This document summarizes three research projects that aim to utilize the genetic resources of Helianthus niveus subsp. tephrodes (Algodones dune sunflower) for the improvement of cultivated sunflower. Project 1 involves comparative genetic mapping between H. niveus and cultivated sunflower to understand chromosomal rearrangements. Project 2 analyzes phylogeographic diversity in H. niveus and develops populations for association mapping. Project 3 develops introgression lines through backcrossing to transfer traits from H. niveus into cultivated sunflower for QTL analysis. Initial crosses between the species showed low fertility requiring alternative approaches like embryo rescue and backcrossing over multiple generations.

1. Recruiting Algodones Dune
Sunflowers for Genetic Improvement
of Cultivated Sunflower
Sameer Khanal
MS, UGA

2. Importance of wild Helianthus species
Crop production and extensive cultivation:
Resistance to several biotic and abiotic stresses
Extending crop to marginal environments
Broadening germplasm base:
Crop security from epiphytotics
Crop stability and sustainable production
Novel traits of interest:
Male sterility and restoration genes
Oil quality traits
Biomass traits

3. Phylogenetic Relationship Among Helianthus
species
Rieseber et al. 1991. Sys. Bot.Source: Wikipedia
H. niveus subsp. tephrodes

4. Helianthus niveus subsp. tephrodes
Mostly obligate perennial psammophiles
(plants restricted to active dunes)
Is a “rare” species, some 12 ecotypes are
collected at NPGS, USA
Are potential sources of novel traits in
cultivated sunflower:
- Drought tolerance
- Biomass traits
Most primitive within the genus (represents
ancestral karyotype?)1
1. Heiser et al. 1965

5. Research Projects
1. Macrosynteny between the common and Algodones dune sunflower genomes
2. Phylogeographic diversity and association mapping in Algodones dune sunflower
3. Development and genetic analysis of Algodones dune sunflower Introgression Lines

6. 1. Macrosynteny Between the Common and
Algodones Dune Sunflower Genomes
Rationale
1.Dune sunflowers are untapped genetic
resources
- Drought and stress
resistance
- Novel alleles
2. Introgressive hybridization is
desirable
3. Karyotipic differences ensure
reproductive barriers among species
2.Rates of chromosomal rearrangements are
very high in genus Helianthus1
Long-term goals
1.Understand chromosomal
rearrangements between common
sunflower (H. annuus) and dune
sunflower (H. niveus ssp. tephrodes)
2.Assess and predict the effects of such
differences on the transmission of
alleles across the species barrier
1. Burke et al. 2004, Genetics

7. 1. Macrosynteny Between the Common and
Algodones Dune Sunflower Genomes
Specific Objectives
1.1. Develop “intraspecific” mapping
population
1.2. Comparative genetic mapping
Synteny
Chromosomal rearrangements
Deletions and duplications
1.3. QTL mapping in an “interspecific”
hybrid population
Hybrid fertility
Flowering time
1.4. Molecular cytogenetics

8. 1. Macrosynteny Between the Common and
Algodones Dune Sunflower Genomes
Methods and Approaches
Develop “interspecific” hybrid population
for “intraspecific” genetic mapping
NIV-E NIV-L
NIV-E NIV-LXNMS373
(NIV-E NIV-L)XXNMS373
Status
About 30 seeds from NIV-1243 (NIV-E,
ultra-early) X Ames 27830 (NIV-L, ultra-
late) ecotypes
2 out of 22 seeds produced apparently
healthy seedlings

9. 1. Macrosynteny Between the Common and
Algodones Dune Sunflower Genomes
Methods and Approaches
Comparative genetic and QTL mapping
Status
Illumina GoldenGate SNP genotyping
arrays are underway
NIV-E NIV-L (NIV-E NIV-L)XNMS373
(NIV-E NIV-L)XXNMS373
SNP screening using the arrays:
SNP genotyping:
(NIV-E NIV-L)XXNMS373Phenotyping:
2. Screening 1,536 SNPs in the mapping population
1. SNP screening against mapping population parents
3. Phenotyping population for hybrid fertility and flowering time

10. 2. Phylogeographic Diversity and Association
Mapping in Algodones Dune Sunflower
Rationale
1.Relatively obscure species, biodiversity is not
known
2.From molecular prospective, it’s almost a
“pristine “species
Long-term goals
1.Understand phylogeographic and
genetic diversity in H. niveus ssp.
tephrodes
2.Assess the allelic diversity within this
species relative to domesticated and
wild H. annuus
3.Develop test cross hybrids for
association mapping

11. 2. Phylogeographic Diversity and Association
Mapping in Algodones Dune Sunflower
Specific Objectives
2.1. Phylogeographic diversity and
population structure
2.2. Developing testcross hybrids
Status
2.3. Association mapping

12. 2. Phylogeographic Diversity and Association
Mapping in Algodones Dune Sunflower
Methods and Approaches
Phylogeographic diversity and population
structure
Procure all 10 ecotypes
Genotype 10 individuals/ecotype
Status

13. 2. Phylogeographic Diversity and Association
Mapping in Algodones Dune Sunflower
Methods and Approaches
Developing testcross hybrid for
association mapping
Crossing 10 ecotypes x CMS-
HA412-HO (or a NMS line)
Association mapping
Phenotype F1 for lignocellulosic
biomass and flowering time traits

14. 3. Development and Genetic Analysis of
Algodones Dune Sunflower Introgression Lines
Specific Objectives
3.1. Develop backcross and advanced
populations from an interspecies
3.2. QTL analysis of biologically and
economically important traits
3.3. Develop a genome-wide introgression
library
3.4. Complete genetic analysis of the
introgression library
Status
About 400 seeds from NMS-373 (early,
male sterile) X Ames 27830 (ultra-late,
male fertile)
F1 showed irregular meiotic behavior

15. 3. Development and Genetic Analysis of
Algodones Dune Sunflower Introgression Lines
Autosyndesis
Heteromorphism

16. 3. Development and Genetic Analysis of
Algodones Dune Sunflower Introgression Lines
Specific Objectives
3.1. Develop backcross and advanced
populations from an interspecies
3.2. QTL analysis of biologically and
economically important traits
3.3. Develop a genome-wide introgression
library
3.4. Complete genetic analysis of the
introgression library
Status
420 seeds from NMS-373 (early, male
sterile) X Ames 27830 (ultra-late, male
fertile)
F1 showed highly irregular meiotic
behavior
Pollen fertility was extremely low (2%)

17. 3. Development and Genetic Analysis of
Algodones Dune Sunflower Introgression Lines

18. 3. Development and Genetic Analysis of
Algodones Dune Sunflower Introgression Lines
Specific Objectives
3.1. Develop backcross and advanced
populations from an interspecies
3.2. QTL analysis of a range of biologically
and economically important traits
3.3. Develop a genome-wide introgression
library
3.4. Complete genetic analysis of the
introgression library
Status
420 seeds from NMS-373 (early, male
sterile) X Ames 27830 (ultra-late, male
fertile)
F1 showed highly irregular meiotic
behavior
Pollen fertility was extremely low (2%)
First initial crosses were unsuccessful

19. 3. Development and Genetic Analysis of
Algodones Dune Sunflower Introgression Lines
Studies: Interspecies between H. annuus and H. niveus ssp. tephrodes
1.Chandler (1986)
Used late flowering accession
Pollen viability of F1 around 3.3% (max. 7.3%)
2.Barros (2004)
Used an early flowering accession
Pollen viability of F1 around 1.98
Used embryo rescue
Pollen viability of BC1 around 36.9
Backcross first is extremely difficult

20. 3. Development and Genetic Analysis of
Algodones Dune Sunflower Introgression Lines
Helianthus annuus
(NMS373)
Helianthus niveus ssp. tephrodes
NIV-L (PI 650020)
NMS373 x NIV-L
F1
NMS373
NMS373 X BC1-1 NMS373 X BC1-2 NMS373 X BC1-n
X
X
BC2-1-1 BC2-1-2 BC2-1-n BC2-2-1 BC2-2-2 BC2-2-n BC2-n-1 BC2-n-2 BC2-n-n
BC2-1-/S1 BC2-2-/S1 BC2-n-/S1
BC3-1--S1 BC3-2--S1 BC3-n--S1
NMS373 X BC2-1-/S1 NMS373 X BC2-2-/S1 NMS373 X BC2-n-/S1
Parents
Backcrossing F1
Backcrossing BC1
Individual BC2 Families
Selfing BC2
Genetic Analysis and Selection
BC3-1--S2 BC3-2—S2 BC3-n—S2
Backcrossing and
Selfing BC2
MethodsandApproaches

21. Thank You