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https://www.readbyqxmd.com/read/28786034/bioinformatics-resources-for-deciphering-the-biogenesis-and-action-pathways-of-plant-small-rnas
#1
REVIEW
Dongliang Yu, Xiaoxia Ma, Ziwei Zuo, Weishan Shao, Huizhong Wang, Yijun Meng
The next-generation sequencing (NGS) technology has revolutionized our previous understanding of the plant genomes, relying on its innate advantages, such as high throughput and deep sequencing depth. In addition to the protein-coding gene loci, massive transcription signals have been detected within intergenic or intragenic regions. Most of these signals belong to non-coding ones, considering their weak protein-coding potential. Generally, these transcripts could be divided into long non-coding RNAs and small non-coding RNAs (sRNAs) based on their sequence length...
December 2017: Rice
https://www.readbyqxmd.com/read/28779340/identification-of-resistant-germplasm-containing-novel-resistance-genes-at-or-tightly-linked-to-the-pi2-9-locus-conferring-broad-spectrum-resistance-against-rice-blast
#2
Gui Xiao, Frances Nikki Borja, Ramil Mauleon, Jonas Padilla, Mary Jeanie Telebanco-Yanoria, Jianxia Yang, Guodong Lu, Maribel Dionisio-Sese, Bo Zhou
BACKGROUND: The rice Pi2/9 locus harbors multiple resistance (R) genes each controlling broad-spectrum resistance against diverse isolates of Magnaporthe oryzae, a fungal pathogen causing devastating blast disease to rice. Identification of more resistance germplasm containing novel R genes at or tightly linked to the Pi2/9 locus would promote breeding of resistance rice cultivars. RESULTS: In this study, we aim to identify resistant germplasm containing novel R genes at or tightly linked to the Pi2/9 locus using a molecular marker, designated as Pi2/9-RH (Pi2/9 resistant haplotype), developed from the 5' portion of the Pi2 sequence which was conserved only in the rice lines containing functional Pi2/9 alleles...
December 2017: Rice
https://www.readbyqxmd.com/read/28766258/panicle-blast-1-pb1-resistance-is-dependent-on-at-least-four-qtls-in-the-rice-genome
#3
Haruhiko Inoue, Mitsuru Nakamura, Tatsumi Mizubayashi, Akira Takahashi, Shoji Sugano, Shuuichi Fukuoka, Nagao Hayashi
BACKGROUND: Rice blast is the most serious disease afflicting rice and there is an urgent need for the use of disease resistance (R) genes in blast tolerance breeding programs. Pb1 is classified as a quantitative resistance gene and it does not have fungal specificity. Pb1-mediated resistance develops in the latter stages of growth. However, some cultivars, such as Kanto209 (K209), cultivar name Satojiman, despite possessing Pb1, do not exert resistance to rice blast during the reproductive stage...
December 2017: Rice
https://www.readbyqxmd.com/read/28730413/updating-the-elite-rice-variety-kongyu-131-by-improving-the-gn1a-locus
#4
Xiaomin Feng, Chen Wang, Jianzong Nan, Xiaohui Zhang, Rongsheng Wang, Guoqiang Jiang, Qingbo Yuan, Shaoyang Lin
BACKGROUND: Kongyu 131 is an elite japonica rice variety of Heilongjiang Province, China. It has the characteristics of early maturity, superior quality, high yield, cold tolerance and wide adaptability. However, there is potential to improve the yield of Kongyu 131 because of the relatively few grains per panicle compared with other varieties. Hence, we rebuilt the genome of Kongyu 131 by replacing the GRAIN NUMBER1a (Gn1a) locus with a high-yielding allele from a big panicle indica rice variety, GKBR...
December 2017: Rice
https://www.readbyqxmd.com/read/28730412/gns4-a-novel-allele-of-dwarf11-regulates-grain-number-and-grain-size-in-a-high-yield-rice-variety
#5
Yong Zhou, Yajun Tao, Jinyan Zhu, Jun Miao, Jun Liu, Yanhua Liu, Chuandeng Yi, Zefeng Yang, Zhiyun Gong, Guohua Liang
BACKGROUND: Rice plays an extremely important role in food safety because it feeds more than half of the world's population. Rice grain yield depends on biomass and the harvest index. An important strategy to break through the rice grain yield ceiling is to increase the biological yield. Therefore, genes associated with organ size are important targets for rice breeding. RESULTS: We characterized a rice mutant gns4 (grain number and size on chromosome 4) with reduced organ size, fewer grains per panicle, and smaller grains compared with those of WT...
December 2017: Rice
https://www.readbyqxmd.com/read/28730411/sugary-endosperm-is-modulated-by-starch-branching-enzyme-iia-in-rice-oryza-sativa-l
#6
Yunjoo Lee, Min-Seon Choi, Gileung Lee, Su Jang, Mi-Ra Yoon, Backki Kim, Rihua Piao, Mi-Ok Woo, Joong Hyoun Chin, Hee-Jong Koh
BACKGROUND: Starch biosynthesis is one of the most important pathways that determine both grain quality and yield in rice (Oryza sativa L.). Sugary endosperm, sugary-1 (sug-1), is a mutant trait for starch biosynthesis. Rice plants carrying sug-1 produce grains that accumulate water-soluble carbohydrates instead of starch, even after maturity. Although this trait enhances the diversity of grain quality, sugary endosperm rice has hardly been commercialized due to the severely wrinkled grains and subsequent problems in milling...
December 2017: Rice
https://www.readbyqxmd.com/read/28710696/mesocotyl-elongation-is-essential-for-seedling-emergence-under-deep-seeding-condition-in-rice
#7
Hyun-Sook Lee, Kazuhiro Sasaki, Ju-Won Kang, Tadashi Sato, Won-Yong Song, Sang-Nag Ahn
BACKGROUND: Direct-seeding cultivation by deep-seeding of seeds (drill seeding) is becoming popular due to the scarcity of land and labor. However, poor emergence and inadequate seedling establishment can lead to yield loss in direct-seeding cultivation by deep-sowing. In rice, mesocotyl and coleoptile are primarily responsible for seedling emergence from deeper levels of soil. RESULTS: Quantitative trait loci (QTLs) for mesocotyl and coleoptile length at 5-cm seeding depth were detected using 98 backcross inbred lines from a cross between Kasalath and Nipponbare...
December 2017: Rice
https://www.readbyqxmd.com/read/28664529/phenology-sterility-and-inheritance-of-two-environment-genic-male-sterile-egms-lines-for-hybrid-rice
#8
R El-Namaky, P A J van Oort
BACKGROUND: There is still limited quantitative understanding of how environmental factors affect sterility of Environment-conditioned genic male sterility (EGMS) lines. A model was developed for this purpose and tested based on experimental data from Ndiaye (Senegal) in 2013-2015. For the two EGMS lines tested here, it was not clear if one or more recessive gene(s) were causing male sterility. This was tested by studying sterility segregation of the F2 populations. RESULTS: Daylength (photoperiod) and minimum temperatures during the period from panicle initiation to flowering had significant effects on male sterility...
December 2017: Rice
https://www.readbyqxmd.com/read/28647924/comparative-expression-analysis-of-rice-and-arabidopsis-peroxiredoxin-genes-suggests-conserved-or-diversified-roles-between-the-two-species-and-leads-to-the-identification-of-tandemly-duplicated-rice-peroxiredoxin-genes-differentially-expressed-in-seeds
#9
Yun-Shil Gho, Sun-A Park, Sung-Ruyl Kim, Anil Kumar Nalini Chandran, Gynheung An, Ki-Hong Jung
BACKGROUND: Peroxiredoxins (PRXs) have recently been identified as plant antioxidants. Completion of various genome sequencing projects has provided genome-wide information about PRX genes in major plant species. Two of these -- Oryza sativa (rice) and Arabidopsis -- each have 10 PRX members. Although significant progress has been made in understanding their biological roles in Arabidopsis, those functions in rice, a model crop plant, have not been well studied. RESULTS: We performed a comparative expression analysis of rice and Arabidopsis PRXs...
December 2017: Rice
https://www.readbyqxmd.com/read/28597326/identification-of-bakanae-disease-resistance-loci-in-japonica-rice-through-genome-wide-association-study
#10
Andrea Volante, Alessandro Tondelli, Maria Aragona, Maria Teresa Valente, Chiara Biselli, Francesca Desiderio, Paolo Bagnaresi, Slavica Matic, Maria Lodovica Gullino, Alessandro Infantino, Davide Spadaro, Giampiero Valè
BACKGROUND: Bakanae disease, caused by seed-borne Fusarium species, mainly F. fujikuroi, is a rice disease whose importance is considerably increasing in several rice growing countries, leading to incremental production losses. RESULTS: A germplasm collection of japonica rice was screened for F. fujikuroi resistance, allowing the identification of accessions with high-to-moderate levels of resistance to bakanae. A GWAS approach uncovered two genomic regions highly associated with the observed phenotypic variation for response to bakanae infection on the short arm of chromosome 1 (named as qBK1_628091) and on the long arm of chromosome 4 (named as qBK4_31750955)...
December 2017: Rice
https://www.readbyqxmd.com/read/28584974/high-resolution-mapping-of-qtls-for-heat-tolerance-in-rice-using-a-5k-snp-array
#11
Shanmugavadivel Ps, Amitha Mithra Sv, Chandra Prakash, Ramkumar Mk, Ratan Tiwari, Trilochan Mohapatra, Nagendra Kumar Singh
BACKGROUND: Heat stress is one of the major abiotic threats to rice production, next to drought and salinity stress. Incidence of heat stress at reproductive phase of the crop results in abnormal pollination leading to floret sterility, low seed set and poor grain quality. Identification of QTLs and causal genes for heat stress tolerance at flowering will facilitate breeding for improved heat tolerance in rice. In the present study, we used 272 F8 recombinant inbred lines derived from a cross between Nagina22, a well-known heat tolerant Aus cultivar and IR64, a heat sensitive popular Indica rice variety to map the QTLs for heat tolerance...
December 2017: Rice
https://www.readbyqxmd.com/read/28577284/overexpression-of-rice-auxilin-like-protein-xb21-induces-necrotic-lesions-up-regulates-endocytosis-related-genes-and-confers-enhanced-resistance-to-xanthomonas-oryzae-pv-oryzae
#12
Chang-Jin Park, Tong Wei, Rita Sharma, Pamela C Ronald
BACKGROUND: The rice immune receptor XA21 confers resistance to the bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo). To elucidate the mechanism of XA21-mediated immunity, we previously performed a yeast two-hybrid screening for XA21 interactors and identified XA21 binding protein 21 (XB21). RESULTS: Here, we report that XB21 is an auxilin-like protein predicted to function in clathrin-mediated endocytosis. We demonstrate an XA21/XB21 in vivo interaction using co-immunoprecipitation in rice...
December 2017: Rice
https://www.readbyqxmd.com/read/28560587/evolutionary-relationships-and-expression-analysis-of-eul-domain-proteins-in-rice-oryza-sativa
#13
Kristof De Schutter, Mariya Tsaneva, Shubhada R Kulkarni, Pierre Rougé, Klaas Vandepoele, Els J M Van Damme
BACKGROUND: Lectins, defined as 'Proteins that can recognize and bind specific carbohydrate structures', are widespread among all kingdoms of life and play an important role in various biological processes in the cell. Most plant lectins are involved in stress signaling and/or defense. The family of Euonymus-related lectins (EULs) represents a group of stress-related lectins composed of one or two EUL domains. The latter protein domain is unique in that it is ubiquitous in land plants, suggesting an important role for these proteins...
December 2017: Rice
https://www.readbyqxmd.com/read/28547737/08sg2-osbak1-regulates-grain-size-and-number-and-functions-differently-in-indica-and-japonica-backgrounds-in-rice
#14
Hua Yuan, Shijun Fan, Juan Huang, Shijie Zhan, Shifu Wang, Peng Gao, Weilan Chen, Bin Tu, Bingtian Ma, Yuping Wang, Peng Qin, Shigui Li
BACKGROUND: Both grain size and grain number are significant for rice yield. In the past decade, a number of genes related to grain size and grain number have been documented, however, the regulatory mechanisms underlying them remains ambiguous. RESULTS: We identified a rice small grain (sg2) mutant in an EMS mutant library generated from an indica variety, Shuhui498. Using the MutMap gene mapping strategy, we identified two linkage regions on chromosome 7 and 8, respectively, consistent with the segregation ratios in the F2 population...
December 2017: Rice
https://www.readbyqxmd.com/read/28547736/rice-bran-metabolome-contains-amino-acids-vitamins-cofactors-and-phytochemicals-with-medicinal-and-nutritional-properties
#15
Iman Zarei, Dustin G Brown, Nora Jean Nealon, Elizabeth P Ryan
BACKGROUND: Rice bran is a functional food that has shown protection against major chronic diseases (e.g. obesity, diabetes, cardiovascular disease and cancer) in animals and humans, and these health effects have been associated with the presence of bioactive phytochemicals. Food metabolomics uses multiple chromatography and mass spectrometry platforms to detect and identify a diverse range of small molecules with high sensitivity and precision, and has not been completed for rice bran...
December 2017: Rice
https://www.readbyqxmd.com/read/28534133/silencing-of-the-rice-gene-lrr1-compromises-rice-xa21-transcript-accumulation-and-xa21-mediated-immunity
#16
Daniel F Caddell, Chang-Jin Park, Nicholas C Thomas, Patrick E Canlas, Pamela C Ronald
BACKGROUND: The rice immune receptor XA21 confers resistance to Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial leaf blight. We previously demonstrated that an auxilin-like protein, XA21 BINDING PROTEIN 21 (XB21), positively regulates resistance to Xoo. RESULTS: To further investigate the function of XB21, we performed a yeast two-hybrid screen. We identified 22 unique XB21 interacting proteins, including LEUCINE-RICH REPEAT PROTEIN 1 (LRR1), which we selected for further analysis...
December 2017: Rice
https://www.readbyqxmd.com/read/28527137/genome-based-identification-of-heterotic-patterns-in-rice
#17
Ulrike Beukert, Zuo Li, Guozheng Liu, Yusheng Zhao, Nadhigade Ramachandra, Vilson Mirdita, Fabiano Pita, Klaus Pillen, Jochen Christoph Reif
BACKGROUND: Hybrid rice breeding facilitates to increase grain yield and yield stability. Long-term success of hybrid breeding depends on the recognition of high-yielding complementary heterotic patterns, which is lacking in crops like rice. RESULT: The main goal of this study was to evaluate the potential and limits to use genomics for establishing heterotic patterns in rice. For this purpose, data of a commercial hybrid rice breeding program targeted to India was analyzed, including 1,960 phenotyped hybrids from three market segments and 262 genotyped parental lines...
December 2017: Rice
https://www.readbyqxmd.com/read/28523639/association-mapping-of-yield-and-yield-related-traits-under-reproductive-stage-drought-stress-in-rice-oryza-sativa-l
#18
B P Mallikarjuna Swamy, Noraziyah Abd Aziz Shamsudin, Site Noorzuraini Abd Rahman, Ramil Mauleon, Wickneswari Ratnam, Ma Teressa Sta Cruz, Arvind Kumar
BACKGROUND: The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS: The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%...
December 2017: Rice
https://www.readbyqxmd.com/read/28500411/a-hairy-leaf-gene-blanket-leaf-of-wild-oryza-nivara-increases-photosynthetic-water-use-efficiency-in-rice
#19
Norimitsu Hamaoka, Hideshi Yasui, Yoshiyuki Yamagata, Yoko Inoue, Naruto Furuya, Takuya Araki, Osamu Ueno, Atsushi Yoshimura
BACKGROUND: High water use efficiency is essential to water-saving cropping. Morphological traits that affect photosynthetic water use efficiency are not well known. We examined whether leaf hairiness improves photosynthetic water use efficiency in rice. RESULTS: A chromosome segment introgression line (IL-hairy) of wild Oryza nivara (Acc. IRGC105715) with the genetic background of Oryza sativa cultivar 'IR24' had high leaf pubescence (hair). The leaf hairs developed along small vascular bundles...
December 2017: Rice
https://www.readbyqxmd.com/read/28500410/erratum-to-aldo-ketoreductase-1-akr1-improves-seed-longevity-in-tobacco-and-rice-by-detoxifying-reactive-cytotoxic-compounds-generated-during-ageing
#20
Kodadinne Narayana Nisarga, Ramu S Vemanna, Babitha Kodekallu Chandrashekar, Hanumantha Rao, Amaranatha Reddy Vennapusa, Ashwini Narasimaha, Udayakumar Makarla, Mohan Raju Basavaiah
No abstract text is available yet for this article.
December 2017: Rice
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