Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback

Abstract

Diseases of Theobroma cacao L. (Malvaceae) disrupt cocoa bean supply and economically impact growers. Vascular streak dieback (VSD), caused by Ceratobasidium theobromae, is a new encounter disease of cacao currently contained to southeast Asia and Melanesia. Resistance to VSD has been tested with large progeny trials in Sulawesi, Indonesia, and in Papua New Guinea with the identification of informative quantitative trait loci (QTLs). Using a VSD susceptible progeny tree (clone 26), derived from a resistant and susceptible parental cross, we assembled the genome to chromosome-level and discriminated alleles inherited from either resistant or susceptible parents. The parentally phased genomes were annotated for all predicted genes and then specifically for resistance genes of the nucleotide-binding site leucine-rich repeat class (NLR). On investigation, we determined the presence of NLR clusters and other potential disease response gene candidates in proximity to informative QTLs. We identified structural variants within NLRs inherited from parentals. We present the first diploid, fully scaffolded, and parentally phased genome resource for T. cacao L. and provide insights into the genetics underlying resistance and susceptibility to VSD.

FIGURE 1

Chromsyn (Edwards et al., 2022) synteny plots of T. cacao parentally phased genome, haplotypes A (top) and B (below). Synteny blocks of collinear “Complete” BUSCO genes (Simão et al., 2015) link scaffolds from adjacent assemblies: blue, same strand; red, inverse strand. Yellow triangles mark “Duplicated” BUSCOs. Filled circles mark telomere predictions from Telociraptor (black) (Edwards, 2023). Assembly gaps are marked as dark red + signs.

FIGURE 2

Physical locations of predicted NLR genes on the paired chromosomes of Theobroma cacao (A) haplotype A (red) and (B) haplotype B (yellow) generated using ChromoMap (Anand & Rodriguez Lopez, 2022) in RStudio.

FIGURE 3

The predicted NLR gene complement in the parentally phased Theobroma cacao genome. The two sets of chromosomes corresponding to (A) haplotypes A and (B) B were independently classified (S. H. Chen et al., 2023) and visualized to present the domain classes using SankeyMatic (Bogart, 2014), including novel integrated domains (IDs) with abbreviations derived from the Pfam database (Mistry et al., 2021). CC, coil–coil domain; NBARC, nucleotide binding domain; RPW8, resistance to powdery mildew 8‐like coiled‐coil; Rx, Potato CC‐NB‐LRR protein Rx; TIR, Toll/interleukin‐1 receptor.

FIGURE 4

Subregions of gene sequence alignment of an NLR cluster matching the quantitative trait locus (QTL) mapped regions at around 29 Mb on chromosome 3 (A) and of single NLR homologs at 31 Mb on chromosome 9 (B) within both parentally inherited alleles, A and B, for Theobroma cacao clone 26. Yellow boxed regions indicate SNPs and indels that lead to amino acid changes in predicted coding regions. All predicted NLRs are annotated as Rx‐NLRs (S. H. Chen et al., 2023) named for resistance to potato virus X.

FIGURE 5

Leaf from Theobroma cacao, VSD susceptible clone 26, growing at the Mars Cocoa Research Institute field trials, Pangkep, South Sulawesi, Indonesia. (Left) The symptomatic leaf apex dieback and some chlorosis indicating Ceratobasidium theobromae. (Right) Visible vascular death caused by the pathogen. Scale bar left ∼5 cm.

FIGURE 6

Theobroma cacao–resistant (S1) and –susceptible (RUQ 1347) parental paired‐end (PE) Illumina sequence reads mapped to the concatenated Hap A and B progeny chromosomes. The reads that were mapped in greater numbers to chromosomes and contigs were used to determine parental assignment and swapped accordingly.