QTL Mapping for Resistance to Cankers Induced by Pseudomonas syringae pv. actinidiae (Psa) in a Tetraploid Actinidia chinensis Kiwifruit Population

Abstract

Polyploidy is a key driver of significant evolutionary changes in plant species. The genus Actinidia (kiwifruit) exhibits multiple ploidy levels, which contribute to novel fruit traits, high yields and resistance to the canker-causing dieback disease incited by Pseudomonas syringae pv. actinidiae (Psa) biovar 3. However, the genetic mechanism for resistance to Psa observed in polyploid kiwifruit is not yet known. In this study we performed detailed genetic analysis of a tetraploid Actinidia chinensis var. chinensis population derived from a cross between a female parent that exhibits weak tolerance to Psa and a highly Psa-resistant male parent. We used the capture-sequencing approach across the whole kiwifruit genome and generated the first ultra-dense maps in a tetraploid kiwifruit population. We located quantitative trait loci (QTLs) for Psa resistance on these maps. Our approach to QTL mapping is based on the use of identity-by-descent trait mapping, which allowed us to relate the contribution of specific alleles from their respective homologues in the male and female parent, to the control of Psa resistance in the progeny. We identified genes in the diploid reference genome whose function is suggested to be involved in plant defense, which underly the QTLs, including receptor-like kinases. Our study is the first to cast light on the genetics of a polyploid kiwifruit and suggest a plausible mechanism for Psa resistance in this species.

Development of a 135K SNP genotyping array for Actinidia arguta and its applications for genetic mapping and QTL analysis in kiwifruit

“…There are very few deviating syntenic regions scattered across the linkage map, these could be due to either the misplaced on the physical map, or different locations across species. For example, the Marey plots indicated an inversion of 20 cM on LG1 of A. arguta , this is more likely to be an assembly error as the inversion was also observed in a separate genetic mapping study in tetraploid A. chinensis (Tahir et al ., 2020 ).…”

“…In contrast, previous genetic mapping studies have mapped the sex‐determining region (SDR) to the subtelomeric region of LG25 in an interspecific population of A. rufa × A. chinensis , as well as a tetraploid A. chinensis var . chinensis population (Tahir et al ., 2020 ; Zhang et al ., 2015 ). Two sex‐determining genes have been identified: Shy Girl acts as a dominant suppressor of carpel development, while friendly boy acts as a male promoting factor for male fertility (Akagi et al ., 2019 ).…”

“…It also naturally occurs in a wide range of ploidy levels, from diploid (2x) to dodecaploid (12x). Global kiwifruit production is mainly dominated by polyploid kiwifruit cultivars, which have the advantage of possessing large fruits and displaying strong disease resistance (Ferguson, 2013 ; Tahir et al ., 2020 ; Wu et al ., 2012 ). The global kiwifruit market is dominated by the yellow‐fleshed A. chinensis var.…”

“…Phenotypic traits such as fruit quality and Pseudomonas syringae pv. Actinidiae resistance are mostly quantitative, genetically controlled by multiple genes and with a large influence from both cultivation management and the growing environment (Tahir et al ., 2019 , 2020 ; Testolin et al ., 2016 ). The genetic basis of these traits is complex in dioecious polyploids, making the breeding for desired traits even more challenging.…”

High-density linkage map construction in an autotetraploid blueberry population and detection of quantitative trait loci for anthocyanin content

“…While there is an abundance of genetic mapping software available for diploids that can be used for allopolyploids, new tools have only recently been released for the construction of linkage maps and for quantitative trait locus (QTL) mapping using allele dosage information in polysomic polyploids ( Grandke et al, 2017 ; Hackett et al, 2017 ; Bourke et al, 2018 , 2021 ; Behrouzi and Wit, 2019 ; Mollinari and Garcia, 2019 ; da Silva Pereira et al, 2020 ; Amadeu et al, 2021 ). These new software tools have allowed the discovery of loci linked to complex traits in a number of important autopolyploid crops, such as forage grasses ( Deo et al, 2020 ), rose ( Cheng et al, 2021 ; Yu et al, 2021 ), potato ( da Silva Pereira et al, 2021 ), sweet potato ( da Silva Pereira et al, 2020 ; Gemenet et al, 2020 ; Oloka et al, 2021 ), kiwifruit ( Tahir et al, 2020 ), and blueberry ( Cappai et al, 2020 ; Mengist et al, 2021 ). Additionally, the release of two reference genomes for V. corymbosum ( Gupta et al, 2015 ; Colle et al, 2019 ; Edger et al, 2022 ; Mengist et al, 2022 ) has facilitated the design of high-quality genotyping tools in this species.…”