Crop yield reduction as a consequence of increasingly severe climatic events threatens global food security. Genetic loci that ensure productivity in challenging environments exist within the germplasm of crops, their wild relatives and species that are adapted to extreme environments. Selective breeding for the combination of beneficial loci in germplasm has improved yields in diverse environments throughout the history of agriculture. An effective new paradigm is the targeted identification of specific genetic determinants of stress adaptation that have evolved in nature and their precise introgression into elite varieties. These loci are often associated with distinct regulation or function, duplication and/or neofunctionalization of genes that maintain plant homeostasis.

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability.

As an essential macroelement for all living cells, phosphorus is indispensable in agricultural production systems. Natural phosphorus reserves are limited, 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. However, its functional mechanism remained elusive until the locus was sequenced, showing the presence of a Pup1-specific protein kinase gene, 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. 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.

The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency

Root system architecture: opportunities and constraints for genetic improvement of crops.

The ionome is defined as the mineral nutrient and trace element composition of an organism and represents the inorganic component of cellular and organismal systems. Ionomics, the study of the ionome, involves the quantitative and simultaneous measurement of the elemental composition of living organisms and changes in this composition in response to physiological stimuli, developmental state, and genetic modifications. Ionomics requires the application of high-throughput elemental analysis technologies and their integration with both bioinformatic and genetic tools. Ionomics has the ability to capture information about the functional state of an organism under different conditions, driven by genetic and developmental differences and by biotic and abiotic factors. The relatively high throughput and low cost of ionomic analysis means that it has the potential to provide a powerful approach to not only the functional analysis of the genes and gene networks that directly control the ionome, but also to the more extended gene networks that control developmental and physiological processes that affect the ionome indirectly. In this review we describe the analytical and bioinformatics aspects of ionomics, as well as its application as a functional genomics tool.

/pdf/ionomics-and-the-study-of-the-plant-ionome-4xqvhphg9u.pdf

Ionomics and the Study of the Plant Ionome

Genetic control of yield under reproductive-stage drought stress was studied in a population of 436 random F 3 -derived lines from a cross between the upland rice (Oryza sativa L.) cultivars Vandana and Way Rarem. Screening was conducted under upland conditions at IRRI during the dry seasons of 2005 and 2006. Lines were evaluated in drought stress and nonstress trials in both years to identify QTL contributing to drought resistance. For QTL detection, a set of random lines and the highest and lowest-yielding lines under both stress and nonstress conditions were genotyped by 126 SSR markers. A QTL (qtl12.1) with a large effect on grain yield under stress was detected on Chromosome 12 in both years. The whole population was genotyped for additional markers on Chromosome 12, allowing QTL localization to a 10.2 cM region between SSR markers RM28048 and RM511. Under stress conditions, the locus also increased harvest index, biomass yield, and plant height while reducing the number of days to flowering. Under nonstress conditions, qtl12.1 did not significantly affect any trait. The additive effect of this QTL on grain yield under stress was 172 kg ha-1 per year over the 2 yr of testing, representing 47% of the average yield under stress and explaining 51% of the genetic variance. The yield-increasing allele was derived from the susceptible parent, Way Rarem, suggesting an epistatic effect. This is the first QTL reported in rice having a large and repeatable effect on grain yield under severe drought stress in the field.

A large-effect QTL for grain yield under reproductive-stage drought stress in upland rice.

A major QTL for P uptake had previously been mapped to a 13-cM marker interval on the long arm of chromosome 12. To map that major QTL with higher precision and certainty, a secondary mapping population was developed by backcrossing a near-isogenic line containing the QTL from the donor parent to the recurrent parent of low P uptake. Two different mapping strategies have been followed in this study. A conventional QTL mapping approach was based on individual F2 RFLP data and the phenotypic evaluation of family means in the F3. The second strategy employed a substitution-mapping approach. Phenotypic and marker data were obtained for 160 F3 individuals of six highly informative families that differed in the size of donor chromosomal segments in the region of the putative QTL. QTL mapping showed that close to 80% of the variation between families was due to a single QTL, hereafter referred to as Pup1 (Phosphorus uptake 1). Pup1 was placed in a 3-cM interval flanked by markers S14025 and S13126, which is within 1 cM of the position identified in the original QTL mapping experiment. Other chromosomal regions and epistatic effects were not significant. Substitution mapping revealed that Pup1 co-segregated with marker S13126 and that the flanking markers, S14025 and S13752, were outside the interval containing Pup1. The two mapping strategies therefore yielded almost identical results and, in combining the advantages of both, Pup1 could be mapped with high certainty. The QTL mapping appoach showed that the phenotypic variation between families was due to only one QTL without any additional epistacic interactions, whereas the advantage of substitution mapping was to place clearly defined borders around the QTL.

Substitution mapping of Pup1: a major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil.

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Substitution mapping of Pup1: a major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil.