background
Test of Significance
Trait
R 2Locus/interaction Source
Results: Gt-QTL x Gm-QTL
Fiber fineness
- Green fuzz (chr. 11) linked to G. mustelinum introgression consistently
associated with fineness Fig. 6 Examples of green fuzz trait. Two F1s from a cross between Gto-QTL x Gm-QTL with characteristic green fuzz pheno

20. Results: Gt-QTL x Gm-QTL
Fiber fineness
- Green fuzz (chr. 11) linked to G. mustelinum introgression consistently
associated with fineness
- Represents phenotypic marker for trait improvement, but map distances
need to be calculated.
Fig. 6 Examples of green fuzz trait. Two F1s from a cross between Gto-QTL x Gm-QTL with characteristic green fuzz pheno
Green White Total
(prob > F) fuzz fuzz (prob > F)
MIC Fuzz color R01-40-08 327 <0.0001 Pop. 01 (013) 35 11 46 0.23 -0.54 0.0005
Pop. 01 (014) 41 8 50 0.08 -0.25 0.2396
Pop. 04 (013) 72 22 94 0.03 -0.26 0.0638
Pop. 11 (013) 50 23 75 0.08 -0.31 0.0074
Pop. 13 (013) 47 14 62 0.01 -0.22 0.1937
GA2004230 81 0.1352 Pop. 06 (014) 28 5 33 0.00 -0.22 0.4290
Pop. 15 (013) 40 8 48 0.14 -0.58 0.0048
Trait Marker
Within
family
(G)
Among
family (G)
Total
number
of plants
Background Population R
2
Diff.
Number of plants

21. Results: Gt-QTL x Gm-QTL
Effects of QTL allele stacking in F2/F2:3 pooled analysis
- decrease in fiber fineness in doubly homozygous lines of pop. 07 (5-11%)
and pop. 11 (16-24%) (compared to the parents)
3.00
3.50
4.00
4.50
5.00
5.50
6.00
6.50
AB BA BB Parentals
3.00
3.50
4.00
4.50
5.00
5.50
6.00
1 2 3 4 5 6
AC HN BN HC BC Parent
pop. 07
pop. 11

22. Results: Gt-QTL x Gm-QTL
Effects of QTL allele stacking in F2/F2:3 pooled analysis
- increase in fiber elongation in doubly homozygous lines of pop. 18 (22-
29%) and pop. 19 (36-48%) (compared to the parents)
5.00
5.50
6.00
6.50
7.00
7.50
8.00
8.50
9.00
9.50
pop. 18 and pop. 19
5.00
5.50
6.00
6.50
7.00
7.50
8.00
8.50
1 2 3 4 5 6 7AA AH HA HB BA BB Parent
pop. 02
5.00
5.50
6.00
6.50
7.00
7.50
1 2 3 4AC BN BC Parents
pop. 04
- Also in pop. 02, pop.
04 and pop. 05
5
5.5
6
6.5
7
7.5
1 2 3 4AB BA BB Parent
pop. 05

23. Results: Gt-QTL x Gt-QTL
Effects of allele stacking: two cases [pop. 10 (Acala SJ4) and pop. 16 (GA230)]
4.00
4.50
5.00
5.50
6.00
6.50
7.00
7.50
8.00
8.50
9.00
AA AH HA AB BA HH BH HB BB Parents
a. NAU2432-NAU5027
Fiberelongation(%)

24. 4.00
4.50
5.00
5.50
6.00
6.50
7.00
7.50
8.00
8.50
9.00
AA AB BA BB Parents
Results: Gt-QTL x Gt-QTL
Effects of allele stacking: validated in F2/F2:3 [pop. 10 (Acala SJ4)]
NAU2432-NAU5027
Fiberelongation(%)

25. Summary
- Two fiber elongation QTLs from G. mustelinum
(qELO-1-1 and qELO-11-1) were shown to be ‘stable’
- Another ‘stable’ QTL for fiber fineness was
associated with green fuzz trait
- G. tomentosum QTLs were ‘elusive’
- Effects of QTL stacking was evident in some cases.
The work goes on!!

26. Thank you
swicofil.com
cotton.org
Acknowledgement
Committee:
Andrew Paterson
Ali Missaoui
Brian Schwartz
Paul Schliekelman
Peng Chee
Cotton crew:
Jeevan Adhikari
Jinesh Patel
Rahul Chandnani
Zining Wang
Nino Brown
Sayan Das
Institutional resources:
Plant Genome Mapping Laboratory
Cotton Molecular Breeding Laboratory
Cotton Incorporated
University of Georgia