American Cultivars Research Articles

K-mer genome-wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel.

Access to broad genomic resources and closely linked marker-trait associations for common beans (Phaseolus vulgaris L.) can facilitate development of improved varieties with increased yield, improved market quality traits, and enhanced disease resistance. The emergence of virulent races of anthracnose (caused by Colletotrichum lindemuthianum) and bean common mosaic virus (BCMV) highlight the need for improved methods to identify and incorporate pan-genomic variation in breeding for disease resistance. We sequenced the P. vulgaris Andean Diversity Panel (ADP) and performed a genome-wide association study (GWAS) to identify associations for resistance to BCMV and eight races of anthracnose. Historical single nucleotide polymorphism (SNP)-chip and phenotypic data enabled a three-way comparison between SNP-chip, reference-based whole genome shotgun sequence (WGS)-SNP, and reference-free k-mer (short nucleotide subsequence) GWAS. Across all traits, there was excellent concordance between SNP-chip, WGS-SNP, and k-mer GWAS results-albeit at a much higher marker resolution for the WGS data sets. Significant k-mer haplotype variation revealed selection of the linked I-gene and Co-u traits in North American breeding lines and cultivars. Due to structural variation, only 9.1 to 47.3% of the significantly associated k-mers could be mapped to the reference genome. Thus, to determine the genetic context of cis-associated k-mers, we generated draft whole genome assemblies of four ADP accessions and identified an expanded local repertoire of disease resistance genes associated with resistance to anthracnose and BCMV. With access to variant data in the context of a pan-genome, high resolution mapping of agronomic traits for common bean is now feasible.

SeqSNP-Based Targeted GBS Provides Insight into the Genetic Relationships among Global Collections of Brassica rapa ssp. oleifera (Turnip Rape).

Turnip rape is a multi-purpose crop cultivated in temperate regions. Due to its ability to fit into crop rotation systems and its role as a food and feed source, spring-type turnip rape cultivation is on the rise. To improve the crop's productivity and nutritional value, it is essential to understand its genetic diversity. In this study, 188 spring-type accessions were genotyped using SeqSNP, a targeted genotyping-by-sequencing method to determine genetic relationships between various groups and assess the potential effects of mutations within genes regulating major desirable traits. Single nucleotide polymorphism (SNP) alleles at six loci were predicted to have high effects on their corresponding genes' functions, whereas nine loci had country/region-specific alleles. A neighbor-joining cluster analysis revealed three major clusters (I to III). About 72% of cluster-I accessions were of Asian origin, whereas 88.5% of European accessions and all North American accessions were placed in cluster-II or cluster-III. A principal coordinate analysis explained 65.3% of the total genetic variation. An analysis of molecular variance revealed significant differentiation among different groups of accessions. Compared to Asian cultivars, European and North American cultivars share more genetic similarities. Hence, crossbreeding Asian and European cultivars may result in improved cultivars due to desirable allele recombination. Compared to landraces and wild populations, the cultivars had more genetic variation, indicating that breeding had not caused genetic erosion. There were no significant differences between Swedish turnip rape cultivars and the NordGen collection. Hence, crossbreeding with genetically distinct cultivars could enhance the gene pool's genetic diversity and facilitate superior cultivar development.

Genome-Wide Association Studies and QTL Mapping Reveal a New Locus Associated with Resistance to Bacterial Pustule Caused by Xanthomonas citri pv. glycines in Soybean.

Bacterial pustule (BP), caused by Xanthomonas citri pv. glycines, is an important disease that, under favorable conditions, can drastically affect soybean production. We performed a genome-wide association study (GWAS) with a panel containing Brazilian and American cultivars, which were screened qualitatively and quantitatively against two Brazilian X. citri isolates (IBS 333 and IBS 327). The panel was genotyped using a genotyping by sequencing (GBS) approach, and we identified two main new regions in soybeans associated with X. citri resistance on chromosomes 6 (IBS 333) and 18 (IBS 327), different from the traditional rxp gene located on chromosome 17. The region on chromosome 6 was also detected by QTL mapping using a biparental cross between Williams 82 (R) and PI 416937 (S), showing that Williams 82 has another recessive resistance gene besides rxp, which was also detected in nine BP-resistant ancestors of the Brazilian cultivars (including CNS, S-100), based on haplotype analysis. Furthermore, we identified additional SNPs in strong LD (0.8) with peak SNPs by exploring variation available in WGS (whole genome sequencing) data among 31 soybean accessions. In these regions in strong LD, two candidate resistance genes were identified (Glyma.06g311000 and Glyma.18g025100) for chromosomes 6 and 18, respectively. Therefore, our results allowed the identification of new chromosomal regions in soybeans associated with BP disease, which could be useful for marker-assisted selection and will enable a reduction in time and cost for the development of resistant cultivars.

Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits.

Fruit quality traits are major breeding targets in cultivated strawberry (Fragaria × ananassa). Taking into account the requirements of both growers and consumers when selecting high-quality cultivars is a real challenge. Here, we used a diversity panel enriched with unique European accessions and the 50K FanaSNP array to highlight the evolution of strawberry diversity over the past 160years, investigate the molecular basis of 12 major fruit quality traits by genome-wide association studies (GWAS), and provide genetic markers for breeding. Results show that considerable improvements of key breeding targets including fruit weight, firmness, composition, and appearance occurred simultaneously in European and American cultivars. Despite the high genetic diversity of our panel, we observed a drop in nucleotide diversity in certain chromosomal regions, revealing the impact of selection. GWAS identified 71 associations with 11 quality traits and, while validating known associations (firmness, sugar), highlighted the predominance of new quantitative trait locus (QTL), demonstrating the value of using untapped genetic resources. Three of the six selective sweeps detected are related to glossiness or skin resistance, two little-studied traits important for fruit attractiveness and, potentially, postharvest shelf life. Moreover, major QTL for firmness, glossiness, skin resistance, and susceptibility to bruising are found within a low diversity region of chromosome 3D. Stringent search for candidate genes underlying QTL uncovered strong candidates for fruit color, firmness, sugar and acid composition, glossiness, and skin resistance. Overall, our study provides a potential avenue for extending shelf life without compromising flavor and color as well as the genetic markers needed to achieve this goal.

Characterization of biologically synthesized copper nanoparticles by Aspergillus carbonarius and evaluation of their activity in reducing the pathogenic stress of tomatoes infected with Fusarium oxysporum

This study was conducted to evaluate the efficiency of the fungus Aspergillus carbonarius in the synthesis of copper nanoparticles (CuNPs) from copper chloride solution, with the characterization of these nanoparticles and the demonstration of their effectiveness in inhibiting the pathogenic fungus Fusarium oxysporum causing tomato root rot disease. The results indicated that the treatment of copper chloride solution at 150 mM with A. carbonarius filtrate led to the production of CuNPs which characterized by a color change from blue to green, with the highest absorbance observed at 300 nm. X-ray diffraction (XRD) results revealed the crystalline structure with peaks at angles 28.47286, 47.43258, and 56.20644 ◦ corresponding to (111), (220), and (311) planes, respectively, matching the JCPDS card number 01-081-1841. Scanning electron microscopy images showed cubic, pyramidal, and prismatic shapes with dimensions ranging from 15 - 84.291 nm. In laboratory experiment, CuNPs inhibited the growth of the pathogenic fungus, with an inhibition zone of 1.6 cm, compared to copper chloride which recorded 0.9 cm. In the field, , the treatment of CuNPs led to an increase in the stress resistance indicators, reaching the highest values for CuNPs when combined with the fungicide Medazim in the American tomato cultivar. The concentrations of total phenols and glutathione in this treatment were 2.56 mg/g and 0.322 µg/g, respectively. The lowest concentration of proline was recorded as 4.31 µg/g in the treatment involving CuNPs against the fungal infection. CuNPs with the fungicide medazim, significantly outperformed other treatments, registering lowest disease severity at 12.22% in the American cultivar, compared to the highest disease severity was recorded in the treatment with the pathogenic fungus alone, reaching 91.16% in the Dutch cultivar. CuNPs significantly increased tomato fruit weight, both in healthy and infected plants. The American, Turkish, and Dutch tomato cultivars infected with the pathogenic fungus and treated with under + medazim showed higher productivity, reaching 6432.55, 6334.34, and 6305.73 g.plant-1, compared to the lowest productivity in the treatment of these cultivars with the pathogenic fungus, reaching 1008.34, 977.45, and 833.78 g.plant-1, respectively

Identification of breadfruit (Artocarpus altilis) and South American crops introduced during early settlement of Rapa Nui (Easter Island), as revealed through starch analysis.

Starch residue analysis was carried out on stone tools recovered from the bottom layer of the Anakena site on Rapa Nui (Easter Island). These deposits have been dated to AD 1000-1300 AD and so far, represent the earliest evidence of human settlement on this island. Twenty obsidian tools were analyzed. Analysis of 46 starch grains recovered from 20 obsidian tools from the earliest dated level of the Anakena site on Rapa Nui provides direct evidence for translocation of traditional crop plants at initial stages of the colonization of this island. The analysis of starch grains was based mainly on statistical methods for species identification but was complemented by visual inspection in some cases. Our results identify taxons previously unknown to have been cultivated on the island, such as breadfruit (Artocarpus altilis), Zingiber officinale (ginger), and starch grains of the Spondias dulcis and Inocarpus fagifer tropical trees. Additionally, starch grains of Colocasia esculenta (taro) and Dioscorea sp. (yam), both common species in Pacific agriculture, were identified. Furthermore, the presence of four American taxa Ipomoea batatas (sweet potato), Canna sp. (achira), Manihot esculenta (manioc), and Xanthosoma sp., was detected. The occurrence of Canna sp., M. esculenta, and Xanthosoma sp. starch grains suggests the translocation of previously not described South American cultivars into the Pacific. The detection of I. batatas from this site in Rapa Nui constitutes the earliest record of this cultigen in the Pacific. Our study provides direct evidence for translocation of a set of traditional Polynesian and South American crop plants at the initial stages of colonization in Rapa Nui.

Classification of cultivars of common peach (Persica vulgaris Mill.)

The existing classifications of peach cultivars are based on the morphological characteristics of vegetative and generative organs, and are of economic importance. The classification by N. I. Ryabov (1939) gained the greatest popularity. The entire cultural assortment of Persica vulgaris Mill. was divided by him into two varieties distinguished by the type of flower. A variety with a rose-shaped flower, P. vulgaris var. rosaeflora Rjab., is divided into 4 groups: 1. American early ripers; 2. Northern Chinese peaches of the ‘Chinese Cling’ type (with cartilage-like flesh texture); 3. cultivars of the Turkestan-Transcaucasian type; 4. South Chinese ‘Honey’ type peaches (honey peaches). A variety with a bell-shaped flower, P. vulgaris var. campanuliflora Rjab., is divided into two groups: 1. Iranian, the ‘Phillips Cling’ type (with cartilage-like flesh texture); 2. Iranian, the ‘Crawford’ type (with a fibrous flesh texture). The work was carried out in the collection orchard of the Research Institute of Plant Genetic Resources of Uzbekistan.Research has shown that the groups do not have a specific geographical area and consist of cultivars from all around the world. Peach cultivars are grouped according to a set of morphological characteristics, therefore, the average values of basic biological properties within a group are very close and the differences are insignificant, which complicates the use of the classification for scientific purposes.The proposed classification of peach cultivars is based on the botanical-geographical principle (Vavilov, 1935). It is proposed to divide all common peach cultivars into groups according to their geographical origin: 1. Chinese; 2. Transcaucasian; 3. European; 4. American; and 5. Central Asian. Each of these groups has its own distribution area. The biological properties of cultivars were formed under the influence of various soil and climatic conditions. Chinese peaches are frost and winter hardy and have a long dormancy period. However, in terms of commercial and taste qualities they are inferior to modern cultivars. They can be used in breeding for creating large-fruited, frostresistant, late flowering varieties. European cultivars were forming under different conditions and they should be used differentially; they are good source material for breeding cultivars with high commercial and taste qualities of fruits. Transcaucasian varieties are superior to other groups in terms of transportability. These are cultivars for canning and high quality processed products. They are relatively resistant to fungous diseases. American cultivars are distinguished by high commercial and taste qualities of fruits. Most cultivars are highly frost-resistant, but they are poorly winterhardy. They can be used for breeding highly productive cultivars with high commercial and taste qualities of fruits, with different ripening periods. Central Asian varieties have a long dormancy period, they are frost-, drought-, and soil salinity resistant. However, they are weakly resistant to fungous diseases. They can be used in breeding according to the indicated characteristics

Phenotypic and Genotypic Variation of Cultivated Panax quinquefolius.

American ginseng (Panax quinquefolius) is widely used due to its medicinal properties. Ontario is a major producer of cultivated American ginseng, where seeds were originally collected from the wild without any subsequent scientific selection, and thus the crop is potentially very diverse. A collection of 162 American ginseng plants was harvested from a small area in a commercial garden and phenotyped for morphological traits, such as root grade, stem length, and fresh and dry weights of roots, leaves, stems, and seeds. All of the traits showed a range of values, and correlations were observed between root and stem weights, root dry weight and leaf dry weight, as well as root and leaf fresh weights. The plants were also genotyped using single nucleotide polymorphisms (SNPs) at the PW16 locus. SNP analysis revealed 22 groups based on sequence relatedness with some groups showing no SNPs and others being more diverse. The SNP groups correlated with significant differences in some traits, such as stem length and leaf weight. This study provides insights into the genetic and phenotypic diversity of cultivated American ginseng grown under similar environmental conditions, and the relationship between different phenotypes, as well as genotype and phenotype, will aid in future selection programs to develop American ginseng cultivars with desirable agronomic traits.

Production of American lettuce cultivars under different colored shade nets

Shading nets are used to reduce the amount of radiant energy reaching crops. The objective of the work was to compare the influence of black and red shading nets on the production of nine American lettuce cultivars in the Autumn period under the conditions of the Central Department of Paraguay. The experiment was carried out in the Experimental Field of the Departmental Agronomic Center (CAD) in the Municipality of Julián Augusto Saldívar. The treatments consisted of the combination of two types of shading netting (red with 35% shade and black with 35% shade) and nine cultivars of American lettuce (Julia, Dora, Angelina, Tainá, Sun Valley, Betty, Lucy Brown, Mara, and Serena) totaling 18 treatments. The experiment consisted in a complete randomized block design, arranged in split blocks 2×9 (the color of shading netting was considered the main plot, and the lettuce cultivars as the secondary plot) with four repetitions. Each experimental unit consisted of four crop rows with seven plants. Plant diameter, plant height, head diameter and height, commercial number of leaves per plant, fresh mass, and commercial productivity were evaluated. The data were subjected to analysis of variance, and when differences were found, the means were compared by the Scott-Knott test at 5% probability. The results indicate that using the red netting with the Serena and Dora cultivars provides greater fresh mass and commercial production.

Exploring the tropical acclimation of European and American hop cultivars (Humulus lupulus L.): Focus on physiology, productivity, and chemical composition

Hop (Humulus lupulus L.) cones are widely used by the beer industry to provide flavor, aroma, and bitterness due to the presence of α-acids, β-acids, and volatile oil components. Although the brewing sector plays an important role in Brazil’s economy, hops are entirely imported. In this study, we aimed to investigate the physiological acclimation potential, productivity, and chemical composition of four hop cultivars in a warm tropical region of Brazil. For this purpose, three North American-bred hop cultivars (‘Cascade’, ‘Chinook’ and ‘Triple Pearl’) and one European hop cultivar (‘Saaz’) that grew under tropical ambient conditions for two consecutive years were used. ‘Saaz’ and ‘Triple Pearl’ showed higher mortality and smaller photosynthetic rates, while ‘Cascade’ and ‘Chinook’ cultivars showed the best physiological and growth performance under a tropical-type climate. With a few exceptions, maximum quantum yield of photosystem II (PSII), chlorophyll content, and antioxidant enzymes activity were very similar between these two cultivars. A higher dry mass of cones was observed in ‘Chinook’ and ‘Cascade’, however, with a higher variability within each cultivar. Both cultivars increased the production of the dry mass of cones in the second year. The average concentration of bitter acids in ‘Cascade’ and ‘Chinook’ was below the expected values, but there was a considerable increase in the volatile oil content between the first and second year of cultivation. We concluded that 'Cascade' and 'Chinook', American cultivars, showed better development and lower mortality compared to 'Triple Pearl' (American cultivar) and 'Saaz' (European cultivar) under tropical climate conditions in Brazil. Although the concentration of bitter acids was lower than expected in the first two years, the concentration may increase with plant maturity.

Genetic Diversity Analysis of Soybean Collection Using Simple Sequence Repeat Markers.

Soybean [Glycine max (L.) Merr.] is a nutrient-rich crop that offers a sustainable source of dietary protein and edible oil. Determining the level of genetic diversity and relationships between various genetic resources involved in breeding programs is very important in crop improvement strategies. This study evaluated 100 soybean accessions with diverse origins for 10 important agronomic traits, including plant height (PH), an important plant adaptation-related trait impacting yield, in conditions in southeastern Kazakhstan for 2 years. The comparison of different groups of PH (tall, middle, and short) using a t-test suggested that the group of plants with the tallest PH provided a higher yield (p < 0.001) in relatively dry field conditions. The genetic diversity of the accessions was estimated using 25 simple sequence repeat (SSR) markers previously known to be associated with plant height. The results showed a significant variation among different groups of origin for all measured agronomic traits, as well as high genetic diversity, with the PIC (polymorphism information content) varying from 0.140 to 0.732, with an average of 0.524. Nei's diversity index ranged between 0.152 and 0.747, with an average of 0.526. The principal coordinate analysis (PCoA) of the studied soybean collection showed that Kazakhstan accessions were genetically distant from European, East Asian, and North American cultivars. Twelve out of twenty-five SSR markers demonstrated significant associations with ten studied agronomic traits, including PH (p < 0.05). Six SSRs with pleiotropic effects for studied traits were selected, and their haplotypes with phenotypic effects were generated for each soybean accession. The obtained results can be used in soybean improvement programs, including molecular-assisted breeding projects.

Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States.

Breeding has dramatically changed the plant architecture of wheat (Triticum aestivum), resulting in the development of high-yielding varieties adapted to modern farming systems. However, how wheat breeding shaped the genomic architecture of this crop remains poorly understood. Here, we performed a comprehensive comparative analysis of a whole-genome resequencing panel of 355 common wheat accessions (representing diverse landraces and modern cultivars from China and the United States) at the phenotypic and genomic levels. The genetic diversity of modern wheat cultivars was clearly reduced compared to landraces. Consistent with these genetic changes, most phenotypes of cultivars from China and the United States were significantly altered. Of the 21 agronomic traits investigated, 8 showed convergent changes between the 2 countries. Moreover, of the 207 loci associated with these 21 traits, more than half overlapped with genomic regions that showed evidence of selection. The distribution of selected loci between the Chinese and American cultivars suggests that breeding for increased productivity in these 2 regions was accomplished by pyramiding both shared and region-specific variants. This work provides a framework to understand the genetic architecture of the adaptation of wheat to diverse agricultural production environments, as well as guidelines for optimizing breeding strategies to design better wheat varieties.

Race Structure and Molecular Diversity of Colletotrichum lindemuthianum of Common Bean in Zambia.

Anthracnose, caused by the fungus Colletotrichum lindemuthianum, is a major disease of common bean (Phaseolus vulgaris L.) worldwide. C. lindemuthianum is genetically highly variable, and understanding the pathogen's diversity and distribution is a key step in developing common bean varieties with durable anthracnose resistance. The objectives of this study were to (i) characterize the race structure of C. lindemuthianum in Zambia and (ii) assess the molecular diversity of C. lindemuthianum in Zambia. A field survey was conducted in 20 bean-growing districts in Zambia to collect anthracnose symptomatic bean plants. A total of 103 C. lindemuthianum isolates were collected and characterized based on their reactions on 12 common bean race differential cultivars. RAM and ERIC-BOX DNA markers were used to assess molecular diversity of 60 isolates. A total of 58 races were characterized from the 103 isolates. Race 5 was the least virulent, and race 1631 was the most virulent based on their reaction on the 12 race differential cultivars. Race 19 had the highest recovery frequency (11%) and was the most extensively dispersed among the 22 bean-growing districts from where the isolates were collected. Only six races had previously been reported in Zambia, and 52 races were identified as new races reported for the first time in Zambia. Two races were virulent only on Andean cultivars, 11 races were virulent only on Middle American cultivars, and 45 races were virulent on both Andean and Middle American cultivars. No individual isolate showed pathogenicity on all the differential cultivars, and no isolate overcame the Co-4, Co-5, and Co-7 resistance gene pyramid that naturally exists in G2333. Phylogenetic analysis categorized the 60 isolates in six major clusters and six subclusters. The 60 isolates showed high genetic heterogeneity among and within a race of the same virulence. The study has revealed the existence of both Andean and Middle American races and extensive molecular diversity of C. lindemuthianum in Zambia. The knowledge on the race structure of C. lindemuthianum that this study has provided will be valuable for making breeding decisions on the host plant resistance genes required for developing common bean varieties with durable resistance to anthracnose in Zambia.

Characterization of Uromyces appendiculatus First Races in Sri Lanka and Identification of Genes for the Development of Rust-Resistant Snap Beans.

Bean rust is a devastating disease of snap beans in Sri Lanka. Our study endeavored to develop snap beans with resistance to Uromyces appendiculatus, the bean rust pathogen reported to have numerous virulent races. Accordingly, we needed a detailed understanding of the virulence of U. appendiculatus and to identify genes conferring effective rust resistance. To investigate the virulence, we collected leaves of snap bean with rust symptoms from four snap bean producing districts of Sri Lanka. From these samples we established 57 single pustule isolates. Each isolate was inoculated on a set of 12 differential cultivars, six from the Andean and six from the Middle American gene pools of common bean. The virulence of the isolates segregated into four distinct groups that comprised the first four reported races of U. appendiculatus in Sri Lanka, 23-5, 31-1, 31-11, and 63-21. All races were significantly more virulent on the Andean than on the Middle American differential cultivars. PI 1819966, a Middle American differential cultivar containing the Ur-11 gene, conferred resistance to all four races. Three other Middle American cultivars were resistant to three races. Conversely, five Andean differential cultivars were susceptible to all four races. PI 160418 was the only Andean differential cultivar with resistance to three races. The results suggested that rust resistance genes from the Middle American differential cultivars could be combined in different ways with the resistance of Andean PI 260418 to develop snap bean varieties with broad resistance to all races of U. appendiculatus in Sri Lanka.

Susceptibility of South American pear cultivars to brown spot of pear caused by Stemphylium vesicarium

Susceptibility of South American pear cultivars to brown spot of pear caused by Stemphylium vesicarium

Effect of Cultivars, Apical Pinching and Copper Nano-Fertilizer on 1-Characteristics of Vegetative Growth of Broad Bean (Vicia faba L.)

Research was conducted at the vegetable field of the University of Mosul’s Department of Horticulture and Landscape Engineering (in the College of Agriculture and Forestry) (2021). The experiment included a study of three factors, the first of which was the use of three different bean sprout cultivars (Spanish, American, and Dutch), the second of which was the condition of apical pinching (apical pinching and without pinching), and the third of which was the use of copper Nano-fertilizer at three different concentrations (zero, one, and 1.5 gm L-1) (2 x 3 x 3). Field research was conducted utilizing a factorial experiment with split-plots in R.C.B.D. Varieties were planted in the main plots, and the correlation between pinching and copper Nano-fertilizer concentrations was observed in the sub-plots. The Duncan multiple range test was used to compare the means of the groups, and a significance threshold of 5% was used for the study. Here’s a rundown of the A- The significant effect of the plants of the three cultivars varied in the characteristics of the vegetative growth, as the plants of the Spanish and American cultivars were significantly superior in plant height and percentage of dry matter, while the plants of the Dutch and Spanish cultivars excelled in the number of branches, while no significant differences were observed between the cultivars in terms of chlorophyll and leaf area. B- The treatment of apical pinching excelled in terms of the number of branches and leaf area compared to the treatment of not pinching. C- The use of copper Nano-fertilizer in two concentrations resulted in significant effects on all vegetative growth traits compared to comparison plants. D- Most of the effects of the binary and triple interaction of the studied factors were consistent with the single effect of each factor for most of the previous characteristics.

Genetic Diversity and Population Structure of European Soybean Germplasm Revealed by Single Nucleotide Polymorphism.

Soybean is the most grown high-protein crop in the world. Despite the rapid increase of acreage and production volume, European soybean production accounts for only 34% of its consumption in Europe. This study aims to support the optimal exploitation of genetic resources by European breeding programs by investigating the genetic diversity and the genetic structure of 207 European cultivars or American introductions registered in Europe, which were genotyped by the SoySNP50K array. The expected heterozygosity (He) was 0.34 for the entire collection and ranged among countries from 0.24 for Swiss cultivars to 0.32 for American cultivars (partly reflecting differences in sample size between countries). Cluster analysis grouped all genotypes into two main clusters with eight subgroups that corresponded to the country of origin of cultivars and their maturity group. Pairwise Fst values between countries of origin showed the highest differentiation of Swiss cultivars from the rest of the European gene pool, while the lowest mean differentiation was found between American introductions and all other European countries. On the other hand, Fst values between maturity groups were much lower compared to those observed between countries. In analysis of molecular variance, the total genetic variation was partitioned either by country of origin or by maturity group, explaining 9.1% and 3.5% of the total genetic variance, respectively. On the whole, our results suggest that the European soybean gene pool still has sufficient diversity due to the different historical breeding practices in western and eastern countries and the relatively short period of breeding in Europe.

Genetic Diversity Analysis of Banana Cultivars (Musa sp.) in Saudi Arabia Based on AFLP Marker.

Banana plantation has been introduced recently to a temperate zone in the southeastern parts of Saudi Arabia (Fifa, Dhamadh, and Beesh, located in Jazan province). The introduced banana cultivars were of a clear origin without a recorded genetic background. In the current study, the genetic variability and structure of five common banana cultivars (i.e., Red, America, Indian, French, and Baladi) were analyzed using the fluorescently labeled AFLP technique. Nine different primer pairs combinations yielded 1468 loci with 88.96% polymorphism. Among all locations, high expected heterozygosity under the Hardy-Weinberg assumption was found (0.249 ± 0.003), where Dhamadh was the highest, followed by Fifa and Beesh, respectively. Based on the PCoA and Structure analysis, the samples were not clustered by location but in pairs in accordance with the cultivar's names. However, the Red banana cultivar was found to be a hybrid between the American and Indian cultivars. Based on ΦST, 162 molecular markers (i.e., loci under selection) were detected among cultivars. Identifying those loci using NGS techniques can reveal the genetic bases and molecular mechanisms involved in the domestication and selection indicators among banana cultivars.

Dry matter partitioning in Bt and non Bt cotton (Gossypium hirsutum) cultivars under different sowing environments of Punjab

A field experiment was conducted at Punjab Agricultural University (PAU), Regional Research Station (RRS), Faridkot and Bathinda during rainy (kharif) season 2017 to evaluate the performance of Bt and non Bt cotton (Gossypium hirsutum L.) cultivars under different sowing environments. The experiment was laid out in split plot design with 3 sowing dates (April 20, May 10 and May 30) in main plots and 4 American cotton cultivars [2 Bt cultivars (NCS 855 BGII and RCH 650 BGII) and 2 non Bt cultivars (F 2228 and F 1861)] in sub-plots. Results of the pooled data indicated that early sown (April 20) crop accumulated more dry matter production, higher crop growth rate (CGR) as well as relative growth rate (RGR) followed by crop sown on May 10 and May 30. Maximum CGR (14.35–15.48 g/m2/day) was obtained during 90–120 DAS (days after sowing) while RGR was highest during 60–90 DAS. Among tested cultivars, F 1861 exhibited better CGR and RGR values and hence, accumulated higher dry matter (1303.0 g/m2) followed by F 2228 (1276.9 g/m2), NCS 855 BGII (1261.1 g/m2) and RCH 650 BGII (1206.7 g/m2). Dry matter accumulation in fruiting bodies has started around 90 DAS and accounted for 30–35% of total above ground biomass. Bt cultivar NCS 855 BGII, accumulated higher dry matter in fruiting bodies (458.1 g/m2), though at par with RCH 650 BGII (432.2 g/m2) but, significantly higher than F 1861 (403.3 g/m2) and F 2228 (401.9 g/m2). Dry matter accumulation towards fruiting bodies in Bt cultivars was ~9% higher than non Bt cultivars which may be prime reason for better yield performance of Bt cotton.

Pedigree reconstruction for triploid apple cultivars using single nucleotide polymorphism array data

Societal Impact StatementMany economically, culturally, and historically important apple cultivars are triploids, which have three copies of each chromosome instead of the more typical two copies in diploids. Despite their prevalence and importance, there have been conflicting reports regarding their origin and their ability to beget diploids. New genetic analysis methodologies outlined in this study have clarified the genetic origin of triploid apple cultivars and suggest that triploidy has been a dead end in historic apple pedigrees. The specific results of this study have resolved the pedigrees of many cultivars, including the famous English cultivar Cox's Orange Pippin and the oldest known US cultivar Roxbury Russet.Summary In apple (Malus × domestica), most cultivars are diploid, though a sizeable number are triploids, which tend to be stronger growing, more robust, and bear larger fruit. However, triploidy is also associated with strongly reduced fertility. Some recorded pedigrees for historical apple cultivars include triploids as parents of diploids, despite this reputation of poor fertility. This information, coupled with some initiatives using triploids in breeding efforts, result in confusion about how possible or common it is for triploids to be parents of diploid offspring. To date, no studies have systematically evaluated and identified pedigrees of triploid apple cultivars to resolve these contradictions. Here, we describe a method to make triploid genotype calls using Illumina Infinium single nucleotide polymorphism (SNP) array data through a novel Python script: ploidyClassifier. SNP data for 219 unique triploids was compared alongside 2498 unique diploid apple accessions to conduct pedigree reconstruction. Unreduced gamete‐donating parents were identified for over half of the triploid accessions. From those, reduced gamete‐donating parents were identified for nearly half. Full or partial pedigrees for many classic triploids were uncovered, including that of the oldest known American cultivar, ‘Roxbury Russet’. All tested pedigrees from literature that listed triploids as parents of diploids were deemed false, including that of the well‐known ‘Cox's Orange Pippin’, whose previously unreported second parent was also identified here as ‘Rosemary Russet’. These results together suggest that historic triploids are mostly or solely the product of diploid parentage and that triploidy has been a dead end in historic apple pedigrees.