The eating and cooking qualities of rice grains are the major determinants of consumer preference and, consequently, the economic value of a specific rice variety. These two qualities are largely determined by the physicochemical properties of the starch, i.e. the starch composition, of the rice grain. In our study, we determined the genetic factors responsible for the physicochemical properties of starch in recombinant inbred lines (RILs) of japonica cv. Tainung 78 × indica cv. Taichung Sen 17 (TCS 17) cultivated over two crop seasons by examining palatability characteristics and several Rapid Viscosity Analyzer (RVA) parameters. Thirty-four quantitative trait loci (QTLs), each explaining between 1.2 and 78.1 % phenotypic variation, were mapped in clusters on eight chromosomes in 190 RILs genotyped with 139 markers. Ten pairs of QTLs were detected in the two environments, of which seven were in agreement with previous findings, suggesting that these QTLs may express stable experimental populations across various environments. Waxy (Wx), which controls amylose synthesis, was determined to be a primary gene regulating the physicochemical properties of cooked rice grains, as indicated by the presence of a major QTL cluster on chromosome 6 and by marker regression analysis. Six starch synthesis-related genes (SSRGs) which were located in the QTL intervals significantly differed in terms of gene expression between the two parents during grain-filling and were important genetic factors affecting physicochemical properties. The expression of four genes, PUL, ISA2, GBSSI, and SSII-3, was significantly upregulated in TCS 17, and this expression was positively correlated with six traits. The effects of the six SSRGs and gene interaction depended on genetic background and environment; grain quality may be fine tuned by selecting for SBE4 for japonica and PUL for indica. We provide valuable information for application in the breeding of new rice varieties as daily staple food and for use in industrial manufacturing by marker-assisted selection.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-014-0065-8) contains supplementary material, which is available to authorized users.

While many tropical plants have been adapted to temperate cultivation, few temperate plants have been adapted to the tropics. Originating in Western Europe, Brassica oleracea vernalization requires a period of low temperature and BoFLC2 regulates the transition to floral development. In B. oleracea germplasm selected in Taiwan, a non-vernalization pathway involving BoFLC3 rather than BoFLC2 regulates curd induction. In 112 subtropical breeding lines, specific haplotype combinations of BoFLC3 and PAN (involved in floral organ identity and a positional candidate for additional curd induction variation) adapt B. oleracea to high ambient temperature and short daylength. Duplicated genes permitted evolution of alternative pathways for control of flowering in temperate and tropical environments, a principle that might be utilized via natural or engineered approaches in other plants. New insight into regulation of Brassica flowering exemplifies translational agriculture, tapping knowledge of botanical models to improve food security under projected climate change scenarios.

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New research frameworks that simultaneously address production and environmental goals are required to identify promising sustainable intensification options in high-yielding cereal systems. Here we estimated potential changes in environmental footprint associated with crop management practices aimed at breaking the yield ceiling for rice production in Uruguay. Results from a regional survey were combined with field experiments to integrate impacts on productivity and sustainability at two different intensification levels (average-yielding and high-yielding). Survey results indicate that high-yielding farmers produced 14% more grain compare to the regional average (7900 kg ha−1), with 25% to 99% lower agrochemical contamination risk and similar nitrogen use efficiency and carbon footprint. In on-farm trials, the alternative management practices increased yield beyond that of high-yielding farmers by up to 7% in small plots (8 site-years) and 15% in field-scale comparisons (6 site-years), yet an ex post assessment of environmental indicators shows significant decline of resource use efficiencies and increased carbon footprint. Thus, yield gains were not able to compensate for increased environmental footprint, highlighting the challenge of advancing the dual goals of SI in production systems nearing the yield ceiling. This study provides a simple but powerful framework for advancing SI in mainstream cereal production systems based on cost-effective modifications to existing agronomic experiments.

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