Cocoa Research Centre, The University of The West Indies, St. Augustine, Trinidad and Tobago.
Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), UMR AGAP Institute, Montpellier, France.
PLoS One. 2022 Oct 6;17(10):e0260907. doi: 10.1371/journal.pone.0260907. eCollection 2022.
A genome-wide association study (GWAS) was undertaken to unravel marker-trait associations (MTAs) between SNP markers and phenotypic traits. It involved a subset of 421 cacao accessions from the large and diverse collection conserved ex situ at the International Cocoa Genebank Trinidad. A Mixed Linear Model (MLM) in TASSEL was used for the GWAS and followed by confirmatory analyses using GAPIT FarmCPU. An average linkage disequilibrium (r2) of 0.10 at 5.2 Mb was found across several chromosomes. Seventeen significant (P ≤ 8.17 × 10-5 (-log10 (p) = 4.088)) MTAs of interest, including six that pertained to yield-related traits, were identified using TASSEL MLM. The latter accounted for 5 to 17% of the phenotypic variation expressed. The highly significant association (P ≤ 8.17 × 10-5) between seed length to width ratio and TcSNP 733 on chromosome 5 was verified with FarmCPU (P ≤ 1.12 × 10-8). Fourteen MTAs were common to both the TASSEL and FarmCPU models at P ≤ 0.003. The most significant yield-related MTAs involved seed number and seed length on chromosome 7 (P ≤ 1.15 × 10-14 and P ≤ 6.75 × 10-05, respectively) and seed number on chromosome 1 (P ≤ 2.38 × 10-05), based on the TASSEL MLM. It was noteworthy that seed length, seed length to width ratio and seed number were associated with markers at different loci, indicating their polygenic nature. Approximately 40 candidate genes that encode embryo and seed development, protein synthesis, carbohydrate transport and lipid biosynthesis and transport were identified in the flanking regions of the significantly associated SNPs and in linkage disequilibrium with them. A significant association of fruit surface anthocyanin intensity co-localised with MYB-related protein 308 on chromosome 4. Testing of a genomic selection approach revealed good predictive value (genomic estimated breeding values (GEBV)) for economic traits such as seed number (GEBV = 0.611), seed length (0.6199), seed width (0.5435), seed length to width ratio (0.5503), seed/cotyledon mass (0.6014) and ovule number (0.6325). The findings of this study could facilitate genomic selection and marker-assisted breeding of cacao thereby expediting improvement in the yield potential of cacao planting material.
进行了一项全基因组关联研究（GWAS），以揭示 SNP 标记与表型性状之间的标记-性状关联（MTAs）。它涉及保存在特立尼达国际可可基因库中的大型和多样化的 421 份可可种质资源的一个子集。使用 TASSEL 中的混合线性模型（MLM）进行 GWAS，并使用 GAPIT FarmCPU 进行确认分析。在几个染色体上发现平均连锁不平衡（r2）为 0.10，达到 5.2 Mb。使用 TASSEL MLM 鉴定了 17 个具有重要意义的（P ≤ 8.17 × 10-5（-log10（p）= 4.088））MTAs，其中 6 个与产量相关性状有关，后者占表达的表型变异的 5 至 17%。在 FarmCPU 中验证了种子长度与宽度比与 TcSNP 733 之间的高度显著关联（P ≤ 8.17 × 10-5）（P ≤ 1.12 × 10-8）。在 TASSEL 和 FarmCPU 模型中，有 14 个 MTAs 在 P ≤ 0.003 时是共同的。与种子数量和长度相关的最显著的与产量相关的 MTAs 涉及 7 号染色体上的种子数量和种子长度（P ≤ 1.15 × 10-14 和 P ≤ 6.75 × 10-05，分别）和 1 号染色体上的种子数量（P ≤ 2.38 × 10-05），基于 TASSEL MLM。值得注意的是，种子长度、种子长度与宽度比和种子数量与不同基因座的标记相关，表明其多基因性质。在显著相关的 SNP 及其与它们连锁不平衡的侧翼区域中，鉴定出大约 40 个编码胚胎和种子发育、蛋白质合成、碳水化合物运输和脂质生物合成和运输的候选基因。果实表面花青素强度与 4 号染色体上的 MYB 相关蛋白 308 的显著关联表明。对基因组选择方法的测试表明，种子数量（GEBV = 0.611）、种子长度（0.6199）、种子宽度（0.5435）、种子长度与宽度比（0.5503）、种子/子叶质量（0.6014）和胚珠数量（0.6325）等经济性状具有良好的预测值（基因组估计育种值（GEBV））。这项研究的结果可以促进可可的基因组选择和标记辅助育种，从而加速可可种植材料产量潜力的提高。
