Relationships among durum wheat accessions. I. Comparative analysis of SSR, AFLP, and phenotypic data

Genome ◽  
2007 ◽  
Vol 50 (4) ◽  
pp. 373-384 ◽  
Author(s):  
M. Maccaferri ◽  
S. Stefanelli ◽  
F. Rotondo ◽  
R. Tuberosa ◽  
M.C. Sanguineti
Keyword(s):  
Durum Wheat ◽  
Genetic Relatedness ◽  
Morphological Characteristics ◽  
Morphological Data ◽  
Phenotypic Traits ◽  
Pedigree Data ◽  
Crop Species ◽  
Phenotypic Data ◽  
Breeding Programs ◽  
Triticum Durum Desf

The determination of genetic relatedness among elite materials of crop species allows for more efficient management of breeding programs and for the protection of breeders’ rights. Seventy simple sequence repeats (SSRs) and 234 amplified fragment length polymorphisms (AFLPs) were used to profile a collection of 58 durum wheat ( Triticum durum Desf.) accessions, representing the most important extant breeding programs. In addition, 42 phenotypic traits, including the morphological characteristics recommended for the official distinctness, uniformity, and stability tests, were recorded. The correlation between the genetic similarities obtained with the 2 marker classes was high (r = 0.81), whereas lower values were observed between molecular and phenotypic data (r = 0.46 and 0.56 for AFLPs and SSRs, respectively). Morphological data, even if sampled in high numbers, largely failed to describe the pattern of genetic similarity, according to known pedigree data and the indications provided by molecular markers.

scholarly journals Major QTL with pleiotropic effects controlling time of leaf budburst and flowering-related traits in walnut (Juglans regia L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Şakir Burak Bükücü ◽  
Mehmet Sütyemez ◽  
Sina Kefayati ◽  
Aibibula Paizila ◽  
Abdulqader Jighly ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Juglans Regia ◽  
Genotypic Variation ◽  
Phenotypic Traits ◽  
Juvenile Period ◽  
Phenotypic Data ◽  
Breeding Programs ◽  
Genome Wide ◽  
A Genome ◽  
Major Qtl

Abstract Breeding studies in walnut (Juglans regia L.) are usually time consuming due to the long juvenile period and therefore, this study aimed to determine markers associated with time of leaf budburst and flowering-related traits by performing a genome-wide association study (GWAS). We investigated genotypic variation and its association with time of leaf budburst and flowering-related traits in 188 walnut accessions. Phenotypic data was obtained from 13 different traits during 3 consecutive years. We used DArT-seq for genotyping with a total of 33,519 (14,761 SNP and 18,758 DArT) markers for genome-wide associations to identify marker underlying these traits. Significant correlations were determined among the 13 different traits. Linkage disequilibrium decayed very quickly in walnut in comparison with other plants. Sixteen quantitative trait loci (QTL) with major effects (R2 between 0.08 and 0.23) were found to be associated with a minimum of two phenotypic traits each. Of these QTL, QTL05 had the maximum number of associated traits (seven). Our study is GWAS for time of leaf budburst and flowering-related traits in Juglans regia L. and has a strong potential to efficiently implement the identified QTL in walnut breeding programs.

scholarly journals Development of Optimized Phenomic Predictors for Efficient Plant Breeding Decisions Using Phenomic-Assisted Selection in Soybean

2019 ◽  
Vol 2019 ◽  
pp. 1-15 ◽  
Author(s):  
Kyle Parmley ◽  
Koushik Nagasubramanian ◽  
Soumik Sarkar ◽  
Baskar Ganapathysubramanian ◽  
Asheesh K. Singh
Keyword(s):  
Seed Yield ◽  
Optimization Techniques ◽  
Phenotypic Traits ◽  
Yield Data ◽  
Crop Species ◽  
Breeding Programs ◽  
High Throughput Phenotyping ◽  
Complex Relationships ◽  
Sensor Package ◽  
Made In

The rate of advancement made in phenomic-assisted breeding methodologies has lagged those of genomic-assisted techniques, which is now a critical component of mainstream cultivar development pipelines. However, advancements made in phenotyping technologies have empowered plant scientists with affordable high-dimensional datasets to optimize the operational efficiencies of breeding programs. Phenomic and seed yield data was collected across six environments for a panel of 292 soybean accessions with varying genetic improvements. Random forest, a machine learning (ML) algorithm, was used to map complex relationships between phenomic traits and seed yield and prediction performance assessed using two cross-validation (CV) scenarios consistent with breeding challenges. To develop a prescriptive sensor package for future high-throughput phenotyping deployment to meet breeding objectives, feature importance in tandem with a genetic algorithm (GA) technique allowed selection of a subset of phenotypic traits, specifically optimal wavebands. The results illuminated the capability of fusing ML and optimization techniques to identify a suite of in-season phenomic traits that will allow breeding programs to decrease the dependence on resource-intensive end-season phenotyping (e.g., seed yield harvest). While we illustrate with soybean, this study establishes a template for deploying multitrait phenomic prediction that is easily amendable to any crop species and any breeding objective.

Morphological characteristics of the experimental allopolyploid Triticum durum × Haynaldia villosa (2n = 42)

1987 ◽  
Vol 65 (9) ◽  
pp. 1948-1951 ◽  
Author(s):  
Agostino Stefani ◽  
Paolo Meletti ◽  
Antonino Onnis
Keyword(s):  
Triticum Durum ◽  
Morphological Characteristics ◽  
Morphological Data ◽  
Haynaldia Villosa ◽  
Triticum Durum Desf

The experimental allopolyploid (2n = 42) Triticum durum Desf. cv. Cappelli (2n = 28) × Haynaldia villosa (L.) Schur. (2n = 14) obtained in 1972 has now reached the 12th generation. In the present paper, morphological data on the allopolyploid plants from the 8th to the 10th generation are reported. A comparison between the characters of the allopolyploid and its parents is also presented.

scholarly journals Morphological characterization of selected papaya (Carica papaya L.) inbreds and hybrids

2009 ◽  
pp. 102-112
Author(s):  
Florence Lasalita-Zapico ◽  
Violeta Villegas
Keyword(s):  
Carica Papaya ◽  
Genetic Relatedness ◽  
Morphological Characteristics ◽  
Morphological Characterization ◽  
Accurate Estimation ◽  
Phenotypic Traits ◽  
Complete Dominance ◽  
Phylogenetic Affinities ◽  
High Degree

Morphological analysis was undertaken to assess the degree of genetic relatedness and to characterize selected papaya (Carica papaya L.) inbreds and hybrids. Transmission of phenotypic traits from inbred parents to hybrid progeny followed the Mendelian pattern (complete dominance). The clustering mechanism separated the papaya genotypes into two groups. It was also revealed that some inbred lines presumably of very diverse origins exhibited similar morphological characteristics, raising the possibility that they have phylogenetic affinities and/or common origins. Screening for morphological traits with a high degree of polymorphism and with invariable expressions of the phenotypes would help in the identification of markers for hybrid identification and also in the accurate estimation of genetic relatedness among these hybrids and their parents.

scholarly journals Analyse De La Variation Morpho-Phenologique Et Genetique De Vingt Accessions Du Ble Dur Algerien (Triticum durum D.E.S.F.)

2016 ◽  
Vol 12 (24) ◽  
pp. 168 ◽  
Author(s):  
Rima Belattar ◽  
Leila Boudour ◽  
Ghania Chaib
Keyword(s):  
Molecular Markers ◽  
Genetic Polymorphism ◽  
Durum Wheat ◽  
Triticum Durum ◽  
Phenotypic Diversity ◽  
Rapd Marker ◽  
Strategic Culture ◽  
Breeding Programs ◽  
Crop Varieties ◽  
Triticum Durum Desf

Durum wheat (Triticum durum Desf.) is a strategic culture in Algeria. Characterization and evaluation of crop varieties allow backup and restoration of this genetic heritage and its use in breeding programs. In this context, the study is subject to the identification of some morpho - phenological parameters and molecular markers in kind RAPD variability of 20 genotypes of collection of Algerian durum wheat (Triticum durum Desf.) Belong to two varieties (rechenbachi and leucomelan). The results of the morpho-phenological and genetic analysis show substantial phenotypic diversity between varieties. RAPD marker showed an intervarietal genetic polymorphism.

Relationships of Campanian olive cultivars: comparative analysis of molecular and phenotypic data

Genome ◽  
2009 ◽  
Vol 52 (8) ◽  
pp. 692-700 ◽  
Author(s):  
Giandomenico Corrado ◽  
Maurizio La Mura ◽  
Orsola Ambrosino ◽  
Giuseppe Pugliano ◽  
Paola Varricchio ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Genetic Relationships ◽  
Virgin Olive Oil ◽  
Extra Virgin Olive Oil ◽  
Phenotypic Traits ◽  
Morphological Marker ◽  
Phenotypic Data ◽  
Campania Region ◽  
Qualitative Traits ◽  
Olive Cultivars

Estimation of the genetic relatedness of traditional olive cultivars with genetic markers and phenotypic data enables progress in plant breeding, management of genetic resources, and protection of both breeders’ rights and certified premium products. We used amplified fragment length polymorphisms (AFLPs), simple sequence repeats (SSRs), and quantitative and qualitative morphological traits, including characteristics recommended for variety registration, to study genetic diversity and relationships in the olive at different levels. The 14 varieties analyzed, which are used for the production of Protected Denomination of Origin extra-virgin olive oil, represent the most important cultivars in the Campania region of Italy and typify a regional diversity characteristic of traditional olive cultivation. The genetic distances obtained with the two DNA marker systems were significantly correlated, as were those obtained by quantitative and qualitative traits. A lower but significant correlation was also observed between distances based on molecular markers and quantitative traits, but qualitative traits, even if sampled in high numbers, failed to describe the pattern of molecular similarity. Our data imply that the type and the number of phenotypic traits scored can greatly influence the outcome of the analysis, and care should be taken when qualitative and quantitative data are combined. Furthermore, the data indicate that the two molecular marker systems are useful for investigating genetic relationships, but they may also be used to complement and assist the traditional registration of varieties. We propose that since the information provided by molecular and morphological marker systems in olive is different, they should serve different purposes.

scholarly journals Atlantean Evolution in Darwin’s Finches—Issues and Perspectives in Species Delimitation using Phenotypic Data

2017 ◽  
Author(s):  
Carlos Daniel Cadena ◽  
Iván Jiménez ◽  
Felipe Zapata
Keyword(s):  
Mixture Models ◽  
Species Delimitation ◽  
Morphological Data ◽  
Phenotypic Traits ◽  
Normal Mixture ◽  
Species Limits ◽  
Phenotypic Data ◽  
Normal Mixture Models ◽  
Multiple Species ◽  
Analytical Approaches

AbstractProgress in the development and use of methods for species delimitation employing phenotypic data lags behind conceptual and practical advances in molecular genetic approaches. The basic evolutionary model underlying the use of phenotypic data to delimit species assumes random mating and quantitative polygenic traits, so that phenotypic distributions within a species should be approximately normal for individuals of the same sex and age. Accordingly, two or more distinct normal distributions of phenotypic traits suggest the existence of multiple species. In light of this model, we show that analytical approaches employed in taxonomic studies using phenotypic data are often compromised by three issues: (1) reliance on graphical analyses of phenotypic space that do not consider the frequency of phenotypes; (2)exclusion of characters potentially important for species delimitation following reduction of data dimensionality; and (3) use of measures of central tendencies to evaluate phenotypic distinctiveness. We outline approaches to overcome these issues based on statistical developments related to normal mixture models and illustrate them empirically with a reanalysis of morphological data recently used to claim that there are no morphologically distinct species of Darwin’s ground-finches (Geospiza). We found negligible support for this claim relative to taxonomic hypotheses recognizing multiple species. Although species limits among ground-finches merit further assessments using additional sources of information, our results bear implications for other areas of inquiry including speciation research: because ground-finches have likely speciated and are not trapped in a process of “Sisyphean” evolution as recently argued, they remain useful models to understand the evolutionary forces involved in speciation. Our work underscores the importance of statistical approaches grounded on appropriate evolutionary models for species delimitation. Approaches allowing one to fit normal mixture models withouta prioriinformation about species limits offer new perspectives in the kind of inferences available to systematists, with significant repercusions on ideas about the structure of biological biodiversity. [morphology; normal mixture model; phenotype; principal components analysis; species limits; variable selection.]

scholarly journals Deployment of Molecular Markers and Marker-assisted Selection in Tomato Breeding

HortScience ◽  
2005 ◽  
Vol 40 (4) ◽  
pp. 1114A-1114
Author(s):  
Majid R. Foolad
Keyword(s):  
Disease Resistance ◽  
Marker Assisted Selection ◽  
Complex Disease ◽  
Morphological Characteristics ◽  
Genetic Maps ◽  
Interspecific Crosses ◽  
Crop Species ◽  
Breeding Programs ◽  
Potential Benefits ◽  
Tomato Breeding

In tomato, Lycopersi conesculentum Mill., currently there are >285 known morphological, physiological and disease resistance markers, 36 isozymes, and >1000 RFLPs, which have been mapped onto the 12 tomato chromosomes. In addition, currently there are >162,000 ESTs, of which ∼3.2% have been mapped. Several tomato genetic maps have been developed, mainly based on interspecific crosses between the cultivated tomato and its related wild species. The markers and maps have been used to locate and tag genes or QTLs for disease resistance and other horticultural characteristics. Such information can be used for various purposes, including marker-assisted selection (MAS) and map-based cloning of desirable genes or QTLs. Many seed companies have adopted using MAS for manipulating genes for a few simple morphological characteristics and several vertical disease resistance traits in tomato. However, MAS is not yet a routine procedure in seed companies for manipulating QTLs although it has been tried for a few complex disease resistance and fruit quality characteristics. In comparison, the use of MAS is less common in public tomato breeding programs, although attempts have been made to transfer QTLs for resistances to a few complex diseases. The potential benefits of marker deployment to plant breeding are undisputed, in particular for pyramiding disease resistance genes. It is expected that in the near future MAS will be routine in many breeding programs, taking advantage of high-resolution markers such as SNPs. For quantitative traits, QTLs must be sought for components of genetic variation before they are applicable to marker-assisted breeding. However, MAS will not be a “silver bullet” solution to every breeding problem or for every crop species.

scholarly journals Combining metabolomic and transcriptomic approaches to assess and improve crop quality traits

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Delphine M. Pott ◽  
Sara Durán-Soria ◽  
Sonia Osorio ◽  
José G. Vallarino
Keyword(s):  
Quality Trait ◽  
Quality Traits ◽  
Crop Species ◽  
Breeding Programs ◽  
Crop Quality ◽  
Crop Varieties ◽  
New Genes ◽  
Technical Advances ◽  
Health Promoting ◽  
Selection Of

AbstractPlant quality trait improvement has become a global necessity due to the world overpopulation. In particular, producing crop species with enhanced nutrients and health-promoting compounds is one of the main aims of current breeding programs. However, breeders traditionally focused on characteristics such as yield or pest resistance, while breeding for crop quality, which largely depends on the presence and accumulation of highly valuable metabolites in the plant edible parts, was left out due to the complexity of plant metabolome and the impossibility to properly phenotype it. Recent technical advances in high throughput metabolomic, transcriptomic and genomic platforms have provided efficient approaches to identify new genes and pathways responsible for the extremely diverse plant metabolome. In addition, they allow to establish correlation between genotype and metabolite composition, and to clarify the genetic architecture of complex biochemical pathways, such as the accumulation of secondary metabolites in plants, many of them being highly valuable for the human diet. In this review, we focus on how the combination of metabolomic, transcriptomic and genomic approaches is a useful tool for the selection of crop varieties with improved nutritional value and quality traits.

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