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Izawa T. Reloading DNA History in Rice Domestication. PLANT & CELL PHYSIOLOGY 2022; 63:1529-1539. [PMID: 35656860 PMCID: PMC9680854 DOI: 10.1093/pcp/pcac073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 04/14/2022] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Although crop domestication is a prehistoric event, DNA (or genome) sequences of modern cultivars and the accession lines of wild relatives contain information regarding the history of crop domestication and the breeding process. Accordingly, with plentiful genomic data, many new findings have been obtained concerning the crop domestication process, for which various (some controversial) interpretations exist. Since approximately 20 years ago, dozens of quantitative trait genes (QTGs) related to the domestication process have been cloned from several crops including rice, a global staple food. However, the determination of how and when these QTGs were involved in rice domestication requires a precise understanding of the DNA code. In addition to the identification of domestication-related QTGs, large-scale rice genome analysis based on short-read Illumina data (but with shallow depth) including more than 1,000 rice cultivars and hundreds of wild rice (or Oryza rufipogon) lines, along with extensive genome analysis including more than 3,000 cultivars with sufficient Illumina data, has been reported. From these data, the genome-wide changes during rice domestication have been explained. However, these genome-wide changes were not interpreted based on QTG changes for domestication-related traits during rice domestication. In addition, a substantial gap remains between the archeological hypothesis based on ancient relics and findings from DNA variations among current cultivars. Thus, this review reconsiders the present status of rice domestication research from a biologist's perspective.
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Kuzbakova M, Khassanova G, Oshergina I, Ten E, Jatayev S, Yerzhebayeva R, Bulatova K, Khalbayeva S, Schramm C, Anderson P, Sweetman C, Jenkins CLD, Soole KL, Shavrukov Y. Height to first pod: A review of genetic and breeding approaches to improve combine harvesting in legume crops. FRONTIERS IN PLANT SCIENCE 2022; 13:948099. [PMID: 36186054 PMCID: PMC9523450 DOI: 10.3389/fpls.2022.948099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/17/2022] [Indexed: 06/16/2023]
Abstract
Height from soil at the base of plant to the first pod (HFP) is an important trait for mechanical harvesting of legume crops. To minimise the loss of pods, the HFP must be higher than that of the blades of most combine harvesters. Here, we review the genetic control, morphology, and variability of HFP in legumes and attempt to unravel the diverse terminology for this trait in the literature. HFP is directly related to node number and internode length but through different mechanisms. The phenotypic diversity and heritability of HFP and their correlations with plant height are very high among studied legumes. Only a few publications describe a QTL analysis where candidate genes for HFP with confirmed gene expression have been mapped. They include major QTLs with eight candidate genes for HFP, which are involved in auxin transport and signal transduction in soybean [Glycine max (L.) Merr.] as well as MADS box gene SOC1 in Medicago trancatula, and BEBT or WD40 genes located nearby in the mapped QTL in common bean (Phaseolus vulgaris L.). There is no information available about simple and efficient markers associated with HFP, which can be used for marker-assisted selection for this trait in practical breeding, which is still required in the nearest future. To our best knowledge, this is the first review to focus on this significant challenge in legume-based cropping systems.
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Affiliation(s)
- Marzhan Kuzbakova
- Faculty of Agronomy, S. Seifullin Kazakh Agro Technical University, Nur-Sultan, Kazakhstan
| | - Gulmira Khassanova
- Faculty of Agronomy, S. Seifullin Kazakh Agro Technical University, Nur-Sultan, Kazakhstan
| | - Irina Oshergina
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Evgeniy Ten
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh Agro Technical University, Nur-Sultan, Kazakhstan
| | - Raushan Yerzhebayeva
- Kazakh Research Institute of Agriculture and Plant Growing, Almalybak, Kazakhstan
| | - Kulpash Bulatova
- Kazakh Research Institute of Agriculture and Plant Growing, Almalybak, Kazakhstan
| | - Sholpan Khalbayeva
- Kazakh Research Institute of Agriculture and Plant Growing, Almalybak, Kazakhstan
| | - Carly Schramm
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Peter Anderson
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Crystal Sweetman
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Colin L. D. Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Kathleen L. Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
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Lu Y, Chuan M, Wang H, Chen R, Tao T, Zhou Y, Xu Y, Li P, Yao Y, Xu C, Yang Z. Genetic and molecular factors in determining grain number per panicle of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:964246. [PMID: 35991390 PMCID: PMC9386260 DOI: 10.3389/fpls.2022.964246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
It was suggested that the most effective way to improve rice grain yield is to increase the grain number per panicle (GN) through the breeding practice in recent decades. GN is a representative quantitative trait affected by multiple genetic and environmental factors. Understanding the mechanisms controlling GN has become an important research field in rice biotechnology and breeding. The regulation of rice GN is coordinately controlled by panicle architecture and branch differentiation, and many GN-associated genes showed pleiotropic effect in regulating tillering, grain size, flowering time, and other domestication-related traits. It is also revealed that GN determination is closely related to vascular development and the metabolism of some phytohormones. In this review, we summarize the recent findings in rice GN determination and discuss the genetic and molecular mechanisms of GN regulators.
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Affiliation(s)
- Yue Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Mingli Chuan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Hanyao Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Rujia Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Tianyun Tao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Yong Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yang Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Pengcheng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Youli Yao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Chenwu Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zefeng Yang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
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Zhang B, Chen S, Liu J, Yan YB, Chen J, Li D, Liu JY. A High-Quality Haplotype-Resolved Genome of Common Bermudagrass ( Cynodon dactylon L.) Provides Insights Into Polyploid Genome Stability and Prostrate Growth. FRONTIERS IN PLANT SCIENCE 2022; 13:890980. [PMID: 35548270 PMCID: PMC9081840 DOI: 10.3389/fpls.2022.890980] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 04/04/2022] [Indexed: 05/03/2023]
Abstract
Common bermudagrass (Cynodon dactylon L.) is an important perennial warm-season turfgrass species with great economic value. However, the reference genome is still deficient in C. dactylon, which severely impedes basic studies and breeding studies. In this study, a high-quality haplotype-resolved genome of C. dactylon cultivar Yangjiang was successfully assembled using a combination of multiple sequencing strategies. The assembled genome is approximately 1.01 Gb in size and is comprised of 36 pseudo chromosomes belonging to four haplotypes. In total, 76,879 protein-coding genes and 529,092 repeat sequences were annotated in the assembled genome. Evolution analysis indicated that C. dactylon underwent two rounds of whole-genome duplication events, whereas syntenic and transcriptome analysis revealed that global subgenome dominance was absent among the four haplotypes. Genome-wide gene family analyses further indicated that homologous recombination-regulating genes and tiller-angle-regulating genes all showed an adaptive evolution in C. dactylon, providing insights into genome-scale regulation of polyploid genome stability and prostrate growth. These results not only facilitate a better understanding of the complex genome composition and unique plant architectural characteristics of common bermudagrass, but also offer a valuable resource for comparative genome analyses of turfgrasses and other plant species.
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Affiliation(s)
- Bing Zhang
- School of Life Sciences, Tsinghua University, Beijing, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Si Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jianxiu Liu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Yong-Bin Yan
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Jingbo Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Dandan Li
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, China
| | - Jin-Yuan Liu
- School of Life Sciences, Tsinghua University, Beijing, China
- *Correspondence: Jin-Yuan Liu,
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Inagaki N, Asami H, Hirabayashi H, Uchino A, Imaizumi T, Ishimaru K. A Rice Ancestral Genetic Resource Conferring Ideal Plant Shapes for Vegetative Growth and Weed Suppression. FRONTIERS IN PLANT SCIENCE 2021; 12:748531. [PMID: 34899776 PMCID: PMC8664436 DOI: 10.3389/fpls.2021.748531] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 10/28/2021] [Indexed: 06/02/2023]
Abstract
To maximize crop growth, crops need to capture sunlight efficiently. This property is primarily influenced by the shape of the crops such as the angle, area, and arrangement of leaves. We constructed a rice (Oryza sativa L.) inbred line that displayed an ideal transition of plant shapes in terms of sunlight receiving efficiency. During vegetative growth, this line exhibited tiller spreading with increased tiller number, which formed a parabolic antenna-like structure. The architecture probably improved light reception efficiency of individuals compared with the recurrent parent. The line achieved not only acceleration of the vegetative growth, but also significant suppression of weed growth under the canopy. The increased light reception efficiency of the line has consequently reduced the amount of incident light to the ground and supplied significant competitiveness against weeds. The spread tillers became erect from the entry of the reproductive growth phase, adaptively sustaining light reception efficiency in thicker stands. The line carries a small chromosomal segment from Oryza rufipogon Griff., a putative progenitor of Asian cultivated rice. The introduced chromosome segment had little effect on grain yield and quality. Our results shed light on potentials hidden in the wild rice chromosome segment to achieve the valuable traits.
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Affiliation(s)
- Noritoshi Inagaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Hidenori Asami
- Western Region Agricultural Research Center (Kinki, Chugoku, and Shikoku Regions), National Agriculture and Food Research Organization (NARO), Fukuyama, Japan
- Institute for Plant Protection, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Hideyuki Hirabayashi
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Akira Uchino
- Central Region Agricultural Research Center (Kanto, Tokai, and Hokuriku Regions), National Agriculture and Food Research Organization (NARO), Tsu, Japan
| | - Toshiyuki Imaizumi
- Institute for Plant Protection, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Ken Ishimaru
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
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