scholarly journals A Digital Image-Based Phenotyping Platform for Analyzing Root Shape Attributes in Carrot

2021 ◽  
Vol 12 ◽  
Author(s):  
Scott H. Brainard ◽  
Julian A. Bustamante ◽  
Julie C. Dawson ◽  
Edgar P. Spalding ◽  
Irwin L. Goldman
Keyword(s):  
Genetic Control ◽  
Digital Image ◽  
Principal Component ◽  
Shape Features ◽  
Narrow Sense Heritability ◽  
Breeding Lines ◽  
Digital Phenotyping ◽  
Diallel Mating Design ◽  
Specific Shape ◽  
Market Class

Root shape in carrot (Daucus carota subsp. sativus), which ranges from long and tapered to short and blunt, has been used for at least several centuries to classify carrot cultivars. The subjectivity involved in determining market class hinders the establishment of metric-based standards and is ill-suited to dissecting the genetic basis of such quantitative phenotypes. Advances in digital image acquisition and analysis has enabled new methods for quantifying sizes of plant structures and shapes, but in order to dissect the genetic control of the shape features that define market class in carrot, a tool is required that quantifies the specific shape features used by humans in distinguishing between classes. This study reports the construction and demonstration of the first such platform, which facilitates rapid phenotyping of traits that are measurable by hand, such as length and width, as well as principal component analysis (PCA) of the root contour and its curvature. This latter approach is of particular interest, as it enabled the detection of a novel and significant quantitative trait, defined here as root fill, which accounts for 85% of the variation in root shape. Curvature analysis was demonstrated to be an effective method for precise measurement of the broadness of the carrot shoulder, and degree of tip fill; the first principal component of the respective curvature profiles captured 87% and 84% of the total variance. This platform’s performance was validated in two experimental panels. First, a diverse, global collection of germplasm was used to assess its capacity to identify market classes through clustering analysis. Second, a diallel mating design between inbred breeding lines of differing market classes was used to estimate the heritability of the key phenotypes that define market class, which revealed significant variation in the narrow-sense heritability of size and shape traits, ranging from 0.14 for total root size, to 0.84 for aspect ratio. These results demonstrate the value of high-throughput digital phenotyping in characterizing the genetic control of complex quantitative phenotypes.

Genetic control of kraft pulp yield in Eucalyptus globulus

2010 ◽  
Vol 40 (5) ◽  
pp. 917-927 ◽  
Author(s):  
Desmond J. Stackpole ◽  
René E. Vaillancourt ◽  
Geoffrey M. Downes ◽  
Christopher E. Harwood ◽  
Brad M. Potts
Keyword(s):  
Genetic Control ◽  
Eucalyptus Globulus ◽  
Kraft Pulp ◽  
Near Infrared ◽  
Genetic Correlations ◽  
Basic Density ◽  
Pulp Yield ◽  
Narrow Sense Heritability ◽  
Selection Gradients ◽  
Economic Worth

Pulp yield is an important breeding objective for Eucalyptus globulus Labill., but evaluation of its genetic control and genetic correlations with other traits has been limited by its high assessment cost. We used near infrared spectroscopy to study genetic variation in pulp yield and other traits in a 16-year-old E. globulus trial. Pulp yield was predicted for 2165 trees from 467 open-pollinated families from 17 geographic subraces. Significant differences between subraces and between families within subraces were detected for all traits. The high pulp yield of southern Tasmanian subraces suggested that their economic worth was previously underestimated. The narrow-sense heritability of pulp yield was medium (0.40). The significant positive genetic correlation between pulp yield and diameter (0.52) was at odds with the generally neutral values reported. The average of the reported genetic correlations between pulp yield and basic density (0.50) was also at odds with our nonsignificant estimate. Pulp yield of the subraces increased with increasing latitude, producing a negative correlation with density (–0.58). The absence of genetic correlations within subraces between pulp yield and density suggests that the correlation may be an independent response of the two traits to the same or different selection gradients that vary with latitude.

scholarly journals Genetic worth of multiple sets of cowpea breeding lines destined for advanced yield testing

Euphytica ◽  
2021 ◽  
Vol 217 (2) ◽  
Author(s):  
Patrick Obia Ongom ◽  
Christian Fatokun ◽  
Abou Togola ◽  
Oluwaseye Gideon Oyebode ◽  
Mansur Sani Ahmad ◽  
...  
Keyword(s):  
Seed Weight ◽  
Genetic Variance ◽  
Principal Component ◽  
Performance Tests ◽  
Genetic Advance ◽  
Breeding Lines ◽  
Lattice Design ◽  
Mean And Variance ◽  
Genotypic Coefficient Of Variation ◽  
Location Interaction

AbstractThe objective of this study was to determine genetic potentials in eight sets of cowpea lines for grain yield (GY), hundred seed weight (HSDWT) and days to 50% flowering (DT50FL). A total of 614 F6 genotypes constituting the sets, grouped by maturity, were evaluated across two locations in Northern Nigeria, in an alpha lattice design, two replications each. Data were recorded on GY, HSDWT and DT50FL.Variance components, genotypic coefficient of variation (GCV), and genetic advance (GA) were used to decode the magnitude of genetic variance within and among sets. Genetic usefulness (Up) which depends on mean and variance to score the genetic merits in historically bi-parental populations was applied to groups of breeding lines with mixed parentage. Principal component analysis (PCA) was used to depict contribution of traits to observed variations. GY and DT50FL explained the variance within and between sets respectively. Genotypes were significantly different, although genotype-by-location and set-by-location interaction effects were also prominent. Genetic variance (δ2G) and GCV were high for GY in Prelim2 (δ2G = 45,897; GCV = 19.58%), HSDWT in Prelim11 (δ2G = 7.137; GCV = 17.07%) and DT50F in Prelim5 (δ2G = 4.54; GCV = 4.4%). Heritability varied among sets for GY (H = 0.21 to 0.57), HSDWT (H = 0.76 to 0.93) and DT50FL (H = 0.20 to 0.81). GA and percentage GA (GAPM) were high for GY in Prelim2 (GAPM = 24.59%; GA = 269.05Kg/ha), HSDWT in Prelim11 (GAPM = 28.54%; GA = 4.47 g), and DT50F in Prelim10 (GAPM = 6.49%; GA = 3.01 days). These sets also registered high values of genetic usefulness, suggesting potential application in non-full sib populations. These approaches can be used during preliminary performance tests to reinforce decisions in extracting promising lines and choose among defined groups of lines.

scholarly journals Assessment of wild tomato accessions for fruit yield, physicochemical and nutritional properties under a rain forest agro-ecology

2020 ◽  
Vol 1 (2) ◽  
pp. 1-11
Author(s):  
Dorcas Ibitoye ◽  
Adesike Kolawole ◽  
Roseline Feyisola
Keyword(s):  
Rain Forest ◽  
Agronomic Traits ◽  
Block Design ◽  
Principal Component ◽  
Fruit Yield ◽  
Soluble Solids ◽  
Forest Zone ◽  
Breeding Lines ◽  
Wild Tomato ◽  
Solanum Lycopersicum L

Tomato (Solanum lycopersicum L.) is a broadly consumed fruit vegetable globally. It is one of the research mandate vegetable of the National Horticultural Research Institute (NIHORT), Ibadan, Nigeria. The institute’s contains diverse collections of tomato accessions and wild relatives, without utilization information for the African continent. With the decline in diversity and potential of cultivars, a robust tomato breeding pipeline with broad genetic base that eliminates redundancy in the development of lines with desired horticultural traits is paramount. This study evaluated the mean performance and variations of thirteen wild tomato accessions obtained from the C.M. Rick Tomato Genetic Resource Center, University of California, Davis, USA, evaluated for agronomic, nutritional and physicochemical traits under a rain forest zone in Nigeria. The accessions were planted and grown in three replications with randomized complete block design. Agronomic traits, physicochemical and nutritional parameters were measured and analyzed. There was significant (P < 0.001) variation among accessions for all traits measured. Accession LA0130 was separated from others by cluster analysis and was outstanding for its unique attributes which include: fruit yield parameters, total soluble solids, acidity and content. The principal component analysis suggests fruit yield related traits, acidity and contributed most to the variation among the 13 accessions. The results obtained can be used to breed materials adapted to a rain forest . These wild tomato accessions have genes with desirable agronomic, nutritional and physicochemical traits that could be into breeding lines to improve commercial tomato varieties.

scholarly journals Genetic characterization of carrot root shape and size using genome-wide association analysis and genomic-estimated breeding values

2021 ◽  
Author(s):  
Scott H. Brainard ◽  
Shelby L. Ellison ◽  
Philipp W. Simon ◽  
Julie C. Dawson ◽  
Irwin L. Goldman
Keyword(s):  
Image Analysis ◽  
Genetic Control ◽  
Digital Image Analysis ◽  
Genome Wide Association ◽  
Carrot Root ◽  
Size And Shape ◽  
Genome Wide ◽  
Market Class ◽  
Selection For ◽  
Estimated Breeding Values

Abstract Key message The principal phenotypic determinants of market class in carrot—the size and shape of the root—are under primarily additive, but also highly polygenic, genetic control. Abstract The size and shape of carrot roots are the primary determinants not only of yield, but also market class. These quantitative phenotypes have historically been challenging to objectively evaluate, and thus subjective visual assessment of market class remains the primary method by which selection for these traits is performed. However, advancements in digital image analysis have recently made possible the high-throughput quantification of size and shape attributes. It is therefore now feasible to utilize modern methods of genetic analysis to investigate the genetic control of root morphology. To this end, this study utilized both genome wide association analysis (GWAS) and genomic-estimated breeding values (GEBVs) and demonstrated that the components of market class are highly polygenic traits, likely under the influence of many small effect QTL. Relatively large proportions of additive genetic variance for many of the component phenotypes support high predictive ability of GEBVs; average prediction ability across underlying market class traits was 0.67. GWAS identified multiple QTL for four of the phenotypes which compose market class: length, aspect ratio, maximum width, and root fill, a previously uncharacterized trait which represents the size-independent portion of carrot root shape. By combining digital image analysis with GWAS and GEBVs, this study represents a novel advance in our understanding of the genetic control of market class in carrot. The immediate practical utility and viability of genomic selection for carrot market class is also described, and concrete guidelines for the design of training populations are provided.

scholarly journals Wheat shovelomics I: A field phenotyping approach for characterising the structure and function of root systems in tillering species

2018 ◽  
Author(s):  
Larry M. York ◽  
Shaunagh Slack ◽  
Malcolm J Bennett ◽  
M John Foulkes
Keyword(s):  
Genetic Control ◽  
Principal Component ◽  
Root Systems ◽  
Wheat Root ◽  
Root Number ◽  
Main Shoot ◽  
Growth Angle ◽  
Nodal Root ◽  
Field Phenotyping ◽  
And Function

AbstractWheat represents a major crop, yet the current rate of yield improvement is insufficient to meet its projected global food demand. Breeding root systems more efficient for water and nitrogen capture represents a promising avenue for accelerating yield gains. Root crown phenotyping, or shovelomics, relies on excavation of the upper portions of root systems in the field and measuring root properties such as numbers, angles, densities and lengths. We report a new shovelomics method that images the whole wheat root crown, then partitions it into the main shoot and tillers for more intensive phenotyping. Root crowns were phenotyped using the new method from the Rialto × Savannah population consisting of both parents and 94 doubled-haploid lines. For the whole root crown, the main shoot, and tillers, root phenes including nodal root number, growth angle, length, and diameter were measured. Substantial variation and heritability were observed for all phenes. Principal component analysis revealed latent constructs that imply pleiotropic genetic control of several related root phenes. Correlational analysis revealed that nodal root number and growth angle correlate among the whole crown, main shoot, and tillers, indicating shared genetic control among those organs. We conclude that this phenomics approach will be useful for breeding ideotype root systems in tillering species.

scholarly journals Evaluating Genetic Parameters and Combining Ability of Starch Viscosity Parameters in Rice Cultivars (Oryza sativa L.)

2019 ◽  
Vol 7 (4) ◽  
pp. 665
Author(s):  
Alireza Haghighi Hasanalideh ◽  
Mehrzad Allahgholipour ◽  
Ezatollah Farshadfar
Keyword(s):  
Combining Ability ◽  
Gene Action ◽  
Oryza Sativa L ◽  
Block Design ◽  
Breeding Methods ◽  
Narrow Sense ◽  
Narrow Sense Heritability ◽  
Gene Effects ◽  
Diallel Mating Design ◽  
Additive Gene

This study was undertaken to assess the combining ability of 6 rice varieties, for viscosity parameters and determining gene action controlling Rapid Visco Analyser (RVA) characters. F2 progenies derived from a 6×6 half diallel mating design with their parents were grown in a randomized complete block design with three replications at the research farm of Rice Research Institute of Iran (RRII) in 2015. The diallel analysis by Griffing`s method indicated the involvement of additive and non-additive gene actions controlling RVA traits. For traits PV and FV RI18447-2 and IR50 were the best combiners for increasing and decreasing, respectively. Deylamani and IR50 were the best combiners for increasing and decreasing BV, respectively. Beside, due to more portion of non-additive gene action in controlling trait SV, The Gilaneh × RI18430-46, and Deylamani × RI18430-46 crosses were the best for increasing and decreasing SV, respectively. The high estimates of broad sense heritability and narrow sense heritability for BV and FV, indicated the importance of additive effects in expression of these traits. Therefore, selection base breeding methods will be useful to improve these traits and selection in the early generations could be done to fix the favourable genes. Low estimate of narrow sense heritability for SV revealed that non-additive gene effects play important role in controlling setback viscosity. So, hybrid base breeding methods will be useful to improve this trait.

scholarly journals Diallel Anaysis of Oil Production Components in Peanut (Arachis hypogaeaL.)

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Jeffrey N. Wilson ◽  
Michael R. Baring ◽  
Mark D. Burow ◽  
William L. Rooney ◽  
Charles E. Simpson
Keyword(s):  
Combining Ability ◽  
Seed Mass ◽  
Heritability Estimate ◽  
General Combining Ability ◽  
Specific Combining Ability ◽  
Narrow Sense Heritability ◽  
Ability Estimates ◽  
Diallel Mating Design ◽  
Oil Concentration ◽  
Very High

Peanut (Arachis hypogaeaL.) has the potential to become a major source of biodiesel, but for market viability, peanut oil yields must increase. Oil yield in peanut is influenced by many different components, including oil concentration, seed mass, and mean oil produced per seed. All of these traits can potentially be improved through selection as long as there is sufficient genetic variation. To assess the variation for these traits, a diallel mating design was used to estimate general combining ability, specific combining ability, and heritability. General combining ability estimates were significant for oil concentration, weight of 50 sound mature kernels (50 SMK), and mean milligrams oil produced per SMK (OPS). Specific combining ability was significant for oil concentration. Reciprocal effects were detected for OPS. Narrow-sense heritability estimates were very high for oil concentration and 50 SMK and low for OPS. The low OPS heritability estimate was caused by the negative correlation between oil concentration and seed size. Consequently, oil concentration and seed mass alone can be improved through early generation selection, but large segregating populations from high oil crosses will be needed to identify progeny with elevated oil concentrations that maintain acceptable seed sizes.

Selected Shape and Texture Features for Automatic Detection of Acute Lymphoblastic Leukemia

2018 ◽  
pp. 162-183
Author(s):  
Vanika Singhal ◽  
Preety Singh
Keyword(s):  
Acute Lymphoblastic Leukemia ◽  
Lymphoblastic Leukemia ◽  
Principal Component ◽  
Texture Features ◽  
Automatic Detection ◽  
Support Vector ◽  
Shape Features ◽  
Geometrical Properties ◽  
Correlation Based Feature Selection ◽  
Human Interpretation

Acute Lymphoblastic Leukemia is a cancer of blood caused due to increase in number of immature lymphocyte cells. Detection is done manually by skilled pathologists which is time consuming and depends on the skills of the pathologist. The authors propose a methodology for discrimination of a normal lymphocyte cell from a malignant one by processing the blood sample image. Automatic detection process will reduce the diagnosis time and not be limited by human interpretation. The lymphocyte images are classified based on two types of extracted features: shape and texture. To identify prominent shape features, Correlation based Feature Selection is applied. Principal Component Analysis is applied on the texture features to reduce their dimensionality. Support Vector Machine is used for classification. It is observed that 16 shape features are able to give a classification accuracy of 92.3% and that changes in the geometrical properties of the nucleus emerge as significant features contributing towards detecting a malignant lymphocyte.

Sign in / Sign up

Export Citation Format

Share Document