The Experts below are selected from a list of 103176 Experts worldwide ranked by ideXlab platform
Detlef Weigel - One of the best experts on this subject based on the ideXlab platform.
-
identifying genetic variants underlying Phenotypic Variation in plants without complete genomes
Nature Genetics, 2020Co-Authors: Yoav Voichek, Detlef WeigelAbstract:Structural variants and presence/absence polymorphisms are common in plant genomes, yet they are routinely overlooked in genome-wide association studies (GWAS). Here, we expand the type of genetic variants detected in GWAS to include major deletions, insertions and rearrangements. We first use raw sequencing data directly to derive short sequences, k-mers, that mark a broad range of polymorphisms independently of a reference genome. We then link k-mers associated with phenotypes to specific genomic regions. Using this approach, we reanalyzed 2,000 traits in Arabidopsis thaliana, tomato and maize populations. Associations identified with k-mers recapitulate those found with SNPs, but with stronger statistical support. Importantly, we discovered new associations with structural variants and with regions missing from reference genomes. Our results demonstrate the power of performing GWAS before linking sequence reads to specific genomic regions, which allows the detection of a wider range of genetic variants responsible for Phenotypic Variation.
-
nonlinear Phenotypic Variation uncovers the emergence of heterosis in arabidopsis thaliana
PLOS Biology, 2019Co-Authors: Francois Vasseur, Louise Fouqueau, Thibault Nidelet, Dominique De Vienne, Cyrille Violle, Detlef WeigelAbstract:Heterosis describes the Phenotypic superiority of hybrids over their parents in traits related to agronomic performance and fitness. Understanding and predicting nonadditive inheritance such as heterosis is crucial for evolutionary biology as well as for plant and animal breeding. However, the physiological bases of heterosis remain debated. Moreover, empirical data in various species have shown that diverse genetic and molecular mechanisms are likely to explain heterosis, making it difficult to predict its emergence and amplitude from parental genotypes alone. In this study, we examined a model of physiological dominance initially proposed by Sewall Wright to explain the nonadditive inheritance of traits like metabolic fluxes at the cellular level. We evaluated Wright's model for two fitness-related traits at the whole-plant level, growth rate and fruit number, using 450 hybrids derived from crosses among natural accessions of A. thaliana. We found that allometric relationships between traits constrain Phenotypic Variation in a nonlinear and similar manner in hybrids and accessions. These allometric relationships behave predictably, explaining up to 75% of heterosis amplitude, while genetic distance among parents at best explains 7%. Thus, our findings are consistent with Wright's model of physiological dominance and suggest that the emergence of heterosis on plant performance is an intrinsic property of nonlinear relationships between traits. Furthermore, our study highlights the potential of a geometric approach of Phenotypic relationships for predicting heterosis of major components of crop productivity and yield.
-
non linear Phenotypic Variation uncovers the emergence of heterosis in arabidopsis thaliana
bioRxiv, 2018Co-Authors: Francois Vasseur, Louise Fouqueau, Thibault Nidelet, Dominique De Vienne, Cyrille Violle, Detlef WeigelAbstract:Heterosis describes the Phenotypic superiority of hybrids over their parents in traits related to fitness. Understanding and predicting non-additive inheritance such as heterosis is crucial for evolutionary biology, as well as for plant and animal breeding. However, the physiological bases of heterosis remain debated. Moreover, empirical data in various species have shown that diverse genetic and molecular mechanisms are likely to explain heterosis, making it difficult to predict its emergence and amplitude from parental genotypes alone. In this study, we evaluated a model of physiological dominance proposed by Sewall Wright to explain the non-additive inheritance of metabolic fluxes at the cellular level. We used 450 hybrids derived from crosses among natural inbred accessions of Arabidopsis thaliana to test model of Wright for two fitness-related traits at the whole-plant level: growth rate and fruit number. We found that allometric relationships between traits constrain Phenotypic Variation in hybrids and inbreds to a similar extent. These allometric relationships behave predictably, in a non-linear manner, explaining up to 75% of heterosis amplitude, while genetic distance among parents at best explains 7%. Thus, our findings are consistent with Wright9s model of physiological dominance on plant performance, and suggest that the emergence of heterosis is an intrinsic property of non-linear relationships between traits. Furthermore, our study highlights the potential of a geometric approach of Phenotypic relationships for predicting heterosis of two major components of crop productivity and yield.
Nobuo Sasaki - One of the best experts on this subject based on the ideXlab platform.
-
© 2009 Molecular Vision Phenotypic Variation and genotype-phenotype discordance in canine cone-rod dystrophy with an RPGRIP1 mutation
2013Co-Authors: Keiko Miyadera, Claudia Busse, Kumiko Kato, Tsuyoshi Tokuriki, Kyohei Morimoto, Hiroyuki Ogawa, Jesús Aguirre-hernández, Keith Barnett, Nigel Holmes, Nobuo SasakiAbstract:Purpose: Previously, a 44 bp insertion in exon 2 of retinitis pigmentosa GTPase interacting protein 1 (RPGRIP1) was identified as the cause of cone-rod dystrophy 1 (cord1), a recessive form of progressive retinal atrophy (PRA) in the Miniature Longhaired Dachshund (MLHD), a dog model for Leber congenital amaurosis. The cord1 locus was mapped using MLHDs from an inbred colony with a homogeneous early onset disease phenotype. In this paper, the MLHD pet population was studied to investigate Phenotypic Variation and genotype-phenotype correlation. Further, the cord1 locus was fine-mapped using PRA cases from the MLHD pet population to narrow the critical region. Other dog breeds were also screened for the RGPRIP1 insertion. Methods: This study examined Phenotypic Variation in an MLHD pet population that included 59 sporadic PRA cases and 18 members of an extended family with shared environment and having six PRA cases. Ophthalmologic evaluations included behavioral abnormalities, responses to menace and light, fundoscopy, and electroretinography (ERG). The RPGRIP1 insertion was screened for in all cases and 200 apparently normal control MLHDs and in 510 dogs from 66 other breed. To fine-map the cord1 locus in the MLHD, 74 PRA cases and 86 controls aged 4 years or more were genotyped for 24 polymorphic markers within the previously mapped cord1 critical region of 14.15 Mb
-
Phenotypic Variation and genotype phenotype discordance in canine cone rod dystrophy with an rpgrip1 mutation
Molecular Vision, 2009Co-Authors: Keiko Miyadera, N G Holmes, Keith C Barnett, Claudia Busse, Kumiko Kato, Jesus Aguirrehernandez, Tsuyoshi Tokuriki, Kyohei Morimoto, Hiroyuki Ogawa, Nobuo SasakiAbstract:Purpose: Previously, a 44 bp insertion in exon 2 of retinitis pigmentosa GTPase interacting protein 1 (RPGRIP1) was identified as the cause of cone-rod dystrophy 1 (cord1), a recessive form of progressive retinal atrophy (PRA) in the Miniature Longhaired Dachshund (MLHD), a dog model for Leber congenital amaurosis. The cord1 locus was mapped using MLHDs from an inbred colony with a homogeneous early onset disease phenotype. In this paper, the MLHD pet population was studied to investigate Phenotypic Variation and genotype-phenotype correlation. Further, the cord1 locus was fine-mapped using PRA cases from the MLHD pet population to narrow the critical region. Other dog breeds were also screened for the RGPRIP1 insertion. Methods: This study examined Phenotypic Variation in an MLHD pet population that included 59 sporadic PRA cases and 18 members of an extended family with shared environment and having six PRA cases. Ophthalmologic evaluations included behavioral abnormalities, responses to menace and light, fundoscopy, and electroretinography (ERG). The RPGRIP1 insertion was screened for in all cases and 200 apparently normal control MLHDs and in 510 dogs from 66 other breed. To fine-map the cord1 locus in the MLHD, 74 PRA cases and 86 controls aged 4 years or more were genotyped for 24 polymorphic markers within the previously mapped cord1 critical region of 14.15 Mb. Results: Among sporadic PRA cases from the MLHD pet population, the age of onset varied from 4 months to 15 years old; MLHDs from the extended family also showed variable onset and rate of progression. Screening for the insertion in RPGRIP1 identified substantial genotype-phenotype discordance: 16% of controls were homozygous for the insertion (RPGRIP1−/−), while 20% of PRA cases were not homozygous for it. Four other breeds were identified to carry the insertion including English Springer Spaniels and Beagles with insertion homozygotes. The former breed included both controls and PRA cases, yet in the latter breed, cone ERG was undetectable in two dogs with no clinically apparent visual dysfunction. Notably, the insertion in the Beagles was a longer variant of that seen in the other breeds. Fine-mapping of the cord1 locus narrowed the critical region on CFA15 from 14.15 Mb to 1.74 Mb which still contains the RPGRIP1 gene. Conclusions: Extensive Phenotypic Variations of onset age and progression rate were observed in PRA cases of the MLHD pet population. The insertion in RPGRIP1 showed the strongest association with the disease, yet additional as well as alternative factors may account for the substantial genotype-phenotype discordance.
Francois Vasseur - One of the best experts on this subject based on the ideXlab platform.
-
nonlinear Phenotypic Variation uncovers the emergence of heterosis in arabidopsis thaliana
PLOS Biology, 2019Co-Authors: Francois Vasseur, Louise Fouqueau, Thibault Nidelet, Dominique De Vienne, Cyrille Violle, Detlef WeigelAbstract:Heterosis describes the Phenotypic superiority of hybrids over their parents in traits related to agronomic performance and fitness. Understanding and predicting nonadditive inheritance such as heterosis is crucial for evolutionary biology as well as for plant and animal breeding. However, the physiological bases of heterosis remain debated. Moreover, empirical data in various species have shown that diverse genetic and molecular mechanisms are likely to explain heterosis, making it difficult to predict its emergence and amplitude from parental genotypes alone. In this study, we examined a model of physiological dominance initially proposed by Sewall Wright to explain the nonadditive inheritance of traits like metabolic fluxes at the cellular level. We evaluated Wright's model for two fitness-related traits at the whole-plant level, growth rate and fruit number, using 450 hybrids derived from crosses among natural accessions of A. thaliana. We found that allometric relationships between traits constrain Phenotypic Variation in a nonlinear and similar manner in hybrids and accessions. These allometric relationships behave predictably, explaining up to 75% of heterosis amplitude, while genetic distance among parents at best explains 7%. Thus, our findings are consistent with Wright's model of physiological dominance and suggest that the emergence of heterosis on plant performance is an intrinsic property of nonlinear relationships between traits. Furthermore, our study highlights the potential of a geometric approach of Phenotypic relationships for predicting heterosis of major components of crop productivity and yield.
-
non linear Phenotypic Variation uncovers the emergence of heterosis in arabidopsis thaliana
bioRxiv, 2018Co-Authors: Francois Vasseur, Louise Fouqueau, Thibault Nidelet, Dominique De Vienne, Cyrille Violle, Detlef WeigelAbstract:Heterosis describes the Phenotypic superiority of hybrids over their parents in traits related to fitness. Understanding and predicting non-additive inheritance such as heterosis is crucial for evolutionary biology, as well as for plant and animal breeding. However, the physiological bases of heterosis remain debated. Moreover, empirical data in various species have shown that diverse genetic and molecular mechanisms are likely to explain heterosis, making it difficult to predict its emergence and amplitude from parental genotypes alone. In this study, we evaluated a model of physiological dominance proposed by Sewall Wright to explain the non-additive inheritance of metabolic fluxes at the cellular level. We used 450 hybrids derived from crosses among natural inbred accessions of Arabidopsis thaliana to test model of Wright for two fitness-related traits at the whole-plant level: growth rate and fruit number. We found that allometric relationships between traits constrain Phenotypic Variation in hybrids and inbreds to a similar extent. These allometric relationships behave predictably, in a non-linear manner, explaining up to 75% of heterosis amplitude, while genetic distance among parents at best explains 7%. Thus, our findings are consistent with Wright9s model of physiological dominance on plant performance, and suggest that the emergence of heterosis is an intrinsic property of non-linear relationships between traits. Furthermore, our study highlights the potential of a geometric approach of Phenotypic relationships for predicting heterosis of two major components of crop productivity and yield.
Yann Froelicher - One of the best experts on this subject based on the ideXlab platform.
-
The effect of cross direction and ploidy level on Phenotypic Variation of reciprocal diploid and triploid mandarin hybrids
Tree Genetics and Genomes, 2020Co-Authors: Dalel Ahmed, Jean-charles Evrard, Patrick Ollitrault, Yann FroelicherAbstract:New citrus fruit varieties with the right pomological and organoleptic characteristics are expected by consumers and the fresh citrus fruit market. Apart from a good balance between sugar content and acidity, seedlessness is particularly demanded. Triploidy is one of the best ways to obtain seedless cultivars, and, taking advantage of diploid gametes, research programs have succeeded in creating them. Triploid hybrids are sterile and, when associated with parthenocarpy, produce seedless fruits. However, no studies have compared the potential agronomic interest of diploid and triploid cultivars to date. The aims of this study were to investigate the effects of (i) cross direction between diploid and triploid reciprocal populations of mandarin hybrids and (ii) the increase in ploidy level from diploidy to triploidy Phenotypic Variation in quantitative agronomic traits. Reciprocal crosses between 'Fortune' mandarin and 'Ellendale' tangor generated two diploid and two triploid populations; we then phenotyped by measuring fruit and juice weights, sugar content and titratable acidity over three harvesting campaigns. Significant differences in sugar and acidity levels were observed between triploid populations. Both triploid progenies varied according to their respective female genitor, unlike diploid populations in which no relationship was found between their Phenotypic Variation and that of their parents. Considering each cross direction separately, the comparison of diploid and triploid populations revealed that triploid hybrids were juicier and sweeter. A genomic dosage effect appears to be the most plausible explanation for these Variations. These innovative results will help optimize triploid citrus breeding programmes by choosing the appropriate diploid gamete producing parent.
Jean Clobert - One of the best experts on this subject based on the ideXlab platform.
-
Seasonal and interpopulational Phenotypic Variation in morphology and sexual signals of Podarcis liolepis lizards
PLoS ONE, 2019Co-Authors: Jesús Ortega, José Martin, Pierre-andré Crochet, Pilar López, Jean ClobertAbstract:Widespread species often show extensive Phenotypic Variation due to the contrasting abiotic and biotic factors that shape selective pressures in different environments. In this context, the gradual and predictable patterns of Variation in climatic and environmental conditions found in mountain areas offer a great opportunity to explore intraspecific Phenotypic Variation. For instance, temperature is negatively correlated with altitude and virtually all aspects of the behavior and physiology of ectotherms are sensitive to body temperature. In this work, we tested the hypothesis that morphology, dorsal and ventral coloration and the chemical profile of femoral secretions show interpopulational and seasonal Variation in the lacertid lizard (Podarcis liolepis). We compared lizards from three populations inhabiting lowland and highland habitats in the French Pyrenees that were closely related genetically. We found that highland lizards were larger, stockier, had longer heads and more femoral pores and had a darker dorsal coloration than lowland ones. In addition, we detected interpopulational differences in both the abundance and the richness of chemical compounds in the glandular secretions, and we also found seasonal Variation in the overall chemical composition. Dorsal and ventral coloration differed seasonally and between populations. Ventral and dorsal brightness were higher in lowland than in highland lizards in the reproductive season whereas the reversed trend was found in the non-reproductive season but only for dorsal brightness. In addition, all lizards had browner dorsal coloration in the non-reproductive season, and lowland lizards were greener in the reproductive season. By integrating information from both visual and chemical systems, our works offers a comprehensive view of how these lizards communicate in a multimodal context.
