Large-scale population structure and genetic architecture of agronomic traits of garlic

Abstract

Garlic, an asexually propagated crop, is the second important bulb crop after the onion and is used as a vegetable and medicinal plant. Abundant and diverse garlic resources have been formed over thousands of years of cultivation. However, genome variation, population structure and genetic architecture of garlic agronomic traits were still not well elucidated. Here, 1 100 258 single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing in 606 garlic accessions collected from 43 countries. Population structure, principal component and phylogenetic analysis showed that these accessions were divided into five subpopulations. Twenty agronomic traits, including above-ground growth traits, bulb-related and bolt-related traits in two consecutive years were implemented in a genome-wide association study. In total, 542 SNPs were associated with these agronomic traits, among which 188 SNPs were repeatedly associated with more than two traits. One SNP (chr6: 1896135972) was repeatedly associated with ten traits. These associated SNPs were located within or near 858 genes, 56 of which were transcription factors. Interestingly, one non-synonymous SNP (Chr4: 166524085) in ribosomal protein S5 was repeatedly associated with above-ground growth and bulb-related traits. Additionally, gene ontology enrichment analysis of candidate genes for genomic selection regions between complete-bolting and non-bolting accessions showed that these genes were significantly enriched in ‘vegetative to reproductive phase transition of meristem’, ‘shoot system development’, ‘reproductive process’, etc. These results provide valuable information for the reliable and efficient selection of candidate genes to achieve garlic genetic improvement and superior varieties.

Acknowledgements

This work was financially supported by the Natural Science Foundation of China (31872946, 32172566, and 32272731), National Key R&D Program of China (2021YFD1200201), China Agriculture Research System of MOF and MARA (CARS-24-A-01), Science and Technology Innovation Project of Chinese Academy of Agricultural Sciences (CAAS-XTCX2018021), Youth Innovation Special Task of Chinese Academy of Agricultural Sciences (Y2023QC06), Agricultural Basic Long-Term Scientific and Technological Work (NAES-GR-005), Safe Preservation Project of Crop Germplasm Resources of MOF (2022NWB037), and National Hoticultural Gerplasm Centre Project (NHGRC2022-NH01).

Author contributions

H.J. and H.W. conceived and designed the research. J.S., X.Z., W.Y., and H.W. prepared the materials. Q.Z., J.S., X.Z., W.Y., Z.D., and Y.Z. performed field experiments and phenotypic determination. H.J., Q.Z., and H.W. performed sampling, sequencing, and data analysis. J.S., X.Z., W.Y., and H.W. contributed to the project discussion. H.J. wrote the manuscript. H.W. revised the manuscript.

Data availability

The raw data of genotyping-by-sequencing of 606 garlic accessions have been deposited in the Genome Sequence Archive in the National Genomics Data Center (https://bigd.big.ac.cn) under accession number CRA007913. The raw data of transcriptome sequencing of 8N362 and 8N652 have also been deposited in the GSA with accession number CRA007870.

Conflict of interest statement

The authors declare that they have no conflicts of interest.

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