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Crown roots (CRs) are essential components of the rice root system. Several genes involved in CR initiation or development have been identified but our knowledge about how they organize to form a gene regulatory network (GRN) is still limited. To characterize the regulatory cascades acting during CR formation, we used a systems biology approach to infer the GRN controlling CR formation downstream of CROWN ROOTLESS 1 (CRL1), coding for an ASL (asymmetric leaves-2-like)/LBD (LOB domain) transcription factor necessary for CR initiation. A time-series transcriptomic dataset was generated after synchronized induction of CR formation by dexamethasone-mediated expression of CRL1 expression in a crl1 mutant background. This time series revealed three different genome expression phases during the early steps of CR formation and was further exploited to infer a GRN using a dedicated algorithm. The predicted GRN was confronted with experimental data and 72% of the inferred links were validated. Interestingly, this network revealed a regulatory cascade linking CRL1 to other genes involved in CR initiation, root meristem specification and maintenance, such as QUIESCENT-CENTER-SPECIFIC HOMEOBOX, and in auxin signalling. This predicted regulatory cascade was validated in vivo using transient activation assays. Thus, the CRL1-dependant GRN reflects major gene regulation events at play during CR formation and constitutes a valuable source of discovery to better understand this developmental process.

International audience; Genetics and molecular biology have contributed to the development of rationalized plant breeding programs. Recent developments in both high-throughput experimental analyses of biological systems and in silico data processing offer the possibility to address the whole gene regulatory network (GRN) controlling a given trait. GRN models can be applied to identify topological features helping to shortlist potential candidate genes for breeding purposes. Time-series data sets can be used to support dynamic modelling of the network. This will enable a deeper comprehension of network behaviour and the identification of the few elements to be genetically rewired to push the system towards a modified phenotype of interest. This paves the way to design more efficient, systems biology-based breeding strategies.

Background Despite recent sequencing efforts, local genetic resources remain underexploited, even though they carry alleles that can bring agronomic benefits. Taking advantage of the recent genotyping with 22,000 single-nucleotide polymorphism markers of a core collection of 180 Vietnamese rice varieties originating from provinces from North to South Vietnam and from different agrosystems characterized by contrasted water regimes, we have performed a genome-wide association study for different root parameters. Roots contribute to water stress avoidance and are a still underexploited target for breeding purpose due to the difficulty to observe them. Results The panel of 180 rice varieties was phenotyped under greenhouse conditions for several root traits in an experimental design with 3 replicates. The phenotyping system consisted of long plastic bags that were filled with sand and supplemented with fertilizer. Root length, root mass in different layers, root thickness, and the number of crown roots, as well as several derived root parameters and shoot traits, were recorded. The results were submitted to association mapping using a mixed model involving structure and kinship to enable the identification of significant associations. The analyses were conducted successively on the whole panel and on its indica (115 accessions) and japonica (64 accessions) subcomponents. The two associations with the highest significance were for root thickness on chromosome 2 and for crown root number on chromosome 11. No common associations were detected between the indica and japonica subpanels, probably because of the polymorphism repartition between the subspecies. Based on orthology with Arabidopsis, the possible candidate genes underlying the quantitative trait loci are reviewed. Conclusions Some of the major quantitative trait loci we detected through this genome-wide association study contain promising candidate genes encoding regulatory elements of known key regulators of root formation and development. Electronic supplementary material The online version of this article (doi:10.1186/s12870-016-0747-y) contains supplementary material, which is available to authorized users.

International audience; In the present study, we have successfully developed a transformation protocol for a rice variety Taichung 65 mediated by Agrobacterium tumefacienswith high efficiency, easy manipulation and reductionin labourwork. In the protocol, we have optimized all steps of transformation, standardized components of culture media and presented several manipulation experiments. Experimental results have shown that using petri dishes with high edge (15mm) and exposing explants not only increased the rate of callus formation, but also enhanced the size and quality of calluses. Using bacterial suspension at density OD600nm= 0.1 was optimal with high GUS expression in callus (81.25%) and low contamination. During the selection phase, transformed callusesgrew better in petri dishes with high edge (15 mm) and exposing explants. Checking for the presence of R4 promoter at the molecular level showed high frequency of regenerated plantlets carrying thetransgenes (up to 90.24%). GUS expression in different tissues of transgenic plants indicated the high activity of promoter R4, leading to initiate transcription and synthesis ofGUS enzyme. Analysis of T1 plants confirmed the stable inheritance of transgene to the next generation.; Trong nghiên cứu này, chúng tôi đã cải tiến thành công quy trình chuyển gen vào giống lúa Taichung 65 thông qua vi khuẩn Agrobacterium tumefaciensvới hiệu suất chuyển gen cao, thao tác đơn giản, giảm thiểu khối lượng công việc phải làm. Trong quy trình đưa ra, chúng tôi đã tối ưu hóa các bước tiến hành, chuẩn hóa thành phần môi trường nuôi cấy và đưa ra một sốnhân tốquan trọng trong thao tác. Kết quảthí nghiệm cho thấy sửdụng đĩa petri có gờcao 15mm và phơi mẫu không chỉlàm tăng tỷlệtạo mô sẹo từphôi mà còn tăng kích thước và chất lượng mô sẹo dùng cho quátrình chuyển gen. Dịch khuẩn với mật độOD600nm= 0,1 là tối ưu với tần sốbiểu hiện gen GUS ởmô sẹo cao (81,25%) và tỷlệmẫu nhiễm thấp. Ởgiai đoạn chọn lọc sau lây nhiễm,mô sẹo phát triển tốt hơn khi tiến hành phơi mẫu và sửdụng đĩa petri có gờcao15mm. Phân tíchsựcó mặt của promoter R4 cho thấy tỷlệcây tái sinh mang cấu trúc gen biến nạp cao (90,24%). Đánh giá sựbiểu hiện của gen GUS ởcây lúa chuyển gen đã chứng tỏsựhoạt động mạnh của promoter R4, điều khiển quá trình phiên mã, dẫn tới tổng hợp enzym GUS. Kết quảphân tích cây chuyển gen ởthếhệT1 đã chứng minh sựdi truyền ổn định của gen biến nạp sang thếhệsau.