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A gene that is present in phosphate-deficiency-tolerant rice but absent from modern rice varieties is characterized and named phosphorus-starvation tolerance 1 ( PSTOL1 ); overexpression of PSTOL1 in rice species that naturally lack this gene confers tolerance to low phosphorus conditions, a finding that may have implications for agricultural productivity in rice-growing countries. Rice tolerant to low-phosphate soils Rice is a staple crop for much of Asia. Rice yields in the region are low, however, with limited availability of phosphorous fertilizers and the susceptibility of rain-fed cultivation systems to climate variation among the problems. In this study, Sigrid Heuer and colleagues report the characterization of a gene called phosphorus-starvation tolerance 1 ( PSTOL1 ), which confers tolerance to phosphorus deficiency. The gene is present in the traditional rice variety Kasalath but absent from the rice reference genome and other phosphorus-starvation-intolerant modern varieties. PSTOL1 is shown to act as an enhancer of early root growth, thereby enabling plants to acquire more phosphorus and other nutrients. Introduction of this gene into locally adapted rice varieties should enhance productivity under low-phosphorus conditions. As an essential macroelement for all living cells, phosphorus is indispensable in agricultural production systems. Natural phosphorus reserves are limited 1 , and it is therefore important to develop phosphorus-efficient crops. A major quantitative trait locus for phosphorus-deficiency tolerance, Pup1 , was identified in the traditional aus -type rice variety Kasalath about a decade ago 2 , 3 . However, its functional mechanism remained elusive 4 , 5 until the locus was sequenced, showing the presence of a Pup1 -specific protein kinase gene 6 , which we have named phosphorus-starvation tolerance 1 ( PSTOL1 ). This gene is absent from the rice reference genome and other phosphorus-starvation-intolerant modern varieties 7 , 8 . Here we show that overexpression of PSTOL1 in such varieties significantly enhances grain yield in phosphorus-deficient soil. Further analyses show that PSTOL1 acts as an enhancer of early root growth, thereby enabling plants to acquire more phosphorus and other nutrients. The absence of PSTOL1 and other genes—for example, the submergence-tolerance gene SUB1A —from modern rice varieties underlines the importance of conserving and exploring traditional germplasm. Introgression of this quantitative trait locus into locally adapted rice varieties in Asia and Africa is expected to considerably enhance productivity under low phosphorus conditions.

A substantial increase in grain yield potential is required, along with better use of water and fertilizer, to ensure food security and environmental protection in future decades. For improvements in photosynthetic capacity to result in additional wheat yield, extra assimilates must be partitioned to developing spikes and grains and/or potential grain weight increased to accommodate the extra assimilates. At the same time, improvement in dry matter partitioning to spikes should ensure that it does not increase stem or root lodging. It is therefore crucial that improvements in structural and reproductive aspects of growth accompany increases in photosynthesis to enhance the net agronomic benefits of genetic modifications. In this article, six complementary approaches are proposed, namely: (i) optimizing developmental pattern to maximize spike fertility and grain number, (ii) optimizing spike growth to maximize grain number and dry matter harvest index, (iii) improving spike fertility through desensitizing floret abortion to environmental cues, (iv) improving potential grain size and grain filling, and (v) improving lodging resistance. Since many of the traits tackled in these approaches interact strongly, an integrative modelling approach is also proposed, to (vi) identify any trade-offs between key traits, hence to define target ideotypes in quantitative terms. The potential for genetic dissection of key traits via quantitative trait loci analysis is discussed for the efficient deployment of existing variation in breeding programmes. These proposals should maximize returns in food production from investments in increased crop biomass by increasing spike fertility, grain number per unit area and harvest index whilst optimizing the trade-offs with potential grain weight and lodging resistance.

When plants go halves: haploids made easy Haploid plants, inheriting chromosomes from one parent only, have important advantages in genetic research but also crucially in plant breeding, where they are used to create instant homozygous diploid lines, circumventing many generations of inbreeding. Maruthachalam Ravi and Simon Chan have now developed a simple method for producing haploid Arabidopsis thaliana via seeds that can be readily extended to crop plants. Previously haploid production involved tissue culture or genome elimination in wide crosses, and many species are intractable to these methods. The new technique involves engineering a single protein, the centromere-specific histone CENH3, to create strains whose genome is eliminated from the zygote after crossing to wild type. This generates haploid plants with chromosomes from the wild-type parent only. CENH3 plays a universal role at eukaryote centromeres, so in principle this should be transferable to all plant species. Making haploid plants — which inherit chromosomes from only one parent — is useful for genetic research and also, crucially, for plant breeding. A new method for generating haploid Arabidopsis plants is now described, involving the manipulation of a single centromeric protein, CENH3. When cenh3 null plants are crossed with wild-type plants, the mutant chromosomes are eliminated, producing haploid progeny. Production of haploid plants that inherit chromosomes from only one parent can greatly accelerate plant breeding 1 , 2 , 3 . Haploids generated from a heterozygous individual and converted to diploid create instant homozygous lines, bypassing generations of inbreeding. Two methods are generally used to produce haploids. First, cultured gametophyte cells may be regenerated into haploid plants 4 , but many species and genotypes are recalcitrant to this process 2 , 5 . Second, haploids can be induced from rare interspecific crosses, in which one parental genome is eliminated after fertilization 6 , 7 , 8 , 9 , 10 , 11 . The molecular basis for genome elimination is not understood, but one theory posits that centromeres from the two parent species interact unequally with the mitotic spindle, causing selective chromosome loss 12 , 13 , 14 . Here we show that haploid Arabidopsis thaliana plants can be easily generated through seeds by manipulating a single centromere protein, the centromere-specific histone CENH3 (called CENP-A in human). When cenh3 null mutants expressing altered CENH3 proteins are crossed to wild type, chromosomes from the mutant are eliminated, producing haploid progeny. Haploids are spontaneously converted into fertile diploids through meiotic non-reduction, allowing their genotype to be perpetuated. Maternal and paternal haploids can be generated through reciprocal crosses. We have also exploited centromere-mediated genome elimination to convert a natural tetraploid Arabidopsis into a diploid, reducing its ploidy to simplify breeding. As CENH3 is universal in eukaryotes, our method may be extended to produce haploids in any plant species.

The narrow genetic base of elite Upland cotton (Gossypium hirsutum L.) germplasm has been a significant impediment to sustained progress in the development of cotton cultivars to meet the needs of growers and industry in recent years. The prospect of widening the genetic base of Upland cotton by accessing the genetic diversity and fiber quality of Pima cotton (Gossypium barbadense L.) has encouraged interspecific hybridization and introgression efforts for the past century. However, success is limited due mainly to genetic barriers between the two species in the forms of divergent gene regulatory systems, accumulated gene mutations, gene order rearrangements and cryptic chromosomal structure differences that have resulted in hybrid breakdown, hybrid sterility and selective elimination of genes. The objective of this paper is to provide a mini-review in interspecific hybridization between Upland and Pima cotton relevant to breeding under the following sections: (1) qualitative genetics; (2) cytogenetic stocks; (3) quantitative genetics; (4) heterosis, and (5) introgression breeding. Case studies of successful examples are provided.

The use of crop wild relatives (CWR) genes to improve crop performance is well established with important examples dating back more than 60 years. In this paper, we review available information on the presence of genes from CWR in released cultivars of 16 mandate crops of the CGIAR institutes, and some selected additional crops, focusing on the past 20 years--the period since a comprehensive review by Robert and Christine Prescott-Allen in 1986. It appears that there has been a steady increase in the rate of release of cultivars containing genes from CWR. While there continues to be a strong emphasis on using pest and disease resistance genes, a wider range of characteristics are being introduced than in the past. Those crops whose wild relatives have traditionally been used as sources of useful traits (e.g., wheat, tomato) continue to be most likely to include new genes from their wild relatives. CWR are continually gaining in importance and prevalence, but, we argue, their contributions to the development of new cultivars remain less than might have been expected given improved procedures for intercrossing species from different gene pools, advances in molecular methods for managing backcrossing programes, increased numbers of wild species accessions in gene banks, and the substantial literature on beneficial traits associated with wild relatives.

Heterosis (or hybrid vigor) is a natural phenomenon whereby hybrid offspring of genetically diverse individuals display improved physical and functional characteristics relative to their parents. Heterosis has been increasingly applied in crop production for nearly a century, with the aim of developing more vigorous, higher yielding and better performing cultivars. In this review we present and compare three categories of crop heterosis utilization: intraspecific heterosis, intersubspecific heterosis and wide-hybridization heterosis, with particular focus on polyploid species. Different pollination-control systems used to breed for heterosis are also comparatively analyzed. Finally, we highlight problems involved in heterosis research and crop improvement. We aim to provide insight into best practices for amplifying heterosis potential.

To unravel the molecular mechanisms of drought responses in tomato, gene expression profiles of two drought-tolerant lines identified from a population of Solanum pennellii introgression lines, and the recurrent parent S. lycopersicum cv. M82, a drought-sensitive cultivar, were investigated under drought stress using tomato microarrays. Around 400 genes identified were responsive to drought stress only in the drought-tolerant lines. These changes in genes expression are most likely caused by the two inserted chromosome segments of S. pennellii, which possibly contain drought-tolerance quantitative trait loci (QTLs). Among these genes are a number of transcription factors and signalling proteins which could be global regulators involved in the tomato responses to drought stress. Genes involved in organism growth and development processes were also specifically regulated by drought stress, including those controlling cell wall structure, wax biosynthesis, and plant height. Moreover, key enzymes in the pathways of gluconeogenesis (fructose-bisphosphate aldolase), purine and pyrimidine nucleotide biosynthesis (adenylate kinase), tryptophan degradation (aldehyde oxidase), starch degradation (β-amylase), methionine biosynthesis (cystathionine β-lyase), and the removal of superoxide radicals (catalase) were also specifically affected by drought stress. These results indicated that tomato plants could adapt to water-deficit conditions through decreasing energy dissipation, increasing ATP energy provision, and reducing oxidative damage. The drought-responsive genes identified in this study could provide further information for understanding the mechanisms of drought tolerance in tomato.

To understand the physiological basis of genetic variation and resulting quantitative trait loci (QTLs) for photosynthesis in a rice (Oryza sativa L.) introgression line population, 13 lines were studied under drought and well-watered conditions, at flowering and grain filling. Simultaneous gas exchange and chlorophyll fluorescence measurements were conducted at various levels of incident irradiance and ambient CO2 to estimate parameters of a model that dissects photosynthesis into stomatal conductance (g s), mesophyll conductance (g m), electron transport capacity (J max), and Rubisco carboxylation capacity (V cmax). Significant genetic variation in these parameters was found, although drought and leaf age accounted for larger proportions of the total variation. Genetic variation in light-saturated photosynthesis and transpiration efficiency (TE) were mainly associated with variation in g s and g m. One previously mapped major QTL of photosynthesis was associated with variation in g s and g m, but also in J max and V cmax at flowering. Thus, g s and g m, which were demonstrated in the literature to be responsible for environmental variation in photosynthesis, were found also to be associated with genetic variation in photosynthesis. Furthermore, relationships between these parameters and leaf nitrogen or dry matter per unit area, which were previously found across environmental treatments, were shown to be valid for variation across genotypes. Finally, the extent to which photosynthesis rate and TE can be improved was evaluated. Virtual ideotypes were estimated to have 17.0% higher photosynthesis and 25.1% higher TE compared with the best genotype investigated. This analysis using introgression lines highlights possibilities of improving both photosynthesis and TE within the same genetic background.

Among the reproductive barriers that can isolate species, hybrid sterility is frequently due to dysfunctional interactions between loci that accumulate between differentiating lineages. Theory describing the evolution of these incompatibilities has generated the prediction, still empirically untested, that loci underlying hybrid incompatibility should accumulate faster than linearly with time— the \"snowball effect.\" We evaluated the accumulation of quantitative trait loci (OTL) between spedes in the plant group Solanum and found evidence for a faster-than-linear accumulation of hybrid seed sterility QTL, thus empirically evaluating and confirming this theoretical prediction. In comparison, loci underlying traits unrelated to hybrid sterility show no evidence for an accelerating rate of accumulation between species.

Hybridization between species can lead to introgression of genes from one species to another, providing a potential mechanism for preserving and recombining key traits during evolution. To determine the molecular basis of such transfers, we analyzed a natural polymorphism for flower-head development in SENECIO: We show that the polymorphism arose by introgression of a cluster of regulatory genes, the RAY locus, from the diploid species S. squalidus into the tetraploid S. vulgaris. The RAY genes are expressed in the peripheral regions of the inflorescence meristem, where they promote flower asymmetry and lead to an increase in the rate of outcrossing. Our results highlight how key morphological and ecological traits controlled by regulatory genes may be gained, lost, and regained during evolution.