Table 3_Development and phenotypic characterization of a native Theobroma cacao L. germplasm bank from the Loreto region of the Peruvian Amazon: implications for Ex situ conservation and genetic improvement.xlsx

IntroductionThe ex situ conservation and characterization of native Theobroma cacao L. genetic resources are critical for sustainable cacao production and breeding programs in the face of climate change and escalating disease pressures. This study aimed to establish and characterize a novel germplasm bank from the Loreto region of the Peruvian Amazon, a key center of cacao diversity.
MethodsWe collected 140 native cacao accessions across 15 river basins in eight provinces of the Loreto region. Accessions were propagated using optimized grafting techniques with IMC 67 rootstock. Phenotypic evaluation was conducted on 402 plants using 36 standardized descriptors (25 quantitative and 11 qualitative). Data analysis included multivariate analysis using Uniform Manifold Approximation and Projection (UMAP) and Shannon-Weaver diversity indices to assess morphological diversity patterns.
ResultsGrafting achieved 100% survival rate, establishing a comprehensive germplasm bank. Phenotypic characterization revealed exceptional morphological diversity, with quantitative traits exhibiting substantial variation, particularly in fruit characteristics (CV = 15.82–50.82%) and pod index (CV = 144.82%). Multivariate analysis identified five distinct phenotypic groups, with reproductive traits showing stronger differentiation than vegetative traits. Shannon-Weaver diversity indices highlighted high overall phenotypic diversity (H' ≈ 0.7), with seed longitudinal shape and fruit apex form displaying the highest trait-specific diversity (H' > 1.0).
ConclusionThis comprehensive characterization establishes a foundation for future multiomics studies and advanced breeding strategies. The documented diversity offers opportunities to leverage CRISPR-Cas-based editing and omics technologies to develop climate-resilient, high-yielding cacao varieties with superior quality traits, contributing significantly to global cacao conservation and improvement programs.

引言
面对气候变化与日益严峻的病害压力，本土可可（Theobroma cacao L.）遗传资源的异位保存（ex situ conservation）及表型表征，对于可可可持续生产及育种项目至关重要。本研究旨在从秘鲁亚马逊河洛雷托地区——可可多样性核心分布区——构建并表征一套全新的种质资源库。

研究方法
我们于洛雷托地区8个省份的15个流域内，共收集了140份本土可可种质（accessions）。采用优化嫁接技术，以IMC 67作为砧木繁育收集的种质。针对402株定植苗木开展表型评估，共采用36项标准化描述符（descriptors），包含25项数量性状与11项质量性状。数据分析采用均匀流形近似与投影（Uniform Manifold Approximation and Projection, UMAP）进行多变量分析，并结合香农-威弗多样性指数（Shannon-Weaver diversity index）解析形态多样性分布模式。

研究结果
嫁接成活率达100%，成功构建了一套完整的可可种质资源库。表型表征结果显示该种质库具有极高的形态多样性，其中数量性状存在显著变异，尤以果实性状（变异系数CV=15.82~50.82%）与荚果指数（CV=144.82%）最为突出。多变量分析共识别出5个具有显著差异的表型类群，且繁殖相关性状较营养生长性状呈现出更强的分化水平。香农-威弗多样性指数分析结果显示整体表型多样性水平较高（H'≈0.7），其中种子纵形与果尖形态的性状特异性多样性最为突出（H'>1.0）。

研究结论
本次全面的种质表征工作为后续多组学（multiomics）研究与先进育种策略奠定了基础。本研究记录的种质多样性为利用CRISPR-Cas基因编辑技术及组学（omics）技术研发抗逆、高产且优质的可可新品种提供了契机，将为全球可可种质资源保护与遗传改良项目提供重要支撑。