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Osakina A, Jia Y. Genetic Diversity of Weedy Rice and Its Potential Application as a Novel Source of Disease Resistance. PLANTS (BASEL, SWITZERLAND) 2023; 12:2850. [PMID: 37571004 PMCID: PMC10421194 DOI: 10.3390/plants12152850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023]
Abstract
Weeds that infest crops are a primary factor limiting agricultural productivity worldwide. Weedy rice, also called red rice, has experienced independent evolutionary events through gene flow from wild rice relatives and de-domestication from cultivated rice. Each evolutionary event supplied/equipped weedy rice with competitive abilities that allowed it to thrive with cultivated rice and severely reduce yields in rice fields. Understanding how competitiveness evolves is important not only for noxious agricultural weed management but also for the transfer of weedy rice traits to cultivated rice. Molecular studies of weedy rice using simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), and whole-genome sequence have shown great genetic variations in weedy rice populations globally. These variations are evident both at the whole-genome and at the single-allele level, including Sh4 (shattering), Hd1 (heading and flowering), and Rc (pericarp pigmentation). The goal of this review is to describe the genetic diversity of current weedy rice germplasm and the significance of weedy rice germplasm as a novel source of disease resistance. Understanding these variations, especially at an allelic level, is also crucial as individual loci that control important traits can be of great target to rice breeders.
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Affiliation(s)
- Aron Osakina
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA;
- USDA ARS Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA
| | - Yulin Jia
- USDA ARS Dale Bumpers National Rice Research Center, Stuttgart, AR 72160, USA
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2
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Shi Y, Zhang Y, Sun Y, Xie Z, Luo Y, Long Q, Feng J, Liu X, Wang B, He D, Ren J, Guo P, Xing J, He L, Fernie AR, Chen W, Liu X, Luo Y, Jin C, Luo J. Natural variations of OsAUX5, a target gene of OsWRKY78, control the neutral essential amino acid content in rice grains. MOLECULAR PLANT 2023; 16:322-336. [PMID: 36540024 DOI: 10.1016/j.molp.2022.12.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 11/02/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Grain essential amino acid (EAA) levels contribute to rice nutritional quality. However, the molecular mechanisms underlying EAA accumulation and natural variation in rice grains remain unclear. Here we report the identification of a previously unrecognized auxin influx carrier subfamily gene, OsAUX5, which encodes an amino acid transporter that functions in uptake of multiple amino acids. We identified an elite haplotype of Pro::OsAUX5Hap2 that enhances grain EAA accumulation without an apparent negative effect on agronomic traits. Natural variations of OsAUX5 occur in the cis elements of its promoter, which are differentially activated because of the different binding affinity between OsWRKY78 and the W-box, contributing to grain EAA variation among rice varieties. The two distinct haplotypes were shown to have originated from different Oryza rufipogon progenitors, which contributed to the divergence between japonica and indica. Introduction of the indica-type Pro::OsAUX5Hap2 genotype into japonica could significantly increase EAA levels, indicating that indica-type Pro::OsAUX5Hap2 can be utilized to increase grain EAAs of japonica varieties. Collectively, our study uncovers an WRKY78-OsAUX5-based regulatory mechanism controlling grain EAA accumulation and provides a potential target for breeding EAA-rich rice.
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Affiliation(s)
- Yuheng Shi
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yuanyuan Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yangyang Sun
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Ziyang Xie
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yu Luo
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Qiyuan Long
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Jiahui Feng
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Xueqing Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Bi Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Dujun He
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Junxia Ren
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Peizhen Guo
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Junwei Xing
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Liqiang He
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianqing Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Yuehua Luo
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Cheng Jin
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
| | - Jie Luo
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
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3
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Maity A, Lamichaney A, Joshi DC, Bajwa A, Subramanian N, Walsh M, Bagavathiannan M. Seed Shattering: A Trait of Evolutionary Importance in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:657773. [PMID: 34220883 PMCID: PMC8248667 DOI: 10.3389/fpls.2021.657773] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 05/21/2021] [Indexed: 05/26/2023]
Abstract
Seed shattering refers to the natural shedding of seeds when they ripe, a phenomenon typically observed in wild and weedy plant species. The timing and extent of this phenomenon varies considerably among plant species. Seed shattering is primarily a genetically controlled trait; however, it is significantly influenced by environmental conditions, management practices and their interactions, especially in agro-ecosystems. This trait is undesirable in domesticated crops where consistent efforts have been made to minimize it through conventional and molecular breeding approaches. However, this evolutionary trait serves as an important fitness and survival mechanism for most weeds that utilize it to ensure efficient dispersal of their seeds, paving the way for persistent soil seedbank development and sustained future populations. Weeds have continuously evolved variations in seed shattering as an adaptation under changing management regimes. High seed retention is common in many cropping weeds where weed maturity coincides with crop harvest, facilitating seed dispersal through harvesting operations, though some weeds have notoriously high seed shattering before crop harvest. However, high seed retention in some of the most problematic agricultural weed species such as annual ryegrass (Lolium rigidum), wild radish (Raphanus raphanistrum), and weedy amaranths (Amaranthus spp.) provides an opportunity to implement innovative weed management approaches such as harvest weed seed control, which aims at capturing and destroying weed seeds retained at crop harvest. The integration of such management options with other practices is important to avoid the rapid evolution of high seed shattering in target weed species. Advances in genetics and molecular biology have shown promise for reducing seed shattering in important crops, which could be exploited for manipulating seed shattering in weed species. Future research should focus on developing a better understanding of various seed shattering mechanisms in plants in relation to changing climatic and management regimes.
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Affiliation(s)
- Aniruddha Maity
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
- Seed Technology Division, ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Amrit Lamichaney
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Dinesh Chandra Joshi
- Division of Crop Improvement, ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, India
| | - Ali Bajwa
- Weed Research Unit, New South Wales Department of Primary Industries, Wagga Wagga, NSW, Australia
| | - Nithya Subramanian
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, United States
| | - Michael Walsh
- Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW, Australia
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4
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Mussurova S, Al-Bader N, Zuccolo A, Wing RA. Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:579980. [PMID: 33072154 PMCID: PMC7539145 DOI: 10.3389/fpls.2020.579980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/04/2020] [Indexed: 05/14/2023]
Abstract
As the world's population expands from 7.6 billion to 10 billion over the next 30 years, scientists and farmers across the globe must explore every angle necessary to provide a safe, stable and sustainable food supply for generations to come. Rice, and its wild relatives in the genus Oryza, will play a significant role in helping to solve this 10 billion people question due to its place as a staple food for billions. The genus Oryza is composed of 27 species that span 15 million years of evolutionary diversification and have been shown to contain a plethora of untapped adaptive traits, e.g., biotic and abiotic resistances, which can be used to improve cultivated rice. Such traits can be introduced into cultivated rice, in some cases by conventional crossing, and others via genetic transformation and gene editing methods. In cases where traits are too complex to easily transfer to cultivated rice [e.g., quantitative trait loci (QTL)], an alternative strategy is to domesticate the wild relative that already contains the desired adaptive traits - i.e., "neodomestication". To utilize the Oryza genus for crop improvement and neodomestication, we first need a set of genomic resources that can be used to efficiently identify, capture, and guide molecular crop improvement. Here, we introduce the concept of platinum standard reference genome sequences (PSRefSeq) - a new standard by which contiguous near-gap free reference genomes can now be produced. By having a set of PSRefSeqs for every Oryza species we set a new bar for how crop wild relatives can be integrated into crop improvement programs.
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Affiliation(s)
- Saule Mussurova
- Center for Desert Agriculture, Biological and Environmental Sciences Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Noor Al-Bader
- Center for Desert Agriculture, Biological and Environmental Sciences Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
- *Correspondence: Andrea Zuccolo, ; Rod A. Wing,
| | - Rod A. Wing
- Center for Desert Agriculture, Biological and Environmental Sciences Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- School of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, AZ, United States
- *Correspondence: Andrea Zuccolo, ; Rod A. Wing,
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5
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Wedger MJ, Topp CN, Olsen KM. Convergent evolution of root system architecture in two independently evolved lineages of weedy rice. THE NEW PHYTOLOGIST 2019; 223:1031-1042. [PMID: 30883803 DOI: 10.1111/nph.15791] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/11/2019] [Indexed: 05/13/2023]
Abstract
Root system architecture (RSA) is a critical aspect of plant growth and competitive ability. Here we used two independently evolved strains of weedy rice, a de-domesticated form of rice, to study the evolution of weed-associated RSA traits and the extent to which they evolve through shared or different genetic mechanisms. We characterised 98 two-dimensional and three-dimensional RSA traits in 671 plants representing parents and descendants of two recombinant inbred line populations derived from two weed × crop crosses. A random forest machine learning model was used to assess the degree to which root traits can predict genotype and the most diagnostic traits for doing so. We used quantitative trait locus (QTL) mapping to compare genetic architecture between the weed strains. The two weeds were distinguishable from the crop in similar and predictable ways, suggesting independent evolution of a 'weedy' RSA phenotype. Notably, comparative QTL mapping revealed little evidence for shared underlying genetic mechanisms. Our findings suggest that despite the double bottlenecks of domestication and de-domestication, weedy rice nonetheless shows genetic flexibility in the repeated evolution of weedy RSA traits. Whereas the root growth of cultivated rice may facilitate interactions among neighbouring plants, the weedy rice phenotype may minimise below-ground contact as a competitive strategy.
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Affiliation(s)
- Marshall J Wedger
- Biology Department, Campus Box 1137, Washington University in St Louis, 1 Brookings Dr., St Louis, MO, 63130, USA
| | - Christopher N Topp
- Donald Danforth Plant Science Center, 975 N Warson Rd, St Louis, MO, 63132, USA
| | - Kenneth M Olsen
- Biology Department, Campus Box 1137, Washington University in St Louis, 1 Brookings Dr., St Louis, MO, 63130, USA
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6
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Discordant Patterns of Introgression Suggest Historical Gene Flow into Thai Weedy Rice from Domesticated and Wild Relatives. J Hered 2019; 110:601-609. [DOI: 10.1093/jhered/esz030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/04/2019] [Indexed: 12/12/2022] Open
Abstract
Abstract
Weedy relatives of crop species infest agricultural fields worldwide, reducing harvests and threatening global food security. These weeds can potentially evolve and adapt through gene flow from both domesticated crop varieties and reproductively compatible wild relatives. We studied populations of weedy rice in Thailand to investigate the role of introgression from cultivated and wild rice in their evolution. We examined 2 complementary sources of genetic data: allelic variation at 3 rice domestication genes (Bh4, controlling hull color; Rc, controlling pericarp color and seed dormancy; and sh4, controlling seed shattering), and 12 previously published SSR markers. Sampling spanned 3 major rice growing regions in Thailand (Lower North, North East, and Central Plain) and included 124 cultivated rice accessions, 166 weedy rice accessions, and 98 wild rice accessions. Weedy rice strains were overall closely related to the cultivated varieties with which they co-occur. Domestication gene data revealed potential adaptive introgression of sh4 shattering alleles from wild rice. Introgression of potentially maladaptive rc crop alleles (conferring reduced dormancy) was also detected, with the frequency of the crop allele highest in northern populations. Although SSR markers also indicated introgression into weed populations from wild and cultivated rice, there was little overlap with domestication genes in the accessions showing admixed ancestry. This suggests that much of the introgression we detected at domestication genes most likely reflects past introgression rather than recent gene flow. This finding has implications for understanding long-term gene flow dynamics between rice and its weedy and wild relatives, including potential risks of transgene escape.
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7
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Lachagari VBR, Gupta R, Lekkala SP, Mahadevan L, Kuriakose B, Chakravartty N, Mohan Katta AVSK, Santhosh S, Reddy AR, Thomas G. Whole Genome Sequencing and Comparative Genomic Analysis Reveal Allelic Variations Unique to a Purple Colored Rice Landrace ( Oryza sativa ssp. indica cv. Purpleputtu). FRONTIERS IN PLANT SCIENCE 2019; 10:513. [PMID: 31134103 PMCID: PMC6516047 DOI: 10.3389/fpls.2019.00513] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 04/03/2019] [Indexed: 05/27/2023]
Abstract
Purpleputtu (Oryza sativa ssp. indica cv. Purpleputtu) is a unique rice landrace from southern India that exhibits predominantly purple color. This study reports the underlying genetic complexity of the trait, associated domestication and de-domestication processes during its coevolution with present day cultivars. Along-with genome level allelic variations in the entire gene repertoire associated with the purple, red coloration of grain and other plant parts. Comparative genomic analysis using 'a panel of 108 rice lines' revealed a total of 3,200,951 variants including 67,774 unique variations in Purpleputtu (PP) genome. Multiple sequence alignment uncovered a 14 bp deletion in Rc (Red colored, a transcription factor of bHLH class) locus of PP, a key regulatory gene of anthocyanin biosynthetic pathway. Interestingly, this deletion in Rc gene is a characteristic feature of the present-day white pericarped rice cultivars. Phylogenetic analysis of Rc locus revealed a distinct clade showing proximity to the progenitor species Oryza rufipogon and O. nivara. In addition, PP genome exhibits a well conserved 4.5 Mbp region on chromosome 5 that harbors several loci associated with domestication of rice. Further, PP showed 1,387 unique when SNPs compared to 3,023 lines of rice (SNP-Seek database). The results indicate that PP genome is rich in allelic diversity and can serve as an excellent resource for rice breeding for a variety of agronomically important traits such as disease resistance, enhanced nutritional values, stress tolerance, and protection from harmful UV-B rays.
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Affiliation(s)
- V. B. Reddy Lachagari
- AgriGenome Labs Pvt. Ltd., Biotechnology Incubation Center, MN iHub, Genome Valley, Hyderabad, India
| | - Ravi Gupta
- Medgenome Labs Ltd., Bengaluru, India
- SciGenom Labs Pvt. Ltd., Cochin, India
| | - Sivarama Prasad Lekkala
- AgriGenome Labs Pvt. Ltd., Biotechnology Incubation Center, MN iHub, Genome Valley, Hyderabad, India
| | - Lakshmi Mahadevan
- Medgenome Labs Ltd., Bengaluru, India
- SciGenom Labs Pvt. Ltd., Cochin, India
| | - Boney Kuriakose
- SciGenom Research Foundation, Cheruthuruthy, India
- AgriGenome Labs Pvt. Ltd., Kakkanad, India
| | - Navajeet Chakravartty
- AgriGenome Labs Pvt. Ltd., Biotechnology Incubation Center, MN iHub, Genome Valley, Hyderabad, India
| | - A. V. S. K. Mohan Katta
- AgriGenome Labs Pvt. Ltd., Biotechnology Incubation Center, MN iHub, Genome Valley, Hyderabad, India
| | - Sam Santhosh
- SciGenom Research Foundation, Cheruthuruthy, India
| | - Arjula R. Reddy
- Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - George Thomas
- SciGenom Research Foundation, Cheruthuruthy, India
- AgriGenome Labs Pvt. Ltd., Kakkanad, India
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Sun J, Ma D, Tang L, Zhao M, Zhang G, Wang W, Song J, Li X, Liu Z, Zhang W, Xu Q, Zhou Y, Wu J, Yamamoto T, Dai F, Lei Y, Li S, Zhou G, Zheng H, Xu Z, Chen W. Population Genomic Analysis and De Novo Assembly Reveal the Origin of Weedy Rice as an Evolutionary Game. MOLECULAR PLANT 2019; 12:632-647. [PMID: 30710646 DOI: 10.1016/j.molp.2019.01.019] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 05/27/2023]
Abstract
Crop weediness, especially that of weedy rice (Oryza sativa f. spontanea), remains mysterious. Weedy rice possesses robust ecological adaptability; however, how this strain originated and gradually formed proprietary genetic features remains unclear. Here, we demonstrate that weedy rice at Asian high latitudes (WRAH) is phylogenetically well defined and possesses unselected genomic characteristics in many divergence regions between weedy and cultivated rice. We also identified novel quantitative trait loci underlying weedy-specific traits, and revealed that a genome block on the end of chromosome 1 is associated with rice weediness. To identify the genomic modifications underlying weedy rice evolution, we generated the first de novo assembly of a high-quality weedy rice genome (WR04-6), and conducted a comparative genomics study between WR04-6 with other rice reference genomes. Multiple lines of evidence, including the results of demographic scenario comparisons, suggest that differentiation between weedy rice and cultivated rice was initiated by genetic improvement of cultivated rice and that the essence of weediness arose through semi-domestication. A plant height model further implied that the origin of WRAH can be modeled as an evolutionary game and indicated that strategy-based selection driven by fitness shaped its genomic diversity.
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Affiliation(s)
- Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Dianrong Ma
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Liang Tang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Minghui Zhao
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Guangchen Zhang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Wenjia Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Jiayu Song
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Xiang Li
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Zimeng Liu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Wenxing Zhang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Quan Xu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Yuncheng Zhou
- College of Information and Electrical Engineering, Shenyang Agricultural University, Shenyang, China
| | - Jianzhong Wu
- Institute of Crop Science, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Toshio Yamamoto
- Institute of Plant Science and Resources, Okayama University, Okayama, Japan
| | - Fei Dai
- Department of Agronomy, Zhejiang Key Lab of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Yan Lei
- Biomarker Technologies Corporation, Beijing, China
| | - Song Li
- Biomarker Technologies Corporation, Beijing, China
| | - Gang Zhou
- Biomarker Technologies Corporation, Beijing, China
| | | | - Zhengjin Xu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Wenfu Chen
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China.
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9
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Chen E, Huang X, Tian Z, Wing RA, Han B. The Genomics of Oryza Species Provides Insights into Rice Domestication and Heterosis. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:639-665. [PMID: 31035826 DOI: 10.1146/annurev-arplant-050718-100320] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Here, we review recent progress in genetic and genomic studies of the diversity of Oryza species. In recent years, unlocking the genetic diversity of Oryza species has provided insights into the genomics of rice domestication, heterosis, and complex traits. Genome sequencing and analysis of numerous wild rice (Oryza rufipogon) and Asian cultivated rice (Oryza sativa) accessions have enabled the identification of genome-wide signatures of rice domestication and the unlocking of the origin of Asian cultivated rice. Moreover, similar studies on genome variations of African rice (Oryza glaberrima) cultivars and their closely related wild progenitor Oryza barthii accessions have provided strong evidence to support a theory of independent domestication in African rice. Integrated genomic approaches have efficiently investigated many heterotic loci in hybrid rice underlying yield heterosis advantages and revealed the genomic architecture of rice heterosis. We conclude that in-depth unlocking of genetic variations among Oryza species will further enhance rice breeding.
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Affiliation(s)
- Erwang Chen
- National Center of Plant Gene Research; Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China;
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100049, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China;
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA;
| | - Bin Han
- National Center of Plant Gene Research; Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences; and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China;
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10
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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: 1.6] [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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11
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Vigueira CC, Qi X, Song B, Li L, Caicedo AL, Jia Y, Olsen KM. Call of the wild rice: Oryza rufipogon shapes weedy rice evolution in Southeast Asia. Evol Appl 2019; 12:93-104. [PMID: 30622638 PMCID: PMC6304679 DOI: 10.1111/eva.12581] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/21/2017] [Indexed: 02/03/2023] Open
Abstract
Agricultural weeds serve as productive models for studying the genetic basis of rapid adaptation, with weed-adaptive traits potentially evolving multiple times independently in geographically distinct but environmentally similar agroecosystems. Weedy relatives of domesticated crops can be especially interesting systems because of the potential for weed-adaptive alleles to originate through multiple mechanisms, including introgression from cultivated and/or wild relatives, standing genetic variation, and de novo mutations. Weedy rice populations have evolved multiple times through dedomestication from cultivated rice. Much of the genomic work to date in weedy rice has focused on populations that exist outside the range of the wild crop progenitor. In this study, we use genome-wide SNPs generated through genotyping-by-sequencing to compare the evolution of weedy rice in regions outside the range of wild rice (North America, South Korea) and populations in Southeast Asia, where wild rice populations are present. We find evidence for adaptive introgression of wild rice alleles into weedy rice populations in Southeast Asia, with the relative contributions of wild and cultivated rice alleles varying across the genome. In addition, gene regions underlying several weed-adaptive traits are dominated by genomic contributions from wild rice. Genome-wide nucleotide diversity is also much higher in Southeast Asian weeds than in North American and South Korean weeds. Besides reflecting introgression from wild rice, this difference in diversity likely reflects genetic contributions from diverse cultivated landraces that may have served as the progenitors of these weedy populations. These important differences in weedy rice evolution in regions with and without wild rice could inform region-specific management strategies for weed control.
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Affiliation(s)
| | - Xinshuai Qi
- Department of Ecology & Evolutionary BiologyUniversity of ArizonaTucsonAZUSA
| | - Beng‐Kah Song
- School of ScienceMonash University MalaysiaSelangorMalaysia
- Genomics FacilityMonash University MalaysiaSelangorMalaysia
| | - Lin‐Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringDepartment of Ecology and Evolutionary BiologyFudan UniversityShanghaiChina
| | - Ana L. Caicedo
- Department of BiologyUniversity of MassachusettsAmherstMAUSA
| | - Yulin Jia
- Dale Bumpers National Rice Research CenterUSDA‐ARSStuttgartARUSA
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12
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Huang Z, Kelly S, Matsuo R, Li LF, Li Y, Olsen KM, Jia Y, Caicedo AL. The Role of Standing Variation in the Evolution of Weedines Traits in South Asian Weedy Rice ( Oryza spp.). G3 (BETHESDA, MD.) 2018; 8:3679-3690. [PMID: 30275171 PMCID: PMC6222575 DOI: 10.1534/g3.118.200605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 09/20/2018] [Indexed: 12/02/2022]
Abstract
Weedy rice (Oryza spp.) is a problematic weed of cultivated rice (O. sativa) around the world. Recent studies have established multiple independent evolutionary origins of weedy rice, raising questions about the traits and genes that are essential for the evolution of this weed. Among world regions, South Asia stands out due to the heterogeneity of its weedy rice populations, which can be traced to at least three origins: two through de-domestication from distinct cultivated rice varieties, and one from local wild rice (O. rufipogon/O. nivara). Here we examine five traits considered typical of or advantageous to weedy rice in weedy, cultivated and wild rice samples from South Asia. We establish that convergence among all three weed groups occurs for easy seed shattering, red pericarp color, and compact plant architecture, suggesting that these traits are essential for weed success in the South Asian agricultural environment. A high degree of convergence for black hull color is also seen among weeds with wild ancestors and weeds evolved from the aus cultivated rice group. We also examine polymorphism in five known domestication candidate genes, and find that Rc and Bh4 are associated with weed seed pericarp color and hull color, respectively, and weedy alleles segregate in the ancestral populations, as do alleles for the seed dormancy-linked gene Sdr4 The presence of a domestication related allele at the seed shattering locus, sh4, in weedy rice populations with cultivated ancestry supports a de-domestication origin for these weedy groups, and raises questions about the reacquisition of the shattering trait in these weedy populations. Our characterization of weedy rice phenotypes in South Asia and their associated candidate genes contribute to the emerging understanding of the mechanisms by which weedy rice evolves worldwide, suggesting that standing ancestral variation is often the source of weedy traits in independently evolved groups, and highlighting the reservoir of genetic variation that is present in cultivated varieties as well as in wild rice, and its potential for phenotypic evolution.
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Affiliation(s)
- Zhongyun Huang
- Department of Biology, University of Massachusetts, Amherst, MA, USA, 01003
| | - Shannon Kelly
- Department of Biology, University of Massachusetts, Amherst, MA, USA, 01003
| | - Rika Matsuo
- Department of Biology, University of Massachusetts, Amherst, MA, USA, 01003
| | - Lin-Feng Li
- Department of Biology, Washington University, St. Louis, MO 63130
| | - Yaling Li
- Department of Biology, Washington University, St. Louis, MO 63130
| | - Kenneth M Olsen
- Department of Biology, Washington University, St. Louis, MO 63130
| | - Yulin Jia
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR 72160
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts, Amherst, MA, USA, 01003
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13
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14
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Singh N, Singh B, Rai V, Sidhu S, Singh AK, Singh NK. Evolutionary Insights Based on SNP Haplotypes of Red Pericarp, Grain Size and Starch Synthase Genes in Wild and Cultivated Rice. FRONTIERS IN PLANT SCIENCE 2017; 8:972. [PMID: 28649256 PMCID: PMC5465369 DOI: 10.3389/fpls.2017.00972] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/23/2017] [Indexed: 05/23/2023]
Abstract
The origin and domestication of rice has been a subject of considerable debate in the post-genomic era. Rice varieties have been categorized based on isozyme and DNA markers into two broad cultivar groups, Indica and Japonica. Among other well-known cultivar groups Aus varieties are closer to Indica and Aromatic varieties including Basmati are closer to Japonica, while deep-water rice varieties share kinship to both Indica and Japonica cultivar groups. Here, we analyzed haplotype networks and phylogenetic relationships in a diverse set of genotypes including Indian Oryza nivara/Oryza rufipogon wild rice accessions and representative varieties of four rice cultivar groups based on pericarp color (Rc), grain size (GS3) and eight different starch synthase genes (GBSSI, SSSI, SSIIa, SSIIb, SSIIIa, SSIIIb, SSIVa, and SSIVb). Aus cultivars appear to have the most ancient origin as they shared the maximum number of haplotypes with the wild rice populations, while Indica, Japonica and Aromatic cultivar groups showed varying phylogenetic origins of these genes. Starch synthase genes showed higher variability in cultivated rice than wild rice populations, suggesting diversified selection during and after domestication. O. nivara/O. rufipogon wild rice accessions belonging to different sub-populations shared common haplotypes for all the 10 genes analyzed. Our results support polyphyletic origin of cultivated rice with a complex pattern of migration of domestication alleles from wild to different rice cultivar groups. The findings provide novel insights into evolutionary and domestication history of rice and will help utilization of wild rice germplasm for genetic improvement of rice cultivars.
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Affiliation(s)
- Nisha Singh
- ICAR – National Research Centre on Plant BiotechnologyNew Delhi, India
- Shaheed Udham Singh College of Engineering & Technology, I. K. Gujral Punjab Technical UniversityJalandhar, India
| | - Balwant Singh
- ICAR – National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Vandna Rai
- ICAR – National Research Centre on Plant BiotechnologyNew Delhi, India
| | - Sukhjeet Sidhu
- Shaheed Udham Singh College of Engineering & Technology, I. K. Gujral Punjab Technical UniversityJalandhar, India
| | - Ashok K. Singh
- Divisions of Genetics, ICAR – Indian Agricultural Research InstituteNew Delhi, India
| | - Nagendra K. Singh
- ICAR – National Research Centre on Plant BiotechnologyNew Delhi, India
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15
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Li LF, Li YL, Jia Y, Caicedo AL, Olsen KM. Signatures of adaptation in the weedy rice genome. Nat Genet 2017; 49:811-814. [PMID: 28369039 DOI: 10.1038/ng.3825] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 03/02/2017] [Indexed: 12/19/2022]
Abstract
Crop domestication provided the calories that fueled the rise of civilization. For many crop species, domestication was accompanied by the evolution of weedy crop relatives, which aggressively outcompete crops and reduce harvests. Understanding the genetic mechanisms that underlie the evolution of weedy crop relatives is critical for agricultural weed management and food security. Here we use whole-genome sequences to examine the origin and adaptation of the two major strains of weedy rice found in the United States. We find that de-domestication from cultivated ancestors has had a major role in their evolution, with relatively few genetic changes required for the emergence of weediness traits. Weed strains likely evolved both early and late in the history of rice cultivation and represent an under-recognized component of the domestication process. Genomic regions identified here that show evidence of selection can be considered candidates for future genetic and functional analyses for rice improvement.
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Affiliation(s)
- Lin-Feng Li
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Ya-Ling Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Yulin Jia
- US Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, USA
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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16
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Little White Lies: Pericarp Color Provides Insights into the Origins and Evolution of Southeast Asian Weedy Rice. G3-GENES GENOMES GENETICS 2016; 6:4105-4114. [PMID: 27729434 PMCID: PMC5144979 DOI: 10.1534/g3.116.035881] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Weedy rice is a conspecific form of cultivated rice (Oryza sativa L.) that infests rice fields and results in severe crop losses. Weed strains in different world regions appear to have originated multiple times from different domesticated and/or wild rice progenitors. In the case of Malaysian weedy rice, a multiple-origin model has been proposed based on neutral markers and analyses of domestication genes for hull color and seed shattering. Here, we examined variation in pericarp (bran) color and its molecular basis to address how this trait evolved in Malaysian weeds and its possible role in weed adaptation. Functional alleles of the Rc gene confer proanthocyanidin pigmentation of the pericarp, a trait found in most wild and weedy Oryzas and associated with seed dormancy; nonfunctional rc alleles were strongly favored during rice domestication, and most cultivated varieties have nonpigmented pericarps. Phenotypic characterizations of 52 Malaysian weeds revealed that most strains are characterized by the pigmented pericarp; however, some weeds have white pericarps, suggesting close relationships to cultivated rice. Phylogenetic analyses indicate that the Rc haplotypes present in Malaysian weeds likely have at least three distinct origins: wild O. rufipogon, white-pericarp cultivated rice, and red-pericarp cultivated rice. These diverse origins contribute to high Rc nucleotide diversity in the Malaysian weeds. Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations, for example, by conferring seed dormancy. This may promote functional Rc introgression from local wild Oryza populations.
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17
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Bessho-Uehara K, Wang DR, Furuta T, Minami A, Nagai K, Gamuyao R, Asano K, Angeles-Shim RB, Shimizu Y, Ayano M, Komeda N, Doi K, Miura K, Toda Y, Kinoshita T, Okuda S, Higashiyama T, Nomoto M, Tada Y, Shinohara H, Matsubayashi Y, Greenberg A, Wu J, Yasui H, Yoshimura A, Mori H, McCouch SR, Ashikari M. Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice. Proc Natl Acad Sci U S A 2016; 113:8969-74. [PMID: 27466405 PMCID: PMC4987784 DOI: 10.1073/pnas.1604849113] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Domestication of crops based on artificial selection has contributed numerous beneficial traits for agriculture. Wild characteristics such as red pericarp and seed shattering were lost in both Asian (Oryza sativa) and African (Oryza glaberrima) cultivated rice species as a result of human selection on common genes. Awnedness, in contrast, is a trait that has been lost in both cultivated species due to selection on different sets of genes. In a previous report, we revealed that at least three loci regulate awn development in rice; however, the molecular mechanism underlying awnlessness remains unknown. Here we isolate and characterize a previously unidentified EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family member named REGULATOR OF AWN ELONGATION 2 (RAE2) and identify one of its requisite processing enzymes, SUBTILISIN-LIKE PROTEASE 1 (SLP1). The RAE2 precursor is specifically cleaved by SLP1 in the rice spikelet, where the mature RAE2 peptide subsequently induces awn elongation. Analysis of RAE2 sequence diversity identified a highly variable GC-rich region harboring multiple independent mutations underlying protein-length variation that disrupt the function of the RAE2 protein and condition the awnless phenotype in Asian rice. Cultivated African rice, on the other hand, retained the functional RAE2 allele despite its awnless phenotype. Our findings illuminate the molecular function of RAE2 in awn development and shed light on the independent domestication histories of Asian and African cultivated rice.
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Affiliation(s)
- Kanako Bessho-Uehara
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Diane R Wang
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853-1901
| | - Tomoyuki Furuta
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Anzu Minami
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Rico Gamuyao
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Kenji Asano
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Rosalyn B Angeles-Shim
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Yoshihiro Shimizu
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Madoka Ayano
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Norio Komeda
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Kazuyuki Doi
- Graduate School of Agriculture, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Kotaro Miura
- Faculty of Biotechnology, Fukui Prefectural University, 4-1-1 Eiheiji-Town, Fukui 910-1195, Japan
| | - Yosuke Toda
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Satohiro Okuda
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Mika Nomoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Yasuomi Tada
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Hidefumi Shinohara
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Yoshikatsu Matsubayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Anthony Greenberg
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853-1901
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan
| | - Hideshi Yasui
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Atsushi Yoshimura
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Hitoshi Mori
- Graduate School of Agriculture, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan;
| | - Susan R McCouch
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853-1901;
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan;
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18
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Differentiation and description of aromatic short grain rice landraces of eastern Indian state of Odisha based on qualitative phenotypic descriptors. BMC Ecol 2016; 16:36. [PMID: 27507255 PMCID: PMC4977617 DOI: 10.1186/s12898-016-0086-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 06/14/2016] [Indexed: 11/10/2022] Open
Abstract
Background Speciality rice, in general, and aromatic rice in particular, possess enormous market potential for enhancing farm profits. However, systematic characterization of the diversity present in this natural wealth is a major pre requisite for using it in the breeding programs. This study reports qualitative phenotypic trait based characterization of 126 short grain aromatic rice genotypes, collected from different areas of the state of Odisha, India. Results Out of the 24 descriptors employed, highest variability (8 different types) was observed for lemma-palea colour with a genetic diversity index (He) of 0.696. The principal component analysis reveals that the tip colour of lemma, colour of awn and colour of stigma, cumulatively explain 74 % of the total variation. The Population STRUCTURE analysis classified the population into two subpopulations which were subdivided further into four distinct groups. The western and southern districts of Odisha are endowed with maximum diversity in comparison to eastern and northern districts and at district level comparisons, Koraput and Puri districts are rich with a genetic diversity values of 0.324 and 0.303 respectively. With this set of morphological qualitative traits, based on ‘phenoprinting’, a newly proposed bar coding system, unique fingerprints of each genotype can be effectively generated that can help in easy identification of these genotypes. Conclusion Though aromatic rices represent a tiny fraction of the total rice germplasm, a small collection of 126 land races did exhibit rich diversity for all the qualitative traits. For lemma-palea colour, eight different types were detected while for tip colour of lemma, six different types were recorded, suggesting the presence of rich variability in short grain aromatic rices that are conserved in this region. The proposed ‘phenoprinting’ can be an effective descriptor with the unique finger prints generated for each genotype and coupled with molecular (DNA) finger printing, we can discriminate and identify each and every aromatic short grain rice genotype. The proposed system not only help in conservation but also can confer IPR protection to these specialty rices. Electronic supplementary material The online version of this article (doi:10.1186/s12898-016-0086-8) contains supplementary material, which is available to authorized users.
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19
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Qi X, Liu Y, Vigueira CC, Young ND, Caicedo AL, Jia Y, Gealy DR, Olsen KM. More than one way to evolve a weed: parallel evolution of US weedy rice through independent genetic mechanisms. Mol Ecol 2015; 24:3329-44. [PMID: 26031196 DOI: 10.1111/mec.13256] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 02/06/2023]
Abstract
Many different crop species were selected for a common suite of 'domestication traits', which facilitates their use for studies of parallel evolution. Within domesticated rice (Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it possible to examine the genetic basis of parallel weed evolution and the extent to which this process occurs through shared genetic mechanisms. We performed comparative QTL mapping of weediness traits using two recombinant inbred line populations derived from crosses between an indica crop variety and representatives of each of the two independently evolved weed strains found in US rice fields, strawhull (S) and blackhull awned (B). Genotyping-by-sequencing provided dense marker coverage for linkage map construction (average marker interval <0.25 cM), with 6016 and 13 730 SNPs mapped in F5 lines of the S and B populations, respectively. For some weediness traits (awn length, hull pigmentation and pericarp pigmentation), QTL mapping and sequencing of underlying candidate genes confirmed that trait variation was largely attributable to individual loci. However, for more complex quantitative traits (including heading date, panicle length and seed shattering), we found multiple QTL, with little evidence of shared genetic bases between the S and B populations or across previous studies of weedy rice. Candidate gene sequencing revealed causal genetic bases for 8 of 27 total mapped QTL. Together these findings suggest that despite the genetic bottleneck that occurred during rice domestication, there is ample genetic variation in this crop to allow agricultural weed evolution through multiple genetic mechanisms.
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Affiliation(s)
- Xinshuai Qi
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
| | - Yan Liu
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, 72160, USA
| | - Cynthia C Vigueira
- Department of Biology, Washington University, St. Louis, MO, 63130, USA.,Department of Biology, High Point University, High Point, NC, 27268, USA
| | - Nelson D Young
- Department of Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts, Amherst, MA, 01003, USA
| | - Yulin Jia
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, 72160, USA
| | - David R Gealy
- Dale Bumpers National Rice Research Center, USDA-ARS, Stuttgart, AR, 72160, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University, St. Louis, MO, 63130, USA
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20
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Song BK, Chuah TS, Tam SM, Olsen KM. Malaysian weedy rice shows its true stripes: wildOryzaand elite rice cultivars shape agricultural weed evolution in Southeast Asia. Mol Ecol 2014; 23:5003-17. [DOI: 10.1111/mec.12922] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/30/2014] [Accepted: 09/03/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Beng-Kah Song
- School of Science; Monash University Malaysia; 46150 Bandar Sunway Selangor Malaysia
- Genomics Facility; Monash University Malaysia; 46150 Bandar Sunway Selangor Malaysia
| | - Tse-Seng Chuah
- Department of Agro-technology; Faculty of Agro-technology and Food Science; Universiti Malaysia Terengganu; 21030 Kuala Terengganu Malaysia
| | - Sheh May Tam
- School of Biosciences; Taylor's University; 47500 Subang Jaya Selangor Malaysia
| | - Kenneth M. Olsen
- Department of Biology; Washington University in St Louis; St. Louis MO 63130 USA
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