Inheritance and genetic mapping of Xiphinema index resistance derived from Vitis arizonica

Van Zyl, Sonet (2012-12)

Thesis (PhD(Agric))--Stellenbosch University, 2012.

Thesis

ENGLISH ABSTRACT: Grapevines are one of the most important and diverse crops in the world, but tend to be susceptible for numerous pests and diseases. The dagger nematode, Xiphinema index (X. index) is a well-known soil-borne pest of grapevine and vector of grapevine fanleaf virus. Several Vitis species showed resistance to this pest. Breeding efforts have been underway for several decades to create resistant rootstocks. However, conventional breeding efforts are time consuming due to grapevines being a perennial crop, its heterozygosity, as well as its long growth cycle. Breeding new grapevine varieties are also expensive and work intensive. The development of marker-assisted selection introduced a way to overcome some of the abovementioned problems. The aim of this study was to broaden the genetic evaluation and breeding efforts for improved X. index resistance in grapevine rootstocks. In 2007 several crosses were made in the University of California, Davis vineyards. The background for all these crosses consisted of V. arizonica. These V. arizonica plants are part of a collection obtained by H.P. Olmo during the 1960’s. In recent studies it was established that X. index resistance is controlled by a single dominant gene. The 0701 (R8916-07 (Wichita Refuge x b40-14) x R8916-32), 0704 (161-49C x b40-14) and 0705 (161-49C x R8916-22) populations were created to confirm the homozygous nature of b40-14, a V. arizonica accession. In addition, several V. arizonica species were screened to confirm their resistance or susceptibility towards X. index feeding. The 0705 population was also used to create a genetic map for X. index resistance. In this study a new and improved screening method was developed to inoculate vines under greenhouse conditions. This screening method proved to be quicker and less damaging on the nematodes than traditional systems. Control varieties were used and O39-16, a commercial rootstock showed no damage, even with high nematode pressure, whereas V. rupestris Saint George had severe root damage and decline after eight weeks of exposure. A range of V. arizonica accessions was tested for their resistance to X. index feeding. Of the 18 genotypes tested, half showed resistance and the rest were susceptible. It is possible that these genotypes are not pure V. arizonica genotypes. Genotypes with V. arizonica in the background were also tested. Wichita Refuge was used as a susceptible female parent and the progeny were expected to be heterozygous resistant. Some of the progeny allowed low levels of feeding damage, which may have been the result of the more effective inoculation method described above. The 0701 population confirmed the hypothesized model of 3:1 (Resistance (R):Susceptible (S)) segregation although 13 of the genotypes showed significantly higher gall numbers than the susceptible female parent. The possibility of transgressive segregation exists, but needs to be confirmed. All progeny from the 0704 population should be heterozygous resistant, but a 1:1 (R:S) segregation pattern was observed. The 0705 population was created as a mapping population to study X. index resistance. This population was also tested in the greenhouse for its X. index resistance and was expected to segregate 1:1 (R:S). The X2 analysis did not fully support this model. A genetic map covering all 19 linkage groups, and positioning 175 polymorphic SSR markers was created for the 164 progeny in the 0705 population. MapQTL analysis revealed a major QTL on linkage group 9 and two minor QTL’s on groups 13 and 19. The major QTL placed between markers VMC1c10 and CTG1032918 with a LOD score of 33.4 explaining 70.5% of the phenotypic variance for X. index. This QTL is the second major QTL discovered for X. index resistance. With the discovery of a second major QTL, the two types of resistance can be pyramided. Work is underway to saturate the area around the major QTL on linkage group 9 and to move towards physical mapping of X. index resistance. The b40-14 V. arizonica accession is also known for its resistance to Pierce’s disease and the possibility of simultaneous expression of two types of resistance is created. The 0705 population can also be used to evaluate phenotypical characteristics in the field to determine if useful rootstocks can be selected. Taken together, the results obtained in this study provide improved methods and highly characterized plant populations to support the efforts in obtaining improved X. index resistance in grapevine rootstocks.

AFRIKAANSE OPSOMMING: Wingerde is van die belangrikste en mees diverse gewasse op aarde, maar hulle neig om vir ‘n verskeidenheid plae en siektes vatbaar te wees. Die dolk-aalwurm, Xiphinema index (X. index), is ‘n bekende grondgedraagde plaag van wingerd en ‘n vektor vir wingerd- netelblaarvirus. Verskeie Vitis-spesies toon weerstand teen hierdie plaag. Daar word reeds vir dekades pogings aangewend om weerstandbiedende onderstokke te kweek. Konvensionele kweekpogings is egter tydrowend omdat wingerd ‘n meerjarige gewas is, op grond van die heterosigositeit van die gewas, sowel as die lang groeisiklus. Dit is ook duur en arbeidsintensief om nuwe wingerdvariëteite te kweek. Die ontwikkeling van merkerondersteunde seleksie het dus ‘n metode verskaf om sommige van bogenoemde probleme te oorkom. Die doelwit van hierdie studie was om die genetiese evaluerings- en kweekpogings vir verbeterde X. index-weerstand in wingerd-onderstokke te verbreed. In 2007 is verskeie kruisings in die wingerde by die Universiteit van Kalifornië, Davis gemaak. Die agtergrond vir al hierdie kruisings het bestaan uit V. arizonica. Hierdie V. arizonica-plante vorm deel van ‘n versameling wat in die 1960’s deur H.P. Olmo verkry is. In onlangse studies is daar bepaal dat X. index-weerstand deur ‘n enkele dominante geen beheer word. Die 0701 (R8916-07 (Wichita Refuge x b40-14) x R8916-32), 0704 (161-49C x b40-14) en 0705 (161-49C x R8916-22) bevolkings is geskep om die homosigotiese geaardheid van b40-14, ’n V. arizonicaafstammeling, te bevestig. Daarbenewens is verskeie V. arizonica-spesies gesif om hulle weerstand teen of vatbaarheid vir X. index voeding te bevestig. Die 0705 bevolking is ook gebruik om ‘n genetiese kaart vir X. indexweerstand te skep. In hierdie studie is ‘n nuwe en verbeterde siftingsmetode ontwikkel om wingerdstokke onder glashuistoestande te inokuleer. Daar is gewys dat hierdie siftingsmetode vinniger en minder skadelik vir die aalwurms as tradisionele metodes is. Beheervariëteite is gebruik en O39-16, ‘n kommersiële onderstok, het geen skade getoon nie, selfs met hoë aalwurmdruk, terwyl V. rupestris Saint George ernstige wortelskade en agteruitgang na agt weke se blootstelling getoon het. ‘n Verskeidenheid V. arizonica-afstammelinge is vir hulle weerstand teen X. index-voeding getoets. Van die 18 genotipes wat getoets is, het die helfte weerstand getoon en die res was vatbaar. Dit is moontlik dat hierdie genotipes nie suiwer V. arizonica-genotipes was nie. Genotipes met V. arizonica in hulle agtergrond is ook getoets. Wichita Refuge is as ‘n vatbare vroulike ouer gebruik en die verwagting was dat die nageslag heterosigoties weerstandbiedend sou wees. Sommige van die nageslag het lae vlakke van voedingskade toegelaat, wat moontlik die gevolg was van die meer doeltreffende inokulasiemetode wat hierbo beskryf word. Die 0701 bevolking het die veronderstelde model van 3:1 (Weerstandbiedend (W):Vatbaar (V)) segregasie bevestig, hoewel 13 van die genotipe noemenswaardig hoër galgetalle as die vatbare vroulike ouer getoon het. Die moontlikheid van transgressiewe segregasie bestaan, maar dit moet nog bevestig word. Alle nageslag van die 0704 bevolking behoort heterosigoties weerstandbiedend te wees, maar ‘n 1:1 (W:V) segregasiepatroon is waargeneem. Die 0705 bevolking is as ‘n karteringsbevolking geskep om X. index-weerstand te bestudeer. Hierdie bevolking is ook in die glashuis vir sy X. index-weerstand getoets en daar is verwag dat dit 1:1 (W:V) sou segregeer. Die X2 analise het nie hierdie model ten volle ondersteun nie. ‘n Genetiese padkaart wat al 19 skakelingsgroepe en die posisies van 175 polimorfiese SSR merkers toon, is vir die 164 afstammelinge in die 0705 bevolking geskep. MapQTL analise het ‘n groot kwantitatiewe eienskap lokus (QTL) op skakelingsgroep 9 en twee kleiner QTL’e op groepe 13 en 19 onthul. Die groot QTL is tussen merkers VMC1c10 en CTG1032918 met ‘n LOD telling van 33.4 geplaas en het 70.5% van die fenotipiese variansie van X. index verklaar. Hierdie QTL is die tweede groot QTL wat vir X. index-weerstand ontdek is. Met die ontdekking van ‘n tweede groot QTL, kan die twee soorte weerstand gepiramideer word. Werk word reeds onderneem om die area rondom die groot QTL op skakelingsgroep 9 te versadig en om na die fisiese kartering van X. index-weerstand te beweeg. Die b40-14 V. arizonica-afstammeling is ook bekend vir sy weerstand teen Pierce se siekte en die moontlikheid word geskep vir die gelyktydige uitdrukking van twee soorte weerstand. Die 0705 bevolking kan ook gebruik word om die fenotipiese kenmerke in die veld te evalueer om te bepaal of bruikbare onderstokke geselekteer kan word. In kombinasie behoort die resultate wat in hierdie studie verkry is, verbeterde metodes en hoogs gekarakteriseerde plantbevolkings te lewer wat die pogings sal ondersteun om verbeterde X. index-weerstand in wingerdonderstokke te verkry.

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