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Ntakirutimana F, Tranchant-Dubreuil C, Cubry P, Chougule K, Zhang J, Wing RA, Adam H, Lorieux M, Jouannic S. Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3 (BETHESDA, MD.) 2023; 13:jkad174. [PMID: 37535690 PMCID: PMC10542218 DOI: 10.1093/g3journal/jkad174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/12/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023]
Abstract
African rice (Oryza glaberrima Steud), a short-day cereal crop closely related to Asian rice (Oryza sativa L.), has been cultivated in Sub-Saharan Africa for ∼ 3,000 years. Although less cultivated globally, it is a valuable genetic resource in creating high-yielding cultivars that are better adapted to diverse biotic and abiotic stresses. While inflorescence architecture, a key trait for rice grain yield improvement, has been extensively studied in Asian rice, the morphological and genetic determinants of this complex trait are less understood in African rice. In this study, using a previously developed association panel of 162 O. glaberrima accessions and new SNP variants characterized through mapping to a new version of the O. glaberrima reference genome, we conducted a genome-wide association study of four major morphological panicle traits. We have found a total of 41 stable genomic regions that are significantly associated with these traits, of which 13 co-localized with previously identified QTLs in O. sativa populations and 28 were unique for this association panel. Additionally, we found a genomic region of interest on chromosome 3 that was associated with the number of spikelets and primary and secondary branches. Within this region was localized the O. sativa ortholog of the PHYTOCHROME B gene (Oglab_006903/OgPHYB). Haplotype analysis revealed the occurrence of natural sequence variants at the OgPHYB locus associated with panicle architecture variation through modulation of the flowering time phenotype, whereas no equivalent alleles were found in O. sativa. The identification in this study of genomic regions specific to O. glaberrima indicates panicle-related intra-specific genetic variation in this species, increasing our understanding of the underlying molecular processes governing panicle architecture. Identified candidate genes and major haplotypes may facilitate the breeding of new African rice cultivars with preferred panicle traits.
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Affiliation(s)
| | | | - Philippe Cubry
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
| | - Hélène Adam
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Mathias Lorieux
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
| | - Stefan Jouannic
- DIADE, University of Montpellier, IRD, CIRAD, 34394 Montpellier, France
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Chigira K, Yamasaki M, Adachi S, Nagano AJ, Ookawa T. Identification of Novel Quantitative Trait Loci for Culm Thickness of Rice Derived from Strong-Culm Landrace in Japan, Omachi. RICE (NEW YORK, N.Y.) 2023; 16:4. [PMID: 36705856 PMCID: PMC9883377 DOI: 10.1186/s12284-023-00621-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Increasing the lodging resistance of rice through genetic improvement has been an important target in breeding. To further enhance the lodging resistance of high-yielding rice varieties amidst climate change, it is necessary to not only shorten culms but strengthen them as well. A landrace rice variety, Omachi, which was established more than 100 years ago, has the largest culm diameter and bending moment at breaking in the basal internodes among 135 temperate japonica accessions. Using unused alleles in such a landrace is an effective way to strengthen the culm. In this study, we performed quantitative trait locus (QTL) analysis to identify the genetic factors of culm strength of Omachi using recombinant inbred lines (RILs) derived from a cross between Omachi and Koshihikari, a standard variety in Japan. We identified three QTLs for the culm diameter of the 5th internode on chromosomes 3 (qCD3) and 7 (qCD7-1, qCD7-2). Among them, qCD7-2 was verified by QTL analysis using the F2 population derived from a cross between one of the RILs and Koshihikari. RNA-seq analysis of shoot apex raised 10 candidate genes underlying the region of qCD7-2. The increase in culm strength by accumulating Omachi alleles of qCD3, qCD7-1 and qCD7-2 was 25.0% in 2020. These QTLs for culm diameter pleiotropically increased spikelet number per panicle but did not affect days to heading or culm length. These results suggest that the Omachi alleles of qCD3, qCD7-1 and qCD7-2 are useful for breeding to increase lodging resistance and yield.
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Affiliation(s)
- Koki Chigira
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509 Japan
| | - Masanori Yamasaki
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-Ku, Niigata City, Niigata 950-2181 Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509 Japan
| | - Atsushi J. Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194 Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata 997-0017 Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509 Japan
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3
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Assessment of allelic and genetic diversity, and population structure among farmers' rice varieties using microsatellite markers and morphological traits. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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4
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Awal Khan MA, Zhang S, Emon RM, Chen F, Song W, Wu T, Yuan S, Wu C, Hou W, Sun S, Fu Y, Jiang B, Han T. CONSTANS Polymorphism Modulates Flowering Time and Maturity in Soybean. FRONTIERS IN PLANT SCIENCE 2022; 13:817544. [PMID: 35371153 PMCID: PMC8969907 DOI: 10.3389/fpls.2022.817544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/15/2022] [Indexed: 06/01/2023]
Abstract
CONSTANS (CO) plays a critical role in the photoperiodic flowering pathway. However, the function of soybean CO orthologs and the molecular mechanisms in regulating flowering remain largely unknown. This study characterized the natural variations in CO family genes and their association with flowering time and maturity in soybeans. A total of 21 soybean CO family genes (GmCOLs) were cloned and sequenced in 128 varieties covering 14 known maturity groups (MG 0000-MG X from earliest to latest maturity). Regarding the whole genomic region involving these genes, GmCOL1, GmCOL3, GmCOL8, GmCOL9, GmCOL10, and GmCOL13 were conserved, and the remaining 15 genes showed genetic variation that was brought about by mutation, namely, all single-nucleotide polymorphisms (SNPs) and insertions-deletions (InDels). In addition, a few genes showed some strong linkage disequilibrium. Point mutations were found in 15 GmCOL genes, which can lead to changes in the potential protein structure. Early flowering and maturation were related to eight genes (GmCOL1/3/4/8/13/15/16/19). For flowering and maturation, 11 genes (GmCOL2/5/6/14/20/22/23/24/25/26/28) expressed divergent physiognomy. Haplotype analysis indicated that the haplotypes of GmCOL5-Hap2, GmCOL13-Hap2/3, and GmCOL28-Hap2 were associated with flowering dates and soybean maturity. This study helps address the role of GmCOL family genes in adapting to diverse environments, particularly when it is necessary to regulate soybean flowering dates and maturity.
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Affiliation(s)
- Mohammad Abdul Awal Khan
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shouwei Zhang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Reza Mohammad Emon
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Plant Breeding Division, Bangladesh Institute of Nuclear Agriculture, Mymensingh, Bangladesh
| | - Fulu Chen
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenwen Song
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tingting Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan Yuan
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cunxiang Wu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensheng Hou
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shi Sun
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongfu Fu
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingjun Jiang
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianfu Han
- MARA Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Vasumathy SK, Alagu M. SSR marker-based genetic diversity analysis and SNP haplotyping of genes associating abiotic and biotic stress tolerance, rice growth and development and yield across 93 rice landraces. Mol Biol Rep 2021; 48:5943-5953. [PMID: 34319545 DOI: 10.1007/s11033-021-06595-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/24/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND As rice is the staple food for more than half of the world's population, enhancing grain yield irrespective of the variable climatic conditions is indispensable. Many traditionally cultivated rice landraces are well adapted to severe environmental conditions and have high genetic diversity that could play an important role in crop improvement. METHODS AND RESULTS The present study revealed a high level of genetic diversity among the unexploited rice landraces cultivated by the farmers of Kerala. Twelve polymorphic markers detected a total of seventy- seven alleles with an average of 6.416 alleles per locus. Polymorphic Information Content (PIC) value ranged from 0.459 to 0.809, and to differentiate the rice genotypes, RM 242 was found to be the most appropriate marker with a high value of 0.809. The current study indicated that the rice landraces are highly diverse with higher values of the adequate number of alleles, PIC, and Shannon information index. Utilizing these informative SSR markers for future molecular characterization and population genetic studies in rice landraces are advisable. Haplotypes are sets of genomic regions within a chromosome inherited together, and haplotype-based breeding is a promising strategy for designing next-generation rice varieties. Here, haplotype analysis explored 270 haplotype blocks and 775 haplotypes from all the chromosomes of landraces under study. The number of SNPs in each haplotype block ranged from two to 28. Haplotypes of genes related to biotic and abiotic stress tolerance, yield-enhancing, and growth and development in rice landraces were also elucidated in the current study. CONCLUSIONS The present investigation revealed the genetic diversity of rice landraces and the haplotype analysis will open the way for genome-wide association studies, QTL identification, and marker-assisted selection in the unexplored rice landraces collected from Kerala.
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Affiliation(s)
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Periye, Kasaragod, Kerala, 671316, India.
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Fujino K, Kawahara Y, Koyanagi KO, Shirasawa K. Translation of continuous artificial selection on phenotype into genotype during rice breeding programs. BREEDING SCIENCE 2021; 71:125-133. [PMID: 34377060 PMCID: PMC8329892 DOI: 10.1270/jsbbs.20089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/25/2020] [Indexed: 06/13/2023]
Abstract
Understanding genetic diversity among local populations is a primary goal of modern crop breeding programs. Here, we demonstrated the genetic relationships of rice varieties in Hokkaido, Japan, one of the northern limits of rice cultivation around the world. Furthermore, artificial selection during rice breeding programs has been characterized using genome sequences. We utilized 8,565 single nucleotide polymorphisms and insertion/deletion markers distributed across the genome in genotype-by-sequencing for genetic diversity analyses. Phylogenetics, genetic population structure, and principal component analysis showed that a total of 110 varieties were classified into four distinct clusters according to different populations geographically and historically. Furthermore, the genome sequences of 19 rice varieties along with historic representations in Hokkaido, nucleotide diversity and FST values in each cluster revealed that artificial selection of elite phenotypes focused on chromosomal regions. These results clearly demonstrated the history of the selections on agronomic traits as genome sequences among current rice varieties from Hokkaido.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, Hokkaido 062-8555, Japan
| | - Yoshihiro Kawahara
- Institute of Crop Science, National Agricultural Research Organization, Tsukuba, Ibaraki 305-8518, Japan
- Advanced Analysis Center, National Agricultural Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Kanako O. Koyanagi
- Faculty of Information Science and Technology, Hokkaido University, Sapporo, Hokkaido 060-0814, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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7
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Bollinedi H, Yadav AK, Vinod KK, Gopala Krishnan S, Bhowmick PK, Nagarajan M, Neeraja CN, Ellur RK, Singh AK. Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain. Front Genet 2020; 11:213. [PMID: 32391041 PMCID: PMC7188789 DOI: 10.3389/fgene.2020.00213] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 02/24/2020] [Indexed: 01/16/2023] Open
Abstract
Micronutrient malnutrition due to Fe and Zn, affects around two billion people globally particularly in the developing countries. More than 90% of the Asian population is dependent on rice-based diets, which is low in these micronutrients. In the present study, a set of 192 Indian rice germplasm accessions, grown at two locations, were evaluated for Fe and Zn in brown rice (BR) and milled rice (MR). A significant variation was observed in the rice germplasm for these micronutrients. The grain Fe concentration was in the range of 6.2–23.1 ppm in BR and 0.8–12.3 ppm in MR, while grain Zn concentration was found to be in the range of 11.0–47.0 ppm and 8.2–40.8 ppm in the BR and MR, respectively. Grain Fe exhibited maximum loss upon milling with a mean retention of 24.9% in MR, while Zn showed a greater mean retention of 74.2% in MR. A genome-wide association study (GWAS) was carried out implementing the FarmCPU model to control the population structure and kinship, and resulted in the identification of 29 marker-trait associations (MTAs) with significant associations for traits viz. FeBR (6 MTAs), FeMR (7 MTAs), ZnBR (11 MTAs), and ZnMR (5 MTAs), which could explain the phenotypic variance from 2.1 to as high as 53.3%. The MTAs governing the correlated traits showed co-localization, signifying the possibility of their simultaneous improvement. The robust MTAs identified in the study could be valuable resource for enhancing Fe and Zn concentration in the rice grain and addressing the problem of Fe and Zn malnutrition among rice consumers.
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Affiliation(s)
- Haritha Bollinedi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ashutosh Kumar Yadav
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - K K Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - M Nagarajan
- ICAR-Indian Agricultural Research Institute, Rice Breeding and Genetics Research Centre, Aduthurai, India
| | - C N Neeraja
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ashok Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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8
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Fujino K, Hirayama Y, Kaji R. Marker-assisted selection in rice breeding programs in Hokkaido. BREEDING SCIENCE 2019; 69:383-392. [PMID: 31598070 PMCID: PMC6776137 DOI: 10.1270/jsbbs.19062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 06/06/2019] [Indexed: 05/27/2023]
Abstract
Rice breeding programs in Hokkaido over the past 100 years have dramatically increased productivity and improved the eating quality of rice. Commercial varieties with high yield and good eating quality, such as Kirara 397, Hoshinoyume, and Nanatsuboshi, have been continuously registered since 1990. Furthermore, varieties with better eating quality using Wx1-1, which reduces amylose content to improve the taste of sticky rice, such as Oborozuki and Yumepirika, were registered in 2006 and 2008, respectively. However, to the best of our knowledge the genomic changes associated with these improvements have not been determined. Better understanding of the relationships between DNA sequences and agricultural traits could facilitate rice breeding programs in Hokkaido. Marker-assisted selection (MAS), which can select the plants with chromosomal regions tagged with DNA markers for desirable traits, is an advanced technology to manage genetic improvements. Here, we summarize the current states of MAS in rice breeding programs in Hokkaido before huge data sets of genome sequences using next-generation sequencing technology come into practical use in rice breeding programs.
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Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
| | - Yuji Hirayama
- Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization,
Pippu, Hokkaido 078-0397,
Japan
| | - Ryota Kaji
- Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
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Cultrera NGM, Sarri V, Lucentini L, Ceccarelli M, Alagna F, Mariotti R, Mousavi S, Ruiz CG, Baldoni L. High Levels of Variation Within Gene Sequences of Olea europaea L. FRONTIERS IN PLANT SCIENCE 2019; 9:1932. [PMID: 30671076 PMCID: PMC6331486 DOI: 10.3389/fpls.2018.01932] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/12/2018] [Indexed: 05/08/2023]
Abstract
Gene sequence variation in cultivated olive (Olea europaea L. subsp. europaea var. europaea), the most important oil tree crop of the Mediterranean basin, has been poorly evaluated up to now. A deep sequence analysis of fragments of four genes, OeACP1, OeACP2, OeLUS and OeSUT1, in 90 cultivars, revealed a wide range of polymorphisms along all recognized allele forms and unexpected allele frequencies and genotype combinations. High linkage values among most polymorphisms were recorded within each gene fragment. The great sequence variability corresponded to a low number of alleles and, surprisingly, to a small fraction of genotype combinations. The distribution, frequency, and combination of the different alleles at each locus is possibly due to natural and human pressures, such as selection, ancestrality, or fitness. Phylogenetic analyses of allele sequences showed distant and complex patterns of relationships among cultivated olives, intermixed with other related forms, highlighting an evolutionary connection between olive cultivars and the O. europaea subspecies cuspidata and cerasiformis. This study demonstrates how a detailed and complete sequence analysis of a few gene portions and a thorough genotyping on a representative set of cultivars can clarify important issues related to sequence polymorphisms, reconstructing the phylogeny of alleles, as well as the genotype combinations. The identification of regions representing blocks of recombination could reveal polymorphisms that represent putatively functional markers. Indeed, specific mutations found on the analyzed OeACP1 and OeACP2 fragments seem to be correlated to the fruit weight.
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Affiliation(s)
- Nicolò G. M. Cultrera
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | - Vania Sarri
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Livia Lucentini
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Marilena Ceccarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Fiammetta Alagna
- ENEA Italian National Agency for New Technologies Energy and Sustainable Economic Development, Trisaia Research Center, Rotondella, Italy
| | - Roberto Mariotti
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | - Soraya Mousavi
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | | | - Luciana Baldoni
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
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Iijima K, Suzuki K, Hori K, Ebana K, Kimura K, Tsujii Y, Takano K. Endosperm enzyme activity is responsible for texture and eating quality of cooked rice grains in Japanese cultivars. Biosci Biotechnol Biochem 2018; 83:502-510. [PMID: 30458671 DOI: 10.1080/09168451.2018.1547624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Eating quality of cooked rice grains is an important determinant of its market price and consumer acceptance. To comprehensively assess the variation of eating-quality traits in 152 Japanese rice cultivars, we evaluated activities of eight endosperm enzymes related to degradation of starch and cell-wall polysaccharides. Endosperm enzyme activities showed a wide range of variations and were lower in recently developed cultivars than in landraces and old improved cultivars. Activities of most endosperm enzymes correlated significantly with the eating-quality score and surface texture of cooked rice grains. Principal component analysis revealed that rice cultivars with high eating-quality scores had high stickiness of the grain surface and low levels of endosperm enzyme activities. These results suggest that endosperm enzyme activities control texture and eating quality of cooked rice grains in Japanese rice cultivars.
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Affiliation(s)
- Ken Iijima
- a Institute of Crop Science , National Agriculture and Food Research Organization (NARO) , Tsukuba , Ibaraki , Japan
| | - Keitaro Suzuki
- a Institute of Crop Science , National Agriculture and Food Research Organization (NARO) , Tsukuba , Ibaraki , Japan
| | - Kiyosumi Hori
- a Institute of Crop Science , National Agriculture and Food Research Organization (NARO) , Tsukuba , Ibaraki , Japan
| | - Kaworu Ebana
- b Genetic Resources Center , NARO , Tsukuba , Japan
| | - Keiichi Kimura
- c Department of Agricultural Chemistry , Tokyo University of Agriculture , Tokyo , Japan
| | - Yoshimasa Tsujii
- c Department of Agricultural Chemistry , Tokyo University of Agriculture , Tokyo , Japan
| | - Katsumi Takano
- c Department of Agricultural Chemistry , Tokyo University of Agriculture , Tokyo , Japan
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11
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Matsubara K, Yonemaru JI, Kobayashi N, Ishii T, Yamamoto E, Mizobuchi R, Tsunematsu H, Yamamoto T, Kato H, Yano M. A follow-up study for biomass yield QTLs in rice. PLoS One 2018; 13:e0206054. [PMID: 30352074 PMCID: PMC6198978 DOI: 10.1371/journal.pone.0206054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 10/07/2018] [Indexed: 12/22/2022] Open
Abstract
The biomass yield (plant weight) of rice fluctuates from year to year. In a previous study, we demonstrated that six quantitative trait loci (QTLs) contribute to the variation in the plant weight of recombinant inbred lines (RILs) of high-yielding Japanese rice cultivars. However, it remains unclear whether the effects of those QTLs are stable over multiple years. Therefore, we evaluated the effect of the alleles on the plant weight of RILs over multiple years, including a change of fertilization level (i.e., in different environments). Even though the biomass yields of all RILs fluctuated among environments, RILs that were selected on the basis of the genotypes of the detected QTLs had a stable rank order of plant weight that corresponded to their genotypes. This multiple-environment experiment reveals the highly significant contribution of both genotypic and environmental variances to the observed variance in plant weight. A marginally significant QTL–environment interaction was detected at only one of the six QTLs, with a subtle contribution. These results support the idea that the biomass yield of rice can be improved through QTL-based allele selection.
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Affiliation(s)
- Kazuki Matsubara
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
- * E-mail:
| | - Jun-ichi Yonemaru
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Nobuya Kobayashi
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Takuro Ishii
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Eiji Yamamoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Ritsuko Mizobuchi
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Hiroshi Tsunematsu
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Toshio Yamamoto
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Hiroshi Kato
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
| | - Masahiro Yano
- Institute of Crop Science, NARO (National Agriculture and Food Research Organization), Tsukuba, Ibaraki, Japan
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12
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Bekele WA, Wight CP, Chao S, Howarth CJ, Tinker NA. Haplotype-based genotyping-by-sequencing in oat genome research. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1452-1463. [PMID: 29345800 PMCID: PMC6041447 DOI: 10.1111/pbi.12888] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 01/05/2018] [Accepted: 01/10/2018] [Indexed: 05/05/2023]
Abstract
In a de novo genotyping-by-sequencing (GBS) analysis of short, 64-base tag-level haplotypes in 4657 accessions of cultivated oat, we discovered 164741 tag-level (TL) genetic variants containing 241224 SNPs. From this, the marker density of an oat consensus map was increased by the addition of more than 70000 loci. The mapped TL genotypes of a 635-line diversity panel were used to infer chromosome-level (CL) haplotype maps. These maps revealed differences in the number and size of haplotype blocks, as well as differences in haplotype diversity between chromosomes and subsets of the diversity panel. We then explored potential benefits of SNP vs. TL vs. CL GBS variants for mapping, high-resolution genome analysis and genomic selection in oats. A combined genome-wide association study (GWAS) of heading date from multiple locations using both TL haplotypes and individual SNP markers identified 184 significant associations. A comparative GWAS using TL haplotypes, CL haplotype blocks and their combinations demonstrated the superiority of using TL haplotype markers. Using a principal component-based genome-wide scan, genomic regions containing signatures of selection were identified. These regions may contain genes that are responsible for the local adaptation of oats to Northern American conditions. Genomic selection for heading date using TL haplotypes or SNP markers gave comparable and promising prediction accuracies of up to r = 0.74. Genomic selection carried out in an independent calibration and test population for heading date gave promising prediction accuracies that ranged between r = 0.42 and 0.67. In conclusion, TL haplotype GBS-derived markers facilitate genome analysis and genomic selection in oat.
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Affiliation(s)
- Wubishet A. Bekele
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
| | - Charlene P. Wight
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
| | - Shiaoman Chao
- USDA‐ARS Cereal Crops Research UnitRed River Valley Agricultural Research CenterFargoNDUSA
| | - Catherine J. Howarth
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Nicholas A. Tinker
- Ottawa Research and Development CentreAgriculture and Agri‐Food CanadaOttawaONCanada
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13
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Ogawa D, Yamamoto E, Ohtani T, Kanno N, Tsunematsu H, Nonoue Y, Yano M, Yamamoto T, Yonemaru JI. Haplotype-based allele mining in the Japan-MAGIC rice population. Sci Rep 2018. [PMID: 29531264 PMCID: PMC5847589 DOI: 10.1038/s41598-018-22657-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multi-parent advanced generation inter-cross (MAGIC) lines have broader genetic variation than bi-parental recombinant inbred lines. Genome-wide association study (GWAS) using high number of DNA polymorphisms such as single-nucleotide polymorphisms (SNPs) is a popular tool for allele mining in MAGIC populations, in which the associations of phenotypes with SNPs are investigated; however, the effects of haplotypes from multiple founders on phenotypes are not considered. Here, we describe an improved method of allele mining using the newly developed Japan-MAGIC (JAM) population, which is derived from eight high-yielding rice cultivars in Japan. To obtain information on the haplotypes in the JAM lines, we predicted the haplotype blocks in the whole chromosomes using 16,345 SNPs identified via genotyping-by-sequencing analysis. Using haplotype-based GWAS, we clearly detected the loci controlling the glutinous endosperm and culm length traits. Information on the alleles of the eight founders, which was based on the effects of mutations revealed by the analysis of next-generation sequencing data, was used to narrow down the candidate genes and reveal the associations between alleles and phenotypes. The haplotype-based allele mining (HAM) proposed in this study is a promising approach to the detection of allelic variation in genes controlling agronomic traits in MAGIC populations.
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Affiliation(s)
- Daisuke Ogawa
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Eiji Yamamoto
- Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Toshikazu Ohtani
- Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Noriko Kanno
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Hiroshi Tsunematsu
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Yasunori Nonoue
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan
| | - Masahiro Yano
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan.,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Toshio Yamamoto
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan. .,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan.
| | - Jun-Ichi Yonemaru
- Institute of Crop Science, National Agricultural and Food Research Organization (NARO), Tsukuba, Japan. .,Agrogenomics Research Centre, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan.
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14
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Hori K, Yamamoto T, Yano M. Genetic dissection of agronomically important traits in closely related temperate japonica rice cultivars. BREEDING SCIENCE 2017; 67:427-434. [PMID: 29398936 PMCID: PMC5790047 DOI: 10.1270/jsbbs.17053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/11/2017] [Indexed: 05/15/2023]
Abstract
Many quantitative trait loci (QTLs) for agronomically important traits such as grain yield, disease resistance, and stress tolerance of rice (Oryza sativa L.) have been detected by using segregating populations derived from crosses between indica and japonica subspecies or with wild relatives. However, the QTLs involved in the control of natural variation in agronomic traits among closely related cultivars are still unclear. Decoding the whole genome sequences of Nipponbare and other temperate japonica rice cultivars has accelerated the collection of a huge number of single nucleotide polymorphisms (SNPs). These SNPs are good resource for developing polymorphic DNA markers and for detecting QTLs distributed across all rice chromosomes. The temperate japonica rice cultivar Koshihikari has remained the top cultivar for about 40 years since 1979 in Japan. Unraveling the genetic factors in Koshihikari will provide important insights into improving agronomic traits in temperate japonica rice cultivars. Here we describe recent progress in our studies as an example of genetic analysis in closely related cultivars.
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15
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Sohn HB, Kim SJ, Hwang TY, Park HM, Lee YY, Markkandan K, Lee D, Lee S, Hong SY, Song YH, Koo BC, Kim YH. Barcode System for Genetic Identification of Soybean [ Glycine max (L.) Merrill] Cultivars Using InDel Markers Specific to Dense Variation Blocks. FRONTIERS IN PLANT SCIENCE 2017; 8:520. [PMID: 28443113 PMCID: PMC5385371 DOI: 10.3389/fpls.2017.00520] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/23/2017] [Indexed: 05/29/2023]
Abstract
For genetic identification of soybean [Glycine max (L.) Merrill] cultivars, insertions/deletions (InDel) markers have been preferred currently because they are easy to use, co-dominant and relatively abundant. Despite their biological importance, the investigation of InDels with proven quality and reproducibility has been limited. In this study, we described soybean barcode system approach based on InDel makers, each of which is specific to a dense variation block (dVB) with non-random recombination due to many variations. Firstly, 2,274 VBs were mined by analyzing whole genome data in six soybean cultivars (Backun, Sinpaldal 2, Shingi, Daepoong, Hwangkeum, and Williams 82) for transferability to dVB-specific InDel markers. Secondly, 73,327 putative InDels in the dVB regions were identified for the development of soybean barcode system. Among them, 202 dVB-specific InDels from all soybean cultivars were selected by gel electrophoresis, which were converted as 2D barcode types according to comparing amplicon polymorphisms in the five cultivars to the reference cultivar. Finally, the polymorphism of the markers were assessed in 147 soybean cultivars, and the soybean barcode system that allows a clear distinction among soybean cultivars is also detailed. In addition, the changing of the dVBs in a chromosomal level can be quickly identified due to investigation of the reshuffling pattern of the soybean cultivars with 27 maker sets. Especially, a backcross-inbred offspring, "Singang" and a recurrent parent, "Sowon" were identified by using the 27 InDel markers. These results indicate that the soybean barcode system enables not only the minimal use of molecular markers but also comparing the data from different sources due to no need of exploiting allele binning in new varieties.
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Affiliation(s)
- Hwang-Bae Sohn
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration (RDA)Gangwon-do, South Korea
| | - Su-Jeong Kim
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration (RDA)Gangwon-do, South Korea
| | - Tae-Young Hwang
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration (RDA)Chungcheongnam-Do, South Korea
| | - Hyang-Mi Park
- Headquarters, National Institute of Crop Science, Rural Development Administration (RDA)Jeolabuk-Do, South Korea
| | - Yu-Young Lee
- Department of Central Area, National Institute of Crop Science, Rural Development Administration (RDA)Gyeonggi-Do, South Korea
| | | | - Dongwoo Lee
- TheragenEtex Bio Institute, TheragenEtex Inc.Gyeonggi-Do, South Korea
| | - Sunghoon Lee
- EONE-DIAGNOMICS Genome CenterIncheon, South Korea
| | - Su-Young Hong
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration (RDA)Gangwon-do, South Korea
| | - Yun-Ho Song
- Gangwondo Agricultural Research and Extension ServicesGangwon-Do, South Korea
| | - Bon-Cheol Koo
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration (RDA)Gangwon-do, South Korea
| | - Yul-Ho Kim
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration (RDA)Gangwon-do, South Korea
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16
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N’Diaye A, Haile JK, Cory AT, Clarke FR, Clarke JM, Knox RE, Pozniak CJ. Single Marker and Haplotype-Based Association Analysis of Semolina and Pasta Colour in Elite Durum Wheat Breeding Lines Using a High-Density Consensus Map. PLoS One 2017; 12:e0170941. [PMID: 28135299 PMCID: PMC5279799 DOI: 10.1371/journal.pone.0170941] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 01/12/2017] [Indexed: 12/30/2022] Open
Abstract
Association mapping is usually performed by testing the correlation between a single marker and phenotypes. However, because patterns of variation within genomes are inherited as blocks, clustering markers into haplotypes for genome-wide scans could be a worthwhile approach to improve statistical power to detect associations. The availability of high-density molecular data allows the possibility to assess the potential of both approaches to identify marker-trait associations in durum wheat. In the present study, we used single marker- and haplotype-based approaches to identify loci associated with semolina and pasta colour in durum wheat, the main objective being to evaluate the potential benefits of haplotype-based analysis for identifying quantitative trait loci. One hundred sixty-nine durum lines were genotyped using the Illumina 90K Infinium iSelect assay, and 12,234 polymorphic single nucleotide polymorphism (SNP) markers were generated and used to assess the population structure and the linkage disequilibrium (LD) patterns. A total of 8,581 SNPs previously localized to a high-density consensus map were clustered into 406 haplotype blocks based on the average LD distance of 5.3 cM. Combining multiple SNPs into haplotype blocks increased the average polymorphism information content (PIC) from 0.27 per SNP to 0.50 per haplotype. The haplotype-based analysis identified 12 loci associated with grain pigment colour traits, including the five loci identified by the single marker-based analysis. Furthermore, the haplotype-based analysis resulted in an increase of the phenotypic variance explained (50.4% on average) and the allelic effect (33.7% on average) when compared to single marker analysis. The presence of multiple allelic combinations within each haplotype locus offers potential for screening the most favorable haplotype series and may facilitate marker-assisted selection of grain pigment colour in durum wheat. These results suggest a benefit of haplotype-based analysis over single marker analysis to detect loci associated with colour traits in durum wheat.
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Affiliation(s)
- Amidou N’Diaye
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Jemanesh K. Haile
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Aron T. Cory
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Fran R. Clarke
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - John M. Clarke
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ron E. Knox
- Semiarid Prairie Agricultural Research Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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17
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Genetic characterization and population structure of Indian rice cultivars and wild genotypes using core set markers. 3 Biotech 2016; 6:95. [PMID: 28330165 PMCID: PMC4808523 DOI: 10.1007/s13205-016-0409-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 03/01/2016] [Indexed: 11/12/2022] Open
Abstract
Genetic diversity among 23 rice genotypes including wild species and cultivars of indica, japonica, aus and aromatic type was investigated using 165 genomewide core set microsatellite (SSR) markers. This genotypic characterization was undertaken to know the genetic similarity among the parental lines to be used in developing a set of chromosome segment substitution lines. In all, 253 alleles were identified using 77 polymorphic SSRs, and polymorphism information content ranged from 0.31 to 0.97 with a mean of 0.79. Cluster analysis grouped the genotypes into three clusters at a genetic similarity of 0.26–0.75. Wild accessions grouped together in cluster-I, indica cultivars formed cluster-II, and aromatic, japonica and aus types came under cluster-III. Principal component analysis also showed similar results. The genotypic data was analyzed using STRUCTURE, and genotypes were grouped into four populations. RM1018 on chromosome 4, RM8009 on chromosome 7, and RM273 on chromosome 12 amplified alleles specific to wild accessions. The information obtained from core set markers would help in selecting diverse parents including wild accessions and for tracking alleles in mapping or breeding populations.
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18
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Matsubara K, Yamamoto E, Kobayashi N, Ishii T, Tanaka J, Tsunematsu H, Yoshinaga S, Matsumura O, Yonemaru JI, Mizobuchi R, Yamamoto T, Kato H, Yano M. Improvement of Rice Biomass Yield through QTL-Based Selection. PLoS One 2016; 11:e0151830. [PMID: 26986071 PMCID: PMC4795639 DOI: 10.1371/journal.pone.0151830] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Accepted: 03/06/2016] [Indexed: 12/31/2022] Open
Abstract
Biomass yield of rice (Oryza sativa L.) is an important breeding target, yet it is not easy to improve because the trait is complex and phenotyping is laborious. Using progeny derived from a cross between two high-yielding Japanese cultivars, we evaluated whether quantitative trait locus (QTL)-based selection can improve biomass yield. As a measure of biomass yield, we used plant weight (aboveground parts only), which included grain weight and stem and leaf weight. We measured these and related traits in recombinant inbred lines. Phenotypic values for these traits showed a continuous distribution with transgressive segregation, suggesting that selection can affect plant weight in the progeny. Four significant QTLs were mapped for plant weight, three for grain weight, and five for stem and leaf weight (at α = 0.05); some of them overlapped. Multiple regression analysis showed that about 43% of the phenotypic variance of plant weight was significantly explained (P < 0.0001) by six of the QTLs. From F2 plants derived from the same parental cross as the recombinant inbred lines, we divergently selected lines that carried alleles with positive or negative additive effects at these QTLs, and performed successive selfing. In the resulting F6 lines and parents, plant weight significantly differed among the genotypes (at α = 0.05). These results demonstrate that QTL-based selection is effective in improving rice biomass yield.
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Affiliation(s)
- Kazuki Matsubara
- NARO Institute of Crop Science, Tsukuba, Ibaraki 305–8518, Japan
- * E-mail:
| | - Eiji Yamamoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305–8602, Japan
| | - Nobuya Kobayashi
- NARO Institute of Crop Science, Tsukuba, Ibaraki 305–8518, Japan
| | - Takuro Ishii
- NARO Institute of Crop Science, Tsukuba, Ibaraki 305–8518, Japan
| | - Junichi Tanaka
- NARO Institute of Crop Science, Tsukuba, Ibaraki 305–8518, Japan
| | | | | | | | - Jun-ichi Yonemaru
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305–8602, Japan
| | - Ritsuko Mizobuchi
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305–8602, Japan
| | - Toshio Yamamoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305–8602, Japan
| | - Hiroshi Kato
- NARO Institute of Crop Science, Tsukuba, Ibaraki 305–8518, Japan
| | - Masahiro Yano
- NARO Institute of Crop Science, Tsukuba, Ibaraki 305–8518, Japan
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19
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Open access resources for genome-wide association mapping in rice. Nat Commun 2016; 7:10532. [PMID: 26842267 PMCID: PMC4742900 DOI: 10.1038/ncomms10532] [Citation(s) in RCA: 225] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 12/22/2015] [Indexed: 01/19/2023] Open
Abstract
Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement. Understanding the link between genotype and phenotype can facilitate efforts by breeders to utilize natural variation and develop new crop varieties. Here the authors present a diverse germplasm collection, a high-density genotyping array and a set of bioinformatic tools to enable association mapping in rice.
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20
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Shinada H, Yamamoto T, Sato H, Yamamoto E, Hori K, Yonemaru J, Sato T, Fujino K. Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping. BREEDING SCIENCE 2015; 65:388-95. [PMID: 26719741 PMCID: PMC4671699 DOI: 10.1270/jsbbs.65.388] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/26/2015] [Indexed: 05/20/2023]
Abstract
Plant breeding programs aim to develop cultivars with high adaptability to the specific conditions in a local region. As a result, unique genes and gene combinations have been accumulated in local elite breeding populations during the long history of plant breeding. Genetic analyses on such genes and combinations may be useful for developing new cultivars with more-desirable agronomic traits. Here, we attempted to detect quantitative trait loci (QTL) for rice blast resistance (BR) using a local breeding rice population from Hokkaido, Japan. Using genotyping data on single nucleotide polymorphisms and simple sequence repeat markers distributed throughout the whole genomic region, we detected genetic regions associated with phenotypic variation in BR by a genome-wide association mapping study (GWAS). An additional association analysis using other breeding cultivars verified the effect and inheritance of the associated region. Furthermore, the existence of a gene for BR in the associated region was confirmed by QTL mapping. The results from these studies enabled us to estimate potential of the Hokkaido rice population as a gene pool for improving BR. The results of this study could be useful for developing novel cultivars with vigorous BR in rice breeding programs.
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Affiliation(s)
- Hiroshi Shinada
- Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization,
Minami 1-5, Pippu, Hokkaido 078-0397,
Japan
- Corresponding author (e-mail: )
| | - Toshio Yamamoto
- Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences,
Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Hirokazu Sato
- Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization,
Minami 1-5, Pippu, Hokkaido 078-0397,
Japan
| | - Eiji Yamamoto
- Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences,
Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kiyosumi Hori
- Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences,
Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Junichi Yonemaru
- Rice Applied Genomics Research Unit, National Institute of Agrobiological Sciences,
Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Takashi Sato
- Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization,
Minami 1-5, Pippu, Hokkaido 078-0397,
Japan
| | - Kenji Fujino
- NARO Hokkaido Agricultural Research Center, National Agricultural Research Organization,
Sapporo, Hokkaido 062-8555,
Japan
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21
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Leung H, Raghavan C, Zhou B, Oliva R, Choi IR, Lacorte V, Jubay ML, Cruz CV, Gregorio G, Singh RK, Ulat VJ, Borja FN, Mauleon R, Alexandrov NN, McNally KL, Sackville Hamilton R. Allele mining and enhanced genetic recombination for rice breeding. RICE (NEW YORK, N.Y.) 2015; 8:34. [PMID: 26606925 PMCID: PMC4659784 DOI: 10.1186/s12284-015-0069-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/20/2015] [Indexed: 05/17/2023]
Abstract
Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources.
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Affiliation(s)
- Hei Leung
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines.
| | - Chitra Raghavan
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Bo Zhou
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Ricardo Oliva
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Il Ryong Choi
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Vanica Lacorte
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Mona Liza Jubay
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Casiana Vera Cruz
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Glenn Gregorio
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Rakesh Kumar Singh
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Victor Jun Ulat
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
| | - Frances Nikki Borja
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
| | - Ramil Mauleon
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
| | - Nickolai N Alexandrov
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
| | - Kenneth L McNally
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
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Yonemaru JI, Choi SH, Sakai H, Ando T, Shomura A, Yano M, Wu J, Fukuoka S. Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar 'Koshihikari'. BREEDING SCIENCE 2015; 65:249-56. [PMID: 26175622 PMCID: PMC4482175 DOI: 10.1270/jsbbs.65.249] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/24/2015] [Indexed: 05/06/2023]
Abstract
Insertion-deletion (indel) polymorphisms, such as simple sequence repeats, have been widely used as DNA markers to identify QTLs and genes and to facilitate rice breeding. Recently, next-generation sequencing has produced deep sequences that allow genome-wide detection of indels. These polymorphisms can potentially be used to develop high-accuracy polymerase chain reaction (PCR)-based markers. Here, re-sequencing of 5 indica, 2 aus, and 3 tropical japonica cultivars and Japanese elite cultivar 'Koshihikari' was performed to extract regions containing large indels (10-51 bp) shared by diverse cultivars. To design indel markers for the discrimination of genomic regions between 'Koshihikari' and other diverse cultivars, we subtracted the indel regions detected in 'Koshihikari' from those shared in other cultivars. Two sets of indel markers, KNJ8-indel (shared in eight or more cultivars, including 'Khao Nam Jen' as a representative tropical japonica cultivar) and C5-indel (shared in five to eight cultivars), were established, with 915 and 9,899 indel regions, respectively. Validation of the two marker sets by using 23 diverse cultivars showed a high PCR success rate (≥95%) for 83.3% of the KNJ8-indel markers and 73.9% of the C5-indel markers. The marker sets will therefore be useful for the effective breeding of Japanese rice cultivars.
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Affiliation(s)
- Jun-ichi Yonemaru
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
- Corresponding author (e-mail: )
| | - Sun Hee Choi
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Hiroaki Sakai
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Tsuyu Ando
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Ayahiko Shomura
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Masahiro Yano
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
- NARO Institute of Crop Science,
2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518,
Japan
| | - Jianzhong Wu
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Shuichi Fukuoka
- Agrogenomics Research Center, National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
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Matsuda F, Nakabayashi R, Yang Z, Okazaki Y, Yonemaru JI, Ebana K, Yano M, Saito K. Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:13-23. [PMID: 25267402 PMCID: PMC4309412 DOI: 10.1111/tpj.12681] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 09/19/2014] [Accepted: 09/19/2014] [Indexed: 05/18/2023]
Abstract
Plants produce structurally diverse secondary (specialized) metabolites to increase their fitness for survival under adverse environments. Several bioactive compounds for new drugs have been identified through screening of plant extracts. In this study, genome-wide association studies (GWAS) were conducted to investigate the genetic architecture behind the natural variation of rice secondary metabolites. GWAS using the metabolome data of 175 rice accessions successfully identified 323 associations among 143 single nucleotide polymorphisms (SNPs) and 89 metabolites. The data analysis highlighted that levels of many metabolites are tightly associated with a small number of strong quantitative trait loci (QTLs). The tight association may be a mechanism generating strains with distinct metabolic composition through the crossing of two different strains. The results indicate that one plant species produces more diverse phytochemicals than previously expected, and plants still contain many useful compounds for human applications.
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Affiliation(s)
- Fumio Matsuda
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University1-5 Yamadaoka, Suita, Osaka, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Zhigang Yang
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Jun-ichi Yonemaru
- National Institute of Agrobiological Sciences2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Kaworu Ebana
- National Institute of Agrobiological Sciences2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Masahiro Yano
- National Institute of Agrobiological Sciences2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba UniversityInohana 1-8-1, Chuo-ku, Chiba, Japan
- *For correspondence (e-mail )
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24
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Matsubara K, Yamamoto E, Mizobuchi R, Yonemaru JI, Yamamoto T, Kato H, Yano M. Hybrid breakdown caused by epistasis-based recessive incompatibility in a cross of rice (Oryza sativa L.). J Hered 2014; 106:113-22. [PMID: 25429024 DOI: 10.1093/jhered/esu065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Viability and fertility in organisms depend on epistatic interactions between loci maintained in lineages. Here, we describe reduced fitness of segregants (hybrid breakdown, HB) that emerged in an F2 population derived from a cross between 2 rice (Oryza sativa L.) cultivars, "Tachisugata" (TS) and "Hokuriku 193" (H193), despite both parents and F1s showing normal fitness. Quantitative trait locus (QTL) analyses detected 13 QTLs for 4 morphological traits associated with the HB and 6 associated with principal component scores calculated from values of the morphological traits in the F2 population. Two-way analysis of variance of the putative QTLs identified 4 QTL pairs showing significant epistasis; among them, a pair on chromosomes 1 and 12 made the greatest contribution to HB. The finding was supported by genetic experiments using F3 progeny. HB emerged only when a plant was homozygous for the TS allele at the QTL on chromosome 1 and homozygous for the H193 allele at the QTL on chromosome 12, indicating that each allele behaves as recessive to the other. Our results support the idea that epistasis is an essential part of hybrid fitness.
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Affiliation(s)
- Kazuki Matsubara
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan.
| | - Eiji Yamamoto
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Ritsuko Mizobuchi
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Jun-ichi Yonemaru
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Toshio Yamamoto
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
| | - Hiroshi Kato
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan.
| | - Masahiro Yano
- From the NARO Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan (Matsubara and Kato); and the National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan (Yamamoto, Mizobuchi, Yonemaru, Yamamoto, and Yano). Eiji Yamamoto is now at the NARO Institute of Vegetable and Tea Science, Tsu, Mie 514-2392, Japan. Masahiro Yano is now at the NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan. Hiroshi Kato is now at the National Institute of Agrobiological Sciences, Hitachiohmiya, Ibaraki 319-2293, Japan
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25
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Liu Q, Wang H, Hu H, Zhang H. Genome-wide identification and evolutionary analysis of positively selected miRNA genes in domesticated rice. Mol Genet Genomics 2014; 290:593-602. [DOI: 10.1007/s00438-014-0943-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Accepted: 10/17/2014] [Indexed: 01/24/2023]
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26
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Kim YH, Park HM, Hwang TY, Lee SK, Choi MS, Jho S, Hwang S, Kim HM, Lee D, Kim BC, Hong CP, Cho YS, Kim H, Jeong KH, Seo MJ, Yun HT, Kim SL, Kwon YU, Kim WH, Chun HK, Lim SJ, Shin YA, Choi IY, Kim YS, Yoon HS, Lee SH, Lee S. Variation block-based genomics method for crop plants. BMC Genomics 2014; 15:477. [PMID: 24929792 PMCID: PMC4229737 DOI: 10.1186/1471-2164-15-477] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 06/03/2014] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for the screening of target loci for agricultural traits. RESULTS We propose the variation block method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the short-read DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in the cultivar set are used to split the genomes, and the resulting sequence regions are termed variation blocks. Finally, the genomes are compared using the variation blocks. The variation block method identified recurring recombination blocks accurately and successfully represented block-level diversities in the publicly available genomes of 31 soybean and 23 rice accessions. The practicality of this approach was demonstrated by the identification of a putative locus determining soybean hilum color. CONCLUSIONS We suggest that the variation block method is an efficient genomics method for the recombination block-level comparison of crop genomes. We expect that this method will facilitate the development of crop genomics by bringing genomics technologies to the field of crop breeding.
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Affiliation(s)
- Yul Ho Kim
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Hyang Mi Park
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Tae-Young Hwang
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Seuk Ki Lee
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Man Soo Choi
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Seungwoo Hwang
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 306-809, Republic of Korea
| | - Hak-Min Kim
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Dongwoo Lee
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Byoung-Chul Kim
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Chang Pyo Hong
- Theragen Bio Institute, TheragenEtex, Suwon 443-270, Republic of Korea
| | - Yun Sung Cho
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Hyunmin Kim
- Theragen Bio Institute, TheragenEtex, Suwon 443-270, Republic of Korea
| | - Kwang Ho Jeong
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Min Jung Seo
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Hong Tai Yun
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Sun Lim Kim
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Young-Up Kwon
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Wook Han Kim
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Hye Kyung Chun
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Sang Jong Lim
- National Institute of Crop Science, Rural Development Administration, Suwon 441-857, Republic of Korea
| | - Young-Ah Shin
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
| | - Ik-Young Choi
- National Instrumentation Center for Environmental Management, College of Agriculture and Life Science, Seoul National University, Seoul 151-921, Republic of Korea
| | - Young Sun Kim
- Department of Biology, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Ho-Sung Yoon
- Department of Biology, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea
| | - Sunghoon Lee
- Personal Genomics Institute, Genome Research Foundation, Suwon 443-270, Republic of Korea
- Theragen Bio Institute, TheragenEtex, Suwon 443-270, Republic of Korea
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27
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Kawasaki-Tanaka A, Fukuta Y. Genetic variation in resistance to blast disease (Pyricularia oryzae Cavara) in Japanese rice (Oryza sativa L.), as determined using a differential system. BREEDING SCIENCE 2014; 64:183-92. [PMID: 24987305 PMCID: PMC4065326 DOI: 10.1270/jsbbs.64.183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Accepted: 03/13/2014] [Indexed: 05/25/2023]
Abstract
A total of 324 Japanese rice accessions, including landrace, improved, and weedy types were used to 1) investigate genetic variations in blast resistance to standard differential isolates, and 2) across the genome using polymorphism data on 64 SSR markers. From the polymorphism data, the accessions were classified into two clusters,. Accessions from irrigated lowland areas were included mainly in cluster I, and upland and Indica types were mainly in cluster II. The accessions were classified into three resistance subgroups, A2, B1 and B2, based on the reaction patterns to blast isolates. The accessions in A2 were postulated to have at least two resistance genes Pish and Pik-s, whereas those in B1 had various combinations of the resistance genes Pish, Pia, Pii, Pi3, Pi5(t), and Pik alleles. The B2 accessions were resistant to almost all isolates, and many accessions of cluster II were included, and had Pish, Pia, Pii, Pi3, Pi5(t), certain Pik, Piz and Pita alleles, and unknown genes. The frequencies of accessions of B1 originating in Hokkaido, and those of B2 originating in the Kanto and Tohoku regions were remarkably higher than in the other regions.
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Affiliation(s)
- Akiko Kawasaki-Tanaka
- Tottori University,
4-101 Koyama-Minami Tottori, Tottori 680-8553,
Japan
- Japan International Research Center for Agricultural Sciences,
1-1 Ohwashi, Tsukuba, Ibaraki 304-8686,
Japan
| | - Yoshimichi Fukuta
- Japan International Research Center for Agricultural Sciences,
1-1 Ohwashi, Tsukuba, Ibaraki 304-8686,
Japan
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28
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Yonemaru JI, Mizobuchi R, Kato H, Yamamoto T, Yamamoto E, Matsubara K, Hirabayashi H, Takeuchi Y, Tsunematsu H, Ishii T, Ohta H, Maeda H, Ebana K, Yano M. Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars. BMC Genomics 2014; 15:346. [PMID: 24885019 PMCID: PMC4035073 DOI: 10.1186/1471-2164-15-346] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 04/28/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND High-yielding cultivars of rice (Oryza sativa L.) have been developed in Japan from crosses between overseas indica and domestic japonica cultivars. Recently, next-generation sequencing technology and high-throughput genotyping systems have shown many single-nucleotide polymorphisms (SNPs) that are proving useful for detailed analysis of genome composition. These SNPs can be used in genome-wide association studies to detect candidate genome regions associated with economically important traits. In this study, we used a custom SNP set to identify introgressed chromosomal regions in a set of high-yielding Japanese rice cultivars, and we performed an association study to identify genome regions associated with yield. RESULTS An informative set of 1152 SNPs was established by screening 14 high-yielding or primary ancestral cultivars for 5760 validated SNPs. Analysis of the population structure of high-yielding cultivars showed three genome types: japonica-type, indica-type and a mixture of the two. SNP allele frequencies showed several regions derived predominantly from one of the two parental genome types. Distinct regions skewed for the presence of parental alleles were observed on chromosomes 1, 2, 7, 8, 11 and 12 (indica) and on chromosomes 1, 2 and 6 (japonica). A possible relationship between these introgressed regions and six yield traits (blast susceptibility, heading date, length of unhusked seeds, number of panicles, surface area of unhusked seeds and 1000-grain weight) was detected in eight genome regions dominated by alleles of one parental origin. Two of these regions were near Ghd7, a heading date locus, and Pi-ta, a blast resistance locus. The allele types (i.e., japonica or indica) of significant SNPs coincided with those previously reported for candidate genes Ghd7 and Pi-ta. CONCLUSIONS Introgression breeding is an established strategy for the accumulation of QTLs and genes controlling high yield. Our custom SNP set is an effective tool for the identification of introgressed genome regions from a particular genetic background. This study demonstrates that changes in genome structure occurred during artificial selection for high yield, and provides information on several genomic regions associated with yield performance.
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Affiliation(s)
- Jun-ichi Yonemaru
- National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
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29
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Shinada H, Yamamoto T, Yamamoto E, Hori K, Yonemaru J, Matsuba S, Fujino K. Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:995-1004. [PMID: 24510168 DOI: 10.1007/s00122-014-2274-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Accepted: 01/26/2014] [Indexed: 05/10/2023]
Abstract
The rice local population was clearly differentiated into six groups over the 100-year history of rice breeding programs in the northern limit of rice cultivation over the world. Genetic improvements in plant breeding programs in local regions have led to the development of new cultivars with specific agronomic traits under environmental conditions and generated the unique genetic structures of local populations. Understanding historical changes in genome structures and phenotypic characteristics within local populations may be useful for identifying profitable genes and/or genetic resources and the creation of new gene combinations in plant breeding programs. In the present study, historical changes were elucidated in genome structures and phenotypic characteristics during 100-year rice breeding programs in Hokkaido, the northern limit of rice cultivation in the world. We selected 63 rice cultivars to represent the historical diversity of this local population from landraces to the current breeding lines. The results of the phylogenetic analysis demonstrated that these cultivars clearly differentiated into six groups over the history of rice breeding programs. Significant differences among these groups were detected in five of the seven traits, indicating that the differentiation of the Hokkaido rice population into these groups was correlated with these phenotypic changes. These results demonstrated that breeding practices in Hokkaido have created new genetic structures for adaptability to specific environmental conditions and breeding objectives. They also provide a new strategy for rice breeding programs in which such unique genes in local populations in the world can explore the genetic potentials of the local populations.
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Affiliation(s)
- Hiroshi Shinada
- Rice Breeding Group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization, Minami 1-5, Pippu, Hokkaido, 078-0397, Japan
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30
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Yonemaru JI, Ebana K, Yano M. HapRice, an SNP haplotype database and a web tool for rice. PLANT & CELL PHYSIOLOGY 2014; 55:e9. [PMID: 24334415 DOI: 10.1093/pcp/pct188] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Genome-wide single nucleotide polymorphism (SNP) analysis is a promising tool to examine the genetic diversity of rice populations and genetic traits of scientific and economic importance. Next-generation sequencing technology has accelerated the re-sequencing of diverse rice varieties and the discovery of genome-wide SNPs. Notably, validation of these SNPs by a high-throughput genotyping system, such as an SNP array, could provide a manageable and highly accurate SNP set. To enhance the potential utility of genome-wide SNPs for geneticists and breeders, analysis tools need to be developed. Here, we constructed an SNP haplotype database, which allows visualization of the allele frequency of all SNPs in the genome browser. We calculated the allele frequencies of 3,334 SNPs in 76 accessions from the world rice collection and 3,252 SNPs in 177 Japanese rice accessions; all these SNPs have been validated in our previous studies. The SNP haplotypes were defined by the allele frequency in each cultivar group (aus, indica, tropical japonica and temperate japonica) for the world rice accessions, and in non-irrigated and three irrigated groups (three variety registration periods) for Japanese rice accessions. We also developed web tools for finding polymorphic SNPs between any two rice accessions and for the primer design to develop cleaved amplified polymorphic sequence markers at any SNP. The 'HapRice' database and the web tools can be accessed at http://qtaro.abr.affrc.go.jp/index.html. In addition, we established a core SNP set consisting of 768 SNPs uniformly distributed in the rice genome; this set is of a practically appropriate size for use in rice genetic analysis.
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Affiliation(s)
- Jun-ichi Yonemaru
- National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602 Japan
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31
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Yang Z, Nakabayashi R, Okazaki Y, Mori T, Takamatsu S, Kitanaka S, Kikuchi J, Saito K. Toward better annotation in plant metabolomics: isolation and structure elucidation of 36 specialized metabolites from Oryza sativa (rice) by using MS/MS and NMR analyses. Metabolomics 2014; 10:543-555. [PMID: 25057267 PMCID: PMC4097337 DOI: 10.1007/s11306-013-0619-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 12/18/2013] [Indexed: 01/05/2023]
Abstract
Metabolomics plays an important role in phytochemical genomics and crop breeding; however, metabolite annotation is a significant bottleneck in metabolomic studies. In particular, in liquid chromatography-mass spectrometry (MS)-based metabolomics, which has become a routine technology for the profiling of plant-specialized metabolites, a substantial number of metabolites detected as MS peaks are still not assigned properly to a single metabolite. Oryza sativa (rice) is one of the most important staple crops in the world. In the present study, we isolated and elucidated the structures of specialized metabolites from rice by using MS/MS and NMR. Thirty-six compounds, including five new flavonoids and eight rare flavonolignan isomers, were isolated from the rice leaves. The MS/MS spectral data of the isolated compounds, with a detailed interpretation of MS fragmentation data, will facilitate metabolite annotation of the related phytochemicals by enriching the public mass spectral data depositories, including the plant-specific MS/MS-based database, ReSpect.
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Affiliation(s)
- Zhigang Yang
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
| | - Tetsuya Mori
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
| | - Satoshi Takamatsu
- School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Funabashi, Chiba 274-8555 Japan
- Present Address: School of Pharmacy, Showa University, 1-5-8 Hatanodai, Shinagawa, Tokyo 142-8555 Japan
| | - Susumu Kitanaka
- School of Pharmacy, Nihon University, 7-7-1 Narashinodai, Funabashi, Chiba 274-8555 Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045 Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chiba, 260-8675 Japan
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Choudhary G, Ranjitkumar N, Surapaneni M, Deborah DA, Vipparla A, Anuradha G, Siddiq EA, Vemireddy LR. Molecular Genetic Diversity of Major Indian Rice Cultivars over Decadal Periods. PLoS One 2013; 8:e66197. [PMID: 23805204 PMCID: PMC3689748 DOI: 10.1371/journal.pone.0066197] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 05/05/2013] [Indexed: 12/03/2022] Open
Abstract
Genetic diversity in representative sets of high yielding varieties of rice released in India between 1970 and 2010 was studied at molecular level employing hypervariable microsatellite markers. Of 64 rice SSR primer pairs studied, 52 showed polymorphism, when screened in 100 rice genotypes. A total of 184 alleles was identified averaging 3.63 alleles per locus. Cluster analysis clearly grouped the 100 genotypes into their respective decadal periods i.e., 1970s, 1980s, 1990s and 2000s. The trend of diversity over the decadal periods estimated based on the number of alleles (Na), allelic richness (Rs), Nei’s genetic diversity index (He), observed heterozygosity (Ho) and polymorphism information content (PIC) revealed increase of diversity over the periods in year of releasewise and longevitywise classification of rice varieties. Analysis of molecular variance (AMOVA) suggested more variation in within the decadal periods than among the decades. Pairwise comparison of population differentiation (Fst) among decadal periods showed significant difference between all the pairs except a few. Analysis of trends of appearing and disappearing alleles over decadal periods showed an increase in the appearance of alleles and decrease in disappearance in both the categories of varieties. It was obvious from the present findings, that genetic diversity was progressively on the rise in the varieties released during the decadal periods, between 1970s and 2000s.
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Affiliation(s)
- Gangaprasad Choudhary
- Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, Andhra Pradesh, India
| | - Nagireddy Ranjitkumar
- Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, Andhra Pradesh, India
| | - Malathi Surapaneni
- Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, Andhra Pradesh, India
| | - Dondapati Annekitty Deborah
- Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, Andhra Pradesh, India
| | - Abhilash Vipparla
- Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, Andhra Pradesh, India
| | - Ghanta Anuradha
- Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, Andhra Pradesh, India
| | - Ebrahimali Abubacker Siddiq
- Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, Andhra Pradesh, India
| | - Lakshminarayana Reddy Vemireddy
- Institute of Biotechnology, Acharya NG Ranga Agricultural University, Rajendranagar, Hyderabad, Andhra Pradesh, India
- * E-mail:
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Shinada H, Iwata N, Sato T, Fujino K. Genetical and morphological characterization of cold tolerance at fertilization stage in rice. BREEDING SCIENCE 2013; 63:197-204. [PMID: 23853514 PMCID: PMC3688381 DOI: 10.1270/jsbbs.63.197] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 02/14/2013] [Indexed: 05/03/2023]
Abstract
Cold temperature during the reproductive phase leads to seed sterility, which reduces yield and decreases the grain quality of rice. The fertilization stage, ranging from pollen maturation to the completion of fertilization, is sensitive to unsuitable temperature. Improving cold tolerance at the fertilization stage (CTF) is an important objective of rice breeding program in cold temperature areas. In this study, we characterized fertilization behavior under cold temperature to define the phenotype of CTF and identified quantitative trait loci (QTLs) for CTF. A wide variation in CTF levels has been identified among local cultivars in Hokkaido, which is one of the most northern regions for rice cultivation in the world. Clear varietal differences in pollen germination, and pollen tube elongation due to cold temperature have been observed. These differences may confer a degree of CTF among this population. We conducted QTL analysis for CTF using 120 backcrossed inbred lines derived from a cross between Eikei88223 (vigorous CTF) and Suisei (very weak CTF). Three QTLs for CTF were identified. A clear effect by QTL, qCTF7, for increasing the level of CTF was validated using advanced progeny. These results will facilitate marker-assist selection for desirable QTLs for CTF in rice breeding program.
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Affiliation(s)
- Hiroshi Shinada
- Rice breeding group, Kamikawa Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization , Minami 1-5, Pippu, Hokkaido 078-0397, Japan ; Present address: Beans breeding group, Tokachi Agricultural Experiment Station, Local Independent Administrative Agency Hokkaido Research Organization , Shinsei minami 9-2, Memuro, Hokkaido 082-0071, Japan ; Corresponding author (e-mail: )
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Ikeda M, Miura K, Aya K, Kitano H, Matsuoka M. Genes offering the potential for designing yield-related traits in rice. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:213-20. [PMID: 23466256 DOI: 10.1016/j.pbi.2013.02.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 02/04/2013] [Indexed: 05/05/2023]
Abstract
Breeding of high-yielding rice is crucial for meeting the food demand of the increasing world population. New technologies have facilitated identification of genes involved in quantitative traits, and many genes underpinning quantitative trait loci involved in rice crop yield have been isolated. Meanwhile, various kinds of mutants have been intensively studied, leading to characterization of many genes related to yield traits. A combination of quantitative trait locus analysis and studies of such mutants has made it possible to compile a list of genes available for breeding rice with higher yield.
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Affiliation(s)
- Mayuko Ikeda
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
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Liu Q, Wang H, Zhu L, Hu H, Sun Y. Genome-wide identification and analysis of miRNA-related single nucleotide polymorphisms (SNPs) in rice. RICE (NEW YORK, N.Y.) 2013; 6:10. [PMID: 24280131 PMCID: PMC4883715 DOI: 10.1186/1939-8433-6-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 04/17/2013] [Indexed: 05/23/2023]
Abstract
BACKGROUND MiRNAs are key regulators in the miRNA-mediated regulatory networks. Single nucleotide polymorphisms (SNPs) that occur at miRNA-related regions may cause serious phenotype changes. To gain new insights into the evolution of miRNAs after SNP variation, we performed a genome-wide scan of miRNA-related SNPs, and analyzed their effects on the stability of miRNAs structure and the alteration of target spectrum in rice. RESULTS We find that the SNP density in pre-miRNAs is significantly higher than that in the flanking regions, owing to the rapid evolution of a large number of species-specific miRNAs in rice. In contrast, it is obvious that deeply conserved miRNAs are under strong purifying selection during evolution. In most cases, the SNPs in stem regions may result in the miRNA hairpin structures changing from stable to unstable status; And SNPs in mature miRNAs have great potential to have either newly created or disrupted the miRNA-target interactions. However, the total number of gained targets is over 2.5 times greater than that are lost after mutation. Notably, 12 putative domestication-related miRNAs have been identified, where the SNP density is significantly lower. CONCLUSIONS The present study provides the first outline of SNP variations occurred in rice pre-miRNAs at the whole genome-wide level. These analyses may deepen our understanding on the effects of SNPs on the evolution of miRNAs in the rice genome.
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Affiliation(s)
- Qingpo Liu
- />College of Agriculture and Food Science, Zhejiang A & F University, Lin’an Hangzhou, 311300 China
| | - Hong Wang
- />College of Agriculture and Food Science, Zhejiang A & F University, Lin’an Hangzhou, 311300 China
| | - Leyi Zhu
- />College of Agriculture and Food Science, Zhejiang A & F University, Lin’an Hangzhou, 311300 China
| | - Haichao Hu
- />College of Agriculture and Food Science, Zhejiang A & F University, Lin’an Hangzhou, 311300 China
| | - Yuqiang Sun
- />College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 310036 China
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Fujino K, Yamanouchi U, Yano M. Roles of the Hd5 gene controlling heading date for adaptation to the northern limits of rice cultivation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:611-8. [PMID: 23090144 DOI: 10.1007/s00122-012-2005-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 10/06/2012] [Indexed: 05/04/2023]
Abstract
During the diversification of cultivated rice after domestication, rice was grown in diverse geographic regions using genetic variations attributed to the combination of alleles in loci for adaptability to various environmental conditions. To elucidate the key gene for adaptation in rice cultivars to the northern limit of rice cultivation, we conducted genetic analyses of heading date using extremely early-heading cultivars. The Hd5 gene controlling heading date (flowering time) generated variations in heading date among cultivars adapted to Hokkaido, where is the northernmost region of Japan and one of the northern limits of rice cultivation in the world. The association of the Hd5 genotype with heading date and genetical analysis clearly showed that the loss-of-function Hd5 has an important role in exhibiting earlier heading among a local population in Hokkaido. Distinct distribution of the loss-of-function Hd5 revealed that this mutation event of the 19-bp deletion occurred in a local landrace Bouzu and that this mutation may have been selected as an early-heading variety in rice breeding programs in Hokkaido in the early 1900s. The loss-of-function Hd5 was then introduced into the rice variety Fanny from France and contributed to its extremely early heading under the presence of functional Ghd7. These results demonstrated that Hd5 plays roles not only in generating early heading in variations of heading date among a local population in Hokkaido, but also in extremely early heading for adaptation to northern limits of rice cultivation.
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Affiliation(s)
- Kenji Fujino
- Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido, 067-1317, Japan.
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