Discovery of a major QTL for root-knot nematode (Meloidogyne incognita) resistance in cultivated sweetpotato (Ipomoea batatas)

Abstract

Key message Utilizing a high-density integrated genetic linkage map of hexaploid sweetpotato, we discovered a major dominant QTL for root-knot nematode (RKN) resistance and modeled its effects. This discovery is useful for development of a modern sweetpotato breeding program that utilizes marker-assisted selection and genomic selection approaches for faster genetic gain of RKN resistance. Abstract The root-knot nematode [Meloidogyne incognita (Kofoid & White) Chitwood] (RKN) causes significant storage root quality reduction and yields losses in cultivated sweetpotato [Ipomoea batatas (L.) Lam.]. In this study, resistance to RKN was examined in a mapping population consisting of 244 progenies derived from a cross (TB) between ‘Tanzania,’ a predominant African landrace cultivar with resistance to RKN, and ‘Beauregard,’ an RKN susceptible major cultivar in the USA. We performed quantitative trait loci (QTL) analysis using a random-effect QTL mapping model on the TB genetic map. An RKN bioassay incorporating potted cuttings of each genotype was conducted in the greenhouse and replicated five times over a period of 10 weeks. For each replication, each genotype was inoculated with ca. 20,000 RKN eggs, and root-knot galls were counted ~62 days after inoculation. Resistance to RKN in the progeny was highly skewed toward the resistant parent, exhibiting medium to high levels of resistance. We identified one major QTL on linkage group 7, dominant in nature, which explained 58.3% of the phenotypic variation in RKN counts. This work represents a significant step forward in our understanding of the genetic architecture of RKN resistance and sets the stage for future utilization of genomics-assisted breeding in sweetpotato breeding programs.

Polyploid QTL‐seq towards rapid development of tightly linked DNA markers for potato and sweetpotato breeding through whole‐genome resequencing

“…QTLs for root‐knot nematode resistance and storage root β‐carotene content were detected through analyses with 5,563 and 5,952 donor parent‐derived SNPs for their expected segregation ratios for simplex, respectively (Haque et al., 2020a ; Sasai et al., 2019 ), and a QTL for AN content in storage roots was presented by an analysis of 15 747 simplex SNPs (Haque et al., 2020b ). QTLs for root‐knot nematode resistance and storage root β‐carotene content were also detected by another reduced representation sequencing‐based platform that consisted of GBSpoly, MAPpoly and QTLpoly (Gemenet et al., 2020 ; Oloka et al., 2021 ). Another approach is the sequencing of individual progenies with low quantity of read data.…”

“…Using these methods, DNA markers linked to late blight resistance in diploid potato (Chen et al., 2018 ), and potato cyst nematode resistance in tetraploid potato (Strachan et al., 2019 ) have been developed. In sweetpotato, restriction site‐associated DNA sequence (RAD‐seq)‐based mapping methods have been developed to identify QTLs for root‐knot nematode resistance (Oloka et al., 2021 ; Sasai et al., 2019 ), AN and β‐carotene content in coloured storage roots (Gemenet et al., 2020 ; Haque et al., 2020a ; Haque et al., 2020b ), and yield (Okada et al., 2019 ). Both sequence capturing and RAD‐seq‐based methods reduced the time and effort required for the development of DNA markers.…”

Rose Rosette Disease Resistance Loci Detected in Two Interconnected Tetraploid Garden Rose Populations

“…The MAPpoly and QTLpoly software have been successfully used to map common scab resistance in autotetraploid potatoes ( da Silva Pereira et al, 2021 ) and fruit firmness in autotetraploid blueberry ( Cappai et al, 2020 ). This software has been used extensively to study autohexaploid sweet potatoes for root-knot nematode resistance ( Oloka et al, 2021 ), carotenoid, and starch biosynthesis ( Gemenet et al, 2020 ) and yield component traits ( da Silva Pereira et al, 2020 ). Several autotetraploid rose maps have been constructed using polymapR ( Bourke et al, 2017b ; Zurn et al, 2018 , 2020 ; Cheng et al, 2021 ; Yu et al, 2021 ) and QTL for stem prickles and flavonoid and carotenoid levels using polyqtlR ( Bourke et al, 2021 ; Cheng et al, 2021 ).…”

Mapping of Nematode Resistance in Hexaploid Sweetpotato Using a Next-Generation Sequencing-Based Association Study

“…Currently, various analytical tools such as MAPpoly and QTLpoly have been developed for polyploid species, which use Mendelian inheritance simplex markers as well as multiplex markers (Mollinari and Garcia, 2019;da Silva Pereira et al, 2020;Mollinari et al, 2020). Recently, Oloka et al (2021) performed QTL mapping for nematode resistance by constructing a highdensity linkage map with single-and multiple-dose SNPs and indels. The authors utilized new bioinformatic tools developed for sweetpotato improvement, such as GBSpoly, a genotyping platform that modifies GBS to polyploid species; MAPpoly, an R package for building linkage maps; and QTLpoly, an R package for QTL mapping.…”