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Marta Brozynska, Dario Copetti, Agnelo Furtado, Rod A Wing, Darren Crayn, Glen Fox, Ryuji Ishikawa, Robert J Henry
The related A genome species of the Oryza genus are the effective gene pool for rice. Here we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short and long read next generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A, has a sequence that is much closer to that of domesticated rice (O...
November 27, 2016: Plant Biotechnology Journal
Yeo-Tae Yun, Chong-Tae Chung, Young-Ju Lee, Han-Jung Na, Jae-Chul Lee, Sun-Gye Lee, Kwang-Won Lee, Young-Hwan Yoon, Ju-Won Kang, Hyun-Sook Lee, Jong-Yeol Lee, Sang-Nag Ahn
BACKGROUND: Improved eating quality is a major breeding target in japonica rice due to market demand. Consequently, quantitative trait loci (QTL) for glossiness of cooked rice and amylose content associated with eating quality have received much research focus because of their importance in rice quality. RESULTS: In this study, QTL associated with 12 grain quality traits were identified using 96 introgression lines (IL) of rice developed from an interspecific cross between the Korean elite O...
December 2016: Rice
Biao-Lin Hu, Jian-Kun Xie, Yong Wan, Jin-Wei Zhang, Fan-Tao Zhang, Xia Li
Hybrid rice breeding using cytoplasmic male sterility/fertility restoration (CMS/Rf) systems plays an important role in ensuring global food security. Two backcross inbred line (BIL) populations derived from either Xieqingzao B (XB)//XB/Dongxiang wild rice (DWR) (XXD) or XB//DWR/XB (XDX) were used to detect quantitative trait loci (QTLs) for fertility restoration of Dwarf wild abortive- (DA-), Indonesia Paddy- (ID-), and DWR-type CMS in rice. Lines with ID- and DA-type CMS were testcrossed with both the XXD- and XDX-BILs, while the line with DWR-type CMS was testcrossed with the XDX-BILs only...
2016: BioMed Research International
Khin Thanda Win, Yoshiyuki Yamagata, Kazuyuki Doi, Kazuhiro Uyama, Yasuko Nagai, Yosuke Toda, Takahiro Kani, Motoyuki Ashikari, Hideshi Yasui, Atsushi Yoshimura
Reduced seed shattering was a critical evolutionary step in crop domestication. Two cultivated rice species, Oryza sativa and Oryza glaberrima, were independently domesticated from the wild species Oryza rufipogon in Asia and Oryza barthii in Africa, respectively. A single nucleotide polymorphism (SNP) in the c gene, which encodes a trihelix transcription factor, causes nonshattering in O. sativa. However, the genetic mechanism of nonshattering in O. glaberrima is poorly understood. We conducted an association analysis for the coding sequences of SH3/SH4 in AA- genome rice species and the mutation suggested to cause nonshattering was demonstrated to do so using a positional-cloning approach in the O...
November 12, 2016: New Phytologist
Tomonobu Toyomasu, Koji Miyamoto, Matthew R Shenton, Arisa Sakai, Chizu Sugawara, Kiyotaka Horie, Hiroshi Kawaide, Morifumi Hasegawa, Masaru Chuba, Wataru Mitsuhashi, Hisakazu Yamane, Nori Kurata, Kazunori Okada
Cultivated rice (Oryza sativa) possesses various labdane-related diterpene synthase genes, homologs of ent-copalyl diphosphate synthase (CPS) and ent-kaurene synthase (KS) that are responsible for the biosynthesis of phytohormone gibberellins. The CPS homologs and KS like (KSL) homologs successively converted geranylgeranyl diphosphate to cyclic diterpene hydrocarbons via ent-copalyl diphosphate or syn-copalyl diphosphate in O. sativa. Consequently, a variety of labdane-related diterpenoids, including phytoalexin phytocassanes, momilactones and oryzalexins, have been identified from cultivated rice...
October 19, 2016: Biochemical and Biophysical Research Communications
Sidhanta Sekhar Bisoi, Swati S Mishra, Jijnasa Barik, Debabrata Panda
The aim of the present study was investigation the effects of fly ash and mining soil on growth and antioxidant protection of two cultivars of Indian wild rice (Oryza nivara and Oryza rufipogon) for possible phytoremediation and restoration of metal contaminated site. In this study, Indian wild rice showed significant changes in germination, growth and biochemical parameters after exposure to different ratio of fly ash and mining soil with garden soil. There was significant reduction of germination, fresh weight, dry weight, leaf chlorophyll content, leaf area, SPAD index, proteins, and activities of antioxidant enzymes in both cultivars of the wild rice grown in 100% fly ash and mining soil compared to the plants grown in 100% garden soil...
October 14, 2016: International Journal of Phytoremediation
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
Yongxia Cui, Beng Kah Song, Lin-Feng Li, Ya-Ling Li, Zhongyun Huang, Ana L Caicedo, Yulin Jia, Kenneth M Olsen
Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation...
October 11, 2016: G3: Genes—Genomes—Genetics
Huiwu Tang, Xingmei Zheng, Chuliang Li, Xianrong Xie, Yuanling Chen, Letian Chen, Xiucai Zhao, Huiqi Zheng, Jiajian Zhou, Shan Ye, Jingxin Guo, Yao-Guang Liu
New gene origination is a major source of genomic innovations that confer phenotypic changes and biological diversity. Generation of new mitochondrial genes in plants may cause cytoplasmic male sterility (CMS), which can promote outcrossing and increase fitness. However, how mitochondrial genes originate and evolve in structure and function remains unclear. The rice Wild Abortive type of CMS is conferred by the mitochondrial gene WA352c (previously named WA352) and has been widely exploited in hybrid rice breeding...
October 11, 2016: Cell Research
Jing Jin, Lei Hua, Zuofeng Zhu, Lubin Tan, Xinhui Zhao, Weifeng Zhang, Fengxia Liu, Yongcai Fu, Hongwei Cai, Xianyou Sun, Ping Gu, Daoxin Xie, Chuanqing Sun
Cultivated rice (Oryza sativa L.) was domesticated from wild rice (Oryza rufipogon Griff.), which typically displays fewer grains per panicle and longer grains than cultivated rice. In addition, wild rice has long awns, whereas cultivated rice has short awns or lacks them altogether. These changes represent critical events in rice domestication. Here, we identified a major gene, GRAIN NUMBER, GRAIN LENGTH AND AWN DEVELOPMENT 1 (GAD1), that regulates those critical changes during rice domestication. GAD1 is located on chromosome 8 and is predicted to encode a small secretary signal peptide belonging to the EPIDERMAL PATTERNING FACTOR-LIKE family...
September 15, 2016: Plant Cell
Pritesh Sundar Roy, Gundimeda Jwala Narasimha Rao, Sudipta Jena, Rashmita Samal, Ashok Patnaik, Sasank Sekhar Chyau Patnaik, Nitiprasad Namdeorao Jambhulkar, Srigopal Sharma, Trilochan Mohapatra
A large number of short grain aromatic rice suited to the agro-climatic conditions and local preferences are grown in niche areas of different parts of India and their diversity is evolved over centuries as a result of selection by traditional farmers. Systematic characterization of these specialty rices has not been attempted. An effort was made to characterize 126 aromatic short grain rice landraces, collected from 19 different districts in the State of Odisha, from eastern India. High level of variation for grain quality and agronomic traits among these aromatic rices was observed and genotypes having desirable phenotypic traits like erect flag leaf, thick culm, compact and dense panicles, short plant stature, early duration, superior yield and grain quality traits were identified...
2016: PloS One
Weihua Qiao, Lan Qi, Zhijun Cheng, Long Su, Jing Li, Yan Sun, Junfang Ren, Xiaoming Zheng, Qingwen Yang
BACKGROUND: Wild rice (Oryza rufipogon) constitutes a primary gene source for rice breed improvement. Chromosome segment substitution line (CSSL) for O. rufipogon is a powerful tool for fine mapping of quantitative traits, new gene discovery, and marker-assisted breeding. Thus, they provide a basis for a wide range of genomic and genetic studies. RESULTS: In this study, a set of 198 CSSLs were developed from a cross between recurrent parent indica var. 9311 and an O...
2016: BMC Genomics
Keisuke Igarashi, Tomohiko Kazama, Kinya Toriyama
Cytoplasmic male sterility (CMS) lines in rice, which have the cytoplasm of a wild species and the nuclear genome of cultivated rice, are of value for the study of genetic interactions between the mitochondrial and nuclear genomes. The RT98-type CMS line RT98A and the fertility restorer line RT98C carry the cytoplasm of the wild species Oryza rufipogon and the nuclear genome of the Taichung 65 cultivar (Oryza sativa L.). Based on a classical crossing experiment, fertility is reported to be restored gametophytically by the presence of a tentative single gene, designated Rf98, which is derived from the cytoplasm donor...
October 2016: Plant & Cell Physiology
Ying Yang, Jiawu Zhou, Jing Li, Peng Xu, Yu Zhang, Dayun Tao
In order to know the genetic nature of hybrid sterility further, three populations, a BC4F2 population derived from Oryza nivara crossed with Yundao 1, a BC4F2 population derived from O. rufipogon crossed with Yundao 1, and a BC10F1 population derived from a cross between O. barthii and Dianjingyou 1 were developed, respectively. Three hybrid sterility QTLs, qHS-6a, qHS-6b, and qHS-6c, detected from those three populations, were mapped into the region between RM190 and RM510, RM190 and RM3414, RM190 and RM587 on chromosome 6, respectively...
June 2016: Breeding Science
V Vishnu Prasanth, Kumari Ramana Basava, M Suchandranath Babu, Venkata Tripura V G N, S J S Rama Devi, S K Mangrauthia, S R Voleti, N Sarla
Rice lines derived from wild species and mutants can serve as a good resource for favorable alleles for heat tolerance. In all, 48 stable lines including 17 KMR3/O. rufipogon introgression lines (KMR3 ILs), 15 Swarna/O. nivara ILs (Swarna ILs) along with their parents, Nagina 22 (N22) and its 4 EMS induced mutants and 7 varieties were evaluated for heat tolerance under irrigated conditions under field in two seasons, wet season 2012 using poly cover house method and dry season 2013 using late sown method. Spikelet fertility (SF), yield per plant (YP) and heat susceptibility index (HSI) for these two traits were considered as criteria to assess heat tolerance compared to control...
April 2016: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
Avishek Dey, Milan Kumar Samanta, Srimonta Gayen, Mrinal K Maiti
BACKGROUND: Family members of sucrose non-fermenting 1-related kinase 2 (SnRK2), being plant-specific serine/threonine protein kinases, constitute the central core of abscisic acid (ABA)-dependent and ABA-independent signaling pathways, and are key regulators of abiotic stress adaptation in plants. We report here the functional characterization of SAPK9 gene, one of the 10 SnRK2s of rice, through developing gain-of-function and loss-of-function phenotypes by transgenesis. RESULTS: The gene expression profiling revealed that the abundance of single gene-derived SAPK9 transcript was significantly higher in drought-tolerant rice genotypes than the drought-sensitive ones, and its expression was comparatively greater in reproductive stage than the vegetative stage...
2016: BMC Plant Biology
Muhammad Abdul Rehman Rashid, Yan Zhao, Hongliang Zhang, Jinjie Li, Zichao Li
Lodging resistance is one of the vital traits in yield improvement and sustainability. Culm wall thickness, diameter, and strength are different traits that can govern the lodging resistance in rice. The genes SCM2 and FC1 have been isolated for culm thickness, strength, and flexibility, but their functional nucleotide variations were still unknown. We used a 13× deep sequence of 795 diverse genotypes to present the functional variation and SNP diversity in SCM2 and FC1. The major functional variant for the SCM2 gene was at position 27480181 and for the FC1 gene at position 31072992...
July 2016: Genome Génome / Conseil National de Recherches Canada
Koji Miyamoto, Masahiro Fujita, Matthew R Shenton, Shota Akashi, Chizu Sugawara, Arisa Sakai, Kiyotaka Horie, Morifumi Hasegawa, Hiroshi Kawaide, Wataru Mitsuhashi, Hideaki Nojiri, Hisakazu Yamane, Nori Kurata, Kazunori Okada, Tomonobu Toyomasu
Plants frequently possess operon-like gene clusters for specialized metabolism. Cultivated rice, Oryza sativa, produces antimicrobial diterpene phytoalexins represented by phytocassanes and momilactones, and the majority of their biosynthetic genes are clustered on chromosomes 2 and 4, respectively. These labdane-related diterpene phytoalexins are biosynthesized from geranylgeranyl diphosphate via ent-copalyl diphosphate or syn-copalyl diphosphate. The two gene clusters consist of genes encoding diterpene synthases and chemical-modification enzymes including P450s...
August 2016: Plant Journal: for Cell and Molecular Biology
Fantao Zhang, Tao Xu, Linyong Mao, Shuangyong Yan, Xiwen Chen, Zhenfeng Wu, Rui Chen, Xiangdong Luo, Jiankun Xie, Shan Gao
BACKGROUND: It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level. RESULTS: Instead of comparing two assembled genomes, this study directly compared the Dongxiang wild rice (DXWR) Illumina sequencing reads with the Nipponbare (O...
2016: BMC Plant Biology
Sajjad Asaf, Abdul Latif Khan, Abdur Rahim Khan, Muhammad Waqas, Sang-Mo Kang, Muhammad Aaqil Khan, Raheem Shahzad, Chang-Woo Seo, Jae-Ho Shin, In-Jung Lee
Oryza minuta (Poaceae family) is a tetraploid wild relative of cultivated rice with a BBCC genome. O. minuta has the potential to resist against various pathogenic diseases such as bacterial blight (BB), white backed planthopper (WBPH) and brown plant hopper (BPH). Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. The mtDNA genome is 515,022 bp, containing 60 protein coding genes, 31 tRNA genes and two rRNA genes. The mitochondrial genome organization and the gene content at the nucleotide level are highly similar (89%) to that of O...
2016: PloS One
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