AGIDB: a versatile database for genotype imputation and variant decoding across species

Author:

Zhang Kaili1,Liang Jiete1ORCID,Fu Yuhua1,Chu Jinyu1,Fu Liangliang123,Wang Yongfei1,Li Wangjiao1,Zhou You1,Li Jinhua1,Yin Xiaoxiao1,Wang Haiyan14,Liu Xiaolei12ORCID,Mou Chunyan5,Wang Chonglong6,Wang Heng7,Dong Xinxing8,Yan Dawei8,Yu Mei12,Zhao Shuhong129ORCID,Li Xinyun12ORCID,Ma Yunlong19ORCID

Affiliation:

1. Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of the Ministry of Education & Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University , Wuhan  430070 , China

2. Hubei Hongshan Laboratory , Wuhan  430070 , China

3. The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University , Wuhan  430070 , China

4. College of Informatics, Huazhong Agricultural University , Wuhan  430070 , China

5. College of Animal Science and Technology, Southwest University , Chongqing  402460 , China

6. Key Laboratory of Pig Molecular Quantitative Genetics of Anhui Academy of Agricultural Sciences, Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Engineering, Institute of Animal Husbandry and Veterinary Medicine, Anhui Academy of Agricultural Sciences , Hefei  230031 , China

7. College of Animal Science and Technology, Shandong Agricultural University , Taian  271018 , China

8. Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming  650201 , China

9. Lingnan Modern Agricultural Science and Technology Guangdong Laboratory , Guangzhou  510642 , China

Abstract

Abstract The high cost of large-scale, high-coverage whole-genome sequencing has limited its application in genomics and genetics research. The common approach has been to impute whole-genome sequence variants obtained from a few individuals for a larger population of interest individually genotyped using SNP chip. An alternative involves low-coverage whole-genome sequencing (lcWGS) of all individuals in the larger population, followed by imputation to sequence resolution. To overcome limitations of processing lcWGS data and meeting specific genotype imputation requirements, we developed AGIDB (https://agidb.pro), a website comprising tools and database with an unprecedented sample size and comprehensive variant decoding for animals. AGIDB integrates whole-genome sequencing and chip data from 17 360 and 174 945 individuals, respectively, across 89 species to identify over one billion variants, totaling a massive 688.57 TB of processed data. AGIDB focuses on integrating multiple genotype imputation scenarios. It also provides user-friendly searching and data analysis modules that enable comprehensive annotation of genetic variants for specific populations. To meet a wide range of research requirements, AGIDB offers downloadable reference panels for each species in addition to its extensive dataset, variant decoding and utility tools. We hope that AGIDB will become a key foundational resource in genetics and breeding, providing robust support to researchers.

Funder

National Key Research and Development Program of China

Laboratory of Lingnan Modern Agriculture Project

Natural Science Foundation of Hubei Province

National Natural Science Foundation of China

China Agriculture Research System of MOF and MARA

Plan for Technology Talent and Platform

Publisher

Oxford University Press (OUP)

Subject

Genetics

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