Using SNP haplotypes to study gene flow in a P. vulgaris wild-weedy-crop complex
from Colombia: A pilot study
C. Quintero1, R.I González-Torres1, E. Gaitán-Solís2; R. Hidalgo4, O. Toro3, D.G Debouck3 and J. Tohme1
1CIAT, Biotechnology Research Unit, AA6713, Cali, Colombia; 2 Donald Danforth Plant Science Center, Missouri, USA;
3CIAT, Genetic Resources Unit, Cali, Colombia; Universidad Nacional de Colombia, Palmira, Colombia
INTRODUCTION SNP haplotypes frequency in the complex
The study of “wild-weedy-crop” complexes along common bean range of Differences between haplotype frequencies allowed the identification of those
distribution in the Americas has shown no preferential gene flow direction in haplotypes that described better each of the parental biological forms. In most
Colombia, Ecuador and Peru (Chacón et al, 2006). We conducted a pilot study cases, haplotypes were classified as wild types when their frequency was at least
in the wild-weedy-crop complex G50879 from Colombia (19, wild; 32 weedy twice the observed in cultivated forms, and vice versa.
and 34 cultivated), previously evaluated with biochemical markers and SSRs, 100
to test the potential of nuclear SNP markers as an alternate tool for the 80 C Wild Weedy Cultivated Block 1, B01
PIC = 0.70
identification of gene flow events and inference about their direction. 60
40
W W
W
MATERIALS 20
0
C W C
A B C D E F G H
Frequency (%)
100
Wild-weedy crop complex G50879 80
Block 2, B01
PIC = 0.76
Seed from the original collection sorrounded by wild, weedy and cultivated forms. 60
C W
40
C Wee W C
20
W C C W C C
Chloroplast haplotypes and SSR most W 0
C
frequent alleles were shared between C 100
A B C D E F G H I J K L
Block 1, B07
wild and cultivated types 80
PIC = 0.73
C C
C 60
W
40
No clear discrimination between
20
W C W
biological forms at the DNA level could 0
C C
be observed Wee A B C D E F G H I J K
C Haplotype variant
No gene flow direction could be C
determined
C Admixture model
Wee Wee Parental truly-wild and truly-cultivated populations were selected based on the
coincidence of their phenotype with their genotype (SNP haplotypes). After
METHODS admixture events, they could give rise to three hybrid subpopulations in this wild-
•Haplotype analysis weedy-crop complex.
SNP Genotyping: (HAP software)
DNA Parental Parental
20 SNPs in linkage groups
extraction •Admixture analysis “Truly” Wild “Truly”cultivated
B01 and B07
(ADMIX 1.0)
Admixture events
RESULTS AND DISCUSSION
SNP genotyping:
Simultaneous genotyping up to 15 alleles in one single base extension reaction was
Wild
achieved using a Luminex100 flow cytometer equipped with a Luminex XY Platform “hybrid”
Weedy
“hybrid” Cultivated
plate reader (Quintero et al., 2005). “hybrid”
Wild SNP Haplotype
A Cultivated SNP Haplotype
Mean Fluorescence Intensity
A A A A A Allele ‘A’
2,000 A
1,500 A A A
1,000 A A more accurate estimation of admixture coefficients (S.D. values close to zero) in
500
0 the hybrid subpopulations was calculated.
464 938 526 691 976 709 791 793 799 858 893 497 523 527 578
G
Allele ‘G’ G
1,200
1,000 Cultivated (hybrid)
800 G
600
400 G Mw SD Mc SD Mc/Mw Gene flow
200
0
464 938 526 691 976 709 791 793 799 858 893 497 523 527 578
0,3237 0,0501 0,6766 0,0495 2,1 C W
SNP ID
Weedy
Haplotype inference: Mw SD Mc SD Mc/Mw Gene flow
Block partition and haplotype prediction within each block was done using HAP
0,4458 0,0436 0,5518 0,043 1,2 C W
software (Halperin and Eskin, 2004). Both linkage groups were divided in three
blocks of limited diversity. 43 SNP haplotypes were observed in the wild-weedy- Wild (hybrid)
crop complex: 84% in weedy forms, 77% in cultivated forms and 70% wild forms. Mw SD Mc SD Mc/Mw Gene flow
Linkage group B01
0,4669 0,055 0,5281 0,0588 1,1 C W
Block SNPs (#) Haplotypes (#) PIC
1 3 8 0,702
2 5 12 0,756 In the weedy and wild-hybrid subpopulations, the contribution of truly-cultivated was
3 2 4 0,310 slightly higher than that of truly-wild meaning that both gene flow directions are
Linkage Group B07
possible and almost symmetric. For the cultivated-hybrid, the contribution of truly-
cultivated was twice that of the truly-wild, suggesting more pollen flow from the
Block SNPs (#) Haplotypes (#) PIC
cultivated types. Although we have looked only at one wild-weedy-crop complex
1 6 11 0,731
2 3 6 0,498 from Colombia our results show that SNP haplotypes are informative enough to
3 1 2 0,288 provide evidence about gene flow dynamics in P. vulgaris.
Initial admixture analysis REFERENCES
The admixture coefficient MY (Bertorelle & Excoffier, 1998) was calculated, based Bertorelle G, Excoffier L. 1998. Molecular Biology and Evolution. 15:1298-1311.
on haplotype frequencies and the molecular distances between them. Chacón, M.I. González-Torres, R.I. & D. G. Debouck. 2006. Council of Science. CIAT. 2006.
Halperin E. and E. Eskin. 2004. Bioinformatics. 20(12):1842-9.
SNP haplotype Quintero, C., E. Gaitán-Solís, C. Quigley, P. Cregan, M.C. Duque and J. Tohme. 2005. Annual
MW1 S.D.2 distribution within and Report SB02-Project. 21-23p.
0.58 0.12 between biological forms
Too high Parental Wild and Cultivated ACKNOWLEDGEMENTS
MC 3 S.D. S.D. values to be re-defined
Blocks with PIC≥0.7: Special thanks go to Drs Perry Cregan and Charles Quigley (Soybean Genomics Lab-USDA)
0.42 0.16
1 y 2 in B01; who kindly shared with us the information and primers of the soybean SNPs they discovered.
1M
1 in B07 To the “Ginés-Mera memorial fellowship fund for postgraduate studies in biodiversity” for partial
W: relative contribution from the wild parental population
2S.D: Standard deviation based on 1000 resampling events. funding of this research and to Myriam C. Duque for helpul comments.
3M
C: relative contribution from the cultivated parental population