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IRRI AR 2012 - Publications 2012

IRRI AR 2012 - Publications 2012

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IRRI Annual Report 2012
IRRI Annual Report 2012

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Published by: International Rice Research Institute on May 08, 2013
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Publications 2012

Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, et al. 2012. A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues. Mass Spectrom. Rev. 9999: 1-32. Akkinepalli H, Ereful N, Liu Y, Malabanan K, Howells R, Stamati K, et al. 2012. Snapshots of gene expression in rice: limitations for allelic expression imbalance determination. Genome 55(5): 400-406. Alberto MCR, Hirano T, Miyata A, Wassmann R, Kumar A, Padre A, et al. 2012. Influence of climate variability on seasonal and interannual variations of ecosystem CO2 exchange in flooded and non-flooded rice fields in the Philippines. Field Crops Res. 134: 80-94. Azam S, Thakur V, Ruperao P, Shah T, Balaji J, Amindala BP, et al. 2012. Coverage-based consensus calling (CBCC) of short sequence reads and comparison of CBCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome. Am. J. Bot. 99(2): 186-192. Banayo NPM, Sta. Cruz PC, Aguilar EA, Badayos RB, Haefele SM. 2012. Evaluation of biofertilizers in irrigated rice: effects on grain yield at different fertilizer rates. Agriculture 2: 73-86. Barboza GA, Pede VO. 2012. A spatial econometric analysis of cultural dimensions, technology knowledge and economic growth. Rev. Dev. Econ. 16(2): 262-275. Barrion AT, Villareal SS, Catindig JLA, Cai D, Yuan QH, Heong KL. 2012. The spider fauna in the rice agricultural landscape of Hainan Island, China: composition, abundance and feeding structure. Asia Life Sci. 21(2): 625-651. Boopathi NM, Swapanshri G, Kavitha P, Sathish S, Nithya R, Ratnam W, et al. 2012. Introgression, evaluation and bulked segregant analysis of major yield QTL under water stress into indigenous elite line for low water availability. Rice Sci. 19(4): 6. Butardo VMJr, Daygon VD, Colgrave ML, Campbell PM, Resurreccion A, Cuevas RP, et al. 2012. Biomolecular analyses of starch and starch granule proteins in the high-amylose rice mutant Goami 2. J. Agric. Food Chem. 60(46): 1157611585. Caemmerer SV, Quick WP, Furbank RT. 2012. The development of C4 rice: current progress and future challenges. Science 336 (6089): 16711672. Calingacion MN, Boualaphanh C, Daygon VD. 2012. A genomics and multi-platform metabolomics approach to identify new traits of rice quality in traditional and improved varieties. Metabolomics 8(5): 771-783. Carasso C, Fusconi A, Hay FR, Dho S, Gallino B, Mucciarelli M. 2012. A threatened alpine

species, Fritillaria tubiformis subsp. l: seed morphology and temperature regulation of embryo growth. Plant Biosyst. 146: 74-83. Chandna P, Ladha JK, Singh UP, Punia M, Gupta R, Sidhu BS. 2012. Using remote sensing technologies to enhance resource conservation and agricultural productivity in underutilized lands of South Asia. Appl. Geogr. 32: 757-765. Chauhan BS. 2012. Can knowledge in seed ecology contribute to improved weed management in direct-seeded rice? Curr. Sci. 103(5): 486-489. Chauhan BS. 2012. Weed ecology and weed management strategies for dry-seeded rice in Asia. Weed Technol. 26(1): 1-13. Chauhan BS. 2012. Weedy rice (Oryza sativa). II. Response of weedy rice to seed burial and flooding depth. Weed Sci. 60(3): 385-388. Chauhan BS, Abugho SB. 2012. Interaction of rice residue and PRE herbicides on emergence and biomass of four weed species. Weed Technol. 26(4): 627-632. Chauhan BS, Abugho SB. 2012. Phenotypic plasticity of spiny amaranth (Amaranthus spinosus) and longfruited primrose-willow (Ludwigia octovalvis) in response to rice interference. Weed Sci. 60(3): 411-415. Chauhan BS, Abugho SB. 2012. Threelobe morningglory (Ipomoea triloba) germination and response to herbicides. Weed Sci. 60: 199-204. Chauhan BS, Mahajan G. 2012. Role of integrated weed management strategies in sustaining conservation agriculture systems. Curr. Sci. 103(2): 135-136. Chauhan BS, Mahajan G, Sardana V, Timsina J, Jat ML. 2012. Productivity and sustainability of the 1 of 10

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Publications rice-wheat cropping system in the Indo-Gangetic Plains of the Indian subcontinent: problems, opportunities, and strategies. Adv. Agron. 117: 315-369. Chauhan BS, Opena J. 2012. Effect of tillage systems and herbicides on weed emergence, weed growth, and grain yield in dry-seeded rice systems. Field Crops Res. 137: 56-59. Chauhan BS, Opena J. 2012. Growth of purple nutsedge (Cyperus rotundus) in response to interference with direct-seeded rice. Weed Technol. 26: 506-509. Chauhan BS, Singh RG, Mahajan G. 2012. Ecology and management of weeds under conservation agriculture: a review. Crop Prot. 38: 57-65. Chemin Y, Phuphak S, Asilo S, Hijmans R. 2012. Determining spatial and temporal patterns of submergence in rice with MODIS satellite data. Int. J. Geoinformatics 8(2): 1-12. Cheng LR, Wang Y, Meng LJ, Hu X, Cui YR, Sun Y, et al. 2012. Identification of salt-tolerant QTLs with strong genetic background effect using two sets of reciprocal introgression lines in rice. Genome 55(1): 45-55. Cheng LR, Wang JM, Uzokwe V, Meng LJ, Wang Y, Sun Y, et al. 2012. Genetic analysis of cold tolerance at seedling stage and heat tolerance at anthesis in rice (Oryza sativa L.). J. Integr. Agric. 11(3): 359-367. Cheng LR, Wang JM, Ye GY, Luo CG, Xu JL, Li ZK. 2012. Identification of stably expressed QTL for heading date using reciprocal introgression line and recombinant inbred line populations in rice. Genet. Res. 94(5): 245-253. Chu SH, Jiang WZ, Lee JH, Chin JH, Koh HJ. 2012. QTL analyses of heterosis for grain yield and yield-related traits in indica-japonica crosses of rice (Oryza sativa L.). Genes Genomics 34: 367377. Chu Thai Hoanh, Ngo Dang Phong, Nguyen Hieu Trung, Le Canh Dung, Nguyen Xuan Hien, Nguyen Van Ngoc, et al. 2012. Modelling to support land and water management: experiences from the Mekong River Delta, Vietnam. Water Int. 37(4): 408-426. Clerget B, Rattunde HFW, Weltzien E. 2012. Why tropical sorghum sown in winter months has delayed flowering and modified morphogenesis in spite of prevailing short days. Field Crops Res. 125: 139-150. Cuc LM, Huyen LTN, Hien PTM, Hang VTT, Dam NQ, Mui PT, Quang VD, Ismail AM, Ham LH. 2012. Application of marker-assisted backcrossing to introgress the submergence tolerance QTL SUB1 into the Vietnam elite rice variety-AS996. Am. J. Plant Sci. 3: 528-536. Dar SR, Thomas T, Dagar JC, Lal K, Mehboob S, Bakshi MR, et al. 2012. Effect of fertilizer nitrogen and varied C:N ratio of mushroom compost on rice yield and nitrogen forms of soil. J. Food Agric. Environ. 10(3/4): 423-427. Dixit S, Swamy BPM, Vikram P, Ahmed HU, Sta. Cruz MT, Amante M, et al. 2012. Fine mapping of QTLs for rice grain yield under drought reveals sub-QTLs conferring a response to variable drought severities. Theor. Appl. Genet. 125(1): 155-169. Dixit S, Swamy BPM, Vikram P, Bernier J, Sta Cruz MT, Amante M, et al. 2012. Increased drought tolerance and wider adaptability of qDTY (12.1) conferred by its interaction with qDTY (2.3) and qDTY (3.2). Mol. Breed. 30(4): 1767-1779. Dobermann A. 2012. Getting back to the field. Nature 485: 176-177. Duan JZ, Zhang MH, Zhang HL, Xiong HY, Liu PL, Ali J, et al. 2012. OsMIOX, a myo-inositol oxygenase gene, improves drought tolerance through scavenging of reactive oxygen species in rice (Oryza sativa L.). Plant Sci. 196: 143-151. Feng BH, Yang Y, Shi YF, Lin L, Chen J, Huang QN, et al. 2012. Genetic analysis and gene mapping of a light brown spotted leaf mutant in rice. Chin. J. Rice Sci. 26(3): 297-301. Fischer KS, Fukai S, Kumar A, Leung H, Jongdee B. 2012. Field phenotyping strategies and breeding for adaptation of rice to drought. Front. Physiol. 3(282): 1-21. Fujita D, Tagle AG, Ebron LA, Fukuta Y, Kobayashi N. 2012. Characterization of near-isogenic lines carrying QTL for high spikelet number with the genetic background of an indica rice variety IR64 (Oryza sativa L.). Breed. Sci. 62(1): 18-26. Gamuyao R, Chin JH, Pariasca-Tanaka J, Pesaresi P, Catausan S, Dalid C, et al. 2012. The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488(7412): 535-541. Gaur VS, Singh US, Gupta AK, Kumar A. 2012. Influence of different nitrogen inputs on the members of ammonium transporter and glutamine synthetase genes in two rice genotypes having differential responsiveness to nitrogen. Mol. Biol. Rep. 39(8): 8035-8044. Gaydon DS, Probert ME, Buresh RJ, Meinke H, Suriadi A, Dobermann A, et al. 2012. Rice 2 of 10

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Publications in cropping systems - modelling transitions between flooded and non-flooded soil environments. Eur. J. Agron. 39: 9-24. Gaydon DS, Probert ME, Buresh RJ, Meinke H, Timsina J. 2012. Modelling the role of algae in rice crop nutrition and soil organic carbon maintenance. Eur. J. Agron. 39: 35-43. Ghimire KH, Quiatchon LA, Vikram P, Swamy BPM, Dixit S, Ahmed H, et al. 2012. Identification and mapping of a QTL (qDTY1.1) with a consistent effect on grain yield under drought. Field Crops Res. 131: 88-96. Gowda VRP, Henry A, Vadez V, Shashidhar HE, Serraj R. 2012. Water uptake dynamics under progressive drought stress in diverse accessions of the OryzaSNP panel of rice (Oryza sativa). Funct. Plant Biol. 10 p. Gumma MK, Daniel VR, Nelson A, Thenkabail PS, Venkat AR, Priyanie A. 2012. Expansion of urban- and wastewater irrigated areas in Hyderabad, India. Irrig. Drain. Syst. 25:135-149. Gurr GM, Read DMY, Catindig JLA, Cheng JA, Liu J, La Phan Lan., et al. 2012. Parasitoids of the rice leaffolder Cnaphalocrocis medinalis and prospects for enhancing biological control with nectar plants. Agric. For. Meteorol. 14 (1): 1-12. Hansen TH, Lombi E, Fitzgerald M. 2012. Losses of essential mineral nutrients by polishing of rice differ among genotypes due to contrasting grain hardness and mineral distribution. J. Cereal Sci. 56(2): 307-315. Hay FR, Thavong P, Taridno P, Timple S. 2012. Evaluation of zeolite seed ‘drying beads’ for drying rice seeds to low moisture content prior to long-term storage. Seed Sci. Technol. 40(3): 374-395. He H, Serraj R. 2012. Involvement of peduncle elongation, anther dehiscence and spikelet sterility in upland rice response to reproductivestage drought stress. Environ. Exp. Bot. 75: 120-127. He Z, Xie F, Chen L, Paz MAD. 2012. Genetic diversity of tropical hybrid rice germplasm measured by molecular markers. Rice Sci. 19(3): 193-201. Henry A, Cal AJ, Batoto TC, Torres RO, Serraj R. 2012. Root attributes affecting water uptake of rice (Oryza sativa) under drought. J. Exp. Bot. 63(13): 4751-4763. Horgan FG. 2012. Effects of leaf damage on oviposition choice in an invasive paropsine beetle. J. Appl. Entomol. 136: 271-281. Horgan FG, Quiring DT, Lagnaoui A, Pelletier Y. 2012. Life histories and fitness of two tuber moth species feeding on native Andean potatoes. Neotrop. Entomol. 41(4): 3330-3340. Huang B, Xu JY, Hou MS, Ali J, Mou TM. 2012. Introgression of bacterial blight resistance genes Xa7, Xa21, Xa22 and Xa23 into hybrid rice restorer lines by molecular marker-assisted selection. Euphytica 187: 449-459. Hussain AJ, Ali J, Siddiq EA, Gupta VS, Reddy UK, Ranjekar PK. 2012. Mapping of tms8 gene for temperature-sensitive genic male sterility (TGMS) in rice (Oryza sativa L.). Plant Breed. 131(1): 4247. Huyen LTN, Cuc LM, Ismail AM, Ham LH. 2012. Introgression of the salinity tolerance QTLs saltol into AS996, the elite rice variety of Vietnam. Am. J. Plant Sci. 3: 981-987. Iftekharuddaula KM, Salam MA, Newaz MA, Ahmed HU, Collard BCY, Septiningsih EM, et al. 2012. Comparison of phenotypic versus markerassisted background selection for the SUB1 QTL during backcrossing in rice. Breed. Sci. 62(3): 216-222. Impa S, Johnson-Beebout SR. 2012. Mitigating zinc deficiency and achieving high grain Zn in rice through integration of soil chemistry and plant physiology research. Plant Soil 361(1/2): 3-41. Islam MR, Gregorio GB, Salam MA, Collard BCY, Singh RK, Hassan L. 2012. Validation of SalTol linked markers and haplotype diversity on chromosome 1 of rice. Mol. Plant Breed. 3(10): 103-114. Jagadish SVK, Septiningsih EM, Kohli A, Thomson MJ, Ye G, Redona E, et al. 2012. Genetic advances in adapting rice to a rapidly changing climate. J. Agron. Crop Sci. 198: 360-373. Jena KK, Kim SM, Suh JP, Yang CI, Kim YG. 2012. Identification of cold-tolerant breeding lines by quantitative trait loci associated with cold tolerance in rice. Crop Sci. 52(2): 517-523. Johnson MTJ, Carpenter EJ, Tian ZJ, Bruskiewich R, Burris JN, Carrigan CT, et al. 2012. Evaluating methods for isolating total RNA and predicting the success of sequencing phylogenetically diverse plant transcriptomes. PLoS One 7(11): e50226. 12 p. Kajisa K. 2012. The double tragedy of irrigation systems in Tamil Nadu, India: assessment of the replacement of traditional systems by private wells. Water Policy 14(3): 371-390. Katayanagi N, Furukawa Y, Fumoto T, Hosen Y. 2012. Validation of the DNDC-Rice model by using CH4 and N2O flux data from rice cultivated 3 of 10

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Publications in pots under alternate wetting and drying irrigation management. Soil Sci. Plant Nutr. 58(3): 360-372. Khin Khin Marlar Myint, Fujita D, Matsumura M, Sonoda T, Yoshimura A, Yasui H. 2012. Mapping and pyramiding of two major genes for resistance to the brown planthopper (Nilaparvata lugens [Stal]) in rice cultivar ADR52. Theor. Appl. Genet. 124 (3): 495-504. Knief C, Delmotte N, Chaffron S, Stark M, Innerebner G, Wassmann R, et al. 2012. Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice. ISME J. 6(7): 1378-1390. Kohli A, Narciso JO, Miro B, Raorane M. 2012. Root proteases: reinforced links between nitrogen uptake and mobilization and drought tolerance. Physiol. Plant. 145(1): 165-179. Kumar S, Verulkar SB, Mandal NP, Variar M, Shukla VD, Dwivedi JL, et al. 2012. High-yielding, drought-tolerant, stable rice genotypes for the shallow rainfed lowland drought-prone ecosystem. Field Crops Res. 133: 37-47. Laborte AG, de Bie KCAJM, Smaling EMA, Moya P, Boling AA, Van Ittersum MK. 2012. Rice yields and yield gaps in Southeast Asia: past trends and future outlook. Eur. J. Agron. 36(1): 9-10. Laborte AG, Maunahan AA, Hijmans RJ. 2012. Opportunities for expanding paddy rice production in Laos: spatial predictive modeling using Random Forest. J. Land Use Sci. 7:21-33. Lee D, Ialicicco M, Akkinepalli H. 2012. Genotyping SSR length variants by isothermal DNA amplification. Genome 55(9): 56(2): 691-695. Liu GF, Zhu HT, Zhang GQ, Li LH, Ye GY. Dynamic analysis of QTLs on tiller number in rice (Oryza sativa L.) with single segment substitution lines. Theor. Appl. Genet. 125(1): 143-153. Mackill DJ, Ismail AM, Singh US, Labios RV, Paris TR. 2012. Development and rapid adoption of submergence-tolerant (Sub1) rice varieties. Adv. Agron. 115: 299-352. Madan P, Jagadish SVK, Craufurd PQ, Fitzgerald M, Lafarge T, Wheeler TR. 2012. Effect of elevated CO2 and high temperature on seed-set and grain quality of rice. J. Exp. Bot. 63(10): 3843-3852. Mahajan G, Chauhan BS, Timsina J, Singh PP, Singh K. 2012. Crop performance and water- and nitrogen-use efficiencies in dry-seeded rice in response to irrigation and fertilizer amounts in northwest India. Field Crops Res. 134: 59-70. Mahajan G, Singh S, Chauhan BS. 2012. Impact of climate change on weeds in the rice-wheat cropping system. Curr. Sci. 102(9): 1254-1255. Mahajan G, Timsina J, Jhanji S, Sekhon NK, Kuldeep S. 2012. Cultivar response, dry-matter partitioning, and nitrogen-use efficiency in dry direct-seeded rice in Northwest India. J. Crop Improv. 26: 767-790. Maredia MK, Raitzer DA. 2012. Review and analysis of documented patterns of agricultural research impacts in Southeast Asia. Agric. Syst. 106(1): 46-58. Masouleh AK, Waters DLE, Reinke RF, Ward R, Henry RJ. 2012. SNP in starch biosynthesis genes associated with nutritional and functional properties of rice. Sci. Rep. 2(557): 1-9. McCouch SR, McNally KL, Wang W, Hamilton RS. 2012. Genomics of gene banks: a case study in rice. Am. J. Bot. 99(2): 17. McKinley JD, Sparks AH, Pede VO. 2012. An economic assessment of the impact of mango pulp weevil on the agricultural sector of Palawan, Philippines. Philipp. Agric. Sci. 95(3): 286-292. Mitra S, Majumda D, Wassmann R. 2012. Methane production and emission in surface and subsurface rice soils and their blends. Agric. Ecosyst. Environ. 158: 94-102. Myint KM, Arikit S, Wanchana S, Yoshihashi T, Choowongkomon K, Vanavichit A. 2012. A PCRbased marker for a locus conferring the aroma in Myanmar rice (Oryza sativa L.). Theor. Appl. Genet. 125(5): 887-896. Nakhoda B, Leung H, Mendioro MS, Mohammadinejad G, Ismail AM. 2012. Isolation, characterization, and field evaluation of rice (Oryza sativa L., Var. IR64) mutants with altered responses to salt stress. Field Crops Res. 127: 191-202. Ndikumana I, Pinel-Galzi A, Negussie Z, Msolla SN, Njau P, Singh RK, et al. 2012. First report of rice yellow mottle virus on rice in Burundi. Plant Dis. 96(8): 1230-1231. Ngo Thi Thanh Truc, Sumalde ZM, Espaldon MVO, Pacardo EP, Rapera CL, Palis FG. 2012. Farmers’ awareness and factors affecting adoption of rapid composting in Mekong Delta, Vietnam and Central Luzon, Philippines. J. Environ. Sci. Manage. 15(2): 59-73. Nie LX, Peng SB, Bouman B, Shah F, Huang JL, Cui KH, et al. 2012. Synergic effect of flooding and nitrogen application on alleviation of soil sickness

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Publications caused by aerobic rice monocropping. Plant Prod. Sci. 15(3): 246-251. Nuruzzaman M, Sharoni AM, Satoh K, Moumeni A, Venuprasad R, Serraj R, et al. 2012. Comprehensive gene expression analysis of the NAC gene family under normal growth conditions, hormone treatment, and drought stress conditions in rice using near-isogenic lines (NILs) generated from crossing Aday Selection (drought tolerant) and IR64. Mol. Genet. Genomics 287(5): 389-410. Nyo Me Htwe, Singleton GR, Hinds LA, Propper CR, Sluydts V. 2012. Breeding ecology of rice field rats, Rattus argentiventer and R. tanezumi in lowland irrigated rice systems in the Philippines. Agric. Ecosyst. Environ. 161: 39-45. Pandey S, Suphanchaimat N, Velasco ML. 2012. The patterns of spread and economics of a laborsaving innovation in rice production: the case of direct seeding in Northeast Thailand. Q. J. Int. Agric. 51(4): 333-356. Pavelic P, Patankar U, Acharya S, Jella K, Gumma MK. 2012. Role of groundwater in buffering irrigation production against climate variability at the basin scale in South-West India. Agric. Water Manage. 103: 78-87. Peltonen-Sainio P, Jauhiainen L, Nissila E. 2012. Improving cereal protein yields for high latitude conditions. Eur. J. Agron. 39: 1-8. Pede VO, McKinley JD, Sharma R, Kumar A. 2012. Guidance and technology: an assessment of project intervention and promoted technologies. GSTF J. Bus. Rev. 2(2): 159-164. Raitzer DA, Maredia MK. 2012. Analysis of agricultural research investment priorities for sustainable poverty reduction in Southeast Asia. Food Policy 37(4): 412-426. Ram H, Singh Y, Saini KS, Kler DS, Timsina J, Humphreys EJ. 2012. Agronomic and economic evaluation of permanent raised beds, no tillage and straw mulching for an irrigated maize-wheat system in Northwest India. Exp. Agric. 48(1): 2138. Raman A, Verulkar SB, Mandal NP, Variar M, Shukla VD, Dwivedi JL, et al. 2012. Drought yield index to select high-yielding rice lines under different drought stress severities. Rice 5(31): 12. Rashid MH, Alam MM, Ladha JK. 2012. Comparative efficacy of pretilachlor and hand weeding in managing weeds and improving the productivity and net income of wet-seeded rice in Bangladesh. Field Crops Res. 128: 17-26. Rebolledo MC, Dingkuhn M, Pere P, McNally KL, Luquet D. 2012. Developmental dynamics and early growth vigor in rice. I. Relationship between development rate (1/phyllochron) and growth. J. Agron. Crop Sci. 198: 374-384. Reflinur, Chin JH, Jang SM, Kim B, Lee JH, Koh HJ. 2012. QTLs for hybrid fertility and their association with female and male sterility in rice. Genes Genomics 34: 355-365. Rejesus RM, Mutuc MEM, Yasar M, Lapitan AV, Palis FG, Truong Thi Ngoc Chi. 2012. Sending Vietnamese rice farmers back to school: further evidence on the impacts of farmer field schools. Can. J. Agric. Econ. 60(3): 407-426. Sarhadi E, Bazargani MM, Sajise AG, Abdolahi S, Vispo NA, Arceta M, et al. 2012. Proteomic analysis of rice anthers under salt stress. Plant Physiol. Biochem. 58: 280-287. Savary S, Horgan F, Willocquet L, Heong KL. 2012. A review of principles for sustainable pest management in rice. Crop Prot. 32: 54-63. Savary S, Nelson A, Willocquet L, Pangga I, Aunario J. 2012. Modeling and mapping potential epidemics of rice diseases globally. Crop Prot. 34: 6-17. Seck PA, Diagne A, Mohanty S, Wopereis MCS. 2012. Crops that feed the world 7: Rice. Food Security 4(1): 7-24. Septiningsih EM, Sanchez DL, Singh N, Sendon PMD, Pamplona AM, Heuer S, et al. 2012. Identifying novel QTLs for submergence tolerance in rice cultivars IR72 and Madabaru. Theor. Appl. Genet. 124(5): 867-874. Sessitsch A, Hardoim P, Doring J, Weilharter A, Krause A, Woyke T, et al. 2012. Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis. Mol. Plant-Microbe Interact. 25(1): 2836. Shackley S, Carter S, Knowles T, Middelink E, Haefele S, Haszeldine S. 2012. Sustainable gasificationbiochar systems? A case-study of rice-husk gasification in Cambodia, Part II: Field trial results, carbon abatement, economic assessment and conclusions. Energy Policy 41: 618-623. Shackley S, Carter S, Knowles T, Middelink E, Haefele S, Sohi S, et al. 2012. Sustainable gasification biochar systems? A case-study of rice-husk gasification in Cambodia, Part I: Context, chemical properties, environmental and health and safety issues. Energy Policy 42: 49-58. Sharoni AM, Nuruzzaman M, Satoh K, Moumeni A, Attia K, Venuprasad R, et al. 2012. Comparative transcriptome analysis of AP2/EREBP gene family 5 of 10

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Publications under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64. Mol. Genet. Genomics 287(1): 1-19. Shen QXJ, Yu DQ, Jeon JS, Piffanelli P, Abbruscato P, Guo ZJ, et al. 2012. Nomenclature report on rice WRKY’s - conflict regarding gene names and its solution. Rice 5(1): 3. Shi BH, Zhang JH, Zheng YM, Liu YQ, Vera Cruz CM, Zheng TQ, et al. 2012. Identification of a new resistance gene Pi-Da(t) from Dacca6 against rice blast fungus (Magnaporthe oryzae) in Jin23B background. Mol. Breed. 30(2): 1089-1096. Shi WJ, Muthurajan R, Rahman H, Selvam J, Peng SB,Zou YB, Jagadish KSV. 2012. Source-sink dynamics and proteomic reprogramming under elevated night temperature and their impact on rice yield and grain quality. New Phytol. 197: 825-837. Singh B, Gaydon DS, Humphreys E, Eberbach PL. 2012. The effects of mulch and irrigation management on wheat in Punjab, India― evaluation of the APSIM model. Field Crops Res. 125: 139-150. Singh R, Saravanan R, Feroze SM, Devarani L, Paris TR. 2012. A case study of drought and its impact on rural livelihood in Meghalaya. Indian J. Dryland Agric. Res. Dev. 27(1): 90-94. Sreenivasulu N, Harshavardhan VT, Govind G, Seiler C, Kohli A. 2012. Contrapuntal role of ABA: does it mediate stress tolerance or plant growth retardation under long-term drought stress? Gene 506(2): 265-273. Sta. Cruz PC, Banayo NPMC, Marundan SR Jr, Magnaye MA, Lalican DJ, Hernandez JE. 2012. Bio-inoculant and foliar fertilizer in combination with soil-applied fertilizer on the yield of lowland rice. Philipp. J. Crop Sci. 37(3): 55-63. Stuart AM, Prescott CV, Singleton GR. 2012. Natal nest locations of the Asian house rat (Rattus tanezumi) in lowland rice-coconut cropping systems: a coconut penthouse or rice bunds with water frontage? Wildlife Res. 39: 496-502. Sudhir-Yadav, Humphreys E, Li T, Gill G, Kukal SS. 2012. Evaluation of tradeoffs in land and water productivity of dry seeded rice as affected by irrigation schedule. Field Crops Res. 128: 180-190. Suh JP, Lee CK, Lee JH, Kim JJ, Kim SM, Cho YC, et al. 2012. Identification of quantitative trait loci for seedling cold tolerance using RILs derived from a cross between japonica and tropical japonica rice cultivars. Euphytica 184 (1): 101-108. Swamy BPM, Kaladhar K, Rani NS, Prasad GSV, Viraktamath BC, Reddy GA, et al. 2012. QTL analysis for grain quality traits in 2 BC2F2 populations derived from crosses between Oryza sativa cv Swarna and 2 accessions of O. nivara. J. Hered. 103(3): 442-452. Tatem AJ, Adamo S, Bharti N, Burgert CR, Castro M, Dorelien A, et al. 2012. Mapping populations at risk: improving spatial demographic data for infectious disease modeling and metric derivation. Popul. Health Metrics 10(8): 14. Tatem AJ, Adamo S, Bharti N, Burgert CR, Castro M, Dorelien A, et al. 2012. Omics technologies to tap genetic variation for rice improvement. In Vitro Cell Dev. Biol. Anim. 48(1): 4-4. Tatlonghari G, Paris T, Pede V, Siliphouthone I, Suhaeti R. 2012. Seed and information exchange through social networks: the case of rice farmers of Indonesia and Lao PDR. Sociol. Mind 2(2):169176. Thenkabail PS, Knox JW, Ozdogan. M., Gumma MK, Congalton R, Wu Z, et al. 2012. Assessing future risks to agricultural productivity, water resources and food security: how can remote sensing help? Photogr. Eng. Remote Sensing 78(8): 773-782. Thomson MJ, Zhao KY, Wright M, McNally KL, Rey J, Tung CW, et al. 2012. High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Mol. Breed. 29(4): 875886. Tolley BJ, Woodfield H, Wanchana S, Bruskiewich R, Hibberd JM. 2012. Light-regulated and cellspecific methylation of the maize PEPC promoter. J. Exp. Bot. 63(3): 1381-1390. Torrion JA, Setiyono TD, Cassman KG, Ferguson RB, Irmak S, Specht JE. 2012. Soybean root development relative to vegetative and reproductive phenology. Agron. J. 104(6): 1702-1709. Venuprasad R, Bool ME, Quiatchon L, Atlin GN. 2012. A QTL for rice grain yield in aerobic environments with large effects in three genetic backgrounds. Theor. Appl. Genet. 124(2): 323-332. Venuprasad R, Bool ME, Quiatchon L, Sta. Cruz MT, Amante M, Atlin GN. 2012. A large-effect QTL for rice grain yield under upland drought stress on chromosome 1. Mol. Breed. 30(1): 535-547.

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Publications Verdier V, Vera Cruz C, Leach JE. 2012. Controlling rice bacterial blight in Africa: needs and prospects. J. Biotechnol. 159(4): 320-328. Vikram P, Swamy BPM, Dixit S, Ahmed H, Sta. Cruz MT, Singh AK, et al. 2012. Bulk segregant analysis: ‘an effective approach for mapping consistent-effect drought grain yield QTLs in rice’. Field Crops Res. 134: 185-192. Villa JE, Henry A, Xie FM, Serraj R. 2012. Hybrid rice performance in environments of increasing drought severity. Field Crops Res. 125: 14-24. Villegas KL, Ambal RGR, Boyd C, Brooks TM, Coroza O, Silva Nde, et al. 2012. Quantitative landscape management targets for biodiversity conservation: method development with an example from the Philippines. Asia Life Sci. 21(2): 565-583. Vleesschauwer Dde, Buyten Ev, Satoh K, Balidion J, Mauleon R, Choi IR, et al. 2012. Brassinosteroids antagonize gibberellin- and salicylate-mediated root immunity in rice. Plant Physiol. 158(4): 1833-1846. Vu HTT, Le DD, Ismail AM, Le HH. 2012. Markerassisted backcrossing (MABC) for improved salinity tolerance in rice (Oryza sativa L.) to cope with climate change in Vietnam. Austr. J. Crop Sci. 6: 1649-1654. Wang H, Pandey S, Velarde O. 2012. Patterns of adoption of improved high-yielding rice varieties and determinants of adoption in Cambodia. GSTF J. Bus. Rev. 2(1): 104-110. Wang P, Xing YZ, Li ZK, Yu SB. 2012. Improving rice yield and quality by QTL pyramiding. Mol. Breed. 29 (4): 903-913. Wang Y, Zang JP, Sun Y, Ali J, Xu JL, Li ZK. 2012. Identification of genetic overlaps for salt and drought tolerance using simple sequence repeat markers on an advanced backcross population in rice. Crop Sci. 52(4): 1583-1592. Wei D, Cui KH, Ye GY, Pan JF, Xiang J, Huang JL, et al. 2012. QTL mapping for nitrogen-use efficiency and nitrogen-deficiency tolerance traits in rice. Plant Soil 359(1/2): 281-295. Wickneswari R, Bhuiyan MAR, Kalluvettankuzhy K. S, Lim LS, Thomson MJ, Narimah MK, et al. 2012. Identification and validation of quantitative trait loci for agronomic traits in advanced backcross breeding lines derived from Oryza rufipogon x Oryza sativa cultivar MR219. Plant Mol. Biol. Rep. 30: 929-939. Xia K, Daws MI, Hay FR, Chen WY, Zhou ZK, Prtichard HW. 2012. A comparative study of desiccation responses of seeds of Asian evergreen oaks, Quercus subgenus Cyclobalanopsis and Quercus subgenus Quercus. South Afr. J. Bot. 78: 47-54. Xie FM, Guo LB, Ren GJ, Hu PS, Wang F, Xu JL, et al. 2012. Genetic diversity and structure of indica rice varieties from two heterotic pools of southern China and IRRI. Plant Genet. Resour. Charact. Util. 10(3): 186-193. Xu YB, Li ZK, Thomson MJ. 2012. Molecular breeding in plants: moving into the mainstream. Mol. Breed. 29 (4): 831-832. Yang SY, Gronlund M, Jakobsen I, Grotomeyer MS, Rentsch D, Miyao A, et al. 2012. Nonredundant regulation of rice arbuscular mycorrhizal symbiosis by two members of the PHOSPHATE TRANSPORTER1 gene family. Plant Cell 24: 4236-4251. Ye CR, Argayoso MA, Redona ED, Sierra SN, Laza MA, Dilla CJ, et al. 2012. Mapping QTL for heat tolerance at flowering stage in rice using SNP markers. Plant Breed. 131(1): 33-41. Yunbo Zhang Y, Tang Q, Peng S,Xing D, Laza RC, Punzalan BR. 2012. Water use efficiency and physiological response of rice cultivars under alternate wetting and drying conditions. Sci. World J. 10 p. doi: 10.1100/2012/287907 Zhang F, Huang LY, Wang WS, Zhao XQ, Zhu LH, Fu BY, et al. 2012. Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background. BMC Genomics 13(461): 1-28. Zhang Z-H, Liu Q, Song H-X, Rong X-M, Ismail AM. 2012. Responses of different rice (Oryza sativa L.) genotypes to salt stress and relation to carbohydrate metabolism and chlorophyll content. Afr. J. Agric. Res. 7(1): 19-27. Zheng TQ, Yang J, Zhong WG, Zhai HQ, Zhu LH, Fan FJ, et al. 2012. Novel loci for field resistance to black-streaked dwarf and stripe viruses identified in a set of reciprocal introgression lines of rice (Oryza sativa L.). Mol. Breed. 29(4): 925-938. Zhou YL, Xie XW, Xu MR, Zang JP, Zhu LH, Xu JL, et al. 2012. Genetic overlap in the quantitative resistance of rice at the seedling and adult stages to Xanthomonas oryzae pv. oryzae. J. Plant Biol. 55(2): 102-113. Ziska LH, Bunce JA, Shimono H, Gealy DR, Baker JT, Newton PCD, et al. 2012. Food security and climate change: on the potential to adapt global crop production by active selection to rising atmospheric carbon dioxide. Proc. R. Soc. Jpn. B (Biol. Sci.) 279: 4097-4105. 7 of 10

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Thursday seminars
Megatrends, innovation, and IRRI’s future business model. Dr. Achim Dobermann. Making the global agrifood system more sustainable: using systems thinking to identify key intervention points.Dr. Erik Mathijs, University of Leuven, Belgium. The dirt on nitrogen, soil, and carbon—a step toward solving the enigma of soil N balance. Dr. J.K. Ladha. Carbon crediting in rice production: realistic outlook or only wishful thinking? Dr. Reiner Wassmann. Recent developments in genetic resources policy: impact on the value chain. Dr. Bert Visser, Wageningen University, The Netherlands. Breeding for resilience: green super rice. Dr. Jauhar Ali. Towards market-oriented breeding programs. Dr. Eero Nissila. Exploring rice diversity from markers through sequences: the history and consequence. Dr. Kenneth McNally. Flooding tolerance: escape or quiescence. Dr. Rens Voesenek, Utrecht University, The Netherlands. Modernizing the IRRI Experiment Station. Mr. Leigh Vial. Can Myanmar do what Vietnam has done? Drs. Randolph Barker, Grant Singleton, and David Johnson. Four decades of socioeconomic studies in a rice village in East Laguna. Dr. Keiji Kajisa. Rice production in the cone of South America—what we can learn for GRiSP. Dr. Bas Bouman.

Rice market forecasts: from guesstimates to estimates. Dr. Samarendu Mohanty. A magical gene for rice improvement. Dr. Kshirod Jena. The STRASA project: reversing the adverse. Dr. Abdelbagi Ismail. Rice breeding in Korea: looking back, looking forward. Dr. Ha Woon-Go. Joint seminar highlighting the work of two prestigious institutions. Dr. Rainer Hoefgen and Dr. Hans-Michael Hubberten, Max Planck Institute of Molecular Plant Physiology, Germany. Linking genome-wide association studies (GWAS) and plant breeding to better utilize natural variation in rice. Dr. Susan McCouch, Cornell University, USA. Cloning of QTLs via next-generation sequencing. Dr. John Platten. Managing rice diseases in a changing rice production scenario. Dr. Casiana Vera Cruz. Rice races against rising temperatures. Dr. Krishna Jagadish. Toward sustainable irrigated rice farming under increasing labor and water scarcity. Dr. Keiji Kajisa. Checking palay quality by image analysis of leaf coloration. Dr. Rodrigo Munoz, Jr., Ms. Maria Crizele de Jesus, and Ms. Graychelle Isidro, Bataan State Peninsula University, Philippines. Using genomic approaches to increase rice yield potential. Dr. Parminder Virk. Working with smallholder farmers for increased rice productivity: the Sulawesi experience. Dr. Madonna Casimero.

Marker-assisted breeding to improve grain yield under drought. Dr. Arvind Kumar. Breeding new flood-tolerant varieties. Dr. Bertrand Collard. Transformations in the lowland rice-based ecosystems in Nyaungdon Township, Mayanmar: implications on farmers’ productivity and incomes. Dr. Lee Garcia. Ecological intensification,: a futuristic view of rice production. Dr. James Quilty. Update on CGIAR reform and strategy and results framework (SRF) action plan. Dr. F. Rijsberman, CGIAR. Panel discussion: Public-private partnerships―getting the balance right. Panelists: Drs. Eero Nissila, Elsie Quaite-Randall, Noel Magor, Sigrid Heuer, James Quilty, and Alfred Schmidley. Breeding approaches for varietal improvement in rice, with special reference to genetic yield enhancement and stability, and reflections on 35 years of rice breeding in eastern India. Dr. S.R. Das. Year-end report. Dr. Robert Zeigler. Nine years at IRRI, nine years of change. Dr. Sigrid Heuer. Three-year journey in eastern and southern Africa. What’s next? Dr. R.K. Singh. Introducing the AgMIP project and improving crop models for response to climate factors. Dr. K.J. Boote, University of Florida, USA. Crop and natural resource management. Dr. Stephan Haefele.

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Division seminars
Crop and Environmental Sciences “Three controls” technology: rice farmer’s choice in Guangdong. Dr Xuhua Zhong, Academy of Agricultural Sciences, China. Machine eyes and human eyes: testing new highthroughput phenotyping methods. Prof. Seishi Ninomiya, The University of Tokyo, Japan. GYGA: a global yield gap atlas overview and protocol. Justin van Wart, University of NebraskaLincoln, and Lenny van Bussel, Wageningen University (joint seminar with Social Sciences Division). Genomics of flooding stress tolerance: exploiting genetic variation in Arabidopsis thaliana. Dr. Rashmi Sasidharan, Institute of Environmental Biology, The Netherlands (joint seminar with Plant Breeding, Genetics, and Biotechnology Division). Towards the development of a stable and high-yielding aerobic rice system in Japan: considerations on physiology, agronomy and breeding. Keisuke Katsura and Midori Okami, Kyoto and Tokyo Universities, Japan. Greenhouse gas emission from rice fields: assessing the impact of elevated temperatures. Yam Kanta Gaihre, PhD scholar. Climate change and rice productivity. Prof. Hiroyuki Shimono, Faculty of Agriculture, Iwate University, Japan. Taking the heat: rice response to high night temperature. Onoriode Coast, PhD research scholar, University of Reading, UK. Rodent management strategies for different species of rice field rats in Southeast Asia. Nyo Me Htwe,

PhD affiliate scholar; PhD scholar, Northern Arizona University, USA. Electromagnetic soil survey techniques, with particular reference to the survey of the IRRI farm. John Medway and John Lucas, Terrabyte Services Ltd., Australia. IRRI Climate Unit: 32 years in providing climate services for the Los Baños community. Ms. Grace Centeno and Dr. Reiner Wassmann. The slow development of the rice plants in aerobic soils. Dr. Benoit Clerget. Time of anthesis in response to environmental conditions in rice (Oryza sativa). Cecile Julia, PhD research scholar. Drought-tolerant transgenic rice: hope or hype? Dr. Amelie Gaudin. Insecticide resistance selection, monitoring and detection in China: from mechanisms to management. Dr Liu Zewen, Nanjing Agricultural University, China. Overcoming the phenotyping bottlenecks: an Australian perspective. Dr. Xavier R.R. Sirault, CSIRO Plant Industry, Australia. Varietal difference of ripening ability in rice. Dr. Fumitaka Shiotsu, Ibaraki University, Japan. Emerging opportunities to adapt agriculture and food systems to a variable climate. Dr. James Hansen, Climate Change, Agriculture, and Food Security. Plant Breeding, Genetics, and Biotechnology Genetic improvement of rice for nutrient deficiency and problem soils: the case of phosphorus deficiency and iron toxicity. Dr. Khady Nani Dramé, AfricaRice, Tanzania.

Time of day and drought: the dynamic plant transcriptome. Dr. Olivia Wilkins, New York University, USA. Functional analyses of the rice protein kinase OsPSTOL1 (phosphorus starvation tolerance 1) gene. Rico Gamuyao, PhD scholar. Strigolactone transport: potential applications in improving parasitic weed resistance? Dr. Tobias Kretzschmar. Analysis of allele-specific expression imbalance in rice during normal and drought conditions. Nelzo C. Ereful, PhD research scholar. Development of C4 rice: rationale and progress. Dr. Shanta Karki, postdoctoral fellow. Microscopy: insights into rice response to drought stress. Ms. Rowena H. Oane. Mapping quantitative trait loci for seed longevity in rice and characterization of near-isogenic lines. Dr. Kazuhiro Sasaki, visiting research fellow. Marker-assisted breeding for high rice yield under drought. Dr. Shalabh Dixit, visiting research fellow. The International Oryza Map Alignment Project: Sequencing the collective Oryza genome to help solve the 9 billion-people question. Dr. Rod A. Wing, University of Arizona, USA. Redesigning rice to combat salt. Dr. Rafiqul Islam, postdoctoral fellow. Challenges for genetic analysis in MAGIC. Dr. Emma Huang, CSIRO, Brisbane, Australia. Cadmium transport in rice. Prof. Hiromi Nakanishi, Tokyo University, Japan. Exploring regulatory networks of secondary cell wall formation during vessel development in 9 of 10

IRRI Annual Report 2012

monocots and dicots. Dr. Lutz Neumetzler, visiting research fellow. MAGIC: a new genetic resource for multiple trait improvement and QTL discovery in rice. Mr. Nonoy B. Bandillo. Genomics, evolution and systems biology in rice and Arabidopsis: finding genes that matter for adaptation. Dr. Michael Purugganan, New York University, USA. Behind the scenes in a marker-assisted backcrossing program: development of Sub1 varieties. Ms. Darlene L. Sanchez. Importance of taxonomy for gene banks. Dr. Ronald G. van den Berg, Wageningen University, The Netherlands. Genetic mechanisms of salinity tolerance at reproductive stage in rice. Reza Mohammadi, PhD scholar. Plants and global change: the ubiquity of plasticity. Dr. Adrienne B. Nicotra, Australian National University, Canberra, Australia. Can agriculture feed and fuel the world? A role for plant biotechnology. Dr. Trevor Stevenson, RMIT University, Melbourne, Australia. Major and consistent drought grain yield QTLs for marker-assisted breeding in rice. Dr. Prashant Vikram, visiting research fellow.

Social Sciences
Ex-ante impact assessment of a combination of drought-and submergence-tolerant rice varieties in the presence of climate change. Dr. K.A. Mottaleb. Optimization sampling for rural household surveys. Ms. Maritess Tiongco, IFPRI, Washington, D.C. Changes in the agro-climate effects on cereal crop yields: panel evidence from India (1972-2002) with implications for sub-Saharan Africa. Dr. T. Tsusaka. Yield gap studies of rice production systems. Kees de Bie, University of Twente, The Netherlands. Long-run time-series analysis of global rice consumption through 2050. Dr. Roderick M. Rejesus, North Carolina State University, USA. What is new in Central Luzon: Irrigation, IMT, AWD, hybrid rice, research needs, etc. Dr. Randolph Barker and Dr. Cristina David. Incorporating process-based crop simulation models into global economic analyses of climate change. Mr. Ricky Robertson, IFPRI, Washington, D.C. Did the commodity price spike increase rural poverty? Evidence from a long-run panel in Bangladesh. Dr. Joseph Balagtas, Purdue University, USA. Consumer preference for rice grain quality. Ms. Frida Matilda Arnell, visitor/collaborator.

Patterns of varietal adoption and economics of rice production in Asia. Dr. Huaiyu Wang. Neigborhood effects and social behavior: the case of irrigated and rainfed rice farmers in Bohol, the Philippines. Preliminary study on behavioral game experiments. Dr. T. Tsusaka and Mr. J. Randall, intern. Guidance and technology: an assessment of project intervention and promoted technologies. Mr. Justin McKinley, intern. From Los Baños to Los Baños, my experience and travel research, summer 2012. Hoa Hoang, intern. Rice income and access to land market: the case of Bangladesh. Dr. K.A. Mottaleb. Possiblity of rice green revolution in sub-Saharan Africa: evidence from Ghana, Tanzania and Mozambique. Ms. Millicent Degraft-Johnson, National Graduate Institute for Policy Studies, Tokyo, Japan. Rice in Odisha: present constraints and future opportunities. Dr. D.P. Ray, Orissa University of Agriculture and Technology, India. Mapping rice areas with radar remote sensing: a case study for Leyte, Philippines. Mr. Roman Skorzus, research scholar. Sharing internship experience in IRRI. Fazleen Abdul Fatah, intern.

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