Development of the rubber tree 40K breeding chip with applications in genetic study and breeding prediction

作者：Xiaobo Wang, Zhi Deng, Yanshi Hu, Fazal Rehman, Zewei An, Tingkai Wu, Yuan Yuan, Runrun Qiang, Wenguan Wu, Xia Zeng, Han Cheng · 发表于：Industrial Crops and Products · 年份：2025 · DOI：10.1016/j.indcrop.2025.120640 · 被引用次数：6 · 研究领域：Genetics and Plant Breeding、Genetic and phenotypic traits in livestock、Genetic Mapping and Diversity in Plants and Animals

As an important industrial crop, rubber tree ( Hevea brasiliensis ) provides the source of natural rubber globally. However, rubber tree breeding is confronted with the challenge of long breeding cycles and corresponding time, land, and labor costs. In this study, we developed a novel high-density breeding chip for rubber tree using genotyping by target sequencing (GBTS) technology, comprising approximately 40 K markers. The developed breeding chip was used to genotype 223 rubber tree clones. Results showed a prevalent low genetic diversity among the rubber tree clones, indicating a limited genetic foundation. Subsequently, markers associated with girth growth rate were identified through genome-wide association study (GWAS). Based on the GWAS results, seven genomic selection (GS) models were used to assess the prediction accuracy of different associated marker datasets for girth growth rate. The Bayesian least absolute shrinkage and selection operator (BayesLASSO), using the marker dataset with a p -value < 0.001, showed the highest prediction accuracy of 0.59, thus being selected as the optimal GS model and genotype dataset for breeding prediction. Fifty superior parental combinations were selected by usefulness criteria calculated based on genome estimated breeding values of simulated F 1 progenies. This study developed a reliable breeding chip applicable in genetic study and breeding prediction and provided a strategy for molecular breeding of rubber trees by determining ...