Genome-wide association mapping for root cone angle in rice.

BACKGROUND: Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. Two genes, DRO1 and SOR1, and several QTLs for root cone angle have been discovered in the last 5 years. RESULTS: To find other QTLs linked to root cone angle, a genome-wide association mapping study was conducted on two panels of 162 indica and 169 japonica rice accessions genotyped with two sets of SNP markers (genotyping-by-sequencing set with approximately 16,000 markers and high-density-rice-array set with approximately 300,000 markers). The root cone angle of all accessions was measured using a screen protractor on images taken after 1 month of plant growth in the Rhizoscope phenotyping system. The distribution of the root cone angle in the indica panel was Gaussian, but several accessions of the japonica panel (all the bulus from Indonesia and three temperate japonicas from Nepal or India) appeared as outliers with a very wide root cone angle. The data were submitted to association mapping using a mixed model with control of structure and kinship. A total of 15 QTLs for the indica panel and 40 QTLs for the japonica panel were detected. Genes underlying these QTLs (+/-50 kb from the significant markers) were analyzed. We focused our analysis on auxin-related genes, kinases, and genes involved in root developmental processes and identified 8 particularly interesting genes. CONCLUSIONS: The present study identifies new sources of wide root cone angle in rice, proposes ways to bypass some drawbacks of association mapping to further understand the genetics of the trait and identifies candidate genes deserving further investigation.

Rice Root Architectural Plasticity Traits and Genetic Regions for Adaptability to Variable Cultivation and Stress Conditions.

Future rice (Oryza sativa) crops will likely experience a range of growth conditions, and root architectural plasticity will be an important characteristic to confer adaptability across variable environments. In this study, the relationship between root architectural plasticity and adaptability (i.e. yield stability) was evaluated in two traditional × improved rice populations (Aus 276 × MTU1010 and Kali Aus × MTU1010). Forty contrasting genotypes were grown in direct-seeded upland and transplanted lowland conditions with drought and drought + rewatered stress treatments in lysimeter and field studies and a low-phosphorus stress treatment in a Rhizoscope study. Relationships among root architectural plasticity for root dry weight, root length density, and percentage lateral roots with yield stability were identified. Selected genotypes that showed high yield stability also showed a high degree of root plasticity in response to both drought and low phosphorus. The two populations varied in the soil depth effect on root architectural plasticity traits, none of which resulted in reduced grain yield. Root architectural plasticity traits were related to 13 (Aus 276 population) and 21 (Kali Aus population) genetic loci, which were contributed by both the traditional donor parents and MTU1010. Three genomic loci were identified as hot spots with multiple root architectural plasticity traits in both populations, and one locus for both root architectural plasticity and grain yield was detected. These results suggest an important role of root architectural plasticity across future rice crop conditions and provide a starting point for marker-assisted selection for plasticity.

Rice panicle plasticity in Near Isogenic Lines carrying a QTL for larger panicle is genotype and environment dependent.

BACKGROUND: Panicle architectural traits in rice (branching, rachis length, spikelet number) are established between panicle initiation and heading stages. They vary among genotypes and are prone to Genotype x Environment interactions. Together with panicle number, panicle architecture determines sink-based yield potential. Numerous studies analyzed genetic and environmental variation of plant morphology, but the plasticity of panicle structure is less well understood. This study addressed the response of rice panicle size and structure to limited light availability at plant level for near-isogenic lines (NILs) with IR64 or IRRI146 backgrounds, carrying the QTL qTSN4 (syn. SPIKE) for large panicles. Full light and shading in the greenhouse and two population densities in the field were implemented. The image analysis tool P-TRAP was used to analyze the architecture of detached panicles. RESULTS: The qTSN4 increased total branch length, branching frequency and spikelet number per panicle in IRRI146 background in the field and greenhouse, and in IR64 background in the greenhouse, but not for IR64 in the field. In the field, however, qTSN4 reduced panicle number, neutralizing any potential yield gains from panicle size. Shading during panicle development reduced spikelet and branch number but qTSN4 mitigated partly this effect. Spikelet number over total branch length (spikelet density) was a stable allometry across genotypes and treatments with variation in spikelet number mainly due to the frequency of secondary branches. Spikelet number on the main tiller was correlated with stem growth rate during panicle development, indicating that effects on panicle size seemed related to resources available per tiller. CONCLUSIONS: The qTSN4 effects on panicle spikelet number appear as indirect and induced by upstream effects on pre-floral assimilate resources at tiller level, as they were (1) prone to G x E interactions, (2) non-specific with respect to panicle architectural traits, and (3) associated with pre-floral stem growth rate.

The qTSN Positive Effect on Panicle and Flag Leaf Size of Rice is Associated with an Early Down-Regulation of Tillering.

The qTSN4 was identified as rice QTL (Quantitative Traits Locus) increasing total spikelet number per panicle and flag leaf area but potentially reducing panicle number depending on the environment. So far, this trade-off was mainly observed at grain maturity and not specifically studied in details, limiting the apprehension of the agronomic interest of qTSN4. This study aimed to understand the effect of qTSN4 and of the environment on panicle sizing, its trade-off with panicle number, and finally plant grain production. It compared two high yielding genotypes to their Near Isogenic Lines (NIL) carrying either QTL qTSN4 or qTSN12, two distinct QTLs contributing to the enlarged panicle size, thereafter designated as qTSN. Traits describing C sink (organ appearance rate, size, biomass) and source (leaf area, photosynthesis, sugar availability) were dynamically characterized along plant and/or panicle development within two trials (greenhouse, field), each comparing two treatments contrasting for plant access to light (with or without shading, high or low planting densities). The positive effect of qTSN on panicle size and flag leaf area of the main tiller was confirmed. More precisely, it could be shown that qTSN increased leaf area and internode cross-section, and in some cases of the photosynthetic rate and starch reserves, of the top 3-4 phytomers of the main tiller. This was accompanied by an earlier tillering cessation, that coincided with the initiation of these phytomers, and an enhanced panicle size on the main tiller. Plant leaf area at flowering was not affected by qTSN but fertile tiller number was reduced to an extent that depended on the environment. Accordingly, plant grain production was enhanced by qTSN only under shading in the greenhouse experiment, where panicle number was not affected and photosynthesis and starch storage in internodes was enhanced. The effect of qTSN on rice phenotype was thus expressed before panicle initiation (PI). Whether early tillering reduction or organ oversizing at meristem level is affected first cannot be entirely unraveled. Further studies are needed to better understand any signal involved in this early regulation and the qTSN × Environment interactions underlying its agronomic interest.

Genome-wide association mapping of root traits in a japonica rice panel.

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 (r(2)>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.