1
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Li X, Lowey D, Lessard J, Caicedo AL. Comparative histology of abscission zones reveals the extent of convergence and divergence in seed shattering in weedy and cultivated rice. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4837-4850. [PMID: 38972665 DOI: 10.1093/jxb/erae221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 05/29/2024] [Indexed: 07/09/2024]
Abstract
The modification of seed shattering has been a recurring theme in rice evolution. The wild ancestor of cultivated rice disperses its seeds, but reduced shattering was selected during multiple domestication events to facilitate harvesting. Conversely, selection for increased shattering occurred during the evolution of weedy rice, a weed invading cultivated rice fields that has originated multiple times from domesticated ancestors. Shattering requires formation of a tissue known as the abscission zone (AZ), but how the AZ has been modified throughout rice evolution is unclear. We quantitatively characterized the AZ characteristics of relative length, discontinuity, and intensity in 86 cultivated and weedy rice accessions. We reconstructed AZ evolutionary trajectories and determined the degree of convergence among different cultivated varieties and among independent weedy rice populations. AZ relative length emerged as the best feature to distinguish high and low shattering rice. Cultivated varieties differed in average AZ morphology, revealing lack of convergence in how shattering reduction was achieved during domestication. In contrast, weedy rice populations typically converged on complete AZs, irrespective of origin. By examining AZ population-level morphology, our study reveals its evolutionary plasticity, and suggests that the genetic potential to modify the ecologically and agronomically important trait of shattering is plentiful in rice lineages.
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Affiliation(s)
- Xiang Li
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Daniel Lowey
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Jessica Lessard
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Ana L Caicedo
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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2
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Bhupenchandra I, Chongtham SK, Gangarani Devi A, Dutta P, Lamalakshmi E, Mohanty S, Choudhary AK, Das A, Sarika K, Kumar S, Yumnam S, Sagolsem D, Rupert Anand Y, Bhutia DD, Victoria M, Vinodh S, Tania C, Dhanachandra Sharma A, Deb L, Sahoo MR, Seth CS, Swapnil P, Meena M. Harnessing weedy rice as functional food and source of novel traits for crop improvement. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38436101 DOI: 10.1111/pce.14868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/05/2024]
Abstract
A relative of cultivated rice (Oryza sativa L.), weedy or red rice (Oryza spp.) is currently recognized as the dominant weed, leading to a drastic loss of yield of cultivated rice due to its highly competitive abilities like producing more tillers, panicles, and biomass with better nutrient uptake. Due to its high nutritional value, antioxidant properties (anthocyanin and proanthocyanin), and nutrient absorption ability, weedy rice is gaining immense research attentions to understand its genetic constitution to augment future breeding strategies and to develop nutrition-rich functional foods. Consequently, this review focuses on the unique gene source of weedy rice to enhance the cultivated rice for its crucial features like water use efficiency, abiotic and biotic stress tolerance, early flowering, and the red pericarp of the seed. It explores the debating issues on the origin and evolution of weedy rice, including its high diversity, signalling aspects, quantitative trait loci (QTL) mapping under stress conditions, the intricacy of the mechanism in the expression of the gene flow, and ecological challenges of nutrient removal by weedy rice. This review may create a foundation for future researchers to understand the gene flow between cultivated crops and weedy traits and support an improved approach for the applicability of several models in predicting multiomics variables.
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Affiliation(s)
- Ingudam Bhupenchandra
- ICAR-Farm Science Centre Tamenglong, ICAR Research Complex for NEH Region, Manipur Centre, Imphal, Manipur, India
| | - Sunil Kumar Chongtham
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Ayam Gangarani Devi
- ICAR Research Complex for North Eastern Hill Region, Tripura Centre Lembucherra, Tripura, India
| | - Pranab Dutta
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Elangbam Lamalakshmi
- ICAR Research Complex for North Eastern Hill Region, Sikkim Centre, Tadong, Sikkim, India
| | - Sansuta Mohanty
- Molecular Biology and Biotechnology Department, Faculty of Agricultural Sciences, Siksha O Anusandhan University, Bhubaneswar, Odisha, India
| | - Anil K Choudhary
- Division of Crop Production, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Anup Das
- ICAR Research Complex for North Eastern Hill Region, Lembucherra, Tripura, India
| | - Konsam Sarika
- ICAR Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | - Sumit Kumar
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
- Department of Plant Pathology, B.M. College of Agriculture, Khandwa, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior, Madhya Pradesh, India
| | - Sonika Yumnam
- All India Coordinated Research Project on Chickpea, Central Agricultural University, Imphal, Manipur, India
| | - Diana Sagolsem
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Y Rupert Anand
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Dawa Dolma Bhutia
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - M Victoria
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - S Vinodh
- Multi Technology Testing Centre and Vocational Training Centre, College of Horticulture, Central Agricultural University, Bermiok, Sikkim, India
| | - Chongtham Tania
- ICAR Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | | | - Lipa Deb
- School of Crop Protection, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, Meghalaya, India
| | - Manas Ranjan Sahoo
- ICAR Research Complex for North Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | | | - Prashant Swapnil
- Department of Botany, School of Basic Science, Central University of Punjab, Bhatinda, Punjab, India
| | - Mukesh Meena
- Laboratory of Phytopathology and Microbial Biotechnology, Department of Botany, Mohanlal Sukhadia University, Udaipur, Rajasthan, India
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3
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Li LF, Pusadee T, Wedger MJ, Li YL, Li MR, Lau YL, Yap SJ, Jamjod S, Rerkasem B, Hao Y, Song BK, Olsen KM. Porous borders at the wild-crop interface promote weed adaptation in Southeast Asia. Nat Commun 2024; 15:1182. [PMID: 38383554 PMCID: PMC10881511 DOI: 10.1038/s41467-024-45447-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 01/24/2024] [Indexed: 02/23/2024] Open
Abstract
High reproductive compatibility between crops and their wild relatives can provide benefits for crop breeding but also poses risks for agricultural weed evolution. Weedy rice is a feral relative of rice that infests paddies and causes severe crop losses worldwide. In regions of tropical Asia where the wild progenitor of rice occurs, weedy rice could be influenced by hybridization with the wild species. Genomic analysis of this phenomenon has been very limited. Here we use whole genome sequence analyses of 217 wild, weedy and cultivated rice samples to show that wild rice hybridization has contributed substantially to the evolution of Southeast Asian weedy rice, with some strains acquiring weed-adaptive traits through introgression from the wild progenitor. Our study highlights how adaptive introgression from wild species can contribute to agricultural weed evolution, and it provides a case study of parallel evolution of weediness in independently-evolved strains of a weedy crop relative.
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Affiliation(s)
- Lin-Feng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63105, USA
| | - Tonapha Pusadee
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Marshall J Wedger
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63105, USA
| | - Ya-Ling Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ming-Rui Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yee-Ling Lau
- Department of Parasitology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | | | - Sansanee Jamjod
- Department of Plant and Soil Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Benjavan Rerkasem
- Plant Genetic Resources and Nutrition Laboratory, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Yan Hao
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Beng-Kah Song
- School of Sciences, Monash University Malaysia, 47500, Bandar Sunway, Selangor, Malaysia.
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63105, USA.
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4
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Ma CY, Chen Y, Zhan X, Dong YW. Tracing the evolution of tissue inhibitor of metalloproteinases in Metazoa with the Pteria penguin genome. iScience 2024; 27:108579. [PMID: 38161420 PMCID: PMC10755359 DOI: 10.1016/j.isci.2023.108579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 09/13/2023] [Accepted: 11/23/2023] [Indexed: 01/03/2024] Open
Abstract
Tissue inhibitors of metalloproteinase (TIMPs) play a pivotal role in regulating extracellular matrix (ECM) dynamics and have been extensively studied in vertebrates. However, understanding their evolution across invertebrate phyla is limited. Utilizing the high-quality Pteria penguin genome, we conducted phylogenomic orthology analyses across metazoans, revealing the emergence and distribution of the TIMP gene family. Our findings show that TIMP repertoires originated during eumetazoan radiation, experiencing independent duplication events in different clades, resulting in varied family sizes. Particularly, Pteriomorphia bivalves within Mollusca exhibited the most significant expansion and displayed the most diverse TIMP repertoires among metazoans. These expansions were attributed to multiple gene duplication events, potentially driven by the demands for functional diversification related to multiple adaptive traits, contributing to the adaptation of Pteriomorphia bivalves as stationary filter feeders. In this context, Pteriomorphia bivalves offer a promising model for studying invertebrate TIMP evolution.
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Affiliation(s)
- Chao-Yi Ma
- Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, P.R. China
- Academy of the Future Ocean, Ocean University of China, Qingdao 266100, P.R. China
| | - Yi Chen
- State Key Laboratory of Marine Resources Utilization in South China Sea, Hainan University, Haikou 570228, P.R. China
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, P.R. China
| | - Xin Zhan
- State Key Laboratory of Marine Resources Utilization in South China Sea, Hainan University, Haikou 570228, P.R. China
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, P.R. China
| | - Yun-Wei Dong
- Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, P.R. China
- Academy of the Future Ocean, Ocean University of China, Qingdao 266100, P.R. China
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5
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Li X, Zhang S, Lowey D, Hissam C, Clevenger J, Perera S, Jia Y, Caicedo AL. A derived weedy rice × ancestral cultivar cross identifies evolutionarily relevant weediness QTLs. Mol Ecol 2023; 32:5971-5985. [PMID: 37861465 DOI: 10.1111/mec.17172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/02/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023]
Abstract
Weedy rice (Oryza spp.) is a weedy relative of the cultivated rice that competes with the crop and causes significant production loss. The BHA (blackhull awned) US weedy rice group has evolved from aus cultivated rice and differs from its ancestors in several important weediness traits, including flowering time, plant height and seed shattering. Prior attempts to determine the genetic basis of weediness traits in plants using linkage mapping approaches have not often considered weed origins. However, the timing of divergence between crossed parents can affect the detection of quantitative trait loci (QTL) relevant to the evolution of weediness. Here, we used a QTL-seq approach that combines bulked segregant analysis and high-throughput whole genome resequencing to map the three important weediness traits in an F2 population derived from a cross between BHA weedy rice with an ancestral aus cultivar. We compared these QTLs with those previously detected in a cross of BHA with a more distantly related crop, indica. We identified multiple QTLs that overlapped with regions under selection during the evolution of weedy BHA rice and some candidate genes possibly underlying the evolution weediness traits in BHA. We showed that QTLs detected with ancestor-descendant crosses are more likely to be involved in the evolution of weediness traits than those detected from crosses of more diverged taxa.
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Affiliation(s)
- Xiang Li
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Shulin Zhang
- College of Biology and Food Engineering, Innovation and Practice Base for Postdoctors, Anyang Institute of Technology, Anyang, China
| | - Daniel Lowey
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Carter Hissam
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Josh Clevenger
- HudsonAlpha Institute of Biotechnology, Huntsville, Alabama, USA
| | - Sherin Perera
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Yulin Jia
- United States Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, USA
| | - Ana L Caicedo
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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6
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Common evolutionary trajectory of short life-cycle in Brassicaceae ruderal weeds. Nat Commun 2023; 14:290. [PMID: 36653415 PMCID: PMC9849336 DOI: 10.1038/s41467-023-35966-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Weed species are detrimental to crop yield. An understanding of how weeds originate and adapt to field environments is needed for successful crop management and reduction of herbicide use. Although early flowering is one of the weed trait syndromes that enable ruderal weeds to overcome frequent disturbances, the underlying genetic basis is poorly understood. Here, we establish Cardamine occulta as a model to study weed ruderality. By genome assembly and QTL mapping, we identify impairment of the vernalization response regulator gene FLC and a subsequent dominant mutation in the blue-light receptor gene CRY2 as genetic drivers for the establishment of short life cycle in ruderal weeds. Population genomics study further suggests that the mutations in these two genes enable individuals to overcome human disturbances through early deposition of seeds into the soil seed bank and quickly dominate local populations, thereby facilitating their spread in East China. Notably, functionally equivalent dominant mutations in CRY2 are shared by another weed species, Rorippa palustris, suggesting a common evolutionary trajectory of early flowering in ruderal weeds in Brassicaceae.
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7
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Ma J, Wei H, Yu X, Lv Y, Zhang Y, Qian Q, Shang L, Guo L. Compared analysis with a high-quality genome of weedy rice reveals the evolutionary game of de-domestication. FRONTIERS IN PLANT SCIENCE 2022; 13:1065449. [PMID: 36466225 PMCID: PMC9716140 DOI: 10.3389/fpls.2022.1065449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
The weedy rice (Oryza sativa f. spontanea) harbors large numbers of excellent traits and genetic diversities, which serves as a valuable germplasm resource and has been considered as a typical material for research about de-domestication. However, there are relatively few reference genomes on weedy rice that severely limit exploiting these genetic resources and revealing more details about de-domestication events. In this study, a high-quality genome (~376.4 Mb) of weedy rice A02 was assembled based on Nanopore ultra-long platform with a coverage depth of about 79.3× and 35,423 genes were predicted. Compared to Nipponbare genome, 5,574 structural variations (SVs) were found in A02. Based on super pan-genome graph, population SVs of 238 weedy rice and cultivated rice accessions were identified using public resequencing data. Furthermore, the de-domestication sites of weedy rice and domestication sites of wild rice were analyzed and compared based on SVs and single-nucleotide polymorphisms (SNPs). Interestingly, an average of 2,198 genes about de-domestication could only be found by F ST analysis based on SVs (SV-F ST) while not by F ST analysis based on SNPs (SNP-F ST) in divergent region. Additionally, there was a low overlap between domestication and de-domestication intervals, which demonstrated that two different mechanisms existed in these events. Our finding could facilitate pinpointing of the evolutionary events that had shaped the genomic architecture of wild, cultivated, and weedy rice, and provide a good foundation for cloning of the superior alleles for breeding.
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Affiliation(s)
- Jie Ma
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Hua Wei
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xiaoman Yu
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Yang Lv
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Yu Zhang
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Qian Qian
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Longbiao Guo
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
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8
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McSteen P, Kellogg EA. Molecular, cellular, and developmental foundations of grass diversity. Science 2022; 377:599-602. [PMID: 35926032 DOI: 10.1126/science.abo5035] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Humans have cultivated grasses for food, feed, beverages, and construction materials for millennia. Grasses also dominate the landscape in vast parts of the world, where they have adapted morphologically and physiologically, diversifying to form ~12,000 species. Sequences of hundreds of grass genomes show that they are essentially collinear; nonetheless, not all species have the same complement of genes. Here, we focus on the molecular, cellular, and developmental bases of grain yield and dispersal-traits that are essential for domestication. Distinct genes, networks, and pathways were selected in different crop species, reflecting underlying genomic diversity. With increasing genomic resources becoming available in nondomesticated species, we anticipate advances in coming years that illuminate the ecological and economic success of the grasses.
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Affiliation(s)
- Paula McSteen
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
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9
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Wu D, Qiu J, Sun J, Song BK, Olsen KM, Fan L. Weedy rice, a hidden gold mine in the paddy field. MOLECULAR PLANT 2022; 15:566-568. [PMID: 35032686 DOI: 10.1016/j.molp.2022.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Dongya Wu
- Zhejiang University City College, Hangzhou 310015, China; College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Beng-Kah Song
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor 46150, Malaysia
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Longjiang Fan
- Zhejiang University City College, Hangzhou 310015, China; College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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10
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Garcia RS, Coronejo S, Concepcion J, Subudhi PK. Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice. Int J Mol Sci 2022; 23:1608. [PMID: 35163531 PMCID: PMC8836195 DOI: 10.3390/ijms23031608] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/16/2022] [Accepted: 01/26/2022] [Indexed: 02/01/2023] Open
Abstract
Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified unique variants within the heading date QTLs. Analyses of the RNA-Seq result under both short-day (SD) and long-day (LD) conditions revealed that many differentially expressed genes (DEGs) colocalized with the flowering QTLs, and some DEGs such as Hd1, OsMADS56, Hd3a, and RFT1 had unique variants in PSRR-1. Ehd1, Hd1, OsMADS15, and OsMADS56 showed different alternate splicing (AS) events between genotypes and day length conditions. OsMADS56 was expressed in PSRR-1 but not in Cypress under both LD and SD conditions. Based on variations in both sequence and expression, the unique flowering response in PSRR-1 may be due to the high-impact variants of flowering genes, and OsMADS56 is proposed as a key regulator for its day-neutral flowering response.
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Affiliation(s)
| | | | | | - Prasanta K. Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA; (R.S.G.); (S.C.); (J.C.)
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11
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Sudo MPS, Yesudasan R, Neik TX, Masilamany D, Jayaraj J, Teo SS, Rahman S, Song BK. The details are in the genome-wide SNPs: Fine scale evolution of the Malaysian weedy rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 310:110985. [PMID: 34315600 DOI: 10.1016/j.plantsci.2021.110985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/24/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Weedy rice (Oryza spp.) is a major nuisance to rice farmers from all over the world. Although the emergence of weedy rice in East Malaysia on the island of Borneo is very recent, the threat to rice yield has reached an alarming stage. Using 47,027 genotyping-by-sequencing (GBS)-derived SNPs and candidate gene analysis of the plant architecture domestication gene TAC1, we assessed the genetic variations and evolutionary origin of weedy rice in East Malaysia. Our findings revealed two major evolutionary paths for genetically distinct weedy rice types. Whilst the cultivar-like weedy rice are very likely to be the weedy descendant of local coexisting cultivars, the wild-like weedy rice appeared to have arisen through two possible routes: (i) accidental introduction from Peninsular Malaysia weedy rice populations, and (ii) weedy descendants of coexisting cultivars. The outcome of our genetic analyses supports the notion that Sabah cultivars and Peninsular Malaysia weedy rice are the potential progenitors of Sabah weedy rice. Similar TAC1 haplotypes were shared between Malaysian cultivated and weedy rice populations, which further supported the findings of our GBS-SNP analyses. These different strains of weedy rice have convergently evolved shared traits, such as seeds shattering and open tillers. A comparison with our previous simple-sequence repeat-based population genetic analyses highlights the strength of genome-wide SNPs, including detection of admixtures and low-level introgression events. These findings could inform better strategic management for controlling the spread of weedy rice in the region.
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Affiliation(s)
- Maggie Pui San Sudo
- School of Science, Monash University Malaysia, 46150 Bandar Sunway, Selangor, Malaysia
| | - Rupini Yesudasan
- School of Science, Monash University Malaysia, 46150 Bandar Sunway, Selangor, Malaysia
| | - Ting Xiang Neik
- School of Science, Monash University Malaysia, 46150 Bandar Sunway, Selangor, Malaysia; School of Biological Sciences, University of Western Australia, Perth, Australia
| | - Dilipkumar Masilamany
- Rice Research Center, Malaysian Agricultural Research and Development Institute (MARDI), MARDI Seberang Perai, 13200 Kepala Batas, Pulau Pinang, Malaysia
| | - Jayasyaliny Jayaraj
- School of Science, Monash University Malaysia, 46150 Bandar Sunway, Selangor, Malaysia
| | - Su-Sin Teo
- Department of Agriculture, Sabah, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, 46150 Bandar Sunway, Selangor, Malaysia; Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, 47500 Bandar Sunway, Selangor, Malaysia
| | - Beng-Kah Song
- School of Science, Monash University Malaysia, 46150 Bandar Sunway, Selangor, Malaysia; Monash University Malaysia Genomics Facility, Tropical Medicine and Biology Multidisciplinary Platform, 47500 Bandar Sunway, Selangor, Malaysia.
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12
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Imaizumi T, Ebana K, Kawahara Y, Muto C, Kobayashi H, Koarai A, Olsen KM. Genomic divergence during feralization reveals both conserved and distinct mechanisms of parallel weediness evolution. Commun Biol 2021; 4:952. [PMID: 34376793 PMCID: PMC8355325 DOI: 10.1038/s42003-021-02484-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/23/2021] [Indexed: 12/28/2022] Open
Abstract
Agricultural weeds are the most important biotic constraints to global crop production, and chief among these is weedy rice. Despite increasing yield losses from weedy rice in recent years worldwide, the genetic basis of weediness evolution remains unclear. Using whole-genome sequence analyses, we examined the origins and adaptation of Japanese weedy rice. We find evidence for a weed origin from tropical japonica crop ancestry, which has not previously been documented in surveys of weedy rice worldwide. We further show that adaptation occurs largely through different genetic mechanisms between independently-evolved temperate japonica- and tropical japonica-derived strains; most genomic signatures of positive selection are unique within weed types. In addition, some weedy rice strains have evolved through hybridization between weedy and cultivated rice with adaptive introgression from the crop. Surprisingly, introgression from cultivated rice confers not only crop-like adaptive traits (such as shorter plant height, facilitating crop mimicry) but also weedy-like traits (such as seed dormancy). These findings reveal how hybridization with cultivated rice can promote persistence and proliferation of weedy rice.
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Affiliation(s)
- Toshiyuki Imaizumi
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan.
| | - Kaworu Ebana
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Yoshihiro Kawahara
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Chiaki Muto
- Research Center of Genetic Resources, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Hiroyuki Kobayashi
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsukuba, Japan
- Center for Weed and Wildlife Management, Utsunomiya University, Utsunomiya, Japan
| | - Akira Koarai
- Institute for Plant Protection, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, USA
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13
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Zhou C, Feng Y, Li G, Wang M, Jian J, Wang Y, Zhang W, Song Z, Li L, Lu B, Yang J. The New Is Old: Novel Germination Strategy Evolved From Standing Genetic Variation in Weedy Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:699464. [PMID: 34234803 PMCID: PMC8256273 DOI: 10.3389/fpls.2021.699464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/28/2021] [Indexed: 06/01/2023]
Abstract
Feralization of crop plants has aroused an increasing interest in recent years, not only for the reduced yield and quality of crop production caused by feral plants but also for the rapid evolution of novel traits that facilitate the evolution and persistence of weedy forms. Weedy rice (Oryza sativa f. spontanea) is a conspecific weed of cultivated rice, with separate and independent origins. The weedy rice distributed in eastern and northeastern China did not diverge from their cultivated ancestors by reverting to the pre-domestication trait of seed dormancy during feralization. Instead, they developed a temperature-sensing mechanism to control the timing of seed germination. Subsequent divergence in the minimum critical temperature for germination has been detected between northeastern and eastern populations. An integrative analysis was conducted using combinations of phenotypic, genomic and transcriptomic data to investigate the genetic mechanism underlying local adaptation and feralization. A dozen genes were identified, which showed extreme allele frequency differences between eastern and northeastern populations, and high correlations between allele-specific gene expression and feral phenotypes. Trancing the origin of potential adaptive alleles based on genomic sequences revealed the presence of most selected alleles in wild and cultivated rice genomes, indicating that weedy rice drew upon pre-existing, "conditionally neutral" alleles to respond to the feral selection regimes. The cryptic phenotype was exposed by activating formerly silent alleles to facilitate the transition from cultivation to wild existence, promoting the evolution and persistence of weedy forms.
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Affiliation(s)
- Chengchuan Zhou
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Yang Feng
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Gengyun Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Mengli Wang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Jinjing Jian
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Yuguo Wang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Wenju Zhang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Zhiping Song
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Linfeng Li
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Baorong Lu
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
| | - Ji Yang
- National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, China
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14
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Wu D, Lao S, Fan L. De-Domestication: An Extension of Crop Evolution. TRENDS IN PLANT SCIENCE 2021; 26:560-574. [PMID: 33648850 DOI: 10.1016/j.tplants.2021.02.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/24/2021] [Accepted: 02/01/2021] [Indexed: 06/12/2023]
Abstract
De-domestication or feralization is an interesting phenomenon in crops and livestock. Previously, evidence for crop de-domestication was based mainly on studies using phenotypic and genotypic data from limited molecular markers or gene segments. Recent genomic studies in rice, barley, and wheat provide comprehensive landscapes of de-domestication on a whole-genome scale. Here, we summarize crop de-domestication processes, ecological roles of de-domesticates, mechanisms underlying crop de-domestication syndromes, and conditions potentially favoring de-domestication events. We further explain how recent de-domestication studies have expanded our understanding of the complexity of crop evolution, and highlight the genetic novelties of de-domesticates beneficial for modern crop breeding.
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Affiliation(s)
- Dongya Wu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sangting Lao
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Longjiang Fan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; Hainan Institute of Zhejiang University, Yonyou Industrial Park, Sanya 572025, China.
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15
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Hoyos V, Plaza G, Li X, Caicedo AL. Something old, something new: Evolution of Colombian weedy rice ( Oryza spp.) through de novo de-domestication, exotic gene flow, and hybridization. Evol Appl 2020; 13:1968-1983. [PMID: 32908598 PMCID: PMC7463356 DOI: 10.1111/eva.12955] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/21/2020] [Accepted: 02/26/2020] [Indexed: 12/17/2022] Open
Abstract
Weedy rice (Oryza spp.) is a worldwide weed of domesticated rice (O. sativa), considered particularly problematic due to its strong competition with the crop, which leads to reduction in yields and harvest quality. Several studies have established multiple independent origins for weedy rice populations in the United States and various parts of Asia; however, the origins of weedy rice in South America have not been examined in a global context. We evaluated the genetic variation of weedy rice populations in Colombia, as well as the contributions of local wild Oryza species, local cultivated varieties, and exotic Oryza groups to the weed, using polymorphism generated by genotyping by sequencing (GBS). We found no evidence for genomic contributions from local wild Oryza species (O. glumaepatula, O. grandiglumis, O. latifolia, and O. alta) to Colombian weedy rice. Instead, Colombian weedy rice has evolved from local indica cultivars and has also likely been inadvertently imported as an exotic pest from the United States. Additionally, weeds comprising de novo admixture between these distinct weedy populations now represent a large proportion of genomic backgrounds in Colombian weedy rice. Our results underscore the impressive ability of weedy rice to evolve through multiple evolutionary pathways, including in situ de-domestication, range expansion, and hybridization.
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Affiliation(s)
- Verónica Hoyos
- Departamento de AgronomíaUniversidad Nacional de ColombiaBogotáColombia
| | - Guido Plaza
- Departamento de AgronomíaUniversidad Nacional de ColombiaBogotáColombia
| | - Xiang Li
- Plant Biology Graduate ProgramUniversity of MassachusettsAmherstMAUSA
| | - Ana L. Caicedo
- Biology DepartmentUniversity of MassachusettsAmherstMAUSA
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16
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Qiu J, Jia L, Wu D, Weng X, Chen L, Sun J, Chen M, Mao L, Jiang B, Ye C, Turra GM, Guo L, Ye G, Zhu QH, Imaizumi T, Song BK, Scarabel L, Merotto A, Olsen KM, Fan L. Diverse genetic mechanisms underlie worldwide convergent rice feralization. Genome Biol 2020; 21:70. [PMID: 32213201 PMCID: PMC7098168 DOI: 10.1186/s13059-020-01980-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/02/2020] [Indexed: 11/21/2022] Open
Abstract
Background Worldwide feralization of crop species into agricultural weeds threatens global food security. Weedy rice is a feral form of rice that infests paddies worldwide and aggressively outcompetes cultivated varieties. Despite increasing attention in recent years, a comprehensive understanding of the origins of weedy crop relatives and how a universal feralization process acts at the genomic and molecular level to allow the rapid adaptation to weediness are still yet to be explored. Results We use whole-genome sequencing to examine the origin and adaptation of 524 global weedy rice samples representing all major regions of rice cultivation. Weed populations have evolved multiple times from cultivated rice, and a strikingly high proportion of contemporary Asian weed strains can be traced to a few Green Revolution cultivars that were widely grown in the late twentieth century. Latin American weedy rice stands out in having originated through extensive hybridization. Selection scans indicate that most genomic regions underlying weedy adaptations do not overlap with domestication targets of selection, suggesting that feralization occurs largely through changes at loci unrelated to domestication. Conclusions This is the first investigation to provide detailed genomic characterizations of weedy rice on a global scale, and the results reveal diverse genetic mechanisms underlying worldwide convergent rice feralization. Electronic supplementary material The online version of this article (10.1186/s13059-020-01980-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jie Qiu
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.,Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200235, China
| | - Lei Jia
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Dongya Wu
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xifang Weng
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Lijuan Chen
- Rice Research Institute, Yunnan Agricultural University, Kunming, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, China
| | - Meihong Chen
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Lingfeng Mao
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Bowen Jiang
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Chuyu Ye
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Guilherme Menegol Turra
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guoyou Ye
- International Rice Research Institute (IRRI), Manila, Philippines
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Toshiyuki Imaizumi
- National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, 305-8666, Japan
| | - Beng-Kah Song
- School of Science, Monash University Malaysia, 46150, Bandar Sunway, Selangor, Malaysia
| | - Laura Scarabel
- Istituto per la Protezione Sostenibile delle Piante (IPSP), CNR, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| | - Aldo Merotto
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
| | - Longjiang Fan
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China. .,James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, 310058, China.
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17
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Goad DM, Jia Y, Gibbons A, Liu Y, Gealy D, Caicedo AL, Olsen KM. Identification of Novel QTL Conferring Sheath Blight Resistance in Two Weedy Rice Mapping Populations. RICE (NEW YORK, N.Y.) 2020; 13:21. [PMID: 32206941 PMCID: PMC7090113 DOI: 10.1186/s12284-020-00381-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/06/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Rice sheath blight (ShB) disease, caused by the pathogenic fungus Rhizoctonia solani, causes significant yield losses globally. US weedy rice populations, which are de-domesticated forms of indica and aus cultivated rice, appear to be more resistant to ShB than local japonica cultivated rice. We mapped quantitative trait loci (QTL) associated with ShB resistance using two F8 recombinant inbred line populations generated from crosses of an indica crop variety, Dee-Geo-Woo-Gen (DGWG), with individuals representing the two major US weed biotypes, straw hull (SH) and black hull awned (BHA). RESULTS We identified nine ShB resistance QTL across both mapping populations. Five were attributable to alleles that affect plant height (PH) and heading date (HD), two growth traits that are known to be highly correlated with ShB resistance. By utilizing an approach that treated growth traits as covariates in the mapping model, we were able to infer that the remaining four QTL are involved in ShB resistance. Two of these, qShB1-2 and qShB4, are different from previously identified ShB QTL and represent new candidates for further study. CONCLUSION Our findings suggest that ShB resistance can be improved through favorable plant growth traits and the combined effects of small to moderate-effect resistance QTL. Additionally, we show that including PH and HD as covariates in QTL mapping models is a powerful way to identify new ShB resistance QTL.
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Affiliation(s)
- David M Goad
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1137, St. Louis, MO, 63110, USA
| | - Yulin Jia
- United States Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, 2890 HWY 130 E, Stuttgart, AR, 72160, USA.
| | - Andrew Gibbons
- University of Arkansas Rice Research and Extension Center, 2900 AR-130, Stuttgart, AR, 72160, USA
- Present address: Arkansas Department of Health, Little Rock, AR, 72205, USA
| | - Yan Liu
- Present address: Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | - David Gealy
- United States Department of Agriculture-Agricultural Research Service, Dale Bumpers National Rice Research Center, 2890 HWY 130 E, Stuttgart, AR, 72160, USA
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts, Amherst, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, 1 Brookings Drive, Campus Box 1137, St. Louis, MO, 63110, USA
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18
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Gering E, Incorvaia D, Henriksen R, Conner J, Getty T, Wright D. Getting Back to Nature: Feralization in Animals and Plants. Trends Ecol Evol 2019; 34:1137-1151. [PMID: 31488326 PMCID: PMC7479514 DOI: 10.1016/j.tree.2019.07.018] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 11/24/2022]
Abstract
Formerly domesticated organisms and artificially selected genes often escape controlled cultivation, but their subsequent evolution is not well studied. In this review, we examine plant and animal feralization through an evolutionary lens, including how natural selection, artificial selection, and gene flow shape feral genomes, traits, and fitness. Available evidence shows that feralization is not a mere reversal of domestication. Instead, it is shaped by the varied and complex histories of feral populations, and by novel selection pressures. To stimulate further insight we outline several future directions. These include testing how 'domestication genes' act in wild settings, studying the brains and behaviors of feral animals, and comparative analyses of feral populations and taxa. This work offers feasible and exciting research opportunities with both theoretical and practical applications.
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Affiliation(s)
- Eben Gering
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Department of Biological Sciences, Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Davie, FL, USA.
| | - Darren Incorvaia
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Rie Henriksen
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
| | - Jeffrey Conner
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA; Kellogg Biological Station and Dept. of Plant Biology, Michigan State University, Hickory Corners, MI, USA
| | - Thomas Getty
- Department of Integrative Biology and Ecology, Evolutionary Biology, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | - Dominic Wright
- IIFM Biology and AVIAN Behavioural Genomics and Physiology Group, Linköping University, Linköping, Sweden
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19
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Jiang YF, Chen Q, Wang Y, Guo ZR, Xu BJ, Zhu J, Zhang YZ, Gong X, Luo CH, Wu W, Liu CH, Kong L, Deng M, Jiang QT, Lan XJ, Wang JR, Chen GY, Zheng YL, Wei YM, Qi PF. Re-acquisition of the brittle rachis trait via a transposon insertion in domestication gene Q during wheat de-domestication. THE NEW PHYTOLOGIST 2019; 224:961-973. [PMID: 31168798 DOI: 10.1111/nph.15977] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 05/28/2019] [Indexed: 05/18/2023]
Abstract
De-domestication is a unique evolutionary process during which crops re-acquire wild-like traits to survive and persist in agricultural fields without the need for human cultivation. The re-acquisition of seed dispersal mechanisms is crucial for crop de-domestication. Common wheat is an important cereal crop worldwide. Tibetan semi-wild wheat is a potential de-domesticated common wheat subspecies. However, the crucial genes responsible for its brittle rachis trait have not been identified. Genetic mapping, functional analyses and phylogenetic analyses were completed to identify the gene associated with Qbr.sau-5A, which is a major locus for the brittle rachis trait of Tibetan semi-wild wheat. The cloned Qbr.sau-5A gene is a new Q allele (Qt ) with a 161-bp transposon insertion in exon 5. Although Qt is expressed normally, its encoded peptide lacks some key features of the APETALA2 family. The abnormal functions of Qt in developing wheat spikes result in brittle rachises. Phylogenetic and genotyping analyses confirmed that Qt originated from Q in common wheat and is naturally distributed only in Tibetan semi-wild wheat populations. The identification of Qt provides new evidence regarding the origin of Tibetan semi-wild wheat, and new insights into the re-acquisition of wild traits during crop de-domestication.
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Affiliation(s)
- Yun-Feng Jiang
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Qing Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yan Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Zhen-Ru Guo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Bin-Jie Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Jing Zhu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Ya-Zhou Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xi Gong
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Cui-Hua Luo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Wang Wu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Cai-Hong Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Li Kong
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Qian-Tao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Xiu-Jin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Ji-Rui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Guo-Yue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yu-Ming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Peng-Fei Qi
- State Key Laboratory of Crop Genetics of Disease Resistance and Disease Control, Chengdu, Sichuan, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
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20
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When West Meets East: The Origins and Spread of Weedy Rice Between Continental and Island Southeast Asia. G3-GENES GENOMES GENETICS 2019; 9:2941-2950. [PMID: 31292156 PMCID: PMC6723143 DOI: 10.1534/g3.119.400021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Weedy crop relatives are among the world’s most problematic agricultural weeds, and their ability to rapidly evolve can be enhanced by gene flow from both domesticated crop varieties and wild crop progenitor species. In this study, we examined the role of modern commercial crop cultivars, traditional landraces, and wild relatives in the recent emergence and proliferation of weedy rice in East Malaysia on the island of Borneo. This region of Malaysia is separated from the Asian continent by the South China Sea, and weedy rice has become a major problem there more recently than on the Malaysian peninsular mainland. Using 24 polymorphic SSR loci and genotype data from the awn-length domestication gene An-1, we assessed the genetic diversity, population structure and potential origins of East Malaysian weeds; 564 weedy, cultivated and wild rice accessions were analyzed from samples collected in East Malaysia, Peninsular Malaysia and neighboring countries. While there is considerable evidence for contributions of Peninsular Malaysian weed ecotypes to East Malaysian populations, we find that local crop cultivars and/or landraces from neighboring countries are also likely contributors to the weedy rice infestations. These findings highlight the implications of genetic admixture from different cultivar source populations in the spread of weedy crop relatives and the urgent need for preventive measurements to maintain sustainable crop yields.
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21
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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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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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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: 40] [Impact Index Per Article: 8.0] [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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De Leon TB, Karn E, Al‐Khatib K, Espino L, Blank T, Andaya CB, Andaya VC, Brim‐DeForest W. Genetic variation and possible origins of weedy rice found in California. Ecol Evol 2019; 9:5835-5848. [PMID: 31161002 PMCID: PMC6540678 DOI: 10.1002/ece3.5167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 03/04/2019] [Accepted: 03/18/2019] [Indexed: 12/12/2022] Open
Abstract
Control of weeds in cultivated crops is a pivotal component in successful crop production allowing higher yield and higher quality. In rice-growing regions worldwide, weedy rice (Oryza sativa f. spontanea Rosh.) is a weed related to cultivated rice which infests rice fields. With populations across the globe evolving a suite of phenotypic traits characteristic of weeds and of cultivated rice, varying hypotheses exist on the origin of weedy rice. Here, we investigated the genetic diversity and possible origin of weedy rice in California using 98 simple sequence repeat (SSR) markers and an Rc gene-specific marker. By employing phylogenetic clustering analysis, we show that four to five genetically distinct biotypes of weedy rice exist in California. Analysis of population structure and genetic distance among individuals reveals diverse evolutionary origins of California weedy rice biotypes, with ancestry derived from indica, aus, and japonica cultivated rice as well as possible contributions from weedy rice from the southern United States and wild rice. Because this diverse parentage primarily consists of weedy, wild, and cultivated rice not found in California, most existing weedy rice biotypes likely originated outside California.
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Affiliation(s)
- Teresa B. De Leon
- Department of Plant SciencesUniversity of California, DavisDavisCalifornia
- Rice Experiment StationCalifornia Cooperative Rice Research Foundation, Inc.BiggsCalifornia
| | - Elizabeth Karn
- Cooperative Extension Sutter‐Yuba CountiesUniversity of California Division of Agricultural and Natural Resources (UC ANR)Yuba CityCalifornia
| | - Kassim Al‐Khatib
- Department of Plant SciencesUniversity of California, DavisDavisCalifornia
| | - Luis Espino
- Cooperative Extension Colusa CountyUniversity of California Division of Agricultural and Natural Resources (UC ANR)ColusaCalifornia
| | - Timothy Blank
- California Crop Improvement AssociationUniversity of California, DavisDavisCalifornia
| | - Cynthia B. Andaya
- Rice Experiment StationCalifornia Cooperative Rice Research Foundation, Inc.BiggsCalifornia
| | - Virgilio C. Andaya
- Rice Experiment StationCalifornia Cooperative Rice Research Foundation, Inc.BiggsCalifornia
| | - Whitney Brim‐DeForest
- Cooperative Extension Sutter‐Yuba CountiesUniversity of California Division of Agricultural and Natural Resources (UC ANR)Yuba CityCalifornia
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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: 27] [Impact Index Per Article: 5.4] [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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Guo L, Qiu J, Li LF, Lu B, Olsen K, Fan L. Genomic Clues for Crop-Weed Interactions and Evolution. TRENDS IN PLANT SCIENCE 2018; 23:1102-1115. [PMID: 30293809 DOI: 10.1016/j.tplants.2018.09.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/10/2018] [Accepted: 09/11/2018] [Indexed: 05/11/2023]
Abstract
Agronomically critical weeds that have evolved alongside crop species are characterized by rapid adaptation and invasiveness, which can result in an enormous reduction in annual crop yield worldwide. We discuss here recent genome-based research studies on agricultural weeds and crop-weed interactions that reveal several major evolutionary innovations such as de-domestication, interactions mediated by allelochemical secondary metabolites, and parasitic genetic elements that play crucial roles in enhancing weed invasiveness in agricultural settings. We believe that these key studies will guide future research into the evolution of crop-weed interactions, and further the development of practical applications in agricultural weed control and crop breeding.
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Affiliation(s)
- Longbiao Guo
- State Key Lab for Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China; These authors contributed equally to this work
| | - Jie Qiu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA; These authors contributed equally to this work
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Baorong Lu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Kenneth Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Longjiang Fan
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.
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27
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Chai C, Shankar R, Jain M, Subudhi PK. Genome-wide discovery of DNA polymorphisms by whole genome sequencing differentiates weedy and cultivated rice. Sci Rep 2018; 8:14218. [PMID: 30242197 PMCID: PMC6155081 DOI: 10.1038/s41598-018-32513-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 09/10/2018] [Indexed: 12/13/2022] Open
Abstract
Analyzing the genome level DNA polymorphisms between weedy and cultivated rice is crucial to elucidate the molecular basis of weedy and agronomic traits, which in turn can enhance our ability to control weedy rice and its utilization for rice improvement. Here, we presented the genome-wide genetic variations between a weedy rice accession PSRR-1 and two cultivated rice accessions, Bengal and Nona Bokra, belonging to japonica and indica subspecies, respectively. The total number of SNPs and InDels in PSRR/Bengal was similar to that of Nona Bokra/Bengal, but was three times greater than that of PSRR/Nona Bokra. There were 11546 large-effect SNPs/InDels affecting 5673 genes, which most likely differentiated weedy rice from cultivated rice. These large effect DNA polymorphisms were mostly resulted in stop codon gain and least by start codon loss. Analysis of the molecular functions and biological processes of weedy rice specific SNPs/InDels indicated that most of these genes were involved in protein modification/phosphorylation, protein kinase activity, and protein/nucleotide binding. By integrating previous QTL mapping results with the DNA polymorphisms data, the candidate genes for seed dormancy and seed shattering were narrowed down. The genomic resource generated in this study will facilitate discovery of functional variants for weedy and agronomic traits.
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Affiliation(s)
- Chenglin Chai
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
- Noble Research Institute, LLC, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Rama Shankar
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Prasanta K Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
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28
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29
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Evolution of invasiveness by genetic accommodation. Nat Ecol Evol 2018; 2:991-999. [DOI: 10.1038/s41559-018-0553-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 04/03/2018] [Indexed: 11/09/2022]
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30
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Subudhi PK, De Leon TB, Tapia R, Chai C, Karan R, Ontoy J, Singh PK. Genetic interaction involving photoperiod-responsive Hd1 promotes early flowering under long-day conditions in rice. Sci Rep 2018; 8:2081. [PMID: 29391460 PMCID: PMC5794782 DOI: 10.1038/s41598-018-20324-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
Although flowering in rice has been extensively investigated, few studies focused on genetic interactions. Flowering evaluation of two recombinant inbred line (RIL) populations involving photo-insensitive rice cultivars, Bengal and Cypress, and a weedy rice accession, PSRR-1, under natural long-day (LD) conditions, revealed six to ten quantitative trait loci (QTLs) and a major QTL interaction. In addition to the validation of several previously cloned genes using an introgression lines (IL) population of PSRR-1, a few novel QTLs were also discovered. Analysis of the marker profiles of the advanced backcross lines revealed that Hd1 allele of PSRR-1 was responsible for the photoperiodic response in the near-isogenic lines (NILs) developed in both cultivar backgrounds. Based on the phenotypic and genotypic data of the NILs, and NIL mapping population and the transcript abundance of key flowering pathway genes, we conclude that Hd1 and its interaction with a novel gene other than Ghd7 play an important role in controlling flowering under LD conditions. Our study demonstrates the important role of genetic interaction that regulates flowering time in rice and the need for further investigation to exploit it for breeding adaptable rice varieties.
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Affiliation(s)
- Prasanta K Subudhi
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA.
| | | | - Ronald Tapia
- Department of Horticultural Science, University of Florida, IFAS Gulf Coast Research and Education Center, 14625 CR 672, Wimauma, FL, 33598, USA
| | - Chenglin Chai
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK, 73401, USA
| | - Ratna Karan
- University of Florida, Gainesville, FL, 32611, USA
| | - John Ontoy
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, 70803, USA
| | - Pradeep K Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, 110012, India
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31
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Qiu J, Zhou Y, Mao L, Ye C, Wang W, Zhang J, Yu Y, Fu F, Wang Y, Qian F, Qi T, Wu S, Sultana MH, Cao YN, Wang Y, Timko MP, Ge S, Fan L, Lu Y. Genomic variation associated with local adaptation of weedy rice during de-domestication. Nat Commun 2017; 8:15323. [PMID: 28537247 PMCID: PMC5477509 DOI: 10.1038/ncomms15323] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/17/2017] [Indexed: 11/09/2022] Open
Abstract
De-domestication is a unique evolutionary process by which domesticated crops are converted into ‘wild predecessor like' forms. Weedy rice (Oryza sativa f. spontanea) is an excellent model to dissect the molecular processes underlying de-domestication. Here, we analyse the genomes of 155 weedy and 76 locally cultivated rice accessions from four representative regions in China that were sequenced to an average 18.2 × coverage. Phylogenetic and demographic analyses indicate that Chinese weedy rice was de-domesticated independently from cultivated rice and experienced a strong genetic bottleneck. Although evolving from multiple origins, critical genes underlying convergent evolution of different weedy types can be found. Allele frequency analyses suggest that standing variations and new mutations contribute differently to japonica and indica weedy rice. We identify a Mb-scale genomic region present in weedy rice but not cultivated rice genomes that shows evidence of balancing selection, thereby suggesting that there might be more complexity inherent to the process of de-domestication. De-domestication is the process by which cultivated plants adopt characteristics similar to that of their wild predecessors. Here Qiu et al. re-sequence de-domesticated weedy rice and matched cultivated varieties and identify genetic variants indicative of convergent evolution across multiple de-domestication events.
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Affiliation(s)
- Jie Qiu
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yongjun Zhou
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Lingfeng Mao
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chuyu Ye
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Weidi Wang
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jianping Zhang
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yongyi Yu
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fei Fu
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yunfei Wang
- Zhejiang Sheng Ting Biotechnology Co., Ltd., Taizhou 318020, China
| | - Feijian Qian
- Zhejiang Sheng Ting Biotechnology Co., Ltd., Taizhou 318020, China
| | - Ting Qi
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sanling Wu
- Analysis Center of Agrobiology and Environmental Sciences, Faculty of Agriculture, Life and Environmental Sciences, Zhejiang University, Hangzhou 310058, China
| | - Most Humaira Sultana
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ya-Nan Cao
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, Zhejiang University, Hangzhou 310058, China
| | - Yu Wang
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, Virginia 22904, USA
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Longjiang Fan
- Institutue of Crop Science &Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yongliang Lu
- China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
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32
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Huang Z, Young ND, Reagon M, Hyma KE, Olsen KM, Jia Y, Caicedo AL. All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian
Oryza. Mol Ecol 2017; 26:3151-3167. [DOI: 10.1111/mec.14120] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 01/21/2017] [Accepted: 03/10/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Zhongyun Huang
- Department of Biology University of Massachusetts Amherst MA USA
| | - Nelson D. Young
- Department of Biology University of Massachusetts Amherst MA USA
| | - Michael Reagon
- Department of Biology Ohio State University Lima Lima OH USA
| | - Katie E. Hyma
- Department of Biology University of Massachusetts Amherst MA USA
| | | | - Yulin Jia
- Dale Bumpers National Rice Research Center USDA‐ARS Stuttgart AR USA
| | - Ana L. Caicedo
- Department of Biology University of Massachusetts Amherst MA USA
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33
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34
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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: 97] [Impact Index Per Article: 13.9] [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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35
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Liao IT, Shan H, Xu G, Zhang R. Bridging evolution and development in plants. THE NEW PHYTOLOGIST 2016; 212:827-830. [PMID: 27874986 DOI: 10.1111/nph.14294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Affiliation(s)
- Irene T Liao
- Department of Biology, Duke University, Durham, NC, USA
| | - Hongyan Shan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Guixia Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rui Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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36
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Dalziel AC, Laporte M, Rougeux C, Guderley H, Bernatchez L. Convergence in organ size but not energy metabolism enzyme activities among wild Lake Whitefish (Coregonus clupeaformis) species pairs. Mol Ecol 2016; 26:225-244. [DOI: 10.1111/mec.13847] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/31/2016] [Accepted: 09/06/2016] [Indexed: 01/01/2023]
Affiliation(s)
- Anne C. Dalziel
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
- Department of Biology; Saint Mary's University; 923 Robie Street Halifax Nova Scotia Canada B3H 3C3
| | - Martin Laporte
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
| | - Clément Rougeux
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
| | - Helga Guderley
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
| | - Louis Bernatchez
- Department of Biology; Institut de Biologie Intégrative et des Systèmes; 1030 Avenue de la Médecine Université Laval Québec City Québec Canada G1V 0A6
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Johnsson M, Gering E, Willis P, Lopez S, Van Dorp L, Hellenthal G, Henriksen R, Friberg U, Wright D. Feralisation targets different genomic loci to domestication in the chicken. Nat Commun 2016; 7:12950. [PMID: 27686863 PMCID: PMC5056458 DOI: 10.1038/ncomms12950] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 08/18/2016] [Indexed: 12/03/2022] Open
Abstract
Feralisation occurs when a domestic population recolonizes the wild, escaping its previous restricted environment, and has been considered as the reverse of domestication. We have previously shown that Kauai Island's feral chickens are a highly variable and admixed population. Here we map selective sweeps in feral Kauai chickens using whole-genome sequencing. The detected sweeps were mostly unique to feralisation and distinct to those selected for during domestication. To ascribe potential phenotypic functions to these genes we utilize a laboratory-controlled equivalent to the Kauai population-an advanced intercross between Red Junglefowl and domestic layer birds that has been used previously for both QTL and expression QTL studies. Certain sweep genes exhibit significant correlations with comb mass, maternal brooding behaviour and fecundity. Our analyses indicate that adaptations to feral and domestic environments involve different genomic regions and feral chickens show some evidence of adaptation at genes associated with sexual selection and reproduction.
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Affiliation(s)
- M. Johnsson
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, 58183 Linköping, Sweden
| | - E. Gering
- Department of Zoology, Michigan University, Michigan 48824, USA
| | - P. Willis
- Department of Biology, University of Victoria, Victoria, British Columbia, Canada V8P 5C2
| | - S. Lopez
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - L. Van Dorp
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Centre for Mathematics, Physics and Engineering in the Life Sciences and EXperimental Biology (CoMPLEX), University College London, London WC1E 6BT, UK
| | - G. Hellenthal
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - R. Henriksen
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, 58183 Linköping, Sweden
| | - U. Friberg
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, 58183 Linköping, Sweden
| | - D. Wright
- AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, 58183 Linköping, Sweden
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Kanapeckas KL, Vigueira CC, Ortiz A, Gettler KA, Burgos NR, Fischer AJ, Lawton-Rauh AL. Escape to Ferality: The Endoferal Origin of Weedy Rice from Crop Rice through De-Domestication. PLoS One 2016; 11:e0162676. [PMID: 27661982 PMCID: PMC5035073 DOI: 10.1371/journal.pone.0162676] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 08/26/2016] [Indexed: 11/30/2022] Open
Abstract
Domestication is the hallmark of evolution and civilization and harnesses biodiversity through selection for specific traits. In regions where domesticated lines are grown near wild relatives, congeneric sources of aggressive weedy genotypes cause major economic losses. Thus, the origins of weedy genotypes where no congeneric species occur raise questions regarding management effectiveness and evolutionary mechanisms responsible for weedy population success. Since eradication in the 1970s, California growers avoided weedy rice through continuous flood culture and zero-tolerance guidelines, preventing the import, presence, and movement of weedy seeds. In 2003, after decades of no reported presence in California, a weedy rice population was confirmed in dry-seeded fields. Our objectives were to identify the origins and establishment of this population and pinpoint possible phenotypes involved. We show that California weedy rice is derived from a different genetic source among a broad range of AA genome Oryzas and is most recently diverged from O. sativa temperate japonica cultivated in California. In contrast, other weedy rice ecotypes in North America (Southern US) originate from weedy genotypes from China near wild Oryza, and are derived through existing crop-wild relative crosses. Analyses of morphological data show that California weedy rice subgroups have phenotypes like medium-grain or gourmet cultivars, but have colored pericarp, seed shattering, and awns like wild relatives, suggesting that reversion to non-domestic or wild-like traits can occur following domestication, despite apparent fixation of domestication alleles. Additionally, these results indicate that preventive methods focused on incoming weed sources through contamination may miss burgeoning weedy genotypes that rapidly adapt, establish, and proliferate. Investigating the common and unique evolutionary mechanisms underlying global weed origins and subsequent interactions with crop relatives sheds light on how weeds evolve and addresses broader questions regarding the stability of selection during domestication and crop improvement.
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Affiliation(s)
- Kimberly L. Kanapeckas
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- South Carolina Department of Natural Resources, Marine Resources Research Institute, Charleston, South Carolina, United States of America
| | - Cynthia C. Vigueira
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
- Department of Biology, High Point University, High Point, North Carolina, United States of America
| | - Aida Ortiz
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Kyle A. Gettler
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
| | - Nilda R. Burgos
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Albert J. Fischer
- Department of Plant Sciences, University of California Davis, Davis, California, United States of America
| | - Amy L. Lawton-Rauh
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina, United States of America
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Affiliation(s)
- Philip E Hulme
- The Bio-Protection Research Centre, Lincoln University, Lincoln 7647, Canterbury, New Zealand.
| | - Johannes J Le Roux
- The Bio-Protection Research Centre, Lincoln University, Lincoln 7647, Canterbury, New Zealand. Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, Matieland 7602, South Africa
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Li LF, Olsen KM. To Have and to Hold: Selection for Seed and Fruit Retention During Crop Domestication. Curr Top Dev Biol 2016; 119:63-109. [PMID: 27282024 DOI: 10.1016/bs.ctdb.2016.02.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Crop domestication provides a useful model system to characterize the molecular and developmental bases of morphological variation in plants. Among the most universal changes resulting from selection during crop domestication is the loss of seed and fruit dispersal mechanisms, which greatly facilitates harvesting efficiency. In this review, we consider the molecular genetic and developmental bases of the loss of seed shattering and fruit dispersal in six major crop plant families, three of which are primarily associated with seed crops (Poaceae, Brassicaceae, Fabaceae) and three of which are associated with fleshy-fruited crops (Solanaceae, Rosaceae, Rutaceae). We find that the developmental basis of the loss of seed/fruit dispersal is conserved in a number of independently domesticated crops, indicating the widespread occurrence of developmentally convergent evolution in response to human selection. With regard to the molecular genetic approaches used to characterize the basis of this trait, traditional biparental quantitative trait loci mapping remains the most commonly used strategy; however, recent advances in next-generation sequencing technologies are now providing new avenues to map and characterize loss of shattering/dispersal alleles. We anticipate that continued application of these approaches, together with candidate gene analyses informed by known shattering candidate genes from other crops, will lead to a rapid expansion of our understanding of this critical domestication trait.
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Affiliation(s)
- L-F Li
- Washington University in St. Louis, St. Louis, MO, United States; Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, PR China.
| | - K M Olsen
- Washington University in St. Louis, St. Louis, MO, United States.
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