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Lacchini E, Kiegle E, Castellani M, Adam H, Jouannic S, Gregis V, Kater MM. CRISPR-mediated accelerated domestication of African rice landraces. PLoS One 2020; 15:e0229782. [PMID: 32126126 PMCID: PMC7053755 DOI: 10.1371/journal.pone.0229782] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/13/2020] [Indexed: 11/18/2022] Open
Abstract
African Oryza glaberrima and Oryza sativa landraces are considered valuable resources for breeding traits due to their adaptation to local environmental and soil conditions. They often possess superior resistance to endemic pests and tolerance to drought and nutrient deficiencies when compared to the "imported" high production Asian rice varieties. In contrast, "domestication traits" such as seed shattering, lodging, and seed yield are not well established in these African landraces. Therefore, the use of these African varieties for high production agriculture is limited by unpredictable yield and grain quality. We are addressing this shortcoming by developing protocols for genetically transforming African landraces to allow the use of CRISPR-Cas mediated breeding approaches. Here we use as proof of concept the cultivated African landrace Kabre to target selected known "domestication loci" and improve the agronomic potential of Kabre rice. Stable genetic transformation with CRISPR-Cas9-based vectors generated single and simultaneous multiple gene knockouts. Plants with reduced stature to diminish lodging were generated by disrupting the HTD1 gene. Furthermore, three loci shown to control seed size and/or yield (GS3, GW2 and GN1A) were targeted using a multiplex CRISPR-Cas9 construct. This resulted in mutants with significantly improved seed yield. Our study provides an example of how new breeding technologies can accelerate the development of highly productive African landrace rice varieties, an important advancement considering that Africa is a hotspot for worldwide population growth and therefore prone to food shortage.
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Affiliation(s)
- Elia Lacchini
- Department of Biosciences, University of Milan, Milan, Italy
| | - Edward Kiegle
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Hélène Adam
- University of Montpellier, DIADE, IRD, Montpellier, France
| | | | - Veronica Gregis
- Department of Biosciences, University of Milan, Milan, Italy
| | - Martin M. Kater
- Department of Biosciences, University of Milan, Milan, Italy
- * E-mail:
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Li J, Zhou J, Xu P, Deng X, Deng W, Zhang Y, Yang Y, Tao D. Mapping five novel interspecific hybrid sterility loci between Oryza sativa and Oryza meridionalis. BREEDING SCIENCE 2018; 68:516-523. [PMID: 30697112 PMCID: PMC6345236 DOI: 10.1270/jsbbs.18001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/22/2018] [Indexed: 05/27/2023]
Abstract
Oryza meridionalis is a potential source for improving Asian cultivated rice O. sativa via direct hybridization and backcrossing. However, hybrid sterility between O. sativa and O. meridionalis is the main barrier of reproduction hindering the transfer of favorable genes from O. meridionalis to O. sativa. To investigate the nature of hybrid sterility between O. sativa and O. meridionalis, three accessions of O. meridionalis were used as male parents to cross Dianjingyou 1, an O. sativa subsp. japonica cultivar following the backcross with the recurrent parent of Dianjingyou 1. Twenty pollen sterility NILs (BC6F1) were obtained and genotyped by using simple sequence repeat (SSR) markers distributed across the 12 rice chromosomes. The heterozygous markers were employed to genotype the corresponding segregation populations for mapping sterility genes. As a result, five novel loci for pollen sterility between O. sativa and O. meridionalis were identified and designated as S51(t), S52(t), S53(t), S54(t) and S55(t), respectively. The genetic behavior of five novel loci followed one-locus allelic interaction model. The disharmonious interaction between Asian cultivated rice allele and wild relative allele led to the partial or full abortion of male gametes for one parent allele in the heterozygotes. These results will be useful for elucidating the mechanism of interspecific hybrid sterility and further utilizing favorable genes from O. meridionalis for enhancement of rice breeding.
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Kanaoka Y, Kuniyoshi D, Inada E, Koide Y, Okamoto Y, Yasui H, Kishima Y. Anther culture in rice proportionally rescues microspores according to gametophytic gene effect and enhances genetic study of hybrid sterility. PLANT METHODS 2018; 14:102. [PMID: 30473723 PMCID: PMC6240274 DOI: 10.1186/s13007-018-0370-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 11/12/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND To investigate plant hybrid sterility, we studied interspecific hybrids of two cultivated rice species, Asian rice (Oryza sativa) and African rice (O. glaberrima). Male gametes of these hybrids display complete sterility owing to a dozen of hybrid sterility loci, termed HS loci, but this complicated genetic system remains poorly understood. RESULTS Microspores from these interspecific hybrids form sterile pollen but are viable at the immature stage. Application of the anther culture (AC) method caused these immature microspores to induce callus. The segregation distortion of 11 among 13 known HS loci was assessed in the callus population. Using many individual calli, fine mapping of the HS loci was attempted based on heterozygotes produced from chromosome segment substitution lines (CSSLs). Transmission ratio distortion (TRD) from microspores was detected at 6 of 11 HS loci in the callus population. The fine mapping of S 1 and S 19 loci using CSSLs revealed precise distances of markers from the positions of HS loci exhibiting excessive TRD. CONCLUSIONS We demonstrated that AC to generate callus populations derived from immature microspores is a useful methodology for genetic study. The callus population facilitated detection of TRD at multiple HS loci and dramatically shortened the process for mapping hybrid sterility genes.
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Affiliation(s)
- Yoshitaka Kanaoka
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Daichi Kuniyoshi
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Eri Inada
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Yohei Koide
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Yoshihiro Okamoto
- Laboratory of Plant Breeding, Rakuno Gakuen University, Bunkyodai-Midorimachi, Ebetsu, 069-8501 Japan
| | - Hideshi Yasui
- Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-ku, Fukuoka, Japan
| | - Yuji Kishima
- Laboratory of Plant Breeding, Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
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Li J, Zhou J, Xu P, Deng X, Deng W, He M, Yang Y, Zhang Y, Tao D. Neutral alleles at hybrid sterility loci of Oryza glaberrima from AA genome relatives in Genus Oryza. BREEDING SCIENCE 2018; 68:343-351. [PMID: 30100801 PMCID: PMC6081293 DOI: 10.1270/jsbbs.18006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/11/2018] [Indexed: 05/10/2023]
Abstract
Hybrid sterility between Oryza sativa and O. glaberrima is a main reproduction barrier when transferring the favorable alleles from O. glaberrima to O. sativa and it happens due to allelic interaction at sterility loci. Neutral alleles at each locus have the potential to overcome the sterility between the two cultivated rice species. In this study, an O. sativa cultivar Dianjingyou 1 (DJY1) and its near-isogenic lines (NILs) harboring the single sterility allele S1-glab, S19-glab, S20-glab, S37-glab, S38-glab and S39-glab as the tested lines were crossed with O. glaberrima, O. rufipogon, O. nivara, O. glumaepatula, O. barthii, O. meridionalis and O. sativa so as to detect the neutral alleles of these loci. Pollen fertility was investigated in the paired F1s based on two seasons' result and genotypic segregation was also analyzed in some F2 populations to confirm the results of pollen fertility investigation. The neutral alleles of S38-n and S39-n were identified based upon the pollen fertility and genotypic segregation analysis for the first time. The neutral alleles of sterility loci detected from present report have the potential to know of the nature of interspecific hybrid sterility, and to overcome the interspecific hybrid sterility between O. sativa and O. glaberrima.
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Affiliation(s)
- Jing Li
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Jiawu Zhou
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Peng Xu
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Xianneng Deng
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Wei Deng
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Mingzhu He
- East China Normal University,
Shanghai 200241,
P. R. China
| | - Ying Yang
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Yu Zhang
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
| | - Dayun Tao
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS),
Kunming 650200,
P. R. China
- Corresponding author (e-mail: )
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Xie Y, Xu P, Huang J, Ma S, Xie X, Tao D, Chen L, Liu YG. Interspecific Hybrid Sterility in Rice Is Mediated by OgTPR1 at the S1 Locus Encoding a Peptidase-like Protein. MOLECULAR PLANT 2017; 10:1137-1140. [PMID: 28533193 DOI: 10.1016/j.molp.2017.05.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 05/11/2017] [Accepted: 05/11/2017] [Indexed: 05/04/2023]
Affiliation(s)
- Yongyao Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Peng Xu
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
| | - Jianle Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shengjian Ma
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Dayun Tao
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650200, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Guangzhou 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China; Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou 510642, China; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.
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