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)