The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Dirk De Waele - One of the best experts on this subject based on the ideXlab platform.
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Identification of quantitative trait loci underlying resistance and tolerance to the Rice root-knot nematode, Meloidogyne graminicola, in Asian Rice (Oryza sativa)
Molecular Breeding, 2020Co-Authors: Judith Galeng-lawilao, B. P. Mallikarjuna Swamy, Tapas Kumer Hore, Arvind Kumar, Dirk De WaeleAbstract:Meloidogyne graminicola is one of the most important plant-parasitic nematodes in Rice. Breeding for natural resistance and tolerance is considered one of the most economical and sustainable approaches to control this damaging pathogen. Quantitative trait loci (QTL) mapping was carried out in a recombinant inbred line (RIL) population derived from a cross between the Asian Rice genotypes IR78877-208-B-1-2 and Dinorado. IR78877-208-B-1-2 is an aerobic Rice genotype that is resistant and tolerant to M. graminicola . Dinorado is a traditional upland Rice genotype from the Philippines that is characterized by its aroma and prized for its cooking quality. The host response of 300 F_4 lines derived from this cross was evaluated in both nematode infested and non-infested concrete beds in the dry seasons of 2013 and 2014. Five genotypes were found consistently resistant while 13 genotypes were consistently partially resistant to M. graminicola. QTL mapping for M. graminicola resistance/tolerance, yield-contributing traits, and yield revealed four main effect QTLs ( qJ _ 2 R S_ 2.1 , qJ _ 2 GRT _ 2.1 , qJ _2 RS _ 3.1 , and qJ _ 2 GRT _ 3. 1) associated with reduced nematode reproduction on chromosomes 2 and 3 and two QTLs ( qGR _ 3.1 and qGR _ 5.1 ) associated with reduced root galling on chromosomes 3 and 5. Twenty main effect QTLs associated with yield-contributing traits and yield were also found. Our study further identified co-locating QTLs associated with nematode resistance, yield-contributing traits, and yield on chromosomes 3 and 5. QTLs harboring candidate genes, such as OsBAK1 , OsDST , OsIPT4 , and DUF26 , for higher grain yield and tolerance to abiotic and biotic stress, were identified. These QTLs and the RILs that are consistently resistant and tolerant to M. graminicola , and which are high-yielding in nematode-infested fields, can be utilized in breeding programs to improve the resistance and tolerance of Asian Rice to this important pathogen.
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effects of initial nematode population density and water regime on resistance and tolerance to the Rice root knot nematode meloidogyne graminicola in african and Asian Rice genotypes
International Journal of Pest Management, 2018Co-Authors: Ma. Teodora Nadong Cabasan, Arvind Kumar, Dirk De WaeleAbstract:ABSTRACTThe Rice root-knot nematode (RKN), Meloidogyne graminicola, is an important pathogen affecting Rice production in South and Southeast Asia. Efficacy of resistance and tolerance in selected M. graminicola-resistant African Rice genotypes TOG5674, TOG5675 and CG14 and -susceptible Asian Rice genotypes IR64 and UPLRi-5 were examined under a range of initial population densities (Pi) and water regimes. Resistance to M. graminicola in resistant Rice genotypes was not broken with increasing pathogen pressure (Pi = 15,000 to 60,000 J2/plant). Resistant Rice genotypes were even tolerant to the damage and yield loss caused by high pathogen pressure. On the other hand, increasing Pi levels caused more damage on susceptible Rice genotypes. Final nematode population densities in the root systems of resistant and susceptible Rice genotypes were significantly lower under flooded conditions than under upland and drought conditions. TOG5674, TOG5675 and CG14 were more tolerant to M. graminicola infection even whe...
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Host status of rotation crops in Asian Rice-based cropping systems to the Rice root-knot nematode Meloidogyne graminicola
Tropical Plant Pathology, 2016Co-Authors: Pa Pa Win, Pyone Pyone Kyi, Ma. Teodora Nadong Cabasan, Zin Thu Zar Maung, Yi Yi Myint, Dirk De WaeleAbstract:Rotation with nonhost crops is an important practice used for root-knot nematode (RKN) management. Screenhouse experiments were conducted to evaluate the response infection of 27 cultivars belonging to 14 crops (blackgram, cabbage, cauliflower, chickpea, cowpea, garlic, ginger, greengram, groundnut, maize, potato, sesame, soybean, sunflower), which are grown in rotation with Rice in lowland and upland Rice-based ecosystems, to the RKN Meloidogyne graminicola. Root galling indices observed on all crop rotation cultivars were significantly lower compared with the Rice cv. Thihtatyin, used as positive control. Differences in host response to M. graminicola infection were observed between cultivars. All 27 cultivars were poor or non-hosts of M. graminicola, except cv. Yezin 4 of chickpea considered as good host. No significant differences in plant growth were observed between non-inoculated and inoculated plants of all plant/species cultivars, with the exception of a reduction in root length in the chickpea cv. Yezin 4 (good host) and the garlic cv. Shan (poor host). Rotation crops identified as poor or non-hosts of M. graminicola could be useful in the management of RKN in Rice-based cropping systems.
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interactions between the oomycete pythium arrhenomanes and the Rice root knot nematode meloidogyne graminicola in aerobic Asian Rice varieties
Rice, 2016Co-Authors: Ruben Verbeek, Dirk De Waele, C G B Banaay, M Sikder, C Vera M Cruz, Godelieve Gheysen, Monica HofteAbstract:Aerobic Rice fields are frequently infested by pathogenic oomycetes (Pythium spp.) and the Rice root-knot nematode Meloidogyne graminicola. Here, the interaction between Pythium arrhenomanes and Meloidogyne graminicola was studied in Rice roots of two aerobic Rice varieties. In different experimental set-ups and infection regimes, plant growth, Rice yield, Pythium colonization, as well as establishment, development and reproduction of M. graminicola were studied. In this study, it is shown that the presence of P. arrhenomanes delays the establishment, development and reproduction of M. graminicola compared to single nematode infected plants. The delay in establishment and development of M. graminicola becomes stronger with higher P. arrhenomanes infection pressure. Our data indicate that P. arrhenomanes antagonizes M. graminicola in the Rice root and that the plant benefits from this antagonism as shown by the yield data, especially when either of the pathogens is present in high levels.
Michael D. Purugganan - One of the best experts on this subject based on the ideXlab platform.
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multiple origin but single domestication led to oryza sativa
G3: Genes Genomes Genetics, 2018Co-Authors: Jae Young Choi, Michael D. PuruggananAbstract:The domestication scenario that led to Asian Rice (Oryza sativa) is a contentious topic. Here, we have reanalyzed a previously published large-scale wild and domesticated Rice data set, which was also analyzed by two studies but resulted in two contrasting domestication models. We suggest that the analysis of false-positive selective sweep regions and phylogenetic analysis of concatenated genomic regions may have been the sources that contributed to the different results. In the end, our result indicates that Asian Rice originated from multiple wild progenitor subpopulations; however, de novo domestication appears to have occurred only once and the domestication alleles were transferred between Rice subpopulations through introgression.
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multiple origin but single domestication led to oryza sativa
bioRxiv, 2018Co-Authors: Jae Young Choi, Michael D. PuruggananAbstract:Abstract The domestication scenario that led to Asian Rice (Oryza sativa) is a contentious topic. Here, we have reanalyzed a previously published large-scale wild and domesticated Rice dataset, which were also analyzed by two studies but resulted in two contrasting domestication models. We suggest the analysis of false positive selective sweep regions and phylogenetic analysis of concatenated genomic regions may have been the sources that contributed to the different results. In the end, our result indicates Asian Rice originated from multiple wild progenitor subpopulations; however, de novo domestication appears to have occurred only once and the domestication alleles were transferred between Rice subpopulation through introgression.
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Multiple origin but single domestication led to domesticated Asian Rice
bioRxiv, 2017Co-Authors: Jae Young Choi, Michael D. PuruggananAbstract:The domestication scenario that led to Asian Rice (Oryza sativa) is a contentious topic. Here, we have reanalyzed a previously published large-scale wild and domesticated Rice dataset, which were also analyzed by two studies but resulted in two contrasting domestication scenario. Our result indicates Asian Rice originated from multiple wild progenitor subpopulations, however, domestication occurred only once and the domestication alleles were transferred between Rice subpopulation through introgression.
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the Rice paradox multiple origins but single domestication in Asian Rice
Molecular Biology and Evolution, 2017Co-Authors: Jae Young Choi, Michael D. Purugganan, Rod A Wing, Dorian Q Fuller, Adrian E Platts, Yueie C HsingAbstract: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. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1-24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild Rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different Rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus Rice.
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levels and patterns of nucleotide variation in domestication qtl regions on Rice chromosome 3 suggest lineage specific selection
PLOS ONE, 2011Co-Authors: Jeanmaire Molina, Andrew R Reynolds, Ryan D Hernandez, Adam R Boyko, Carlos Bustamante, Michael D. PuruggananAbstract:Oryza sativa or Asian cultivated Rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL) mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different Rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa—indica and tropical japonica—as well as the ancestral wild Rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of Rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica Rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian Rice varietal groups.
Kaworu Ebana - One of the best experts on this subject based on the ideXlab platform.
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genetic architecture of variation in heading date among Asian Rice accessions
BMC Plant Biology, 2015Co-Authors: Kiyosumi Hori, Kaworu Ebana, Taeko Shibaya, Kazuki Matsubara, Yasunori Nonoue, Nozomi Ono, Eri Ogisotanaka, Takanari Tanabata, Kazuhiko Sugimoto, Fumio TaguchishiobaraAbstract:Heading date, a crucial factor determining regional and seasonal adaptation in Rice (Oryza sativa L.), has been a major selection target in breeding programs. Although considerable progress has been made in our understanding of the molecular regulation of heading date in Rice during last two decades, the previously isolated genes and identified quantitative trait loci (QTLs) cannot fully explain the natural variation for heading date in diverse Rice accessions. To genetically dissect naturally occurring variation in Rice heading date, we collected QTLs in advanced-backcross populations derived from multiple crosses of the japonica Rice accession Koshihikari (as a common parental line) with 11 diverse Rice accessions (5 indica, 3 aus, and 3 japonica) that originate from various regions of Asia. QTL analyses of over 14,000 backcrossed individuals revealed 255 QTLs distributed widely across the Rice genome. Among the detected QTLs, 128 QTLs corresponded to genomic positions of heading date genes identified by previous studies, such as Hd1, Hd6, Hd3a, Ghd7, DTH8, and RFT1. The other 127 QTLs were detected in different chromosomal regions than heading date genes. Our results indicate that advanced-backcross progeny allowed us to detect and confirm QTLs with relatively small additive effects, and the natural variation in Rice heading date could result from combinations of large- and small-effect QTLs. We also found differences in the genetic architecture of heading date (flowering time) among maize, Arabidopsis, and Rice.
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exploring the areas of applicability of whole genome prediction methods for Asian Rice oryza sativa l
Theoretical and Applied Genetics, 2015Co-Authors: Akio Onogi, Kaworu Ebana, Osamu Ideta, Yuto Inoshita, Takuma Yoshioka, Masanori Yamasaki, Hiroyoshi IwataAbstract:Our simulation results clarify the areas of applicability of nine prediction methods and suggest the factors that affect their accuracy at predicting empirical traits. Whole-genome prediction is used to predict genetic value from genome-wide markers. The choice of method is important for successful prediction. We compared nine methods using empirical data for eight phenological and morphological traits of Asian Rice cultivars (Oryza sativa L.) and data simulated from real marker genotype data. The methods were genomic BLUP (GBLUP), reproducing kernel Hilbert spaces regression (RKHS), Lasso, elastic net, random forest (RForest), Bayesian lasso (Blasso), extended Bayesian lasso (EBlasso), weighted Bayesian shrinkage regression (wBSR), and the average of all methods (Ave). The objectives were to evaluate the predictive ability of these methods in a cultivar population, to characterize them by exploring the area of applicability of each method using simulation, and to investigate the causes of their different accuracies for empirical traits. GBLUP was the most accurate for one trait, RKHS and Ave for two, and RForest for three traits. In the simulation, Blasso, EBlasso, and Ave showed stable performance across the simulated scenarios, whereas the other methods, except wBSR, had specific areas of applicability; wBSR performed poorly in most scenarios. For each method, the accuracy ranking for the empirical traits was largely consistent with that in one of the simulated scenarios, suggesting that the simulation conditions reflected the factors that affected the method accuracy for the empirical results. This study will be useful for genomic prediction not only in Asian Rice, but also in populations from other crops with relatively small training sets and strong linkage disequilibrium structures.
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uncovering of major genetic factors generating naturally occurring variation in heading date among Asian Rice cultivars
Theoretical and Applied Genetics, 2011Co-Authors: Kaworu Ebana, Taeko Shibaya, Kazuki Matsubara, Hiroyuki Kanamori, Hiroko Yamane, Utako Yamanouchi, Tatsumi Mizubayashi, Izumi Kono, Ayahiko Shomura, Sachie ItoAbstract:To dissect the genetic factors controlling naturally occurring variation of heading date in Asian Rice cultivars, we performed QTL analyses using F2 populations derived from crosses between a japonica cultivar, Koshihikari, and each of 12 cultivars originating from various regions in Asia. These 12 diverse cultivars varied in heading date under natural field conditions in Tsukuba, Japan. Transgressive segregation was observed in 10 F2 combinations. QTL analyses using multiple crosses revealed a comprehensive series of loci involved in natural variation in flowering time. One to four QTLs were detected in each cross combination, and some QTLs were shared among combinations. The chromosomal locations of these QTLs corresponded well with those detected in other studies. The allelic effects of the QTLs varied among the cross combinations. Sequence analysis of several previously cloned genes controlling heading date, including Hd1, Hd3a, Hd6, RFT1, and Ghd7, identified several functional polymorphisms, indicating that allelic variation at these loci probably contributes to variation in heading date. Taken together, the QTL and sequencing results indicate that a large portion of the phenotypic variation in heading date in Asian Rice cultivars could be generated by combinations of different alleles (possibly both loss- and gain-of-function) of the QTLs detected in this study.
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genetic structure revealed by a whole genome single nucleotide polymorphism survey of diverse accessions of cultivated Asian Rice oryza sativa l
Breeding Science, 2010Co-Authors: Kaworu Ebana, Hiroyuki Kanamori, Hiroyoshi Iwata, Junichi Yonemaru, Shuichi Fukuoka, Nobukazu Namiki, Hideki Nagasaki, Masahiro YanoAbstract:To reveal the sequence diversity and population structure of Asian Rice (Oryza sativa L.) cultivars, we surveyed genome-wide single-nucleotide polymorphisms (SNPs) in 140 diverse accessions. We identified 4357 SNPs distributed on the 12 chromosomes by sequencing PCR amplicons from the exons and introns of anonymous Rice genes. We detected 4.87 SNPs per 1 kb genome-wide. By classifying the 140 accessions on the basis of these SNPs, we identified seven cultivar groups that reflected the geographical distribution of the accessions. Three cultivar groups were defined from tropical japonica that corresponded to previous categories, and three indica cultivar groups were also defined within indica. The linkage disequilibrium (LD) distance between SNPs was approximately 250 kb, except for a longer LD detected in the Indica I cultivar group (corresponding to the previously identified aus group). The allele frequency of the SNPs varied among cultivar groups, reflecting the level of genetic diversity in each group. These SNPs for the diverse accessions enhance our understanding of natural variation in Rice.
Monica Hofte - One of the best experts on this subject based on the ideXlab platform.
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interactions between the oomycete pythium arrhenomanes and the Rice root knot nematode meloidogyne graminicola in aerobic Asian Rice varieties
Rice, 2016Co-Authors: Ruben Verbeek, Dirk De Waele, C G B Banaay, M Sikder, C Vera M Cruz, Godelieve Gheysen, Monica HofteAbstract:Aerobic Rice fields are frequently infested by pathogenic oomycetes (Pythium spp.) and the Rice root-knot nematode Meloidogyne graminicola. Here, the interaction between Pythium arrhenomanes and Meloidogyne graminicola was studied in Rice roots of two aerobic Rice varieties. In different experimental set-ups and infection regimes, plant growth, Rice yield, Pythium colonization, as well as establishment, development and reproduction of M. graminicola were studied. In this study, it is shown that the presence of P. arrhenomanes delays the establishment, development and reproduction of M. graminicola compared to single nematode infected plants. The delay in establishment and development of M. graminicola becomes stronger with higher P. arrhenomanes infection pressure. Our data indicate that P. arrhenomanes antagonizes M. graminicola in the Rice root and that the plant benefits from this antagonism as shown by the yield data, especially when either of the pathogens is present in high levels.
Rod A Wing - One of the best experts on this subject based on the ideXlab platform.
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high resolution introgressive region map reveals spatiotemporal genome evolution in Asian Rice domestication
bioRxiv, 2020Co-Authors: Hajime Ohyanagi, Rod A Wing, Kosuke Goto, Sonia Negrao, Mark Tester, Kenneth L Mcnally, Vladimir B Bajic, Katsuhiko Mineta, Takashi GojoboriAbstract:Domestication is anthropogenic evolution that fulfills mankind9s critical food demand. As such, elucidating the molecular mechanisms behind this process promotes the development of future new food resources including crops. With the aim of understanding the long-term domestication process of Asian Rice and by employing the Oryza sativa subspecies (indica and japonica) as an Asian Rice domestication model, we scrutinized past genomic introgressions between them as traces of domestication. Here we show the genome-wide introgressive region (IR) map of Asian Rice, by utilizing 4,587 accession genotypes with a stable outgroup species, particularly at the finest resolution through a machine learning-aided method. The IR map revealed that 14.2% of the Rice genome consists of IRs, including both wide IRs (recent) and narrow IRs (ancient). This introgressive landscape with their time calibration indicates that introgression events happened in multiple genomic regions over multiple periods. From the correspondence between our wide IRs and the so-called selective sweep regions, we provide a definitive answer to a long-standing controversy over the evolutionary origin of Asian Rice domestication, single or multiple origins: It heavily depends upon which regions you pay attention to, implying that wider genomic regions represent immediate short history of Asian Rice domestication as a likely support to the single origin, while its ancient history is interspersed in narrower traces throughout the genome as a possible support to the multiple origin.
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machine learning reveals spatiotemporal genome evolution in Asian Rice domestication
bioRxiv, 2019Co-Authors: Hajime Ohyanagi, Rod A Wing, Kosuke Goto, Sonia Negrao, Mark Tester, Kenneth L Mcnally, Vladimir B Bajic, Katsuhiko Mineta, Takashi GojoboriAbstract:Domestication is anthropogenic evolution that fulfills mankind’s critical food demand. As such, elucidating the molecular mechanisms behind this process promotes the development of future new crops. With the aim of understanding the whole domestication process of Asian Rice and by employing the Oryza sativa subspecies (indica and japonica) as an Asian Rice domestication model, we scrutinized genomic introgressions between them as traces of domestication. Here we show the genome-wide introgressive region (IR) map of Asian Rice, by utilizing 4,587 accession genotypes with a stable outgroup species, particularly at the finest resolution through a machine learning-aided method. The IR map revealed that 14.2% of the Rice genome consists of IRs, including both wide IRs (recent) and narrow IRs (ancient). This introgressive landscape with their time calibration indicates that introgression events happened in multiple genomic regions over multiple periods. From the correspondence between our wide IRs and so-called Selective Sweep Regions, we provide a definitive answer to a long-standing controversy in plant science: Asian Rice phylogeny appears to depend on which regions and time frames are examined.
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a single nucleotide polymorphism causes smaller grain size and loss of seed shattering during african Rice domestication
Nature plants, 2017Co-Authors: Xiangkun Wang, Wenguang Wu, Rachel S Meyer, Marie Noelle Ndjiondjop, Muhua Wang, Jianzhong Wu, Jianwei Zhang, Rod A WingAbstract:Grain size is one of the most important components of grain yield and selecting large seeds has been a main target during plant domestication. Surprisingly, the grain of African cultivated Rice (Oryza glaberrima Steud.) typically is smaller than that of its progenitor, Oryza barthii. Here we report the cloning and characterization of a quantitative trait locus, GL4, controlling the grain length on chromosome 4 in African Rice, which regulates longitudinal cell elongation of the outer and inner glumes. Interestingly, GL4 also controls the seed shattering phenotype like its orthologue SH4 gene in Asian Rice. Our data show that a single-nucleotide polymorphism (SNP) mutation in the GL4 gene resulted in a premature stop codon and led to small seeds and loss of seed shattering during African Rice domestication. These results provide new insights into diverse domestication practices in African Rice, and also pave the way for enhancing crop yield to meeting the challenge of cereal demand in West Africa.
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the Rice paradox multiple origins but single domestication in Asian Rice
Molecular Biology and Evolution, 2017Co-Authors: Jae Young Choi, Michael D. Purugganan, Rod A Wing, Dorian Q Fuller, Adrian E Platts, Yueie C HsingAbstract: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. rufipogon was O. sativa ssp. japonica, occurring at ∼13.1-24.1 ka, which is an order of magnitude older then the earliest archeological date of domestication. This date is consistent, however, with the expansion of O. rufipogon populations after the Last Glacial Maximum ∼18 ka and archeological evidence for early wild Rice management in China. We also show that there is significant gene flow from japonica to both indica (∼17%) and aus (∼15%), which led to the transfer of domestication alleles from early-domesticated japonica to proto-indica and proto-aus populations. Our results provide support for a model in which different Rice subspecies had separate origins, but that de novo domestication occurred only once, in O. sativa ssp. japonica, and introgressive hybridization from early japonica to proto-indica and proto-aus led to domesticated indica and aus Rice.
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evolutionary analysis of the sub1 locus across the oryza genomes
Rice, 2017Co-Authors: Railson Schreinert Dos Santos, Daniel Da Rosa Farias, Takeshi Fukao, Cesar Valmor Rombaldi, Camila Pegoraro, Rod A Wing, Antonio Costa De OliveiraAbstract: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. Chromosomal location, phylogenetic, and gene structure analyses have revealed that the SUB1 locus is conserved in the long arm of chromosome 9 in most Oryza species. We also show that the SUB1A-like gene of O. nivara is on chromosome 1 and that Leersia perrieri, a grass-tolerant to deep-flooding, presents three ERF genes in the SUB1 locus. We provide here a deeper insight into the evolutionary origin and variation of the SUB1 locus and raise the possibility that an association of these genes with flooding tolerance in L. perrieri may exist.
