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Railson Schreinert Dos Santos, Daniel da Rosa Farias, Camila Pegoraro, Cesar Valmor Rombaldi, Takeshi Fukao, Rod A Wing, Antonio Costa de Oliveira
BACKGROUND: Tolerance to complete submergence is recognized in a limited number of Asian rice (Oryza sativa L.) varieties, most of which contain submergence-inducible SUB1A on the polygenic SUBMERGENCE-1 (SUB1) locus. It has been shown that the SUB1 locus encodes two Ethylene-Responsive Factor (ERF) genes, SUB1B and SUB1C, in all O. sativa varieties. These genes were also found in O rufipogon and O nivara, wild relatives of O. sativa. However, detailed analysis of the polygenic locus in other Oryza species has not yet been made...
December 2017: Rice
Tomoyuki Furuta, Kanako Uehara, Rosalyn B Angeles-Shim, Junghyun Shim, Keisuke Nagai, Motoyuki Ashikari, Tomonori Takashi
Chromosome segment substitution lines (CSSLs) are rich genetic resources that can be mined for novel, agriculturally useful loci or that can be used directly as materials for breeding. To date, a number of rice CSSLs have been developed by crossing rice cultivars with its wild relatives as a means to tap into the potential of wild alleles in rice improvement. Oryza nivara is a wild relative of rice that is thought to be a progenitor of O. sativa spp. indica. In the present study, 26 CSSLs that covers the entire genome of O...
December 2016: Breeding Science
Jae Young Choi, Adrian E Platts, Dorian Q Fuller, Yue-Ie Hsing, Rod A Wing, Michael D Purugganan
The origin of domesticated Asian rice (Oryza sativa) has been a contentious topic, with conflicting evidence for either single or multiple domestication of this key crop species. We examined the evolutionary history of domesticated rice by analyzing de novo assembled genomes from domesticated rice and its wild progenitors. Our results indicate multiple origins, where each domesticated rice subpopulation (japonica, indica, and aus) arose separately from progenitor O. rufipogon and/or O. nivara Coalescence-based modeling of demographic parameters estimate that the first domesticated rice population to split off from O...
January 12, 2017: Molecular Biology and Evolution
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
Divya Balakrishnan, Desiraju Subrahmanyam, Jyothi Badri, Addanki Krishnam Raju, Yadavalli Venkateswara Rao, Kavitha Beerelli, Sukumar Mesapogu, Malathi Surapaneni, Revathi Ponnuswamy, G Padmavathi, V Ravindra Babu, Sarla Neelamraju
Advanced backcross introgression lines (BILs) developed from crosses of Oryza sativa var. Swarna/O. nivara accessions were grown and evaluated for yield and related traits. Trials were conducted for consecutive three seasons in field conditions in a randomized complete block design with three replications. Data on yield traits under irrigated conditions were analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) and modified rank-sum statistic (YSi) for yield stability...
2016: Frontiers in Plant Science
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
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
Hengjian Xu, Kenneth A Watanabe, Liyuan Zhang, Qingxi J Shen
The WRKY transcription factor family is one of the largest gene families involved in plant development and stress response. Although many WRKY genes have been studied in cultivated rice (Oryza sativa), the WRKY genes in the wild rice species Oryza nivara, the direct progenitor of O. sativa, have not been studied. O. nivara shows abundant genetic diversity and elite drought and disease resistance features. Herein, a total of 97 O. nivara WRKY (OnWRKY) genes were identified. RNA-sequencing demonstrates that OnWRKY genes were generally expressed at higher levels in the roots of 30-day-old plants...
August 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Rong Liu, Xiao-Ming Zheng, Lian Zhou, Hai-Fei Zhou, Song Ge
Ecological speciation plays a primary role in driving species divergence and adaptation. Oryza rufipogon and Oryza nivara are two incipient species at the early stage of speciation with distinct differences in morphology, life history traits and habitat preference, and therefore provide a unique model for the study of ecological speciation. However, the population genetic structure of the ancestral O. rufipogon has been controversial despite substantial study, and the origin of the derivative O. nivara remains unclear...
October 2015: Molecular Ecology
Tomoyuki Furuta, Norio Komeda, Kenji Asano, Kanako Uehara, Rico Gamuyao, Rosalyn B Angeles-Shim, Keisuke Nagai, Kazuyuki Doi, Diane R Wang, Hideshi Yasui, Atsushi Yoshimura, Jianzhong Wu, Susan R McCouch, Motoyuki Ashikari
A long awn is one of the distinct morphological features of wild rice species. This organ is thought to aid in seed dispersal and prevent predation by animals. Most cultivated varieties of Oryza sativa and Oryza glaberrima, however, have lost the ability to form long awns. The causal genetic factors responsible for the loss of awn in these two rice species remain largely unknown. Here, we evaluated three sets of chromosome segment substitution lines (CSSLs) in a common O. sativa genetic background (cv. Koshihikari) that harbor genomic fragments from Oryza nivara, Oryza rufipogon, and Oryza glaberrima donors...
November 2015: G3: Genes—Genomes—Genetics
Yanping Tan, Xin Xu, Chuntai Wang, Gang Cheng, Shaoqing Li, Xuequn Liu
BACKGROUND: Cytoplasmic male sterility (CMS) is a maternally inherited inability to produce functional pollen found in numerous flowering plant species. CMS is associated with mitochondrial DNA mutation, novel chimeric open reading frames (ORFs), and rearrangement of coding and noncoding regions of the mitochondrial genome. RESULTS: BLAST (Basic Local Alignment Search Tool) analysis indicated that L-sp1, a new sequence-characterized amplified region, is non-homologous to atp6-orfH79 (or atp6-orf79) and WA352 cloned CMS-associated genes...
2015: BMC Genetics
Waikhom Bimolata, Anirudh Kumar, Sai Kiran Reddy M, Raman Meenakshi Sundaram, Gouri Sankar Laha, Insaf Ahmed Qureshi, Irfan Ahmad Ghazi
Nucleotide sequence polymorphisms among R gene alleles influence the process of co-evolutionary interaction between host and pathogen by shaping the response of host plants towards invading pathogens. Here, we present the DNA sequence polymorphisms and diversities present among natural alleles of three rice bacterial blight resistance genes, Xa21, Xa26 and xa5. The diversity was examined across different wild relatives and cultivars of Oryza species. Functional significance of selected alleles was evaluated through semi-quantitative reverse transcription polymerase chain reaction and real time PCR...
2015: PloS One
J B Li, Y D Sun, H Liu, Y Y Wang, Y L Jia, M H Xu
Studying natural variation in rice resistance genes of cultivated and wild rice relatives can predict resistance stability to rice blast fungus. In the present study, the protein coding regions of the rice R gene Pi-d2 in 35 rice accessions, including Oryza sativa L. subsp. indica Kato (Aus), indica (IND), temperate japonica (TEJ), tropical japonica (TRJ), aromatic (ARO); subgroups of Oryza sativa; 6 accessions of wild rice varieties; O. nivara; and O. rufipogon were analyzed. A total of 13 nucleotide differences were found in the open reading frames (ORFs) of Pi-d2...
2015: Genetics and Molecular Research: GMR
Trees-Juen Chuang, Min-Yu Yang, Chuang-Chieh Lin, Ping-Hung Hsieh, Li-Yuan Hung
BACKGROUND: Crop plants such as rice, maize and sorghum play economically-important roles as main sources of food, fuel, and animal feed. However, current genome annotations of crop plants still suffer false-positive predictions; a more comprehensive registry of alternative splicing (AS) events is also in demand. Comparative genomics of crop plants is largely unexplored. RESULTS: We performed a large-scale comparative analysis (ExonFinder) of the expressed sequence tag (EST) library from nine grass plants against three crop genomes (rice, maize, and sorghum) and identified 2,879 previously-unannotated exons (i...
2015: BMC Plant Biology
B P Mallikarjuna Swamy, K Kaladhar, G Ashok Reddy, B C Viraktamath, N Sarla
Advanced backcross QTL (AB-QTL) analysis was carried out in two Oryza nivara-derived BC2F2 populations. For nine traits, we identified 28 QTL in population 1 and 26 QTL in population 2. The two most significant yield-enhancing QTL, yldp9.1 and yldp2.1 showed an additive effect of 16 and 7 g per plant in population 1, while yld2.1 and yld11.1 showed an additive effect of 11 and 10 g per plant in population 2. At least one O. nivara-derived QTL with a phenotypic variance of >15% was detected for seven traits in population 1 and three traits in population 2...
December 2014: Journal of Genetics
Qun-Jie Zhang, Ting Zhu, En-Hua Xia, Chao Shi, Yun-Long Liu, Yun Zhang, Yuan Liu, Wen-Kai Jiang, You-Jie Zhao, Shu-Yan Mao, Li-Ping Zhang, Hui Huang, Jun-Ying Jiao, Ping-Zhen Xu, Qiu-Yang Yao, Fan-Chun Zeng, Li-Li Yang, Ju Gao, Da-Yun Tao, Yue-Ju Wang, Jeffrey L Bennetzen, Li-Zhi Gao
Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation...
November 18, 2014: Proceedings of the National Academy of Sciences of the United States of America
Kiran B Gaikwad, Naveen Singh, Dharminder Bhatia, Rupinder Kaur, Navtej S Bains, Tajinder S Bharaj, Kuldeep Singh
Utilization of "hidden genes" from wild species has emerged as a novel option for enrichment of genetic diversity for productivity traits. In rice we have generated more than 2000 lines having introgression from 'A' genome-donor wild species of rice in the genetic background of popular varieties PR114 and Pusa44 were developed. Out of these, based on agronomic acceptability, 318 lines were used for developing rice hybrids to assess the effect of introgressions in heterozygous state. These introgression lines and their recurrent parents, possessing fertility restoration ability for wild abortive (WA) cytoplasm, were crossed with cytoplasmic male sterile (CMS) line PMS17A to develop hybrids...
2014: PloS One
Brian J Atwell, Han Wang, Andrew P Scafaro
Oryza sativa and Oryza glaberrima have been selected to acquire and partition resources efficiently as part of the process of domestication. However, genetic diversity in cultivated rice is limited compared to wild Oryza species, in spite of 120,000 genotypes being held in gene banks. By contrast, there is untapped diversity in the more than 20 wild species of Oryza, some having been collected from just a few coastal locations (e.g. Oryza schlechteri), while others are widely distributed (e.g. Oryza nivara and Oryza rufipogon)...
February 2014: Plant Science: An International Journal of Experimental Plant Biology
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