A bi-parental mapping population was constructed from Nachinyaya (a landrace from northern Mozambique and southern Tanzania, known to have tolerance to CBSD root necrosis that has been durable for several decades, and susceptible to CMD) and AR37-80 (selected for the CMD2 gene and CGM resistance, but susceptible to CBSD (Blair et al., 2007; Okogbenin et al., 2012)). The final population size used for QTL analysis was 186 individuals. This population was phenotyped for CBSD root necrosis and CBSD foliar symptoms over three seasons (2013/14, 2014/15, and 2015/16) in two hotspot locations, Naliendele and Chambezi, Tanzania.
QTL and candidate genes associated with CBSD resistance
A total of 42 QTL have been defined for tolerance to CBSD (
Supplementary File S4
) across five populations developed, phenotyped and genotyped at the same time as this population (NDL06/132 × AR37-80 (NDLAR) (Kapinga, 2017), Namikonga × Albert (NxA) (Masumba et al., 2017), Kiroba × AR37-80 (KAR) (Nzuki et al., 2017) and AR40-6 × Albert (ARAL) (Garcia-Oliveira et al., 2020). To prioritise QTL results for further investigation, they are considered in conjunction with other information (1) co-localisation across populations; (2) identity by descent (IBD) analysis of parents based on whole genome sequence information (Bredeson et al., 2016) and (3) introgression segments from M. glaziovii (Bredeson et al., 2016). Viewing results across populations, particularly with a knowledge of the relatedness of parents, and identifying QTL that occur in more than one population provides confidence in the validity of QTL.
Identity-by-descent analysis reveals the close relationship between the CBSD tolerance donor parents (Nachinyaya, Namikonga and NDL06/132) of three of the populations (NCAR, NxA and NDLAR), whereas the CBSD tolerant donors (Kiroba and AR40-6) of the other two populations are more independent (Bredeson et al., 2016; Nzuki et al., 2017). This has implications for interpreting the results. NDL06/132 and Nachinyaya appear to be full siblings, with Nachinyaya a full sibling of Albert, which in turn is a full sibling of TMEB117 (Bredeson et al., 2016). Namikonga is also closely related, with a parent–offspring relationship with TMEB117. TMEB117 is a Nigerian landrace that has been widely used in the IITA breeding program for poundability characteristics. TMEB117 was almost identical to TMEB693 (apart from CMD resistance) (Ferguson et al., 2019) and appeared to be widely distributed in Africa. This variety is possibly an early introduction to East Africa (Ferguson et al., 2019) and a parent in the Amani breeding program. This would explain the relationship between Nachinyaya, Albert and Namikonga. Namikonga is the Amani hybrid 46106/27, a third backcross of M. glaziovii, and mentioned by Hillocks and Jennings (2003) as one the best Amani hybrids. In Kenya, it is also known as Kaleso (Amuge et al., 2017). Interestingly NDL06/132 was thought to be a cross from female parent NDL90/34 and likely male parent Nachinyaya that was selected from a crossing block in Naliendele, southern Tanzania, although Bredeson et al. (2016) shows NDL06/132 and Nachinyaya to be full siblings. There was no M. glaziovii wild species introgression segment detected in either NDL06/132 or Nachinyaya (Bredeson et al., 2016). Many years ago, TMEB117 was reported to be ‘highly resistant’ (immune) to CBSV and, thus, maybe a source of CBSD resistance/tolerance (Stephan Winter, per. comm.).
In contrast, Kiroba is a landrace from around Dar es Salaam, which occasionally shows severe leaf symptoms of CBSV but no root symptoms, even under high disease pressure. The results from whole genome re-sequencing data, suggest Kiroba has a parent–offspring relationship with tree cassava (an M. esculenta – M. glaziovii hybrid) and is more related to West African and South American germplasm than East African germplasm (Nzuki et al., 2017). Introgression segments from M. glaziovii were identified by Nzuki et al. (2017) on chromosomes 1, 17 and 18. This, together with the fact that it has good yield and vigour, suggests it may be derived from the Amani breeding program. AR40-6 is a cross between a CMD-resistant line from West Africa and South American/Asian breeding lines. It clusters with the South American and West African germplasm (Nzuki et al., 2017) as opposed to East African germplasm.
In the NCAR population reported here, consistent QTL associated with resistance to CBSD root necrosis were detected on chromosomes 7, 11 and 12, all of which were identified within data from C1 and C2, cultivated under high disease pressure (
Table 2
). A fourth region was detected on chromosome 18 in C1 only, characterised by two QTL, one quite specific (chrXVIII:6,327,979–6,801,336), the other encompassing the first (chrXVIII:4,212,438–8,916,735) (
Table 2
). This also co-locates with QTL for foliar symptoms from this population. In addition, 17 significant QTL were associated with foliar symptoms. Here, we initially highlight QTL and chromosomal regions which are found in more than one population and provide possible explanations for this based on the relatedness of parents. We then highlight QTL that occur in only one population but either occur in many sites/seasons or, for other reasons, appear to warrant further investigation.
Two QTL on chromosome 4 are of interest; qCBSDFc4_L was associated with resistance to foliar symptoms in KAR (C1, C2) and NCAR (N1, N2) populations overlapping from 2.4 to 3.4 Mbp. This is noteworthy even though the donor parents of these populations are not particularly closely related. Of possibly greater interest is the QTL qCBSDFc4_R associated with foliar symptoms from NCAR and NDLAR (with CBSD tolerant donor parents Nachinyaya and NDL06/132, respectively). These parents are likely full sibs with an identity by descent (IBD) of 0.5411 based on whole genome sequence information (Bredeson et al., 2016). Neither Nachinyaya nor NDL06/132 have M. glaziovii introgression segments in their genome (Bredeson et al., 2016), implying that these QTL regions are derived from the M. esculenta genome.
Kayondo et al. (2018) using GWAS found many SNPs in high linkage disequilibrium, defining a QTL covering both arms of chromosome 4. This supports the evidence presented here. In contrast, Kayondo et al. (2018) suggest that this QTL is derived from an introgression segment from M. glaziovii and confirmed the presence and segregation of the introgressed genome segment in both panels using a set of diagnostic markers from M. glaziovii. Due to the high level of linkage disequilibrium at the QTL location, they do not highlight a single locus or loci as candidate gene(s) associated with CBSD foliar severity. Interestingly Somo et al. (2020), also using GWAS, detected a QTL on chromosome 4 (QTL-cbsd4|cmd-1), tagged by marker S4_24670203, which showed significant associations with both CBSD foliar symptoms and CMD resistance in the K4_cluster1 dataset. This is relatively close to the qCBSDFc4_R region (16,481,626–20,065,474 bp (v5.1).
Three populations with closely related CBSD donor parents (Namikonga, Nachinyaya and NDL06/132) all mapped the qCBSDRNc11 locus (
Figure 1
and
Table 5
). This locus is supported by evidence from 11 site/season combinations. The locus currently stretches over 3.7 Mbp from positions 3.6–7.3 Mbp, although the regions around 4.5 Mbp seem to be well supported with NCAR having a QTL covering only 144 kbp from 4,383,294 to 4,527,454 bp (6,683,896–6,886,880 bp in v8.1, a distance of 202,984 bp) from C1 and C2 and accounting for 32% of the variation in each site. In addition, NxA has a QTL covering just 25 kbp from 4,502,175 to 4,527,454 bp (6,861,782–6,886,880 bp in v8.1, 25,098 bp) from the same site/seasons but, in this case, accounts for an average of 6.4% of the phenotypic variation. There are no M. glaziovii introgression regions on chromosome 11 (Bredeson et al., 2016), so qCBSDRNc11 is likely to be derived from the M. esculenta genome. Given these data, we believe this region warrants further investigation.
In contrast to the study here, Kayondo et al. (2018) found 83 significant SNP markers on chromosome 11 associated with foliar symptoms at 3 MAP and 33 SNPs at 6 MAP, but around ~23 Mbp. They could not identify SNPs surpassing the Bonferroni threshold for CBSD root severity across two panels. However, analysis of the multi-location data for Panel 1 identified significant regions of CBSD association on chromosomes 5, 11 and 18 (−log10(P-value) > 6.5), which explained 8, 6 and 10% of the phenotypic variance, respectively. This supports the observations reported here regarding QTL on chromosome 11 and their association with CBSD root necrosis. In addition, Somo et al. (2020) identified a QTL associated with CBSD foliar symptoms, similar to that of Kayondo et al. (2018), but again these do not coincide with the QTL identified for root necrosis here.
A third region on chromosome 18 is more complex. A QTL occurs across a large region from 4.2 to 8.9 Mbp in NCAR and is associated with both foliar symptoms (C2, C3 and N2) and root necrosis (C1). The only other population showing a QTL associated with foliar symptoms within this region is KAR in C2 from 5.7–6.0 Mbp, albeit with a low LOD score of 2.79 with a PVE of 9.6%. It seems that there is more evidence for QTL associated with root necrosis in this region (qCBSDRNc18). Within the QTL region of NCAR (4.2–8.9 Mbp), there are two, more specific, regions defined by other populations. NxA, NCAR and the population ARAL with the unrelated donor parent AR40-6 have QTL from 6.3–6.8 Mbp, all associated with root necrosis in a total of five site/season environments. A neighbouring QTL from 6.8–9.0 Mbp in a further two populations (NDLAR (6.8–9.0 Mbp) and NxA (8.6–8.9 Mbp)) is associated with root necrosis in a total of three sites/seasons. Thus, all three related CBSD tolerant parents (NDL06/132, Nachinyaya and Namikonga) with good levels of tolerance to root necrosis have QTL for root necrosis between 6.3–9.0 Mbp on chromosome 18 (
Table 6
and
Figure 1
). Although this region is large, it appears to be genuine. ARAL shows a QTL for foliar symptoms from 10 to 10.9 Mbp in both C1 and C2, which may be of additional interest. There are no M. glaziovii introgression regions on chromosome 18 (Bredeson et al., 2016), so the QTL described here are likely to be derived from the M. esculenta genome. Kayondo et al. (2018) identified significant regions of CBSD root severity association from multi-location data for Panel 1 on 18 (−log10 (P-value) > 6.5), in addition to chromosomes 5 and 11, which explained 10% of the phenotypic variance.
Some QTL, not shared across populations, are worthy of mention and further investigation. The NCAR population, with donor parent Nachinyaya, apart from possessing the important qCBSDFc4_L, qCBSDFc4_R and qCBSDFc18 loci, contain other important QTL associated with foliar symptoms, including six QTL distributed across chromosome 1 and on chromosomes 5, 6, 7, 8, 10, 11, 14 and 17 (
Table 3
). Chromosome 1 has a large M. glaziovii introgression segment in some Amani-derived varieties (Bredeson et al., 2016), but interestingly M. glaziovii introgression segments were not found in Nachinyaya, and QTL associated with foliar symptoms were not found on chromosome 1 of other varieties with introgression segments. This indicates that foliar symptom resistance on chromosome 1 comes from the cultivated M. esculenta. In addition, QTL on chromosomes 7 (qCBSDRNc7NC) and 12 (qCBSDRNc12NC) were associated with root necrosis in C1 and C2 under high disease pressure, although these did have slightly lower PVEs compared to qCBSDRNc11NC and qCBSDRNc18NC. Somo et al. (2020) detected two QTL associated with both CMD and CBSD foliar symptoms on chromosome 12 (QTL-cbsd12|cmd-1 and QTL-cbsd12|cmd-2), the latter SNP tag S12_7929439 which is close to the QTL detected here for CBSD root necrosis 6,934,834–10,102,374 bp (v5.1), 8,250,631–12,995,530 bp (v8.1). It also overlaps with another QTL for CMD severity detected by Somo et al. (2020) at 6.3–8.7 Mbp (v5.1).
In Namikonga, a QTL on chromosome 2 named qCBSDRNFc2Nm from 3.5–3.6 Mbp (v5.1) was associated with foliar symptoms in all site/season combinations and root necrosis in both years in Naliendele and should be of particular interest. Somo et al. (2020) detected a QTL for root necrosis in the Tanzanian Ukiriguru GWAS population with SNP tagged at S2_9258334.
As Kiroba and AR40-6 are more distantly related to the other CBSD donor parents, they may possess unique QTL. For CBSD root necrosis and foliar symptoms, a small region (15.7–15.8 Mbp which corresponds with 26.956–27.058 Mbp in v8.1) on the other arm of chromosome 11 to the QTL from the Nachinyaya-NDL06/132-Naminkonga group, is implicated in the KAR population (qCBSDRNFc11KR). It is significant in C1, N1 and N2 and is worthy of further investigation (Nzuki et al., 2017). Somo et al. (2020) detected a QTL for CBSD foliar symptoms from between 22.88 and 22.94 Mbp in an Ukiriguru population.
In addition, a QTL on chromosome 15 (qCBSDRNFc15K) (4.2–4.7 Mbp) in the KAR population is significant for root necrosis in N2 and foliar symptoms in N1 and N2, but interestingly this was not detected under the higher disease pressure of Chambezi. Two further QTL related solely to root necrosis from the KAR population are also interesting; qCBSDRNc12K on chromosome 12 (16.4–17.3 Mbp), which is significant in C1, N1 and N2 and qCBSDRNc5K, although this is less consistent (Nzuki et al., 2017). The QTL found here does not coincide with that detected by Somo et al. (2020) for CMD and CBSD foliar symptoms. In ARAL, a QTL on chromosome 14 for root necrosis was detected when scoring was done using a 1–5 scale (qCBSDRNSc14AR) (12.1–13.9 Mbp) in N1, N2 and C2 and by area of necrosis (qCBSDRNAc14AR) (12.9–13.6 Mbp) in the same environments. This is worthy of further investigation and, for convenience, is designated here as qCBSDRNc14AR.
In summary, the polygenic nature of tolerance to CBSD root necrosis and foliar symptoms in the populations studied here is evident, as is their instability across environments. This was also noted by Kayondo et al. (2018). It appears that although tolerance to foliar symptoms and root necrosis are largely under different genetic controls, there are some regions of the genome which may influence both. It is recommended that the following two QTL are targeted, as first priority, for marker development for use in marker-assisted breeding for foliar symptom resistance; qCBSDFc4_L and qCBSDFc4_R; four for CBSD-induced root necrosis qCBSDRNc11, qCBSDRNc18 (which may also confer some tolerance to foliar symptoms), qCBSDRNc12K and qCBSDRNc14AR; and three QTL for both root necrosis and foliar symptom resistance: qCBSDRNFc2Nm, qCBSDRNFc11KR and qCBSDRNFc15K. Due to the large number of QTL detected across various mapping populations and panels, it is important that QTL should be mapped onto the most recent version of the cassava reference genome (Mbanjo et al., 2021).
Candidate genes associated with CBSD resistance
A literature survey was carried out on the 1,168 genes contained within the priority QTL regions on chromosomes 4, 11 and 18 (
Supplementary File S5
) to determine those most likely to contribute to CBSD resistance (
Table 7
). Those considered the most significant are discussed below.
PAL and CCR
Of particular relevance are two genes, phenylalanine ammonia-lyase (PAL) (Manes.04G018000) and cinnamoyl-CoA reductase (CCR) (Manes.04G103200), found in QTL regions for foliar symptoms (chromosome 4). A second CCR (Manes.11G065500) is found within the QTL for root necrosis on chromosome 11. A second PAL gene (Manes.10G047500) was also identified on chromosome 10 (5,218,254–5,221,121 bp (v8.1)). CCR proteins operate downstream of PAL within the lignin biosynthetic pathway (Wadenbäck et al., 2008) and catalyse the production of several of its components (Yadav et al., 2020). We examined key genes of the cassava lignification pathway (Wang et al., 2023) using previously published transcriptomic data from Amuge et al. (2017). We found these to be strongly upregulated in the CBSD-resistant landrace Namikonga compared to the susceptible landrace Albert (
Supplementary File S6
) throughout the lignification pathway. This was the case in both uninfected and infected plants, strongly suggesting Namikonga has a higher level of basal lignin deposition. Wild cassava species, or those with introgression segments, tend to have more fibrous storage roots, commensurate with greater lignin content. Manes.11G065500 was upregulated 2.4x to 14.3x and 1.6x to 11.8x in Namikonga-infected and uninfected plants, respectively.
For long-distance and systemic infection, CBSVs, like other plant viruses, are translocated through the plant in both external and internal phloem vessels with the source-sink flow of photoassimilates (Graciano-Ribeiro et al., 2009; Nassar et al., 2010; Hipper et al., 2013; Sheat et al., 2021). Virus particles then pass from sieve elements of the phloem into the companion cells (SE–CC complex) to translocate to parenchyma and mesophyll cells, where they replicate. Resistance to long-distance movement is achieved either by preventing the virus from entering (loading) or exiting (unloading) the SE–CC complex (Rajamäki and Valkonen, 2009; Vuorinen et al., 2011). Sheat et al. (2021) demonstrated the extensive distribution of U/CBSV virus particles in phloem and non-phloem cells in leaves, stems and roots in CBSD susceptible varieties using RNAscope® in situ hybridisation. In contrast, in a highly resistant variety from South America they demonstrated very few virus particles in the external phloem cells of the stem, with no accumulation, and an absence of viral particles in the parenchyma tissue. This indicates a restriction of movement, most likely in the unloading, of CBSV from the SE–CC to surrounding cells, thus preventing the virus from reaching sites of replication. In other clones, the virus was restricted to stems and roots or roots only, with organ-specific, variable phloem uploading implicated. This supports the observation here of different QTL for root and foliar CBSD symptoms implying that different mechanisms or conditions may exist for virus restriction in these tissues. Sheat et al. (2021) suggest that phloem restriction is a specific resistance response of the host since the viruses otherwise move and replicate extensively in susceptible cassava varieties.
CCR-mediated lignin synthesis and its contribution to pathogen resistance are reported in the case of fungal (Xu et al., 2011), bacterial (Liu et al., 2021) and viral resistance (tomato yellow leaf curl virus, Sade et al., 2015). It is thought that the increase in lignin deposition contributes to cell wall thickening, which acts as a physical barrier to unloading from the phloem to parenchyma cells at the onset of infection in resistant lines. However, the upregulation of components of the lignification pathway does not necessarily correlate with increased lignification (Kofalvi and Nassuth, 1995), suggesting further function of components of this pathway. CCR has also been shown to be an effector of Rac1, a small GTPase operating within plant defence signalling pathways and is an elicitor of the hypersensitive response to infection by Tobacco mosaic virus (Moeder et al., 2005; Kawasaki et al., 2006). The value of plant-derived lignin as an antiviral agent in non-plants has been an area of substantial research (reviewed in Ullah et al. (2022)). These studies have shown that lignin-derived material effectively inactivate a range of viral pathogens. The precise mechanism by which this is achieved is yet to be fully understood. However, mutants or overexpression lines within the lignin pathway suggest it performs an important role in pathogen resistance, both as a passive or active regulatory component of the immune response (Xu et al., 2011).
Although PAL operates upstream of CCR in the lignification pathway (thus polymorphisms within PAL are more likely to account for its up-regulation than CCR) the known functions and increased basal expression of CCR in Namikonga, seen in the Amuge et al. (2017) data, suggest it is a strong candidate for CBSD resistance
eIF
We identified eukaryotic initiation factor (elF) genes within QTL on chromosomes 4 (eIF4A), 11 (eIF4AIII, eIF3) and 18 (eIF5 and eIF2D). eIFs protein complexes or subunits are required to recruit mRNA to ribosomes for translation. This process can be co-opted by viruses for their own replication (Zhang et al., 2015). eIF4F complexes contain a 5´cap recognition subunit required for the correct placement of mRNA within the ribosome. Many viral transcripts, including those from members of Potyviridae, lack a 5´ cap but can utilise eIF complexes for translation through the binding of a cap-independent translation element (CITE) to an eIF4F subunit, eIF4G (Kneller et al., 2006). eIF4A functions as an RNA helicase, removing tertiary structures from mRNA prior to translation and is also likely to contribute to efficient viral RNA translation by substantially increasing the binding affinity of eIF4F to the CITE (Zhao et al., 2017). eIF4 and elF5 genes are known to be major contributors to plant virus recessive resistance, as minor sequence changes can prevent viral translation. This protection can be broad-ranging and mutations as minor as a single nucleotide have been shown to confer protection (Ling et al., 2009; Rodríguez-Hernández et al., 2012). While eIF4 has been a major focus of elF contribution to viral resistance (including the poly-A binding protein eIF4E in CBSD resistance (Shi et al., 2017)), more recently, eIF3 has been shown to be involved in barley yellow dwarf virus replication by facilitating binding viral 5′ UTR to the 40S subunit (Powell et al., 2022). We also note Manes.11G073900 within a QTL region on chromosome 11. This is annotated as a DEAD BOX HELICASE but has very high homology with other eIF4 proteins and may represent a third eIF on chromosome 11. A possible role of eIF2D in viral resistance has recently been proposed (Kim et al., 2023). It has been suggested that, upon viral infection, translation can be switched from the standard 5´cap dependent mechanism to one using non-AUG codons facilitated by eIF2A and/or eIF2D (Green et al., 2022). The cell uses this switch to prevent viral replication through interaction with eIF4 in the manner described above. However, positive-stranded RNA viruses are also able to utilise this mechanism and continue replication.
PEPR1
Chromosome 4 contains a cluster of three PEPR1-related kinase genes. PEPR1/2 proteins act as peptide receptors as part of an innate immunity activation network. Arabidopsis plants with disruptions in this pathway show reduced root callose and lignin deposition and are more susceptible to infection by Pseudomonas syringae (Jing et al., 2023). AtPEPR1 is one of several proteins which can act as co-receptors within this network with BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1 (BAK1). Mutant forms of AtBAK1 show increased susceptibility to a range of viral infections, while AtPEPR1 mutants do not show variation in viral load (Yang et al., 2010; Kørner et al., 2013). AtPEPR1/2 gene expression is linked with increased salicylic acid (SA) production, a major factor in plant viral defence (reviewed in Alazem and Lin, 2015). Additionally, AtPEPR1 is induced upon wounding by feeding insects, including whitefly (Wang et al., 2019), presumably to prime the immune response against invasive microbes. PEPR1 studies have been largely restricted to Arabidopsis, and a role in viral defence in other species should not be ruled out.
WRKY
The data contained a single WRKY 40 transcription factor gene underlying the QTL on chromosome 4 and two WRKY 25 transcription factor genes on chromosome 18. The WKRY gene family is manifold, performing a variety of functions, including regulation of biotic stress response (Chen et al., 2017; Jiang et al., 2017). In Arabidopsis, WKRY40 and WKRY25 proteins are negative regulators of key resistance genes and mutants show decreased susceptibility to P. syringae infection (Zheng et al., 2007; Pandey et al., 2010). Notably, transcriptional profiling indicates a possible role for another WKRY40 homologue in resistance to the South African cassava mosaic virus (Freeborough et al., 2021).
MAPK3
We identified a mitogen-activated protein kinase 3 (MAPK3) gene on chromosome 4 (Manes.04G026700). MAPK proteins are a component of signalling cascades with several known functions, including being strongly associated with SA and jasmonic acid (JA) mediated immunity. In tomato, SlMAPK3 enhances tolerance to tomato yellow leaf curl virus (TYLCV) and is upregulated in infected plants (Li et al., 2017). Although cassava contains multiple MAPK3 genes, Manes.04G026700 has the highest peptide similarity (84%) to SlMAPK3. In a variety of plant species, endogenous application of JA increases resistance to viral infection and increases transcription of MAPK genes (Shang et al., 2011).
HOPW1-1
M. esculenta HOPW1-1-interacting1 (MeWIN1) protein is a member of the plant-specific AP2/EREBP transcription factor family. MeWIN1 is a homologue of AtSHN1/WIN1, which contributes to infection resistance by various fungi by regulating the induction of pathogenesis-related and redox-related genes (Sela et al., 2013). Besides, WIN1 possibly regulates SA in Arabidopsis through interaction with hopW1-1 effector proteins in response to Pseudomonas syringae infection (Lee et al., 2008). In cotton, GhWIN2 positively regulates JA biosynthesis but negatively influences SA biosynthesis (Li et al., 2019). WIN1 is strongly linked with cuticle formation, and increased expression has been shown to enhance the physical barrier against leaf-feeding insects and, by extension, their viral load. Beyond this function, WIN1 has been shown to perform multiple roles including pathogen defence and hormone regulation.
DCL-4
Manes.11G064002, annotated as a DICER-LIKE 4 (DLC-4) protein-encoding gene, was strongly up-regulated in Namikonga, five days post-infection, compared to Albert (Amuge et al., 2017). DCL-4 proteins form part of the plant RNAi immunity system and are involved in virus-induced RNA silencing (VIGS) by mediating the biogenesis, at the site of viral infection, of small interfering RNAs. These can be triggered upon infection and act non-cell autonomously to enable viral defence mechanisms in uninfected tissue (Garcia-Ruiz et al., 2010).
LSM3
Members of the LSM family of proteins are involved in eukaryotic mRNA turnover through de-adenylation and de-capping mechanisms. Positive-stranded RNA viruses require host translation to produce RNA replication proteins which, in turn, replicate viral RNA by recruiting it from the host translation mechanism (Chen and Ahlquist, 2000; Schwartz et al., 2002). To distinguish viral from host RNA, Brome mosaic virus has been shown to utilise the mRNA processing function of LSM proteins, and LSM deficiency blocks viral RNA translation (Noueiry et al., 2003).
Rab5/6 GTPase effector protein
Rab GTPases are present on the surface of organelles where they act as recognition and binding platforms for intracellular proteins but are also widely involved in viral infection (reviewed in Spearman, 2018). Positive-stranded RNA virus replication utilises membrane-bound viral replication proteins as well as host membrane proteins, including Rab5 and Rab5 effectors (Stone et al., 2007).
LRR
The most frequent class of plant resistance genes (R genes) are denoted as NBS-LRR, which usually contain both a nucleotide-binding site domain and a leucine-rich repeat domain (McHale et al., 2006). The LRR domain is thought to be a major determinant of pathogen recognition specificity (Collier and Moffett, 2009). A total of 228 NBS-LRR type genes and 99 partial genes (without the NBS domain) were located on v4.1 of the casava genome sequence (Lozano et al., 2015). There were several LRR proteins underlying all target QTL investigated here, with 11 such genes within a 1.28 Mbp region underlying the QTL on chromosome 11. Although Kayondo et al. (2018) identified a cluster of NBS-LRR genes on chromosome 11 through genome-wide associated mapping and genomic selection, this region was outside of the QTL region investigated here. Neither Maruthi et al. (2014) nor Lozano et al. (2015) found any significant differential expression of NBS-LRR genes in cassava infected with CBSV; however, NBS-LRR genes were implicated in resistance to cassava anthracnose disease (Utsumi et al., 2016). Zhang et al. (2022) selected four NBS-LRR genes from the transcriptome databases of Lozano et al. (2015) and Utsumi et al. (2016) for further investigation and found that they were significantly induced by Xanthomonas axonopodis pv. manihotis (Xam) and salicylic acid treatment. Of these, the MeLRR1 gene (Manes. 11G053000.1) is within the QTL region on chromosome 11 investigated here.