Desired base upper half mean length (UHML) of upland cotton (G. hirsutum) in the U.S. has been set a 27.0 mm and is shorter than the standard set by the international community. Upland cotton genotypes from China, South Africa, West Africa, and the U.S. were test crossed to an extra long staple upland (ELSU) and a short staple upland (SSU) and selected genotypes that included both ELSU and MSU phenotypes were crossed in a half-diallel mating scheme to estimate general combing ability (GCA) effects and specific combining ability (SCA) effects. A recombinant inbred line (RIL) population was established to determine the narrow sense heritability (h^2) of AFIS short fiber content by weight (SFCw) and lower half mean length (LHML) and to estimate SFCw using HVI fiber properties. Obsolete cultivars from China are not likely sources for UHML improvement, cultivars from Africa and the U.S. could harbor alleles not being used in current elite short staple cultivars or modern ELSU cultivars. Two ELSU lines used in this study derived through interspecific hybridization with G. barbadense could contain alleles for UHML improvement in modern ELSU cultivars developed without any apparent G. barbadense introgression. A third line D&PL 45-867, might contain alleles for UHML improvement in long staple upland cotton genotypes. Narrow sense heritability estimates indicated a much higher heritability of LHML than AFIS SFCw. Correlation between AFIS SFCw and LHML did not agree with previous studies when using an ELSU X MSU cross. Further study is needed to understand this complex relationship.

Recent initiatives for biofuel production have increased research and development of sweet sorghum. Currently, the initial major limitation to integrating sweet sorghum into existing production systems is the lack of sweet sorghum hybrids adapted to industrial production systems. Hybrid development is now underway, and the application of genetic markers can be used to define the genetic basis of sugar yield and its components, as well as reduce the time required to deliver new sweet sorghum hybrids to market. The purpose of this research was to further characterize the genetic components that influence sweet sorghum productivity, agronomics, and composition. Specifically, a grain x sweet sorghum recombinant inbred line (RIL) population developed for quantitative trait locus (QTL) analysis related to sugar production was evaluated for 24 phenotypic traits including brix, percent moisture, and biomass yield across four environments. The 185 F4 RILs were derived from the parents 'BTx3197' and 'Rio', which are pithy stalk grain and juicy stalk sweet sorghums respectively. Following screening, two genetic maps were constructed with 372 and 381 single nucleotide polymorphisms (SNPs) evaluated using an Illumina GoldenGate assay. Analysis of the data in QTL Cartographer revealed a major and previously reported QTL for soluble solids on chromosome 3, but in contrast to previous studies, this QTL co-localized with other QTLs that have a negative influence on biomass and seed production. Therefore, selection for this QTL may not be advantageous. Because only a few QTLs for percent moisture were found, the results indicated that the pithy stalk phenotype does not have a major effect on percent moisture as measured in this study. Thus, breeding for high or low moisture content will be more challenging than previously expected. The absence of dominance effects indicated that brix must be high in both parents to produce high brix in the hybrid.

Des changements de méthylation de l’ADN peuvent affecter l’expression des gènes et pour certains être transmis au travers des générations. De telles « épimutations » qui concernent des groupes de cytosines à proximité ou dans les gènes sont donc une source potentielle de variation phénotypique héritable en absence de changements de la séquence de l’ADN. Chez les plantes la méthylation de l’ADN est cependant principalement observée au niveau des séquences répétées. Il reste à déterminer dans quelle mesure les changements de méthylation au niveau de ce type de séquences peuvent être héritées et affecter les phénotypes. Afin de répondre à ces questions, plus de 500 épiRIL (epigenetic Recombinant Inbred Lines) quasi-isogéniques a été générée chez Arabidopsis thaliana. Cette population a été obtenue par le croisement d’un parent sauvage et d’un parent mutant pour le gène DDM1 présentant une très forte réduction du taux de méthylation de l’ADN. Après un rétrocroisement de la F1 avec une plante sauvage, les individus sauvages pour le gène DDM1 ont été sélectionnés et propagées sur 6 générations par autofécondation. Nous avons montré par l’analyse du méthylome de plus de 100 épiRIL que l’hypométhylation induite par ddm1 présente selon les séquences affectées différents degrés de transmission au travers des générations. La réversion de l’hypométhylation concerne des régions associées à une abondance élevée en sRNA de 24 nt. Nous avons utilisé l’hypométhylation stablement transmise dans les épiRIL induite par ddm1 afin de détecter des QTL (Quantitative Trait Loci) affectant le temps de floraison et la longueur de la racine primaire, deux caractères pour lesquels les variations observées dans les épiRIL présentent une héritabilité importante. En dernier lieu, nous avons recherché par différentes approches les variations causales de ces QTL. / Loss or gain of DNA methylation can affect gene expression and is sometimes transmitted across generations. Such epigenetic alterations, which concern clusters of cytosines located near or within genes, are thus a source of heritable phenotypic variation in the absence of DNA sequence change. In plants however, DNA methylation targets repeat elements predominantly and it remains unclear to which extent DNA methylation changes over repeat sequences can be inherited and affect phenotypes. To address these issues, a population of near-isogenic, epigenetic Recombinant Inbred Lines (epiRILs) was generated in Arabidopsis thaliana. These were derived from a cross between a wild type and an isogenic ddm1 mutant line, in which DNA methylation is compromised specifically over repeat elements. After backcrossing of the F1 and selection of the progeny homozygous for wild-type DDM1, the epiRILs were propagated through six rounds of selfing. Analysis of the methylomes of more than 100 epiRILs and of the parents, indicates that ddm1-induced hypomethylation exhibit different patterns of inheritance through generations. Reversion of ddm1-induced hypomethylation is observed for regions associated with high level of 24 nt siRNA. Based on these findings, stable ddm1-induced hypomethylated regions were used to map quantitative trait loci (QTL) for flowering time and primary root length, two complex traits for which substantial heritable variation is observed in the epiRIL population. We finally analysed these QTL by different approaches to find their causal variations.

No description available.

Previously seed coat color in flax has been used as a phenotypic marker for specialty quality traits and currently there is an increasing demand to use seed coat color in flax to market flax for human and animal nutrition uses. Seed coat color was studied to 1) understand the inheritance of seed coat color conditioned by the b1 locus, to 2) understand the relationship of other important flax traits with seed coat color as well as to 3) identify markers that are linked to seed coat color for future marker assisted selection of seed coat color. Spearman’s rank correlation and an allelism test was used to show the inheritance of the alleles at the b1 locus. Bulked segregant analysis (BSA) was used to identify putatively linked markers with the b1 locus, these were then screened on the CDC Bethune x M96006 recombinant inbred line population. Furthermore, the CDC Bethune x M96006 and CDC Bethune x USDA-ARS Crystal recombinant inbred line populations were used to identify any important flax traits that had a significant relationship with seed coat color. It was shown that seed coat color conditioned by the b1 locus was stably inherited and that b1vg and b1 are allelic to one another. The results of the BSA showed that there were 17 candidates for linkage but when these markers were screened on the population only the Lu456 from linkage group (LG) six was identified to have linkage (χ²=3.90; P<0.05) with the b1 locus. Additionally, it was shown that the b1 seed coat color allele of the b1 locus had a pleiotropic effect on flower color and flower shape and that seed coat color was associated with linolenic fatty acid content. None of the traits examined were found to be associated with the b1vg allele of this locus. These results show that the b1 locus is likely present on linkage group six, more marker coverage on linkage group six of markers that are polymorphic between the two seed coat color parents would increase the accuracy of detection. Lastly, this study showed that plant breeders should consider using the b1vg allele that conditions the variegated seed coat color to mark unique lines with important combinations of traits because it sorted independently for seed quality traits. Whereas, the yellow seed coat color conditioned by the b1 allele was found to be associated with higher linolenic fatty acid content and the semi-lethality of this allele would make it not suitable for use in parental lines.

Des changements de méthylation de l'ADN peuvent affecter l'expression des gènes et pour certains être transmis au travers des générations. De telles " épimutations " qui concernent des groupes de cytosines à proximité ou dans les gènes sont donc une source potentielle de variation phénotypique héritable en absence de changements de la séquence de l'ADN. Chez les plantes la méthylation de l'ADN est cependant principalement observée au niveau des séquences répétées. Il reste à déterminer dans quelle mesure les changements de méthylation au niveau de ce type de séquences peuvent être héritées et affecter les phénotypes. Afin de répondre à ces questions, plus de 500 épiRIL (epigenetic Recombinant Inbred Lines) quasi-isogéniques a été générée chez Arabidopsis thaliana. Cette population a été obtenue par le croisement d'un parent sauvage et d'un parent mutant pour le gène DDM1 présentant une très forte réduction du taux de méthylation de l'ADN. Après un rétrocroisement de la F1 avec une plante sauvage, les individus sauvages pour le gène DDM1 ont été sélectionnés et propagées sur 6 générations par autofécondation. Nous avons montré par l'analyse du méthylome de plus de 100 épiRIL que l'hypométhylation induite par ddm1 présente selon les séquences affectées différents degrés de transmission au travers des générations. La réversion de l'hypométhylation concerne des régions associées à une abondance élevée en sRNA de 24 nt. Nous avons utilisé l'hypométhylation stablement transmise dans les épiRIL induite par ddm1 afin de détecter des QTL (Quantitative Trait Loci) affectant le temps de floraison et la longueur de la racine primaire, deux caractères pour lesquels les variations observées dans les épiRIL présentent une héritabilité importante. En dernier lieu, nous avons recherché par différentes approches les variations causales de ces QTL.

Chickpea (Cicer arietinum L.) was recently introduced to the Canadian prairies, a region which has a short growing season in which crop maturation often occurs under cool and wet conditions. To improve the yield of chickpea, crop duration must closely match the available growing season. The objectives of this study were to: i) examine the days to flowering of diverse chickpea accessions grown in either long or short-days; ii) examine the days to flowering of selected chickpea accessions grown in a range of thermal regimes combined with either long or short days and to examine the interaction between photoperiod and day and night temperatures on crop duration; iii) determine the timing and duration of the photoperiod-sensitive phase in selected chickpea accessions, and vi) determine the genetic basis of the association between flowering time and reaction to ascochyta blight in chickpea. A wide variation was observed in chickpea accessions for their response to flowering under long (16/8 hours day /night) and short days (10/14 hours day/night). Earlier flowering was observed under long photoperiod regimes compared with the short photoperiod regimes. Variability was detected among chickpea accessions for their flowering responses when different temperatures were combined with different photoperiods. Earlier flowering was observed under long days (16/8 hours day/night) coupled with high to moderate temperature regimes (24/16 ºC and 20/12 ºC, day and night respectively) compared to short-days (10/14 hours day and night) and moderate to low temperature regimes (20/12 ºC and 16/8 ºC day and night, respectively). Those chickpea accessions such as ICC 6821 and ICCV 96029 which originated from the lower latitudes of Ethiopia and India, respectively, flowered earlier compared to accessions such as CDC Corinne and CDC Frontier which originated from the higher latitudes and cooler temperate environments of western Canada. Photoperiod sensitivity phases were detected in chickpea accessions adapted to the cold environments of western Canada, whereas no photoperiod sensitivity phase was identified in the extra-early flowering cultivar ICCV 96029. The duration of the photoperiod sensitive phase in the chickpea accessions was longer under short days compared to long days. Field and growth chamber evaluation of a chickpea RIL population (CP-RIL-1) revealed the presence of variability among the lines and the two parents for their days to flowering and level of resistance to ascochyta blight. Broad sense heritability across different site-years for days to flower 0.45 to 0.78, plant height 0.48 to 0.78, ascochyta blight resistance 0.14 to 0.68, days to maturity 0.26, photoperiod sensitivity 0.83 and nodes number of first flowering 0.37 to 0.75 were estimated. Days to flower and photoperiod sensitivity were significantly r = -0.21 to -0.58 (P ≤ 0.05 to 0.001) and -0.28 to -0.41 (P ≤ 0.01 to 0.001), respectively and negatively correlated with ascochyta blight resistance in the CP-RIL-1 population. A genetic linkage map consisting of eight linkage groups was developed using 349 SNP markers. Seven QTLs were identified for days to flowering under growth chamber and field conditions on chromosomes 3, 5, 6 and 8 each and 3 QTLs on chromosome 4. The total phenotypic variation explained by QTLs for days to flowering ranged from 7 to 44%. Two QTLs for days to maturity were identified on chromosomes 3 and 8. Three QTLs, one each on chromosomes 3, 4 and 5 were identified for photoperiod sensitivity. The total phenotypic variation explained by each QTL for photoperiod sensitivity ranged from 7 to 41%. A total of three QTL for node of first flowering, one on chromosomes 3 and 8 each, and two on chromosome 4 were identified. The two QTL on chromosome 4 explained total phenotypic variations of 11 and 32%, respectively. Ten QTLs distributed across all chromosomes, except chromosomes 2 and 5, were identified for ascochyta blight resistance. The phenotypic variability explained by each QTL for ascochyta blight resistance ranged from 7 to 17%. The molecular markers associated with these QTLs have potential for use in chickpea breeding.