This document outlines Sameer Khanal's proposed research on dissecting quantitative variation in bermudagrass and upland cotton. For bermudagrass, the research involves developing EST-SSR markers to characterize genetic diversity, constructing genetic linkage maps, and performing QTL analysis of morphological traits. For upland cotton, the research aims to use QTL-stacked lines introgressed with favorable alleles from wild cotton species to dissect the genetic basis of fiber quality traits. The document provides background on the economic importance of bermudagrass and cotton, as well as prior research establishing genetic resources and QTL for the proposed studies.

1. Dissecting quantitative variation introgressed
into bermudagrass and Upland cotton
Sameer Khanal
Plant Genome Mapping Laboratory
Department of Crop and Soil Sciences
Picture source: google images
Doctoral Dissertation Defense
Dr. Andrew Paterson (Chair)
Dr. Ali Missaoui, Dr. Brian Schwartz,
Dr. Paul Schliekelman, Dr. Peng Chee
Advisory committee

2.  Dissecting quantitative variation in fiber quality traits using
QTL-stacked Gossypium hirsutum (Upland cotton) lines
Proposed research:
 Application of molecular markers in Cynodon spp.
(bermudagrass) for genetic diversity, linkage mapping and
QTL analyses

3. Introduction
Materials and Methods
Results/Discussion
Summary
Outline: bermudagrass
www.pixabay.comImage credits: seanheritage.com

4. Introduction: economy
www.abatti.com
• Most prominent pasture grass of
the south
• Lawn and sport turf, ground cover
• Turfgrass industry ~ $40 billion
Images.google

5. Introduction: taxonomy
Genus Cynodon
• Family of grasses (Poaceae);
subfamily: Chloridoideae
• Zoysia grass, finger millet and tef
• C4 photosynthetic pathway
• 8 perennial species
• Highly heterozygous and self
incompatible
www.abatti.comstaffordsod.comwww.wiki.org

6. Introduction: taxonomy
• A series of ploidy levels
(n = x = 9)
• Common bermudagrass
(C. dactylon) 2n = 4x = 36
• Leading turf varieties are
triploids
(C. dactylon x
transvaalensis)
www.abatti.comstaffordsod.comwww.wiki.org
A. Diploid B. Triploid C. Tetraploid
Source: Brillman (1978)

7. Introduction: genetic resources
 Single mapping population
 Pseudo-testcross scheme
Two parental maps:
T89 map:
155 single dose,17 double dose
35 linkage groups
T574 map:
77 single dose
18 linkage groups
C. dactylon acc. T89 x C. transvaalensis acc. T574
113 F1
Genetic material used to
construct the interspecific
genetic linkage map
(Bethel et al. 2006).
Single dose: Ao (simplex) x oo (nulliplex)
Ao : oo
(1:1)
Double dose: AAoo or Ao/Ao (duplex) x oo (nulliplex)
A/- : oo
(5:1 or 3:1)
Marker Classes
Genetic linkage map
Biparental: Ao (simplex) x Ao (simplex)
A/- : oo
(3:1)Genetic linkage maps need to be updated

8. Introduction: inheritance
Classical evidences (cytological, species distribution)
suggest autopolyploid origin of the tetraploid species
Molecular evidences:
 Marker segregation
- Harris et al. (2010) and Guo et al. (2015) : 14 and 13
codominant SSRs, alleles completely complementary
 Repulsion to coupling ratio
- Bethel et al. (2006): very few repulsion linkages;
suggestive of polysomic inheritance
Mode of inheritance needs further assessment

9. Introduction: comparative genomics
Chloridoids lag in genome evolution studies
Basic ancestral chromosome number of grasses was 7; after
WGD and two mergers, ancestral species had 12
chromosomes (Wang 2014)
Rice remains stable - zoysia grass and tef (x = 10), finger millet
and bermudagrass (x = 9)
Compared to rice, 12-to-10 chromosome reduction is understood
in zoysia grass and finger millet; two species share two
nested chromosome fusion (NCF) events
NCFs experienced by chloridoid common ancestor?

10. Introduction: DNA markers
 Paucity of DNA markers
 Bermudagrass sequences
- Kim et al. (2008): cDNA library
- Kamps et al. (2011): SSR enriched genomic library
- Tan et al. (2014): SSR enriched genomic library
 Already screened for SSR polymorphisms
Number of DNA markers need to be increased

11. Introduction: DNA markers
 Cultivar identification
- Clonal variants: mutants
- Contaminants: seeds, sprigs
 Linkage mapping and mode of
inheritance
 Genome evolution and
comparative analysis
 QTL and association mapping
gsrpdf.lib.msu.edu/

12. Research objectives: bermudagrass
• Objective:
- To develop and
characterize EST-SSR
markers
- To construct integrated
genetic linkage maps
- QTL analysis of turf
quality traits
plant-shed.com
 Application of
molecular markers in
Cynodon spp.
(bermudagrass) for
genetic diversity,
linkage mapping and
QTL analyses

13. Introduction
Materials and Methods
Results/Discussion
Summary
Materials and methods
www.pixabay.comImage credits: seanheritage.com

14. Project outline: bermudagrass
Phase I (diversity): Cross-taxon application of sugarcane EST-
SSRs to characterize bermudagrass accessions
- DNA markers
- Molecular diversity
Phase II (linkage): Building an integrated genetic linkage map of
bermudagrass (C. dactylon x transvaalenesis)
- Genetic linkage map
- Comparative mapping
- Mode of inheritance
Phase III (QTL mapping): QTL mapping of morphological traits
- Height, Internode length, length of longest stolon
- Leaf length and width

15. Project outline: diversity
Phase I: Cross-taxon application of sugarcane EST-
SSRs to characterize bermudagrass accessions
Marker resource:
- Preexisting sugarcane
EST- SSRs (~ 2,000)
- Miscanthus and Sorghum
Plant materials:
- 2 parents (T89 and T574)
- 10 varieties (Tif series)
- 2 Sorghum spp.
- 10 F1s
Accession Epithet Ploidy
T574 C. transvaalensis Burtt-Davy 2n = 2x = 18
Tifway C. transvaalensis x C. dactylon 2n = 3x = 27
Tifway II C. transvaalensis x C. dactylon 2n = 3x = 27
Tifgreen C. dactylon x C. transvaalensis 2n = 3x = 27
Tifgreen II C. dactylon x C. transvaalensis 2n = 3x = 27
Tifdwarf C. dactylon x C. transvaalensis 2n = 3x = 27
TifEagle C. dactylon x C. transvaalensis 2n = 3x = 27
TifGrand C. transvaalensis x C. dactylon 2n = 3x = 27
Tifsport C. transvaalensis x C. dactylon 2n = 3x = 27
T89 C. dactylon (L.) Pers. 2n = 4x = 36
Tiflawn C. dactylon x C. dactylon 2n = 4x = 36
Tifton 10 C. dactylon 2n = 6x = 54
F1-1 to F1-10 C. dactylon x C. transvaalensis 2n = 3x = 27
BTx623 Sorghum bicolor (L.) Moench. 2n = 2x = 20
Gypsum-9E S. halepense (L.) Pers. 2n = 4x = 40

16. Project outline: diversity
Phase I: Cross-taxon application of sugarcane EST-
SSRs to characterize bermudagrass accessions
- Additional 7 varieties
- TifTuf: promising recent
release from Tifton
- 5 varieties from
OSU breeding program
- Three experimental lines
from UGA breeding
program
Accession Epithet Ploidy
TifTuf C. dactylon x C. transvaalensis 2n = 3x = 27
Latitude 36 C. dactylon x C. transvaalensis 2n = 3x = 27
Northbridge C. dactylon x C. transvaalensis 2n = 3x = 27
Patriot C. dactylon x C. transvaalensis 2n = 4x = 36
Premier C. dactylon x C. transvaalensis? --
Discovery C. dactylon 2n = 4x = 36
Celebration C. dactylon 2n = 4x = 36
UGB-70 Experimental line --
11-T-56 Experimental line --
09-T-31 Experimental line --

17. Project outline: linkage
Phase II: Building genetic linkage map of
bermudagrass (C. dactylon x transvaalenesis)
C. dactylon acc. T89 x C. transvaalensis acc. T574
F1
(Bethel et al. 2006, Harris et
al. 2010a, 2010b)
Genetic linkage mapMapping population:
- 102 F1s
Marker resource:
~300 Phase I selections
Software tool:
- OneMap (R package)
- TetraploidMap

18. Project outline: QTL mapping
Phase III: QTL mapping of morphological traits
Phenotypic data (Griffin and Tifton):
- Canopy height (seven times, 2010-2012)
- Internode length (four times, 2011-2012)
- Length of the longest stolon (four times, 2010)
- Leaf length (twice, 2012)
- Leaf width (thrice, 2011-2012)
Software tools:
- Single marker analysis, Interval mapping (QTL
Cartographer/QTL network)

19. Introduction
Materials and Methods
Results/Discussion
Summary
Results and discussion
www.pixabay.comImage credits: seanheritage.com

20. Results: diversity
Phase I: Cross-taxon application of sugarcane EST-
SSRs to characterize bermudagrass accessions
Manuscript (published):
Khanal S, Schwartz BM, Kim C, Adhikari J, Rainville LK, Auckland SA, Paterson AH
(2017) Cross-taxon application of sugarcane EST-SSR to genetic diversity analysis of
bermudagrass (Cynodon spp.). Genet Resour Crop Evol 64(8):2059-2070
doi: 10.1007/s10722-017-0496-2

21. Results: linkage
Phase II: Building an integrated genetic linkage map of
bermudagrass (C. dactylon x C. transvaalenesis)
Manuscript (published):
Khanal S, Kim C, Auckland SA, Rainville LK, Adhikari J, Schwartz BM, Paterson AH
(2017) SSR-enriched genetic linkage maps of bermudagrass (Cynodon dactylon x
transvaalensis), and their comparison with allied plant genomes. Theor Appl Genet
130(4):119-139
doi: 10.1007/x00122-017-2854-z

22. Phase III: QTL mapping of bermudagrass
morphological traits
Results: QTL
Manuscript (to be submitted):
Khanal S, Dunne JC, Schwartz BM, Kim C, Milla-Lewis S, Raymer PL, Adhikari J,
Auckland SA, Rainville L, Paterson AH. Molecular dissection of quantitative variation
in bermudagrass hybrids (Cynodon dactylon x transvaalensis): morphological traits (to
be submitted to G3: Genes | Genomes | Genetics)

23. Introduction
Materials and Methods
Results/Discussion
Summary
Summary: bermudagrass
www.pixabay.comImage credits: seanheritage.com

24. Summary: bermudagrass
- Diversity manuscript: reported the development
and characterization of hundreds of SSR markers
useful for bermudagrass breeding and genetic
studies
- Linkage manuscript: reported the construction of
SSR-enriched linkage maps, performed
comparative mapping, and proposed mode of
inheritance in the tetraploid species
- QTL manuscript: reported early QTL study on
bermudagrass morphological traits

25.  Dissecting quantitative variation in fiber quality traits using
QTL-stacked Gossypium hirsutum (Upland cotton) lines
Proposed research:
 Application of molecular markers in Cynodon spp.
(bermudagrass) for genetic diversity, linkage mapping and
QTL analyses

26. Outline: cotton
Introduction
Materials and Methods
Results/Discussion
Summary
www.pixabay.comImage credits: seanheritage.com

27. Data source: USDA-NASS, 2014, Image source: cotton.org
Introduction: cotton economy
• 9-12 million acres
• 4th biggest crop
• $6 billion industry
• $3 billion from export

28. Introduction: cotton economy
200
0
1200
1000
800
600
400
1600
1400
2006 2007 2008 2009 2010 2011
Area planted (in thousand acres)
georgiaagforecast.com
Cotton
Peanut
Corn
SoybeanWheat
Georgia

29. Introduction: New World cotton
 Upland Cotton:
G. hirsutum
 Pima/Egyptian:
G. barbadense
flickr.combotanicalgarden.ubc.ca

30. Introduction: cotton types
EasternAcala DeltaPlains
cotton.org
Pima
Upland cotton:Pima/Egyptian cotton:

31. Introduction: fiber quality traits
Recent interest in fiber quality
influenced by:
evolution of efficient spinning
technologies
competition from synthetic fibers
increased demand for quality fibers
better price premium

32. Introduction: instrument
uster.com
High volume instrument
-Fiber fineness, length, elongation, strength

33. Introduction: favorable alleles
 Gossypium tomentosum (Gto)
- Endemic to Hawaiian islands
 Gossypium mustelinum (Gm)
- Endemic to Brazil
flickr.com
luirig.altervista.org/
128.192.141.98/CottonFiber/pages/phylogeny/genomeEvo.aspx

34. Introduction: Gto- and Gm-QTLs
G. tomentosum Maps G. mustelinum Maps
Genetic material used to detect
QTL alleles for improved fiber
quality traits (Wang et al.
2017)

35. Introduction: Gto-QTLs
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

36. Introduction: Gm-QTLs
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)

37. Gto- and Gm-QTL synopsis
- Favorable alleles were recovered from seemingly
unfavorable parents and at QTL hotspots
- Majority of favorable alleles for fiber elongation and
fiber fineness were contributed by Gto or Gm
- Targeted selection for elongation and fineness do
not have a long breeding history
- Some elongation QTLs mapped at same
chromosomal regions in both populations

38. Proposed research: cotton
 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

39. Materials and methods
Introduction
Materials and Methods
Results/Discussion
Summary
www.pixabay.comImage credits: seanheritage.com

40. Project outline
Phase I: Introducing Gto-QTL from advanced-
backcross populations to different G. hirsutum
genetic backgrounds
Phase II: Stacking Gto- and Gm-QTL in six different
genetic backgrounds of G. hirsutum
Phase III: Identifying QTL stacked lines, targeted
genotyping, and analyzing marker-trait
associations in QTL-stacked F2 populations
Phase IV: Validating QTL effects by phenotyping F2:3
progenies of QTL-stacked selections for fiber
quality traits

41. 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 (also carries a fiber length QTL)
4. GA2004089
5. Paymaster HS26
6. Acala SJ-4
Actions:
- Four QTL regions were
tagged with SSR markers
(Fall 2011)
- BC3F3 lines screened for
target QTLs (Spring 2012)
- Gto-QTL x Elite crosses were
made
(Spring 2012)
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 QTL targets
List Elite lines

42. 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
(Summer 2012)
- BC3F3 (Gm selections) were
also genotyped for target
QTLs (Summer 2012)
- Gto- x Gto-QTL crosses were
made in all combinations
- Gto- x Gm-QTL crosses were
made in all combinations
- All crosses were made in the
field (Summer 2012)
(QTL target B)

43. 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 (Winter 2012)
- QTL stacked lines were selfed
to constitute QTL mapping
populations (Spring 2013)

44. Phase III: Identifying QTL stacked lines, targeted
genotyping, and analyzing marker-trait associations
in QTL-stacked F2 populations
Project outline: populations
Gt-QTL x Gt-QTL selections
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

45. Phase III: Identifying QTL stacked lines, targeted
genotyping, and analyzing marker-trait associations
in QTL-stacked F2 populations
Project outline: populations
Gt-QTL x Gm-QTL selections
Control crosses:
GA2004230 X PD94042
R01-40-08 X PD94042
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

46. Phase III: Identifying QTL stacked lines, targeted
genotyping, and analyzing marker-trait associations
in QTL-stacked F2 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
Project outline: populations
Actions:
- Mapping populations were
planted at Watkinsville Plant
Science farm (Summer 2013)
- DNA extraction, harvesting
(Fall 2013)
- HVI analysis and genotyping
was done (Spring 2014)

47. 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
(Spring 2014)
- Selectively advanced lines were
planted at 2 locations (Athens,
Tifton; 2 reps/location) (Summer
2014)
- Harvesting (Winter 2014)
- HVI analysis (Spring 2015)

48. Results and discussion
Introduction
Materials and Methods
Results/Discussion
Summary
www.pixabay.comImage credits: seanheritage.com

49. Results: Gt-QTL x Gm-QTL
Gt-QTL x Gm-QTL dissertation chapter:
Manuscript (under preparation):
Khanal S, Patel JD, Adhikari J, Chandnani R, Wang Z, Das S, Brown N, Jones D,
Chee PW, Paterson AH. Dissecting quantitative variation introgressed into Upland
cotton (G. hirsutum L.) using QTL-stacked segregating populations (to be submitted)

50. Results: Gt-QTL x Gt-QTL
Gt-QTL x Gt-QTL dissertation chapter:
Manuscript (under preparation):
Khanal S, Patel JD, Adhikari J, Chandnani R, Wang Z, Das S, Brown N, Jones D,
Chee PW, Paterson AH. Dissecting biometric parameters of fiber quality variation
using Gossypium tomentosum introgressions stacked in Upland cotton (to be
submitted)

51. Summary: cotton
Introduction
Materials and Methods
Results/Discussion
Summary
www.pixabay.comImage credits: seanheritage.com

52. Summary: cotton
- Development and characterization of multi-species
QTL stacks and phenotypically superior lines
- A total of 38 early generation QTL-stacked
populations were studied
- 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
- Two fiber elongation QTLs and one fiber fineness QTL
were associated with G. tomentosum introgressions at
chr. 7, chr. 14 and chr. 11, respectively
- Valuable resource for marker-assisted breeding in
cultivar development

53. 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 Incorporated
University of Georgia