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Suganami M, Kojima S, Yoshida H, Mori M, Kawamura M, Koketsu E, Matsuoka M. Low mutation rate of spontaneous mutants enables detection of causative genes by comparing whole genome sequences. Front Plant Sci 2024; 15:1366413. [PMID: 38638359 PMCID: PMC11024370 DOI: 10.3389/fpls.2024.1366413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 03/19/2024] [Indexed: 04/20/2024]
Abstract
In the early 1900s, mutation breeding to select varieties with desirable traits using spontaneous mutation was actively conducted around the world, including Japan. In rice, the number of fixed mutations per generation was estimated to be 1.38-2.25. Although this low mutation rate was a major problem for breeding in those days, in the modern era with the development of next-generation sequencing (NGS) technology, it was conversely considered to be an advantage for efficient gene identification. In this paper, we proposed an in silico approach using NGS to compare the whole genome sequence of a spontaneous mutant with that of a closely related strain with a nearly identical genome, to find polymorphisms that differ between them, and to identify the causal gene by predicting the functional variation of the gene caused by the polymorphism. Using this approach, we found four causal genes for the dwarf mutation, the round shape grain mutation and the awnless mutation. Three of these genes were the same as those previously reported, but one was a novel gene involved in awn formation. The novel gene was isolated from Bozu-Aikoku, a mutant of Aikoku with the awnless trait, in which nine polymorphisms were predicted to alter gene function by their whole-genome comparison. Based on the information on gene function and tissue-specific expression patterns of these candidate genes, Os03g0115700/LOC_Os03g02460, annotated as a short-chain dehydrogenase/reductase SDR family protein, is most likely to be involved in the awnless mutation. Indeed, complementation tests by transformation showed that it is involved in awn formation. Thus, this method is an effective way to accelerate genome breeding of various crop species by enabling the identification of useful genes that can be used for crop breeding with minimal effort for NGS analysis.
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Affiliation(s)
- Mao Suganami
- Faculty of Food and Agricultural Sciences, Institute of Fermentation Sciences, Fukushima University, Fukushima, Japan
| | - Soichi Kojima
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Hideki Yoshida
- Faculty of Food and Agricultural Sciences, Institute of Fermentation Sciences, Fukushima University, Fukushima, Japan
| | - Masaki Mori
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Mayuko Kawamura
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Eriko Koketsu
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Makoto Matsuoka
- Faculty of Food and Agricultural Sciences, Institute of Fermentation Sciences, Fukushima University, Fukushima, Japan
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Vlahova A, Antonova Z, Rangelov E, Kartulev N, Oparanova V, Gabrovska N, Spasova A, Velizarova S, Shivachev H. Surgical Treatment of Lung Abscess Due to an Awn Aspiration in a 9-Year-Old Child: A Case Report. Children (Basel) 2023; 10:910. [PMID: 37371142 DOI: 10.3390/children10060910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/09/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023]
Abstract
INTRODUCTION Foreign body aspiration is a common condition in the child population and is one of the leading causes of accidental deaths in children. The aspiration of an awn (grass inflorescences) is extremely rare. AIM OF THE STUDY This study aims to describe the symptoms, diagnosis, therapeutic difficulties, and results of the aspiration of grass inflorescence. They are all related to the shape of the awn's head and its behavior in the tracheobronchial tree. CASE DESCRIPTION We present a 9-year-old boy with a history of an awn aspiration and recurrent respiratory infections. After antibiotic and symptomatic treatment, two bronchoscopies were performed, and both showed stenosis and obturation of the segmental and subsegmental bronchi of the left posterior basal segment, but no foreign body was found. After recanalization and continuous medicamentous treatment, a computed tomography (CT) verified the lung abscess. Video-assisted thoracoscopic surgery (VATS) was performed, and an atypical lung resection was conducted. During the surgery, a foreign body-grass inflorescence from the species Hordeum murinum-was found in the resected tissue. The patient recovered uneventfully after the surgery. CONCLUSIONS Grass inflorescence aspiration in the child population is an extremely rare event, and it represents a diagnostic and therapeutic issue. The exact timing of surgery is very important to reduce complications and avoid death.
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Affiliation(s)
- Angelina Vlahova
- Department of Pediatric Surgery, University Multiprofile Hospital for Active Treatment and Emergency Medicine "N.I.Pirogov", 1606 Sofia, Bulgaria
| | - Zdravka Antonova
- Department of Pediatric Surgery, University Multiprofile Hospital for Active Treatment and Emergency Medicine "N.I.Pirogov", 1606 Sofia, Bulgaria
| | - Edmond Rangelov
- Department of Pediatric Surgery, University Multiprofile Hospital for Active Treatment and Emergency Medicine "N.I.Pirogov", 1606 Sofia, Bulgaria
| | - Nikola Kartulev
- Department of Pediatric Surgery, University Multiprofile Hospital for Active Treatment and Emergency Medicine "N.I.Pirogov", 1606 Sofia, Bulgaria
| | - Velichka Oparanova
- Department of Pediatric Surgery, University Multiprofile Hospital for Active Treatment and Emergency Medicine "N.I.Pirogov", 1606 Sofia, Bulgaria
| | - Natalia Gabrovska
- Department of Pediatrics, Medical University-Sofia, Specialized Hospital for Active Treatment of Children's Diseases "Prof. Ivan Mitev", 1606 Sofia, Bulgaria
| | - Albena Spasova
- Department of Pediatrics, Medical University-Sofia, Specialized Hospital for Active Treatment of Children's Diseases "Prof. Ivan Mitev", 1606 Sofia, Bulgaria
| | - Svetlana Velizarova
- Department of Pediatrics, Medical University-Sofia, Specialized Hospital for Active Treatment of Children's Diseases "Prof. Ivan Mitev", 1606 Sofia, Bulgaria
| | - Hristo Shivachev
- Department of Pediatric Surgery, University Multiprofile Hospital for Active Treatment and Emergency Medicine "N.I.Pirogov", 1606 Sofia, Bulgaria
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Bessho-Uehara K, Masuda K, Wang DR, Angeles-Shim RB, Obara K, Nagai K, Murase R, Aoki SI, Furuta T, Miura K, Wu J, Yamagata Y, Yasui H, Kantar MB, Yoshimura A, Kamura T, McCouch SR, Ashikari M. Regulator of Awn Elongation 3, an E3 ubiquitin ligase, is responsible for loss of awns during African rice domestication. Proc Natl Acad Sci U S A 2023; 120:e2207105120. [PMID: 36649409 DOI: 10.1073/pnas.2207105120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Two species of rice have been independently domesticated from different ancestral wild species in Asia and Africa. Comparison of mutations that underlie phenotypic and physiological alterations associated with domestication traits in these species gives insights into the domestication history of rice in both regions. Asian cultivated rice, Oryza sativa, and African cultivated rice, Oryza glaberrima, have been modified and improved for common traits beneficial for humans, including erect plant architecture, nonshattering seeds, nonpigmented pericarp, and lack of awns. Independent mutations in orthologous genes associated with these traits have been documented in the two cultivated species. Contrary to this prevailing model, selection for awnlessness targeted different genes in O. sativa and O. glaberrima. We identify Regulator of Awn Elongation 3 (RAE3) a gene that encodes an E3 ubiquitin ligase and is responsible for the awnless phenotype only in O. glaberrima. A 48-bp deletion may disrupt the substrate recognition domain in RAE3 and diminish awn elongation. Sequencing analysis demonstrated low nucleotide diversity in a ~600-kb region around the derived rae3 allele on chromosome 6 in O. glaberrima compared with its wild progenitor. Identification of RAE3 sheds light on the molecular mechanism underlying awn development and provides an example of how selection on different genes can confer the same domestication phenotype in Asian and African rice.
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Cuellar-Garrido LF, Ruiz-Sanchez E, Vargas-Ponce O, Whipple CJ. Ontogeny and anatomy of Bouteloua (Poaceae: Chloridoideae) species display a basipetal branch formation and a novel modified leaf structure in grasses. Ann Bot 2022; 130:737-747. [PMID: 35961673 PMCID: PMC9670754 DOI: 10.1093/aob/mcac104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Shoot ontogenesis in grasses follows a transition from a vegetative phase into a reproductive phase. Current studies provide insight into how branch and spikelet formation occur during the reproductive phase. However, these studies do not explain all the complex diversity of grass inflorescence forms and are mostly focused on model grasses. Moreover, truncated inflorescences of the non-model grass genus Urochloa (Panicoideae) with formation of primary branches have basipetal initiation of branches. Bouteloua species (Chloridoideae) are non-model grasses that form truncated inflorescences of primary branches with apical vestiges of uncertain homology at the tips of branching events and sterile florets above the lowermost fertile floret. Sterile florets are reduced to rudimentary lemmas composed of three large awns diverging from an awn column. Conflict about the awn column identity of this rudimentary lemma is often addressed in species descriptions of this genus. We test if Bouteloua species can display basipetal initiation of branches and explore the identity of vestiges and the awn column of rudimentary lemmas. METHODS We surveyed the inflorescence ontogeny and branch/awn anatomy of Bouteloua species and compared results with recent ontogenetic studies of chloridoids. KEY RESULTS Bouteloua arizonica has florets with basipetal maturation. Branches display basipetal branch initiation and maturation. Branch vestiges are formed laterally by meristems during early branching events. The spikelet meristem forms the awn column of rudimentary lemmas. Vestiges and sterile floret awns have anatomical similarities to C4 leaves. CONCLUSIONS Basipetal initiation of branches is a novel feature for Chloridoideae grasses. Branch vestiges are novel vegetative grass structures. Sterile floret awn columns are likely to be extensions of the rachilla.
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Affiliation(s)
- Luis Fernando Cuellar-Garrido
- Doctorado en Ciencias en Biosistemática, Ecología y Manejo de Recursos Naturales y Agrícolas (BEMARENA), Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ing. Ramón Padilla Sánchez 2100, Zapopan, Jalisco 45200, México
- Laboratorio Nacional de Identificación y Caracterización Vegetal, Instituto de Botánica, Universidad de Guadalajara, Camino Ing. Ramón Padilla Sánchez 2100, Zapopan, Jalisco 45200, México
| | - Eduardo Ruiz-Sanchez
- Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ing. Ramón Padilla Sánchez 2100, Zapopan, Jalisco 45200, México
- Laboratorio Nacional de Identificación y Caracterización Vegetal, Instituto de Botánica, Universidad de Guadalajara, Camino Ing. Ramón Padilla Sánchez 2100, Zapopan, Jalisco 45200, México
| | - Ofelia Vargas-Ponce
- Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Camino Ing. Ramón Padilla Sánchez 2100, Zapopan, Jalisco 45200, México
- Laboratorio Nacional de Identificación y Caracterización Vegetal, Instituto de Botánica, Universidad de Guadalajara, Camino Ing. Ramón Padilla Sánchez 2100, Zapopan, Jalisco 45200, México
| | - Clinton J Whipple
- Department of Biology, Brigham Young University, 4102 LSB, Provo, UT 84602, USA
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Wu J, Qiao L, Liu Y, Fu B, Nagarajan R, Rauf Y, Jia H, Yan L. Rapid identification and deployment of major genes for flowering time and awn traits in common wheat. Front Plant Sci 2022; 13:992811. [PMID: 36092425 PMCID: PMC9459131 DOI: 10.3389/fpls.2022.992811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/08/2022] [Indexed: 06/01/2023]
Abstract
Molecular markers are developed to accelerate deployment of genes for desirable traits segregated in a bi-parental population of recombinant inbred lines (RILs) or doubled haplotype (DH) lines for mapping. However, it would be the most effective if such markers for multiple traits could be identified in an F2 population. In this study, single nucleotide polymorphisms (SNP) chips were used to identify major genes for heading date and awn in an F2 population without developing RILs or DH lines. The population was generated from a cross between a locally adapted spring wheat cultivar "Ningmaizi119" and a winter wheat cultivar "Tabasco" with a diverse genetic background. It was found that the dominant Vrn-D1 allele could make Ningmaizi119 flowered a few months earlier than Tabasco in the greenhouse and without vernalization. The observed effects of the allele were validated in F3 populations. It was also found that the dominant Ali-A1 allele for awnless trait in Tabasco or the recessive ali-A1 allele for awn trait in Ningmaizi119 was segregated in the F2 population. The allelic variation in the ALI-A1 gene relies not only on the DNA polymorphisms in the promoter but also on gene copy number, with one copy ali-A1 in Ningmaizi119 but two copies Ali-A1 in Tabasco based on RT-PCR results. According to wheat genome sequences, cultivar "Mattis" has two copies Ali-A1 and cultivar "Spelta" has four copies Ali-A in a chromosome that was uncharacterized (ChrUN), in addition to one copy on chromosome 5A. This study rapidly characterized the effects of the dominant Vrn-D1 allele and identified the haplotype of Ali-A1 in gene copy number in the F2 segregation population of common wheat will accelerate their deployment in cycling lines in breeding.
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Affiliation(s)
- Jizhong Wu
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Linyi Qiao
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Ying Liu
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Bisheng Fu
- Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Ragupathi Nagarajan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Yahya Rauf
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Haiyan Jia
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
- The Applied Plant Genomics Laboratory, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Liuling Yan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, United States
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Wang Z, Deng Z, Kong X, Wang F, Guan J, Cui D, Sun G, Liao R, Fu M, Che Y, Hao C, Geng S, Zhang X, Zhou P, Mao L, Liu S, Li A. InDels Identification and Association Analysis with Spike and Awn Length in Chinese Wheat Mini-Core Collection. Int J Mol Sci 2022; 23:5587. [PMID: 35628397 DOI: 10.3390/ijms23105587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/17/2022] Open
Abstract
Diversity surveys of germplasm are important for gaining insight into the genomic basis for crop improvement; especially InDels, which are poorly understood in hexaploid common wheat. Here, we describe a map of 89,923 InDels from exome sequencing of 262 accessions of a Chinese wheat mini-core collection. Population structure analysis, principal component analysis and selective sweep analysis between landraces and cultivars were performed. Further genome-wide association study (GWAS) identified five QTL (Quantitative Trait Loci) that were associated with spike length, two of them, on chromosomes 2B and 6A, were detected in 10 phenotypic data sets. Assisted with RNA-seq data, we identified 14 and 21 genes, respectively that expressed in spike and rachis within the two QTL regions that can be further investigated for candidate genes discovery. Moreover, InDels were found to be associated with awn length on chromosomes 5A, 6B and 4A, which overlapped with previously reported genetic loci B1 (Tipped 1), B2 (Tipped 2) and Hd (Hooded). One of the genes TaAGL6 that was previously shown to affect floral organ development was found at the B2 locus to affect awn length development. Our study shows that trait-associated InDels may contribute to wheat improvement and may be valuable molecular markers for future wheat breeding.
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Liu T, Shi X, Wang J, Song J, Xiao E, Wang Y, Gao X, Nan W, Wang Z. Mapping and Characterization of QTLs for Awn Morphology Using Crosses between "Double-Awn" Wheat 4045 and Awnless Wheat Zhiluowumai. Plants (Basel) 2021; 10:2588. [PMID: 34961059 PMCID: PMC8703630 DOI: 10.3390/plants10122588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/20/2021] [Accepted: 11/21/2021] [Indexed: 12/03/2022]
Abstract
Awns play important roles in seed dispersal, protection against predators, and photosynthesis. The characterization of genes related to the formation of awns helps understand the regulation mechanisms of awn development. In the present study, the "double-awn" wheat 4045, which features super-long lemma awns and long glume awns, and an awnless wheat line, Zhiluowumai, were used to investigate QTLs or genes involved in awn development. QTL analysis identified three loci-Qawn-1D, Qawn-5A, and Qawn-7B-using a population of 101 4045 × ZLWM F2 plants. Fine mapping with a total of 9018 progenies narrowed the mapping interval of Qawn-5A to an 809-kb region, which was consistent with the B1 locus, containing five genes on chromosome 5AL. Gene structure and expression analysis indicated that TraesCS5A02G542800 was the causal gene, which was subsequently verified by overexpression of TraesCS5A02G542800 in a "double-awn" wheat, Yangmai20. The retained "double-awn" phenotype of transgenic plants suggested that B1 represses the elongation but does not influence the emergence of the awns. Moreover, 4045 harbors a new allele of B1 with a 261-bp insertion in the promoter region and a lack of the EAR2 motif in the encoding region, which influences several important agronomic traits. In this study, we identify two novel QTLs and a novel allele of B1, providing new resources for exploration of awn development.
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Affiliation(s)
- Tianxiang Liu
- Department of Agronomy, Northwest Agriculture and Forestry University, Xianyang 712100, China; (T.L.); (X.S.); (J.W.); (E.X.); (Y.W.); (X.G.)
| | - Xue Shi
- Department of Agronomy, Northwest Agriculture and Forestry University, Xianyang 712100, China; (T.L.); (X.S.); (J.W.); (E.X.); (Y.W.); (X.G.)
| | - Jun Wang
- Department of Agronomy, Northwest Agriculture and Forestry University, Xianyang 712100, China; (T.L.); (X.S.); (J.W.); (E.X.); (Y.W.); (X.G.)
| | - Jiawang Song
- Key Laboratory of Plant Development and Stress Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China;
| | - Enshi Xiao
- Department of Agronomy, Northwest Agriculture and Forestry University, Xianyang 712100, China; (T.L.); (X.S.); (J.W.); (E.X.); (Y.W.); (X.G.)
| | - Yong Wang
- Department of Agronomy, Northwest Agriculture and Forestry University, Xianyang 712100, China; (T.L.); (X.S.); (J.W.); (E.X.); (Y.W.); (X.G.)
| | - Xin Gao
- Department of Agronomy, Northwest Agriculture and Forestry University, Xianyang 712100, China; (T.L.); (X.S.); (J.W.); (E.X.); (Y.W.); (X.G.)
| | - Wenzhi Nan
- College of Life Sciences, Yulin University, Yulin 719000, China
| | - Zhonghua Wang
- Department of Agronomy, Northwest Agriculture and Forestry University, Xianyang 712100, China; (T.L.); (X.S.); (J.W.); (E.X.); (Y.W.); (X.G.)
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Zhou L, Zhu C, Fang X, Liu H, Zhong S, Li Y, Liu J, Song Y, Jian X, Lin Z. Gene duplication drove the loss of awn in sorghum. Mol Plant 2021; 14:1831-1845. [PMID: 34271177 DOI: 10.1016/j.molp.2021.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/18/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Loss of the awn in some cereals, including sorghum, is a key transition during cereal domestication or improvement that has facilitated grain harvest and storage. The genetic basis of awn loss in sorghum during domestication or improvement remains unknown. Here, we identified the awn1 gene encoding a transcription factor with the ALOG domain that is responsible for awn loss during sorghum domestication or improvement. awn1 arose from a gene duplication on chromosome 10 that translocated to chromosome 3, recruiting a new promoter from the neighboring intergenic region filled with "noncoding DNA" and recreating the first exon and intron. awn1 acquired high expression after duplication and represses the elongation of awns in domesticated sorghum. Comparative mapping revealed high collinearity at the awn1 paralog locus on chromosome 10 across cereals, and awn growth and development were successfully reactivated on the rice spikelet by inactivating the rice awn1 ortholog. RNA-seq and DAP-seq revealed that as a transcriptional repressor, AWN1 bound directly to a motif in the regulatory regions of three MADS genes related to flower development and two genes, DL and LKS2, involved in awn development. AWN1 downregulates the expression of these genes, thereby repressing awn elongation. The preexistence of regulatory elements in the neighboring intergenic region of awn1 before domestication implicates that noncoding DNA may serve as a treasure trove for evolution during sorghum adaptation to a changing world. Taken together, our results suggest that gene duplication can rapidly drive the evolution of gene regulatory networks in plants.
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Affiliation(s)
- Leina Zhou
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Can Zhu
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Xiaojian Fang
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Hangqin Liu
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Shuyang Zhong
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Yan Li
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Jiacheng Liu
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Yang Song
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Xing Jian
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Zhongwei Lin
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China.
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Abstract
Barley awns are highly active in photosynthesis and account for 30–50% of grain weight in barley. They are diverse in length, ranging from long to awnless, and in shape from straight to hooded or crooked. Their diversity and importance have intrigued geneticists for several decades. A large collection of awnness mutants are available—over a dozen of them have been mapped on chromosomes and a few recently cloned. Different awnness genes interact with each other to produce diverse awn phenotypes. With the availability of the sequenced barley genome and application of new mapping and gene cloning strategies, it will now be possible to identify and clone more awnness genes. A better understanding of the genetic basis of awn diversity will greatly facilitate development of new barley cultivars with improved yield, adaptability and sustainability.
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Affiliation(s)
- Biguang Huang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Fujian Collegiate Key Laboratory of Applied Plant Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Weiren Wu
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Z.H.)
| | - Zonglie Hong
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
- Correspondence: (W.W.); (Z.H.)
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10
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Huang B, Wu W, Hong Z. Genetic Interactions of Awnness Genes in Barley. Genes (Basel) 2021; 12:606. [PMID: 33924025 DOI: 10.3390/genes12040606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/08/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
Awns are extending structures from lemmas in grasses and are very active in photosynthesis, contributing directly to the filling of the developing grain. Barley (Hordeum vulgare L.) awns are highly diverse in shape and length and are known to be controlled by multiple awn-related genes. The genetic effects of these genes on awn diversity and development in barley are multiplexed and include complementary effect, cumulative effect, duplicate effect, recessive epistasis, dominant epistasis, and inhibiting effect, each giving a unique modified Mendelian ratio of segregation. The complexity of gene interactions contributes to the awn diversity in barley. Excessive gene interactions create a challenging task for genetic mapping and specific strategies have to be developed for mapping genes with specific interactive effects. Awn gene interactions can occur at different levels of gene expression, from the transcription factor-mediated gene transcription to the regulation of enzymes and metabolic pathways. A better understanding of gene interactions will greatly facilitate deciphering the genetic mechanisms underlying barley awn diversity and development.
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Bessho-Uehara K, Yamagata Y, Takashi T, Makino T, Yasui H, Yoshimura A, Ashikari M. Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species. Plants (Basel) 2021; 10:725. [PMID: 33917982 DOI: 10.3390/plants10040725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022]
Abstract
Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the novel loci regulating awn development and understand the conservation of genes in other wild rice relatives belonging to the AA genome group, we analyzed the chromosome segment substitution lines (CSSL). In this study, we compared a number of CSSL sets derived by crossing wild rice species in the AA genome group with the cultivated species Oryza sativa ssp. japonica. Two loci on chromosomes 7 and 11 were newly discovered to be responsible for awn development. We also found wild relatives that were used as donor parents of the CSSLs carrying the functional alleles responsible for awn elongation, REGULATOR OF AWN ELONGATION 1 (RAE1) and RAE2. To understand the conserveness of RAE1 and RAE2 in wild rice relatives, we analyzed RAE1 and RAE2 sequences of 175 accessions among diverse AA genome species retrieved from the sequence read archive (SRA) database. Comparative sequence analysis demonstrated that most wild rice AA genome species maintained functional RAE1 and RAE2, whereas most Asian rice cultivars have lost either or both functions. In addition, some different loss-of-function alleles of RAE1 and RAE2 were found in Asian cultivated species. These findings suggest that different combinations of dysfunctional alleles of RAE1 and RAE2 were selected after the speciation of O. sativa, and that two-step loss of function in RAE1 and RAE2 contributed to awnlessness in Asian cultivated rice.
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12
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Wang D, Yu K, Jin D, Sun L, Chu J, Wu W, Xin P, Gregová E, Li X, Sun J, Yang W, Zhan K, Zhang A, Liu D. Natural variations in the promoter of Awn Length Inhibitor 1 (ALI-1) are associated with awn elongation and grain length in common wheat. Plant J 2020; 101:1075-1090. [PMID: 31628879 DOI: 10.1111/tpj.14575] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/27/2019] [Indexed: 06/10/2023]
Abstract
Wheat awn plays a vital role in photosynthesis, grain production, and drought tolerance. However, the systematic identification or cloning of genes controlling wheat awn development is seldom reported. Here, we conducted a genome-wide association study (GWAS) with 364 wheat accessions and identified 26 loci involved in awn length development, including previously characterized B1, B2, Hd, and several rice homologs. The dominant awn suppressor B1 was fine mapped to a 125-kb physical interval, and a C2 H2 zinc finger protein Awn Length Inhibitor 1 (ALI-1) was confirmed to be the underlying gene of the B1 locus through the functional complimentary test with native awnless allele. ALI-1 expresses predominantly in the developing spike of awnless individuals, transcriptionally suppressing downstream genes. ALI-1 reduces cytokinin content and simultaneously restrains cytokinin signal transduction, leading to a stagnation of cell proliferation and reduction of cell numbers during awn development. Polymorphisms of four single nucleotide polymorphisms (SNPs) located in ALI-1 promoter region are diagnostic for the B1/b1 genotypes, and these SNPs are associated with awn length (AL), grain length (GL) and thousand-grain weight (TGW). More importantly, ali-1 was observed to increase grain length in wheat, which is a valuable attribute of awn on grain weight, aside from photosynthesis. Therefore, ALI-1 pleiotropically regulates awn and grain development, providing an alternative for grain yield improvement and addressing future climate changes.
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Affiliation(s)
- Dongzhi Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Kang Yu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- BGI Institute of Applied Agriculture, BGI-Agro, Shenzhen, 518120, China
| | - Di Jin
- College of Agronomy/The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, Zhengzhou, 450002, China
| | - Linhe Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenying Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Peiyong Xin
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Edita Gregová
- National Agricultural and Food centre, Research Institute of Plant Production, Bratislavská cesta 122, 921 68, Piešťany, Slovakia
| | - Xin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kehui Zhan
- College of Agronomy/The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, Zhengzhou, 450002, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Biology and Agriculture Research Center, University of Science and Technology Beijing, Beijing, 100024, China
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13
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Pongrac P, Arčon I, Castillo-Michel H, Vogel-Mikuš K. Mineral Element Composition in Grain of Awned and Awnletted Wheat ( Triticum aestivum L.) Cultivars: Tissue-Specific Iron Speciation and Phytate and Non-Phytate Ligand Ratio. Plants (Basel) 2020; 9:plants9010079. [PMID: 31936205 PMCID: PMC7020463 DOI: 10.3390/plants9010079] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/04/2020] [Accepted: 01/06/2020] [Indexed: 11/16/2022]
Abstract
In wheat (Triticum aestivum L.), the awns—the bristle-like structures extending from lemmas—are photosynthetically active. Compared to awned cultivars, awnletted cultivars produce more grains per unit area and per spike, resulting in significant reduction in grain size, but their mineral element composition remains unstudied. Nine awned and 11 awnletted cultivars were grown simultaneously in the field. With no difference in 1000-grain weight, a larger calcium and manganese—but smaller iron (Fe) concentrations—were found in whole grain of awned than in awnletted cultivars. Micro X-ray absorption near edge structure analysis of different tissues of frozen-hydrated grain cross-sections revealed that differences in total Fe concentration were not accompanied by differences in Fe speciation (64% of Fe existed as ferric and 36% as ferrous species) or Fe ligands (53% were phytate and 47% were non-phytate ligands). In contrast, there was a distinct tissue-specificity with pericarp containing the largest proportion (86%) of ferric species and nucellar projection (49%) the smallest. Phytate ligand was predominant in aleurone, scutellum and embryo (72%, 70%, and 56%, respectively), while nucellar projection and pericarp contained only non-phytate ligands. Assuming Fe bioavailability depends on Fe ligands, we conclude that Fe bioavailability from wheat grain is tissue specific.
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Affiliation(s)
- Paula Pongrac
- Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; (I.A.); (K.V.-M.)
- Correspondence: ; Tel.: +386-51-222-963; Fax: +386-477-31-51
| | - Iztok Arčon
- Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; (I.A.); (K.V.-M.)
- Laboratory for quantum optics, University of Nova Gorica, Vipavska 13, SI-5000 Nova Gorica, Slovenia
| | | | - Katarina Vogel-Mikuš
- Jožef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia; (I.A.); (K.V.-M.)
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
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14
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Huang D, Zheng Q, Melchkart T, Bekkaoui Y, Konkin DJF, Kagale S, Martucci M, You FM, Clarke M, Adamski NM, Chinoy C, Steed A, McCartney CA, Cutler AJ, Nicholson P, Feurtado JA. Dominant inhibition of awn development by a putative zinc-finger transcriptional repressor expressed at the B1 locus in wheat. New Phytol 2020; 225:340-355. [PMID: 31469444 PMCID: PMC6916588 DOI: 10.1111/nph.16154] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/16/2019] [Indexed: 05/22/2023]
Abstract
Awns, bristle-like structures extending from grass lemmas, provide protection against predators, contribute to photosynthesis and aid in grain dispersal. In wheat, selection of awns with minimal extension, termed awnletted, has occurred during domestication by way of loci that dominantly inhibit awn development, such as Tipped1 (B1), Tipped2 (B2), and Hooded (Hd). Here we identify and characterize the B1 gene. B1 was identified using bulked segregant RNA-sequencing of an F2 durum wheat population and through deletion mapping of awned bread wheat mutants. Functional characterization was accomplished by gene overexpression while haplotype analyses assessed B1 polymorphisms and genetic variation. Located on chromosome 5A, B1 is a C2H2 zinc finger encoding gene with ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motifs. Constitutive overexpression of B1 in awned wheat produced an awnletted phenotype with pleiotropic effects on plant height and fertility. Transcriptome analysis of B1 overexpression plants suggests a role as transcriptional repressor, putatively targeting pathways involved in cell proliferation. Haplotype analysis revealed a conserved B1 coding region with proximal polymorphisms and supported the contention that B1 is mainly responsible for awnletted wheats globally. B1, predominantly responsible for awn inhibition in wheat, encodes a C2H2 zinc finger protein with EAR motifs which putatively functions as a transcriptional repressor.
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Affiliation(s)
- Daiqing Huang
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Qian Zheng
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Tancey Melchkart
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Yasmina Bekkaoui
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - David J. F. Konkin
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Sateesh Kagale
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Martial Martucci
- Morden Research and Development CentreAgriculture and Agri‐Food Canada101 Route 100MordenMBR6M 1Y5Canada
| | - Frank M. You
- Ottawa Research and Development CentreAgriculture and Agri‐Food Canada960 Carling AvenueOttawaONK1A 0C6Canada
| | - Martha Clarke
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - Nikolai M. Adamski
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - Catherine Chinoy
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - Andrew Steed
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - Curt A. McCartney
- Morden Research and Development CentreAgriculture and Agri‐Food Canada101 Route 100MordenMBR6M 1Y5Canada
| | - Adrian J. Cutler
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
| | - Paul Nicholson
- Department of Crop GeneticsJohn Innes CentreNorwich Research Park, Colney LaneNorwichNR4 7UHUK
| | - J. Allan Feurtado
- Aquatic and Crop Resource DevelopmentNational Research Council of CanadaSaskatoonSKS7N 0W9Canada
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15
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Bessho-Uehara K, Wang DR, Furuta T, Minami A, Nagai K, Gamuyao R, Asano K, Angeles-Shim RB, Shimizu Y, Ayano M, Komeda N, Doi K, Miura K, Toda Y, Kinoshita T, Okuda S, Higashiyama T, Nomoto M, Tada Y, Shinohara H, Matsubayashi Y, Greenberg A, Wu J, Yasui H, Yoshimura A, Mori H, McCouch SR, Ashikari M. Loss of function at RAE2, a previously unidentified EPFL, is required for awnlessness in cultivated Asian rice. Proc Natl Acad Sci U S A 2016; 113:8969-74. [PMID: 27466405 PMCID: PMC4987784 DOI: 10.1073/pnas.1604849113] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Domestication of crops based on artificial selection has contributed numerous beneficial traits for agriculture. Wild characteristics such as red pericarp and seed shattering were lost in both Asian (Oryza sativa) and African (Oryza glaberrima) cultivated rice species as a result of human selection on common genes. Awnedness, in contrast, is a trait that has been lost in both cultivated species due to selection on different sets of genes. In a previous report, we revealed that at least three loci regulate awn development in rice; however, the molecular mechanism underlying awnlessness remains unknown. Here we isolate and characterize a previously unidentified EPIDERMAL PATTERNING FACTOR-LIKE (EPFL) family member named REGULATOR OF AWN ELONGATION 2 (RAE2) and identify one of its requisite processing enzymes, SUBTILISIN-LIKE PROTEASE 1 (SLP1). The RAE2 precursor is specifically cleaved by SLP1 in the rice spikelet, where the mature RAE2 peptide subsequently induces awn elongation. Analysis of RAE2 sequence diversity identified a highly variable GC-rich region harboring multiple independent mutations underlying protein-length variation that disrupt the function of the RAE2 protein and condition the awnless phenotype in Asian rice. Cultivated African rice, on the other hand, retained the functional RAE2 allele despite its awnless phenotype. Our findings illuminate the molecular function of RAE2 in awn development and shed light on the independent domestication histories of Asian and African cultivated rice.
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Affiliation(s)
- Kanako Bessho-Uehara
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Diane R Wang
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853-1901
| | - Tomoyuki Furuta
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Anzu Minami
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Rico Gamuyao
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Kenji Asano
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Rosalyn B Angeles-Shim
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Yoshihiro Shimizu
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Madoka Ayano
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Norio Komeda
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Kazuyuki Doi
- Graduate School of Agriculture, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Kotaro Miura
- Faculty of Biotechnology, Fukui Prefectural University, 4-1-1 Eiheiji-Town, Fukui 910-1195, Japan
| | - Yosuke Toda
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Satohiro Okuda
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Mika Nomoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Yasuomi Tada
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Hidefumi Shinohara
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Yoshikatsu Matsubayashi
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8602, Japan
| | - Anthony Greenberg
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853-1901
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan
| | - Hideshi Yasui
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Atsushi Yoshimura
- Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
| | - Hitoshi Mori
- Graduate School of Agriculture, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan;
| | - Susan R McCouch
- Section of Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY 14853-1901;
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan;
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16
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Gu B, Zhou T, Luo J, Liu H, Wang Y, Shangguan Y, Zhu J, Li Y, Sang T, Wang Z, Han B. An-2 Encodes a Cytokinin Synthesis Enzyme that Regulates Awn Length and Grain Production in Rice. Mol Plant 2015; 8:1635-50. [PMID: 26283047 DOI: 10.1016/j.molp.2015.08.001] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 07/17/2015] [Accepted: 08/03/2015] [Indexed: 05/03/2023]
Abstract
A wide range of morphological and physiological traits have changed between cultivated rice Oryza sativa and wild rice Oryza rufipogon under domestication. Here, we report cloning of the An-2 gene, encoding the Lonely Guy Like protein 6 (OsLOGL6), which catalyzes the final step of cytokinin synthesis in O. rufipogon. The near-isogenic line harboring a wild allele of An-2 in the genetic background of the awnless indica Guangluai 4 shows that An-2 promotes awn elongation by enhancing cell division, but decreases grain production by reducing grains per panicle and tillers per plant. We reveal that a genetic variation in the An-2 locus has a large impact on reducing awn length and increasing tiller and grain numbers in domesticated rice. Analysis of gene expression patterns suggests that An-1 regulates the formation of awn primordial, and An-2 promotes awn elongation. Nucleotide diversity of the An-2 locus in cultivated rice was found to be significantly reduced compared with that of wild rice, suggesting that the An-2 locus was subjected to artificial selection. We therefore propose that the selection of genetic variation in An-2 was due to reduced awn length and increased grain yield in cultivated rice.
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Affiliation(s)
- Benguo Gu
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Taoying Zhou
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jianghong Luo
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Hui Liu
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yongchun Wang
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yingying Shangguan
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Jingjie Zhu
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Yan Li
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Tao Sang
- State Key Laboratory of Systematic and Evolutionary Botany, Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Zixuan Wang
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Bin Han
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
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17
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Furuta T, Komeda N, Asano K, Uehara K, Gamuyao R, Angeles-Shim RB, Nagai K, Doi K, Wang DR, Yasui H, Yoshimura A, Wu J, McCouch SR, Ashikari M. Convergent Loss of Awn in Two Cultivated Rice Species Oryza sativa and Oryza glaberrima Is Caused by Mutations in Different Loci. G3 (Bethesda) 2015; 5:2267-74. [PMID: 26338659 DOI: 10.1534/g3.115.020834] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A long awn is one of the distinct morphological features of wild rice species. This organ is thought to aid in seed dispersal and prevent predation by animals. Most cultivated varieties of Oryza sativa and Oryza glaberrima, however, have lost the ability to form long awns. The causal genetic factors responsible for the loss of awn in these two rice species remain largely unknown. Here, we evaluated three sets of chromosome segment substitution lines (CSSLs) in a common O. sativa genetic background (cv. Koshihikari) that harbor genomic fragments from Oryza nivara, Oryza rufipogon, and Oryza glaberrima donors. Phenotypic analyses of these libraries revealed the existence of three genes, Regulator of Awn Elongation 1 (RAE1), RAE2, and RAE3, involved in the loss of long awns in cultivated rice. Donor segments at two of these genes, RAE1 and RAE2, induced long awn formation in the CSSLs whereas an O. sativa segment at RAE3 induced long awn formation in O. glaberrima. These results suggest that the two cultivated rice species, O. sativa and O. glaberrima, have taken independent paths to become awnless.
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18
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Toriba T, Hirano HY. The DROOPING LEAF and OsETTIN2 genes promote awn development in rice. Plant J 2014; 77:616-26. [PMID: 24330191 DOI: 10.1111/tpj.12411] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 11/27/2013] [Accepted: 12/05/2013] [Indexed: 05/18/2023]
Abstract
The awn is a long needle-like appendage that, in some grass species, is formed on the lemma that encloses floral organs together with the palea. In rice, most wild species and most strains of Oryza sativa ssp. indica generate an awn, whereas most strains of O. sativa ssp. japonica do not. In japonica, the long-awn characteristic appears to have been lost during domestication and breeding programs. Here, we found that the genes DROOPING LEAF (DL) and OsETTIN2 (OsETT2) are involved in awn development in the awned indica strain Kasalath. Genetic analyses and RNA-silencing experiments indicate that DL and OsETT2 act independently in awn formation, and that either gene alone is not sufficient for awn development. Scanning electron microscopy revealed that the top region of the lemma (a putative awn primordium) is larger in an awned floret than in an awnless floret. OsETT2 is expressed in the awn primordium in the awned indica floret, but not in the awnless japonica floret except in the provascular bundle. DL is expressed underneath the primordium at similar levels in both indica and japonica florets, suggesting non-cell-autonomous action. We hypothesize that loss of expression of OsETT2 in the awn primordium is probably associated with the failure of awn formation in japonica strains.
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Affiliation(s)
- Taiyo Toriba
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
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