Fig 1.
Variation in RKN resistance traits within the 524B x IT84S-2049 RIL population.
The number of RKN egg masses per root system was measured in pouch tests conducted in a growth chamber.
Fig 2.
Manhattan plot of SNPs associated to M. javanica resistance.
The blue line represents the Bonferroni correction using a threshold of p = 0.05. The Infinite (INF) values of -log10(p) were represented as a numeral “18”.
Fig 3.
Mean numbers of Meloidogyne javanica egg masses per root system in nine groups of near-isogenic lines (NIL) based on allele condition of two QTLs.
The mean number of egg masses per root system was measured in growth-pouch inoculation assays conducted in a controlled environment chamber. * Number of NILs per group; Het = heterozygous.
Fig 4.
Nematode penetration and development on resistant and susceptible cowpea NILs.
Roots of 12-day-old seedlings were infected with an equal number of RKN juveniles, and stained with acid fuchsin at different DAI. (A) NIL-S, 3 DAI. (B) NIL-S, 3 DAI. (C) NIL-S, 6 DAI. (D) NIL-S, 6 DAI. (E) NIL-S, 9 DAI. (F) NIL-S, 9 DAI. (G) NIL-S, 12 DAI. (H) NIL-S, 12 DAI. Bars = 250μm.
Fig 5.
Differentially expressed genes (DEG) during RKN infection of near-isogenic lines of Vigna unguiculata roots.
(A) Venn diagram showing DEG at 3 and 9 DAI of resistant NIL plants compared to susceptible NIL plants. The intersections represent genes commonly expressed between both time-points. (B) Venn diagram showing DEG up-regulated 3 and 9 DAI. The intersection represents genes commonly up-regulated. (C) Venn diagram showing DEG down-regulated 3 and 9 DAI. The intersection represents genes commonly up-regulated. FDR ≤ 0.1, fold change >± 1.
Fig 6.
Gene ontology (GO) enrichment analysis of DEG 3 and 9 DAI of the resistant NIL compared to the susceptible NIL.
(A) Number of DEG 3 DAI characterized according to biological process. (B) Number of DEG 9 DAI characterized according to biological process. GO based on Phaseolus vulgaris annotations.
Table 1.
List of differentially expressed genes in RKN-inoculated cowpea plants, identified in BAC sequences [16] containing SNP markers for the QRk-vu9.1 and QRk-vu11.1 regions and filtered by the best synteny and blast hit between Phaseolus vulgaris and Vigna unguiculata.
Fig 7.
Differential expression of three RKN candidate genes in mock and inoculated cowpea plants 3 and 9 DAI.
The expression was measured by qRT-PCR using cowpea Elongation factor gene as reference (Housekeeping gene) and the susceptible NIL as control.
Table 2.
Fold change (Log2FC) of eight differentially expressed genes using qRT-PCR for RNA-Seq validation using the susceptible near-isogenic line as control.
Table 3.
Percent identity matrix among cowpea predicted proteins homologous to common bean Phvul.011G300000, Phvul.004G140400 and Phvul.004G140500 proteins.
Fig 8.
Conserved domains of three cowpea predicted proteins encoded by candidate genes constitutively higher expressed in RKN resistant plants.
Protein encoded by the cowpea gene homolog of (A) Phvul.004G140400 in common bean, (B) Phvul.004G140500 and (C) Phvul.011G300000. The scale bar represents the number of amino acids.