Comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchi.

Yanwei Hao, Qian Yan, Kan Huang, Rui Xia, Junting Feng, Jiezhen Chen, Yingjie Wen, Yonghua Jiang, Yingxiao Mai, Hailun Liu, Hongsen Liu, Fachao Shi, Changhe Cai, Canye Yu, Liangxi Ou

Journal: Genome biology 2025;26(1):222

PMID: 40708030

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Abstract

BACKGROUND

Litchi, an economically important fruit crop in Southeast Asia, is renowned for its distinctive flavor and nutrient value, but its genetic diversity and genetic basis underlying fruit quality regulation remain largely unexplored.

RESULTS

We re-sequence 276 litchi accessions collected globally and identify 54 million high-quality biallelic SNPs. We then analyze the population structure and reveal four main subgroups within the population. By phenotypic profiling of 21 fruit-quality-related traits, followed with genome-wide association study, we identify a plethora of candidate genes and genomic loci that are responsible for regulating seed and fruit quality traits. In particular, we characterize and experimentally validate an invertase gene, LcSAI, encoding an enzyme catalyzing the conversion of sucrose into reducing sugars, as a key regulator of sugar composition in litchi fruit, affecting the sweetness of litchi fruits.

CONCLUSIONS

Our study demonstrates the genetic diversity and population structure of litchi. We delineate the genetic basis of fruit quality through comprehensive genomic analyses and phenotypic profiling. These findings provide valuable resources and knowledge for understanding the genetic basis of fruit quality in litchi, which contribute to the theoretical basis for further genetic improvement.

Address: Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Science and Technology Research on Fruit Tree, Guangzhou, Guangdong, 510640, China.; State Key Laboratory of Tropical Crop Breeding, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China.; Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops (South China) at Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, China.; Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs; Guangdong Provincial Key Laboratory of Science and Technology Research on Fruit Tree, Guangzhou, Guangdong, 510640, China. [email protected].; Guangdong Basic Research Center of Excellence for Precise Breeding of Future Crops, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops (South China) at Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, 510642, China. [email protected].

DOI: 10.1186/s13059-025-03693-5

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MeSH Terms: Fruit, Phenotype, Litchi, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Genome, Plant, Genomics, Genetic Variation, Plant Proteins, beta-Fructofuranosidase