Rice is a crop prone to drought stress in upland and rainfed lowland ecosystems. A deep root system is recognized as the best drought avoidance mechanism. Genome-wide association mapping offers higher resolution for locating quantitative trait loci (QTLs) than QTL mapping in biparental populations. We performed an association mapping study for root traits using a panel of 167 japonica accessions, mostly of tropical origin. The panel was genotyped at an average density of one marker per 22.5 kb using genotyping by sequencing technology. The linkage disequilibrium in the panel was high (r2>0.6, on average, for 20 kb mean distances between markers). The plants were grown in transparent 50 cm × 20 cm × 2 cm Plexiglas nailboard sandwiches filled with 1.5 mm glass beads through which a nutrient solution was circulated. Root system architecture and biomass traits were measured in 30-day-old plants. The panel showed a moderate to high diversity in the various traits, particularly for deep (below 30 cm depth) root mass and the number of deep roots. Association analyses were conducted using a mixed model involving both population structure and kinship to control for false positives. Nineteen associations were significant at P<1e-05, and 78 were significant at P<1e-04. The greatest numbers of significant associations were detected for deep root mass and the number of deep roots, whereas no significant associations were found for total root biomass or deep root proportion. Because several QTLs for different traits were co-localized, 51 unique loci were detected; several co-localized with meta-QTLs for root traits, but none co-localized with rice genes known to be involved in root growth. Several likely candidate genes were found in close proximity to these loci. Additional work is necessary to assess whether these markers are relevant in other backgrounds and whether the genes identified are robust candidates.

Cotton fiber properties are essential predictors of yarn performance. The suite of fiber quality traits that collectively affect the utility of the fiber for the textile industry include the length, the strength, the fineness and the color. These properties have been shown to be moderately to highly heritable. In an attempt to overcome the limitations of conventional breeding we undertook a marker‐assisted selection program aimed at introgressing fiber quality QTLs from Gossypium barbadense L. into G. hirsutum L. We describe the QTL analysis of 11 fiber properties measured on three phenotypic data sets. The three populations studied were the 1st (BC1) and 2nd (BC2 and BC2S1) backcross generations derived from the cross between ‘Guazuncho 2’, G. hirsutum, and ‘VH8’, G. barbadense Collectively we detected 80 QTLs, of which 50 surpassed the permutation‐based LOD thresholds (3.2–5.7). The most economically important traits, length (two correlated properties), strength, fineness (four properties), and color (two properties) were influenced by 15, 12, 21, and 16 QTLs, respectively, that could be detected in one or more populations. As expected, for the majority of QTLs, the favorable alleles came from the G. barbadense parent. Altogether one third (26) of the QTLs confirmed the map position and phenotypic effect of QTLs reported in the literature also detected in interspecific G. hirsutum × G. barbadense populations. Cases of colocalization of QTLs for different traits were more frequent than isolated positioning. Taking these QTL‐rich chromosomal regions into consideration, 19 regions on 15 different chromosomes, were identified as target regions for the marker‐assisted introgression strategy.

In greenhouse experiments, Aychade, a fragrant rice variety, was grown under one level of salt solution (EC of 3800 ± 400 μS·cm(-1)) sufficient to induce salt stress in rice. Timing and duration of salt solution application varied according to the growth stages. 2-Acetyl-1-pyrroline (2AP), a characteristic flavor compound of fragrant rice as well as biogenetically related compounds, proline, and γ-aminobutyric acid (GABA) were quantified. Salt treatments induced 2AP synthesis in the leaves, but the increase was often higher in the vegetative phase. This increase was correlated with proline level but not with that of GABA. Interestingly the grains from all the salt treated plants contained significantly higher levels of 2AP (733-998 μg·kg(-1)) than those from the control (592 μg·kg(-1)). The highest 2AP synthesis occurred when the plants were subjected to salt treatment during whole vegetative or reproductive phases. However in the latter case crop yield decreased significantly.