The Experts below are selected from a list of 1119 Experts worldwide ranked by ideXlab platform
Joshua A Udall - One of the best experts on this subject based on the ideXlab platform.
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quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed brassica napus l 2 identification of alleles from unadapted germplasm
Theoretical and Applied Genetics, 2006Co-Authors: Joshua A Udall, Pablo A Quijada, Bart Lambert, Thomas C OsbornAbstract:Unadapted germplasm may contain alleles that could improve hybrid cultivars of spring oilseed Brassica napus. Quantitative trait loci (QTL) mapping was used to identify potentially useful alleles from two unadapted germplasm sources, a Chinese winter cultivar and a re-synthesized B. napus, that increase seed yield when introgressed into a B. napus spring hybrid combination. Two populations of 160 doubled haploid (DH) lines were created from crosses between the unadapted germplasm source and a genetically engineered male-fertility restorer line (P1804). A genetically engineered male-sterile tester line was used to create hybrids with each DH line (Testcrosses). The two DH line populations were evaluated in two environments and the two testcross populations were evaluated in three or four environments for seed yield and other agronomic traits. Several genomic regions were found in the two testcross populations which contained QTL for seed yield. The map positions of QTL for days to flowering and resistance to a bacterial leaf blight disease coincided with QTL for seed yield and other agronomic traits, suggesting the occurrence of pleiotropic or linked effects. For two hybrid seed yield QTL, the favorable alleles increasing seed yield originated from the unadapted parents, and one of these QTL was detected in multiple environments and in both populations. In this QTL region, a chromosome rearrangement was identified in P1804, which may have affected seed yield.
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quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed brassica napus l 1 identification of genomic regions from winter germplasm
Theoretical and Applied Genetics, 2006Co-Authors: Pablo A Quijada, Joshua A Udall, Bart Lambert, Thomas C OsbornAbstract:The introgression of winter germplasm into spring canola (Brassica napus L.) represents a novel approach to improve seed yield of hybrid spring canola. In this study, quantitative trait loci (QTL) for seed yield and other traits were genetically mapped to determine the effects of genomic regions introgressed from winter germplasm into spring canola. Plant materials used comprised of two populations of doubled haploid (DH) lines having winter germplasm introgression from two related French winter cultivars and their Testcrosses with a spring line used in commercial hybrids. These populations were evaluated for 2 years at two locations (Wisconsin, USA and Saskatchewan, Canada). Genetic linkage maps based on RFLP loci were constructed for each DH population. Six QTL were detected in the testcross populations for which the winter alleles increased seed yield. One of these QTL explained 11 and 19% of the phenotypic variation in the two Canadian environments. The winter allele for another QTL that increased seed yield was linked in coupling to a QTL allele for high glucosinolate content, suggesting that the transition of rapeseed into canola could have resulted in the loss of favorable seed yield alleles. Most QTL for which the introgressed allele decreased seed yield of hybrids mapped to genomic regions having homoeologous non-reciprocal transpositions. This suggests that allelic configurations created by these rearrangements might make an important contribution to genetic variation for complex traits in oilseed B. napus and could account for a portion of the heterotic effects in hybrids.
Albrecht E. Melchinger - One of the best experts on this subject based on the ideXlab platform.
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Association mapping for cold tolerance in two large maize inbred panels
BMC Plant Biology, 2016Co-Authors: Pedro Revilla, Albrecht E. Melchinger, Amando Ordás, Renaud Rincent, Alain Charcosset, Catherine Giauffret, Eva Bauer, Victor Manuel Rodriguez, Chris-carolin Schoen, Thomas AltmannAbstract:Background: Breeding for cold tolerance in maize promises to allow increasing growth area and production in temperate zones. The objective of this research was to conduct genome-wide association analyses (GWAS) in temperate maize inbred lines and to find strategies for pyramiding genes for cold tolerance. Two panels of 306 dent and 292 European flint maize inbred lines were evaluated per se and in Testcrosses under cold and control conditions in a growth chamber. We recorded indirect measures for cold tolerance as the traits number of days from sowing to emergence, relative leaf chlorophyll content or quantum efficiency of photosystem II. Association mapping for identifying genes associated to cold tolerance in both panels was based on genotyping with 49,585 genome-wide single nucleotide polymorphism (SNP) markers. Results: We found 275 significant associations, most of them in the inbreds evaluated per se, in the flint panel, and under control conditions. A few candidate genes coincided between the current research and previous reports. A total of 47 flint inbreds harbored the favorable alleles for six significant quantitative trait loci (QTL) detected for inbreds per se evaluated under cold conditions, four of them had also the favorable alleles for the main QTL detected from the Testcrosses. Only four dent inbreds (EZ47, F924, NK807 and PHJ40) harbored the favorable alleles for three main QTL detected from the evaluation of the dent inbreds per se under cold conditions. There were more QTL in the flint panel and most of the QTL were associated with days to emergence and FPSII. Conclusions: These results open new possibilities to genetically improve cold tolerance either with genome-wide selection or with marker assisted selection.
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Additional file 1: Table S1. of Association mapping for cold tolerance in two large maize inbred panels
2016Co-Authors: Pedro Revilla, Albrecht E. Melchinger, Víctor Rodríguez, Amando Ordás, Renaud Rincent, Alain Charcosset, Catherine Giauffret, Chris-carolin Schön, Eva Bauer, Thomas AltmannAbstract:Summary of the compression mixed linear model analysis for cold tolerance traits in two panels of dent and flint maize inbred lines evaluated in a cold chamber under cold and control conditions per se and as Testcrosses, and number of SNPs declared as significantly associated to each trait. (DOC 372 kb
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variation and covariation for gibberella ear rot resistance and agronomic traits in Testcrosses of doubled haploid maize lines
Euphytica, 2012Co-Authors: Matthias Martin, Thomas Miedaner, B S Dhillon, Wolfgang Schipprack, Bettina Kessel, Milena Ouzunova, Albrecht E. MelchingerAbstract:Gibberella ear rot (GER) of maize caused by Fusarium graminearum reduces grain yield and leads to contamination of the grains with deoxynivalenol (DON), a mycotoxin that adversely affects the health of humans and animals. The objectives of this study were to (1) analyze means and genotypic variances for line per se performance (LP) and testcross performance (TP) of doubled haploid (DH) lines for GER severity and DON concentration as well as for some agronomic traits, (2) examine correlations among these traits, (3) validate QTL for resistance detected in previous studies for LP and their effect on TP and (4) investigate the relative efficiency of indirect selection (RE) for LP to improve TP. Testcross progenies of 94 DH lines originating from four flint populations were developed using a susceptible dent tester as pollinator. Artificial inoculations with F. graminearum led to appreciable disease development. Average TP for GER severity and DON concentration were lower than the mean mid-parent values of the tester and DH lines, indicating mid-parent heterosis for resistance. Genotypic variation for resistance was significant for LP and TP. Genotypic correlations between LP and TP were low and resistance QTL for LP had no significant effects on TP. Accordingly, RE for resistance was low, suggesting to allocate resources mostly to the evaluation of Testcrosses. Correlations of resistance to GER and DON contamination with grain yield (measured under non-inoculated conditions) were not significant, indicating that selection for resistance and higher grain yield can be carried out simultaneously.
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genetic variation in Testcrosses and relationship between line per se and testcross performance for resistance to gibberella ear rot in maize
Crop Science, 2010Co-Authors: Christof Bolduan, Thomas Miedaner, B S Dhillon, H F Utz, Albrecht E. MelchingerAbstract:Gibberella ear rot (GER), caused by Fusarium spp., is a major concern in maize production in Central Europe, and development of hybrid cultivars having GER resistance is an important breeding goal. The objectives of the present study were to (i) evaluate the variation in testcross performance (TP) of European maize germplasm for GER resistance and deoxynivalenol (DON) contamination, (ii) estimate variance components, heritabilities, and correlations of these traits, and (iii) examine the relationship between line per se performance (LP) and TP. Testcrosses of 30 diverse flint inbred lines with two dent inbred testers were evaluated in four environments under artificial inoculation. Data were recorded on severity of GER and concentration of DON. There was substantial GER development and the range of both traits was greater for LP than TP. Estimates of genotypic and genotype x environment interaction variances were significant for Testcrosses with both testers. Genotypic variances were generally higher for LP than for TP in each testcross set. Correlations between LP and TP were moderate (ȓ p ≤ 0.57) for GER rating and DON concentration. We recommend multi-stage selection to develop GER resistant maize hybrids based on evaluation of GER resistance under artificial inoculation for (1) LP in one environment followed by (2) TP evaluation in two to three environments. Only the most promising Testcrosses should be tested for DON concentration.
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the role of epistasis in the manifestation of heterosis a systems oriented approach
Genetics, 2007Co-Authors: Albrecht E. Melchinger, Zhaobang Zeng, Hans-peter Piepho, C C SchonAbstract:Heterosis is widely used in breeding, but the genetic basis of this biological phenomenon has not been elucidated. We postulate that additive and dominance genetic effects as well as two-locus interactions estimated in classical QTL analyses are not sufficient for quantifying the contributions of QTL to heterosis. A general theoretical framework for determining the contributions of different types of genetic effects to heterosis was developed. Additive × additive epistatic interactions of individual loci with the entire genetic background were identified as a major component of midparent heterosis. On the basis of these findings we defined a new type of heterotic effect denoted as augmented dominance effect di* that comprises the dominance effect at each QTL minus half the sum of additive × additive interactions with all other QTL. We demonstrate that genotypic expectations of QTL effects obtained from analyses with the design III using Testcrosses of recombinant inbred lines and composite-interval mapping precisely equal genotypic expectations of midparent heterosis, thus identifying genomic regions relevant for expression of heterosis. The theory for QTL mapping of multiple traits is extended to the simultaneous mapping of newly defined genetic effects to improve the power of QTL detection and distinguish between dominance and overdominance.
Brecca R Miller - One of the best experts on this subject based on the ideXlab platform.
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Testcrosses are an efficient strategy for identifying cis regulatory variation bayesian analysis of allele specific expression bayesase
G3: Genes Genomes Genetics, 2021Co-Authors: Brecca R Miller, Alison M Morse, Jacqueline E Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy R B NewmanAbstract:Allelic imbalance (AI) occurs when alleles in a diploid individual are differentially expressed and indicates cis acting regulatory variation. What is the distribution of allelic effects in a natural population? Are all alleles the same? Are all alleles distinct? The approach described applies to any technology generating allele-specific sequence counts, for example for chromatin accessibility and can be applied generally including to comparisons between tissues or environments for the same genotype. Tests of allelic effect are generally performed by crossing individuals and comparing expression between alleles directly in the F1. However, a crossing scheme that compares alleles pairwise is a prohibitive cost for more than a handful of alleles as the number of crosses is at least (n2-n)/2 where n is the number of alleles. We show here that a testcross design followed by a hypothesis test of AI between Testcrosses can be used to infer differences between nontester alleles, allowing n alleles to be compared with n crosses. Using a mouse data set where both Testcrosses and direct comparisons have been performed, we show that the predicted differences between nontester alleles are validated at levels of over 90% when a parent-of-origin effect is present and of 60%-80% overall. Power considerations for a testcross, are similar to those in a reciprocal cross. In all applications, the testing for AI involves several complex bioinformatics steps. BayesASE is a complete bioinformatics pipeline that incorporates state-of-the-art error reduction techniques and a flexible Bayesian approach to estimating AI and formally comparing levels of AI between conditions. The modular structure of BayesASE has been packaged in Galaxy, made available in Nextflow and as a collection of scripts for the SLURM workload manager on github (https://github.com/McIntyre-Lab/BayesASE).
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Testcrosses are an efficient strategy for identifying cis regulatory variation bayesian analysis of allele specific expression base
bioRxiv, 2020Co-Authors: Brecca R Miller, Alison M Morse, Jacqueline E Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy R B NewmanAbstract:Allelic imbalance (AI) occurs when alleles in a diploid individual are differentially expressed and indicates cis acting regulatory variation. What is the distribution of allelic effects in a natural population? Are all alleles the same? Are all alleles distinct? Tests of allelic effect are performed by crossing individuals and comparing expression between alleles directly in the F1. However, a crossing scheme that compares alleles pairwise is a prohibitive cost for more than a handful of alleles as the number of crosses is at least (n2-n)/2 where n is the number of alleles. We show here that a testcross design followed by a hypothesis test of AI between Testcrosses can be used to infer differences between non-tester alleles, allowing n alleles to be compared with n crosses. Using a mouse dataset where both Testcrosses and direct comparisons have been performed, we show that ~75% of the predicted differences between non-tester alleles are validated in a background of ~10% differences in AI. The testing for AI involves several complex bioinformatics steps. BASE is a complete bioinformatics pipeline that incorporates state-of-the-art error reduction techniques and a flexible Bayesian approach to estimating AI and formally comparing levels of AI between conditions. The modular structure of BASE has been packaged in Galaxy, made available in Nextflow and sbatch on github (https://github.com/McIntyre-Lab/BASE_2020). In the mouse data, the direct test identifies more cis effects than the testcross. Cis-by-trans interactions with trans-acting factors on the X contributing to observed cis effects in autosomal genes in the direct cross remains a possible explanation for the discrepancy.
Thomas C Osborn - One of the best experts on this subject based on the ideXlab platform.
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quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed brassica napus l 2 identification of alleles from unadapted germplasm
Theoretical and Applied Genetics, 2006Co-Authors: Joshua A Udall, Pablo A Quijada, Bart Lambert, Thomas C OsbornAbstract:Unadapted germplasm may contain alleles that could improve hybrid cultivars of spring oilseed Brassica napus. Quantitative trait loci (QTL) mapping was used to identify potentially useful alleles from two unadapted germplasm sources, a Chinese winter cultivar and a re-synthesized B. napus, that increase seed yield when introgressed into a B. napus spring hybrid combination. Two populations of 160 doubled haploid (DH) lines were created from crosses between the unadapted germplasm source and a genetically engineered male-fertility restorer line (P1804). A genetically engineered male-sterile tester line was used to create hybrids with each DH line (Testcrosses). The two DH line populations were evaluated in two environments and the two testcross populations were evaluated in three or four environments for seed yield and other agronomic traits. Several genomic regions were found in the two testcross populations which contained QTL for seed yield. The map positions of QTL for days to flowering and resistance to a bacterial leaf blight disease coincided with QTL for seed yield and other agronomic traits, suggesting the occurrence of pleiotropic or linked effects. For two hybrid seed yield QTL, the favorable alleles increasing seed yield originated from the unadapted parents, and one of these QTL was detected in multiple environments and in both populations. In this QTL region, a chromosome rearrangement was identified in P1804, which may have affected seed yield.
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quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed brassica napus l 1 identification of genomic regions from winter germplasm
Theoretical and Applied Genetics, 2006Co-Authors: Pablo A Quijada, Joshua A Udall, Bart Lambert, Thomas C OsbornAbstract:The introgression of winter germplasm into spring canola (Brassica napus L.) represents a novel approach to improve seed yield of hybrid spring canola. In this study, quantitative trait loci (QTL) for seed yield and other traits were genetically mapped to determine the effects of genomic regions introgressed from winter germplasm into spring canola. Plant materials used comprised of two populations of doubled haploid (DH) lines having winter germplasm introgression from two related French winter cultivars and their Testcrosses with a spring line used in commercial hybrids. These populations were evaluated for 2 years at two locations (Wisconsin, USA and Saskatchewan, Canada). Genetic linkage maps based on RFLP loci were constructed for each DH population. Six QTL were detected in the testcross populations for which the winter alleles increased seed yield. One of these QTL explained 11 and 19% of the phenotypic variation in the two Canadian environments. The winter allele for another QTL that increased seed yield was linked in coupling to a QTL allele for high glucosinolate content, suggesting that the transition of rapeseed into canola could have resulted in the loss of favorable seed yield alleles. Most QTL for which the introgressed allele decreased seed yield of hybrids mapped to genomic regions having homoeologous non-reciprocal transpositions. This suggests that allelic configurations created by these rearrangements might make an important contribution to genetic variation for complex traits in oilseed B. napus and could account for a portion of the heterotic effects in hybrids.
Jeremy R B Newman - One of the best experts on this subject based on the ideXlab platform.
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Testcrosses are an efficient strategy for identifying cis regulatory variation bayesian analysis of allele specific expression bayesase
G3: Genes Genomes Genetics, 2021Co-Authors: Brecca R Miller, Alison M Morse, Jacqueline E Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy R B NewmanAbstract:Allelic imbalance (AI) occurs when alleles in a diploid individual are differentially expressed and indicates cis acting regulatory variation. What is the distribution of allelic effects in a natural population? Are all alleles the same? Are all alleles distinct? The approach described applies to any technology generating allele-specific sequence counts, for example for chromatin accessibility and can be applied generally including to comparisons between tissues or environments for the same genotype. Tests of allelic effect are generally performed by crossing individuals and comparing expression between alleles directly in the F1. However, a crossing scheme that compares alleles pairwise is a prohibitive cost for more than a handful of alleles as the number of crosses is at least (n2-n)/2 where n is the number of alleles. We show here that a testcross design followed by a hypothesis test of AI between Testcrosses can be used to infer differences between nontester alleles, allowing n alleles to be compared with n crosses. Using a mouse data set where both Testcrosses and direct comparisons have been performed, we show that the predicted differences between nontester alleles are validated at levels of over 90% when a parent-of-origin effect is present and of 60%-80% overall. Power considerations for a testcross, are similar to those in a reciprocal cross. In all applications, the testing for AI involves several complex bioinformatics steps. BayesASE is a complete bioinformatics pipeline that incorporates state-of-the-art error reduction techniques and a flexible Bayesian approach to estimating AI and formally comparing levels of AI between conditions. The modular structure of BayesASE has been packaged in Galaxy, made available in Nextflow and as a collection of scripts for the SLURM workload manager on github (https://github.com/McIntyre-Lab/BayesASE).
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Testcrosses are an efficient strategy for identifying cis regulatory variation bayesian analysis of allele specific expression base
bioRxiv, 2020Co-Authors: Brecca R Miller, Alison M Morse, Jacqueline E Borgert, Zihao Liu, Kelsey Sinclair, Gavin Gamble, Fei Zou, Jeremy R B NewmanAbstract:Allelic imbalance (AI) occurs when alleles in a diploid individual are differentially expressed and indicates cis acting regulatory variation. What is the distribution of allelic effects in a natural population? Are all alleles the same? Are all alleles distinct? Tests of allelic effect are performed by crossing individuals and comparing expression between alleles directly in the F1. However, a crossing scheme that compares alleles pairwise is a prohibitive cost for more than a handful of alleles as the number of crosses is at least (n2-n)/2 where n is the number of alleles. We show here that a testcross design followed by a hypothesis test of AI between Testcrosses can be used to infer differences between non-tester alleles, allowing n alleles to be compared with n crosses. Using a mouse dataset where both Testcrosses and direct comparisons have been performed, we show that ~75% of the predicted differences between non-tester alleles are validated in a background of ~10% differences in AI. The testing for AI involves several complex bioinformatics steps. BASE is a complete bioinformatics pipeline that incorporates state-of-the-art error reduction techniques and a flexible Bayesian approach to estimating AI and formally comparing levels of AI between conditions. The modular structure of BASE has been packaged in Galaxy, made available in Nextflow and sbatch on github (https://github.com/McIntyre-Lab/BASE_2020). In the mouse data, the direct test identifies more cis effects than the testcross. Cis-by-trans interactions with trans-acting factors on the X contributing to observed cis effects in autosomal genes in the direct cross remains a possible explanation for the discrepancy.
