Population Structure and Phylogeny of Some U.S. Peach Cultivars

Peach (Prunus persica) cultivars maintained at the U.S. Department of Agriculture program at Byron, GA, have never been characterized with any molecular markers. In this study, 20 microsatellite markers were used to genotype 112 cultivars and the data were analyzed to discern their population structure and phylogenetic relationships. STRUCTURE simulations revealed four K clusters and broad genetic admixture among the cultivars. Principal coordinate analysis (PCoA) showed the cultivar groups from western, northeastern, and southeastern U.S. states were adjacent to each other except cultivars from Michigan (close to most southeastern state groups) and Florida (most distant from the other groups). Principal component analysis (PCA) showed that these cultivars had no obvious PCA partitioning boundaries. The intertwined distribution in both PCoA and PCA partitions suggested many of them were genetically closely related to each other largely because most shared same ancestral parentages. Most pairwise distance means within and between the cultivar groups were relatively low, suggesting close phylogenetic relations among those cultivars, as were demonstrated in the phylogenetic tree. Limiting factors and perspectives relevant to peach breeding are discussed.

Analysis of varietal diversity, decorativeness and peculiarities of growth and development of cultivars Dahlia cultorum Thorsrud & Reisaeter in the collection of the biostationary of Bila Tserkva NAU

Aim. In order to identify promising cultivars of Dahlia cultorum for use in landscaping in Kyiv region, the analysis of the system of qualitative and quantitative indicators of cultivars of dahlias, the peculiarities of their growth and development in the absence of irrigation is conducted. Methods. To analyze the diversity of Dahlia cultorum cultivars at the biostationary of Bila Tserkva NAU, the classification developed by the American Society of Dahlia (ADS classification) was used. The cultivar assortment of dahlias was studied according to the descriptions of the catalog of the company “SontseSad”, which transferred 108 cultivars of Dahlia cultorum to Bila Tserkva NAU biostationary in 2014. Phenological rhythms of growth and development of dahlias were studied according to the methods of B. K. Shybniev, H. D. Yurkevych, and D. S. Holod. The increment of dahlias was measured during the period of active growth, the size of the flower — during the period of its full opening with the help of a measuring ruler on 5 specimens of each cultivar every decade. Results. Based on the analysis of the varietal composition of Dahlia cultorum collection of dahlia cultivars of Bila Tserkva NAU biostationary, it was found that the largest number of 36% belongs to the cultivar group of decorative dahlias, 12% — to cactus, 7% — to spherical and 1% to pompoms and anemones. The mixed cultivar of dahlias is 43.4%, among them the most numerous group of dahlias with dissected leaves “Deer antlers” — 48%, “Karma” — 19%, pot — 12%, French collection — 21%. According to the color spectrum, the collection is dominated by dahlias of red color — 29%, pink — 19%, yellow and orange — 16% each, violet — 12%, white color — 6%. Two-color cultivars amount to only 2%. Observations show that in May–June, due to the long and dry period and the lack of artificial irrigation, all cultivars of dahlias at Bila Tserkva NAU biostationary were marked by very slow growth. As of July 15, the height of dahlia bushes averaged 30–50 cm, which was significantly less than the size presented in the catalog of the magazine “SontseSad”. Conclusions. The collection of dahlias at Bila Tserkva NAU biostationary includes 108 cultivars belonging to seven main cultivar groups, including 11 cultivars from the new French collection. Early in the first decade of July, the cultivars ‘Islande’, ‘Maki’, ‘Sir Alf Ramsay’, ‘Mingus Alex’, ‘Glorie van Heemstede’ begin to bloom. Latest of all, in August, cultivars ‘Babylon Rose’, ‘Amanda’, ‘Aitara Bronwyn’, ’Karma Gold’, ‘Gallery Rembrandt’, ‘Lilac Time’, and ‘Star Spectacle’ began flowering. It is established that the period from the appearance of the bud to the opening of the flower in dahlia cultivars lasts 25-30 days. The first buds appeared in early July, but their peduncles were very short and such flowers were not suitable for cutting. In fact, the blooming central flower itself was 5-10 cm lower than the second-order buds around it, and therefore had a limited view from the inflorescence, which led to a loss of decorativeness in the cultivars ‘Romance’, ‘Candlelight’, and “Karma Bon Bini”. The duration of flowering of one dahlia flower in different cultivars ranged from 5 to 17 days. The longest period of blooming of one flower is 14-17 days in ‘Autumn Fairy’, ‘Nagano’, ‘Idylle’, ‘Babylon Brons’, ‘Duet’ cultivars. The shortest blooming period of one flower is 5-7 days for ‘Ellen Huston’, ‘Champs Elysees’, ‘ThykiYori No Shisha’, ‘Aspen’ cultivars. Due to the high air temperature and the long rainless period, the peak of flowering of dahlias in the conditions of Bila Tserkva NAU biostationary was at the beginning of September.

Potential Markers for Selecting Self-Eliminating Apple Genotypes

The heavy blooming of apple trees results in the inefficient usage of energy and nutritional material, and additional expenditure on fruitlet thinning is required to maintain fruit quality. A possible solution for controlling the fruit load on trees is the development of new cultivars that self-eliminate excess fruitlets, thus controlling yield. The aim of our study was to identify biological differences in apple cultivars in terms of blooming intensity and fruitlet load self-regulation. In total, 19 apple cultivars were studied in the years 2015–2017. The dynamics of fruitlet self-elimination, seed development in fruitlets and fruits, photosynthetic parameters, carbohydrates, and plant hormones were evaluated. We established that apple cultivars self-eliminating a small number of fruitlets need a lower number of well-developed seeds in fruit, and their number of leaves and area per fruit on a bearing branch are larger, compared to cultivars, self-eliminating large numbers of fruitlets. A higher carbohydrate amount in the leaves may be related to smaller fruitlet self-elimination. The amount of auxin and a high indole-3-acetic acid/zeatin ratio between leaves of cultivar groups with heavy blooming were higher than in cultivars with moderate blooming. A lower amount of abscisic acid was found in heavy-blooming cultivars during drought stress. All these parameters may be used as markers for the selection of different apple genotypes that self-eliminate fruitlets.

Cultivar-Groups in Cucurbita maxima Duchesne: Diversity and Possible Domestication Pathways

Domesticated Cucurbita has been remarked as one of the plant genera with the highest diversity in color, shape and fruit dimensions. Their economic and cultural values are related to the consumption of the mature or immature fruits, seeds, flowers, and to the use as decoration. The wild ancestor of C. maxima, the ssp. andreana has an actual scattered and disjointed distribution, associated with megafauna seed disperser syndrome. It was domesticated in South America around 9000–7000 years BP. The cultivar-group is a subspecific category for assembling cultivars on the basis of defined similarity. The work describes and pictures nine cultivar-groups for the species, Banana, Turban, Hubbard, Show, Buttercup, Zapallito, Plomo, Zipinka and Nugget. The molecular and a morphological join data analysis scatter biplot showed Turban and Buttercup in a central position, suggesting a first step in the domestication pathway associated with seed and immature fruit consumption; afterward, bigger bearing fruits groups were selected for their mature fruit flesh quality on one hand, and bush type, short day induction and temperate climate adaptation on the other hand. The striking domesticated Brazilian accession MAX24 intermediate between cultigens and ssp. andreana strengthens, in concordance with archeological remains, the possible domestication place of the species more easternward than previously believed.

Comparative analysis of sour cherry cultivars on their ecological and biological indicators

Sour cherries developed in the northern hemisphere, an alloploid hybrid of dwarf sour cherries (Prunus fruticosa) and bird cherries (P. avium), born in the confluence of the two species. However, the ecological and, above all, cold tolerance of the ancestor of cultivated sour cherries is higher than that of wild cherries (De Candolle, 1894; Rehder, 1954; Terpó, 1974; Iezzoni et al., 1991; Faust & Surányi, 1997). The cultivation limits are in the northern hemisphere 38-44. degree. The Carpathian Basin, the Balkans and Asia Minor are considered to be the main birthplaces for sour cherries. The genetic and morphological diversity of sour cherries is greater than that of the basic species (Iezzoni et al. 1991; Faust & Surányi, 1997). In the study, 472 sour cherry cultivars were compared based on 7 relative ecological indicators and 3 biological values. Compared to other Prunus species, we mostly found less variability in sour cherries - not counting their salt tolerance (SB). The partial similarity between open pollination (OP), frost tolerance (FR) and disease resistance (DR) - partly true in terms of varieties, but also reflected the effects of purposeful breeding and selection. The cultivars together - in comparison, showed balance, but in the highlighting, the differences of the 3 cultivar groups became significant. Indeed, the differences between the species of the former Hungarian cultural flora are clearly different (Surányi, 2004), which is also the case when comparing a large number of apricot (Surányi, 2014), plum (Surányi, 2015) and peach (Surányi, 2020) varieties.

Genetic Diversity Assessment and Cultivar Identification of Cucumber (Cucumis sativus L.) Using the Fluidigm Single Nucleotide Polymorphism Assay

Genetic diversity analysis and cultivar identification were performed using a core set of single nucleotide polymorphisms (SNPs) in cucumber (Cucumis sativus L.). For the genetic diversity study, 280 cucumber accessions collected from four continents (Asia, Europe, America, and Africa) by the National Agrobiodiversity Center of the Rural Development Administration in South Korea and 20 Korean commercial F1 hybrids were genotyped using 151 Fluidigm SNP assay sets. The heterozygosity of the SNP loci per accession ranged from 4.76 to 82.76%, with an average of 32.1%. Population genetics analysis was performed using population structure analysis and hierarchical clustering (HC), which indicated that these accessions were classified mainly into four subpopulations or clusters according to their geographical origins. The subpopulations for Asian and European accessions were clearly distinguished from each other (FST value = 0.47), while the subpopulations for Korean F1 hybrids and Asian accessions were closely related (FST = 0.34). The highest differentiation was observed between American and European accessions (FST = 0.41). Nei’s genetic distance among the 280 accessions was 0.414 on average. In addition, 95 commercial F1 hybrids of three cultivar groups (Baekdadagi-, Gasi-, and Nakhap-types) were genotyped using 82 Fluidigm SNP assay sets for cultivar identification. These 82 SNPs differentiated all cultivars, except seven. The heterozygosity of the SNP loci per cultivar ranged from 12.20 to 69.14%, with an average of 34.2%. Principal component analysis and HC demonstrated that most cultivars were clustered based on their cultivar groups. The Baekdadagi- and Gasi-types were clearly distinguished, while the Nakhap-type was closely related to the Baekdadagi-type. Our results obtained using core Fluidigm SNP assay sets provide useful information for germplasm assessment and cultivar identification, which are essential for breeding and intellectual right protection in cucumber.

Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of nonclassic domestication

The genetic architecture of quantitative traits is determined by both Mendelian and polygenic factors, yet classic examples of plant domestication focused on selective sweep of newly mutated Mendelian genes. Here we report the chromosome-level genome assembly and the genomic investigation of a nonclassic domestication example, bitter gourd (Momordica charantia), an important Asian vegetable and medicinal plant of the family Cucurbitaceae. Population resequencing revealed the divergence between wild and South Asian cultivars about 6,000 y ago, followed by the separation of the Southeast Asian cultivars about 800 y ago, with the latter exhibiting more extreme trait divergence from wild progenitors and stronger signs of selection on fruit traits. Unlike some crops where the largest phenotypic changes and traces of selection happened between wild and cultivar groups, in bitter gourd large differences exist between two regional cultivar groups, likely reflecting the distinct consumer preferences in different countries. Despite breeding efforts toward increasing female flower proportion, a gynoecy locus exhibits complex patterns of balanced polymorphism among haplogroups, with potential signs of selective sweep within haplogroups likely reflecting artificial selection and introgression from cultivars back to wild accessions. Our study highlights the importance to investigate such nonclassic example of domestication showing signs of balancing selection and polygenic trait architecture in addition to classic selective sweep in Mendelian factors.

Multiple streams of genetic diversity in Japonica rice

In-depth studies on the genetic diversity of crops indicate that domestication is likely a drawn-out process that differs from the traditional representation of a simple rapid bottleneck. Asian cultivated rice provides a clear picture of multiple foundations of crop diversity. Among them, Japonica rice is likely the group derived from the first human manipulations of this species. We make use of the 3,000 Rice Genomes (3K RG) data set, first described in 2018, to explore the genetic diversity of traditional Japonica rice. After delineating introgressions from the Indica and cAus cultivar groups, we mask these traces to analyse Japonica diversity in more depth. We find differentiation between the established “temperate”, “subtropical” and “tropical” subgroups, and identify stream-like traces of highly divergent sources from broad geographic ranges and subgroups. We characterize five such streams, most visible respectively in: 1) Indonesia, 2) continental Southeast Asia, 3) China, 4) uplands of Japan, and 5) Bhutan. These streams likely consist of ancient alien introgressions propagated through geneflow to different degrees. They currently appear as long genome segments conserved among specific germplasm groups, as well as shorter segments more broadly distributed across diverse germplasm along what could be adaptive corridors. They are all represented in the Japonica component of cBasmati varieties, thought to have emerged over two millennia ago. We thus provide strong evidence that Japonica, the group posited as being the most direct product of a simple domestication process in China, is an aggregate derived from multiple waves of admixture and represents a composite gene pool with ancient Asia-wide population dynamics.

Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of domestication

Bitter gourd (Momordica charantia) is a vegetable and medicinal plant of the family Cucurbitaceae. Here we report a chromosome-level assembly, with highest contig N50 (close to 10 Mb) and proportion of sequences placed on chromosomes (96%) in Cucurbitaceae. Population resequencing revealed the divergence between wild and cultivars at about 6000 years ago. Different cultivar groups have distinct allelic compositions in loci associated with domestication traits, suggesting phenotypic changes were achieved by allele frequency shifts in independent loci. Noticeably, one candidate locus for fruit size locates within a region missing from a recent Illumina-based assembly. Despite breeding efforts to increase female flower proportion, the gynoecy locus exhibits high variation within and low differentiation between wild and cultivar groups, likely because artificial directional selection could not overwhelm natural balancing selection. Our study provides resources to further investigate the genetic architecture of bitter gourd as well highlights the importance of a well-assembled genome.