Integrated genome-wide association and transcriptomic studies reveal genetic architecture of bulb storability of plentiful garlic germplasm resources

Abstract

Garlic is a widely utilized condiment and health product. However, garlic bulbs are prone to quality deterioration resulting in decrease of economic value during postharvest. In this study, the storability of 501 garlic accessions worldwide was evaluated based on the examination of decay index (DI), decay rate, sprouting rate, and bud-to-clove ratio in two consecutive years. The DI was employed as a primary index for evaluating the storability of garlic. Among these garlic, 43 accessions exhibited strong storability with DI of 0%-5%. Phenotypic and cytological observations revealed that strong storability accessions displayed delayed sprouting and decay, a slow rate of nutrient transfer to vascular bundles. Through genome-wide association study (GWAS), 234 single-nucleotide polymorphism loci (SNPs) were associated with the storability, which were located in or near 401 genes, which were annotated the functions of resistance, storage substances transport, etc. A total of 44 genes were screened using selective sweep analysis. Transcriptomic analysis was performed at four periods after storage in the 8N035 accession with strong storability and 8N258 accession with weak storability. Compared with 8N035, the upregulated genes in the 8N258 were enriched in photosynthesis and stress response, whereas the downregulated genes were enriched in response of biotic and abiotic stress and defense response. A co-expression network and GWAS identified three hub genes as key regulatory genes. Conjoint analysis of GWAS, selective sweep, and transcriptomic analysis identified 21 important candidate genes. These findings provided excellent resources with storability and vital candidate genes regulating storability for biological breeding of garlic.

Acknowledgements

This work was financially supported by the Natural Science Foundation of China (32172566, 32272731, and 31872946), Youth Innovation Special Task of Chinese Academy of Agricultural Sciences (Y2023QC06), Key R&D Program of Shandong Province of China (2022LZGCQY015),Innovation Engineering Project of Chinese Academy of Agricultural Sciences (CAAS-ASTIP-2021-IVF), Safe Preservation Project Of Crop Germplasm Resources of MOF (2024NWB037), National Horticultural Germplasm Centre Project (NHGRC2024-NH01), and National Modern Agricultural Industry Technology System Construction Special Fund Project (CARS-24-A-01).

Author contributions

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

Data availability

The raw RNA-Seq data have been deposited into the BIG Submission Genome Sequence Archive (GSA) under the project accession numbers CRA014298. The other supplementary figures and tables are summarized in the Supplementary Data files.

Conflict of interest statement

The authors declared that they had no known competing financial interests.

Supplementary data

Supplementary data is available at Horticulture Research online.

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