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Juan L Reig-Valiente, Juan Viruel, Ester Sales, Luis Marqués, Javier Terol, Marta Gut, Sophia Derdak, Manuel Talón, Concha Domingo
BACKGROUND: After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a valuable resource for crop improvement. In general, current rice breeding programs have to deal with a lack of both germplasm accessions specifically adapted to local agro-environmental conditions and adapted donors carrying desired agronomical traits...
December 2016: Rice
Wei Tong, Tae-Sung Kim, Yong-Jin Park
BACKGROUND: Chloroplast genome variations have been detected, despite its overall conserved structure, which has been valuable for plant population genetics and evolutionary studies. Here, we described chloroplast variation architecture of 383 rice accessions from diverse regions and different ecotypes, in order to mine the rice chloroplast genome variation architecture and phylogenetic. RESULTS: A total of 3677 variations across the chloroplast genome were identified with an average density of 27...
December 2016: Rice
HyunJung Kim, Janelle Jung, Namrata Singh, Anthony Greenberg, Jeff J Doyle, Wricha Tyagi, Jong-Wook Chung, Jennifer Kimball, Ruaraidh Sackville Hamilton, Susan R McCouch
BACKGROUND: Understanding population structure of the wild progenitor of Asian cultivated rice (O. sativa), the Oryza rufipogon species complex (ORSC), is of interest to plant breeders and contributes to our understanding of rice domestication. A collection of 286 diverse ORSC accessions was evaluated for nuclear variation using genotyping-by-sequencing (113,739 SNPs) and for chloroplast variation using Sanger sequencing (25 polymorphic sites). RESULTS: Six wild subpopulations were identified, with 25 % of accessions classified as admixed...
December 2016: Rice
Ning Yu, Yaping Liang, Xinxiang Peng, Xuewen Hou
BACKGROUND: ROOT UV-B SENSITIVE (RUS) genes exist in most eukaryotic organisms, and encode proteins that contain a DUF647 (domain of unknown function 647). Although the RUS genes are known to play essential roles in Arabidopsis seedling development, their precise functions are not well understood in other plants, including rice. FINDINGS: In this study, six OsRUS genes were cloned from rice root and leaf cDNA libraries. Our analysis showed that the sequence and open reading frame of cloned OsRUS3 cDNA differs from the predictions reported in the RAP-DB and RGAP databases...
December 2016: Rice
Chan-Mi Lee, Jonghwa Park, Backki Kim, Jeonghwan Seo, Gileung Lee, Su Jang, Hee-Jong Koh
No abstract text is available yet for this article.
December 2016: Rice
Hongbo Wang, Shengtuo Ye, Tongmin Mou
BACKGROUND: The development of hybrid rice is a practical approach for increasing rice production. However, the brown planthopper (BPH), Nilaparvata lugens Stål, causes severe yield loss of rice (Oryza sativa L.) and can threaten food security. Therefore, breeding hybrid rice resistant to BPH is the most effective and economical strategy to maintain high and stable production. Fortunately, numerous BPH resistance genes have been identified, and abundant linkage markers are available for molecular marker-assisted selection (MAS) in breeding programs...
December 2016: Rice
Teresa B De Leon, Steven Linscombe, Prasanta K Subudhi
BACKGROUND: Salinity is one of the many abiotic stresses limiting rice production worldwide. Several studies were conducted to identify quantitative trait loci (QTLs) for traits associated to salinity tolerance. However, due to large confidence interval for the position of QTLs, utility of reported QTLs and the associated markers has been limited in rice breeding programs. The main objective of this study is to construct a high-density rice genetic map for identification QTLs and candidate genes for salinity tolerance at seedling stage...
December 2016: Rice
Bijayalaxmi Mohanty, Hirokazu Takahashi, Benildo G de Los Reyes, Edward Wijaya, Mikio Nakazono, Dong-Yup Lee
BACKGROUND: Rice is the only crop that germinates and elongates the coleoptile under complete submergence. It has been shown that alcohol dehydrogenase 1 (ADH1)-deficient mutant of rice with reduced alcohol dehydrogenase activity (rad) and reduced ATP level, is viable with much reduced coleoptile elongation under such condition. To understand the altered transcriptional regulatory mechanism of this mutant, we aimed to establish possible relationships between gene expression and cis-regulatory information content...
December 2016: Rice
Nelzo C Ereful, Li-Yu Liu, Eric Tsai, Shu-Min Kao, Shalabh Dixit, Ramil Mauleon, Katrina Malabanan, Michael Thomson, Antonio Laurena, David Lee, Ian Mackay, Andy Greenland, Wayne Powell, Hei Leung
BACKGROUND: Information on the effect of stress on the allele-specific expression (ASE) profile of rice hybrids is limited. More so, the association of allelically imbalanced genes to important traits is yet to be understood. Here we assessed allelic imbalance (AI) in the heterozygote state of rice under non- and water-stress treatments and determined association of asymmetrically expressed genes with grain yield (GY) under drought stress by in-silico co-localization analysis and selective genotyping...
December 2016: Rice
B P Mallikarjuna Swamy, Mohammad Akhlasur Rahman, Mary Ann Inabangan-Asilo, Amery Amparado, Christine Manito, Prabhjit Chadha-Mohanty, Russell Reinke, Inez H Slamet-Loedin
Zinc (Zn) is one of the most essential micronutrients required for the growth and development of human beings. More than one billion people, particularly children and pregnant women suffer from Zn deficiency related health problems in Asia. Rice is the major staple food for Asians, but the presently grown popular high yielding rice varieties are poor supplier of Zn in their polished form. Breeding rice varieties with high grain Zn has been suggested to be a sustainable, targeted, food-based and cost effective approach in alleviating Zn deficiency...
December 2016: Rice
Likai Chen, Weiwei Gao, Siping Chen, Liping Wang, Jiyong Zou, Yongzhu Liu, Hui Wang, Zhiqiang Chen, Tao Guo
BACKGROUND: Grain appearance quality is a main determinant of market value in rice and one of the highly important traits requiring improvement in breeding programs. The genetic basis of grain shape and endosperm chalkiness have been given significant attention because of their importance in affecting grain quality. Meanwhile, the introduction of NGS (Next Generation Sequencing) has a significant part to play in the area of genomics, and offers the possibility for high-resolution genetic map construction, population genetics analysis and systematic expression profile study...
December 2016: Rice
Zhijian Liang, Ling Wang, Qinghua Pan
BACKGROUND: Rice blast (causative pathogen Magnaporthe oryzae) represents a major biotic constraint over rice production. While numerous genes for resistance have been found in both japonica and indica germplasm, as yet the diversity harbored by aus germplasm has not been widely exploited. RESULTS: The blast resistance present in the aus type cultivar AS20-1 was shown, via an analysis of segregation in the F2 generation bred from a cross with the highly blast susceptible cultivar Aichi Asahi, to be due to the action of a single recessive gene, denoted pi66(t)...
December 2016: Rice
Ying-Ying Li, Ao Shen, Wei Xiong, Qiong-Lin Sun, Qian Luo, Ting Song, Zheng-Long Li, Wei-Jiang Luan
BACKGROUND: The Class III homeodomain Leu zipper (HD-Zip III) gene family plays important roles in plant growth and development. Here, we analyze the function of OsHox32, an HD-Zip III family member, and show that it exhibits pleiotropic effects on regulating plant type architecture and leaf development in rice. RESULTS: Transgenic lines overexpressing OsHox32 (OsHox32-OV) produce narrow leaves that roll towards the adaxial side. Histological analysis revealed a decreased number of bulliform cells in OsHox32-OV lines...
December 2016: Rice
R Abdul Fiyaz, Ashutosh K Yadav, S Gopala Krishnan, Ranjith K Ellur, Bishnu M Bashyal, Nitasha Grover, Prolay K Bhowmick, M Nagarajan, K K Vinod, Nagendra K Singh, Kumble V Prabhu, Ashok K Singh
BACKGROUND: Bakanae or foot rot disease caused by Fusarium fujikuroi [teleomorph: Gibberella fujikuroi (Sawada) Ito] is emerging as a serious disease in rice. The disease causes both quantitative and qualitative losses to the grains under the field conditions. Breeding for resistance to Bakanae disease is a promising strategy to manage this emerging disease. In this study, we used a population of 168 F14 recombinant inbred lines (RILs) derived from two indica rice parents Pusa 1342, a highly resistant variety and Pusa Basmati 1121, a highly susceptible variety to map quantitative trait loci (QTLs) governing resistance against Bakanae disease...
December 2016: Rice
Dan Zhu, Houxiang Kang, Zhiqiang Li, Minghao Liu, Xiaoli Zhu, Yue Wang, Dan Wang, Zhilong Wang, Wende Liu, Guo-Liang Wang
BACKGROUND: Breeding of rice cultivars with long-lasting resistance to the rice blast fungus Magnaporthe oryzae is difficult, and identification of new resistance genes is essential. Most of the loci associated with blast resistance against M. oryzae in rice have been identified in controlled environments and with single isolates, and such loci may confer resistance to only a small faction of the M. oryzae strains. In the field, however, rice is commonly attacked by multiple strains. Research is therefore needed to identify loci that confer resistance in the field, i...
December 2016: Rice
Hong-Yu Zhang, Ming Luo, Susan D Johnson, Xiao-Wei Zhu, Lei Liu, Fang Huang, Yu-Tong Liu, Pei-Zhou Xu, Xian-Jun Wu
BACKGROUND: Reproductive isolation between rice of different ploidy levels is manifested as endosperm and embryo abortion in seeds produced by interploidy crosses. Genomic imprinting is considered to be the underlying mechanism establishing the post-zygotic hybridization barrier. We characterized disrupted seed development in reciprocal crosses between a diploid Japonica rice and a tetraploid Indica rice. RESULTS: Triploid seeds from these crosses had aborted development and could not germinate in soil but could be rescued in culture medium with significantly more seeds developing to seedlings in the 4n × 2n (♀-♂) cross with excess maternal genomes than in the 2n × 4n cross with excess paternal genome...
December 2016: Rice
Matthew Shenton, Chie Iwamoto, Nori Kurata, Kazuho Ikeo
BACKGROUND: Deposition and secretion from roots influences the composition of the microbial communities surrounding them in the rhizosphere, and microbial activities influence the growth and health of the plant. Different host plant genotypes result in differences in those microbial communities. Crop genomes may have a narrow genetic base because of bottlenecks that occurred when domesticated crops were derived from small populations within the progenitor species. Desirable traits influencing root-associated microbial communities might therefore have been lost in the transition from wild species to modern cultivars...
December 2016: Rice
Yang Gao, Chaolei Liu, Yuanyuan Li, Anpeng Zhang, Guojun Dong, Lihong Xie, Bin Zhang, Banpu Ruan, Kai Hong, Dawei Xue, Dali Zeng, Longbiao Guo, Qian Qian, Zhenyu Gao
BACKGROUND: An ideal appearance is of commercial value for rice varieties. Chalkiness is one of the most important appearance quality indicators. Therefore, clarification of the heredity of chalkiness and its molecular mechanisms will contribute to reduction of rice chalkiness. Although a number of QTLs related to chalkiness were mapped, few of them have been cloned so far. RESULTS: In this study, using recombinant inbred lines (RILs) of PA64s and 9311, we identified 19 QTLs associated with chalkiness on chromosomes 1, 4, 6, 7, 9 and 12, which accounted for 5...
December 2016: Rice
Anil Kumar Nalini Chandran, Yo-Han Yoo, Peijian Cao, Rita Sharma, Manoj Sharma, Christopher Dardick, Pamela C Ronald, Ki-Hong Jung
BACKGROUND: Protein kinases catalyze the transfer of a phosphate moiety from a phosphate donor to the substrate molecule, thus playing critical roles in cell signaling and metabolism. Although plant genomes contain more than 1000 genes that encode kinases, knowledge is limited about the function of each of these kinases. A major obstacle that hinders progress towards kinase characterization is functional redundancy. To address this challenge, we previously developed the rice kinase database (RKD) that integrated omics-scale data within a phylogenetics context...
December 2016: Rice
Lei Gao, Jiadong Chang, Ruijie Chen, Hubo Li, Hongfei Lu, Longxing Tao, Jie Xiong
Iron (Fe) is essential for rice growth and humans consuming as their staple food but is often deficient because of insoluble Fe(III) in soil for rice growth and limited assimilation for human bodies, while cadmium (Cd) is non-essential and toxic for rice growth and humans if accumulating at high levels. Over-accumulated Cd can cause damage to human bodies. Selecting and breeding Fe-rich but Cd-free rice cultivars are ambitious, challenging and meaningful tasks for researchers. Although evidences show that the mechanisms of Fe/Cd uptake and accumulation in rice are common to some extent as a result of similar entry routes within rice, an increasing number of researchers have discovered distinct mechanisms between Fe/Cd uptake and accumulation in rice...
December 2016: Rice
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