Variability and synchronism of leaf appearance and leaf elongation rates of eleven contrasting rice genotypes

Leaf appearance and leaf elongation rates in rice play an essential role in determining the development of the plants' architecture which affects their adaptability to varying environments. This study aimed to characterize the rates of leaf appearance and elongation on all leaves of the main culms of rice plants for 11 contrasting varieties and to determine if the decrease in the leaf appearance rate was related to a simultaneous decrease in the rate of leaf elongation. Forty four 13-L pots were sown with one plant from one genotype and laid out in 4 randomized complete blocks. The experiment, conducted inside a greenhouse, was repeated twice. The increase in length of the leaves expanding on the main stems was monitored daily until flag leaf. Data were used to estimate the rates of leaf appearance and leaf elongation. Significant variability in the rate of leaf appearance, rate of leaf elongation, and leaf length was found across varieties. The kinetics of leaf appearance had linear phases intermediated by a curvilinear phase, without sharp changes in the phyllochron duration. Maximal leaf elongation rate (LER) of all genotypes (except for one) increased linearly with leaf rank until it reached its maximum value at leaf 8 to 10 (11 - 12 for Azucena) where it stabilized before decreasing linearly with leaf rank for the last leaves. Finally, both rates of leaf appearance and leaf elongation evolved with time more smoothly than expected so no sharp decrease in LER occurred at the time of the decrease in leaf appearance rate of the last leaves. However, the trilinear model fits the data well enough to remain useful in efficiently comparing the leaf appearance kinetics of contrasting varieties. (Résumé d'auteur

Variabilité de la vitesse de développement chez le sorgho cultivé (Sorghum bicolor (L.) Moench) et relation avec le photopériodisme

The rate of development of highly photoperiodic and consequently late sorghums adapted to the West-African savannas is reduced during the phases of jointing and panicle development. Slow development, expressed by a long phyllochron or time between the appearances of two successive leaves, is related to the limited size of the panicles of late sorghums. Therefore, variation for phyllochron during plant development could be a way of increasing the potential grain yield of this type of sorghum. Variability for this trait was assessed in the Cirad (Centre de coopération internationale en recherche agronomique pour le développement) sorghum mini core-collection but none was detected. On the contrary, the rates of development appear to be homogeneous within the species. There was no significant variation observed for the initial phyllochron, following emergence. Although there was large variation in the secondary phyllochron expressed during the jointing period, there were no significant differences among varieties of a similar maturity. Secondary phyllochron was strongly correlated with vegetative phase duration and thus appears to be one of the functions affected by the photoperiod-sensitive response

Past, present and future criteria to breed crops for water-limited environments in West Africa

Asia's Green Revolution of the 1960s and 1970s has largely bypassed West Africa, and "modern" (high-yielding, input responsive) germplasm for staple crops has found comparatively little adoption, except for systems that are have good access to markets and sufficient water resources. It is unlikely, however, that breeding objectives conserving traditional crop characteristics as found in extensive systems would have been more successful. The authors identify systems caught in the agricultural transition from subsistence to intensified, market-oriented production as the most important target for crop improvement, and provide examples of new breeding objectives for cowpea, sorghum and upland rice. In each of these cases, breeders, with the help of physiologists, have developed innovative plant-type concepts that combine improved yield potential and input responsiveness with specific traditional crop characteristics that remain essential during the agricultural transition. In the case of cowpea, dual-purpose varieties were developed that produce a good grain yield due to an erect plant habit, then produce new leaves enabling a second harvest of green foliage. For upland rice systems that are limited by labour (mainly needed to control weeds that abound due to shortened fallow periods), a weed competitive plant type was developed from Oryza sativa × Oryza glaberrima crosses. Lastly, sorghum breeders who had previously deselected photoperiod sensitivity are now re-inserting sensitivity into plants having "modern" architecture, in order to allow for flexible sowing dates while maintaining an agro-ecologically optimal time of flowering near the end of the wet season. The ecophysiological basis of these plant types, their place in current and future cropping systems, as well as the problem of under-funding for their realisation, are discussed

Surprising flowering response to photoperiod: Preliminary characterization of West and Central African pearl millet germplasm

Pearl millet (Pennisetum glaucum) is considered to be a short-day species that flowers, or flowers earlier, when day lengths are short. A few studies with two to six planting dates and few selected entries have been conducted in USA (Burton 1965), Senegal (Ramond 1968), and India (Patil et al. 1978, Das 1991). However, there is no known research on the flowering response of pearl millet to photoperiod changes over the entire year. Likewise, knowledge about the photoperiod-sensitivity in West and Central African pearl millets is insufficient

A "Candidate-Interactome" Aggregate Analysis of Genome-Wide Association Data in Multiple Sclerosis

Though difficult, the study of gene-environment interactions in multifactorial diseases is crucial for interpreting the relevance of non-heritable factors and prevents from overlooking genetic associations with small but measurable effects. We propose a “candidate interactome” (i.e. a group of genes whose products are known to physically interact with environmental factors that may be relevant for disease pathogenesis) analysis of genome-wide association data in multiple sclerosis. We looked for statistical enrichment of associations among interactomes that, at the current state of knowledge, may be representative of gene-environment interactions of potential, uncertain or unlikely relevance for multiple sclerosis pathogenesis: Epstein-Barr virus, human immunodeficiency virus, hepatitis B virus, hepatitis C virus, cytomegalovirus, HHV8-Kaposi sarcoma, H1N1-influenza, JC virus, human innate immunity interactome for type I interferon, autoimmune regulator, vitamin D receptor, aryl hydrocarbon receptor and a panel of proteins targeted by 70 innate immune-modulating viral open reading frames from 30 viral species. Interactomes were either obtained from the literature or were manually curated. The P values of all single nucleotide polymorphism mapping to a given interactome were obtained from the last genome-wide association study of the International Multiple Sclerosis Genetics Consortium & the Wellcome Trust Case Control Consortium, 2. The interaction between genotype and Epstein Barr virus emerges as relevant for multiple sclerosis etiology. However, in line with recent data on the coexistence of common and unique strategies used by viruses to perturb the human molecular system, also other viruses have a similar potential, though probably less relevant in epidemiological terms

Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes

<p>Abstract</p> <p>Background</p> <p>During the replication process of bacteria with circular chromosomes, an odd number of homologous recombination events results in concatenated dimer chromosomes that cannot be partitioned into daughter cells. However, many bacteria harbor a conserved dimer resolution machinery consisting of one or two tyrosine recombinases, XerC and XerD, and their 28-bp target site, <it>dif</it>.</p> <p>Results</p> <p>To study the evolution of the <it>dif/</it>XerCD system and its relationship with replication termination, we report the comprehensive prediction of <it>dif </it>sequences <it>in silico </it>using a phylogenetic prediction approach based on iterated hidden Markov modeling. Using this method, <it>dif </it>sites were identified in 641 organisms among 16 phyla, with a 97.64% identification rate for single-chromosome strains. The <it>dif </it>sequence positions were shown to be strongly correlated with the GC skew shift-point that is induced by replicational mutation/selection pressures, but the difference in the positions of the predicted <it>dif </it>sites and the GC skew shift-points did not correlate with the degree of replicational mutation/selection pressures.</p> <p>Conclusions</p> <p>The sequence of <it>dif </it>sites is widely conserved among many bacterial phyla, and they can be computationally identified using our method. The lack of correlation between <it>dif </it>position and the degree of GC skew suggests that replication termination does not occur strictly at <it>dif </it>sites.</p

Genetic Structure, Linkage Disequilibrium and Signature of Selection in Sorghum: Lessons from Physically Anchored DArT Markers

Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r2 decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod

Yield of Photoperiod-sensitive Sorghum Hybrids Based on Guinea-race Germplasm under Farmers’ Field Conditions in Mali

The first sorghum [Sorghum bicolor (L.) Moench] hybrids based on West African Guinea-race-derived parents were created to enhance farmer’s food security and income through increased yields. To assess their performance, eight hybrids, six experimental pure-line cultivars, one pure-line check (Lata), and a highly adapted landrace cultivar (Tieble) were evaluated in 27 farmer-managed and two on-station yield trials in Mali, West Africa, from 2009 to 2011. The hybrids were confirmed to have photoperiod sensitivity similar to the well-adapted Guinea landrace check cultivar. Genotypic differences for on-farm grain yield were highly significant and genotype × environment crossover interactions were limited. The yield superiorities of individual hybrids, relative to the landrace check, ranged from 17 to 37% over the 27 on-farm trials. The three top yielding hybrids showed 30% yield advantages across productivity levels, with absolute yield advantages averaging 380 kg ha−1 under lower (1.0–1.5 t ha−1) and 660 kg ha−1 under higher (2.0–3.5 t ha−1) productivity conditions. A mean male-parent (better parent) heterosis of 26% was observed for the four hybrids having Lata as a male parent. As the hybrids studied here were obtained with a low intensity of selection using a limited number of parents, even greater yield superiorities may be attained with development of distinct parental pools and scaled-up hybrid breeding