Evidence map›Paper›PMID 40708030›Full record

ArticleGenome biology2025

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

Qian Yan, Junting Feng, Jiezhen Chen, Yingjie Wen, Yonghua Jiang, Yingxiao Mai, Kan Huang, Hailun Liu, Hongsen Liu, Fachao Shi and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Qian Yan *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.
Junting Feng *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.
Jiezhen Chen *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.
Yingjie WenInstitute 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.
Yonghua JiangInstitute 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.
Yingxiao MaiGuangdong 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.
Kan HuangInstitute 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.
Hailun LiuInstitute 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.
Hongsen LiuGuangdong 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.
Fachao ShiInstitute 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.
Yanwei HaoGuangdong 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.
Changhe CaiInstitute 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.
Canye YuInstitute 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.
Liangxi OuInstitute 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. gdglxo2015@126.com.
Rui XiaGuangdong 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. rxia@scau.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundLitchi, 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.

resultsWe 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.

conclusionsOur 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.

Indexed as

FruitLitchibeta-FructofuranosidaseGenetic VariationGenome, PlantGenome-Wide Association StudyGenomicsPhenotypePlant ProteinsPolymorphism, Single Nucleotidebeta-FructofuranosidasePlant ProteinsFruit qualityGenetic basisGenetic diversityInvertase geneLitchi (Litchi chinensis Sonn.)

Identifiers

PMID40708030
PMCPMC12291274

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.