ENGLISH ABSTRACT: Late blight caused by Phytophthora infestans on potato and tomato causes major
economic losses worldwide. Until the 1980s, P. infestans populations outside its centre of
origin (either central Mexico or the Andean region) only consisted of one mating type
(A1), which prevented the pathogen from reproducing sexually. Pathogen populations
outside the centre of origin most likely only consisted of a few genotypes prior to the
1980’s. Pan globally, these genotypes probably first consisted of genotype/s that had
mitochondrial DNA (mtDNA) haplotype Ia, which was subsequently replaced by a
mtDNA haplotype Ib genotype known as the US-1 lineage. This relative simple
population structure of the pathogen changed almost worldwide in the late 1970s and
early 1980s, when a second set of migrations took place from the centre of origin. These
populations contained both A1 and A2 mating type isolates that consisted of several
different genotypes, which were more virulent than the pre-1970s genotypes and resulted
in the displacement of these genotypes almost worldwide. Some of the new genotypes
were also resistant to metalaxyl, the fungicide that was most effective in controlling late
blight.
In Sub-Saharan Africa (SSA), the characteristics of P. infestans populations are
not well documented in most countries except South Africa, Kenya and Uganda. Previous
studies in SSA showed that populations were dominated by the US-1 lineage and its
variants. The exceptions were reports of the presence of a few mtDNA haplotype Ia
isolates in Rwanda and Ethiopia. The current study aimed to determine the population
structure of P. infestans in eight selected SSA countries (Burundi, Kenya, Rwanda,
Tanzania, Uganda, Malawi, Mozambique and South Africa), mainly on potato and on a
limited scale on tomato and petunia, using ‘old’ markers (mating type determination,
glucose-6-phosphate isomerase [Gpi] genotyping, mtDNA haplotyping, DNA
fingerprinting with probe RG-57 and metalaxyl sensitivity). Populations were further also
genotyped using seven recently published Simple Sequence Repeats (SSRs) markers.
This information would help to define the population structure of P. infestans in
SSA for the first time on a regional basis, and will also determine whether new
migrations have taken place since the last characterization studies took place in 2001.
A survey in the eight SSA countries yielded a total of 281 P. infestans isolates,
mainly obtained from potato fields (Tanzania, Kenya, Uganda, Rwanda, Burundi, Malawi
and South Africa), but also from tomato (Malawi, Mozambique and South Africa) and
Petunia ´ hybrida (South Africa) that were characterized. Characterization of subsets of
the isolates with the ‘old’ markers (176 isolates for mating type, 281 isolates for mtDNA,
70 isolates for [Gpi] and 49 isolates with restriction fragment length polymorphism
analysis with probe RG-57), showed that most of the isolates belonged to the US-1
genotype or its variants (US-1.10 and US-1.11). The exception were isolates that
belonged to genotype KE-1 (A1 mating type, mtDNA haplotype Ia, Gpi 90/100 and
unique RG-57 genotype) that was identified in two fields in Kenya. Genotype KE-1,
based on the ‘old’ marker data, is related to genotypes (RW-1 and RW-2) previously
identified in Rwanda, and several Ecuadorean and European genotypes. Metalaxyl
sensitivity testing of 64 isolates showed that metalaxyl resistant potato isolates were
present in all the countries except Malawi, whereas all the tomato isolates were sensitive.
Genotyping of 176 isolates with seven recently published simple sequence repeat (SSR)
markers revealed a high number (79) of multi-locus genotypes (MLGs) in SSA.
However, when locus D13, which was difficult to score, was excluded only 35 MLGs
were identified. When locus D13 was excluded from analyses of molecular variance
(AMOVA), (i) there was no significant genetic differentiation between
populations from central-east Africa (Burundi, Kenya, Rwanda, Tanzania and Uganda),
south-east Africa (Malawi and Mozambique) and South Africa, (ii) the KE-1 population
was genetically differentiated (Fst = 0.33; P = 0.001) from the US-1 and US-1.10
populations and (iii) genetic differentiation between populations from potato and tomato
was low (Fst = 0.07; P = 0.004).
The study has expanded the worldwide genotypic database of P. infestans for
SSA. Previously, no populations were characterized from Burundi, Malawi and
Mozambique. The characterization work showed that migrations seem unlikely to have
taken place in SSA, or if these did occur, it was on a very limited scale. The more severe
epidemics in some SSA countries could be due to the presence of metalaxyl resistance.
Furthermore, the occurrence of mutations or mitotic recombination might have resulted in
more aggressive and/or better adapted genotypes, for example the US-1.10 lineage that
was only detected in the Western Cape Province of South Africa. The significance of the
discovery of the KE-1 genotype in Kenya needs further investigation since it might (i) be
an asexual descendent of genotypes (RW-1 and RW-2) that were previously reported in
Rwanda in the 1980s, (ii) previously have gone undetected due to the small surveys that
were conducted in SSA, (iii) be a new migrant from countries other than SSA or (iv) have
been introduced in the very first introductions into Kenya prior to the 1970s. The SSR
results from the survey will allow comparison of the SSA late blight populations with
other populations worldwide through the EucaBlight database in future studies.
AFRIKAANSE OPSOMMING: Laatroes, veroorsaak deur Phytophthora infestans op aartappel en tamatie,
veroorsaak groot ekonomiese verliese wêreldwyd. Phytophthora infestans populasies
buite hul kern van oorsprong (óf sentraal Meksiko óf die Andes area), het tot die 1980’s
slegs uit een paringstipe (A1) bestaan, wat verhoed het dat die patogeen geslagtelik
vermeerder. Patogeenpopulasies buite die kern van oorsprong, het heel moontlik vóór die
1980’s slegs uit ‘n paar genotipes bestaan. Wêreldwyd, het hierdie genotipes moontlik
aanvanklik uit genotipe(s) bestaan wat mitokondriale DNS (mtDNS) haplotipe Ia bevat
het, wat later met ‘n mtDNS haplotipe Ib genotipe, bekend as die US-1 genotipe, vervang
is. Hierdie relatiewe eenvoudige populasiestruktuur van die patogeen, het omtrent
wêreldwyd in die láát 1970’s en vroeë 1980’s verander, toe ‘n tweede stel migrasies
vanaf die patogeen se kern van oorsprong plaasgevind het. Hierdie populasies het beide
A1 en A2 paringstipe isolate ingesluit, wat uit verskeie verskillende genotipes bestaan
het, wat meer virulent as die vóór-1970’s genotipes was, en wat die verskuiwing van
hierdie genotipes omtrent wêrelwyd tot gevolg gehad het. Sommige van die nuwe
genotipes was ook weerstandbiedend teen metalaksiel, die fungisied wat mees effektief in
die beheer van laatroes was.
Die kenmerke van P. infestans populasies is nie goed in die meeste lande in Sub-
Sahara Afrika (SSA) gedokumenteer nie, behalwe vir Suid-Afrika, Kenia en Uganda.
Vorige studies in SSA het aangedui dat populasies deur die US-1 genotipe en sy variante
gedomineer word. Die uitsonderings was aantekeninge oor die teenwoordigheid van ‘n
paar mtDNS haplotipe Ia isolate in Rwanda en Etiopië. Die huidige studie was daarop
gemik om die populasiestruktuur van P. infestans in agt geselekteerde SSA lande
(Burundi, Kenia, Rwanda, Tanzanië, Uganda, Malawi, Mosambiek en Suid-Afrika),
hoofsaaklik op aartappel en op ‘n beperkte skaal op tamatie en petunia, vas te stel, deur
die gebruik van ‘ou’ merkers (paringstipe-bepaling, glukose-6-fosfaat isomerase [Gpi]
genotipering, mtDNS haplotipering, DNS fingerafdrukke met RG-57 en metalaksielsensitiwiteit).
Die genotipe van populasies is verder ook bepaal deur gebruik te maak van
sewe onlangs-gepubliseerde “Simple Sequence Repeats (SSRs)” merkers. Hierdie
inligting sal help om die populasiestruktuur van P. infestans in
SSA vir die eerste keer op ‘n streeksbasis vas te stel, en sal ook bepaal of nuwe migrasies
sedert die laaste karakteriseringstudies wat in 2001 uitgevoer is, plaasgevind het.
‘n Opname in die agt SSA lande, het ‘n totaal van 281 P. infestans isolate
opgelewer, hoofsaaklik vanaf aartappellande (Tanzanië, Kenia, Uganda, Rwanda,
Burundi, Malawi en Suid-Afrika), maar ook vanaf tamatie (Malawi, Mosambiek en Suid-
Afrika) en Petunia ´ hybrida (Suid-Afrika) wat gekarakteriseer is. Karakterisering van
geselekteerde isolate met die ‘ou’ merkers (176 isolate vir paringstipe, 281 isolate vir
mtDNS, 70 isolate vir Gpi en 49 isolate met restriksiefragment-lengte-polimorfismeanalise
met RG-57), het aangetoon dat die meeste van die isolate aan die US-1 genotipe
of sy variante (US-1.10 en US-1.11) behoort het. Die uitsondering was isolate wat tot die
genotipe KE-1 behoort het (A1 paringstipe, mtDNS haplotipe Ia, Gpi 90/100 en unieke
RG-57 genotipe) wat in twee velde in Kenia geïdentifiseer is. Genotipe KE-1, gebaseer
op die ‘ou’ merkerdata, is aan genotipes (RW-1 en RW-2) verwant, wat voorheen in
Rwanda, en verskeie Ekwadoreaanse en Europese lande geïdentifiseer is. Metalaksielsensitiwiteitstoetsing
van 64 isolate het aangetoon dat metalaksiel-weerstandbiedende
aartappel-isolate in al die lande teenwoordig was, behalwe vir Malawi, terwyl al die
tamatie-isolate sensitief was. Genotipering van 176 isolate met sewe onlangs
gepubliseerde “Simple Sequence Repeat” (SSR) merkers, het ‘n hoë aantal (79) multilokus
genotipes (MLGs) in SSA aangedui. Met die uitsluiting van lokus D13, wat
moeilik was om te evalueer, is slegs 35 MLGs egter geïdentifiseer. Met die uitsluiting
van lokus D13 uit die analise van molekulêre variansie (AMOVA), was (i) daar geen
betekenisvolle genetiese differensiasie tussen populasies van sentraal-oos
Afrika (Burundi, Kenia, Rwanda, Tanzanië en Uganda), suid-oos Afrika (Malawi en
Mosambiek) en Suid-Afrika nie, (ii) die KE-1 populasie geneties (Fst = 0.33; P = 0.001)
van die US-1 en US-1.10 populasies gedifferensieerd en (iii) genetiese differensiasie
tussen populasies vanaf aartappel en tamatie laag (Fst = 0.07; P = 0.004).
Die studie het die wêreldwye genotipe-databasis van P. infestans vir SSA
uitgebrei. Voorheen is geen populasies vanuit Burundi, Malawi en Mosambiek
gekarakteriseer nie. Die karakteriseringswerk het aangetoon dat die waarskynlikheid
klein is dat migrasies in SSA plaasgevind het, of indien dit wel plaasgevind het, dit op ‘n
baie beperkte skaal plaasgevind. Die meer ernstige epidemies in sommige SSA lande kan
die gevolg wees van die teenwoordigheid van metalaksiel-weerstand. Die voorkoms van
mutasies of mitotiese rekombinasie kon verder meer aggressiewe en/of beter aangepaste
genotipes tot gevolg gehad het, byvoorbeeld die US-1.10 genotipe wat slegs in die
Westelike Kaapprovinsie van Suid-Afrika waargeneem is. Die betekenis van die
ontdekking van die KE-1 genotipe in Kenia benodig verdere ondersoek aangesien dit (i)
‘n ongeslagtelike afstammeling van genotipes (RW-1 en RW-2) mag wees wat voorheen
in die 1980’s in Rwanda aangeteken is, (ii) voorheen nie waargeneem is nie weens die
klein opnames wat in SSA uitgevoer is, (iii) ‘n nuwe genotipe van lande buite die SSA
kan wees of (iv) ingebring is tydens die heel eerste inkoms in Kenia vóór die 1970’s. Die
SSR resultate van die opname sal vergelykings tussen die SSA laatroespopulasies en
ander populasies wêreldwyd toelaat, deur gebruik te maak van die EucaBlight databasis
in toekomstige studies.
