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: Kazuyoshi Hosaka Nuclear and chloroplast DNA differentiation in Andean potatoes Genome (2004) 47: Thitaporn 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

(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:

Cultivated potato chloroplast DNA differs from the wild type by one deletion – Evidence and Implications Hosaka et al. (1988) TAG 75:

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) may Therefore, S.tuberosum spp. tuberosum may 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:

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:

Evolutionary Pathway of T-type Chloroplast DNA in Potato American Journal of Potato Research (2004) 81: Kazuyoshi Hosaka

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 / from NW Argentina, 1 – Chile, 1 - Ecuador spp. tuberosum (Chilean) – 24 / 28 All Chilean

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:

How did tuberosum arise from andigena? Hypotheses 1.S.tarijensessp.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

Evolution and historical migration route for potato

Nuclear and chloroplast DNA differentiation in Andean potatoes Genome (2004) 47: Thitaporn 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 : 2W – A : 2C – A : 1 T – A : 3 T – S : 3W – 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 dendrogram polymorphic RFLP bands scored (9 unique bands) 3. All except S.curtilobum can be distinguished (avg. difference pf 24 bands) 4. ssp. tuberosum 5A’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 haplotyper =  nDNA RFLP versus ctDNA typer = 

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

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)