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.

The propagation of cultivated garlic relies on vegetative cloves, thus flowers become non-essential for reproduction in this species, driving the evolution of reproductive feature-derived traits. To obtain insights into the evolutionary alteration of reproductive traits in the clonally propagated garlic, the evolutionary histories of two main reproduction-related traits, bolting and flower differentiation, were explored by genome analyses using 134 accessions displaying wide diversity in these two traits. Resequencing identified 272.8 million variations in the garlic genome, 198.0 million of which represent novel variants. Population analysis identified five garlic groups that have evolved into two clades. Gene expression, single-cell transcriptome sequencing, and genome-wide trait association analyses have identified numerous candidates that correlate with reproductive transition and flower development, some of which display distinct selection signatures. Selective forces acting on the B-box zinc finger protein-encoding Asa2G00291.1, the global transcription factor group E protein-encoding Asa5G01527.1, and VERNALIZATION INSENSITIVE 3-like Asa3G03399.1 appear to be representative of the evolution of garlic bolting. Plenty of novel genomic variations and trait-related candidates represent valuable resources for biological studies of garlic. Numerous selective signatures from genes associated with the two chosen reproductive traits provide important insights into the evolutionary history of reproduction in this clonally propagated crop.

Open access peer-reviewed chapter

Clubroot disease, caused by Plasmodiophora brassicae, poses a significant global threat to cruciferous crops. The epidemic area of clubroot disease is expanding rapidly. In response to this pressing issue, there is a compelling need for the development of clubroot disease-resistant radish cultivars. China boasts an extensive array of radish varieties and germplasm resources. However, a comprehensive assessment of their resistance to clubroot has not yet been carried out, thereby impeding the effective utilization of germplasm and clubroot-resistant breeding. Therefore, it is urgent to systematically evaluate the clubroot resistance of the radish germplasm and identify resistant resources. In this study, clubroot resistance evaluations were conducted on 268 excellent radish varieties derived from 30 provinces in China, as well as seven accessions from Russia, North Korea, France, South Korea, and Germany. The resistance evaluation revealed a diverse range of resistance indices, with a mean disease index (DI) ranging from 0.6 to 58.5, showing significant disparities in clubroot resistance among these radish resources. A total of six accessions were characterized as highly resistant to clubroot, and a further 50 accessions were characterized as resistant. The disease-resistant radishes showed diversity in horticultural traits. Provinces in South China contributed significantly more resistance germplasm than those of North China. These materials are of great value for both genetic investigation and the crop breeding of clubroot resistance. Furthermore, we employed a previously established clubroot-resistance-linked SSR marker to analyze the clubroot-resistant resources. The accessions exhibited dissimilar genetic profiles from known clubroot-resistant germplasm, suggesting their potential status as novel sources of clubroot resistance. Conclusively, these newly identified accessions enriched the genetic diversity within the clubroot-resistant gene pool and may contribute to the future cloning of previously undiscovered clubroot-resistant genes.

Polyethylene mulch film (PEM) is widely utilized in garlic cultivation, significantly enhancing garlic yield. However, the prolonged use of this material leads to serious environmental issues that adversely affect soil health and plant growth. To promote the adoption of biodegradable mulch film (BDM) in garlic cultivation, we investigate the effects of BDMs with thicknesses of 0.006 mm, 0.008 mm, and 0.010 mm on garlic growth and soil properties, comparing them with the commonly used PEM 0.008 mm. The results indicated that the agronomic traits of garlic were significantly improved under both PEM and BDMs compared to no mulching, with yield increases ranging from 75.42% to 90.39%. The highest garlic yield was observed with the BDM 0.008 mm. Most above-ground agronomic traits of garlic did not exhibit significant differences between PEM and BDMs, although a few traits showed slight increases under the BDMs 0.008 mm and 0.010 mm. The quality characteristics of garlic bulbs, including the contents of soluble sugar, vitamin C, and allicin, did not differ significantly between PEM and BDMs. Soil temperature was significantly higher under both PEM and BDMs compared to no mulching. In comparison to PEM 0.008 mm, the application of BDMs 0.006 mm and 0.008 mm significantly enhanced potassium availability in the soil. Furthermore, the activities of catalase, phosphatase, and invertase were notably increased under the BDM 0.008 mm, suggesting that this type of mulch could improve the physicochemical properties of the soil. Additionally, the BDM 0.008 mm remained intact throughout the low-temperature overwintering period, began to partially degrade as temperatures rose in March and April, and exhibited considerable fragmentation during the maturity and harvest periods of garlic. Its degradation rate was well aligned with the growth requirements of garlic. Taken together, these findings suggested that the BDM 0.008 mm is particularly effective, resulting in significant yield increase and an appropriate degradation rate. These results provided a valuable reference for the selection and application of BDM in garlic cultivation.