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Additional file 2: Figure S2. Manhattan plots of the SL-GWAS and ML-GWAS for yield. (A-E) Manhattan maps representing five traits of GL, GW, GT, TGW, and YPP, respectively; The x-axis displays the chromosome label, and the y-axis displays -log10 (p-value). The dotted and solid gray lines show significant associations between SNPs and phenotype value with threshold levels of p-value

Additional file 1. Figure S1. The survival rate of rice seedlings (Luohui 9, RPY geng, and RILs) after 7 days of salt stress treatment and 7 days of recovery; Figure S2. Three randomly selected candidate genes were verified by RT-PCR. Figure S3. Expression levels of LOC_Os05g14880, LOC_Os06g01250, and LOC_Os06g37300 in rice tissues from http://www.mbkbase.org/rice. Figure S4. Variant sites and haplotype results of LOC_Os05g14880, LOC_Os06g01250, and LOC_Os06g37300 from the rice genome variation database of 4,726 rice accessions (Rice Variation Map v2.0, http://ricevarmap.ncpgr.cn/).

Hybrid rice has been researched and utilized in China for 50 years. Three mainly cytoplasmic male sterile rice are wild abortive (WA), boro-II (BT), and Honglian (HL). Honglian (HL) type hybrid rice has made important contributions to the development of hybrid rice by combining scientific research, application research and industrial utilization. We identified Honglian cytoplasmic male sterile (HL-CMS) gene, orfH79 , which located downstream of atp6 in mitochondrial genome. CMS RNA, atp6-orfH79 , were translated into a cytotoxic protein, ORFH79. Data showed ORFH79 interacts with P61, which is a subunit of complex III of mitochondrial electron transfer chain. This interaction may impair energy production and leads to the accumulation of reactive oxygen species (ROS) in mitochondria, consequently resulting in abnormal pollen development. Furthermore, we cloned two restorer of fertility ( Rf ) genes, Rf5 and Rf6 , both of which are PPR genes. Neither RF5 nor RF6 binds to CMS RNA, atp6-orfH79 , directly. RF5 interacts with glycine rich protein 162 (GRP162) and RFC3 (restoration of fertility complex subunit 3) thus forming a restoration of fertility complex (RFC) to process CMS RNA. GRP162 can form homodimer and bind to CMS RNA with two binding sites directly. RCF3 is transported into the mitochondria as a membrane protein and functions as a scaffold protein for the assembly of the RFC complex. The RFC complex was detected with a size ranging from 400 to 500 kD. Moreover, Rf6 encodes a novel pentatricopeptide repeat (PPR) family protein with a characteristic duplication of PPR motifs 3 to 5. Results show RF6 is also targeted to mitochondria, where it physically associates with hexokinase 6 (OsHXK6) and promotes the processing of the aberrant CMS RNA, atp6-orfH79 , to restore the fertility of CMS line. To create more available germplasm in hybrid rice, we developed a molecular marker of orfH79 to screen wild rice and bred some novel CMS lines. We also developed molecular markers of Rf5 and Rf6 to breed novel stronger restore lines which contain two Rf genes. Consequently, we bred several combinations such as Honglian you 6, Yueyou 938, Luoyou 8 and Luoyou 9348 with high yield, good quality, multiple resistance and wide adaptation. HL hybrid rice has been widely planted in Yangzte river areas and South China with the yield of 10 to 12 tons per hectare. HL hybrid rice combinations also have been planted in Southeast Asian countries, such as Vietnam, Indonesia, Malaysia, Bangladesh and Phillippine. Most combinations exhibited 140% or more of yield compared with the local rice cultivars in Southeast Asian countries. HL hybrid rice even more is becoming the leading hybrid rice and priority choice in most of Asian countries and other Africa countries.

Gene expression profiles between submergence rice (Oryza sativa ssp. indica) varieties, tolerant FR13A and sensitive IR39595-503-2-1-2, under submergence stress were identified using differential display reverse transcriptase-polymerase chain reaction (DDRT-PCR). A total of 1428 bands were amplified with 40 pairs of primers, of which 102 were significantly different between the two lines. The differential display ratio was 7.1%. Among 42 differential display bands derived from the submergence tolerant variety, the expression of seven fragments was confirmed by Northern blot analysis. The analysis of their sequences indicated that four of them showed high homology with genes related to a water stress response: genes encoding ATP-binding protein, isocitrate dehydrogenase, NADH dehydrogenase and terminal acetyltransferase, respectively. The remaining three fragments were novel cDNA fragments.

Summary Using different phase encoding schemes, a composite record comprising of different single-shot da ta can be acquired at different locations through simultaneous sweep with multiple vibrators. There are many ways to decompose this composite record into independent singleshot records. This paper analyzes the cause that leads to illconditioned matrix during data separation, introduces the basic principles of the singular value decomposition(SVD) method and gives a real case of data separation using the method. Other methods such as Gauss-Jordan elimination method can also achieve data separation; however, comparison of the data separation results between the singular value decomposition method and Gauss-Jordan elimination method in this paper shows that compared to the later, the S/N ratio of the single-shot record obtained with the former is much higher. A 90-degree phase shift of the original data is performed using Hilbert transform before data separation operation.

Recovering worn-out tools/parts could have significant economic benefits. Traditionally, only some of these worn-out components can be repaired by conventional welding processes. Laser cladding is a material depositing method by which injected powder material is melted by a laser beam and re-solidified to form a dense coating with metallurgical bonding onto a substrate. This technology can be used in the component repair to restore undersized worn-out areas. Compared to conventional welding processes, laser cladding utilizes much less heat input with much better control, which drastically reduces or even eliminates distortion, and, therefore, enables the repair of complex components that cannot be repaired using conventional welding processes. Original CAD model does not represent the worn out component anymore and cannot be used directly for the component repair. Therefore, the first step in the laser cladding repair procedure is to extract the actual geometry of the components. Non-contact freeform surface measurement is widely used for this purpose. We developed a unique software system for laser cladding repair of worn-out components, which integrates the non-contact freeform surface measurement, the cladding path creation and the cladding program generation seamlessly. The surface contour is measured along with the predesigned scanning paths based on its original CAD model. The measured results are filtered to remove noise, and then compared with the CAD model. Finally, the cladding path planner creates the cladding program (G-code) based on the selected laser cladding parameters. Through this integrated software, the undersized worn-out components could be repaired effectively and easily by laser cladding process., 21st International Solid Freeform Fabrication Symposium, August 2010, Austin TX, USA

The 28th International Congress on Applications of Lasers & Electro Optics (ICALEO 2009): Orlando, Florida, USA: November 02, 2009

Non-contact freeform surface measurement is widely used in industry. To acquire the surface data, a laser displacement sensor and a motion system are typically used. One of the factors that affect the measuring accuracy is the sensor’s resolution. A high resolution sensor usually has a short measuring range. However, an unknown component’s profile with a large peak-to-valley height variation can not usually be measured using a short range sensor. We designed and developed a measuring system based on an existing 3-axis motion system with a laser displacement sensor mounted on its Z axis. This measuring system can be easily integrated to an existing laser processing system by standard communication ports to extend its applications into tool path planning, in-line inspection and monitoring. With the developed system, the real-time distance from the sensor to the component surface is acquired, and used as a feedback signal to control the sensor’s position on the Z axis to automatically maintain its distance with a given value. Through this development, the measuring range of the system is extended from the sensor’s measuring range up to the Z axis travelling range of the motion system so that a surface with large peak-to-valley height variation can be easily measured by a short range sensor with substantially improved accuracy., 20th International Solid Freeform Fabrication Symposium, August 3-5 2009, Austin, Texas, USA

Laser consolidation (LC) is a novel manufacturing process that produces net-shape functional components directly from a CAD model without and moulds or dies. Parts are built layer by layer using a laser beam to melt a controlled amount of injected powder on a substrate to deposit the first layer and on previous passes for the subsequent layers. As an alternative to conventional machining processes, the LC process builds complete net-shape functional parts or features on existing parts by adding instead of removing material. In this paper, laser consolidation of various metallic alloys is demonstrated. The LC process successfully built metallurgically sound Ni-alloys and Ti-alloys samples. The laser consolidated materials exhibit the mechanical properties comparable to respective wrought materials. In addition, several laser consolidated samples were presented to demonstrate the capability of the process to make net-shaped functional components for aerospace applications. Based on the same principle as the laser consolidation but covers surface areas, laser cladding of Ni-alloys and Ti-alloys can also be used to repair damaged aerospace components with much less heat input than the conventional welding methods., Materials Science and Technology 2007 Conference and Exhibition, September 16th to 20th, Detriot Michigan

Laser consolidation (LC) is a novel manufacturing process that produces net-shape functional and metallurgically sound components by adding material based on a CAD model. Parts are built using a laser beam to melt a controlled amount of injected powder on a base plate to deposit the first layer and on previous passes for the subsequent layers. As an alternative to conventional machining processes, the LC process builds complete net-shape functional parts or features on existing parts by adding instead of removing material. In this paper, laser consolidation of Al 4047 alloy is demonstrated. The LC process successfully built metallurgically sound Al 4047 alloy samples on Al substrate. The microstructure of LC Al 4047 material was examined using optical microscope, scanning electron microscope (SEM) and x-ray diffraction (XRD). The mechanical properties of the LC Al 4047 material were evaluated and compared with reference data. In addition, several LC Al 4047 samples were produced to demonstrate the capability of the process. Laser consolidation of Alalloys has many potential applications in aerospace, mold making and other industries for rapid tooling, small quantity production, and repair of expensive components., Materials Science and Technology 2006, October 15th to 19th 2006, Cincinnati USA