PhenoRoots: an inexpensive non-invasive phenotyping system to assess the variability of the root system architecture

The root system architecture (RSA) of plants and its functioning play a fundamental role in a number of plant growth mechanisms including water and nutrient uptake. Optimization of the RSA is important for stable and increased plant productivity under adverse conditions. Despite its great importance, studying the RSA is notoriously laborious because of the difficulty of accessing the rooting system of plants. We developed a root phenotyping platform, PhenoRoots, which allows for the non-invasive study of plant RSA. The system was built using inexpensive material and was designed to provide medium throughput. Substrate or soil-filled rhizotrons are used to grow plantlets, whose roots are directly visible through a glass plate. An experiment conducted on a panel of twenty Upland cotton (Gossypium hirsutum L.) varieties demonstrated the usefulness of the platform in assessing RSA traits. A number of traits, destructive and non-destructive, related to the RSA were measured and statistically analyzed. The non-destructive traits based on image analysis of roots were more accurate and showed high correlation with the time-consuming destructive measurements. The platform allowed for capturing the phenotypic and genetic variability found in the panel of cotton varieties, and to define three contrasting RSA patterns. PhenoRoots provides an inexpensive alternative to the medium throughput analysis of RSA traits in plants.(AU)

PhenoRoots: an inexpensive non-invasive phenotyping system to assess the variability of the root system architecture

The root system architecture (RSA) of plants and its functioning play a fundamental role in a number of plant growth mechanisms including water and nutrient uptake. Optimization of the RSA is important for stable and increased plant productivity under adverse conditions. Despite its great importance, studying the RSA is notoriously laborious because of the difficulty of accessing the rooting system of plants. We developed a root phenotyping platform, PhenoRoots, which allows for the non-invasive study of plant RSA. The system was built using inexpensive material and was designed to provide medium throughput. Substrate or soil-filled rhizotrons are used to grow plantlets, whose roots are directly visible through a glass plate. An experiment conducted on a panel of twenty Upland cotton (Gossypium hirsutum L.) varieties demonstrated the usefulness of the platform in assessing RSA traits. A number of traits, destructive and non-destructive, related to the RSA were measured and statistically analyzed. The non-destructive traits based on image analysis of roots were more accurate and showed high correlation with the time-consuming destructive measurements. The platform allowed for capturing the phenotypic and genetic variability found in the panel of cotton varieties, and to define three contrasting RSA patterns. PhenoRoots provides an inexpensive alternative to the medium throughput analysis of RSA traits in plants.

Anatomía comparada de plantas de Dioscorea alata L. clon Caraqueño cultivadas en tres ambientes de crecimiento in vitro / Compared anatomy of Dioscorea alata L. clone Caraqueño plants cultivated in three in vitro growth environments

La conservación in vitro de Dioscorea alata L. clon Caraqueño es fundamental para garantizar la propagación y distribución de material de plantación sano a los productores, y disponer de un banco in vitro de un clon de gran valor agronómico y comercial en la región oriental de Cuba. Con el fin de evaluar las modificaciones anatómicas que se producen en plantas de ñame en tres condiciones de cultivo in vitro: plantas conservadas por métodos de mínimo crecimiento, plantas regeneradas y plantas en fase de multiplicación en el medio MS 75 %, se realizó un análisis de la anatomía foliar y caulinar a partir de cortes transversales de la lámina foliar y del tallo, y cortes longitudinales y transversales de microtubérculos formados durante el proceso de conservación. Las hojas de las plantas conservadas mostraron menor espesor del mesófilo y la epidermis y el área de los haces conductores del tallo también fue menor, debido al proceso de stress durante la conservación in vitro. Sin embargo, durante la recuperación del material conservado a través de la regeneración y la multiplicación in vitro se restablecieron de manera normal estos parámetros. También se evidenció que los microtubérculos formados en la conservación in vitro, poseen parénquima amilífero con abundantes gránulos de almidón, capa delgada de parénquima cortical, y haces conductores poco desarrollados, todo lo cual indica la presencia de actividad meristemática.

The in vitro conservation of Dioscorea alata L. clone Caraqueño is fundamental to guarantee the propagation and distribution of healthy plantation material to the farmers and the establishment of one in vitro bank of this clone of great agronomic and commercial value in the Oriental Region of Cuba. With the purpose of evaluating the anatomical modifications that take place in yam plants under three in vitro culture conditions: conserved plants by slow growth, regenerated plants and in plants multiplication phase in MS 75% medium, was carried out an analysis of the foliar and caulinar anatomy from transversal cuts of the foliar sheet and of the stem, and longitudinal and transversal cuts of microtubers formed during the conservation process. Smaller thickness of the mesophyll and of the epidermis in the leaves of the conserved plants were showed and the conductive sheaves area of the stem were also smaller, due to the stress process during the in vitro conservation. However during the recovery of the conserved material through the regeneration and the in vitro multiplication were reestablished to their normal state these parameters. It was also evidenced that the microtubers formed in the in vitro conservation, have reserve parenchyma with abundant starch granules, thin cortical parenchyma and conductive sheaves little developed were determined. All this characteristics indicated the presence of meristematic activity.

Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars.

BACKGROUND: Drought is a widespread limiting factor in coffee plants. It affects plant development, fruit production, bean development and consequently beverage quality. Genetic diversity for drought tolerance exists within the coffee genus. However, the molecular mechanisms underlying the adaptation of coffee plants to drought are largely unknown. In this study, we compared the molecular responses to drought in two commercial cultivars (IAPAR59, drought-tolerant and Rubi, drought-susceptible) of Coffea arabica grown in the field under control (irrigation) and drought conditions using the pyrosequencing of RNA extracted from shoot apices and analysing the expression of 38 candidate genes. RESULTS: Pyrosequencing from shoot apices generated a total of 34.7 Mbp and 535,544 reads enabling the identification of 43,087 clusters (41,512 contigs and 1,575 singletons). These data included 17,719 clusters (16,238 contigs and 1,575 singletons) exclusively from 454 sequencing reads, along with 25,368 hybrid clusters assembled with 454 sequences. The comparison of DNA libraries identified new candidate genes (n = 20) presenting differential expression between IAPAR59 and Rubi and/or drought conditions. Their expression was monitored in plagiotropic buds, together with those of other (n = 18) candidates genes. Under drought conditions, up-regulated expression was observed in IAPAR59 but not in Rubi for CaSTK1 (protein kinase), CaSAMT1 (SAM-dependent methyltransferase), CaSLP1 (plant development) and CaMAS1 (ABA biosynthesis). Interestingly, the expression of lipid-transfer protein (nsLTP) genes was also highly up-regulated under drought conditions in IAPAR59. This may have been related to the thicker cuticle observed on the abaxial leaf surface in IAPAR59 compared to Rubi. CONCLUSIONS: The full transcriptome assembly of C. arabica, followed by functional annotation, enabled us to identify differentially expressed genes related to drought conditions. Using these data, candidate genes were selected and their differential expression profiles were confirmed by qPCR experiments in plagiotropic buds of IAPAR59 and Rubi under drought conditions. As regards the genes up-regulated under drought conditions, specifically in the drought-tolerant IAPAR59, several corresponded to orphan genes but also to genes coding proteins involved in signal transduction pathways, as well as ABA and lipid metabolism, for example. The identification of these genes should help advance our understanding of the genetic determinism of drought tolerance in coffee.