This Provisional PDF corresponds to the article as it appeared upon acceptance. Copyedited and fu... more This Provisional PDF corresponds to the article as it appeared upon acceptance. Copyedited and fully formatted PDF and full text (HTML) versions will be made available soon. Intraspecific variation of recombination rate in maize
L'invention concerne un procede ameliore mis en œuvre par ordinateur permettant de predire un... more L'invention concerne un procede ameliore mis en œuvre par ordinateur permettant de predire une valeur agronomique et une valeur de reproduction d'une plante appartenant a une population, le procede comprenant les etapes suivantes : - obtenir au moins certaines donnees de genotype d'un sous-ensemble de lignes de la population, - obtenir au moins certaines donnees de phenotype d'un sous-ensemble de lignes de la population, - fournir un modele statistique recevant en entrees lesdites donnees de genotype et donnees de phenotype, - utiliser ledit modele statistique pour fournir en sortie au moins une valeur agronomique estimee pour ladite plante. En particulier, le modele statistique est un modele mixte combinant des effets fixes et des effets aleatoires.
Medicago truncatula has all the characteristics required for a concerted analysis of nitrogen-fix... more Medicago truncatula has all the characteristics required for a concerted analysis of nitrogen-fixing symbiosis with Rhizobium using the tools of molecular biology, cellular biology and genetics. M. tru ncatula is a diploid and autogamous plant, has a relatively small genome, and preliminary molecular analysis suggests that allelic heterozygosity is minimalcompared with the cross-fertilising tetraploid alfalfa (Medicago sativa). The M. truncatula cultivar Jemalong is
Association mapping is based on linkage disequilibrium (LD) resulting from historical recombinati... more Association mapping is based on linkage disequilibrium (LD) resulting from historical recombinations and helps understanding the genetic basis of complex traits. Many factors affect LD and, therefore, it must be determined empirically in the germplasm under investigation to examine the prospects of successful genome-wide association mapping. The objectives of our study were to (1) examine the extent of LD with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in 1,537 commercial maize inbred lines belonging to four heterotic pools, (2) compare the LD patterns determined by these two marker types, (3) evaluate the number of SNP markers needed to perform genome-wide association analyses, and (4) investigate temporal trends of LD. Mean values of the squared correlation coefficient (" R) were almost identical for unlinked, linked, and adjacent SSR marker pairs. In contrast, " R values were lowest for the unlinked SNP loci and highest for the SNPs within amplicons. LD decay varied across the different heterotic pools and the individual chromosomes. The SSR markers employed in the present study are not adequate for association analysis, because of insufficient marker density for the germplasm evaluated. Based on the decay of LD in the various heterotic pools, we would need between 4,000 and 65,000 SNP markers to detect with a reasonable power associations with rather large quantitative trait loci (QTL). A much higher marker density is required to identify QTL with smaller effects. However, not only the total number of markers but also their distribution among and along the chromosomes are primordial for undertaking powerful association analyses. Communicated by A. Charcosset.
Vingt individus issus de populations ou cultivars tétraploïdes et diploïdes de Medicago sativa L.... more Vingt individus issus de populations ou cultivars tétraploïdes et diploïdes de Medicago sativa L. et de l'espèce Medicago falcata L. ont été évalués pour leur aptitude à la régénération à partir de cals. Les différences interet intra-populations ou cultivars sont très importantes. Les cals issus de 6 génotypes ont permis la régénération de plantes soit par organogenèse (2 génotypes) soit par embryogenèse somatique (4 génotypes). La qualité et le rendement des embryons somatiques ont été améliorés par l'utilisation d'une nouvelle séquence de milieux (UM-UMo). Deux génotypes de M. sativa tétraploïdes, l'un issu de la population chinoise « Mestnaya », l'autre du cultivar « Europe » ont un potentiel embryogène et de régénération très élevé, nettement supérieur à Regen S utilisé comme témoin.
Multiparental designs combined with dense genotyping of parents have been proposed as a way to in... more Multiparental designs combined with dense genotyping of parents have been proposed as a way to increase the diversity and resolution of quantitative trait loci (QTL) mapping studies, using methods combining linkage disequilibrium information with linkage analysis (LDLA). Two new nested association mapping designs adapted to European conditions were derived from the complementary dent and flint heterotic groups of maize (Zea mays L.). Ten biparental dent families (N = 841) and 11 biparental flint families (N = 811) were genotyped with 56,110 single nucleotide polymorphism markers and evaluated as test crosses with the central line of the reciprocal design for biomass yield, plant height, and precocity. Alleles at candidate QTL were defined as (i) parental alleles, (ii) haplotypic identity by descent, and (iii) single-marker groupings. Between five and 16 QTL were detected depending on the model, trait, and genetic group considered. In the flint design, a major QTL (R(2) = 27%) with p...
The efficiency of marker-assisted prediction of phenotypes has been studied intensively for diffe... more The efficiency of marker-assisted prediction of phenotypes has been studied intensively for different types of plant breeding populations. However, one remaining question is how to incorporate and counterbalance information from biparental and multiparental populations into model training for genome-wide prediction. To address this question, we evaluated testcross performance of 1652 doubled-haploid maize (Zea mays L.) lines that were genotyped with 56,110 single nucleotide polymorphism markers and phenotyped for five agronomic traits in four to six European environments. The lines are arranged in two diverse half-sib panels representing two major European heterotic germplasm pools. The data set contains 10 related biparental dent families and 11 related biparental flint families generated from crosses of maize lines important for European maize breeding. With this new data set we analyzed genome-based best linear unbiased prediction in different validation schemes and compositions of estimation and test sets. Further, we theoretically and empirically investigated marker linkage phases across multiparental populations. In general, predictive abilities similar to or higher than those within biparental families could be achieved by combining several half-sib families in the estimation set. For the majority of families, 375 half-sib lines in the estimation set were sufficient to reach the same predictive performance of biomass yield as an estimation set of 50 full-sib lines. In contrast, prediction across heterotic pools was not possible for most cases. Our findings are important for experimental design in genome-based prediction as they provide guidelines for the genetic structure and required sample size of data sets used for model training.
Association mapping has permitted the discovery of major QTLs in many species. It can be applied ... more Association mapping has permitted the discovery of major QTLs in many species. It can be applied 68 to existing populations and, as a consequence, it is generally necessary to take into account structure 69 and relatedness among individuals in the statistical model to control false positives. We studied 70
Background: In sexually reproducing organisms, meiotic crossovers ensure the proper segregation o... more Background: In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such genetic reassortment is exploited in breeding to combine favorable alleles, and in genetic research to identify genetic factors underlying traits of interest via linkage or association-based approaches. Crossover numbers and distributions along chromosomes vary between species, but little is known about their intraspecies variation.
Mapping quantitative trait loci (QTL) in plants is usually conducted using a population derived f... more Mapping quantitative trait loci (QTL) in plants is usually conducted using a population derived from a cross between two inbred lines. The power of such QTL detection and the estimation of the effects highly depend on the choice of the two parental lines. Thus, the QTL found represent only a small part of the genetic architecture and can be of limited economical interest in marker-assisted selection. On the other hand, applied breeding programmes evaluate large numbers of progeny derived from multiple-related crosses for a wide range of agronomic traits. It is assumed that the development of statistical techniques to deal with pedigrees in existing plant populations would increase the relevance and cost effectiveness of QTL mapping in a breeding context. In this study, we applied a two-step IBD-based-variance component method to a real wheat breeding population, composed of 374 F6 lines derived from 80 different parents. Two bread wheat quality related traits were analysed by the method. Results obtained show very close agreement with major genes and QTL already known for those two traits. With this new QTL mapping strategy, inferences about QTL can be drawn across the breeding programme rather than being limited to the sample of progeny from a single cross and thus the use of the detected QTL in assisting breeding would be facilitated.
Association mapping is based on linkage disequilibrium (LD) resulting from historical recombinati... more Association mapping is based on linkage disequilibrium (LD) resulting from historical recombinations and helps understanding the genetic basis of complex traits. Many factors affect LD and, therefore, it must be determined empirically in the germplasm under investigation to examine the prospects of successful genome-wide association mapping. The objectives of our study were to (1) examine the extent of LD with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in 1,537 commercial maize inbred lines belonging to four heterotic pools, (2) compare the LD patterns determined by these two marker types, (3) evaluate the number of SNP markers needed to perform genome-wide association analyses, and (4) investigate temporal trends of LD. Mean values of the squared correlation coefficient ( " R) were almost identical for unlinked, linked, and adjacent SSR marker pairs. In contrast, " R values were lowest for the unlinked SNP loci and highest for the SNPs within amplicons. LD decay varied across the different heterotic pools and the individual chromosomes.
In order to evaluate the impact of ethylene in maize tissue culture, silver nitrate has been used... more In order to evaluate the impact of ethylene in maize tissue culture, silver nitrate has been used as an inhibitor of ethylene action. Type II callus initiation rate was improved when immature embryos were cultured on a modified Murashige & Skoog medium containing various concentrations of silver nitrate (5, 10, 20 mg 1-J ). Regeneration ability of calli initiated and maintained in presence of silver nitrate was enhanced. No modification of callus growth rate neither of ethylene production has been detected.
ABSTRACT Saponins have been extracted from callus and suspension cultures from Medicago sativa an... more ABSTRACT Saponins have been extracted from callus and suspension cultures from Medicago sativa and M. truncatula. Acid hydrolysis of the saponins has provided soyasapogenol B and medicagenic acid as the main genins; they were identified by TLC and HPLC. .
In order to evaluate the importance of ethylene on embryogenic callus initiation from immature co... more In order to evaluate the importance of ethylene on embryogenic callus initiation from immature corn embryos, AVG, ACC, AgN03 and STS were used and ethylene measurements performed during embryo culture. Ethylene was a restrictive factor of type 11callus initiation for several culture conditions. AVG (0.5-5~) and Ag+ (5.9-59I-'M) increased the type 11callus initiation rate 3-10 fold (to 20-70%) while ACC (10-100~) decreased it. Type I callus production was irregularly influenced by ethylene. Regeneration ability of type 11calli maintained in the presence of ethylene inhibitors was enhanced (3 fold by 51-'M AVG or 59~AgN03) while no modification of callus growth rate was detected.
A MONG the different methods that use molecular markers for selection, genomic selection (GS) has... more A MONG the different methods that use molecular markers for selection, genomic selection (GS) has received considerable attention in the last decade. The objective of this approach is to predict the breeding values of candidates based on their molecular marker genotypes. A prediction formula is developed using the genotypes and phenotypes of reference individuals forming a calibration set (Meuwissen
This Provisional PDF corresponds to the article as it appeared upon acceptance. Copyedited and fu... more This Provisional PDF corresponds to the article as it appeared upon acceptance. Copyedited and fully formatted PDF and full text (HTML) versions will be made available soon. Intraspecific variation of recombination rate in maize
L'invention concerne un procede ameliore mis en œuvre par ordinateur permettant de predire un... more L'invention concerne un procede ameliore mis en œuvre par ordinateur permettant de predire une valeur agronomique et une valeur de reproduction d'une plante appartenant a une population, le procede comprenant les etapes suivantes : - obtenir au moins certaines donnees de genotype d'un sous-ensemble de lignes de la population, - obtenir au moins certaines donnees de phenotype d'un sous-ensemble de lignes de la population, - fournir un modele statistique recevant en entrees lesdites donnees de genotype et donnees de phenotype, - utiliser ledit modele statistique pour fournir en sortie au moins une valeur agronomique estimee pour ladite plante. En particulier, le modele statistique est un modele mixte combinant des effets fixes et des effets aleatoires.
Medicago truncatula has all the characteristics required for a concerted analysis of nitrogen-fix... more Medicago truncatula has all the characteristics required for a concerted analysis of nitrogen-fixing symbiosis with Rhizobium using the tools of molecular biology, cellular biology and genetics. M. tru ncatula is a diploid and autogamous plant, has a relatively small genome, and preliminary molecular analysis suggests that allelic heterozygosity is minimalcompared with the cross-fertilising tetraploid alfalfa (Medicago sativa). The M. truncatula cultivar Jemalong is
Association mapping is based on linkage disequilibrium (LD) resulting from historical recombinati... more Association mapping is based on linkage disequilibrium (LD) resulting from historical recombinations and helps understanding the genetic basis of complex traits. Many factors affect LD and, therefore, it must be determined empirically in the germplasm under investigation to examine the prospects of successful genome-wide association mapping. The objectives of our study were to (1) examine the extent of LD with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in 1,537 commercial maize inbred lines belonging to four heterotic pools, (2) compare the LD patterns determined by these two marker types, (3) evaluate the number of SNP markers needed to perform genome-wide association analyses, and (4) investigate temporal trends of LD. Mean values of the squared correlation coefficient (" R) were almost identical for unlinked, linked, and adjacent SSR marker pairs. In contrast, " R values were lowest for the unlinked SNP loci and highest for the SNPs within amplicons. LD decay varied across the different heterotic pools and the individual chromosomes. The SSR markers employed in the present study are not adequate for association analysis, because of insufficient marker density for the germplasm evaluated. Based on the decay of LD in the various heterotic pools, we would need between 4,000 and 65,000 SNP markers to detect with a reasonable power associations with rather large quantitative trait loci (QTL). A much higher marker density is required to identify QTL with smaller effects. However, not only the total number of markers but also their distribution among and along the chromosomes are primordial for undertaking powerful association analyses. Communicated by A. Charcosset.
Vingt individus issus de populations ou cultivars tétraploïdes et diploïdes de Medicago sativa L.... more Vingt individus issus de populations ou cultivars tétraploïdes et diploïdes de Medicago sativa L. et de l'espèce Medicago falcata L. ont été évalués pour leur aptitude à la régénération à partir de cals. Les différences interet intra-populations ou cultivars sont très importantes. Les cals issus de 6 génotypes ont permis la régénération de plantes soit par organogenèse (2 génotypes) soit par embryogenèse somatique (4 génotypes). La qualité et le rendement des embryons somatiques ont été améliorés par l'utilisation d'une nouvelle séquence de milieux (UM-UMo). Deux génotypes de M. sativa tétraploïdes, l'un issu de la population chinoise « Mestnaya », l'autre du cultivar « Europe » ont un potentiel embryogène et de régénération très élevé, nettement supérieur à Regen S utilisé comme témoin.
Multiparental designs combined with dense genotyping of parents have been proposed as a way to in... more Multiparental designs combined with dense genotyping of parents have been proposed as a way to increase the diversity and resolution of quantitative trait loci (QTL) mapping studies, using methods combining linkage disequilibrium information with linkage analysis (LDLA). Two new nested association mapping designs adapted to European conditions were derived from the complementary dent and flint heterotic groups of maize (Zea mays L.). Ten biparental dent families (N = 841) and 11 biparental flint families (N = 811) were genotyped with 56,110 single nucleotide polymorphism markers and evaluated as test crosses with the central line of the reciprocal design for biomass yield, plant height, and precocity. Alleles at candidate QTL were defined as (i) parental alleles, (ii) haplotypic identity by descent, and (iii) single-marker groupings. Between five and 16 QTL were detected depending on the model, trait, and genetic group considered. In the flint design, a major QTL (R(2) = 27%) with p...
The efficiency of marker-assisted prediction of phenotypes has been studied intensively for diffe... more The efficiency of marker-assisted prediction of phenotypes has been studied intensively for different types of plant breeding populations. However, one remaining question is how to incorporate and counterbalance information from biparental and multiparental populations into model training for genome-wide prediction. To address this question, we evaluated testcross performance of 1652 doubled-haploid maize (Zea mays L.) lines that were genotyped with 56,110 single nucleotide polymorphism markers and phenotyped for five agronomic traits in four to six European environments. The lines are arranged in two diverse half-sib panels representing two major European heterotic germplasm pools. The data set contains 10 related biparental dent families and 11 related biparental flint families generated from crosses of maize lines important for European maize breeding. With this new data set we analyzed genome-based best linear unbiased prediction in different validation schemes and compositions of estimation and test sets. Further, we theoretically and empirically investigated marker linkage phases across multiparental populations. In general, predictive abilities similar to or higher than those within biparental families could be achieved by combining several half-sib families in the estimation set. For the majority of families, 375 half-sib lines in the estimation set were sufficient to reach the same predictive performance of biomass yield as an estimation set of 50 full-sib lines. In contrast, prediction across heterotic pools was not possible for most cases. Our findings are important for experimental design in genome-based prediction as they provide guidelines for the genetic structure and required sample size of data sets used for model training.
Association mapping has permitted the discovery of major QTLs in many species. It can be applied ... more Association mapping has permitted the discovery of major QTLs in many species. It can be applied 68 to existing populations and, as a consequence, it is generally necessary to take into account structure 69 and relatedness among individuals in the statistical model to control false positives. We studied 70
Background: In sexually reproducing organisms, meiotic crossovers ensure the proper segregation o... more Background: In sexually reproducing organisms, meiotic crossovers ensure the proper segregation of chromosomes and contribute to genetic diversity by shuffling allelic combinations. Such genetic reassortment is exploited in breeding to combine favorable alleles, and in genetic research to identify genetic factors underlying traits of interest via linkage or association-based approaches. Crossover numbers and distributions along chromosomes vary between species, but little is known about their intraspecies variation.
Mapping quantitative trait loci (QTL) in plants is usually conducted using a population derived f... more Mapping quantitative trait loci (QTL) in plants is usually conducted using a population derived from a cross between two inbred lines. The power of such QTL detection and the estimation of the effects highly depend on the choice of the two parental lines. Thus, the QTL found represent only a small part of the genetic architecture and can be of limited economical interest in marker-assisted selection. On the other hand, applied breeding programmes evaluate large numbers of progeny derived from multiple-related crosses for a wide range of agronomic traits. It is assumed that the development of statistical techniques to deal with pedigrees in existing plant populations would increase the relevance and cost effectiveness of QTL mapping in a breeding context. In this study, we applied a two-step IBD-based-variance component method to a real wheat breeding population, composed of 374 F6 lines derived from 80 different parents. Two bread wheat quality related traits were analysed by the method. Results obtained show very close agreement with major genes and QTL already known for those two traits. With this new QTL mapping strategy, inferences about QTL can be drawn across the breeding programme rather than being limited to the sample of progeny from a single cross and thus the use of the detected QTL in assisting breeding would be facilitated.
Association mapping is based on linkage disequilibrium (LD) resulting from historical recombinati... more Association mapping is based on linkage disequilibrium (LD) resulting from historical recombinations and helps understanding the genetic basis of complex traits. Many factors affect LD and, therefore, it must be determined empirically in the germplasm under investigation to examine the prospects of successful genome-wide association mapping. The objectives of our study were to (1) examine the extent of LD with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in 1,537 commercial maize inbred lines belonging to four heterotic pools, (2) compare the LD patterns determined by these two marker types, (3) evaluate the number of SNP markers needed to perform genome-wide association analyses, and (4) investigate temporal trends of LD. Mean values of the squared correlation coefficient ( " R) were almost identical for unlinked, linked, and adjacent SSR marker pairs. In contrast, " R values were lowest for the unlinked SNP loci and highest for the SNPs within amplicons. LD decay varied across the different heterotic pools and the individual chromosomes.
In order to evaluate the impact of ethylene in maize tissue culture, silver nitrate has been used... more In order to evaluate the impact of ethylene in maize tissue culture, silver nitrate has been used as an inhibitor of ethylene action. Type II callus initiation rate was improved when immature embryos were cultured on a modified Murashige & Skoog medium containing various concentrations of silver nitrate (5, 10, 20 mg 1-J ). Regeneration ability of calli initiated and maintained in presence of silver nitrate was enhanced. No modification of callus growth rate neither of ethylene production has been detected.
ABSTRACT Saponins have been extracted from callus and suspension cultures from Medicago sativa an... more ABSTRACT Saponins have been extracted from callus and suspension cultures from Medicago sativa and M. truncatula. Acid hydrolysis of the saponins has provided soyasapogenol B and medicagenic acid as the main genins; they were identified by TLC and HPLC. .
In order to evaluate the importance of ethylene on embryogenic callus initiation from immature co... more In order to evaluate the importance of ethylene on embryogenic callus initiation from immature corn embryos, AVG, ACC, AgN03 and STS were used and ethylene measurements performed during embryo culture. Ethylene was a restrictive factor of type 11callus initiation for several culture conditions. AVG (0.5-5~) and Ag+ (5.9-59I-'M) increased the type 11callus initiation rate 3-10 fold (to 20-70%) while ACC (10-100~) decreased it. Type I callus production was irregularly influenced by ethylene. Regeneration ability of type 11calli maintained in the presence of ethylene inhibitors was enhanced (3 fold by 51-'M AVG or 59~AgN03) while no modification of callus growth rate was detected.
A MONG the different methods that use molecular markers for selection, genomic selection (GS) has... more A MONG the different methods that use molecular markers for selection, genomic selection (GS) has received considerable attention in the last decade. The objective of this approach is to predict the breeding values of candidates based on their molecular marker genotypes. A prediction formula is developed using the genotypes and phenotypes of reference individuals forming a calibration set (Meuwissen
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