Tim L. Setter

Comparative Transcriptional Profiling of Placenta and Endosperm in Developing Maize Kernels in Response to Water Deficit

The early post-pollination phase of maize (Zea mays) development is particularly sensitive to water deficit stress. Using cDNA microarray, we studied transcriptional profiles of endosperm and placenta/pedicel tissues in developing maize kernels under water stress. At 9 d after pollination (DAP), placenta/pedicel and endosperm differed considerably in their transcriptional responses. In placenta/pedicel, 79 genes were significantly affected by stress and of these 89% were up-regulated, whereas in endosperm, 56 genes were significantly affected and 82% of these were down-regulated. Only nine of the stress-regulated genes were in common between these tissues. Hierarchical cluster analysis indicated that different sets of genes were regulated in the two tissues. After rewatering at 9 DAP, profiles at 12 DAP suggested that two regulons exist, one for genes responding specifically to concurrent imposition of stress, and another for genes remaining affected after transient stress. In placenta, genes encoding recognized stress tolerance proteins, including heat shock proteins, chaperonins, and major intrinsic proteins, were the largest class of genes regulated, all of which were up-regulated. In contrast, in endosperm, genes in the cell division and growth category represented a large class of down-regulated genes. Several cell wall-degrading enzymes were expressed at lower levels than in controls, suggesting that stress delayed normal advance to programmed cell death in the central endosperm. We suggest that the responsiveness of placenta to whole-plant stress factors (water potential, abscisic acid, and sugar flux) and of endosperm to indirect factors may play key roles in determining the threshold for kernel abortion.

Agricultural use of wetlands: opportunities and limitations

BACKGROUND Wetlands are species-rich habitats performing valuable ecosystem services such as flood protection, water quality enhancement, food chain support and carbon sequestration. Worldwide, wetlands have been drained to convert them into agricultural land or industrial and urban areas. A realistic estimate is that 50 % of the worlds wetlands have been lost. SCOPE This paper reviews the relationship between wetlands and agriculture with the aim to identify the successes and failures of agricultural use in different types of wetlands, with reference to short-term and long-term benefits and issues of sustainability. It also addresses a number of recent developments which will lead to pressure to reclaim and destroy natural wetlands, i.e. the continuous need for higher production to feed an increasing world population and the increasing cultivation of energy crops. Finally, attention is paid to the development of more flood-tolerant crop cultivars. CONCLUSIONS Agriculture has been carried out in several types of (former) wetlands for millennia, with crop fields on river floodplain soils and rice fields as major examples. However, intensive agricultural use of drained/reclaimed peatlands has been shown to lead to major problems because of the oxidation and subsidence of the peat soil. This does not only lead to severe carbon dioxide emissions, but also results in low-lying land which needs to be protected against flooding. Developments in South-East Asia, where vast areas of tropical peatlands are being converted into oil palm plantations, are of great concern in this respect. Although more flood-tolerant cultivars of commercial crop species are being developed, these are certainly not suitable for cultivation in wetlands with prolonged flooding periods, but rather will survive relatively short periods of waterlogging in normally improved agricultural soils. From a sustainability perspective, reclamation of peatlands for agriculture should be strongly discouraged. The opportunities for agriculture in naturally functioning floodplains should be further investigated. The development and use of crop cultivars with an even stronger flood tolerance could form part of the sustainable use of such floodplain systems. Extensive use of wetlands without drastic reclamation measures and without fertilizer and pesticides might result in combinations of food production with other wetland services, with biodiversity remaining more or less intact. There is a need for research by agronomists and environmental scientists to optimize such solutions.

Role of Auxin in Maize Endosperm Development (Timing of Nuclear DNA Endoreduplication, Zein Expression, and Cytokinin)

The timing of developmental events and regulatory roles of auxin were examined in maize (Zea mays L.) endosperms. Zeatin, zeatin riboside, and indole-3-acetic acid (IAA) levels were determined by enzyme-linked immunosorbent (ELISA). Zeatin and zeatin riboside increased to maximal concentrations at an early stage (9 d after pollination [DAP]), corresponding to the stage when cell division rate was maximal. In contrast, IAA concentration was low at 9 DAP and abruptly increased from 9 to 11 DAP, thus creating a sharp decline in the cytokinin to auxin ratio. Coincident with the increase in IAA was an increase in DNA content per nucleus, attributed to postmitotic DNA replication via endoreduplication. Exogenous application of 2,4-dichlorophenoxyacetic acid (2,4-D) at 5 or 7 DAP hastened the time course of DNA accumulation per nucleus and increased the average nuclear diameter, whereas 2-(para-chlorophenoxy)isobutyric acid delayed such development. Exogenously applied 2,4-D hastened the accumulation of the zein polypeptides of apparent molecular masses of 12, 14, and 16 kD and the expression of mRNA hybridizing with a zein DNA probe. We conclude that an abrupt increase in auxin induces cellular differentiation events in endosperm, including endoredupliction and expression of particular zein storage proteins.

Drought Tolerance in Maize

Drought is the single most common cause of severe crop production shortage in developing countries, and global warming is predicted to further exacerbate droughts impact. This chapter describes how to best evaluate segregating germplasm under water-limited conditions, what are the secondary traits to be included in the selection and why is it important to identify key regulatory genes involved in selected metabolic pathways and signaling. The chapter also summarizes the current understanding of the genetic basis for drought tolerance. From this review, one can project that sustained progress in breeding for drought tolerance in maize is likely to entail the selection of plants with a reduced leaf area (especially in the upper part of the plant), short thick stems, small tassels, erect leaves, delayed senescence, smaller root biomass, and a deep root system with little lateral root branching. Tolerant genotypes are also expected to have robust spikelet and kernel growth at the cell-division and expansion-growth phases, with good osmotic adjustment to assist in cell retention of water during drought. In this way, root and ear growth is not completely inhibited, and leaf survival is enhanced despite limited water. Extensive genetic dissections of drought tolerance traits have been carried out in maize over the last decade, yielding numerous QTL involved in the determination of morphological traits and regularoty pathways. A better understanding of the physiological mechanisms and the genetic basis of the response of maize to drought should make it increasingly feasible and efficient to stack favorable alleles at key genes, so as to select for genotypes that will develop phenotypes described above. The final section of this chapter focuses on the genetic gains achieved in maize via an interdisciplinary approach, and includes an exploration of new strategies combining marker-assisted breeding and phenotyping selection to accelerate drought tolerance breeding in maize.

Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought

In maize, water stress at flowering causes loss of kernel set and productivity. While changes in the levels of sugars and abscisic acid (ABA) are thought to play a role in this stress response, the mechanistic basis and genes involved are not known. A candidate gene approach was used with association mapping to identify loci involved in accumulation of carbohydrates and ABA metabolites during stress. A panel of single nucleotide polymorphisms (SNPs) in genes from these metabolic pathways and in genes for reproductive development and stress response was used to genotype 350 tropical and subtropical maize inbred lines that were well watered or water stressed at flowering. Pre-pollination ears, silks, and leaves were analysed for sugars, starch, proline, ABA, ABA-glucose ester, and phaseic acid. ABA and sugar levels in silks and ears were negatively correlated with their growth. Association mapping with 1229 SNPs in 540 candidate genes identified an SNP in the maize homologue of the Arabidopsis MADS-box gene, PISTILLATA, which was significantly associated with phaseic acid in ears of well-watered plants, and an SNP in pyruvate dehydrogenase kinase, a key regulator of carbon flux into respiration, that was associated with silk sugar concentration. An SNP in an aldehyde oxidase gene was significantly associated with ABA levels in silks of water-stressed plants. Given the short range over which decay of linkage disequilibrium occurs in maize, the results indicate that allelic variation in these genes affects ABA and carbohydrate metabolism in floral tissues during drought.

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.

A GH3-like gene, CcGH3, isolated from Capsicum chinense L. fruit is regulated by auxin and ethylene*

Auxin, which has been implicated in multiple biochemical and physiological processes, elicits three classes of genes (Aux/IAAs, SAURs and GH3s) that have been characterized by their early or primary responses to the hormone. A new GH3-like gene was identified from a suppressive subtraction hybridization (SSH) library of pungent pepper (Capsicum chinense L.) cDNAs. This gene, CcGH3, possessed several auxin- and ethylene-inducible elements in the putative promoter region. Upon further investigation, CcGH3 was shown to be auxin-inducible in shoots, flower buds, sepals, petals and most notably ripening and mature pericarp and placenta. Paradoxically, this gene was expressed in fruit when auxin levels were decreasing, consistent with ethylene-inducibility. Further experiments demonstrated that CcGH3 was induced by endogenous ethylene, and that transcript accumulation was inhibited by 1-methylcyclopropene, an inhibitor of ethylene perception. When over-expressed in tomato, CcGH3 hastened ripening of ethylene-treated fruit. These results implicate CcGH3 as a factor in auxin and ethylene regulation of fruit ripening and suggest that it may be a point of intersection in the signaling by these two hormones.

Phenotypic approaches to drought in cassava: review

Cassava is an important crop in Africa, Asia, Latin America, and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12–18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance breeding.

Regulation of endoreduplication in maize (Zea mays L.) endosperm. Isolation of a novel B1-type cyclin and its quantitative analysis

To investigate the involvement of cyclin in mitotic and endoreduplicative cell cycle control, we have isolated a mitotic cyclin clone from a maize endosperm cDNA library. The deduced amino acid sequence of this clone identifies a novel B1-type cyclin with distinctly different sequence in regions with putative involvement in intracellular localization. This cyclin, designated Zeama;CycB1;3 (CycZme1), was shown by RNA gel blots and quantitative RT-PCR to be specific for tissues engaging in cell proliferation. It accumulated in metaphase-arrested cells and declined rapidly upon release into G1 phase. During the transition from mitosis to endoreduplication in maize endosperm, CycZme1 transcript declined precipitously while transcripts associated with S phase (histone-H3 and PCNA) and multiple phases of the cell cycle (Cdc2, α-tubulin) remained at moderate to high levels. We conclude that CycZme1 down-regulation is involved in the cellular transition to endoreduplication.

Field-Based High-Throughput Plant Phenotyping Reveals the Temporal Patterns of Quantitative Trait Loci Associated with Stress-Responsive Traits in Cotton

The application of high-throughput plant phenotyping (HTPP) to continuously study plant populations under relevant growing conditions creates the possibility to more efficiently dissect the genetic basis of dynamic adaptive traits. Toward this end, we employed a field-based HTPP system that deployed sets of sensors to simultaneously measure canopy temperature, reflectance, and height on a cotton (Gossypium hirsutum L.) recombinant inbred line mapping population. The evaluation trials were conducted under well-watered and water-limited conditions in a replicated field experiment at a hot, arid location in central Arizona, with trait measurements taken at different times on multiple days across 2010–2012. Canopy temperature, normalized difference vegetation index (NDVI), height, and leaf area index (LAI) displayed moderate-to-high broad-sense heritabilities, as well as varied interactions among genotypes with water regime and time of day. Distinct temporal patterns of quantitative trait loci (QTL) expression were mostly observed for canopy temperature and NDVI, and varied across plant developmental stages. In addition, the strength of correlation between HTPP canopy traits and agronomic traits, such as lint yield, displayed a time-dependent relationship. We also found that the genomic position of some QTL controlling HTPP canopy traits were shared with those of QTL identified for agronomic and physiological traits. This work demonstrates the novel use of a field-based HTPP system to study the genetic basis of stress-adaptive traits in cotton, and these results have the potential to facilitate the development of stress-resilient cotton cultivars.