Population genomics of Mediterranean oat (A. sativa) reveals high genetic diversity and three loci for heading date.

KEY MESSAGE: Genomic analysis of Mediterranean oats reveals high genetic diversity and three loci for adaptation to this environment. This information together with phenotyping and passport data, gathered in an interactive map, will be a vital resource for oat genetic improvement. During the twentieth century, oat landraces have increasingly been replaced by modern cultivars, resulting in loss of genetic diversity. However, landraces have considerable potential to improve disease and abiotic stress tolerance and may outperform cultivars under low input systems. In this work, we assembled a panel of 669 oat landraces from Mediterranean rim and 40 cultivated oat varieties and performed the first large-scale population genetic analysis of both red and white oat types of Mediterranean origin. We created a public database associated with an interactive map to visualize information for each accession. The oat collection was genotyped with 17,288 single-nucleotide polymorphism (SNP) loci to evaluate population structure and linkage disequilibrium (LD); to perform a genome-wide association study (GWAs) for heading date, a key character closely correlated with performance in this drought-prone area. Population genetic analysis using both structure and PCA distinguished two main groups composed of the red and white oats, respectively. The white oat group was further divided into two subgroups. LD decay was slower within white lines in linkage groups Mrg01, 02, 04, 12, 13, 15, 23, 33, whereas it was slower within red lines in Mrg03, 05, 06, 11, 21, 24, and 28. Association analysis showed several significant markers associated with heading date on linkage group Mrg13 in white oats and on Mrg01 and Mrg08 in red oats.

Development of genic-microsatellite markers for sorghum staygreen QTL using a comparative genomic approach with rice.

The already available comprehensive genome sequence information of model crops along with the transcriptomic resource from other crops provides an excellent opportunity for comparative genome analysis. We studied the synteny between each of the four major sorghum staygreen quantitative trait loci (QTL) regions with that in the rice genome and attempted to increase marker density around the QTL with genic-microsatellites from the sorghum transcriptomic resource using the rice genome as template. For each of the sorghum QTL regions, the reported RFLP markers were compiled, used for sequence similarity searches against the rice genome which identified syntenous regions on rice chromosome 1 for Stg1 and Stg2 QTL, on chromosome 9 for Stg3 QTL, and on chromosome 11 for Stg4 QTL. Using the Gramene genome browsing tool, 869 non-redundant sorghum expressed sequence tags (ESTs) were selected and 50 genic-microsatellites (18, 12, 15, and 5, for Stg1, Stg2, Stg3, and Stg4 QTL, respectively) could be developed. We could experimentally establish synteny of the Stg1, Stg2, Stg3, and Stg4 QTL regions with that of the rice genome by mapping ten polymorphic genic-microsatellite markers (20%) to the positions of the staygreen QTL. The simple strategy demonstrated in the present study could readily be extrapolated to other cereals of the Poaceae family. The markers developed in this study provide a basis for the isolation of genes underling these QTL using an association study or map-based gene isolation approach, and create an additional option for MAS of the staygreen trait in sorghum.

Breeding for abiotic stresses for sustainable agriculture.

Using cereal crops as examples, we review the breeding for tolerance to the abiotic stresses of low nitrogen, drought, salinity and aluminium toxicity. All are already important abiotic stress factors that cause large and widespread yield reductions. Drought will increase in importance with climate change, the area of irrigated land that is salinized continues to increase, and the cost of inorganic N is set to rise. There is good potential for directly breeding for adaptation to low N while retaining an ability to respond to high N conditions. Breeding for drought and salinity tolerance have proven to be difficult, and the complex mechanisms of tolerance are reviewed. Marker-assisted selection for component traits of drought in rice and pearl millet and salinity tolerance in wheat has produced some positive results and the pyramiding of stable quantitative trait locuses controlling component traits may provide a solution. New genomic technologies promise to make progress for breeding tolerance to these two stresses through a more fundamental understanding of underlying processes and identification of the genes responsible. In wheat, there is a great potential of breeding genetic resistance for salinity and aluminium tolerance through the contributions of wild relatives.

Mapping and characterisation of QTL x E interactions for traits determining grain and stover yield in pearl millet.

A mapping population of 104 F(3) lines of pearl millet, derived from a cross between two inbred lines H 77/833-2 x PRLT 2/89-33, was evaluated, as testcrosses on a common tester, for traits determining grain and stover yield in seven different field trials, distributed over 3 years and two seasons. The total genetic variation was partitioned into effects due to season (S), genotype (G), genotype x season interaction (G x S), and genotype x environment-within-season interaction [G x E(S)]. QTLs were determined for traits for their G, G x S, and G x E(S) effects, to assess the magnitude and the nature (cross over/non-crossover) of environmental interaction effects on individual QTLs. QTLs for some traits were associated with G effects only, while others were associated with the effects of both G and G x S and/or G, G x S and G x E(S) effects. The major G x S QTLs detected were for flowering time (on LG 4 and LG 6), and mapped to the same intervals as G x S QTLs for several other traits (including stover yield, harvest index, biomass yield and panicle number m(-2)). All three QTLs detected for grain yield were unaffected by G x S interaction however. All three QTLs for stover yield (mapping on LG 2, LG 4 and LG 6) and one of the three QTLs for grain yield (mapping on LG 4) were also free of QTL x E(S) interactions. The grain yield QTLs that were affected by QTL x E(S) interactions (mapping on LG 2 and LG 6), appeared to be linked to parallel QTL x E(S) interactions of the QTLs for panicle number m(-2) on (LG 2) and of QTLs for both panicle number m(-2) and harvest index (LG 6). In general, QTL x E(S) interactions were more frequently observed for component traits of grain and stover yield, than for grain or stover yield per se.

Quantitative trait loci associated with traits determining grain and stover yield in pearl millet under terminal drought-stress conditions.

Drought stress during the reproductive stage is one of the most important environmental factors reducing the grain yield and yield stability of pearl millet. A QTL mapping approach has been used in this study to understand the genetic and physiological basis of drought tolerance in pearl millet and to provide a more-targeted approach to improving the drought tolerance and yield of this crop in water-limited environments. The aim was to identify specific genomic regions associated with the enhanced tolerance of pearl millet to drought stress during the flowering and grain-filling stages. Testcrosses of a set of mapping-population progenies, derived from a cross of two inbred pollinators that differed in their response to drought, were evaluated in a range of managed terminal drought-stress environments. A number of genomic regions were associated with drought tolerance in terms of both grain yield and its components. For example, a QTL associated with grain yield per se and for the drought tolerance of grain yield mapped on linkage group 2 and explained up to 23% of the phenotypic variation. Some of these QTLs were common across stress environments whereas others were specific to only a particular stress environment. All the QTLs that contributed to increased drought tolerance did so either through better than average maintenance (compared to non-stress environments) of harvest index, or harvest index and biomass productivity. It is concluded that there is considerable potential for marker-assisted backcross transfer of selected QTLs to the elite parent of the mapping population and for their general use in the improvement of pearl millet productivity in water-limited environments.

Pharmacological characterisation of 5-hydroxytryptamine-induced contractile effects in the isolated gut of the lepidopteran caterpillar Spodoptera frugiperda.

The indolealkylamine 5-hydroxytryptamine (5-HT, 0.1nM-1&mgr;M) caused dose-dependent increases in the number of contractions observed in guts isolated from the caterpillar Spodoptera frugiperda. Of the 5-HT analogues tested for agonist action, 2-methyl-5-HT (0.1-10&mgr;M) was a full agonist with reduced potency while alpha-methyl-5-HT (0.1-100&mgr;M), 5-carboxamidotryptamine (0.1-100&mgr;M), 5-methoxytryptamine (5-MeOT) (10nM-10&mgr;M), and tryptamine (1-100&mgr;M) were partial agonists. Incubation of isolated guts with proven mammalian 5-HT receptor antagonists showed that cyproheptadine (10nM-1&mgr;M), MDL 72222 (1-10&mgr;M), tropisetron (1-10&mgr;M) and 5-benzoyloxygramine (1-10&mgr;M) were potent non-competitive antagonists of 5-HT-induced tissue contraction. In comparison, ketanserin (0.1-1&mgr;M) was a competitive antagonist. The mammalian selective serotonin reuptake inhibitors, clomipramine (10nM-10&mgr;M) and fluoxetine (10nM-10&mgr;M) also caused non-competitive inhibition of 5-HT-induced contraction while fluvoxamine (10nM-10&mgr;M) was a weak competitive antagonist. Low doses of clomipramine (0.1&mgr;M) caused potentiation of 5-HT-induced gut contraction thereby suggesting the presence of 5-HT reuptake systems in this tissue. The contractile effects of 5-HT were inhibited by verapamil, Li(+) and H7 and potentiated by theophylline thereby indicating that L-type Ca(2+) channels, phosphatidylinositol second messengers and cAMP, respectively, are involved in 5-HT-induced tissue contraction. The 5-HT receptors mediating contractility in the gut of S. frugiperda have properties in common with mammalian 5-HT(2) and Drosophila 5-HT(dro2A/2B) receptors. In addition, these data suggest that the tissue also contains receptors that are similar to mammalian 5-ht(6) and 5-HT(7) as well as Drosophila(dro1) receptors. However, the primary amino acid sequence of these lepidopteran 5-HT receptors will have to be elucidated before full comparisons can be made.

Structure-activity relationship of contractile effects induced by helicokinins in the isolated gut of the lepidopteran caterpillar Spodoptera frugiperda.

The diuretic helicokinins YFSPWG-amide (Hez KI), VRFSPWG-amide (Hez KII) and KVKFSAWG-amide (Hez KIII) are potent contractants of the isolated gut of the caterpillar Spodoptera frugiperda at doses ranging from 0.1 to 10nM. In comparison, the pentapeptide FSPWG-amide was a full agonist with greatly reduced potency while SPWG-amide and PWG-amide were weak partial agonists. Substitution of individual amino acids in Hez KI with alanine revealed that replacement of the [phenylalanine(2)] residue caused a large fall in potency while replacement of [tryptophan(5)] residue caused complete loss of myogenic activity. The striking fall in potency of YASPWG-amide and the lack of activity of YFSPAG-amide confirm the requirement for aromatic groups in positions 2 and 3 of the core pentapeptide as well as supporting the ideas that the active core of these peptides adopts a beta-turn when interacting with receptors, bringing together the [Phe] and [Trp] residues that are critical for activity. Neither the pentapeptide proctolin nor the potent mammalian gut contractant Substance P were able to cause contraction when applied to caterpillar gut tissue. Incubation of isolated gut tissue in the phosphodiesterase inhibitor theophylline (10-100&mgr;M) caused significant potentiation of the response to applied Hez KI. Conversely, in the presence of the L-type Ca(2+) channel blocker verapamil (10&mgr;M-1mM) or Co(2+) (1-50mM) the contractile effects of Hez KI were attentuated significantly. These data suggest that the gut of S. frugiperda contains G-protein-linked kinin receptors that utilise cyclic AMP as their second messenger system and cause contraction by promoting the entry of extracellular Ca(2+).

Five ways to stay green.

The relationship between carbon income and expenditure over the life of a leaf is described and related to the productivity benefits of altering the timing of senescence initiation. In genetic variants with delayed leaf senescence ('stay-greens') deconstruction of the photosynthetic apparatus during leaf senescence is partially or completely prevented. Although the staygreen phenotype is superficially similar in all species and genotypes, the genetic and physiological routes to the trait are diverse. In one type of stay-green, chlorophyll catabolism is disabled. Legumes and monocots with pigment breakdown lesions are discussed. Sorghum is presented as an example of another kind of stay-green in which perennial tendencies have been bred into a monocarpic annual crop species. Transgenic approaches are briefly discussed (enhanced endogenous cytokinins, reduced ethylene production or perception). An alternative route towards making a stay-green phenotype is through quantitative trait mapping and marker-assisted selection. Loci for greenness in pearl millet have been identified, some of which are associated with drought responses or flowering time. Finally the question of the limits on stay-green as a productivity-enhancing character is addressed.

Temperature shock proteins in plants.

Plant tissue generally responds rapidly to sudden increases in temperature by curtailing or abolishing normal protein synthesis and producing new polypeptides known as heat shock proteins (HSP). Some of the methods used for monitoring the expression of heat shock genes are described, and the characteristics of the heat shock response in higher plants are discussed with special reference to tropical cereals. The possible role for heat shock proteins in conferring thermo-tolerance upon plant tissue is considered. The behaviour of plant tissue subjected to temperature decreases has been much less intensively studied, and varies greatly according to species and the nature of the cold treatment. No homology has yet been detected between the heat shock and the cold shock response in any plant system. Cold-induced changes in gene expression observed in a wide range of plant species are discussed with particular reference to parallel changes in cold-hardiness. Marked contrasts have been observed between the response of temperate grasses and that of tropical cereals to cold treatment, and these are discussed in relation to growth and survival at suboptimal temperatures.

Population ecology of the ring-tailed lemur, Lemur catta, and the white sifaka, Propithecus verreauxi verreauxi, at Berenty, Madagascar, 1981.

The diurnal lemurs Propithecus verreauxi verreauxi and Lemur catta at Berenty in southern Madagascar, have been studied for the last 30 years. The August 1981 census indicates that the population size of L. catta remains stable at 150 adults but that P. v. verreauxi troops have become fragmented and scattered and the population is apparently increasing. Eight different vegetation types were classified within the reserve and their influence on the distribution of L. catta and P. v. verreauxi investigated. Behavioural data obtained shows the niche separation between these two, potentially competitive, sympatric lemurs.