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N'Diaye A, Tonessia DC, Le Cunff L, Hamon P, Hamon S. RETRACTED ARTICLE: Evidence of weak genetic differentiation of Striga gesnerioides populations collected in Senegal: possible relationship with traditional cowpea seed management. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1. [PMID: 19484430 DOI: 10.1007/s00122-009-1073-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2008] [Accepted: 05/13/2009] [Indexed: 05/27/2023]
Affiliation(s)
- Amidou N'Diaye
- INRA, UMR DIAPC, 2 Place Pierre Viala, 34060, Montpellier Cedex 01, France.
| | | | - Loïc Le Cunff
- INRA, UMR DIAPC, 2 Place Pierre Viala, 34060, Montpellier Cedex 01, France
| | - Perla Hamon
- IRD, UMR DIAPC, 911 Av Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
| | - Serge Hamon
- IRD, UMR DIAPC, 911 Av Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
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Population Dynamics of Wide Compatibility System and Evaluation of Intersubspecific Hybrids by indica-japonica Hybridization in Rice. PLANTS 2022; 11:plants11151930. [PMID: 35893634 PMCID: PMC9332614 DOI: 10.3390/plants11151930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 11/17/2022]
Abstract
The exploitation of heterosis through intersubspecific hybridisation between indica and japonica has been a major breeding target in rice, but is marred by the cross incompatibility between the genomes. Wide compatibility (WC) is a triallelic system at the S5 locus on chromosome 6 that ensures the specificity of hybridisation within and between indica and japonica. The S5n allele that favours intercrossing is sparsely distributed in the rice gene pool and therefore warrants identification of diverse WC sources to develop superior intersubspecific hybrids. In this study, we have identified several novel WC sources through the marker-assisted screening of a large set of 950 rice genotypes. Seventeen percent of the genotypes carried S5n, which fell into two subpopulations. The WC genotypes showed wide phenotypic and genotypic variability, including both indica and japonica lines. Based on phenotypic performance, the WC varieties were grouped into three clusters. A subset of 41 WC varieties was used to develop 164 hybrids, of which WC/japonica hybrids showed relative superiority over WC/indica hybrids. The multilocation evaluation of hybrids indicated that hybrids derived from WC varieties, such as IRG137, IRG143, OYR128, and IRGC10658, were higher yielding across all the three different locations. Most of the hybrids showed the stability of performance across locations. The identified diverse set of wide compatible varieties (WCVs) can be used in the development of intersubspecific hybrids and also for parental line development in hybrid rice breeding.
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Sah RP, Behera S, Dash SK, Azharudheen TPM, Meher J, Kumar A, Marndi BC, Kar MK, Subudhi HN, Anilkumar C. Unravelling genetic architecture and development of core set from elite rice lines using yield-related candidate gene markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1217-1232. [PMID: 35910441 PMCID: PMC9334483 DOI: 10.1007/s12298-022-01190-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 05/08/2022] [Accepted: 05/17/2022] [Indexed: 06/03/2023]
Abstract
Assessing genetic diversity and development of a core set of elite breeding lines is a prerequisite for selective hybridization programes intended to improve the yield potential in rice. In the present study, the genetic diversity of newly developed elite lines derived from indicax tropical japonica and indicax indica crosses were estimated by 38 reported molecular markers. The markers used in the study consist of 24 gene-based and 14 random markers related to grain yield-related QTLs distributed across the rice genome. Genotypic characterization was carried out to determine the genetic similarities between the elite lines. In total, 75 alleles were found using 38 polymorphic markers, with polymorphism information content ranging from 0.10 to 0.51 with an average of 0.35. The genotypes were divided into three groups based on cluster analysis, structure analysis and also dispersed throughout the quadrangle of PCA, but nitrogen responsive lines clustered in one quadrangle. Seven markers (GS3_RGS1, GS3_RGS2, GS5_Indel1, Ghd 7_05SNP, RM 12289, RM 23065 and RM 25457) exhibited PIC values ≥ 0.50 indicating that they were effective in detecting genetic relationships among elite rice. Additionally, a core set of 11 elite lines was made from 96 lines in order to downsize the diversity of the original population into a small set for parental selection. In general, the genetic information collected in this work will aid in the study of grain yield traits at molecular level for other sets of rice genotypes and for selecting diverse elite lines to develop a strong crossing programme in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01190-8.
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Affiliation(s)
- Rameswar Prasad Sah
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Sasmita Behera
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Sushant Kumar Dash
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | | | - Jitendriya Meher
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Awadhesh Kumar
- Crop Physiology and Biochemistry, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Bishnu Charan Marndi
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Meera Kumari Kar
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - H. N. Subudhi
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - C. Anilkumar
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, Odisha India
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Population Structure of a Worldwide Collection of Tropical Japonica Rice Indicates Limited Geographic Differentiation and Shows Promising Genetic Variability Associated with New Plant Type. Genes (Basel) 2022; 13:genes13030484. [PMID: 35328038 PMCID: PMC8956019 DOI: 10.3390/genes13030484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/15/2022] Open
Abstract
Abating the approaching yield plateau in rice requires taking advantage of potential technologies that requires knowledge on genetic diversity. Hybrid breeding, particularly in indica rice, requires the recruitment of large genetic variability from outside because the available genetic diversity of the cultivated pool has already been utilized to a great extent. In this study, we examined an assembly of 200 tropical japonica lines collected worldwide for population genetic structure and variability in yield-associated traits. Tested along with 30 indica and six wild rice lines belonging to India, the tropical japonica lines indicated great phenotypic variability, particularly related to new plant type (NPT) phenology, and formed six clusters. Furthermore, a marker-based characterization using a universal diversity marker panel classified the genotype assembly into four clusters, of which three encompassed tropical japonica lines, while the last cluster included mostly indica lines. The population structure of the panel also revealed a similar pattern, with tropical japonica lines forming three subpopulations. Remarkable variation in the allelic distribution was observed between the subpopulations. Superimposing the geographical sources of the genotypes over the population structure did not reveal any pattern. The genotypes sourced closer to the center of origin of rice showed relatively little diversity compared with the ones obtained from other parts of the world, suggesting migration from a common region of origin. The tropical japonica lines can be a great source of parental diversification for hybrid development after confirming the presence of widely compatible genes.
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Su D, Xie F, Liu H, Xie D, Li J, He X, Guo X, Zhou S. Comparative analysis of complete plastid genomes from Lilium lankongense Franchet and its closely related species and screening of Lilium-specific primers. PeerJ 2021; 9:e10964. [PMID: 33717697 PMCID: PMC7938781 DOI: 10.7717/peerj.10964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 01/28/2021] [Indexed: 11/20/2022] Open
Abstract
Lilium lankongense Franchet is a lily species found on the Qinghai-Tibet Plateau. It is pink with deep red spots, has a high ornamental value, and is used in hybrid breeding of horticultural lily varieties. We have insufficient knowledge of the genetic resources of L. lankongense and its phylogenetic relationships with related species. Recent molecular phylogenetic studies have shown a very close phylogenetic relationship between L. lankongense and the five species L. duchartrei, L. stewartianum, L. matangense, L. lophophorum, and L. nanum. However, molecular markers still lack sufficient signals for population-level research of the genus Lilium. We sequenced and compared the complete plastid sequences of L. lankongense and its five related species. The genomes ranged from 152,307 bp to 152,611 bp. There was a slight inconsistency detected in inverted repeat and single copy boundaries and there were 53 to 63 simple sequence repeats in the six species. Two of the 12 highly variable regions (trnC-petN and rpl32-trnL) were verified in 11 individuals and are promising for population-level studies. We used the complete sequence of 33 plastid genomes, the protein-coding region sequence, and the nuclear ITS sequence to reconstruct the phylogenetic tree of Lilium species. Our results showed that the plastid gene tree and nuclear gene tree were not completely congruent, which may be caused by hybridization, insufficient information contained in the nuclear ITS, or the small number of samples. The results of phylogenetic analysis based on plastid genomes indicated that the six Lilium species were closely related. Our study provides a preliminarily rebuilt backbone phylogeny that is significant for future molecular and morphological studies of Lilium.
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Affiliation(s)
- Danmei Su
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Fumin Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Haiying Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Dengfeng Xie
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Juan Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xingjin He
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Xianlin Guo
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| | - Songdong Zhou
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
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Genetic and Genomic Diversity in a Tarwi (Lupinus mutabilis Sweet) Germplasm Collection and Adaptability to Mediterranean Climate Conditions. AGRONOMY-BASEL 2019. [DOI: 10.3390/agronomy10010021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Lupinus mutabilis (tarwi) is a species of Andean origin with high protein and oil content and regarded as a potential crop in Europe. The success in the introduction of this crop depends in part on in depth knowledge of the intra-specific genetic variability of the collections, enabling the establishment of breeding and conservation programs. In this study, we used morphological traits, Inter-Simple Sequence Repeat markers and genome size to assess genetic and genomic diversity of 23 tarwi accessions under Mediterranean conditions. Phenotypic analyses and yield component studies point out accession LM268 as that achieving the highest seed production, producing large seeds and efficiently using primary branches as an important component of total yield, similar to the L. albus cultivars used as controls. By contrast, accession JKI-L295 presents high yield concentrated on the main stem, suggesting a semi-determinate development pattern. Genetic and genomic analyses revealed important levels of diversity, however not relatable to phenotypic diversity, reflecting the recent domestication of this crop. This is the first study of genome size diversity within L. mutabilis, revealing an average size of 2.05 pg/2C (2001 Mbp) with 9.2% variation (1897–2003 Mbp), prompting further studies for the exploitation of this diversity.
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Kumar A, Singh VJ, Krishnan SG, Vinod KK, Bhowmick PK, Nagarajan M, Ellur RK, Bollinedi H, Singh AK. WA-CMS-based iso-cytoplasmic restorers derived from commercial rice hybrids reveal distinct population structure and genetic divergence towards restorer diversification. 3 Biotech 2019; 9:299. [PMID: 31355108 DOI: 10.1007/s13205-019-1824-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 07/01/2019] [Indexed: 12/27/2022] Open
Abstract
One hundred diverse iso-cytoplasmic restorer (ICR) lines carrying WA cytoplasm indicated significant but moderate variability for agro-morphological traits as well as for the microsatellite-based allele patterns. There were two major groups of ICRs based on agro-morphological clustering. Simple sequence repeat (SSR) markers identified allelic variants with an average of 2.48 alleles per locus and the gene diversity (GD) ranged from 0.02 to 0.62 at different loci. ICR lines showed a genetic structure involving two sub-populations, POP1 and POP2. Both the subpopulations had the presence of admixture lines. Nearest ancestry-based grouping of ICRs by neighbour-joining (NJ) method showed near similar grouping as that of sub-population division. The POP2 was the largest group but with fewer admixed lines. POP1 was more distinct than POP2. Since the hybrid parents of the ICRs had limited diversity on maternal lineage, paternal lineage was concluded as the major contributor to the observed divergence and population differentiation. ICRs developed from certain hybrids were more genetically distinct than other hybrids. Even with the moderate variability, ICRs could be considered as a potential source of fertility restoration in hybrid development because of their distinct population structure and the full complement of restorer genes they contained. ICR lines with high per se performance can be utilized in hybrid rice development by estimating their combining ability.
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Affiliation(s)
- Amit Kumar
- 1Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012 India
- Plant Breeding, ICAR-Research Complex for North Eastern Hill Region, Umiam, 793103 India
| | - Vikram Jeet Singh
- 1Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012 India
| | - S Gopala Krishnan
- 1Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012 India
| | - K K Vinod
- Rice Breeding and Genetics Research Centre, ICAR-IARI, Aduthurai, 612101 India
| | - Prolay Kumar Bhowmick
- 1Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012 India
| | - M Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR-IARI, Aduthurai, 612101 India
| | - Ranjith Kumar Ellur
- 1Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012 India
| | - Haritha Bollinedi
- 1Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012 India
| | - Ashok Kumar Singh
- 1Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012 India
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Abstract
Sake is a Japanese traditional alcoholic beverage made from rice and water. Recently, its export and its production in countries other than Japan have increased. In accordance, both the breeding and the cultivation of sake rice varieties have been extended to wide areas of Japan. To breed new sake rice cultivars and to cultivate rice with high suitability for sake production, an understanding of the properties of the ingredient rice grains and the factors affecting sake making is important. The influence of various rice properties, such as starch structure, protein, water absorption, and grain polishing, on sake making are being revealed in detail. In this review, the properties of rice used for sake making are summarized in terms of fermentation science and rice cultivation.
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Affiliation(s)
- Masaki Okuda
- a National Research Institute of Brewing , Higashihiroshima , Japan
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Roy PS, Rao GJN, Jena S, Samal R, Patnaik A, Patnaik SSC, Jambhulkar NN, Sharma S, Mohapatra T. Nuclear and Chloroplast DNA Variation Provides Insights into Population Structure and Multiple Origin of Native Aromatic Rices of Odisha, India. PLoS One 2016; 11:e0162268. [PMID: 27598392 PMCID: PMC5012674 DOI: 10.1371/journal.pone.0162268] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 08/20/2016] [Indexed: 11/23/2022] Open
Abstract
A large number of short grain aromatic rice suited to the agro-climatic conditions and local preferences are grown in niche areas of different parts of India and their diversity is evolved over centuries as a result of selection by traditional farmers. Systematic characterization of these specialty rices has not been attempted. An effort was made to characterize 126 aromatic short grain rice landraces, collected from 19 different districts in the State of Odisha, from eastern India. High level of variation for grain quality and agronomic traits among these aromatic rices was observed and genotypes having desirable phenotypic traits like erect flag leaf, thick culm, compact and dense panicles, short plant stature, early duration, superior yield and grain quality traits were identified. A total of 24 SSR markers corresponding to the hyper variable regions of rice chromosomes were used to understand the genetic diversity and to establish the genetic relationship among the aromatic short grain rice landraces at nuclear genome level. SSR analysis of 126 genotypes from Odisha and 10 genotypes from other states revealed 110 alleles with an average of 4.583 and the Nei’s genetic diversity value (He) was in the range of 0.034–0.880 revealing two sub-populations SP 1 (membership percentage-27.1%) and SP 2 (72.9%). At the organelle genomic level for the C/A repeats in PS1D sequence of chloroplasts, eight different plastid sub types and 33 haplotypes were detected. The japonica (Nipponbare) subtype (6C7A) was detected in 100 genotypes followed by O. rufipogon (KF428978) subtype (6C6A) in 13 genotypes while indica (93–11) sub type (8C8A) was seen in 14 genotypes. The tree constructed based on haplotypes suggests that short grain aromatic landraces might have independent origin of these plastid subtypes. Notably a wide range of diversity was observed among these landraces cultivated in different parts confined to the State of Odisha.
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Affiliation(s)
- Pritesh Sundar Roy
- National Rice Research Institute (formerly Central Rice Research Institute), Cuttack, Odisha, India
| | | | - Sudipta Jena
- National Rice Research Institute (formerly Central Rice Research Institute), Cuttack, Odisha, India
| | - Rashmita Samal
- National Rice Research Institute (formerly Central Rice Research Institute), Cuttack, Odisha, India
| | - Ashok Patnaik
- National Rice Research Institute (formerly Central Rice Research Institute), Cuttack, Odisha, India
| | | | | | - Srigopal Sharma
- National Rice Research Institute (formerly Central Rice Research Institute), Cuttack, Odisha, India
| | - Trilochan Mohapatra
- National Rice Research Institute (formerly Central Rice Research Institute), Cuttack, Odisha, India
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Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice. Nat Genet 2016; 48:927-34. [PMID: 27322545 DOI: 10.1038/ng.3596] [Citation(s) in RCA: 360] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 05/26/2016] [Indexed: 02/07/2023]
Abstract
A genome-wide association study (GWAS) can be a powerful tool for the identification of genes associated with agronomic traits in crop species, but it is often hindered by population structure and the large extent of linkage disequilibrium. In this study, we identified agronomically important genes in rice using GWAS based on whole-genome sequencing, followed by the screening of candidate genes based on the estimated effect of nucleotide polymorphisms. Using this approach, we identified four new genes associated with agronomic traits. Some genes were undetectable by standard SNP analysis, but we detected them using gene-based association analysis. This study provides fundamental insights relevant to the rapid identification of genes associated with agronomic traits using GWAS and will accelerate future efforts aimed at crop improvement.
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Arai-Kichise Y, Shiwa Y, Ebana K, Shibata-Hatta M, Yoshikawa H, Yano M, Wakasa K. Genome-wide DNA polymorphisms in seven rice cultivars of temperate and tropical japonica groups. PLoS One 2014; 9:e86312. [PMID: 24466017 PMCID: PMC3897683 DOI: 10.1371/journal.pone.0086312] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 12/09/2013] [Indexed: 01/04/2023] Open
Abstract
Elucidation of the rice genome is expected to broaden our understanding of genes related to the agronomic characteristics and the genetic relationship among cultivars. In this study, we conducted whole-genome sequencings of 6 cultivars, including 5 temperate japonica cultivars and 1 tropical japonica cultivar (Moroberekan), by using next-generation sequencing (NGS) with Nipponbare genome as a reference. The temperate japonica cultivars contained 2 sake brewing (Yamadanishiki and Gohyakumangoku), 1 landrace (Kameji), and 2 modern cultivars (Koshihikari and Norin 8). Almost >83% of the whole genome sequences of the Nipponbare genome could be covered by sequenced short-reads of each cultivar, including Omachi, which has previously been reported to be a temperate japonica cultivar. Numerous single nucleotide polymorphisms (SNPs), insertions, and deletions were detected among the various cultivars and the Nipponbare genomes. Comparison of SNPs detected in each cultivar suggested that Moroberekan had 5-fold more SNPs than the temperate japonica cultivars. Success of the 2 approaches to improve the efficacy of sequence data by using NGS revealed that sequencing depth was directly related to sequencing coverage of coding DNA sequences: in excess of 30× genome sequencing was required to cover approximately 80% of the genes in the rice genome. Further, the contigs prepared using the assembly of unmapped reads could increase the value of NGS short-reads and, consequently, cover previously unavailable sequences. These approaches facilitated the identification of new genes in coding DNA sequences and the increase of mapping efficiency in different regions. The DNA polymorphism information between the 7 cultivars and Nipponbare are available at NGRC_Rices_Build1.0 (http://www.nodai-genome.org/oryza_sativa_en.html).
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Affiliation(s)
- Yuko Arai-Kichise
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
- * E-mail:
| | - Yuh Shiwa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Kaworu Ebana
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Mari Shibata-Hatta
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
| | - Masahiro Yano
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Kyo Wakasa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Setagaya, Tokyo, Japan
- Department of Bioscience, Tokyo University of Agriculture, Tokyo, Japan
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12
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Dong Z, Wang H, Dong Y, Wang Y, Liu W, Miao G, Lin X, Wang D, Liu B. Extensive microsatellite variation in rice induced by introgression from wild rice (Zizania latifolia Griseb.). PLoS One 2013; 8:e62317. [PMID: 23638037 PMCID: PMC3634730 DOI: 10.1371/journal.pone.0062317] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/20/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND It is widely accepted that interspecific hybridization may induce genomic instability in the resultant hybrids. However, few studies have been performed on the genomic analysis of homoploid hybrids and introgression lines. We have reported previously that by introgressive hybridization, a set of introgression lines between rice (Oryza sativa L.) and wild rice (Zizania latifolia Griseb.) was successfully generated, and which have led to the release of several cultivars. METHODOLOGY Using 96 microsatellite markers located in the nuclear and organelle genomes of rice, we investigated microsatellite stability in three typical introgression lines. Expression of a set of mismatch repair (MMR) genes and microsatellite-containing genes was also analyzed. RESULTS/CONCLUSIONS Compared with the recipient rice cultivar (Matsumae), 55 of the 96 microsatellite loci revealed variation in one or more of the introgression lines, and 58.2% of the altered alleles were shared by at least two lines, indicating that most of the alterations had occurred in the early stages of introgression before their further differentiation. 73.9% of the non-shared variations were detected only in one introgression line, i.e. RZ2. Sequence alignment showed that the variations included substitutions and indels that occurred both within the repeat tracts and in the flanking regions. Interestingly, expression of a set of MMR genes altered dramatically in the introgression lines relative to their rice parent, suggesting participation of the MMR system in the generation of microsatellite variants. Some of the altered microsatellite loci are concordant with changed expression of the genes harboring them, suggesting their possible cis-regulatory roles in controlling gene expression. Because these genes bear meaningful homology to known-functional proteins, we conclude that the introgression-induced extensive variation of microsatellites may have contributed to the novel phenotypes in the introgression lines.
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Affiliation(s)
- Zhenying Dong
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
- The State Key Laboratory of Plant Cell and Chromosomal Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Hongyan Wang
- Faculty of Life Science, Liaoning University, Shenyang, China
| | - Yuzhu Dong
- School of Life Sciences, Changchun Normal University, Changchun, China
| | - Yongming Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Wei Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Gaojian Miao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Xiuyun Lin
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Daqing Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics and Cytology, Northeast Normal University, Changchun, China
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13
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Morphological and genetic diversity analysis of rice accessions (Oryza sativa L.) differing in iron toxicity tolerance. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s12892-012-0104-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Yamasaki M, Ideta O. Population structure in Japanese rice population. BREEDING SCIENCE 2013; 63:49-57. [PMID: 23641181 PMCID: PMC3621445 DOI: 10.1270/jsbbs.63.49] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 11/21/2011] [Indexed: 05/04/2023]
Abstract
It is essential to elucidate genetic diversity and relationships among even related individuals and populations for plant breeding and genetic analysis. Since Japanese rice breeding has improved agronomic traits such as yield and eating quality, modern Japanese rice cultivars originated from narrow genetic resource and closely related. To resolve the population structure and genetic diversity in Japanese rice population, we used a total of 706 alleles detected by 134 simple sequence repeat markers in a total of 114 cultivars composed of 94 improved varieties and 20 landraces, which are representative and important for Japanese rice breeding. The landraces exhibit greater gene diversity than improved lines, suggesting that landraces can provide additional genetic diversity for future breeding. Model-based Bayesian clustering analysis revealed six subgroups and admixture situation in the cultivars, showing good agreement with pedigree information. This method could be superior to phylogenetic method in classifying a related population. The leading Japanese rice cultivar, Koshihikari is unique due to the specific genome constitution. We defined Japanese rice diverse sets that capture the maximum number of alleles for given sample sizes. These sets are useful for a variety of genetic application in Japanese rice cultivars.
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Affiliation(s)
- Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, 1348 Uzurano, Kasai, Hyogo 675-2103, Japan
- Corresponding author (e-mail: )
| | - Osamu Ideta
- National Agriculture and Food Research Organization, Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Present address: National Agriculture and Food Research Organization, Western Region Agricultural Research Center, 6-12-1 Nishifukatsu, Fukuyama, Hiroshima 721-8514, Japan
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Chakhonkaen S, Pitnjam K, Saisuk W, Ukoskit K, Muangprom A. Genetic structure of Thai rice and rice accessions obtained from the International Rice Research Institute. RICE (NEW YORK, N.Y.) 2012; 5:19. [PMID: 27234241 PMCID: PMC5520827 DOI: 10.1186/1939-8433-5-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 06/13/2012] [Indexed: 05/22/2023]
Abstract
BACKGROUND Although the genetic structure of rice germplasm has been characterized worldwide, few studies investigated germplasm from Thailand, the world's largest exporter of rice. Thailand and the International Rice Research Institute (IRRI) have diverse collections of rice germplasm, which could be used to develop breeding lines with desirable traits. This study aimed to investigate the level of genetic diversity and structures of Thai and selected IRRI germplasm. Understanding the genetic structure and relationships among these germplasm will be useful for parent selection used in rice breeding programs. RESULTS From the 98 InDel markers tested for single copy and polymorphism, 19 markers were used to evaluate 43 Thai and 57 IRRI germplasm, including improved cultivars, breeding lines, landraces, and 5 other Oryza species. The Thai accessions were selected from all rice ecologies such as irrigated, deep water, upland, and rainfed lowland ecosystems. The IRRI accessions were groups of germplasm having agronomic desirable traits, including temperature-sensitive genetic male sterility (TGMS), new plant type, early flowering, and biotic and abiotic stress resistances. Most of the InDel markers were genes with diverse functions. These markers produced the total of 127 alleles for all loci, with a mean of 6.68 alleles per locus, and a mean Polymorphic Information Content (PIC) of 0.440. Genetic diversity of Thai rice were 0.3665, 0.4479 and 0.3972 for improved cultivars, breeding lines, and landraces, respectively, while genetic diversity of IRRI improved and breeding lines were 0.3272 and 0.2970, respectively. Cluster, structure, and differentiation analyses showed six distinct groups: japonica, TGMS, deep-water, IRRI germplasm, Thai landraces and breeding lines, and other Oryza species. CONCLUSIONS Thai and IRRI germplasm were significantly different. Thus, they can be used to broaden the genetic base and trait improvements. Cluster, structure, and differentiation analyses showed concordant results having six distinct groups, in agreement with their development, and ecologies.
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Affiliation(s)
- Sriprapai Chakhonkaen
- Laboratory of Plant Molecular Genetics, National Center for Genetic Engineering and Biotechnology, Pathum thani, 12120 Thailand
| | - Keasinee Pitnjam
- Laboratory of Plant Molecular Genetics, National Center for Genetic Engineering and Biotechnology, Pathum thani, 12120 Thailand
| | - Wachira Saisuk
- Department of Biotechnology, Faculty of Science and Technology, Thammasart University, Rangsit, Pathum thani, 12120 Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasart University, Rangsit, Pathum thani, 12120 Thailand
| | - Amorntip Muangprom
- Laboratory of Plant Molecular Genetics, National Center for Genetic Engineering and Biotechnology, Pathum thani, 12120 Thailand
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Bezugliy MD, Sivolap YM, Galaev AV, Dudchenko VV, Vozhegova RA. DNA-identification of rice varieties (Oriza sativa L.) of Ukrainian breeding. CYTOL GENET+ 2011. [DOI: 10.3103/s0095452711010063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Caser M, Torello Marinoni D, Scariot V. Microsatellite-based genetic relationships in the genus Camellia: potential for improving cultivars. Genome 2010; 53:384-99. [PMID: 20616869 DOI: 10.1139/g10-012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
There is a lack of published microsatellite data that characterizes Camellia spp. To address this, an initial study of sequence tagged microsatellite site (STMS) variation was undertaken with 132 accessions of Camellia spp., which included 24 accessions representing 22 different species or varieties as well as 63 cultivars of C. japonica, 33 cultivars of C. sasanqua, 7 cultivars of C. x vernalis, 3 cultivars of C. x hiemalis, and 2 cultivars of C. hybrida. The four primer sets used (MSCJAF37, MSCJAH46, MSCJAF25, and MSCJAH38) successfully amplified polymorphic alleles in all the species analysed, showing cross-transferability. Overall, 96 alleles were scored. MSCJAH38 primers produced the highest number of bands (30), while MSCJAH46 primers yielded the lowest number (15). The genetic distance between pairs of accessions was estimated on the basis of the Nei coefficient and a principal coordinate analysis was performed. The plot revealed a main differentiation between the C. japonica cultivars and the winter camellias. The distribution of the genetic variation, attributed by AMOVA, particularly highlighted genetic overlap among C. sasanqua cultivars and the cultivars belonging to C. x vernalis, C. x hiemalis, and C. hybrida. In conclusion, this study demonstrated that STMS markers offer a suitable method for detection of genetic variability and molecular study of camellia genotypes.
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Affiliation(s)
- Matteo Caser
- Department of Agronomy, Forest and Land Management, University of Turin, via L. da Vinci 44, 10095 Grugliasco (TO), Italy.
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Nakamura S, Haraguchi K, Mitani N, Ohtsubo K. Novel preparation method of template DNAs from wine for PCR to differentiate grape (Vitis vinifera L.) cultivar. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:10388-10395. [PMID: 17994688 DOI: 10.1021/jf072407u] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Template DNAs were extracted from wine and purified for use as samples for PCR to differentiate grape cultivars. It has been pointed out that the authentication of grape material by PCR using wine as a material is very difficult. The problems are (1) decomposition of DNAs during fermentation; (2) contamination of DNAs from microorganisms such as yeast; (3) interference of DNA extraction by polysaccharides and polypeptides in the beverages; and (4) coexistence of PCR inhibitors, such as polyphenols. For this study was developed a novel preparation method of template DNA from wine to differentiate grape cultivars using PCR by (1) lyophilizing and pulverizing the fermented beverage to concentrate the DNAs; (2) decomposition of polysaccharides and proteins so as not to inhibit DNA extraction using heat-resistant amylase and proteinase K without DNA damage by endogenous DNase; and (3) separation of the template DNAs for PCR from PCR inhibitors, such as polyphenols, by purification using 70% EtOH extraction and isopropyl alcohol precipitation. To prevent the amplification of microorganisms' DNAs during PCR, suitable PCR primers closely related to the specific plant DNAs, such as chloroplast DNA and mitochondrial DNA, were selected. The sequences of the amplified DNAs by PCR were ascertained to be the same as those of grape materials.
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Affiliation(s)
- Sumiko Nakamura
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba Science City, Ibaraki 305-8642 Japan
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Ohtsubo K, Suzuki K, Haraguchi K, Nakamura S. Novel method for preparation of the template DNA and selection of primers to differentiate the material rice cultivars of rice wine by PCR. ACTA ACUST UNITED AC 2007; 70:1020-8. [PMID: 17675162 DOI: 10.1016/j.jbbm.2007.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2006] [Revised: 07/01/2007] [Accepted: 07/01/2007] [Indexed: 11/15/2022]
Abstract
As many rice wine brewers label the name of the cultivar of the material rice, authentication technology is necessary. The problems are (1) decomposition of DNAs during the fermentation, (2) contamination of DNAs from microorganisms, (3) co-existence of PCR inhibitors, such as polyphenols. The present authors improved the PCR method by (1) lyophilizing and pulverizing the rice wine to concentrate DNAs, (2) decomposition of starches and proteins so as not to inhibit DNA extraction by the use of heat-resistant amylase and proteinase K, (3) purification of the template DNA by the combination of CTAB method and fractional precipitation by 70% EtOH. To prevent the amplification of microorganism's DNAs during PCR, the present authors selected the suitable plant-specific primers. It became possible to prepare the template DNAs for PCR from the rice wine. The sequences of the amplified DNAs by PCR were ascertained to be same with those of material rice. Mislabeling of material rice cultivar was detected by PCR using the commercial rice wine. It became possible to extract and purify the template DNAs for PCR from the rice wine and to differentiate the material rice cultivars by the PCR using the rice wine as a sample.
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Affiliation(s)
- Ken'ichi Ohtsubo
- National Food Research Institute, 2-1-12, Kan-nondai, Tsukuba Science City, Ibaraki, 305-8642 Japan.
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Yang W, Glover BJ, Rao GY, Yang J. Molecular evidence for multiple polyploidization and lineage recombination in the Chrysanthemum indicum polyploid complex (Asteraceae). THE NEW PHYTOLOGIST 2006; 171:875-86. [PMID: 16918557 DOI: 10.1111/j.1469-8137.2006.01779.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The Chrysanthemum indicum polyploid complex comprises morphologically differentiated diploids, tetraploids and hybrids between C. indicum and C. lavandulifolium. The relationships between species and cytotypes within this complex remain poorly understood. Random amplified polymorphic DNAs (RAPDs), intersimple sequence repeats (ISSRs) and chloroplast SSR markers were used to elucidate the genetic diversity and relationships of the C. indicum polyploid complex. Molecular analysis of three diploid and nine tetraploid populations provided strong evidence for recurrent origins and lineage recombination in the C. indicum polyploid complex. The high similarity in molecular marker profiles and cpDNA haplotypes between the diploids and tetraploids distributed in the Shen-Nong-Jia Mountain area of China suggested an autopolyploid origin of the tetraploids, while the tetraploids from other populations may have originated via allopolyploidization. Lineage recombination was revealed by the extensive sharing of chloroplast haplotypes and genetic markers among the tetraploid populations with different origins. Multiple differentiation and hybridization/polyploidization cycles have led to an evolutionary reticulation in the C. indicum polyploid complex, and resulted in the difficulties in systematic classification.
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Affiliation(s)
- Wenhua Yang
- College of Life Sciences, Peking University, Beijing 100871, China
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Diéguez MJ, Altieri E, Ingala LR, Perera E, Sacco F, Naranjo T. Physical and genetic mapping of amplified fragment length polymorphisms and the leaf rust resistance Lr3 gene on chromosome 6BL of wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:251-7. [PMID: 16215730 DOI: 10.1007/s00122-005-0122-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Accepted: 09/15/2005] [Indexed: 05/04/2023]
Abstract
The Argentinian wheat cultivar Sinvalocho MA carries the Lr3 gene for leaf rust resistance on distal chromosome 6BL. In this cultivar, 33 spontaneous susceptible lines were isolated and cytogenetically characterized by C-banding. The analysis revealed deletions on chromosome 6BL in most lines. One line was nulli-6B, two lines were ditelo 6BS, two, three, and ten lines had long terminal deletions of 40, 30, and 20%, respectively, three lines showed very small terminal deletions, and one line had an intercalary deletion of 11%. Physical mapping of 55 amplified fragment length polymorphism (AFLP) markers detected differences between deletions and led to the division of 6BL into seven bins delimited by deletion breakpoints. The most distal bin, with a length smaller than 5% of 6BL, contained 22 AFLP markers and the Lr3 gene. Polymorphism for nine AFLPs between Sinvalocho MA and the rust leaf susceptible cultivar Gamma 6 was used to construct a linkage map of Lr3. This gene is at a genetic distance of 0.9 cM from a group of seven closely linked AFLPs. The location of the gene in a high recombinogenic region indicated a physical distance of approximately 1 Mb to the markers.
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Affiliation(s)
- M J Diéguez
- Instituto de Genética Ewald A. Favret CICVyA-INTA CC25 (1712), Castelar, Argentina.
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