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28 November 2016, Volume 23 Issue 6 Previous Issue    Next Issue
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Association Mapping and Marker Development of Genes for Starch Lysophospholipid Synthesis in Rice Chuan Tong, Lei Liu, L. E. Waters Daniel, Jin-song Bao 2016, 23(6): 287-296.  DOI: 10.1016/j.rsci.2016.09.002 Abstract ( )   HTML ( )   PDF (1117KB) ( )   Phospholipids are a major kind of lipids in rice grains and have fundamental nutritional and functional benefits to the plant. Their lyso forms (lysophospholipids, LPLs) often form inclusion complexes with amylose or independently influence the physicochemical and functional properties of rice starch. However, the genetic basis for LPL synthesis in rice endosperm is largely unknown. Here, we performed a preliminary association test of 13 LPL compositions among 20 rice accessions, and identified 22 putative main-effect quantitative trait loci responsible for all LPLs except for LPC14:0 and LPE14:0. Five derived cleaved amplified polymorphic sequences and one insertion/deletion marker for three LPL-synthesis-related candidate genes were developed. Association analysis revealed two markers significantly associated with starch LPL traits. These results provide an insight into the genetic basis of phospholipid biosynthesis in rice and may contribute to the rice quality breeding programs using functional markers.

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Identification and Characterization of OsWRKY72 Variant in Indica Genotypes Ashwini Narasimha, Sivarajan Sajeevan Radha, Udayakumar Makarla, Nalkur Nataraja Karaba 2016, 23(6): 297-305.  DOI: 10.1016/j.rsci.2016.07.002 Abstract ( )   HTML ( )   PDF (891KB) ( )   Plant WRKY transcription factors (TFs) constitute one of the largest families of proteins involved in biotic and abiotic stress responses. These TFs have a conserved 60 amino acid WRKY domain at the N-terminal and a zinc finger motif at the C-terminal. To examine the relevance of OsWRKY72 in imparting salinity stress tolerance, two indica rice genotypes, Rasi (tolerant genotype) and Tellahamsa (susceptible genotype), were used. In Rasi seedlings at 12 h under 100 mmol/L NaCl stress, OsWRKY72 expression was up-regulated, whereas in Tellahamsa, it was highly up-regulated at lethal stress. Full-length OsWRKY72 cDNA was cloned from these two rice genotypes for further analysis. We identified a variant, termed as OsWRKY72b that carries an additional sequence of 111 bp within the WRKY domain. Expression of OsWRKY72b was higher under salinity stress in Rasi than in Tellahamsa. Disorder prediction of OsWRKY72b showed that the additional sequence in the WRKY domain is ordered thereby maintaining the tertiary structure that might interact with the major groove of DNA. Prediction of phosphorylation sites in OsWRKY72b indicated that a few serine residues could be the potential phosphorylation sites. In this study, we firstly reported a OsWRKY72 variant that could have a role in abiotic stress responses.

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Marker-Assisted Pyramiding of Genes Conferring Resistance Against Bacterial Blight and Blast Diseases into Indian Rice Variety MTU1010 Arunakumari K., V. Durgarani C., Satturu V., R. Sarikonda K., D. R. Chittoor P., Vutukuri B., S. Laha G., P. K. Nelli A., Gattu S., Jamal M., Prasadbabu A., Hajira S., M. Sundaram R. 2016, 23(6): 306-316.  DOI: 10.1016/j.rsci.2016.04.005 Abstract ( )   HTML ( )   PDF (646KB) ( )   Abstract: Two major bacterial blight (BB) resistance genes (Xa21 and xa13) and a major gene for blast resistance (Pi54) were introgressed into an Indian rice variety MTU1010 through marker-assisted backcross breeding. Improved Samba Mahsuri (possessing Xa21 and xa13) and NLR145 (possessing Pi54) were used as donor parents. Marker-assisted backcrossing was continued till BC2 generation wherein PCR based functional markers specific for the resistance genes were used for foreground selection and a set of parental polymorphic microsatellite markers were used for background selection at each stage of backcrossing. Selected BC2F1 plants from both crosses, having the highest recoveries of MTU1010 genome (90% and 92%, respectively), were intercrossed to obtain intercross F1 (ICF1) plants, which were then selfed to generate 880 ICF2 plants possessing different combinations of the BB and blast resistance genes. Among the ICF2 plants, seven triple homozygous plants (xa13xa13Xa21Xa21Pi54Pi54) with recurrent parent genome recovery ranging from 82% to 92% were identified. All the seven ICF2 plants showed high resistance against the bacterial blight disease with a lesion lengths of only 0.53-2.28 cm, 1%-5% disease leaf areas and disease scoring values of ‘1’ or ‘3’. The seven ICF2 plants were selfed to generate ICF3, which were then screened for blast resistance, and all were observed to be highly resistant to the diseases. Several ICF3 lines possessing high level of resistance against BB and blast, coupled with yield, grain quality and plant type on par with MTU1010 were identified and advanced for further selection and evaluation.

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Haplotyping of Rice Genotypes Using Simple Sequence Repeat Markers Associated with Salt Tolerance D. Chowdhury A., Haritha G., Sunitha T., L. Krishnamurthy S., Divya B., Padmavathi G., Ram T., Sarla N. 2016, 23(6): 317-325.  DOI: 10.1016/j.rsci.2016.05.003 Abstract ( )   HTML ( )   PDF (627KB) ( )   Salt stress is a major problem in most of the rice growing areas in the world. A major QTL Saltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice. This study aimed to characterize the haplotype diversity at Saltol and additional QTLs associated with salt tolerance. Salt tolerance at the seedling stage was assessed in 54 rice genotypes in the scale of 1 to 9 score at EC = 10 dSm-1 under controlled environmental conditions. Seven new breeding lines including three KMR3/O. rufipogon introgression lines showed similar salt tolerant ability as FL478 and can be good sources of new genes/alleles for salt tolerance. Simple sequence repeat (SSR) marker RM289 showed only two alleles and RM8094 showed seven alleles. Polymorphic information content value varied from 0.55 for RM289 to 0.99 for RM8094 and RM493. Based on 14 SSR markers, the 54 lines were clearly separated into two major clusters. Fourteen haplotypes were identified based on Saltol linked markers with FL478 as the reference. Alleles of RM8094 and RM3412 can discriminate between the salt tolerant and susceptible genotypes clearly and hence can be useful in marker-assisted selection at the seedling stage. Other markers RM10720 on chromosome 1 and RM149 and RM264 on chromosome 8 can also distinguish tolerant and susceptible lines but with lesser stringency.

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Influence of Organic and Inorganic Nitrogen on Grain Yield and Yield Components of Hybrid Rice in Northwestern Pakistan Amanullah, Hidayatullah 2016, 23(6): 326-333.  DOI: 10.1016/j.rsci.2016.02.007 Abstract ( )   HTML ( )   PDF (412KB) ( )   Field experiments were conducted to assess the impact of various organic sources, inorganic nitrogen (N) and the different combinations of inorganic N (urea) + organic source on the yield components (YC) and grain yield (GY) of hybrid rice (Oryza sativa L., Pukhraj) under rice-wheat system. The experiments were conducted at Batkhela (Malakand), Northwestern Pakistan, in 2011 and 2012. Our results revealed that YC and GY ranked first for the hybrid rice when applied with sole inorganic N (urea), followed by the application of N in mixture (urea + organic sources), while the control plots (no N applied) ranked in the bottom. Among the six organic sources (three animal manures: poultry, sheep and cattle; three crop residues: onion, berseem and wheat), application of N in the form of poultry manure was superior in terms of higher YC and GY. When applying 120 kg/hm2 N source, 75% N from urea + 25% N from organic source resulted in higher YC and GY in 2011, while applying 50% N from urea + 50% N from organic sources caused higher YC and GY in 2012. Therefore, the combined application of N sources in the form of urea + organic source can produce good performances in terms of higher YC and GY of rice under rice-wheat cropping system.

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Investigation of Polymorphisms in Coding Region of OsHKT1 in Relation to Salinity in Rice Quynh-Hoa Pham, Xuan-An Tran, Thi-Nha-Trang Nguyen, Thi-Thuy-Anh Tran, Hai-Yen Hoang, Thi-Hong-Van Nguyen, Thi-Hanh Tang, Thi-Phuc Do 2016, 23(6): 334-338.  DOI: 10.1016/j.rsci.2016.05.004 Abstract ( )   HTML ( )   PDF (466KB) ( )   Rice (Oryza sativa) is sensitive to salinity, but the salt tolerance level differs among cultivars, which might result from natural variations in the genes that are responsible for salt tolerance. High-affinity potassium transporter (HKTs) has been proven to be involved in salt tolerance in plants. Therefore, we screened for natural nucleotide polymorphism in the coding sequence of OsHKT1, which encodes the HKT protein in eight Vietnamese rice cultivars differing in salt tolerance level. In total, seven nucleotide substitutions in coding sequence of OsHKT1 were found, including two non-synonymous and five synonymous substitutions. Further analysis revealed that these two non-synonymous nucleotide substitutions (G50T and T1209A) caused changes in amino acids (Gly17Val and Asp403Glu) at signal peptide and the loop of the sixth transmembrane domain, respectively. To assess the potential effect of these substitutions on the protein function, the 3D structure of HKT protein variants was modelled by using PHYRE2 webserver. The results showed that no difference was observed when compared those predicted 3D structure of HKT protein variants with each other. In addition, the codon bias of synonymous substitutions cannot clearly show correlation with salt tolerance level. It might be interesting to further investigate the functional roles of detected non-synonymous substitutions as it might correlate to salt tolerance in rice.

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Relationship Between Degree of Starch Gelatinization and Quality Attributes of Parboiled Rice During Steaming Taghinezhad Ebrahim, Hadi Khoshtaghaza Mohammad, Minaei Saeid, Suzuki Toru, Brenner Tom 2016, 23(6): 339-344.  DOI: 10.1016/j.rsci.2016.06.007 Abstract ( )   HTML ( )   PDF (581KB) ( )   Paddy rice samples were parboiled by soaking at 65 °C for 180 min and steaming at 96 °C for 2-10 min, and then dried to achieve the final moisture content of 11% ± 1%. The degree of starch gelatinization (DSG) and several quality attributes (head rice yield (HRY), color value and hardness) of parboiled rice were measured. Results showed that DSG (46.8%-77.9%), color value (18.08-19.04) and hardness (118.6-219.2 N) all increased following steaming. In contrast, the HRY increased (64.8%-67.1%) for steaming times between 2-4 min but decreased (67.1%-65.0%) for steaming times between 4-10 min. Linear relations between DSG and color value (R2 = 0.87), and DSG and hardness (R2 = 0.88) were observed. The suitable DSG of parboiled rice leading to the highest HRY was found to be 62.5%, obtained following 4 min of steaming.