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Flor Rodriguez' presentation in the framework of the expert consultation on the use of crop wild relatives for pre-breeding in potato
 

Flor Rodriguez' presentation in the framework of the expert consultation on the use of crop wild relatives for pre-breeding in potato

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The expert consultation on the use of crop wild relatives for pre-breeding in potato was a workshop organized by the Global Crop Diversity Trust in collaboration with CIP and took place from the 22nd ...

The expert consultation on the use of crop wild relatives for pre-breeding in potato was a workshop organized by the Global Crop Diversity Trust in collaboration with CIP and took place from the 22nd – 24th of February 2012.

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    Flor Rodriguez' presentation in the framework of the expert consultation on the use of crop wild relatives for pre-breeding in potato Flor Rodriguez' presentation in the framework of the expert consultation on the use of crop wild relatives for pre-breeding in potato Presentation Transcript

    • Do potatoes have a single evolutionary history? Flor Rodríguez February 22nd, 2012 Lima, Peru
    • Previous phylogenetic studies plastid DNA restriction site S. bulbocastanum Clade 2 S. cardiophyllum subsp. cardiophyllum S. cardiophyllum subsp. ehrenbergii Clade 3 all ser. Piurana Clade 4 Remaining SA species NA & CA polyploid species and S. verrucosum Clade 1 Most US, Mexican & Central American diploids Outgroup (S. palustre) Hosaka et al., 1984; Spooner & Sytsma, 1992; al., Castillo & Spooner, 1997; Rodríguez & Spooner, 1997
    • Previous phylogenetic studies DNA sequences, WAXY 900 bp 1200 characters Ser. Longipedicellata c1+2 c4b Ser. Conicibaccata c3 c4a Iopetala Group : S. schenkii & iopetalum c3 c4a c4b S. hougasii c3 c4b S. demisum c4a c4b Rodriguez et al., 2008 al.,
    • Previous phylogenetic studies DNA sequences nitrate reductase 1.00 S. lycopersicum S. acaule 1 1.00 S. acaule 2 0.59 S. demisum 1 0.97 S. demisum 2 S. raphanifolium 2 1200 bp, 0.78 S. raphanifolium 1 0.77 0.99 S. agrimonifolium 1 1.00 S. colombianum 1 0.74 S longiconicum 1 0.78 S. violaceimarmoratum 1500 characters S. microdontum 0.71 S. lignicaule 1 S. berthaultii 0.69 S. tarijense 0.95 S. infundibuliforme 1 S. sparsipilum 1 0.98 0.98 0.96 S. brevicaule 1 S. infundibuliforme 2 S. chacoense Clade 4 Genome A 1.00 S. gandarillasii S. boliviense S. megistacrolobum 1.00 S. brachycarpum 1 0.85 S. S. verrucosum hjertingii 1 1.00 S. stoloniferum 1 Ser. Longipedicellata c1+2 c4b Ser. Conicibaccata c3 c4a S. demisum 3 1.00 S. demisum 4 S. fendleri 1 S. schenkii 10.98 0.96 0.96 1 S. demisum 5 S. demisum 6 S. fendleri 2 Iopetala Group: S. iopetalum c3 c4b 0.83 S. schenkii 2 1 S. oplosence A1 1 S. oplosence A2 S. oplosence A3 0.94 0.52 S. brevicaule 2 S. leptophyes S. sparsipilum 2 S. schenckii c1+2 c3 c4b 0.96 S. oplosence A4 1.00 S. oplocense B1 S. oplosence B2 S. demissum c4a c4b 1 S. oplosence A5 0.99 S. oplosence A6 0.91 S. oplosence B3 0.98 S. oplosence B4 0.76 S. stenophyllidium 0.69 S cardiophyllum S. bulbocastanum 0.97 0.98 S. cardiophyllum subsp.ehrenbergii 1 S. cardiophyllum subsp.ehrenbergii 2 0.99 S. fendleri 3 S. fendleri 4 Diploid species 1.00 S. hjertingii 2 0.93 S. stoloniferum 2 S. stoloniferum 3 S. stoloniferum 4 Clade 1+2 Polyploid species ser. Longipedicellata Polyploid species ser. Connicibaccata Genome B 0.75 S. jamesii 0.74 S. pinnatisectum 1.00 0.68 1.00 S. schenkii 3 S. schenkii 4 Polyploid species Acaulia Group S.trifidum S. clarum 0.98 1.00 S. morelliforme Polyploid species Iopetalum Group 1.00 S. lesteri S. polyadenium S. agrimonifolium 2 Polyploid species ser. Piurana 0.79 S. agrimonifolium 3 0.68 S. agrimonifolium 4 S. brachycarpum 2 Polyploid species ser. Tuberosa 1.00 S. colombianum 2 0.56 S. colombianum 3 72 S longiconicum 2 0.66 Clade 3 1 S. tuquerrense 1 S. tuquerrense 2 0.95 S. andreanum 1 S. paucijugum 1 0.96 0.95 S. paucijugum 2 S. schenkii 5 S. schenkii 6 Piurana Clade Genome C or D or P 0.57 0.59 S. albornozii 0.97 S. paucijugum 3 0.57 1 S. paucijugum 4 S. tuquerrense 3 S. tuquerrense 4 S. immite Rodríguez & Spooner, 2009
    • Objectives Identify COS appropriate for wild potato phylogenetic studies Generate a molecular data set to reconstruct the phylogeny of diploid and polyploid wild potatoes
    • COS selection criteria Chromosome coverage Single-copy in potato Sequence amplification length Intron and exon content
    • Predominant history …. and others too 12 COSII, 10,886 total charactersThe predominant history The other two different histories History 1 History 3 History 2 with 12COS or 6COS with 1COS with 3COS
    • Another way to see alternative evolutionary historiesBayesian concordance analysis (12 COSII)α = 1, 10 and infiniteThe numbers supporting the branches are concordancevalues indicating the proportion of the genes supportingthese branches
    • Conclusions COS are useful for potato phylogenetic studies Intron contents more than 60% are the best to investigate relationships among closely related species The total evidence approach produce a completely resolved potato phylogeny The “prior agreement” approach and “concordance analysis” identified two more histories in potato Additional studies using more accessions and more nuclear orthologs will show and bring up more details of potato evolution
    • Challenges Sequence more COS/genes Identify COS appropriate for wild potato phylogenetic studies Identify all alleles of a genotype
    • Domestication-related loci Summary of domestication-related loci with putative conservation in Solanaceae reported in 15 publications At least 3 common markers among maps were used to determine co-linearity with Tomato-EXPEN2000 map 171 COSII close to them: 130 of them are single copy in potato and 76 in potato and tomato
    • Domestication-related loci 25 traits :
    • Identifying all alleles of a genotype Cloning was the traditional approach for uncovering allelic variants Cloning issues: PCR recombination and heteroduplex fixation Asymmetric PCR SSCP
    • Current research the number of potato diploid species in each main clade was incresed up to 70 species 28 new COS were selected for having a single band in agarose gel direct sequencing and asymmetric-PCR-SSCP
    • Preliminary results blb bst 76 ehr ehr.2 75 cph Clade 1+2 trf cph.2 jam pnt 24 COS pld les clr 24,844 characters clr.2 mrl cmm blv blv.2 69 mga mga.2 ber * tar tar.2 ifd * ifd.2 lph lph.2 71 brc * ver spl spl2 Clade 4 gnd 78 78 gnd.2 chc 75 chc.2 ktz ktz.2 vio lxs 79 lmb lmb.2 54 igl rap rap.2 buk buk.2 chm * chm.2 pcs chl p 65 chm B chq B jlc 79 dcm abz Clade 3 60 adr mtp 72 imt 68 imt.2 mcq smp hcr hcb hcb.2 crc crc.2 etb pls dul 50 changes
    • What does COS tell on the evolution ofwild potato polyploid species? 6 COS sequenced 11 polyploid species, 2-10 accessions per species, in total 44 accessions 37 diploid accessions of 30 species
    • Results in polyploid species Number ofSpecies accessions/species Clade 1+2 Clade 3 Clade 4 examined Precise origin not identified, but at S. lignicaule; S. candolleanum andSolanum acaule 3/3 least 1 allele with BS=0.96 S. raphanifolium clade S. candolleanum and S. 3/4 S. hypacrarthrum raphanifolium cladeS. albicans S. chilliasense and S. piurae clade; S. candolleanum and S. 1/4 S. chomatophilum raphanifolium clade S. andreanum and S. albornozii S. laxissimum, S. limbaniense, andS. agrimonifolium 2/2 clade S. violaceimarmoratum cladeS. colombianum 2/2 S. andreanum and S. albornozii S. laxissimum, S. limbaniense, and 2/2S. moscopanum clade; S. chomatophilum S. violaceimarmoratum clade Precise origin not identified, but at S. berthaultii; S. verrucosum; S. 6/7 least 1 allele with BS>0.96 for all candolleanum and S. accessions raphanifolium cladeS. demissum S. berthaultii, S. verrucosum, S. Precise origin not identified, but at 1/7 S. trifidum candolleanum and S. least 1 allele with BS=0.95 raphanifolium clade
    • Results in polyploid species Number ofSpecies accessions/species Clade 1+2 Clade 3 Clade 4 examined S. stenophyllidium; S. S. andreanum and S.S. hougasii 5/5 S. berthaultii, S. verrucosum trifidum albornozii clade S. berthaultii, S. verrucosum; S. laxissimum, S. andreanum and S.S. iopetalum 7/7 S. limbaniense, and S. violaceimarmoratum albornozii clade clade S. polyadenium; S. S. andreanum and S. 5/6 S. berthaultii; S. verrucosum stenophyllidium; S. trifidum albornozii cladeS. schenckii 1/6 S. stenophyllidium S. berthaultii; S. verrucosum 7/10 S. stenophyllidium S. berthaultii; S. verrucosumS. stoloniferum 2/10 S. chomatophilum S. candolleanum and S. raphanifolium clade 1/10 S. andreanum and S. S. polyadenium, S. trifidum S. berthaultii; S. verrucosum albornozii cladeS. hjertingii 6/6 S. stenophyllidium S. berthaultii; S. verrucosum
    • Conclusions Phylogenetic results are often incongruent among different phylogenetic markers COS are useful for potato phylogenetic studies There are much diversity and genomic complexity that was known within traditional recognized polyploid species At least 4 polyploid species have multiple origins and allele losses Additional studies using more accessions and more nuclear orthologs will show and bring up more details of potato evolution
    • Conclusions Results could be useful for designing crossing strategies to incorporate wild species germplasm into cultivated potato To use wild species effectively in potato breeding programs, it is important to consider both genomes and endosperm balance number The identification of the genomes that have contributed to allopolyploid species may provide a strategy for their use in bridging crosses
    • AcknowledgementsDr. David SpoonerPeople in Spooner’s labDr. David Baum and Cecile AneUniversity of Wisconsin Plant Breeding and PlantGenetics ProgramUS Potato genebank