potato plastidic and nuclear dna evolution and its relation to species evolution anandkumar...
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Potato plastidic and nuclear DNA evolution and its relation to
species evolution
Anandkumar Surendrarao
VC221
April 19, 2006
Evolutionary Pathway of T-type Chloroplast DNA in Potato
Am. J. Potato Res. (2004) 81: 153-158Kazuyoshi Hosaka
Nuclear and chloroplast DNA differentiation in Andean potatoes
Genome (2004) 47: 46-56Thitaporn Sukhotu, Osamu Kamijima and Kazuyoshi Hosaka
Molecular studies of chloroplast DNA (cpDNA) by restriction analysis in the different potato species (Hosaka et al 1984,1986, 2002) shed more light into the problem of the potato origin and evolution.
On the basis of 5 restriction endonucleases, 5 main chloroplast genomes were identified.
Recently AFLP for a 241bp deletion is verified by appropriate PCR primers, along with other Ct DNA markers viz., H2, H3, NTCP6, NTCP7, NTCP14, NTCP18 (Hosaka, 2003)
Chloroplast DNA types
Chloroplast DNA types
(W, W’, W”), C, S, A, T
ct DNA is derived maternally and
paternal contribution is zero or vanishingly small
The chloroplast DNA types were determined by RFLP analyses using 5 different restriction
enzymes
Cultivated potato chloroplast DNA differs from the wild type by one deletion – Evidence and Implications
Hosaka et al. (1988) TAG 75: 741-745
Cultivated potato chloroplast DNA differs from the wild type by one deletion – Evidence and Implications
Hosaka et al. (1988) TAG 75: 741-745
Conclusions from Hosaka et al., 1998
There is only one (not five as reported in Hosaka 1986) deletion detected between W type Ct DNA (predominantly found in wild ancestral species) and T type Ct DNA (predominantly found in cultivated European and common potato)
Therefore, S.tuberosum spp. tuberosum maymay have evolved from S. tuberosum spp. andigena by just one physical deletion
Assumptions:
1. Invoking maximum parsimony for Ct DNA evolution
2. Ct DNA change exactly reflects species evolution.
Hosaka et al. (1988) TAG 75: 741-745
Evolutionary origins of cultivated potato species?
S. tuberosum (4X)S.tuberosum ssp. tuberosum T type Ct DNA
S.tuberosum ssp. andigena A,S type Ct DNA
(Hosaka 1986; Hosaka et al, 1988)
S. stenotomum (2X)
Hosaka and Hanneman. (1988) TAG 76: 172-176
Evolutionary Pathway of T-type Chloroplast DNA in Potato
American Journal of Potato Research (2004) 81: 153-158Kazuyoshi Hosaka
T-type Ct DNA occuranceExisting data:
ssp. andigena accessions : 5 / 113 (N. Argentina and Chile)
ssp. stenotomum accessions: 1 / 54 (Bolivia)
Results from this paper (compliation of 529 accessions):
spp. goniocalyx – 0 / 11
spp. stenotomum – 0 / 204 (1 4X discarded)
spp. Andigena – 9 / 286
7 from NW Argentina, 1 – Chile, 1 - Ecuador
spp. tuberosum (Chilean) – 24 / 28
All Chilean
http://www2.kobe-u.ac.jp/~hosaka/Res1.html
Ct-DNA type distributions in ancestral and cultivated potato species
Experimental results
T-type CtDNA occurance
S.Stenotomum - 0 / 204
S. Goniocalyx – 0 / 11
S. Phureja – none (Hosaka and Hanneman, 1988)
S. Ajanhuiri – none (Sukhotu et al., 2004)
ONLY some S.tarijense populations have T-type Ct DNA. (2X, wild type species)
A few NW Argentine ssp. andigena have T-type Ct DNA
Most all Chilean ssp. tuberosum have T-type Ct DNA
S.tuberosum ssp. tuberosum likely arose from S.tuberosum ssp.andigena
Rationale:1 No 2X or 4X wild species in coastal Southern
Chile,2 Early European potato was actually short-day
ssp. andigena from which artificial is believed to have given ssp. tuberosum,
3 “Neo-tuberosum” has been experimentally selected for from ssp. andigena,
4 Geographical cline in the frequency of Ct DNA types from Northern Andes to Southern Chile supports this selection hypothesis.
Geographical cline of ctDNA
Hosaka and Hanneman. (1988) TAG 76: 172-176
How did tuberosum arise from andigena?
Hypotheses
1. S.tarijense ssp.tuberosum
2. S.tarijense ssp.andigena ssp.tuberosum
3. ♀S.tarijense × S.stenotomum ♂ ssp.andigena
ssp.tuberosum
4. ♀S.tarijense × S.andigena ♂
Which of the hypotheses is correct?
S.tarijense is very different from other ssp. tuberosum species morphologically and by using RFLP markers on nuclear DNA.
Therefore S.tarijense cannot be the direct ancestor to the Chilean tuberosum.
So hypothesis 1 and 2 cannot be true
If ♀S.tarijense × S.stenotomum ♂, S.stenotomum progeny with T-type Ct DNA is expected. But none was found in this study and others.
These two species do not have the same geographic range
So hypothesis 3 cannot be true
Hosaka’s hypothesis #4 for ssp.tuberosum evolution
(T-type Ct DNA) ♀ S.tarijense × S.andigena ♂ (A/S-type Ct DNA)
(overlapping gepgraphical range in NW Argentina)
S. tuberosum (T-type Ct DNA)
(Direct hybrid selected or introgressed further into ssp. andigena?)
Ct-DNA type distributions in ancestral and cultiated potato species
http://www2.kobe-u.ac.jp/~hosaka/Res1.html
Evolution and historical migration route for potato
http://www2.kobe-u.ac.jp/~hosaka/Res1.html
Nuclear and chloroplast DNA differentiation in Andean potatoes
Genome (2004) 47: 46-56Thitaporn Sukhotu, Osamu Kamijima and Kazuyoshi
Hosaka
Determination of Ct DNA-type, Ct DNA marker haplotypes and nDNA marker haplotypes
Cultivated species – 7
Accessions – 76
Putative ancestral wild type species – 8
Accessions – 17
Distantly related wild type species – 1 (S.chacoense)
Accessions – 2
Methodology:
Ct DNA type determination – RFLP (classical method)
Ct marker haplotype – AFLP marker set (microsatellites, H3)
nDNA haplotype – RFLP analyses followed by Southern
Determination of Ct type, Ct DNA marker haplotypes and nDNA marker haplotypes
Determination of haplotype: Ct DNA-type, Ct DNA markers and nDNA markers
Define steps required for change between any two Cp-DNA types
as the minimum number of steps required to change from one type to another.
For example,A – S : 2 W – A : 2 C – A : 1T – A : 3 T – S : 3 W – C: 1
7/25 haplotypes only in cultivated species
Haplotype 1- A type
Haplotype 2 - S type
Haplotype 6- T type
10 haplotypes – C type
12 haplotypes – W type
From dendrogram,
Group 1 – Types A, C, S
Group 2 – Types W
Group 3 – Types W , T
UPGMA dendrogram of Ct marker haplotypes
Based on dendrogram:
W gave rise to T and C independently
C gave rise to S and A independently
In agreement with Hosaka & Hanneman (1988)
Ct type and Ct haplotype dendrogram
edff
Dendrogram of nDNA markers
1. Cluster 1 not resolved into sub-clades compared to Ct-DNA haplotypes dendrogram2. 111 polymorphic RFLP bands scored (9 unique bands)3. All except S.curtilobum can be distinguished (avg. difference pf 24 bands) 4. ssp. tuberosum5A’s + 1T and tbr3(T,6) with adg26(C,3) and adg16(S,2 – common in ancestral cultivates species))
Correlation between distance matrices from nuclear and Ct DNA differences
ctDNA type versus ctDNA haplotyper=0.822
nDNA RFLP versus ctDNA haplotype r = 0.415
nDNA RFLP versus ctDNA type r = 0.217
Conclusions
From Ct type / haplotype dendrogram, T type arose within W type supporting evolution of ssp. tuberosum from S.tarijense
Lack of correlation between nDNA and Ct haplotype / type means frequent hybridizations occurred between cultivated species
nDNA RFLP haplotypes may help differentiate within ssp. tuberosum about evolutionary distances from ssp. Andigena
CtDNA and nDNA differentiated into two groups:Group1. With A, C and S type CtDNA in domesticated
species and their putative ancestral species in PeruGroup 2: Wild type species with W type CtDNA in Argentina
and Bolivia
Phylogenetic implications
None of the Andean cultivated species has an unique haplotype (either at CtDA or nDNA levels)
Therefore, a shared gene pool from the most ancestral cultivated species S. stenotomum contributed to the genetic diversity of all derived species.
Inference of the parents involved in hybridization to give rise to extant progeny can be made from combination of Ct DNA type / haplotypes and nDNA haplotype. Eg. S. chauca from andigena × stenotomum, but NOT S.sparsipilum or S.vernie ssp. andigena
Shared CtDNA types / haplotypes indicates successive domestication of species and parallel evolution of wild type species from the S.brevicaule super-species (S.canasense and S.leptophyes close to cultivated species based on nDNA RFLPs)