Clonal Selection Programs Research Articles

Behavior of New and Promising Egyptian Garlic Clones Resulting from Clonal Selection Program

Behavior of New and Promising Egyptian Garlic Clones Resulting from Clonal Selection Program

Genomic relationship–based genetic parameters and prospects of genomic selection for growth and wood quality traits in Eucalyptus benthamii

The unique adaptation of Eucalyptus benthamii to low temperatures coupled to fast growth and versatile wood quality has made it a valued plantation species in frost-prone areas worldwide, but little is known on its quantitative genetic parameters for key industrial traits. We used GBLUP additive (GA), additive-dominant (GAD), single-step (HBLUP), and pedigree-based predictive models to estimate lignin, extractives, carbohydrates, and wood density at age 4 and tree volume at age 6. By capturing hidden relatedness and correcting pedigree errors, SNP data disentangled non-additive from additive variance providing more realistic estimates of narrow-sense heritability than pedigrees, and more accurate predictions of trait values. Predictive abilities (PAs) ranged from 0.12 for volume (pedigree-based model) to 0.44 for wood density (models H, GA, and GAD). Considerable dominance variance was seen for all traits, growth was the trait most influenced by it, resulting in PAs 48.9% higher when this effect is considered, a result with important consequences both for clonal propagation and overall selection efficiency (Seff). Using a HBLUP model, phenotypes of non-genotyped trees increased PAs by increasing sample size and provided realized relationships with reduced genotyping cost. In a recurrent selection program, the preclusion of progeny testing provides an increase in Seff between 232% and 299%. In a clonal selection program, the elimination of both progeny and initial clonal trial may increase Seff between 134% and 277%. Increasing selection intensity by genomic prediction resulted in an additional impact on Seff. This study provides groundwork to implement genomic selection in E. benthamii breeding.

Utilization Clonal Selection Program to Improve Resistance Garlic (Allium sativum L.) Against Onion Maggot (Delia antiqua M.)

Onion maggot (Delia antiqua M) is an economically important pest of Allium crops throughout the world; thus, management of this pest is required to achieve economic returns. Accordingly, this study aimed to select some clones of garlic resistant to infestation with onion maggot through the implementation three cycles of clonal selection program within some improved garlic clones derived from Balady cultivar. Afterwards, the developed clones and their original population were evaluated in a randomized complete block design with three replicates. Thus, this study was conducted during four successive winter seasons of 2016/2017 to 2019/2020. The obtained results showed, clearly, significant differences among garlic selected clones, as well as their original population in their response to Delia antiqua M. and their bulb characteristics. Where, the selected clones varied between resistant and ability of infestation by onion maggot that was between 0.00% and 22.45%, with classification into five groups by cluster analysis: HR (highly resistant), R (resistant), MR (moderately resistant), MS (moderately susceptible) and S susceptible. Among the 16 selected clones three clones were HR; and six clones were R to onion maggot. Moreover, improvement percentage for the same character using clonal selection program was between 100% to 48.97%, which reflected that clonal selection could be an effective way to improve onion maggot resistance. Also, utilization of these improved clones will promise in minimize environmental pollution.

Peach Tree Short Life in Rio Grande do Sul State, Brazil

The Peach Tree Short Life (PTSL) is a syndrome that causes severe damage to peach trees, usually between one and eight-years-old, which can lead to the scion death. In Brazil, it has importance mainly in the Rio Grande do Sul State, which is the largest Brazilian peach producer. First reported in the Pelotas area, in late 1970s, the syndrome continues to cause damage, with varying intensities among years. Several causes have been reported in national and international literature, involving biotic and abiotic factors. In Rio Grande do Sul, due to the predominant use of mixtures of scion peach pits from canning industry for rootstock production, it is not possible to know varietal identity of tree root system in commercial orchards. This genetic variability which causes heterogeneity among trees, can at the same time under the environmental selection pressure, be used in a clonal selection program in situ, in search for tolerant sources. In another strategy developed by Embrapa Clima Temperado, evaluation of cultivars, species and interspecific hybrids as rootstocks are also underway. In the present paper, we report main technical and scientific advances on PTSL in Rio Grande do Sul and the focus on search for tolerant rootstocks and quality of nursery trees.

Differential expression of transcription factor- and further growth-related genes correlates with contrasting cluster architecture in Vitis vinifera \u2018Pinot Noir\u2019 and Vitis spp. genotypes

Grapevine (Vitis vinifera L.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid fungal damage. Grapevine cultivars with loose cluster architecture enable reducing protective treatments due to their enhanced resilience against fungal infections, such as Botrytis cinerea-induced gray mold. A recent study identified transcription factor gene VvGRF4 as determinant of pedicel length, an important component of cluster architecture, in samples of two loose and two compact quasi-isogenic ‘Pinot Noir’ clones. Here, we extended the analysis to 12 differently clustered ‘Pinot Noir’ clones from five diverse clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons. Two phenotypically opposite clones were grown at all three locations and served for standardization. Data were correlated with the phenotypic variation of cluster architecture sub-traits. A set of 14 genes with consistent expression differences between loosely and compactly clustered clones—independent from season and location—was newly identified. These genes have annotations related to cellular growth, cell division and auxin metabolism and include two more transcription factor genes, PRE6 and SEP1-like. The differential expression of VvGRF4 in relation to loose clusters was exclusively found in ‘Pinot Noir’ clones. Gene expression studies were further broadened to phenotypically contrasting F1 individuals of an interspecific cross and OIV reference varieties of loose cluster architecture. This investigation confirmed PRE6 and six growth-related genes to show differential expression related to cluster architecture over genetically divergent backgrounds.

Distribucija devet virusa kod hrvatskih autohtonih sorata vinove loze (Vitis vinifera L.) s područja Dalmacije uključenih u klonsku selekciju

The investigation of virus incidence was conducted on 14 autochthonous Croatian grapevine cultivars on vines from 51 vineyard located in the Dalmatian region. A total of 1,116 vines were tested by ELISA on nine viruses: Arabis mosaic virus (ArMV), Grapevine fanleaf virus (GFLV), Grapevine fleck virus (GFkV), Grapevine leafroll-associated virus 1, 2, 3 and 7 (GLRaV-1, GLRaV-2, GLRaV-3 and GLRaV-7), Grapevine virus A and B (GVA and GVB). ELISA confirmed presence of eight viruses: GLRaV-3 in 888 vines (79.6%), GVA 685 (61.4%), GLRaV-1 455 (40.8%), GFkV 223 (19.9%), GFLV 219 (19.6%), GLRaV-2 46 (4.1%), ArMV 36 (3.2%) and GVB 35 (3.1%). Altogether 93 vines (8.3%) were free of all tested viruses, 168 (15.1%) were infected with a single virus, 368 (32.9%) with two, 314 (28.1%) with three, 127 (11.4%) with four, 43 (3.9%) with five, and 3 (0.3%) vines with six viruses. Symptoms of premature leaf color change and downward curling of leaf blades were common, while abnormal branching, short internodes, double nodes and irregular ripening were detected sporadically. The investigation confirms deteriorated sanitary status of all cultivars except Grk and Plavina and indicates the necessity of intensifying grapevine clonal and sanitary selection programs.

Evaluation of Various Sugarcane Genotypes for Association of Quality Characters with Cane Yield

The present investigation was carried out to study the association of quality traits with cane yield to establish an appropriate selection strategy based on quality characters. Sixteen sugarcane genotypes comprising two check cultivars were assessed during 2012-15 using RCB design with three replications. Data were collected on brix (%), polarized sugar (%), purity (%), sugar recovery (%) and cane yield (t ha-1). Analysis of variance exhibited highly significant differences between crops for all parameters except brix (%). Among the genotypes highly significant differences were observed for brix (%), polarized sugar (%) and cane yield (t ha-1). Crops × genotypes revealed highly significant differences for cane yield (t ha-1). Genotypes MS-92-CP-99 (72.92 t ha-1), MS-2000-Ho-360 (72.13 t ha-1), MS-2003-HS-274 (72.04 t ha-1) and MS-91-CP-523(71.58 t ha-1) showed superiority regarding cane yield. Positive phenotypic and genotypic correlations were observed for all the traits with cane yield (t/ha) except purity %. Brix % and polarized sugar % showed highly significant and positive correlation with sugar recovery % at genotypic (0.66**, 0.74**) and phenotypic (0.67**, 0.79**) levels. Brix % showed highly significant correlation with polarized sugar (%) at genotypic (1.00**) and phenotypic (0.95**) level. Path analysis showed that highest positive direct effect on cane yield (t ha-1) is exerted by sugar recovery % at genotypic (0.42) and phenotypic (1.94) level showing its importance in clonal selection program for evolving improved sugarcane genotypes. It is suggested that the quality parameters should be taken in to consideration in clonal selection program for evolving improved sugarcane genotypes. Moreover, the genotypes with high cane yield and sugar recovery should be evaluated further.

Genomic predictions of breeding values in a cloned Eucalyptus globulus population in Chile

In Chile, an intensive Eucalyptus globulus clonal selection program is being carried out to increase forest productivity for pulp production. A breeding population was used to investigate the predicted ability of single nucleotide polymorphism (SNP) markers for genomic selection (GS). A total of 310 clones from 53 families were used. Stem volume and wood density were measured on all clones. Trees were genotyped at 12 K polymorphic markers using the EUChip60K genotype array. Genomic best linear unbiased prediction, Bayesian lasso regression, Bayes B, and Bayes C models were used to predict genomic estimated breeding values (GEBV). For cross-validation, 260 individuals were sampled for model training and 50 individuals for model validation, using 2 folds and 10 replications each. The average predictive ability estimates for wood density and stem volume across the models were 0.58 and 0.75, respectively. The average rank correlations were 0.59 and 0.71, respectively. Models produced very similar bias for both traits. When clones were ranked based on their GEBV, models had similar phenotypic mean for the top 10% of the clones. The predicted ability of markers will likely decrease if the models are used to predict GEBV of new material coming from the breeding program, because of a different marker–trait phase introduced by recombination. The results should be validated with larger populations and across two generations before routine applications of GS in E. globulus. We suggest that GS is a viable strategy to accelerate clonal selection program of E. globulus in Chile.

Evaluación de la diversidad genética de la Monastrell, una variedad antigua en la provincia de Alicante (España) mediante Genotipado por Secuenciación (GBS)

Monastrell variety, also known as Mourvedre, is cultivated mainly in the southeast of Spain in more than 45,000 ha. It is an ancient variety, whose origins are not known with certainty, highly adapted to the dry and warm climate of the southeast Spanish. The existence of a great clonal diversity is well known but, although some clonal selection programs have been carried out (Murcia, Bandol, etc.), the genetic diversity has not been evaluated to date. The measure of this diversity is urgent, since very old vines have been plucked in recent years. We have initiated a project to estimate the genetic diversity of the conserved clones of this variety through GBS (Genotyping by Sequencing). To carry out this analysis, a survey was carried out covering the whole area of Monastrell cultivation in the Alicante Denomination of Origin (D.O.). We selected 46 vines from 46 different vineyards, always prioritizing the oldest vines at each sampling site. The GBS has allowed us to obtain between 0.54 and 1.17 million of reads per sample, of which between 73 and 78% have been mapped to the reference genome developed by the French-Italian consortium (vvinifera.IGGP 12x) with a mapping quality above threshold. More than 100,000 SNPs have been identified, ranging from 14,000 to 43,000 per sample, with a coverage greater than 10X. A high percentage of these variants are polymorphic among Monastrell clones, confirming the existence of significant levels of genetic diversity. In addition, this analysis provides a high number of high quality SNPs well distributed across the genome, suitable for clone genotyping, which will allow the design of strategies to optimize its conservation and use.

Using Two Retrotransposon Based Marker Systems (IRAP and REMAP) for Molecular Characterization of Olive (<i>Olea europaea</i> L.) Cultivars

Olive (Olea europaea L.) is one of the most characteristic agricultural trees of the Mediterranean region and has a large number of cultivar diversity. Olive cultivar characterization is very important especially for the fruit productivity and olive oil quality. In the present study, 46 clones belonging to Turkey (eight cultivars, each having five clones) and Italy (two cultivars, each having three clones) were assessed for cultivar characterization via inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) marker systems using 10 LTR and 10 ISSR primers. In total, 368 band profiles were obtained, 358 of which are polymorphic (97.28% polymorphism). The cultivars were segregated into three main groups, each group having several branches, where all the clones of each cultivar were belonging to the same main group. The only exception to that was the distribution of the clones of cultivar Yaglik, 'Yaglik 4' and 'Yaglik 5', into different main groups. IRAP and REMAP analysis showed a high level of genetic variability among the olive cultivars in this study and this marker systems would be useful tool for clonal selection programs.

Using Two Retrotransposon Based Marker Systems (IRAP and REMAP) for Molecular Characterization of Olive (<i>Olea europaea</i> L.) Cultivars

Olive (Olea europaea L.) is one of the most characteristic agricultural trees of the Mediterranean region and has a large number of cultivar diversity. Olive cultivar characterization is very important especially for the fruit productivity and olive oil quality. In the present study, 46 clones belonging to Turkey (eight cultivars, each having five clones) and Italy (two cultivars, each having three clones) were assessed for cultivar characterization via inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) marker systems using 10 LTR and 10 ISSR primers. In total, 368 band profiles were obtained, 358 of which are polymorphic (97.28% polymorphism). The cultivars were segregated into three main groups, each group having several branches, where all the clones of each cultivar were belonging to the same main group. The only exception to that was the distribution of the clones of cultivar Yaglik, ‘Yaglik 4’ and ‘Yaglik 5’, into different main groups. IRAP and REMAP analysis showed a high level of genetic variability among the olive cultivars in this study and this marker systems would be useful tool for clonal selection programs.

ISSR Analysis for Determination of Genetic Diversity and Relationship in Eight Turkish Olive (Olea europaea L.) Cultivars

Olive cultivar identification is very important especially for fruit productivity and olive oil quality. Up to date, numerous techniques have been used for characterization of olive cultivars and detection of genetic variability. In the present study, 40 clones specific to Turkey (8 cultivars, each having 5 clones) were assessed for cultivar determination via inter simple sequence repeat (ISSR) marker systems using 10 ISSR primers. In total, 217 band profiles were obtained, 206 of which were polymorphic (94.9% polymorphism). The cultivars were segregated into two main clusters, each cluster being subdivided into two groups, while all the clones of a cultivar belong to the same main cluster. The only exception was the distribution of the clones of cultivar 'Tekir': 'Tekir 1', 'Tekir 2' and 'Tekir 3' on cluster III, while 'Tekir 4' and 'Tekir 5' were on cluster IV, therefore grouped into different main clusters. In the present study, ISSR analysis displayed a high level of genetic variability among Turkish olive cultivars, indicating a potential resource for the use of this germplasm in clonal selection programs.

ISSR Analysis for Determination of Genetic Diversity and Relationship in Eight Turkish Olive (Olea europaea L.) Cultivars

Olive cultivar identification is very important especially for fruit productivity and olive oil quality. Up to date, numerous techniques have been used for characterization of olive cultivars and detection of genetic variability. In the present study, 40 clones specific to Turkey (8 cultivars, each having 5 clones) were assessed for cultivar determination via inter simple sequence repeat (ISSR) marker systems using 10 ISSR primers. In total, 217 band profiles were obtained, 206 of which were polymorphic (94.9% polymorphism). The cultivars were segregated into two main clusters, each cluster being subdivided into two groups, while all the clones of a cultivar belong to the same main cluster. The only exception was the distribution of the clones of cultivar 'Tekir': 'Tekir 1', 'Tekir 2' and 'Tekir 3' on cluster III, while 'Tekir 4' and 'Tekir 5' were on cluster IV, therefore grouped into different main clusters. In the present study, ISSR analysis displayed a high level of genetic variability among Turkish olive cultivars, indicating a potential resource for the use of this germplasm in clonal selection programs.

MOLECULAR MARKERS TO DETECT GENETIC VARIATION IN SUPERIOR CLONES OF GRAPEVINE (VITIS VINIFERA L. 'KESHMESHI')

To assess the genetic differences among clones of grapevine (Vitis vinifera L.) ?Keshmeshi?, ten selected clones from a clonal selection program were analyzed by 23 Simple Sequence Repeats (SSR) and 7 AFLP primer combinations. No intra-varietal differences could be detected by SSRs among clones whereas 8 out of the 499 AFLP fragments generated by the seven primer combinations were polymorphic. The number of markers ranged from 44 (E34-M34) to 97 (E31-M32) with an average of 71.3 fragments per primer combination. Cluster analysis based on AFLP data separate all the clones of ?Keshmeshi? into two groups. The first group includes nine white berry skin clones, without any genetic differences and the second group has only a red berry skin clone. AFLP analyses could only detect the red berry clone of ?Keshmeshi? from the other white berry clones.

THE VITIS GERMPLASM REPOSITORY AT THE CRA-VIT, CONEGLIANO (ITALY): CONSERVATION, CHARACTERIZATION AND VALORISATION OF GRAPEVINE GENETIC RESOURCES

One of the main concerns for public research in viticulture is the need to safeguard grapevine biodiversity. Among the many ampelographic collections, one of the oldest and richest is maintained by the Agricultural Research Council - Viticulture Research Centre (CRA-VIT) in Conegliano, Italy. This grapevine repository was founded in 1923. As result of a continuous enrichment nowadays it consists of over 3600 accessions from 45 different countries, and it includes several species of the Vitis genus. The primary mission of this facility is the long-term conservation of a broad spectrum of wine and table grape cultivars as well as grape rootstock, both commercially used and not. The collection also includes various biotypes, representative of existing intra-varietal genetic variability, identified during the clonal selection programs. Specific objectives include the acquisition, maintenance, characterization, evaluation, documentation and distribution of grapevine germplasm. The accessions are maintained ex situ in field collections, and partially in vitro. The plants are characterized and evaluated on the basis of morphological, physiological, biochemical, genetic and agronomical characteristics. The collected accessions display a very wide phenotypic variability for many characters (e.g., shape and size of the leaves and bunches, colour, shape and size of the berries, presence of seeds, berry skin thickness, sugar accumulation, phenological periods, susceptibility to various pathogens, etc.). Selected nuclear simple sequence repeats (SSR) markers are routinely used for DNA fingerprinting of the whole collection to determine accession redundancy and to identify synonyms, homonyms, and mislabeling. The germplasm collection provides a valuable source of genes potentially useful in grapevine genetic improvement programmes. Moreover, the collection assembles a large number of different cultivars in a single environment and allows comparative studies on phenological models and evaluation of resistance/tolerance to biotic and abiotic stresses.

DIFFERENCES OF IN VITRO THERMOTOLERANCE TO HIGH TEMPERATURES IN AUTOCHTHONOUS SWEET CHERRY VARIETIES FROM THE JERTE VALLEY (SPAIN)

Different clones of the autochthonous sweet cherry varieties ‘Ambrunes’, ‘Pico Negro’ and ‘Pico Colorado’ from the ‘Clonal Selection Program’ were subjected to different temperature regimes to optimize in vitro heat therapy to obtain virus-free plants. These varieties were especially sensitive to high temperature treatments: ‘Ambrunes and ‘Pico Colorado’ had similar thermotolerance, and ‘Pico Negro’ was less tolerant. However, one of the ‘Pico Negro’ clones had similar thermotolerance to ‘Ambrunes’ and ‘Pico Colorado’. It is necessary to establish a period of adaptation to high temperatures for increasing both the plant and the isolated apex survival.

Selection of A clones from Thymbra spicata var. spicata by clonal selection method

The main objectives of our research were: (1) to evaluate clones among 28 locations of Thymbra spicata populations from the South-eastern Anatolia and Mediterranean region of Turkey, (2) comparing phytochemical content between populations under cultivated conditions, (3) to determine possible correlations between phytochemical content and morphological traits, along with (4) identifying yield-related traits for use in clonal selection programs. The investigated characters were plant height, plant canopy diameter, spike length, fresh herbage weight per plant, dry herbage weight per plant, dry leaf weight per plant, stem weight per plant, leaf/stem ratio and essential oil content per plant. Statistical analysis showed that populations had significant effect on most morphological parameters except stem weight per plant. Simple correlation analysis showed that dry leaf weight had significant and positive correlation with plant height, canopy diameter, fresh herbage and dry herbage (r=0.623, 0.784, 0.954 and 0.983, respectively).Major compounds of essential oil of T. spicata are carvacrol, alpha-terpinene, 4-terpineole, 4-carene and alpha phellandrene. Carvacrol content of different populations ranged 62.2–78.8%. Due to high variability among wild populations these were considered important sources for breeding. The results further emphasize the possibility of selecting high yielding clones with high agronomic traits for development of a new variety or varieties, which will definitely reduce pressure on the nature for obtaining these plants.

A Survey of Maltese Grapevine Germplasm Using SSR Markers

The paper reports the results of a project of recovery and molecular characterization aimed at identifying the local vine varieties cultivated on the archipelago of Malta. A total of 58 accessions from the two major islands, Malta and Gozo, were sampled within the framework of a clonal and sanitary selection program. DNA analyses were conducted using 13 SSR markers and the profiles obtained compared with the CRA-VIT archive. A total of 28 different genotypes were identified, eight of which correspond to imported varieties: Ansonica, Axina de tres bias, Calabrese, Gold, Koenigin der weingaerten, Muscat fleur d’oranger, Muscat Hamburg, and Negroamaro. Reference SSR profiles have been produced for the most important local varieties, Girgentina (Insolja tal-Girgenti), Gellewza, and Gennarua (Insolja ta’ Gennaru).

Selection Efficiency for Solid Wood Traits in Pinus taeda using Time-of-Flight Acoustic and Micro-Drill Resistance Methods

Abstract Conventional sampling and laboratory analysis of solid wood properties to facilitate clonal screening in tree improvement programs are prohibitively time-consuming and expensive. Alternative methods—time-of-flight acoustics and micro-drilling resistance—were assessed for efficiency in screening clones for wood stiffness (modulus of elasticity [MOE]), strength (modulus of rupture [MOR]), and density. Ninety clones, consisting of 30 from each of 3 full-sib families, were screened in an 8-year-old loblolly pine (Pinus taeda L.) field test using a TreeSonic time-of-flight tool and Resistograph drill resistance tool. The same clones were sampled for wood specimens for laboratory tests of MOE, MOR, and density. TreeSonic stress wave speed measurements produced highly repeatable clonal phenotypes that facilitated efficient selection for MOE and to a lesser extent for MOR. Resistograph amplitude measurements had a strong genetic correlation with wood density and facilitated highly efficient selection for density, with correlated responses for MOR and MOE. Combining the indirect traits into a selection index improved gain for mechanical wood traits. Both tools provided high measurement rates that resulted in cost efficiencies. Indirect measurements of solid wood properties should be attractive for clonal selection programs that must screen thousands of clones under a finite budget.

Genetic variation and heritability of agro-morphological and phytochemical traits in Iranian saffron ( Crocus sativus L.) populations

Saffron is highly valued for its unique aroma, taste, colour and medicinal properties. Iran is known, as one of the most important saffron producing countries but the genetic variability present in crocus in Iran is currently unknown. The main objectives of our research were: (1) evaluate phenotypic diversity among Iranian saffron populations; (2) compare phytochemical content between populations originating from different ecological areas; (3) determine possible correlations between phytochemical content and morphological traits; (4) identify yield-related traits for use in clonal selection programs and (5) estimate the broad sense heritability ( h b 2 ) for the traits evaluated. In this study a combined analysis of variance was used to evaluate eight Iranian populations of Crocus sativus over a two-year period. The investigated characters were leaf number per plant, leaf length, flower number per plot, dry stigma weight per plot, spathe number and the content of crocins, picrocrocin and safranal. Statistical analysis showed that population had significant effect on most morphological parameters except leaf length and spathe number. Also it had significant effect on all phytochemical contents. Duncan's multiple range tests showed that populations were significantly different for most evaluated traits. Simple correlation analysis showed that dry stigma weight had significant and positive correlation with leaf number, flower number, picrocrocin and safranal ( r = 0.954, 0.998, 0.830 and 0.881, respectively). The estimates of broad sense heritability were higher for flower related traits ( h b 2 = 0.76 − 0.99 ). Cluster analysis did not reveal a clear relationship between diversity pattern and geographical origin.