Genetic diversity studies of Brazilian garlic cultivars and quality control of garlic-clover production

Turning Garlic into a Modern Crop: State of the Art and Perspectives

Garlic is cultivated worldwide for the value of its bulbs, but its cultivation is challenged by the infertility of commercial cultivars and the accumulation of pathogens over time, which occurs as a consequence of vegetative (clonal) propagation. In this review, we summarize the state of the art of garlic genetics and genomics, highlighting recent developments that will lead to its development as a modern crop, including the restoration of sexual reproduction in some garlic strains. The set of tools available to the breeder currently includes a chromosome-scale assembly of the garlic genome and multiple transcriptome assemblies that are furthering our understanding of the molecular processes underlying important traits like the infertility, the induction of flowering and bulbing, the organoleptic properties and resistance to various pathogens.

Garlic (Allium sativum) feature-specific nutrient dosage based on using machine learning models

Brazil presents large yield gaps in garlic crops partly due to nutrient mismanagement at local scale. Machine learning (ML) provides powerful tools to handle numerous combinations of yield-impacting factors that help reducing the number of assumptions about nutrient management. The aim of the current study is to customize fertilizer recommendations to reach high garlic marketable yield at local scale in a pilot study. Thus, collected 15 nitrogen (N), 24 phosphorus (P), and 27 potassium (K) field experiments conducted during the 2015 to 2017 period in Santa Catarina state, Brazil. In addition, 61 growers’ observational data were collected in the same region in 2018 and 2019. The data set was split into 979 experimental and observational data for model calibration and into 45 experimental data (2016) to test ML models and compare the results to state recommendations. Random Forest (RF) was the most accurate ML to predict marketable yield after cropping system (cultivar, preceding crops), climatic indices, soil test and fertilization were included features as predictor (R² = 0.886). Random Forest remained the most accurate ML model (R² = 0.882) after excluding cultivar and climatic features from the prediction-making process. The model suggested the application of 200 kg N ha^-1 to reach maximum marketable yield in a test site in comparison to the 300 kg N ha^-1 set as state recommendation. P and K fertilization also seemed to be excessive, and it highlights the great potential to reduce production costs and environmental footprint without agronomic loss. Garlic root colonization by arbuscular mycorrhizal fungi likely contributed to P and K uptake. Well-documented data sets and machine learning models could support technology transfer, reduce costs with fertilizers and yield gaps, and sustain the Brazilian garlic production.

Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult

Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology.

DNA profiling and assessment of genetic diversity of relict species Allium altaicum Pall. on the territory of Altai

Analysis of the genetic diversity of natural populations of threatened and endangered species of plants is a main aspect of conservation strategy. The endangered species Allium altaicum is a relict plant of the Ice Age and natural populations are located in extreme climatic conditions of Kazakstan's Altai Mountains. Mobile genetic elements and other interspersed repeats are basic components of a eukaryote genome, which can activate under stress conditions and indirectly promote the survival of an organism against environmental stresses. Detections of chromosomal changes related to recombination processes of mobile genetic elements are performed by various PCR methods. These methods are based on interspersed repeat sequences and are an effective tool for research of biological diversity of plants and their variability. In our research, we used conservative sequences of tRNA primer binding sites (PBS) when initializing the retrotransposon replication as PCR primers to research the genetic diversity of 12 natural populations of A. altaicum found in various ecogeographic conditions of the Kazakhstani Altai. High efficiency of the PBS amplification method used was observed already at the intrapopulation level. Unique amplicons representative of a certain population were found at the intrapopulation level. Analysis of molecular dispersion revealed that the biodiversity of populations of mountainous and lowland A. altaicum is due to intrapopulation differences for climatic zones of habitation. This is likely conditional upon predominance of vegetative reproduction over seed reproduction in some populations. In the case of vegetative reproduction, somatic recombination related to the activity of mobile genetic elements are preserved in subsequent generations. This leads to an increase of intrapopulation genetic diversity. Thus, high genetic diversity was observed in populations such as A. altaicum located in the territory of the Kalbinskii Altai, whereas the minimum diversity was observed in the populations of the Leninororsk ecogeographic group. Distinctions between these populations were also identified depending on the areas of their distribution. Low-land and mid-mountain living environments are characterized by a great variety of shapes and plasticity. This work allowed us to obtain new genetic data on the structure of A. altaicum populations on the territory of the Kazakhstan Altai for the subsequent development of preservation and reproduction strategies for this relict species.

Genomic relationship and physiochemical properties among raw materials used for Thai black garlic processing

Raw materials used for black garlic (BG) processing were collected from the major garlic production areas in Northern Thailand. Five of those were identified as of Thai origin (accession G1-G5), and accession G6 was of the Chinese variety. They were initially analyzed for varietal differences using morphological characteristics and genetic variation. Fresh materials from each accession were dried to the same moisture content (55%-60%) and BG processed at 75°C, 90% relative humidity (RH) for 15 days. Thereafter, physiochemical and chemical profiles were analyzed and compared. The dendrogram from random amplified polymorphic DNA fingerprints grouped G2, G3, G4, and G5 as closely related while G1 and G6 were out-groups. Prior to BG processing, the pH of fresh garlic was approximately 6.3 and decreased to 3.7, thereafter. The contents of chemical properties were independent with genotypes. BG processing improved phenolic, flavonoid, and antioxidant but the content of thiosulfinate was minimized in all BG samples. Overall, result indicated that garlics grown in Northern Thailand were genotypically variable. BG processing altered physical and chemical appearance, and these changes were independent with the genotypes.

Ecotype-Level Genetic Biodiversity of Five Italian Traditional Crops

Italy displays a high level of agrobiodiversity due to its diversified pedoclimatic zones. The Administrative Region of Campania includes several and divergent biomes, occurring close to each other. In fact, the distance between a sea level environment and that of high mountains can be less than 20 km. These environmental conditions allow the cultivation of many different crops and vegetables, represented by diverse ecotypes and varieties that are well adapted to the distribution range where they have been selected and grown. Efforts to maintain and further increase biodiversity in farming systems require a better understanding of the existing diversity created by traditional farming practices. The aim of our study was to identify and molecularly characterize several ecotypes belonging to five horticultural species commonly cultivated in Campania. In particular, we analysed five ecotypes of maize, two of garlic, four of onion, one of escarole, and two of courgette by means of simple sequence repeat (SSR) markers in order to evaluate their level of genetic biodiversity. The results reveal, for the first time, the high genetic biodiversity of horticultural ecotypes of the Campania Region. This feature is very important to improve the quality and productivity of agroecosystems.

Diversity evaluation based on morphological, physiological and isozyme variation in genetic resources of garlic (Allium sativum L.) collected worldwide

The aim of this study was to obtain primary information about the global diversity of garlic (Allium sativum L.) by evaluating morphological, physiological and isozyme variation. A total of 107 garlic accessions collected worldwide were grown in Yamaguchi, Japan. Five morphological traits (bulb weight, bulb diameter, number of cloves per bulb, number of bulbils and scape length) and one physiological trait (bolting period) of the collected garlic showed wide variation. Meanwhile, a total of 140 garlic accessions, including the 107 mentioned above, were characterized by leucine aminopeptidase (LAP) and phosphoglucoisomerase (PGI) isozyme analyses; they clearly showed polymorphisms in putative isozyme loci (Lap-1, Lap-2 and Pgi-1). Allelic frequencies were estimated in each group of accessions categorized by their geographical origin, and the observed (H_o) and expected (H_e) heterozygosities were calculated. The allelic frequencies differed between groups. A principal component analysis based on morpho-physiological data indicated a grouping of the garlic accessions into Central Asian and Northern Mediterranean groups as well as others. We discuss the roles of artificial and natural selection that may have caused differentiation in these traits, on the assumption that ancestral domesticated garlic populations have adapted in various regions using standing variation or mutations that accumulated during expansion, and have evolved along with human-preferred traits over a long history of cultivation.

SSR-based genetic diversity and structure of garlic accessions from Brazil

Garlic is a spice and a medicinal plant; hence, there is an increasing interest in 'developing' new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, HO of 0.5, and HE of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall FST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide.

Genetic divergence among Brazilian garlic cultivars based on morphological characters and AFLP markers

Outside its centers of origin, garlic propagates only asexually. Since asexual reproduction leads to the absence of meiotic recombination, the main garlic cultivars available for cultivation have arisen from the accumulation of somatic mutations in early cultivars. Thus, it is common for a single clone to have different names in different regions. This study aimed to evaluate the genetic diversity of 20 garlic cultivars by using morphological characters and amplified fragment length polymorphism (AFLP) markers to identify possible duplicate cultivars. We assessed 28 morphological characters related to the leaves, bulbs, and bulbils of the garlic plant and divided them into two categories: quantitative and qualitative (14 characters each). For molecular marker-based analysis, we used three AFLP primer combinations. Genetic divergence was calculated using the Jaccard coefficient; the cultivars were grouped using unweighted pair-group mean analysis. The average genetic divergence detected using the morphological characters was 2.30 (range, 0.45-4.70). Plant height and coat adhesion exhibited the highest divergence among the cultivars. The average genetic diversity based on AFLP data was 43% (range, 0-79%). Dendrograms derived from both techniques divided the cultivars into two groups: noble and semi-noble. Together with the divergence within groups, the correlation between morphological and molecular data suggested that the cultivars in the noble group had greater phenotypic stability than those in the semi-noble group. Analysis of Jonas and Quitéria cultivars using these two techniques revealed only slight differences, suggesting that these cultivars may be clones or have a high degree of kinship.