Potato plastidic and nuclear DNA evolution and its relation to species evolution

1
Potato plastidic and nuclear DNA evolution and
its relation to species evolution

• Anandkumar Surendrarao
• VC221
• April 19, 2006

2
Evolutionary Pathway of T-type Chloroplast DNA in
Potato

• Am. J. Potato Res. (2004) 81 153-158
• Kazuyoshi Hosaka

Nuclear and chloroplast DNA differentiation in
Andean potatoes
Genome (2004) 47 46-56 Thitaporn Sukhotu, Osamu
Kamijima and Kazuyoshi Hosaka
3
(No Transcript)
4
Chloroplast DNA types

• 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)

5
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
6
Cultivated potato chloroplast DNA differs from
the wild type by one deletion Evidence and
Implications
Hosaka et al. (1988) TAG 75 741-745
7
Cultivated potato chloroplast DNA differs from
the wild type by one deletion Evidence and
Implications
Hosaka et al. (1988) TAG 75 741-745
8
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 may have
  evolved from S. tuberosum spp. andigena by just
  one physical deletion
• Assumptions
• Invoking maximum parsimony for Ct DNA evolution
• Ct DNA change exactly reflects species evolution.

Hosaka et al. (1988) TAG 75 741-745
9
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
10
Evolutionary Pathway of T-type Chloroplast DNA in
Potato

• American Journal of Potato Research (2004) 81
  153-158
• Kazuyoshi Hosaka

11
T-type Ct DNA occurance

• Existing 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

12
Ct-DNA type distributions in ancestral and
cultivated potato species
http//www2.kobe-u.ac.jp/hosaka/Res1.html
13
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

14
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.

15
Geographical cline of ctDNA
Hosaka and Hanneman. (1988) TAG 76 172-176
16
How did tuberosum arise from andigena?

• Hypotheses
• S.tarijense ssp.tuberosum
• S.tarijense ssp.andigena
  ssp.tuberosum
• ?S.tarijense S.stenotomum ?
  ssp.andigena
• 
  ssp.tuberosum
• 4. ?S.tarijense S.andigena ?

17
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

18
Hosakas 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?)

19
Ct-DNA type distributions in ancestral and
cultiated potato species
http//www2.kobe-u.ac.jp/hosaka/Res1.html
20
Evolution and historical migration route for
potato
http//www2.kobe-u.ac.jp/hosaka/Res1.html
21
Nuclear and chloroplast DNA differentiation in
Andean potatoes
Genome (2004) 47 46-56 Thitaporn Sukhotu, Osamu
Kamijima and Kazuyoshi Hosaka
22
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

23
Determination of Ct type, Ct DNA marker
haplotypes and nDNA marker haplotypes
24
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 1 T A
3 T S 3 W C 1
25
UPGMA dendrogram of Ct marker haplotypes

• 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

26
Ct type and Ct haplotype dendrogram

• 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)

27
Dendrogram of nDNA markers
1. Cluster 1 not resolved into sub-clades
compared to Ct-DNA haplotypes dendrogram 2. 111
polymorphic RFLP bands scored (9 unique bands) 3.
All except S.curtilobum can be distinguished
(avg. difference pf 24 bands) 4. ssp.
tuberosum 5As 1T and tbr3(T,6) with
adg26(C,3) and adg16(S,2 common in ancestral
cultivates species))

• edff

28
Correlation between distance matrices from
nuclear and Ct DNA differences

• ctDNA type versus ctDNA haplotype r0.822 ?
• nDNA RFLP versus ctDNA haplotype r 0.415 ?
• nDNA RFLP versus ctDNA type r 0.217 ?

29
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 Peru
• Group 2 Wild type species with W type CtDNA in
  Argentina and Bolivia

30
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)