Morphological and molecular characterization of Pratylenchus species from Yam (Dioscorea spp.) in West Africa

Publications

Share / Export Citation / Email / Print / Text size:

Journal of Nematology

Society of Nematologists

Subject: Life Sciences

GET ALERTS DONATE

ISSN: 0022-300X
eISSN: 2640-396X

DESCRIPTION

119
Reader(s)
254
Visit(s)
0
Comment(s)
0
Share(s)

SEARCH WITHIN CONTENT

FIND ARTICLE

Volume / Issue / page

Related articles

Morphological and molecular characterization of Pratylenchus species from Yam (Dioscorea spp.) in West Africa

Yao A. Kolombia * / Oluwadamilola Ogundero / Emmanuel Olajide / Nicole Viaene / P. Lava Kumar / Danny L. Coyne / Wim Bert *

Keywords : COI, D2-D3, Dioscorea, DNA, Ghana, Identification, Molecular, Morphology, Morphometrics, Nigeria, Phylogeny, Pratylenchus, Root-lesion nematodes, Taxonomy, West Africa, Yam

Citation Information : Journal of Nematology. Volume 52, Pages 1-25, DOI: https://doi.org/10.21307/jofnem-2020-126

License : (CC-BY-4.0)

Received Date : 12-October-2020 / Published Online: 22-January-2021

ARTICLE

ABSTRACT

The root-lesion nematodes (RLN), Pratylenchus spp., are among the major plant-parasitic nematodes affecting yam (Dioscorea spp.) production in West Africa. The distribution and diversity of RLN species associated with yam was investigated through a soil and tuber survey of the main producing areas in Nigeria and Ghana. Pratylenchus spp. were detected in the yam rhizosphere in 59% of 81 soil samples from Ghana and 39% of 114 soil samples from Nigeria. Pratylenchus spp. were detected in 24 of 400 tubers examined, in combination with root-knot nematodes (Meloidogyne spp.) and their associated damage of galls and crazy roots (79%), and with yam nematode (Scutellonema bradys) and their associated damage of dry rot (17%), although no specific additional symptoms were observed for Pratylenchus spp. Species of Pratylenchus were identified by their morphological features and by sequences of the D2-D3 region of the 28 S rDNA gene and the mitochondrial cytochrome oxidase I gene (COI). Pratylenchus brachyurus was the most frequent RLN species in both the rhizosphere and tubers of yam. Pratylenchus hexincisus was recovered from one tuber collected in Nigeria. While further investigations are required to establish the host status of yam for this nematode, this appears to be the first record of P. hexincisus on yam. The present taxonomical status of P. scribneri and P. hexincisus is discussed.

Graphical ABSTRACT

Yam (Dioscorea spp. L.) is an economically important crop of tropical and sub-tropical areas of the world. West Africa accounts for over 93% of the total production of this tuber with Nigeria and Ghana being the main cultivating yam countries. In these countries, yam is an important staple food providing a valuable source of carbohydrates, proteins and minerals for over 380 million people from an estimated annual production of 67 MT (Nweke et al., 1991; Orkwor, 1998; Nweke, 2016; FAO, 2018). The most important yam species cultivated for food are D. rotundata Poir., D. cayenensis Lam., D. alata L., D. dumetorum (Kunth) Pax., D. bulbifera L. and D. esculenta (Lour.) Burk. Also, yam plays an important socio-cultural role among communities and its cultivation and sale serve as a major income-generating activity for the people in yam-growing areas (Onwueme and Charles, 1994). Yam production is constrained by numerous biotic factors, however, of which plant-parasitic nematodes are among the most damaging. They affect yield and tuber quality, reducing yam production and tuber storability (Ayensu and Coursey, 1972; Bridge et al., 2005; Coyne and Affokpon, 2018). The major plant-parasitic nematodes known to cause serious damage on yam tubers are the yam nematode (Scutellonema bradys (Steiner and LeHew, 1933; Andrássy, 1958), root-knot nematodes (Meloidogyne spp.) and root-lesion nematodes (RLN) (Pratylenchus spp.) (Bridge et al., 2005; Bridge and Starr, 2007; Kolombia et al., 2016b; Coyne and Affokpon, 2018). RLN, however, have been much less studied, even though they are known to cause dry rot symptoms in tubers, indistinguishable from the symptoms caused by S. bradys (Coyne et al., 2016).

Pratylenchus coffeae (Zimmermann, 1898) Filipjev and Schuurmans Stekhoven, 1941 is the most important RLN of yam, occurring in Central America, the Caribbean Islands and the Pacific Islands (Acosta and Ayala, 1975; Coates-Beckford and Brathwaite, 1977; Bridge, 1988; Moura and Monteiro, 1995; Bridge et al., 2005; Muniz et al., 2012; Coyne and Affokpon, 2018). In Africa, P. brachyurus (Godfrey, 1929) Filipjev and Schuurmans Stekhoven, 1941, P. pseudopratensis (Seinhorst, 1968) and P. sudanensis (Loof and Yassin, 1971) are known to cause damage to yam (Coyne et al., 2003; Mudiope et al., 2007; Coyne et al., 2018) with indications that they are relatively common in the yam rhizosphere and on tubers (Adegbite et al., 2008; Kolombia et al., 2020). It was also observed that Pratylenchus spp. were associated with the galls and crazy roots caused by root-knot nematodes, or with dry rot caused by S. bradys, although with no specific additional symptoms (Kolombia et al., 2016a). Being a stenomorphic genus, Pratylenchus is easily recognizable at the genus level (low and flattened labial region, esophageal gland lobe overlapping the intestine mostly ventrally, posterior vulva V = 70–80%, with one ovary), while morphological identification at the species level is problematic due to the low number of diagnostic features and high intraspecific variability (Luc, 1987; Duncan et al., 1999; Castillo and Vovlas, 2007). To establish the diversity of Pratylenchus spp., associated with yam, surveys were conducted in the main yam producing areas in Nigeria and Ghana. The Pratylenchus populations obtained from yam tuber tissue and yam rhizosphere were morphologically characterized and molecularly confirmed by sequencing of the D2-D3 of 28 S rDNA and mitochondrial COI genes.

Materials and methods

Nematode samples

Nematode populations used in this study were obtained soil and tuber sampling undertaken across agro-ecological zones in Ghana and Nigeria during surveys conducted between 2012 and 2015 (Table 1). Nematodes from 195 yam rhizosphere and 400 tubers were recovered using the Whitehead tray immersion technique (Hooper et al., 2005). Extraction from rhizosphere was set using 100 ml soil sub-samples including all roots retrieved from soil per sample. Tubers were peeled using a kitchen peeler, chopped and three sub-samples of 5 g tuber peels were used for the extraction (Coyne et al., 2006). Extracted nematodes were collected on 28 μm sieves, rinsed and divided: one part was heat killed and fixed in 4% formalin, the other part was fixed directly in DESS solution (Yoder et al., 2006). In total, 127 nematodes, including 75 specimens from yam tubers, were used for species identification.

Table 1.

Pratylenchus spp. recovered from yam in Ghana and Nigeria, origin, code, host, altitude and GenBank numbers.

10.21307_jofnem-2020-126-t001.jpg

Morphological characterization

Nematodes from 27 samples fixed in formalin were processed to anhydrous glycerin following the glycerin-ethanol method (Seinhorst, 1959) as modified by De Grisse (1969). Permanent slides were prepared and used to record morphometrics and morphological features (Castillo and Vovlas, 2007; Inserra et al., 2007) using an Olympus BX51 DIC microscope equipped with a Nikon digital camera. Additional morphological and morphometrical data were recorded from temporary slides made from DESS fixed specimens, before DNA extraction (see Table 1).

Molecular characterization

Following morphological identification, the same individual nematodes were picked from temporary slides and used for extraction of genomic DNA using a quick alkaline lysis protocol (Janssen et al., 2016). DNA was amplified by preparing 24 μl PCR master mix comprising 16 μl double sterilized distilled water, 2.5 μl 10x buffers, 2 μl MgCl2, 0.05 μl of dNTP (10 mM), 1 μl of reverse and forward primers, 0.05 μl of Toptaq and 2 μl of nematode template DNA. The primer set D2A (5’–ACA AGT ACC GTG AGG GAA AGT TG–3’) and D3B (5’–TCG GAA GGA ACC AGC TAC TA–3’) (Subbotin et al., 2006) was used for amplification of the D2-D3 expansion regions of 28 S rDNA gene and the cytochrome c oxidase subunit 1 (COI) gene fragment was amplified using the primer set JB3Prat (5’–TTT TTT GGG CAT CCT GAA GTC TAT–3’) and JB4Prat (5’–CCT ATT CTT AAA ACA TAA TGA AAA TG–3’) following DNA amplification profile described in Kolombia (2017).

PCR products were electrophoretically separated on a 1% agarose gel and stained with ethidium bromide. PCR products were purified using the Wizard® SV Gel and PCR Clean-Up System Kit (Promega, the Netherlands) as described in the manufacturer’s instructions and sequenced by Macrogen Inc. (the Netherlands) in forward and reverse directions. Consensus sequences were assembled using GENEIOUS 9.15 (Biomatters; http://www.geneious.com) and deposited in the NCBI GenBank (Table 1).

Phylogenetic analysis

Both D2-D3 of 28 S rDNA and COI of mtDNA sequence datasets were aligned using MUSCLE (Edgar, 2004) with default settings. Outgroup taxa of each dataset were chosen based on previously published data (Subbotin et al., 2008; Liu et al., 2016). The best fit models of DNA evolution were estimated using the program jModeltest 0.1.1 (Posada, 2008) under the Akaike information criterion (AIC). Bayesian phylogenetic analysis (BI) was undertaken using MrBayes 3.2.6 for 1 × 106 generations with a general time-reversible model with a gamma distribution for the remaining sites (GTR + I + G), four runs, 20% burn-in, and subsampling frequency of 500 generations (Huelsenbeck and Ronquist, 2001) for both D2-D3 and COI.

Results

Occurrence and morphological characterization of Pratylenchus spp. from yam

From the rhizosphere, Pratylenchus spp. were detected in 48 samples (59%) collected in Ghana (Fig. 1A) and 45 samples (39%) in Nigeria (Fig. 1B). The density of Pratylenchus spp. from the rhizosphere varied from 2 to 704 individuals per 100 ml soil and roots in Ghana, and from 2 to 398 individuals in 100 ml of soil and roots in Nigeria. From 400 tubers examined, Pratylenchus spp. were recovered from just 6% of the 400 tuber peels (Figure 1C). Twenty-four tubers were infected with Pratylenchus spp., of which, 19 tubers (79%) also had galling and crazy root damage caused by the root-knot nematode (Meloidogyne spp.), 4 tubers (17%) showed dry rot symptoms caused by the yam nematode (Scutellonema bradys) while no symptoms were observed in one tuber, which had a density of 50 specimens of Pratylenchus brachyurus, per 5 g of yam peels (Figure 1D). Densities of Pratylenchus spp. were as higher as 340 nematodes in tubers with symptoms and up to 525 individuals per 5 g of yam peels in tubers with dry rot and galling, respectively. Twenty-eight populations from 12 yam tubers and 16 rhizosphere samples were studied using morphological and molecular data, which resulted in the identification of Pratylenchus brachyurus and P. hexincisus (Taylor and Jenkins, 1957) and P. zeae (Graham, 1951).

Figure 1:

Proportion of Pratylenchus spp. in the yam rhizosphere from Ghana “n = 81” (A) and Nigeria “n = 114” (B), in yam tubers “n = 400” (C) and of nematode damage symptoms on yam tubers (D)

10.21307_jofnem-2020-126-f001.jpg

Pratylenchus brachyurus was the most prevalent RLN species in Ghana and Nigeria, present in 11 of the 12 tubers used for species identification and 88% of Pratylenchus-positive rhizosphere samples. Twenty-five specimens per 5 g of yam peels of Pratylenchus hexincisus were recovered in just one tuber showing galls from Nigeria, and P. zeae was detected in 12% of the rhizosphere samples from Ghana (26 nem/100 ml soil) and Nigeria (3 nem/100 ml soil).

Systematics

Pratylenchus brachyurus Godfrey, 1929 Filipjev and Schuurmans Stekhoven, 1941 (Figures 2 and 3; Tables 2 and 3).

Table 2.

Measurements of thirteen Pratylenchus brachyurus populations from Ghana. All measurements are in μm and in the form: mean ± s.d. (range).

10.21307_jofnem-2020-126-t002.jpg
Table 3.

Measurements of thirteen Pratylenchus brachyurus populations from Nigeria.

10.21307_jofnem-2020-126-t003.jpg
Figure 2:

Pratylenchus brachyurus. Light micrographs of Female: A: Entire body; B: Esophageal region; C: Spermatheca with sperm cells; D: Posterior end of gravid female; E: Tail end; F: Lateral field at mid body; G: Vulva; H: Tail; (scale bars: B-H = 10 μm; A = 100 μm).

10.21307_jofnem-2020-126-f002.jpg
Figure 3:

Morphological variations in Pratylenchus brachyurus. A-F: Anterior regions (A-F); Lateral field at mid body (G-J); Tail region (K-Q); and Tail end (R-Y); (scale bars: 10 μm).

10.21307_jofnem-2020-126-f003.jpg

Female:

Body small 390–679 μm long, stout to moderately slender. Habitus almost straight when heat-relaxed. Lateral fields usually with four longitudinal lines; sometimes 4 to 6 lateral lines at mid body or 2 additional lateral fields faint or broken. Cephalic region slightly offset from body, with two lip annuli. Robust stylet (16.3–20.9 μm long) with stout and rounded basal knobs, 3.8–6.6 μm wide, with irregular shape on the surface. The dorsal esophageal gland opening (DEGO) at 2.0–4.3 μm posterior the stylet base. Median bulb muscular, rounded to oval. Excretory pore just anterior to region of esophago-intestinal junction, but often indistinct. Esophageal glands overlapping intestine ventrally and sometimes laterally. Reproductive system monodelphic-prodelphic, ovary with oocytes in one row, occasionally two rows. Spermatheca usually indistinct, if present, well developed, rounded to spherical, filled with sperm cells in a few specimens. Vulva at 77–88% of body length. Post-vulval uterine sac generally shorter than body diameter length (12.3–34.9 μm long). Vulva-anus distance about twice the tail length. Tail slightly tapering, terminus mostly bluntly rounded, varying from somewhat narrower, flat to slightly indented; terminus smooth.

Males: Not observed.

P. brachyurus populations described were collected from yam tubers and rhizosphere from five districts in Ghana and ten Local Government Areas (LGA) in Nigeria.

From the morphology and the morphometrics, the studied populations are in agreement with the original description of P. brachyurus, and to subsequent descriptions (Roman and Hirschmann, 1969; Corbett, 1976; Castillo and Vovlas, 2007). However, the spermatheca was filled with sperm cells in two specimens (of the same sample), which has not previously been observed. In addition, in one specimen, the vulva was located at 77% of the body, while the vulva is normally located at 81–88% of the body.

Pratylenchus hexincisus Taylor and Jenkins, 1957. (Figure 4 and Table 4).

Table 4.

Measurements of a Pratylenchus hexincisus population from Nigeria.

10.21307_jofnem-2020-126-t004.jpg
Figure 4:

Light micrographs of female Pratylenchus hexincisus. A: Anterior end; B: Entire body; C: Head; D-E: Reproductive track; F-G: Lateral field at mid body; H-I: Tail; (scale bars: A, C-I = 10 μm; B = 100 μm).

10.21307_jofnem-2020-126-f004.jpg

Female:

Body small, 367–625 μm long, stout to moderately slender. Habitus slightly straight when heat-relaxed. Lateral fields indistinct; when observed, with four to six longitudinal lines at mid body. Lateral field 6.8–7.2 μm wide at mid body with crenated margins (Figure 4). Short stylet 15 µm (11.8–16.1 μm), with rounded knobs. Median bulb oval. Cephalic region slightly offset from body, with two annuli. Esophageal glands overlapping intestine ventrally and laterally. Spermatheca rounded and obscure. Vulva located at 72.6–78%. Tail slightly tapering, terminus mostly broadly rounded.

Males: Not observed.

Remarks: The population used in this study is from one location (Otukpo) in Nigeria collected from a yam tuber.

The studied population was in agreement with the original description of P. hexincisus and to subsequent descriptions (Castillo and Vovlas, 2007; Inserra et al., 2007).

Pratylenchus zeae Graham, 1951.

(Figure 5 and Table 5).

Table 5.

Measurements of two Pratylenchus zeae populations from Ghana and Nigeria.

10.21307_jofnem-2020-126-t005.jpg
Figure 5:

Light micrographs of female Pratylenchus zeae. A: Entire body; B: Anterior region; C: Head; D: esophageal region; E-F: Lateral field at mid body; G-H: Reproductive tract showing small round spermatheca; I-K: Tail; (scale bars: B-K, = 10 μm; A = 100 μm).

10.21307_jofnem-2020-126-f005.jpg

Female:

Body slender, short 381–561 μm long, and near-straight when heat-relaxed. Cephalic region continuous with body and bearing three annuli. Lateral fields with four lines at mid body. Stylet 14.6–16.9 µm long, with broad, anteriorly flattened basal knobs. Esophageal glands overlapping intestine ventrally and laterally. Ovary usually long. DEGO at 3 μm posterior to the stylet base. Excretory pore just anterior to the esophago-intestinal junction. Spermatheca rounded, without sperm. Vulva at 70–73.2%. Post-vulval uterine sac short, about 1 body diam. long. Tail tapering, with 18–21 annuli terminating in an almost pointed tip.

Males: Not observed.

Remarks: Based on the morphology and the morphometrics, the studied populations were in agreement with the original description of P. zeae and to the neotype female and other descriptions of P. zeae (Fortuner, 1976; Castillo and Vovlas, 2007).

Molecular characterization of Pratylenchus spp. from yam

The D2-D3 of 28 S rDNA gene

The D2-D3 alignment included 80 Pratylenchus sequences, and two outgroup sequences. Thirteen new D2-D3 sequences were obtained in the present study. Following the numbering proposed by Subbotin et al. (2008), the BI tree contained five highly supported clades except for clade III (Figure 6).

Figure 6:

Bayesian 50% majority rule consensus tree from four runs as inferred from analysis of the D2-D3 of 28 S rRNA gene sequence alignment under the GTR + I + G model. (-lnL = 11091.5259; AIC = 22563.051780; freqA = 0.1873; freqC = 0.2354; freqG = 0.3250; freqT = 0.2523; R(a) = 1.0893; R(b) = 3.9431; R(c) = 2.1703; R(d) = 0.4799; R(e) = 5.3436; R(f) = 1.0000; p-inv = 0.3210; gamma shape = 0.8480). Posterior probability values exceeding 50% are given on appropriate clades). New sequences are indicated by bold font.

10.21307_jofnem-2020-126-f006.jpg

The sequences of P. hexincisus generated in this study formed a very well supported clade without internal resolution with P. hexincisus sequences from China (MT362902 and MT362903), P. hexincisus sensu Inserra et al., 2007 obtained from the type locality (DQ498832 and DQ498833), P. scribneri Steiner in Sherbakoff & Stanley, 1943 (EU130864, EU130865, JX047001 and KM094196) and P. agilis (Thorne and Malek, 1968) (EU130841). However, sequences of P. scribneri sensu Inserra et al. (2007) (DQ498830) and P. scribneri from California U47554 (Al-Banna et al., 1997) formed a separate clade. The intraspecific variation of our P. hexincisus populations was 1–2 bp (0.1–0.3%) and differed only 0–2 bp (0–0.3%) with P. hexincisus from the type location (Inserra et al., 2007) (DQ498832 and DQ498833) and 0–3 bp (0–0.4%) with P. agilis (EU130841) and 1–5 bp (0.1–0.6%) with P. scribneri (EU130864, EU130865, JX047001 and KM094196), while it was clearly different (14–17 bp, 2.5–5.7%) from P. scribneri sensu Inserra et al. (2007) (DQ498830).

Sequences of P. brachyurus from this study, together with P. brachyurus sequences from GenBank were grouped in a well-supported subclade C of the clade III. The intraspecific variation of P. brachyurus was 2–51 bp (0.3–6.6%) and nucleotide difference between P. brachyurus and the most similar sequence, P. penetrans, was 152–177 bp (19.5–23%).

Pratylenchus zeae sequences formed a well-supported clade together with P. zeae sequences from GenBank. The intraspecific sequence variation of P. zeae was 23–65 bp (3.2–9%) and the interspecific sequence difference with the closest related species, Pratylenchus sp. (JX261959), was 23–80 bp (3.2–11.1%).

The mitochondrial COI gene

The COI sequences alignment was 422 bp in length and included 58 sequences of Pratylenchus including eight newly generated sequences, and four outgroup taxa (Meloidogyne, Hirschmanniella, Pratylenchoides and Radopholus). The BI tree contained five highly supported clades following numbering proposed by Subbotin et al. (2008) (Figure 7).

Figure 7:

Bayesian 50% majority rule consensus tree from four runs as inferred from analysis of the COI mtDNA gene sequence alignment under the GTR + I + G model. (-lnL = 6250.9879; AIC = 12821.975780; freqA = 0.2952; freqC = 0.0915; freqG = 0.1808; freqT = 0.4325; R(a) = 0.1894; R(b) = 6.2295; R(c) = 1.8356; R(d) = 5.2302; R(e) = 5.3626; R(f) = 1.0000; p-inv = 0.2340; gamma shape = 0.6370). Posterior probability values exceeding 50% are given on appropriate clades). Original sequences are indicated by bold font.

10.21307_jofnem-2020-126-f007.jpg

Sequences of P. hexincisus from yam formed a well-supported clade with P. hexincisus sequences from China, Italy and the USA and P. scribneri sequences from China and the USA, with P. loosi (PP 0.84) as sister species. The sequences of P. hexincisus generated in this study and P. hexincisus sequences from Italy (KY828322) and China (KY828321) and P. scribneri (MK877999: USA; MK878000: USA; MK878268: USA, KY424093: China; KY424090: China; KY424089: China; KX349425: China) were very similar 0–8 bp (0–1.93%). However, these sequences were different from the recently deposited P. hexincisus sequences from Wheat and Corn in the USA (MK877467, MK877469, MK877471, MK877482, MK877492) with 51–81 bp (19.8–21.1%). Sequences of the closest related species, P. loosi, differed 54–102 bp (19.1–24.5%).

Sequences of P. brachyurus from this study, together with other P. brachyurus sequences available in the NCBI GenBank database formed a well-supported subclade C of clade III, sister to P. oleae (clade IV) (Palomares-Rius et al., 2014). The intraspecific variation of P. brachyurus was 0–16 bp (0–4.1%) and the interspecific sequence difference between P. brachyurus and P. oleae was 78–81 bp (21.1–22%).

Pratylenchus zeae sequences formed a well-supported clade (VI) together with P. zeae sequences from GenBank. The intraspecific sequence variations of P. zeae were 0–37 bp (0–9.6%) and the interspecific sequence difference was 99–112 bp (25.9–28.6%) with P. parazeae, the closest related species.

Discussion

Prior to the current study, seven RLN species, i.e. P. brachyurus, P. crenatus (Loof, 1960), P. coffeae, P. loosi (Loof, 1960), P. sudanensis, P. pseudopratensis and P. zeae have been reported from yam rhizosphere and yam tubers (Caveness, 1967; Bridge, 1973, 1988; Coyne et al., 2003; Varghese and Mohandas, 2004; Bridge and Starr, 2007; Mudiope et al., 2007; Osei et al., 2015; Coyne et al., 2018). Using a combination of morphological and molecular identification, P. brachyurus and P. hexincisus were identified from yam tubers, while P. zeae was recovered from the yam rhizosphere only. Pratylenchus brachyurus, a cosmopolitan species, appears as the predominant species on yam in Nigeria and Ghana, which is in agreement with other studies that have reported P. brachyurus from yam in Nigeria and West Africa (Luc and de Guiran, 1960; Unny and Jerath, 1965; Caveness, 1967; Bridge, 1972, 1973). In this region, the polyphagous P. brachyurus has also been recorded as a pest of numerous crops (Miège, 1957; Luc and de Guiran, 1960; Bridge, 1973; Egunjobi, 1974; Egunjobi and Larinde, 1975; Guerout, 1975; Coyne et al., 1999; Castillo and Vovlas, 2007), including an interception from Colocasia sp. (another tuber crop) from Nigeria to China (Zhao et al., 2011). Also, it is known to affect plant growth and the yield of crops in West Africa, for instance on pineapple (Guerout, 1975) and cassava (De Guiran, 1965).

Pratylenchus species, and in particular P. coffeae are known to cause “dry rot” on yam tubers, a condition similar to that caused by S. bradys, based on what is known for P. coffeae and P. sudanensis (Bridge et al., 2005; Bridge and Starr, 2007; Coyne and Affokpon, 2018). However, symptoms of P. brachyurus or its effects on yam production are not well known, Given the predominance of P. brachyurus in yam tubers and yam rhizosphere, it appears that this species is a major RLN on yam in West Africa. However, more work is necessary to clearly establish the effect of this species on yam growth, yield and tuber quality. The ability of P. brachyurus to survive a long period without a host and its polyphagous nature, could make its management particularly difficult, without the use of resistant cultivars.

Pratylenchus zeae, retrieved only from the yam rhizosphere of one sample in Ghana and one in Nigeria, is a commonly occurring species on other crops in West Africa (Fortuner, 1976; Plowright and Hunt, 1994; Coyne et al., 1996; Castillo and Vovlas, 2007). Pratylenchus zeae was reported on yam in Nigeria (Bridge, 1973) but has never been reported on yam rhizosphere in Ghana. Its absence from tuber tissue, however, indicates that yam tubers may not support P. zeae and that its occurrence in this case may be related to other plant species occurring together with the sampled yam.

Pratylenchus coffeae, one of the major plant-parasitic nematodes of yam in the Americas and the Pacific Islands was not recorded in any of the samples collected from Ghana and Nigeria. A similar observation was reported by Kwoseh et al. (2005) in Ghana. This remarkable absence from P. coffeae supports the statement of Duncan and Moens (2013) that “P. coffeae is a pest of yam, interestingly, not in Africa”, despite being present on other crops in both localities (Duncan et al., 1999; Pourjam et al., 1999; Speijer et al., 2001; Bridge et al., 2005; Kwoseh et al., 2005; Coyne and Affokpon, 2018). Although Osei et al. (2015) recorded P. coffeae on yam in Ghana, but its identity was not ascertained by molecular method.

Traditional taxonomy can have serious limitations for differentiating species of Pratylenchus (Luc, 1987; Subbotin et al., 2008). In the current study, however, populations of P. brachyurus were, despite a remarkable intraspecific variation, relatively easily identified based on morphology and morphometrics, including the number of lip annuli (2), stylet length (17–21 µm), vulva position (77–88%), and a bluntly rounded tail, which while highly variable was never conically pointing, posteriorly confirmed by molecular data. Our observations agree with the descriptions provided by Corbett (1976) and Castillo and Vovlas (2007), including its well-known intraspecific variation on the tail, lips and knobs shape (Roman and Hirschmann, 1969; Corbett, 1976; Tarjan and Frederick, 1978; Payan, 1989). However, the presence of a developed sperm-filled spermatheca in 2 of the 108 analysed specimens was observed for the first time.

In this study, P. hexincisus was recorded from yam for the first time, although just from one sample. The relatively high number of specimens retrieved from yam peels unequivocally demonstrates its association with the tuber. Therefore, infection studies to prove Koch’s postulates are required to demonstrate that P. hexincisus is a pest of yam. Pratylenchus hexincisus recorded from Benue State, Nigeria, is morphologically very similar to P. scribneri, which has been reported on maize in the neighbouring Western region of Nigeria (Anonymous, 1975). Molecular researches are necessary to establish if both species represent two different species or are conspecific.

The observed morphology and morphometrics of P. hexincisus agreed with the original description (Taylor and Jenkins, 1957), although variability in the number of lines in the lateral field, with four to six lines have been observed. This variation is known for P. brachyurus (Castillo and Vovlas, 2007) as well as other members of the genus Pratylenchus, for example four to seven lines in the lateral field have been reported in P. neglectus (Rensch, 1924) Filipjev and Schuurmans Stekhoven, 1941 (Corbett and Clark, 1983) and four to six lines in P. scribneri (Roman and Hirschmann, 1969; Loof, 1985; Inserra et al., 2007). Originally described from corn in Maryland, USA (Taylor and Jenkins, 1957), P. hexincisus was distinguished as a new species, separate from P. scribneri, by the presence of 6 lines in the lateral field, its smaller size and the fact that no spermatheca was observed. However, morphological studies of both species have revealed high morphological similarities, including the presence of empty spermatheca and variation in the number of lines in the lateral field (Roman and Hirschmann, 1969; Corbett and Clark, 1983; Castillo and Vovlas, 2007; Inserra et al., 2007; Ozbayrak et al., 2019). Yet, a comprehensive investigation by Inserra et al., (2007), including P. hexincisus from the type locality (DQ498832-33) and a reference population of P. scribneri (DQ498830), showed a molecular distinction between P. hexincisus and P. scribneri, based on the D2-D3 region of the 28 S rDNA. Moreover, this reference P. scribneri population (DQ498830) also formed a distinct clade with P. scribneri (U47551) reported by Al-Banna et al. (1997). Furthermore, the authors also highlighted morphological characters that could discriminate both species, including the presence of a rectangular-elongated spermatheca in P. hexincisus versus rounded in P. scribneri. However, although the D2-D3 sequences of the isolates of yam were virtually identical to the sequences of P. hexincisus (Inserra et al., 2007), our population did not show an elongated spermatheca but always a rounded spermatheca. On the other hand, our population showed crenated outer incisures of the lateral field (Figure 4) as described in the original description of P. hexincisus (Taylor and Jenkins, 1957). The number of lateral lines appeared to be less discriminative to distinguish P. hexincisus and P. scribneri as six lateral lines were also observed in P. scribneri (Inserra et al., 2007). Similar variability on the lateral lines was observed in P. brachyurus reported in this study indicating that caution is needed when using this character to discriminate species in the genus Pratylenchus.

Although the D2-D3 sequences of P. hexincisus in our study were similar with those of P. scribneri from Imperial Valley, California and Vero Beach, Florida (EU130864-65) the uncertainty of the identification of the isolates was already mentioned by Subbotin et al. (2008) and these sequences may therefore represent P. hexincisus.

Augmenting the problem to delimitate both species, the COI sequences P. hexincisus (MK877467, MK877469, MK877485, MK877471, MK877482, MK877492) in the study reported by Ozbayrak et al. (2019) were clearly different from P. hexincisus from yam when assessed in the current study. Remarkably, our P. hexincisus COI sequences were similar to the sequences of P. scribneri (MK877999, MK878000, MK878268) Ozbayrak et al. (2019). Also, P. scribneri D2-D3 and COI sequences from China (JX047001, KM094196, KX349425) were similar to our P. hexincisus sequences and these Chinese D2-D3 sequences are also similar to those from the P. hexincisus type locality (Inserra et al., 2007). The unclear identity of the COI sequences could be resolved if the materials from Al-Banna et al. (1997) and Inserra et al. (2007) could be linked to COI sequences, i. e. if the P. hexincisus and P. scribneri COI sequences sensu Ozbayrak et al. (2019) agree with the identity of the material from Al-Banna et al. (1997) and Inserra et al. (2007). However, this is likely not the case since, according to the supplementary D2D3 tree in Ozbayrak et al. (2019), their P. scribneri sequences are different to the P. scribneri (DQ498830) from Inserra et al. (2007).

In summary, P. hexincisus and P. scribneri have similar, indeed overlapping, morphometric characteristics and shared morphological characters, leading to a confuse and difficult identification. Hence, a topotype population of P. scribneri is needed to solve the identity and validity of P. scribneri and P. hexincisus, as suggested by Inserra et al. (2007) and Subbotin et al. (2008). Likewise, the D2-D3 sequence of P. agilis Thorne and Malek, 1968 is also similar to P. hexincisus sensu Inserra et al. (2007), as provided and mentioned by Subbotin et al. (2008). Loof (1978) had already doubted the validity of P. agilis and the species was considered as species inquerendae (Frederick and Tarjan, 1989). This was confirmed by ITS sequences and isozyme analysis. Pratylenchus agilis was proposed as a junior synonym of P. scribneri (Hernández et al., 2000), although Waeyenberge et al. (2000) indicated differences between P. scribneri and P. agilis with respect to ITS-rDNA length and the RFLPs.

Evidently, additional morphological and molecular characterizations are required to further analyses the species group of P. scribneri, P. hexincisus and P. agilis.

Acknowledgements

This work was supported by the special research funds UGent (BOF-DOS B/12892/01 and BOF18/DOS/066); the Yam Improvement for Income and Food Security in West Africa (YIIFSWA) project funded by the Bill & Melinda Gates Foundation (BMGF) to IITA; and the CGIAR Research Program on Roots, Tubers and Bananas (CRP-RTB). The authors thank Marjolein Couvreur, University of Ghent, Nematology Research Unit, for technical assistance.

References


  1. Acosta, N. and Ayala, A. 1975. Pathogenicity of Pratylenchus coffeae, Scutellonema bradys, Meloidogyne incognita, and Rotylenchus reniformis on Dioscorea rotundata . Journal of Nematology 7:1–6.
  2. Adegbite, A. A. , Saka, J. O. , Agbaje, G. O. and Osuloye, F. O. 2008. Survey of plant-parasitic nematodes associated with yams in Ogun and Osun states of Nigeria. Journal of Plant Protection Research 48:421–428.
  3. Andrássy, I. 1958. Hoplolaimus tylenchifonnis Daday, 1905 (syn. H. coronatus Cobb, 1923) und die Gattungen der Unterfamilie Hoplolaiminae Filipjev, 1936. Nematologica 3:44–56.
  4. Anonymous 1975. Annual Report 1973-74, Nigeria Federal Department of Agricultural Research.
  5. Ayensu, E. S. and Coursey, D. G. 1972. Guinea yams:the botany, ethno-botany, use and possible future of yams in West Africa. Economic Botany 26:301–318.
  6. Bridge, J. 1972. Nematode problems with yams (Dioscorea spp.) in Nigeria. Tropical Pest Management 18:89–91.
  7. Bridge, J. 1973. Nematodes as pests of yams in Nigeria. Mededelingen van de Faculteit Landbouwwetenschappen, Rijksuniversiteit Gent 38:841–852.
  8. Bridge, J. 1988. Plant-parasitic nematode problems in the Pacific islands. Journal of Nematology 20:173–183.
  9. Bridge, J. and Starr, J. L. 2007. Plant nematodes of agriculture importance:a color handbook Manson Publishing, London.
  10. Bridge, J. , Coyne, D. L. and Kwoseh, C. K. 2005. “Nematode parasites of tropical root and tuber crops (excluding potatoes)”, In Luc, M. , Sikora, R. A. and Bridge, J. (Eds), Plant Parasitic Nematodes in Subtropical and Tropical Agriculture CABI, Wallingford, pp. 221–258.
  11. Castillo, P. and Vovlas, N. 2007. Pratylenchus (Nematoda: Pratylenchidae): diagnosis, biology, pathogenicity and management. Nematology Monographs and Perspectives, 6. Brill, Leiden and Boston, MA.
  12. Caveness, F. E. 1967. Nematology Studies. End of Tour Progress Report on the Nematology Project USAID, Lagos, 135pp.
  13. Coates-Beckford, P. L. and Brathwaite, C. W. D. 1977. Comparison of various treatments for the control of Pratylenchus coffeae in yam. Nematropica 7:20–26.
  14. Corbett, D. C. M. 1976. Pratylenchus brachyurus. C.I.H. Description of plant-parasitic nematodes, Set 6, No. 89. CAB International, Wallingford.
  15. Corbett, D. C. M. and Clark, S. A. 1983. Surface features in the taxonomy of Pratylenchus species. Revue de Nématologie 6:85–98.
  16. Coyne, D. L. and Affokpon, A. 2018. “Nematode parasites of tropical root and tuber crops”, In Sikora, R. A. , Coyne, D. L. , Hallman, J. and Timper, P. (Eds), 2018. Plant Parasitic Nematodes in Subtropical and Tropical Agriculture 3rd edition, CAB International, Wallingford, pp. 252–289.
  17. Coyne, D. L. , Plowright, R. A. and Fofana, I. 1996. Preliminary investigations of nematodes associated with rice in Guinea, Benin and Togo. Afro-Asian Journal of Nematology 6:70–73.
  18. Coyne, D. L. , Plowright, R. A. , Twumasi, J. and Hunt, D. J. 1999. Prevalence of plant parasitic nematodes associated with rice in Ghana with a discussion of their importance. Nematology 1:399–405.
  19. Coyne, D. L. , Talwana, H. A. L. and Maslen, N. R. 2003. Plant-parasitic nematodes associated with root and tuber crops in Uganda. African Plant Protection 9:87–98.
  20. Coyne, D. L. , Kolombia, Y. A. , Kariuki, G. , Luambano, N. and Bert, W. 2016. First report of dry rot disease of yam caused by Scutellonema bradys in East Africa. Plant Disease 100:1794.
  21. Coyne, D. L. , Tchabi, A. , Baimey, H. , Labuschagne, N. and Rotifa, I. 2006. Distribution and prevalence of nematodes (Scutellonema bradys and Meloidogyne spp.) on marketed yam (Dioscorea spp.) in West Africa. Field Crops Research 96:142–150.
  22. Coyne, D. L. , Cortada, L. , Dalzell, J. J. , Claudius-Cole, A. O. , Haukeland, S. , Luambano, N. and Talwana, H. 2018. Plant-parasitic nematodes and food security in Sub-Saharan Africa. Annual Review of Phytopathology 56:381–403.
  23. De Grisse, A. T. 1969. Redescription ou modification de quelques techniques utilisées dans l’étude des nematodes phytoparasitaires. Landbouwwetenschappen Gent 34:351–369.
  24. De Guiran, G. 1965. “Nematodes associes au manioc dans le sud du Togo”, Comptes Rendues des Travaux du Congres de la Protection Culture Tropicales, Chambre de commerce et d’industrie, Marseilles, pp. 677–680.
  25. Duncan, L. W. and Moens, M. 2013. “Migratory endoparasitic nematodes”, In Perry, R. N. and Moens, M. (Eds), Plant nematology CAB International, Wallingford, pp. 144–178.
  26. Duncan, L. W. , Inserra, R. N. , Thomas, W. K. , Dunn, D. , Mustika, I. , Frisse, L. M. , Mendes, M. L. , Morris, K. and Kaplan, D. T. 1999. Molecular and morphological analysis of isolates of Pratylenchus coffeae and closely related specie. Nematropica 29:61–80.
  27. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792–1797.
  28. Egunjobi, O. A. 1974. Nematodes and maize growth in Nigeria. I. Population dynamics of Pratylenchus brachyurus in and about the roots of maize and its effects on maize production at Ibadan. Nematologica 20:181–186.
  29. Egunjobi, O. A. and Larinde, M. A. 1975. Nematodes and maize growth in Nigeria. II. Effects of some amendments on populations of Pratylenchus brachyurus and on the growth and production of maize (Zea mays) in Nigeria. Nematologia Mediterranea 3:65–73.
  30. FAO . 2018. Food and Agriculture Organization of the United Nations, Rome, Available at http://www.fao.org/faostat/en/ (accessed August 15, 2020).
  31. Filipjev, I. N. and Schuurmans Stekhoven, J. H. Jr. 1941. A manual of agricultural helminthology E. J. Brill, Leiden, p. 878.
  32. Fortuner, R. 1976. Pratylenchus zeae. C. I. H. Description of plant-parasitic nematodes, Set 6, No. 77.
  33. Frederick, J. J. and Tarjan, A. C. 1989. A compendium of the genus Pratylenchus Filipjev, 1936 (Nemata: Pratylenchidae). Revue de nématologie 12:243–256.
  34. Godfrey, G. H. 1929. A destructive root disease of pineapple and other plants due to Tylenchus brachyurus . Phytopathology 19:611–629.
  35. Graham, T. W. 1951. Nematode root rot of tobacco and other plants. Bulletin 390. South Carolina Agricultural Experiment Station, Clemson Agricultural College.
  36. Guerout, R. 1975. Nematodes of pineapple: a review. Pest Management 21:123–140.
  37. Hernández, M. A. , Jordana, R. , Goldaracena, A. and Pinochet, J. 2000. SEM observations on nine species of the genus Pratylenchus Filipjev, 1936 (Nematoda: Pratylenchidae). Journal of Nematode Morphology and Systematics 3:165–174.
  38. Hooper, D. J. , Hallmann, J. and Subbotin, S. A. 2005. “Methods for extraction, processing and detection of plant and soil nematodes”, In Luc, M. , Sikora, R. A. and Bridge, J. (Eds), Plant parasitic nematodes in subtropical and tropical agriculture CAB International, Wallingford, pp. 53–86.
  39. Huelsenbeck, J. P. and Ronquist, F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755.
  40. Inserra, R. N. , Troccoli, A. , Gozel, U. , Bernard, E. C. , Dunn, D. and Duncan, L. W. 2007. Pratylenchus hippeastri n. sp. (Nematoda: Pratylenchidae) from amaryllis in Florida with notes on P. scribneri and P. hexincisus . Nematology 9:25–42.
  41. Janssen, T. , Karssen, G. , Verhaeven, M. , Coyne, D. and Bert, W. 2016. Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution. Scientific Reports 6:22591.
  42. Kolombia, Y. A. 2017. Diversity and characterization of plant-parasitic nematodes associated with yam (Dioscorea spp.) in West Africa and a novel approach for rapid resistance screening. PhD Thesis, University of Ghent, Ghent.
  43. Kolombia, Y. A. , Kumar, L. P. , Viaene, N. , Bert, W. and Coyne, D. L. 2016a. “Nematodes on yam in Nigeria: situation on the ground”, 32nd Symposium of European Society of Nematologists, Braga, Brada, 271.
  44. Kolombia, Y. A. , Kumar, P. L. , Claudius-Cole, A. O. , Karssen, G. , Viaene, N. , Coyne, D. and Bert, W. 2016b. First report of Meloidogyne enterolobii causing tuber galling damage on white yam (Dioscorea rotundata) in Nigeria. Plant Disease 100:10.
  45. Kolombia, Y. A. , Kumar, P. L. , Adewuyi, O. , Korie, S. , Viaene, N. , Bert, W. and Coyne, D. L. 2020. Distribution, prevalence and severity of damages caused by nematodes on yam (Dioscorea rotundata) in Nigeria. Nematropica 50:1–18.
  46. Kwoseh, C. K. , Plowright, R. A. , Bridge, J. and Asiedu, R. 2005. Yam-based farm practices and nematode problems in stored yams (Dioscorea spp.) in Ghana. Journal of Science and Technology 25:35–43.
  47. Liu, X. , Wang, H. , Lin, B. , Tao, Y. , Zhuo, K. and Liao, J. 2016. Loop-mediated isothermal amplification based on the mitochondrial COI region to detect Pratylenchus zeae . European Journal of Plant Pathology 48:435–446.
  48. Loof, P. A. A. 1985. Pratylenchus scribneri. C. I. H. Description of plant-parasitic nematodes, Set 6, No. 89.
  49. Loof, P. A. A. and Yassin, A. M. 1971. Three new plant-parasitic nematodes from the Sudan, with notes on Xiphinema basiri Siddiqi, 1959. Nematologica 16: 537–546.
  50. Luc, M. 1987. A reappraisal of Tylenchida (Nemata). 7. The family Pratylenchidae Thorne, 1949. Revue de Nématologie 10:203–218.
  51. Luc, M. and de Guiran, G. 1960. Les nématodes associés aux plantes de l’Ouest africain: liste préliminaire. L’Agronomie Tropicale 15:434–449.
  52. Miège, J. 1957. Influence de quelques caractères des tubercules semences sur la levée et le rendement des ignames cultivées. Journal d’ Agriculture Tropicale et de Botanique Appliquée 4:314–342.
  53. Moura, R. M. and Monteiro, A. R. 1995. Pratylenchus coffeae on yams in Brazil. Fitopatologia Brasileira 20:256.
  54. Mudiope, J. , Speijer, P. R. , Coyne, D. L. , Maslen, R. N. and Adipala, E. 2007. Nematode distribution and damage to yam in Central and Eastern Uganda. African Crop Science Journal 15:93–99.
  55. Muniz, M. F. S. , Silva, E. J. , Castro, J. M. C. , Rocha, F. S. , Alencar, L. M. C. and Gonzaga, V. 2012. Intensity of dry rot disease of yam in the state of Alagoas, Brazil. Nematropica 42:198–200.
  56. Nweke, F. I. 2016. Yam in West Africa: food, money, and more Michigan State University Press.
  57. Nweke, F. I. , Ugwu, B. O. , Asadu, C. L. A. and Ay, P. 1991. Production costs in the yam-based cropping systems of south-western Nigeria. Resource and Crop Management Division. Research Monograph 6. IITA, Ibadan.
  58. Onwueme, I. C. and Charles, W. B. 1994. Tropical root and tuber crops: production, perspectives and future prospects. (FAO Plant Product. Protect. Paper 126). FAO, Rome.
  59. Orkwor, G. C. 1998. “The importance of yams”, In Orkwor, G. C. , Asiedu, R. and Ekanayake, I. J. (Eds), Food Yams: Advances in Research IITA/NRCRI, Nigeria, pp. 1–12.
  60. Osei, K. , Danso, Y. , Otoo, E. , Adomako, J. , Sackey-Asante, J. and Abugri, B. 2015. Evaluation of yam varieties for reaction to plant parasitic nematodes infestation in three agro - ecologies of Ghana. Academic Research Journal of Agricultural Science and Research 3:201–206.
  61. Ozbayrak, M. , Todd, T. , Harris, T. , Higgins, R. , Powers, K. , Mullin, P. , Sutton, L. and Powers, T. 2019. A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North America. Journal of Nematology 51:1–21.
  62. Palomares-Rius, J. E. , Guesmi, I. , Horrigue-Raouani, N. , Cantalapiedra-Navarrete, C. , Liébanas, G. and Castillo, P. 2014. Morphological and molecular characterisation of Pratylenchus oleae n. sp.(Nematoda: Pratylenchidae) parasitizing wild and cultivated olives in Spain and Tunisia. European Journal of Plant Pathology 140:53–67.
  63. Payan, L. A. 1989. The intraspecific variation of Pratylenchus brachyurus University of Florida.
  64. Plowright, R. A. and Hunt, D. J. 1994. Plant parasitic nematodes of upland, hydromorphic and inland swamp rice ecosystems in Côte d’Ivoire. Afro-Asian Journal of Nematology 4:61–67.
  65. Posada, D. 2008. jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25:1253–1256.
  66. Pourjam, E. , Waeyenberge, L. , Moens, M. and Geraert, E. 1999. Morphological, morphometrical and molecular study of Pratylenchus coffeae and P. loosi (Nematoda: Pratylenchidae). Mededelingen Faculteit Landbouwkundige En Toegepaste Biologische Wetenschappen, Universiteit Gent 64:391–401.
  67. Rensch, D. 1924. Aphelenchus neglectus sp. n. eine neue parasitäre Nematodenart. Sonderabdruck aus dem Zoologischen Anzeiger. 59:277–280.
  68. Roman, J. and Hirschmann, H. 1969. Morphology and morphometrics of six species of Pratylenchus . Journal of Nematology 1:363–386.
  69. Seinhorst, J. W. 1959. A rapid method for the transfer of nematodes from fixative to anhydrous glycerin. Nematologica 4:67–69.
  70. Seinhorst, J. W. 1968. Three new Pratylenchus species with a discussion of the structure of the cephalic framework and of the spermatheca in this genus. Nematologica 14:497–510.
  71. Sherbakoff, C. D. and Stanley, W. W. 1943. The more important diseases and insect pests of crops in Tennessee. Tennessee Agriculture Experiment Station Bulletin 186:1–142.
  72. Speijer, P. R. , De Waele, D. and Rotimi, M. O. 2001. Plant parasitic nematodes associated with plantain (Musa spp., AAB-group) in southern Nigeria and their relative importance compared to other biotic constraints. Nematology 3:423–436.
  73. Steiner, G. R. and LeHew, R. R. 1933. Hoplolaimus bradys n. sp. (Tylenchidae, Nematoda), the cause of a disease of yam (Dioscorea sp.). Zoologischer Anzeiger 101:260–264.
  74. Subbotin, S. A. , Sturhan, D. , Chizhov, V. N. , Vovlas, N. and Baldwin, J. G. 2006. Phylogenetic analysis of Tylenchida Thorne, 1949 as inferred from D2 and D3 expansion fragments of the 28S rRNA gene sequences. Nematology 8:455–474.
  75. Subbotin, S. A. , Ragsdale, E. J. , Mullens, T. , Roberts, P. A. , Mundo-Ocampo, M. and Baldwin, J. G. 2008. A phylogenetic framework for root lesion nematodes of the genus Pratylenchus (Nematoda): evidence from 18S and D2-D3 expansion segments of 28S ribosomal RNA genes and morphological characters. Molecular Phylogenetics and Evolution 48:491–505.
  76. Tarjan, A. C. and Frederick, J. J. 1978. Intraspecific morphological variation among populations of Pratylenchus brachyurus and P. coffeae . Journal of Nematology 10:152–160.
  77. Taylor, D. and Jenkins, W. 1957. Variation within the nematode genus Pratylenchus, with the descriptions of P. hexincisus, n. sp. and P. subpenetrans, n. sp. Nematologica 2:159–174.
  78. Thorne, G. and Malek, R. B. 1968. Nematodes of the Northern Great Plains. I. Tylenchida. South Dakota Agricultural Experimental Station. Technical Bulletin 31:111.
  79. Unny, K. L. and Jerath, M. L. 1965. Parasitic nematodes. Plant Disease Reporter 49:875–876.
  80. Varghese, R. and Mohandas, C. 2004. Pratylenchus loosi, a new record on Dioscorea rotundata . Indian Journal of Nematology 34:221–222.
  81. Waeyenberge, L. , Ryss, A. , Moens, M. , Pinochet, J. and Vrain, T. C. 2000. Molecular characterisation of 18 Pratylenchus species using rDNA restriction fragment length polymorphism. Nematology 2:135–142.
  82. Yoder, M. , De Ley, I. T. , King, I. W. , Mundo-Ocampo, M. , Mann, J. , Blaxter, M. , Poiras, L. and De Ley, P. 2006. DESS: a versatile solution for preserving morphology and extractable DNA of nematodes. Nematology 8:367–376.
  83. Zimmermann, A. W. P. 1898. De nematoden der koffiewortels. Deel I. Mededelingen uit’s Lands Plantentuin 27:1–64.
  84. Zhao, L. , Cui, R. , Wang, J. , Hu, X. , Zhong, G. and Zhang, Z. 2011. Pratylenchus brachyurus was intercepted in Colocasia sp. from Nigeria. Plant Quarantine 25:35–38.
XML PDF Share

FIGURES & TABLES

Figure 1:

Proportion of Pratylenchus spp. in the yam rhizosphere from Ghana “n = 81” (A) and Nigeria “n = 114” (B), in yam tubers “n = 400” (C) and of nematode damage symptoms on yam tubers (D)

Full Size   |   Slide (.pptx)

Figure 2:

Pratylenchus brachyurus. Light micrographs of Female: A: Entire body; B: Esophageal region; C: Spermatheca with sperm cells; D: Posterior end of gravid female; E: Tail end; F: Lateral field at mid body; G: Vulva; H: Tail; (scale bars: B-H = 10 μm; A = 100 μm).

Full Size   |   Slide (.pptx)

Figure 3:

Morphological variations in Pratylenchus brachyurus. A-F: Anterior regions (A-F); Lateral field at mid body (G-J); Tail region (K-Q); and Tail end (R-Y); (scale bars: 10 μm).

Full Size   |   Slide (.pptx)

Figure 4:

Light micrographs of female Pratylenchus hexincisus. A: Anterior end; B: Entire body; C: Head; D-E: Reproductive track; F-G: Lateral field at mid body; H-I: Tail; (scale bars: A, C-I = 10 μm; B = 100 μm).

Full Size   |   Slide (.pptx)

Figure 5:

Light micrographs of female Pratylenchus zeae. A: Entire body; B: Anterior region; C: Head; D: esophageal region; E-F: Lateral field at mid body; G-H: Reproductive tract showing small round spermatheca; I-K: Tail; (scale bars: B-K, = 10 μm; A = 100 μm).

Full Size   |   Slide (.pptx)

Figure 6:

Bayesian 50% majority rule consensus tree from four runs as inferred from analysis of the D2-D3 of 28 S rRNA gene sequence alignment under the GTR + I + G model. (-lnL = 11091.5259; AIC = 22563.051780; freqA = 0.1873; freqC = 0.2354; freqG = 0.3250; freqT = 0.2523; R(a) = 1.0893; R(b) = 3.9431; R(c) = 2.1703; R(d) = 0.4799; R(e) = 5.3436; R(f) = 1.0000; p-inv = 0.3210; gamma shape = 0.8480). Posterior probability values exceeding 50% are given on appropriate clades). New sequences are indicated by bold font.

Full Size   |   Slide (.pptx)

Figure 7:

Bayesian 50% majority rule consensus tree from four runs as inferred from analysis of the COI mtDNA gene sequence alignment under the GTR + I + G model. (-lnL = 6250.9879; AIC = 12821.975780; freqA = 0.2952; freqC = 0.0915; freqG = 0.1808; freqT = 0.4325; R(a) = 0.1894; R(b) = 6.2295; R(c) = 1.8356; R(d) = 5.2302; R(e) = 5.3626; R(f) = 1.0000; p-inv = 0.2340; gamma shape = 0.6370). Posterior probability values exceeding 50% are given on appropriate clades). Original sequences are indicated by bold font.

Full Size   |   Slide (.pptx)

REFERENCES

  1. Acosta, N. and Ayala, A. 1975. Pathogenicity of Pratylenchus coffeae, Scutellonema bradys, Meloidogyne incognita, and Rotylenchus reniformis on Dioscorea rotundata . Journal of Nematology 7:1–6.
  2. Adegbite, A. A. , Saka, J. O. , Agbaje, G. O. and Osuloye, F. O. 2008. Survey of plant-parasitic nematodes associated with yams in Ogun and Osun states of Nigeria. Journal of Plant Protection Research 48:421–428.
  3. Andrássy, I. 1958. Hoplolaimus tylenchifonnis Daday, 1905 (syn. H. coronatus Cobb, 1923) und die Gattungen der Unterfamilie Hoplolaiminae Filipjev, 1936. Nematologica 3:44–56.
  4. Anonymous 1975. Annual Report 1973-74, Nigeria Federal Department of Agricultural Research.
  5. Ayensu, E. S. and Coursey, D. G. 1972. Guinea yams:the botany, ethno-botany, use and possible future of yams in West Africa. Economic Botany 26:301–318.
  6. Bridge, J. 1972. Nematode problems with yams (Dioscorea spp.) in Nigeria. Tropical Pest Management 18:89–91.
  7. Bridge, J. 1973. Nematodes as pests of yams in Nigeria. Mededelingen van de Faculteit Landbouwwetenschappen, Rijksuniversiteit Gent 38:841–852.
  8. Bridge, J. 1988. Plant-parasitic nematode problems in the Pacific islands. Journal of Nematology 20:173–183.
  9. Bridge, J. and Starr, J. L. 2007. Plant nematodes of agriculture importance:a color handbook Manson Publishing, London.
  10. Bridge, J. , Coyne, D. L. and Kwoseh, C. K. 2005. “Nematode parasites of tropical root and tuber crops (excluding potatoes)”, In Luc, M. , Sikora, R. A. and Bridge, J. (Eds), Plant Parasitic Nematodes in Subtropical and Tropical Agriculture CABI, Wallingford, pp. 221–258.
  11. Castillo, P. and Vovlas, N. 2007. Pratylenchus (Nematoda: Pratylenchidae): diagnosis, biology, pathogenicity and management. Nematology Monographs and Perspectives, 6. Brill, Leiden and Boston, MA.
  12. Caveness, F. E. 1967. Nematology Studies. End of Tour Progress Report on the Nematology Project USAID, Lagos, 135pp.
  13. Coates-Beckford, P. L. and Brathwaite, C. W. D. 1977. Comparison of various treatments for the control of Pratylenchus coffeae in yam. Nematropica 7:20–26.
  14. Corbett, D. C. M. 1976. Pratylenchus brachyurus. C.I.H. Description of plant-parasitic nematodes, Set 6, No. 89. CAB International, Wallingford.
  15. Corbett, D. C. M. and Clark, S. A. 1983. Surface features in the taxonomy of Pratylenchus species. Revue de Nématologie 6:85–98.
  16. Coyne, D. L. and Affokpon, A. 2018. “Nematode parasites of tropical root and tuber crops”, In Sikora, R. A. , Coyne, D. L. , Hallman, J. and Timper, P. (Eds), 2018. Plant Parasitic Nematodes in Subtropical and Tropical Agriculture 3rd edition, CAB International, Wallingford, pp. 252–289.
  17. Coyne, D. L. , Plowright, R. A. and Fofana, I. 1996. Preliminary investigations of nematodes associated with rice in Guinea, Benin and Togo. Afro-Asian Journal of Nematology 6:70–73.
  18. Coyne, D. L. , Plowright, R. A. , Twumasi, J. and Hunt, D. J. 1999. Prevalence of plant parasitic nematodes associated with rice in Ghana with a discussion of their importance. Nematology 1:399–405.
  19. Coyne, D. L. , Talwana, H. A. L. and Maslen, N. R. 2003. Plant-parasitic nematodes associated with root and tuber crops in Uganda. African Plant Protection 9:87–98.
  20. Coyne, D. L. , Kolombia, Y. A. , Kariuki, G. , Luambano, N. and Bert, W. 2016. First report of dry rot disease of yam caused by Scutellonema bradys in East Africa. Plant Disease 100:1794.
  21. Coyne, D. L. , Tchabi, A. , Baimey, H. , Labuschagne, N. and Rotifa, I. 2006. Distribution and prevalence of nematodes (Scutellonema bradys and Meloidogyne spp.) on marketed yam (Dioscorea spp.) in West Africa. Field Crops Research 96:142–150.
  22. Coyne, D. L. , Cortada, L. , Dalzell, J. J. , Claudius-Cole, A. O. , Haukeland, S. , Luambano, N. and Talwana, H. 2018. Plant-parasitic nematodes and food security in Sub-Saharan Africa. Annual Review of Phytopathology 56:381–403.
  23. De Grisse, A. T. 1969. Redescription ou modification de quelques techniques utilisées dans l’étude des nematodes phytoparasitaires. Landbouwwetenschappen Gent 34:351–369.
  24. De Guiran, G. 1965. “Nematodes associes au manioc dans le sud du Togo”, Comptes Rendues des Travaux du Congres de la Protection Culture Tropicales, Chambre de commerce et d’industrie, Marseilles, pp. 677–680.
  25. Duncan, L. W. and Moens, M. 2013. “Migratory endoparasitic nematodes”, In Perry, R. N. and Moens, M. (Eds), Plant nematology CAB International, Wallingford, pp. 144–178.
  26. Duncan, L. W. , Inserra, R. N. , Thomas, W. K. , Dunn, D. , Mustika, I. , Frisse, L. M. , Mendes, M. L. , Morris, K. and Kaplan, D. T. 1999. Molecular and morphological analysis of isolates of Pratylenchus coffeae and closely related specie. Nematropica 29:61–80.
  27. Edgar, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792–1797.
  28. Egunjobi, O. A. 1974. Nematodes and maize growth in Nigeria. I. Population dynamics of Pratylenchus brachyurus in and about the roots of maize and its effects on maize production at Ibadan. Nematologica 20:181–186.
  29. Egunjobi, O. A. and Larinde, M. A. 1975. Nematodes and maize growth in Nigeria. II. Effects of some amendments on populations of Pratylenchus brachyurus and on the growth and production of maize (Zea mays) in Nigeria. Nematologia Mediterranea 3:65–73.
  30. FAO . 2018. Food and Agriculture Organization of the United Nations, Rome, Available at http://www.fao.org/faostat/en/ (accessed August 15, 2020).
  31. Filipjev, I. N. and Schuurmans Stekhoven, J. H. Jr. 1941. A manual of agricultural helminthology E. J. Brill, Leiden, p. 878.
  32. Fortuner, R. 1976. Pratylenchus zeae. C. I. H. Description of plant-parasitic nematodes, Set 6, No. 77.
  33. Frederick, J. J. and Tarjan, A. C. 1989. A compendium of the genus Pratylenchus Filipjev, 1936 (Nemata: Pratylenchidae). Revue de nématologie 12:243–256.
  34. Godfrey, G. H. 1929. A destructive root disease of pineapple and other plants due to Tylenchus brachyurus . Phytopathology 19:611–629.
  35. Graham, T. W. 1951. Nematode root rot of tobacco and other plants. Bulletin 390. South Carolina Agricultural Experiment Station, Clemson Agricultural College.
  36. Guerout, R. 1975. Nematodes of pineapple: a review. Pest Management 21:123–140.
  37. Hernández, M. A. , Jordana, R. , Goldaracena, A. and Pinochet, J. 2000. SEM observations on nine species of the genus Pratylenchus Filipjev, 1936 (Nematoda: Pratylenchidae). Journal of Nematode Morphology and Systematics 3:165–174.
  38. Hooper, D. J. , Hallmann, J. and Subbotin, S. A. 2005. “Methods for extraction, processing and detection of plant and soil nematodes”, In Luc, M. , Sikora, R. A. and Bridge, J. (Eds), Plant parasitic nematodes in subtropical and tropical agriculture CAB International, Wallingford, pp. 53–86.
  39. Huelsenbeck, J. P. and Ronquist, F. 2001. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17:754–755.
  40. Inserra, R. N. , Troccoli, A. , Gozel, U. , Bernard, E. C. , Dunn, D. and Duncan, L. W. 2007. Pratylenchus hippeastri n. sp. (Nematoda: Pratylenchidae) from amaryllis in Florida with notes on P. scribneri and P. hexincisus . Nematology 9:25–42.
  41. Janssen, T. , Karssen, G. , Verhaeven, M. , Coyne, D. and Bert, W. 2016. Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution. Scientific Reports 6:22591.
  42. Kolombia, Y. A. 2017. Diversity and characterization of plant-parasitic nematodes associated with yam (Dioscorea spp.) in West Africa and a novel approach for rapid resistance screening. PhD Thesis, University of Ghent, Ghent.
  43. Kolombia, Y. A. , Kumar, L. P. , Viaene, N. , Bert, W. and Coyne, D. L. 2016a. “Nematodes on yam in Nigeria: situation on the ground”, 32nd Symposium of European Society of Nematologists, Braga, Brada, 271.
  44. Kolombia, Y. A. , Kumar, P. L. , Claudius-Cole, A. O. , Karssen, G. , Viaene, N. , Coyne, D. and Bert, W. 2016b. First report of Meloidogyne enterolobii causing tuber galling damage on white yam (Dioscorea rotundata) in Nigeria. Plant Disease 100:10.
  45. Kolombia, Y. A. , Kumar, P. L. , Adewuyi, O. , Korie, S. , Viaene, N. , Bert, W. and Coyne, D. L. 2020. Distribution, prevalence and severity of damages caused by nematodes on yam (Dioscorea rotundata) in Nigeria. Nematropica 50:1–18.
  46. Kwoseh, C. K. , Plowright, R. A. , Bridge, J. and Asiedu, R. 2005. Yam-based farm practices and nematode problems in stored yams (Dioscorea spp.) in Ghana. Journal of Science and Technology 25:35–43.
  47. Liu, X. , Wang, H. , Lin, B. , Tao, Y. , Zhuo, K. and Liao, J. 2016. Loop-mediated isothermal amplification based on the mitochondrial COI region to detect Pratylenchus zeae . European Journal of Plant Pathology 48:435–446.
  48. Loof, P. A. A. 1985. Pratylenchus scribneri. C. I. H. Description of plant-parasitic nematodes, Set 6, No. 89.
  49. Loof, P. A. A. and Yassin, A. M. 1971. Three new plant-parasitic nematodes from the Sudan, with notes on Xiphinema basiri Siddiqi, 1959. Nematologica 16: 537–546.
  50. Luc, M. 1987. A reappraisal of Tylenchida (Nemata). 7. The family Pratylenchidae Thorne, 1949. Revue de Nématologie 10:203–218.
  51. Luc, M. and de Guiran, G. 1960. Les nématodes associés aux plantes de l’Ouest africain: liste préliminaire. L’Agronomie Tropicale 15:434–449.
  52. Miège, J. 1957. Influence de quelques caractères des tubercules semences sur la levée et le rendement des ignames cultivées. Journal d’ Agriculture Tropicale et de Botanique Appliquée 4:314–342.
  53. Moura, R. M. and Monteiro, A. R. 1995. Pratylenchus coffeae on yams in Brazil. Fitopatologia Brasileira 20:256.
  54. Mudiope, J. , Speijer, P. R. , Coyne, D. L. , Maslen, R. N. and Adipala, E. 2007. Nematode distribution and damage to yam in Central and Eastern Uganda. African Crop Science Journal 15:93–99.
  55. Muniz, M. F. S. , Silva, E. J. , Castro, J. M. C. , Rocha, F. S. , Alencar, L. M. C. and Gonzaga, V. 2012. Intensity of dry rot disease of yam in the state of Alagoas, Brazil. Nematropica 42:198–200.
  56. Nweke, F. I. 2016. Yam in West Africa: food, money, and more Michigan State University Press.
  57. Nweke, F. I. , Ugwu, B. O. , Asadu, C. L. A. and Ay, P. 1991. Production costs in the yam-based cropping systems of south-western Nigeria. Resource and Crop Management Division. Research Monograph 6. IITA, Ibadan.
  58. Onwueme, I. C. and Charles, W. B. 1994. Tropical root and tuber crops: production, perspectives and future prospects. (FAO Plant Product. Protect. Paper 126). FAO, Rome.
  59. Orkwor, G. C. 1998. “The importance of yams”, In Orkwor, G. C. , Asiedu, R. and Ekanayake, I. J. (Eds), Food Yams: Advances in Research IITA/NRCRI, Nigeria, pp. 1–12.
  60. Osei, K. , Danso, Y. , Otoo, E. , Adomako, J. , Sackey-Asante, J. and Abugri, B. 2015. Evaluation of yam varieties for reaction to plant parasitic nematodes infestation in three agro - ecologies of Ghana. Academic Research Journal of Agricultural Science and Research 3:201–206.
  61. Ozbayrak, M. , Todd, T. , Harris, T. , Higgins, R. , Powers, K. , Mullin, P. , Sutton, L. and Powers, T. 2019. A COI DNA barcoding survey of Pratylenchus species in the Great Plains Region of North America. Journal of Nematology 51:1–21.
  62. Palomares-Rius, J. E. , Guesmi, I. , Horrigue-Raouani, N. , Cantalapiedra-Navarrete, C. , Liébanas, G. and Castillo, P. 2014. Morphological and molecular characterisation of Pratylenchus oleae n. sp.(Nematoda: Pratylenchidae) parasitizing wild and cultivated olives in Spain and Tunisia. European Journal of Plant Pathology 140:53–67.
  63. Payan, L. A. 1989. The intraspecific variation of Pratylenchus brachyurus University of Florida.
  64. Plowright, R. A. and Hunt, D. J. 1994. Plant parasitic nematodes of upland, hydromorphic and inland swamp rice ecosystems in Côte d’Ivoire. Afro-Asian Journal of Nematology 4:61–67.
  65. Posada, D. 2008. jModelTest: phylogenetic model averaging. Molecular Biology and Evolution 25:1253–1256.
  66. Pourjam, E. , Waeyenberge, L. , Moens, M. and Geraert, E. 1999. Morphological, morphometrical and molecular study of Pratylenchus coffeae and P. loosi (Nematoda: Pratylenchidae). Mededelingen Faculteit Landbouwkundige En Toegepaste Biologische Wetenschappen, Universiteit Gent 64:391–401.
  67. Rensch, D. 1924. Aphelenchus neglectus sp. n. eine neue parasitäre Nematodenart. Sonderabdruck aus dem Zoologischen Anzeiger. 59:277–280.
  68. Roman, J. and Hirschmann, H. 1969. Morphology and morphometrics of six species of Pratylenchus . Journal of Nematology 1:363–386.
  69. Seinhorst, J. W. 1959. A rapid method for the transfer of nematodes from fixative to anhydrous glycerin. Nematologica 4:67–69.
  70. Seinhorst, J. W. 1968. Three new Pratylenchus species with a discussion of the structure of the cephalic framework and of the spermatheca in this genus. Nematologica 14:497–510.
  71. Sherbakoff, C. D. and Stanley, W. W. 1943. The more important diseases and insect pests of crops in Tennessee. Tennessee Agriculture Experiment Station Bulletin 186:1–142.
  72. Speijer, P. R. , De Waele, D. and Rotimi, M. O. 2001. Plant parasitic nematodes associated with plantain (Musa spp., AAB-group) in southern Nigeria and their relative importance compared to other biotic constraints. Nematology 3:423–436.
  73. Steiner, G. R. and LeHew, R. R. 1933. Hoplolaimus bradys n. sp. (Tylenchidae, Nematoda), the cause of a disease of yam (Dioscorea sp.). Zoologischer Anzeiger 101:260–264.
  74. Subbotin, S. A. , Sturhan, D. , Chizhov, V. N. , Vovlas, N. and Baldwin, J. G. 2006. Phylogenetic analysis of Tylenchida Thorne, 1949 as inferred from D2 and D3 expansion fragments of the 28S rRNA gene sequences. Nematology 8:455–474.
  75. Subbotin, S. A. , Ragsdale, E. J. , Mullens, T. , Roberts, P. A. , Mundo-Ocampo, M. and Baldwin, J. G. 2008. A phylogenetic framework for root lesion nematodes of the genus Pratylenchus (Nematoda): evidence from 18S and D2-D3 expansion segments of 28S ribosomal RNA genes and morphological characters. Molecular Phylogenetics and Evolution 48:491–505.
  76. Tarjan, A. C. and Frederick, J. J. 1978. Intraspecific morphological variation among populations of Pratylenchus brachyurus and P. coffeae . Journal of Nematology 10:152–160.
  77. Taylor, D. and Jenkins, W. 1957. Variation within the nematode genus Pratylenchus, with the descriptions of P. hexincisus, n. sp. and P. subpenetrans, n. sp. Nematologica 2:159–174.
  78. Thorne, G. and Malek, R. B. 1968. Nematodes of the Northern Great Plains. I. Tylenchida. South Dakota Agricultural Experimental Station. Technical Bulletin 31:111.
  79. Unny, K. L. and Jerath, M. L. 1965. Parasitic nematodes. Plant Disease Reporter 49:875–876.
  80. Varghese, R. and Mohandas, C. 2004. Pratylenchus loosi, a new record on Dioscorea rotundata . Indian Journal of Nematology 34:221–222.
  81. Waeyenberge, L. , Ryss, A. , Moens, M. , Pinochet, J. and Vrain, T. C. 2000. Molecular characterisation of 18 Pratylenchus species using rDNA restriction fragment length polymorphism. Nematology 2:135–142.
  82. Yoder, M. , De Ley, I. T. , King, I. W. , Mundo-Ocampo, M. , Mann, J. , Blaxter, M. , Poiras, L. and De Ley, P. 2006. DESS: a versatile solution for preserving morphology and extractable DNA of nematodes. Nematology 8:367–376.
  83. Zimmermann, A. W. P. 1898. De nematoden der koffiewortels. Deel I. Mededelingen uit’s Lands Plantentuin 27:1–64.
  84. Zhao, L. , Cui, R. , Wang, J. , Hu, X. , Zhong, G. and Zhang, Z. 2011. Pratylenchus brachyurus was intercepted in Colocasia sp. from Nigeria. Plant Quarantine 25:35–38.

EXTRA FILES

COMMENTS