ArticleHorticulture research2025
Mango pangenome reveals dramatic impacts of reference bias on population genomic analyses.
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Article in Horticulture research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6citing papers in PubMed
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6 citing papers in PubMed.
- Dissecting the genetic basis of climatic adaptation in wild relatives (Malus baccata) for climate-resilient apple breeding.Journal of integrative plant biology · 2026Article
- Integrative genetic and hormonal coordination of endocarp/stone development in drupe fruit.Horticulture research · 2026Review
- The Rise of Plant Pan-Genomes: From Genome Variation to Predictive Breeding.Advanced genetics (Hoboken, N.J.) · 2026Article
- Next-Generation Genotyping: Innovations Driving Plant Genomic Improvement.Life (Basel, Switzerland) · 2026Review
- Genomic epidemiology and phylogenomics ofFrontiers in cellular and infection microbiology · 2026Article
- Integrative genomics for mango genetics and breeding.Horticulture research · 2026Article
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Authors and funding
28 authors.
Bilal AhmadState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.
Ying SuState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.ORCID https://orcid.org/0009-0000-0162-3777
Yani HaoState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.
Tayyaba RazzaqState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.
Rida ArshadState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.
Yi ZhangState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.
Yingchun ZhangState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.
Xingyi WangState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.
Guizhou HuangState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.ORCID https://orcid.org/0009-0000-8381-6299
Xiangnian SuState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.
Ting HouState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.ORCID https://orcid.org/0009-0002-4325-5567
Chaochao LiState Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China.
Xuanwen YangState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.ORCID https://orcid.org/0000-0002-3596-4112
Chuanning LiKey Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi University Engineering Research Center of Bioinformation and Genetic Improvement of Specialty Crops, Guangxi 541006, China.
Zhenzhou ChuXinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang 830046, China.ORCID https://orcid.org/0009-0001-1002-8280
Qiuyan WangKey Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Ministry of Education) & Guangxi Key Laboratory of Landscape Resources Conservation and Sustainable Utilization in Lijiang River Basin, Guangxi University Engineering Research Center of Bioinformation and Genetic Improvement of Specialty Crops, Guangxi 541006, China.
Yu ZhangGuangxi Subtropical Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530001,China.
Zhongxin JinState Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China.
Qi XuState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.
Xiaodong XuState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.
Yanling PengState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.ORCID https://orcid.org/0000-0003-3172-3722
Guiqi BiState Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China.
Chengjie ChenState Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China.
Yeyuan ChenSanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China.
Hua XiaoState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.ORCID https://orcid.org/0000-0003-3407-7009
Jianfeng HuangState Key Laboratory of Tropical Crop Breeding, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571100, China.
Yongfeng ZhouState Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences 518000, Shenzhen, China.ORCID https://orcid.org/0000-0003-0780-2973
Xinmin TianXinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, Xinjiang 830046, China.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most genomic studies start by mapping sequencing data to a reference genome. The quality of reference genome assembly, genetic relatedness to the studied population, and the mapping method employed directly impact variant calling accuracy and subsequent genomic analyses, introducing reference bias and resulting in erroneous conclusions. However, the impacts of reference bias have gained limited attention. This study compared population genomic analyses using four different reference genomes of mango (
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