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Kehinde BO, Xie L, Song BK, Zheng X, Fan L. African Cultivated, Wild and Weedy Rice ( Oryza spp.): Anticipating Further Genomic Studies. BIOLOGY 2024; 13:697. [PMID: 39336124 PMCID: PMC11428565 DOI: 10.3390/biology13090697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Revised: 08/31/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024]
Abstract
Rice is a staple crop in sub-Saharan Africa, and it is mostly produced by Asian cultivars of Oryza sativa that were introduced to the continent around the fifteenth or sixteenth century. O. glaberrima, the native African rice, has also been planted due to its valuable traits of insect and drought tolerance. Due to competition and resistance evolution, weedy rice has evolved from O. sativa and O. glaberrima, posing an increasing threat to rice production. This paper provides an overview of current knowledge on the introduction and domestication history of cultivated rice in Africa, as well as the genetic properties of African weedy rice that invades paddy fields. Recent developments in genome sequencing have made it possible to uncover findings about O. glaberrima's population structure, stress resilience genes, and domestication bottleneck. Future rice genomic research in Africa should prioritize producing more high-quality reference genomes, quantifying the impact of crop-wild hybridization, elucidating weed adaptation mechanisms through resequencing, and establishing a connection between genomic variation and stress tolerance phenotypes to accelerate breeding efforts.
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Affiliation(s)
- Babatunde O Kehinde
- Institute of Crop Science, Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
- Department of Zoology, University of Lagos, Akoka-Yaba, Lagos 101245, Nigeria
| | - Lingjuan Xie
- Institute of Crop Science, Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Beng-Kah Song
- School of Science, Monash University Malaysia, Bandar Sunway 46150, Selangor, Malaysia
| | - Xiaoming Zheng
- Yazhouwan National Laboratory, Yazhou District, Sanya 572024, China
| | - Longjiang Fan
- Institute of Crop Science, Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
- Yazhouwan National Laboratory, Yazhou District, Sanya 572024, China
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Labroo MR, Clark LV, Zhang S, Hu F, Tao D, Hamilton RS, Sacks EJ. Solving the mystery of Obake rice in Africa: population structure analyses of Oryza longistaminata reveal three genetic groups and evidence of both recent and ancient introgression with O. sativa. FRONTIERS IN PLANT SCIENCE 2023; 14:1278196. [PMID: 38034553 PMCID: PMC10684938 DOI: 10.3389/fpls.2023.1278196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
The undomesticated rice relative Oryza longistaminata is a valuable genetic resource for the improvement of the domesticated Asian rice, Oryza sativa. To facilitate the conservation, management, and use of O. longistaminata germplasm, we sought to quantify the population structure and diversity of this species across its geographic range, which includes most of sub-Saharan Africa, and to determine phylogenetic relationships to other AA-genome species of rice present in Africa, including the prevalence of interspecific hybridization between O. longistaminata and O. sativa. Though past plant breeding efforts to introgress genes from O. longistaminata have improved biotic stress resistance, ratooning ability, and yield in O. sativa, progress has been limited by substantial breeding barriers. Nevertheless, despite the strong breeding barriers observed by plant breeders who have attempted this interspecific cross, there have been multiple reports of spontaneous hybrids of O. sativa and O. longistaminata (aka "Obake") obtained from natural populations in Africa. However, the frequency and extent of such natural introgressions and their effect on the evolution of O. longistaminata had not been previously investigated. We studied 190 O. longistaminata accessions, primarily from the International Rice Research Institute genebank collection, along with 309 O. sativa, 25 Oryza barthii, and 83 Oryza glaberrima control outgroups, and 17 control interspecific O. sativa/O. longistaminata hybrids. We analyzed the materials using 178,651 single-nucleotide polymorphisms (SNPs) and seven plastid microsatellite markers. This study identified three genetic subpopulations of O. longistaminata, which correspond geographically to Northwestern Africa, Pan-Africa, and Southern Africa. We confirmed that O. longistaminata is, perhaps counterintuitively, more closely related to the Asian species, O. sativa, than the African species O. barthii and O. glaberrima. We identified 19 recent spontaneous interspecific hybrid individuals between O. sativa and O. longistaminata in the germplasm sampled. Notably, the recent introgression between O. sativa and O. longistaminata has been bidirectional. Moreover, low levels of O. sativa alleles admixed in many predominantly O. longistaminata accessions suggest that introgression also occurred in the distant past, but only in Southern Africa.
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Affiliation(s)
- Marlee R. Labroo
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Lindsay V. Clark
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Shilai Zhang
- School of Agriculture, Research Center for Perennial Rice Engineering and Technology in Yunnan, Yunnan University, Kunming, China
| | - Fengyi Hu
- School of Agriculture, Research Center for Perennial Rice Engineering and Technology in Yunnan, Yunnan University, Kunming, China
| | - Dayun Tao
- Yunnan Seed Laboratory & Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Ruaraidh Sackville Hamilton
- T.T. Chang Genetic Resources Center, International Rice Research Institute (IRRI), Los Baños, Philippines
- CGIAR Genebank Initiative, Salisbury, United Kingdom
| | - Erik J. Sacks
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Htet AH, Makabe S, Takahashi H, Samuel PA, Sato YI, Nakamura I. A large deletion within intron 20 sequence of single-copy PolA1 gene as a useful marker for the speciation in Oryza AA-genome species. BREEDING SCIENCE 2022; 72:267-273. [PMID: 36408325 PMCID: PMC9653197 DOI: 10.1270/jsbbs.21075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/04/2022] [Indexed: 06/16/2023]
Abstract
Oryza AA-genome complex comprises five wild species, O. rufipogon, O. barthii, O. longistaminata, O. glumaepatula, and O. meridionalis. Evolutionary relationships among these five wild species have remained contentious and inconclusive. We found that intron 20 of PolA1, a single-copy nuclear gene, was short (S-type: 141-142 bp) in O. rufipogon, O. barthii, and O. glumaepatula, while long (L-type: ca. 1.5 kb) introns were apparent in O. longistaminata and O. meridionalis. Because Oryza species containing BB, CC, EE, FF, and GG genome showed L-type introns, the S-type intron was probably derived from the L-type intron by the deletion of a 1.4 kb fragment through intramolecular homologous recombination between two tandem TTTTGC repeats. Excluding the large deletion sequence, intron 20 sequence of O. barthii was identical to that of O. longistaminata. As more than 3,470 accessions of O. rufipogon and O. sativa also contained the same intron 20 sequence with O. longistaminata except for single T-nucleotide deletion, which was shared with O. glumaepatuala, the deletion of the T-nucleotide probably occurred in the L-type intron 20 of O. logistaminata. Deletions of a large 1.4 kb fragment and single T-nucleotide within the intron 20 of PolA1 gene were considered as useful DNA markers to study the evolutionary relationships among Oryza AA-genome species.
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Affiliation(s)
- Aung Htut Htet
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - So Makabe
- BEX Co. Ltd., Itabashi-ku, Tokyo 173-0004, Japan
| | | | - Poku Aduse Samuel
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan
| | - Yo-ichiro Sato
- Kyoto Washoku Institute, Kyoto Prefectural University, Kyoto 606-8522, Japan
| | - Ikuo Nakamura
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba 271-8510, Japan
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Xie C, An W, Liu S, Huang Y, Yang Z, Lin J, Zheng X. Comparative genomic study on the complete plastomes of four officinal Ardisia species in China. Sci Rep 2021; 11:22239. [PMID: 34782652 PMCID: PMC8594775 DOI: 10.1038/s41598-021-01561-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 10/21/2021] [Indexed: 11/23/2022] Open
Abstract
Ardisia Sw. (Primulaceae) is naturally distributed in tropical and subtropical areas. Most of them possess edible and medicinal values and are popular in clinical and daily use in China. However, ambiguous species delineation and genetic information limit the development and utilization of this genus. In this study, the chloroplast genomes of four Ardisia species, namely A. gigantifolia Stapf, A. crenata Sims, A. villosa Roxb. and A. mamillata Hance, were sequenced, annotated, and analyzed comparatively. All the four chloroplast genomes possess a typical quadripartite structure, and each of the genomes is about 156 Kb in size. The structure and gene content of the Ardisia plastomes were conservative and showed low sequence divergence. Furthermore, we identified five mutation hotspots as candidate DNA barcodes for Ardisia, namely, trnT-psbD, ndhF-rpl32, rpl32-ccsA, ccsA-ndhD and ycf1. Phylogenetic analysis based on the whole-chloroplast genomes data showed that Ardisia was sister to Tapeinosperma Hook. f. In addition, the results revealed a great topological profile of Ardisia's with strong support values, which matches their geographical distribution patterns. Summarily, our results provide useful information for investigations on taxonomic differences, molecular identification, and phylogenetic relationships of Ardisia plants.
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Affiliation(s)
- Chunzhu Xie
- grid.411866.c0000 0000 8848 7685Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Wenli An
- grid.411866.c0000 0000 8848 7685School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Shanshan Liu
- grid.411866.c0000 0000 8848 7685Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Yuying Huang
- grid.411866.c0000 0000 8848 7685Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Zerui Yang
- grid.411866.c0000 0000 8848 7685School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong China
| | - Ji Lin
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong, China.
| | - Xiasheng Zheng
- Institute of Medicinal Plant Physiology and Ecology, School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, 232th Waihuandong Road, Panyu District, Guangzhou, Guangdong, China.
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Wambugu PW, Ndjiondjop MN, Henry R. Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication. RICE (NEW YORK, N.Y.) 2021; 14:6. [PMID: 33415579 PMCID: PMC7790969 DOI: 10.1186/s12284-020-00449-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
African rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of times the crop has been domesticated. Advances in genomics have provided unprecedented opportunities for understanding the genetic architecture of domestication related traits. For most of the domestication traits, the underlying genes and mutations have been identified. Comparative analysis of domestication genes between Asian and African rice has revealed that the two species went through an independent but convergent evolution process. The genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species. Analysis of genome data and its interpretation is emerging as a major challenge facing studies of domestication in African rice as key studies continue giving contradictory findings and conclusions. Insights obtained on the domestication of this species are vital for guiding crop improvement efforts.
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Affiliation(s)
- Peterson W. Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, Nairobi, 00100 Kenya
| | - Marie-Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551 Bouaké 01, Côte d’Ivoire
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
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6
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Ndjiondjop MN, Alachiotis N, Pavlidis P, Goungoulou A, Kpeki SB, Zhao D, Semagn K. Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1145-1158. [PMID: 30578434 PMCID: PMC6449321 DOI: 10.1007/s00122-018-3268-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/11/2018] [Indexed: 05/20/2023]
Abstract
The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1-32.1 and 16.3-37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10-4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10-2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.
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Affiliation(s)
- Marie Noelle Ndjiondjop
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Alphonse Goungoulou
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Sèdjro Bienvenu Kpeki
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Dule Zhao
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Kassa Semagn
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
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7
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Molecular Diversity of Tidal Swamp Rice (Oryza sativa L.) in South Kalimantan, Indonesia. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10020022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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8
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Morphological and molecular dissection of wild rices from eastern India suggests distinct speciation between O. rufipogon and O. nivara populations. Sci Rep 2018; 8:2773. [PMID: 29426872 PMCID: PMC5807453 DOI: 10.1038/s41598-018-20693-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 01/22/2018] [Indexed: 11/14/2022] Open
Abstract
The inter relationships between the two progenitors is interesting as both wild relatives are known to be the great untapped gene reservoirs. The debate continues on granting a separate species status to Oryza nivara. The present study was conducted on populations of Oryza rufipogon and Oryza nivara from Eastern India employing morphological and molecular characteristics. The cluster analysis of the data on morphological traits could clearly classify the two wild forms into two separate discrete groups without any overlaps i.e. lack of intermediate forms, suggesting the non-sympatric existence of the wild forms. Amplification of hyper variable regions of the genome could reveal 144 alleles suggesting high genetic diversity values (average He = 0.566). Moreover, with 42.37% of uncommon alleles between the two wild relatives, the molecular variance analysis (AMOVA) could detect only 21% of total variation (p < 0.001) among them and rest 59% was within them. The population structure analysis clearly classified these two wild populations into two distinct sub-populations (K = 2) without any overlaps i.e. lack of intermediate forms, suggesting the non-sympatric existence of the wild forms. Clear differentiation into two distinct groups indicates that O. rufipogon and O. nivara could be treated as two different species.
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Kim K, Lee SC, Lee J, Yu Y, Yang K, Choi BS, Koh HJ, Waminal NE, Choi HI, Kim NH, Jang W, Park HS, Lee J, Lee HO, Joh HJ, Lee HJ, Park JY, Perumal S, Jayakodi M, Lee YS, Kim B, Copetti D, Kim S, Kim S, Lim KB, Kim YD, Lee J, Cho KS, Park BS, Wing RA, Yang TJ. Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. Sci Rep 2015; 5:15655. [PMID: 26506948 PMCID: PMC4623524 DOI: 10.1038/srep15655] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/30/2015] [Indexed: 12/15/2022] Open
Abstract
Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis.
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Affiliation(s)
- Kyunghee Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Junki Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Yeisoo Yu
- Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea.,Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Kiwoung Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Department of Horticulture, Sunchon National University, Suncheon, 540-950, Republic of Korea
| | - Beom-Soon Choi
- Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea
| | - Hee-Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hong-Il Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Nam-Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Woojong Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hyun-Seung Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jonghoon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hyun Oh Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea
| | - Ho Jun Joh
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hyeon Ju Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sampath Perumal
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Yun Sun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Backki Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Soonok Kim
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Sunggil Kim
- Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Young-Dong Kim
- Department of Life Science, Hallym University, Chuncheon, Kangwon-do, 200-702, Republic of Korea
| | - Jungho Lee
- Green Plant Institute, #2-202 Biovalley, 89 Seoho-ro, Kwonseon-gu, Suwon, Republic of Korea
| | - Kwang-Su Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang-gun, Kangwon-do, 232-955, Republic of Korea
| | - Beom-Seok Park
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, 560-500, Republic of Korea
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
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10
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Henry RJ, Nevo E. Exploring natural selection to guide breeding for agriculture. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:655-62. [PMID: 24975385 DOI: 10.1111/pbi.12215] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 04/13/2014] [Accepted: 05/15/2014] [Indexed: 05/02/2023]
Abstract
Climate change threatens reduced crop production and poses major challenges to food security. The breeding of climate-resilient crop varieties is increasingly urgent. Wild plant populations evolve to cope with changes in their environment due to the forces of natural selection. This adaptation may be followed over time in populations at the same site or explored by examining differences between populations growing in different environments or across an environmental gradient. Survival in the wild has important differences to the objective of agriculture to maximize crop yields. However, understanding the nature of adaptation in wild populations at the whole genome level may suggest strategies for crop breeding to deliver agricultural production with more resilience to climate variability.
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Affiliation(s)
- Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Qld, Australia
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Brozynska M, Omar ES, Furtado A, Crayn D, Simon B, Ishikawa R, Henry RJ. Chloroplast Genome of Novel Rice Germplasm Identified in Northern Australia. TROPICAL PLANT BIOLOGY 2014; 7:111-120. [PMID: 25485030 PMCID: PMC4245483 DOI: 10.1007/s12042-014-9142-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/13/2014] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa L.) was probably domesticated from O. rufipogon in Asia in the last 10,000 years. Relatives of cultivated rice (A genome species of Oryza) are found in South America, Africa, Australia and Asia. These A genome species are the close relatives of cultivated rice and represent the effective gene pool for rice improvement. Members of this group in Northern Australia include, an annual species, O. meridionalis, and two recently distinguished perennial taxa, to one of which the name O. rufipogon has been applied and the other a perennial form of O. meridionalis. Comparison of whole chloroplast genome sequences of these taxa has now been used to determine the relationships between the wild taxa and cultivated rice. The chloroplast genomes of the perennials were both found to be distinguished from O. rufipogon from Asia by 124 or 125 variations and were distinguished from each other by 53 variations. These populations have remained isolated from the overwhelming genetic impact of the large domesticated rice populations in Asia and may be unique descendants of the gene pool from which domesticated rice arose. The conservation of this wild genetic resource may be critical for global food security.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Ernnie Syafika Omar
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Darren Crayn
- Australian Tropical Herbarium, James Cook University, Cairns, Australia
| | - Bryan Simon
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Aomori Japan
| | - Robert James Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
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Wambugu PW, Furtado A, Waters DLE, Nyamongo DO, Henry RJ. Conservation and utilization of African Oryza genetic resources. RICE (NEW YORK, N.Y.) 2013; 6:29. [PMID: 24280189 PMCID: PMC4883696 DOI: 10.1186/1939-8433-6-29] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/23/2013] [Indexed: 05/20/2023]
Abstract
Africa contains a huge diversity of both cultivated and wild rice species. The region has eight species representing six of the ten known genome types. Genetic resources of these species are conserved in various global germplasm repositories but they remain under collected and hence underrepresented in germplasm collections. Moreover, they are under characterized and therefore grossly underutilized. The lack of in situ conservation programs further exposes them to possible genetic erosion or extinction. In order to obtain maximum benefits from these resources, it is imperative that they are collected, efficiently conserved and optimally utilized. High throughput molecular approaches such as genome sequencing could be employed to more precisely study their genetic diversity and value and thereby enhance their use in rice improvement. Oryza sativa was the first crop plant to have its reference genome sequence released marking a major milestone that opened numerous opportunities for functional characterization of the entire rice genome. Studies have however demonstrated that one reference genome sequence is not enough to fully explore the genetic variation in the Oryza genus, hence the need to have reference sequences for other species in the genus. An overview of the state of conservation and utilization of African Oryza is hereby presented. Progress in the release of reference genome sequences for these species is also highlighted.
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Affiliation(s)
- Peterson W Wambugu
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
- />Kenya Agricultural Research Institute, Nairobi, Kenya
| | - Agnelo Furtado
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
| | - Daniel LE Waters
- />Southern Cross Plant Science, Southern Cross University, Lismore, NSW Australia
| | | | - Robert J Henry
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
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13
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Zhu T, Xu PZ, Liu JP, Peng S, Mo XC, Gao LZ. Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions. Mol Phylogenet Evol 2013; 70:348-61. [PMID: 24148990 DOI: 10.1016/j.ympev.2013.10.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Revised: 08/17/2013] [Accepted: 10/09/2013] [Indexed: 12/17/2022]
Abstract
Rapid radiations have long been regarded as the most challenging issue for elucidating poorly resolved phylogenies in evolutionary biology. The eight diploid AA- genome species in the genus Oryza represent a typical example of a closely spaced series of recent speciation events in plants. However, questions regarding when and how they diversified have long been an issue of extensive interest but remain a mystery. Here, a data set comprising >60 kb of 53 singleton fragments and 16 intergenic regions is used to perform phylogenomic analyses of all eight AA- genome species plus four diploid Oryza species with BB-, CC-, EE- and GG- genomes. We fully reconstruct phylogenetic relationships of AA- genome species with confidence. Oryza meridionalis, native to Australia, is found to be the earliest divergent lineage around 2.93 mya, whereas O. punctata, a BB- genome species, serves as the best outgroup to distinguish their phylogenetic relationships. They separated from O. punctata approximately 9.11 mya during the Miocene epoch, and subsequently radiated to generate the entire AA- genome lineage diversity. The success in resolving the phylogeny of AA- genome species highlights the potential of phylogenomics to determine their divergence and evolutionary histories.
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Affiliation(s)
- Ting Zhu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming 650204, China; University of the Chinese Academy of Sciences, Beijing 100039, China.
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14
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Banaticla-Hilario MCN, van den Berg RG, Hamilton NRS, McNally KL. Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon. Ecol Evol 2013; 3:3047-62. [PMID: 24101993 PMCID: PMC3790550 DOI: 10.1002/ece3.689] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 06/17/2013] [Accepted: 06/23/2013] [Indexed: 11/11/2022] Open
Abstract
Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local-level species separation is recognized by Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by F ST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (H E = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (H E = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.
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Affiliation(s)
- Maria Celeste N Banaticla-Hilario
- T.T. Chang Genetic Resources Center, International Rice Research Institute Los Baños, Laguna, Philippines ; Biosystematics Group, Wageningen University and Research Center Wageningen, The Netherlands
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Scafaro AP, Yamori W, Carmo-Silva AE, Salvucci ME, von Caemmerer S, Atwell BJ. Rubisco activity is associated with photosynthetic thermotolerance in a wild rice (Oryza meridionalis). PHYSIOLOGIA PLANTARUM 2012; 146:99-109. [PMID: 22324885 DOI: 10.1111/j.1399-3054.2012.01597.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Oryza meridionalis is a wild species of rice, endemic to tropical Australia. It shares a significant genome homology with the common domesticated rice Oryza sativa. Exploiting the fact that the two species are highly related but O. meridionalis has superior heat tolerance, experiments were undertaken to identify the impact of temperature on key events in photosynthesis. At an ambient CO(2) partial pressure of 38 Pa and irradiance of 1500 µmol quanta m(-2) s(-1), the temperature optimum of photosynthesis was 33.7 ± 0.8°C for O. meridionalis, significantly higher than the 30.6 ± 0.7°C temperature optimum of O. sativa. To understand the basis for this difference, we measured gas exchange and rubisco activation state between 20 and 42°C and modeled the response to determine the rate-limiting steps of photosynthesis. The temperature response of light respiration (R(light)) and the CO(2) compensation point in the absence of respiration (Γ(*)) were determined and found to be similar for the two species. C3 photosynthesis modeling showed that despite the difference in susceptibility to high temperature, both species had a similar temperature-dependent limitation to photosynthesis. Both rice species were limited by ribulose-1,5-bisphosphate (RuBP) regeneration at temperatures of 25 and 30°C but became RuBP carboxylation limited at 35 and 40°C. The activation state of rubisco in O. meridionalis was more stable at higher temperatures, explaining its greater heat tolerance compared with O. sativa.
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Affiliation(s)
- Andrew P Scafaro
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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Scafaro AP, Von Caemmerer S, Evans JR, Atwell BJ. Temperature response of mesophyll conductance in cultivated and wild Oryza species with contrasting mesophyll cell wall thickness. PLANT, CELL & ENVIRONMENT 2011; 34:1999-2008. [PMID: 21752031 DOI: 10.1111/j.1365-3040.2011.02398.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A critical component of photosynthetic capacity is the conductance of CO(2) from intercellular airspaces to the sites of CO(2) fixation in the stroma of chloroplasts, termed mesophyll conductance (g(m)). Leaf anatomy has been identified as an important determinant of g(m). There are few studies of the temperature response of g(m) and none has examined the implications of leaf anatomy. Hence, we compared a cultivar of Oryza sativa with two wild Oryza relatives endemic to the hot northern savannah of Australia, namely Oryza meridionalis and Oryza australiensis. All three species had similar leaf anatomical properties, except that the wild relatives had significantly thicker mesophyll cell walls than O. sativa. Thicker mesophyll cell walls in the wild rice species are likely to have contributed to the reduction in g(m) , which was associated with a greater drawdown of CO(2) into chloroplasts (C(i) -C(c) ) compared with O. sativa. Mesophyll conductance increased at higher temperatures, whereas the rate of CO(2) assimilation was relatively stable between 20 and 40 °C. Consequently, C(i) -C(c) decreased for all three species as temperature increased.
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Affiliation(s)
- Andrew P Scafaro
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
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Griffin PC, Robin C, Hoffmann AA. A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses. BMC Biol 2011; 9:19. [PMID: 21429199 PMCID: PMC3078099 DOI: 10.1186/1741-7007-9-19] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 03/23/2011] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Polyploidy is important from a phylogenetic perspective because of its immense past impact on evolution and its potential future impact on diversification, survival and adaptation, especially in plants. Molecular population genetics studies of polyploid organisms have been difficult because of problems in sequencing multiple-copy nuclear genes using Sanger sequencing. This paper describes a method for sequencing a barcoded mixture of targeted gene regions using next-generation sequencing methods to overcome these problems. RESULTS Using 64 3-bp barcodes, we successfully sequenced three chloroplast and two nuclear gene regions (each of which contained two gene copies with up to two alleles per individual) in a total of 60 individuals across 11 species of Australian Poa grasses. This method had high replicability, a low sequencing error rate (after appropriate quality control) and a low rate of missing data. Eighty-eight percent of the 320 gene/individual combinations produced sequence reads, and >80% of individuals produced sufficient reads to detect all four possible nuclear alleles of the homeologous nuclear loci with 95% probability.We applied this method to a group of sympatric Australian alpine Poa species, which we discovered to share an allopolyploid ancestor with a group of American Poa species. All markers revealed extensive allele sharing among the Australian species and so we recommend that the current taxonomy be re-examined. We also detected hypermutation in the trnH-psbA marker, suggesting it should not be used as a land plant barcode region. Some markers indicated differentiation between Tasmanian and mainland samples. Significant positive spatial genetic structure was detected at <100 km with chloroplast but not nuclear markers, which may be a result of restricted seed flow and long-distance pollen flow in this wind-pollinated group. CONCLUSIONS Our results demonstrate that 454 sequencing of barcoded amplicon mixtures can be used to reliably sample all alleles of homeologous loci in polyploid species and successfully investigate phylogenetic relationships among species, as well as to investigate phylogeographic hypotheses. This next-generation sequencing method is more affordable than and at least as reliable as bacterial cloning. It could be applied to any experiment involving sequencing of amplicon mixtures.
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Affiliation(s)
- Philippa C Griffin
- Department of Genetics, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Charles Robin
- Department of Genetics, University of Melbourne, Parkville 3010, Victoria, Australia
| | - Ary A Hoffmann
- Department of Genetics, University of Melbourne, Parkville 3010, Victoria, Australia
- Department of Zoology, University of Melbourne, Parkville 3010, Victoria, Australia
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Sanyal A, Ammiraju JSS, Lu F, Yu Y, Rambo T, Currie J, Kollura K, Kim HR, Chen J, Ma J, San Miguel P, Mingsheng C, Wing RA, Jackson SA. Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and disruptions to microsynteny in Sorghum. Mol Biol Evol 2010; 27:2487-506. [PMID: 20522726 DOI: 10.1093/molbev/msq133] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Heading date is one of the most important quantitative traits responsible for the domestication of rice. We compared a 155-kb reference segment of the Oryza sativa ssp. japonica cv. Nipponbare genome surrounding Hd1, a major heading date gene in rice, with orthologous regions from nine diploid Oryza species that diverged over a relatively short time frame (∼16 My) to study sequence evolution around a domestication locus. The orthologous Hd1 region from Sorghum bicolor was included to compare and contrast the evolution in a more distant relative of rice. Consistent with other observations at the adh1/adh2, monoculm1, and sh2/a1 loci in grass species, we found high gene colinearity in the Hd1 region amidst size differences that were lineage specific and long terminal repeat retrotransposon driven. Unexpectedly, the Hd1 gene was deleted in O. glaberrima, whereas the O. rufipogon and O. punctata copies had degenerative mutations, suggesting that other heading date loci might compensate for the loss or nonfunctionality of Hd1 in these species. Compared with the japonica Hd1 region, the orthologous region in sorghum exhibited micro-rearrangements including gene translocations, seven additional genes, and a gene triplication and truncation event predating the divergence from Oryza.
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Roulin A, Chaparro C, Piégu B, Jackson S, Panaud O. Paleogenomic analysis of the short arm of chromosome 3 reveals the history of the African and Asian progenitors of cultivated rices. Genome Biol Evol 2010; 2:132-9. [PMID: 20333229 PMCID: PMC2839358 DOI: 10.1093/gbe/evq005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2010] [Indexed: 11/12/2022] Open
Abstract
Rice is one of the most important crops, feeding more than half of the world population. There are two cultivated species, the African rice Oryza glaberrima and the Asian rice O. sativa. Although the African species is gradually replaced by O. sativa in most of African rice agrosystems, this species represents an important reservoir of genes of agronomical interest. Their exploitation for the development of modern African rice varieties requires a good understanding of the genetic relationships between the two cultivated species. We took advantage of the recent availability of the sequence of the chromosome 3 short arm of O. glaberrima to estimate the date of radiation between O. glaberrima and O. sativa lineages, using all the long terminal repeat (LTR)-retrotransposons as paleogenomic markers. We first demonstrated that in two distinct lineages, LTR-retrotransposons mutate at the same rate. Based on LTR-retrotransposons shared by both species in orthologous position, we then estimated that O. glaberrima and O. sativa progenitors diverged 1.2 Ma. This constitutes one of the first studies using such a large sample of transposable elements to reconstruct the phylogeny of species. Given the number of genome sequencing projects, there is no doubt that such approach will allow to resolve phylogenetic incongruities. The application of this method to other plant genomes will also facilitate further understanding of evolution of LTR-retrotransposons and eventually of the whole genome in divergent plant lineages.
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Affiliation(s)
- Anne Roulin
- Laboratoire Génome et Développement des Plantes, Unite Mixte de Recherche Centre National de la Recherche Scientifique/Institut de Recherche pour le Developpement/Universite de Perpignan Via Domitia, Université de Perpignan, Perpignan, Cedex, France
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Tao J, Luo ZY, Msangi CI, Shu XS, Wen L, Liu SP, Zhou CQ, Liu RX, Hu WX. Relationships among genetic makeup, active ingredient content, and place of origin of the medicinal plant Gastrodia tuber. Biochem Genet 2009; 47:8-18. [PMID: 19037723 DOI: 10.1007/s10528-008-9201-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Gastrodia tuber and its component gastrodin have many pharmacological effects. The chemical fingerprints and gastrodin contents of eight Gastrodia populations were determined, and the genomic DNA polymorphism of the populations was investigated. Genetic distance coefficients among the populations were calculated using the DNA polymorphism data. A dendrogram of the genetic similarities between the populations was constructed using the genetic distance coefficients. The results indicated that the genomic DNA of Gastrodia tubers was highly polymorphic; the eight populations clustered into three major groups, and the gastrodin content varied greatly among these groups. There were obvious correlations among genetic makeup, gastrodin content, and place of origin. The ecological environments in Guizhou and Shanxi may be conducive to evolution and to gastrodin biosynthesis, and more suitable for cultivation of Gastrodia tubers. These findings may provide a scientific basis for overall genetic resource management and for the selection of locations for cultivating Gastrodia tubers.
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Affiliation(s)
- Jun Tao
- School of Biology and Food Engineering, Changsha University of Science and Technology, Changsha, Hunan, 410076, P.R. China.
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Xu Z, Ramakrishna W. Retrotransposon insertion polymorphisms in six rice genes and their evolutionary history. Gene 2008; 412:50-8. [PMID: 18291601 DOI: 10.1016/j.gene.2008.01.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Revised: 01/05/2008] [Accepted: 01/08/2008] [Indexed: 01/08/2023]
Abstract
Retrotransposons are abundant in higher plant genomes. Although retrotransposons associated with plant genes have been identified, little is known about their evolutionary conservation at the level of species and subspecies. In the present study, we investigated the phylogenetic distribution of long terminal repeat (LTR) retrotransposon, long interspersed nuclear element (LINE) and short interspersed nuclear element (SINE) insertions in six genes in 95 cultivated and wild rice genotypes. These six genes are likely to be functional based on nonsynonymous (Ka) to synonymous (Ks) substitution ratios which were found to be significantly <1. Different conservation patterns of these retrotransposons in genes were observed in cultivated and wild rice species. Four out of seven retrotransposon insertions appear to predate the ancestral Oryza AA genome. Two of these insertions in genes 4 and 5 occurred early in the evolutionary history of Oryza. Two retrotransposon insertions in gene 1 arose after the divergence of Asian cultivated rice from its wild ancestor. Furthermore, the retrotransposon insertion in gene 3 appears to have occurred in the ancestral lineage leading to temperate japonicas. Conservation of retrotransposon insertions in genes in specific groups, species, and lineages might be related to their specific function.
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Affiliation(s)
- Zijun Xu
- Department of Biological Sciences, Michigan Technological University, Houghton, Michigan 49931, USA
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New insights into the history of rice domestication. Trends Genet 2007; 23:578-87. [DOI: 10.1016/j.tig.2007.08.012] [Citation(s) in RCA: 357] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2007] [Revised: 08/16/2007] [Accepted: 08/21/2007] [Indexed: 11/18/2022]
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