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Wang J, Li S, Lan L, Xie M, Cheng S, Gan X, Huang G, Du G, Yu K, Ni X, Liu B, Peng G. De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance. BMC PLANT BIOLOGY 2021; 21:271. [PMID: 34118890 PMCID: PMC8196518 DOI: 10.1186/s12870-021-03003-8] [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: 11/24/2020] [Accepted: 05/04/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Setaria italica is the second-most widely planted species of millets in the world and an important model grain crop for the research of C4 photosynthesis and abiotic stress tolerance. Through three genomes assembly and annotation efforts, all genomes were based on next generation sequencing technology, which limited the genome continuity. RESULTS Here we report a high-quality whole-genome of new cultivar Huagu11, using single-molecule real-time sequencing and High-throughput chromosome conformation capture (Hi-C) mapping technologies. The total assembly size of the Huagu11 genome was 408.37 Mb with a scaffold N50 size of 45.89 Mb. Compared with the other three reported millet genomes based on the next generation sequencing technology, the Huagu11 genome had the highest genomic continuity. Intraspecies comparison showed about 94.97 and 94.66% of the Yugu1 and Huagu11 genomes, respectively, were able to be aligned as one-to-one blocks with four chromosome inversion. The Huagu11 genome contained approximately 19.43 Mb Presence/absence Variation (PAV) with 627 protein-coding transcripts, while Yugu1 genomes had 20.53 Mb PAV sequences encoding 737 proteins. Overall, 969,596 Single-nucleotide polymorphism (SNPs) and 156,282 insertion-deletion (InDels) were identified between these two genomes. The genome comparison between Huagu11 and Yugu1 should reflect the genetic identity and variation between the cultivars of foxtail millet to a certain extent. The Ser-626-Aln substitution in acetohydroxy acid synthase (AHAS) was found to be relative to the imazethapyr tolerance in Huagu11. CONCLUSIONS A new improved high-quality reference genome sequence of Setaria italica was assembled, and intraspecies genome comparison determined the genetic identity and variation between the cultivars of foxtail millet. Based on the genome sequence, it was inferred that the Ser-626-Aln substitution in AHAS was responsible for the imazethapyr tolerance in Huagu11. The new improved reference genome of Setaria italica will promote the genic and genomic studies of this species and be beneficial for cultivar improvement.
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Affiliation(s)
- Jie Wang
- Genetic, Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- BGI-Agro Seed Service (Wuhan) Co., Ltd, BGI-Shenzhen, Wuhan, 430090, China
| | - Shiming Li
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- BGI-Agro Seed Service (Wuhan) Co., Ltd, BGI-Shenzhen, Wuhan, 430090, China
| | - Lei Lan
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Mushan Xie
- Genetic, Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 401331, China
| | - Shu Cheng
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xiaolong Gan
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China
- Key Laboratory of Crop Molecular Breeding, Xining, 810008, Qinghai, China
| | - Gang Huang
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- BGI-Agro Seed Service (Wuhan) Co., Ltd, BGI-Shenzhen, Wuhan, 430090, China
| | - Guohua Du
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
| | - Kang Yu
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China
- BGI-Agro Seed Service (Wuhan) Co., Ltd, BGI-Shenzhen, Wuhan, 430090, China
| | - Xuemei Ni
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Baolong Liu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810008, Qinghai, China.
- Key Laboratory of Crop Molecular Breeding, Xining, 810008, Qinghai, China.
| | - Guoxiong Peng
- Genetic, Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 401331, China.
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Singh RK, Muthamilarasan M, Prasad M. Biotechnological approaches to dissect climate-resilient traits in millets and their application in crop improvement. J Biotechnol 2021; 327:64-73. [PMID: 33422569 DOI: 10.1016/j.jbiotec.2021.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/21/2020] [Accepted: 01/02/2021] [Indexed: 10/22/2022]
Abstract
'Small millets' is a generic term that includes all the millets except pearl millet and sorghum. These small or minor millets constitute eleven species that are marginally cultivated and consumed worldwide. These small millets possess excellent agronomic-, climate-resilient, and nutritional traits, although they lack popularity. Small millets withstand a broad spectrum of environmental stresses and possess better water-use and nitrogen-use efficiencies. Of note, small millets are five- to seven-fold nutritionally rich in terms of protein, bioactive compounds, micro- and macro-nutrients as compared to major cereals. Irrespective of these merits, small millets have received little research attention compared to major millets and cereals. However, the knowledge generated from such studies is significant for the improvement of millets per se and for translating the information to improve major cereals through breeding and transgene-based approaches. Given this, the review enumerates the efforts invested in dissecting the climate-resilient traits in small millets and provides a roadmap for deploying the information in crop improvement of millets as well as cereals in the scenario of climate change.
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Affiliation(s)
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi 110067, India.
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