P lant breeding programs producing inbred lines have two concurrent goals: (i) identifying new inbreds (either for varieties or parents of hybrids) and (ii) identifying parents for subsequent breeding cycles. We believe the most effective strategy for using genomic selection in these plant breeding programs would address each goal separately. This two-part strategy would reorganize traditional breeding programs into two distinct components: a product development component, to develop and screen for inbred lines, and a population improvement component, to increase the frequency of favorable alleles through rapid recurrent genomic selection.Genomic selection uses estimates of genetic value from a genomewide set of molecular markers to make selections (Meuwissen et al., 2001;Bernardo and Yu, 2007). The process involves training a statistical model for associations between molecular ABSTRACTWe propose a strategy for implementing genomic selection in plant breeding programs for developing inbred lines that reorganizes traditional breeding programs into two distinct components. These components are: (i) a population improvement component to develop improved germplasm through rapid recurrent selection and (ii) a product development component to identify new inbred varieties or parents for hybrids using traditional breeding program designs. Stochastic simulations of entire breeding programs over 40 yr were used to evaluate the effectiveness of this strategy relative to a conventional program without genomic selection and programs using three standard strategies of implementing genomic selection. Cost effectiveness was measured by constraining all programs to approximately equal annual operating costs and directly comparing each program's overall performance. Programs using the two-part strategy generated between 2.36 and 2.47 times more genetic gain than the conventional program and between 1.31 and 1.46 times more genetic gain than the best performing standard genomic selection strategy. These results indicate that the two-part strategy is a cost-effective strategy for implementing genomic selection in plant breeding programs.

By 2050, the world population is likely to be 9.1 billion, the CO2 concentration 550 ppm, the ozone concentration 60 ppb and the climate warmer by ca 2°C. In these conditions, what contribution can increased crop yield make to feeding the world?CO2 enrichment is likely to increase yields of most crops by approximately 13 per cent but leave yields of C4 crops unchanged. It will tend to reduce water consumption by all crops, but this effect will be approximately cancelled out by the effect of the increased temperature on evaporation rates. In many places increased temperature will provide opportunities to manipulate agronomy to improve crop performance. Ozone concentration increases will decrease yields by 5 per cent or more.Plant breeders will probably be able to increase yields considerably in the CO2-enriched environment of the future, and most weeds and airborne pests and diseases should remain controllable, so long as policy changes do not remove too many types of crop-protection chemicals. However, soil-borne pathogens are likely to be an increasing problem when warmer weather will increase their multiplication rates; control is likely to need a transgenic approach to breeding for resistance. There is a large gap between achievable yields and those delivered by farmers, even in the most efficient agricultural systems. A gap is inevitable, but there are large differences between farmers, even between those who have used the same resources. If this gap is closed and accompanied by improvements in potential yields then there is a good prospect that crop production will increase by approximately 50 per cent or more by 2050 without extra land. However, the demands for land to produce bio-energy have not been factored into these calculations.

Drought is one of the major factors limiting the yield of sugar beet (Beta vulgaris L.). The identification of candidate genes for marker-assisted selection (MAS) could greatly improve the efficiency of breeding for increased drought tolerance. Drought-induced changes in the proteome could highlight important genes. Two genotypes of sugar beet (7112 and 7219-P.69) differing in genetic background were cultivated in the field. A line-source sprinkler irrigation system was used to apply irrigated and water deficit treatments beginning at the four-leaf stage. At 157 days after sowing, leaf samples were collected from well-watered and drought-stressed plants for protein extraction and to measure shoot biomass and leaf relative water content. Changes induced in leaf proteins were studied by two-dimensional gel electrophoresis and quantitatively analyzed using image analysis software. Out of more than 500 protein spots reproducibly detected and analyzed, 79 spots showed significant changes under drought. Some proteins showed genotype-specific patterns of up- or downregulation in response to drought. Twenty protein spots were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS), leading to identification of Rubisco and 11 other proteins involved in redox regulation, oxidative stress, signal transduction, and chaperone activities. Some of these proteins could contribute a physiological advantage under drought, making them potential targets for MAS.

Polyethylene glycol (PEG), which is often used to impose low water potentials ( w ) in solution culture, decreases O 2 movement by increasing solution viscosity. We investigated whether this property causes O 2 deficiency that affects the elongation or metabolism of maize (Zea mays L.) primary roots. Seedlings grown in vigorously aerated PEG solutions at ambient solution O 2 partial pressure (pO 2 ) had decreased steady-state root elongation rates, increased root-tip alanine concentrations, and decreased root-tip proline concentrations relative to seedlings grown in PEG solutions of above-ambient pO 2 (alanine and proline accumulation are responses to hypoxia and low w , respectively). Measurements of root pO 2 were made using an O 2 microsensor to ensure that increased solution pO 2 did not increase root pO 2 above physiological levels. In oxygenated PEG solutions that gave maximal root elongation rates, root pO 2 was similar to or less than (depending on depth in the tissue) pO 2 of roots growing in vermiculite at the same w . Even without PEG, high solution pO 2 was necessary to raise root pO 2 to the levels found in vermiculite-grown roots. Vermiculite was used for comparison because it has large air spaces that allow free movement of O 2 to the root surface. The results show that supplemental oxygenation is required to avoid hypoxia in PEG solutions. Also, the data suggest that the O 2 demand of the root elongation zone may be greater at low relative to high w , compounding the effect of PEG on O 2 supply. Under O 2 -sufficient conditions root elongation was substantially less sensitive to the low w imposed by PEG than that imposed by dry vermiculite.In studies of plant responses to water deficit, low w is often imposed by decreasing the supply of water in the soil or other solid media in which the plants are grown. Our previous studies of maize (Zea mays L.) primary root growth at low w were conducted by transplanting seedlings to vermiculite containing limited amounts of water (e.g. Sharp et al., 1988). However, in certain types of experiments there are advantages to imposing low w using osmotica in solution culture, e.g. when radiolabeled compounds must be supplied to the roots in a controlled manner. Despite its convenience, a liquid medium could potentially complicate the results because terrestrial plants such as maize do not normally grow in an environment in which the roots are surrounded by water. Solution culture has been used extensively at both high and low w , but there have been few attempts to verify that plants grown under such conditions are physiologically similar to those grown in solid media.When studying the behavior of roots at low w in solution culture, two factors are centrally important: the osmoticum used and aeration of the solution. It is desirable to use a compound that does not interact with plants in any way other than lowering the w of the medium. Thus, slowly penetrating osmotica such as mannitol or sorbitol (Hohl and Schopfer, 1991) or inorganic salts (Termaat and Munns, ...

Highlights Strategies for future high throughput, non-destructive and cost-efficient measurement of plant traits are highlighted. Use of low-cost and DIY approaches in phenomics provides opportunities for rapid prototyping and sensor development. Robust protocols, data harmonization and provenance are critical to allow data reuse and cross validation of phenotypes. Below-ground phenotyping is a major bottleneck and new technologies allowing the measurement of root-related traits are needed.