Comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchi
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 colle...
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2025-07-01
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| Online Access: | https://doi.org/10.1186/s13059-025-03693-5 |
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| author | Qian Yan Junting Feng Jiezhen Chen Yingjie Wen Yonghua Jiang Yingxiao Mai Kan Huang Hailun Liu Hongsen Liu Fachao Shi Yanwei Hao Changhe Cai Canye Yu Liangxi Ou Rui Xia |
| author_facet | Qian Yan Junting Feng Jiezhen Chen Yingjie Wen Yonghua Jiang Yingxiao Mai Kan Huang Hailun Liu Hongsen Liu Fachao Shi Yanwei Hao Changhe Cai Canye Yu Liangxi Ou Rui Xia |
| author_sort | Qian Yan |
| collection | DOAJ |
| description | 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. |
| format | Article |
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| institution | Kabale University |
| issn | 1474-760X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
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| series | Genome Biology |
| spelling | doaj-art-101cbcd7799a429880803e5e2ca728fa2025-08-20T04:02:51ZengBMCGenome Biology1474-760X2025-07-0126112110.1186/s13059-025-03693-5Comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchiQian Yan0Junting Feng1Jiezhen Chen2Yingjie Wen3Yonghua Jiang4Yingxiao Mai5Kan Huang6Hailun Liu7Hongsen Liu8Fachao Shi9Yanwei Hao10Changhe Cai11Canye Yu12Liangxi Ou13Rui Xia14Institute 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 TreeState Key Laboratory of Tropical Crop Breeding, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural SciencesInstitute 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 TreeInstitute 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 TreeInstitute 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 TreeGuangdong 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 UniversityInstitute 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 TreeInstitute 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 TreeGuangdong 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 UniversityInstitute 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 TreeGuangdong 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 UniversityInstitute 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 TreeInstitute 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 TreeInstitute 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 TreeGuangdong 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 UniversityAbstract 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.https://doi.org/10.1186/s13059-025-03693-5Genetic diversityGenetic basisFruit qualityLitchi (Litchi chinensis Sonn.)Invertase gene |
| spellingShingle | Qian Yan Junting Feng Jiezhen Chen Yingjie Wen Yonghua Jiang Yingxiao Mai Kan Huang Hailun Liu Hongsen Liu Fachao Shi Yanwei Hao Changhe Cai Canye Yu Liangxi Ou Rui Xia Comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchi Genome Biology Genetic diversity Genetic basis Fruit quality Litchi (Litchi chinensis Sonn.) Invertase gene |
| title | Comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchi |
| title_full | Comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchi |
| title_fullStr | Comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchi |
| title_full_unstemmed | Comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchi |
| title_short | Comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchi |
| title_sort | comprehensive genomic and phenotypic analyses reveal the genetic basis of fruit quality in litchi |
| topic | Genetic diversity Genetic basis Fruit quality Litchi (Litchi chinensis Sonn.) Invertase gene |
| url | https://doi.org/10.1186/s13059-025-03693-5 |
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