1
|
Han B, Zhang W, Wang F, Yue P, Liu Z, Yue D, Zhang B, Ma Y, Lin Z, Yu Y, Wang Y, Zhang X, Yang X. Dissecting the Superior Drivers for the Simultaneous Improvement of Fiber Quality and Yield Under Drought Stress Via Genome-Wide Artificial Introgressions of Gossypium barbadense into Gossypium hirsutum. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400445. [PMID: 38984458 DOI: 10.1002/advs.202400445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 05/07/2024] [Indexed: 07/11/2024]
Abstract
Global water scarcity and extreme weather intensify drought stress, significantly reducing cotton yield and quality worldwide. Drought treatments are conducted using a population of chromosome segment substitution lines generated from E22 (G. hirsutum) and 3-79 (G. barbadense) as parental lines either show superior yields or fiber quality under both control and drought conditions. Fourteen datasets, covering 4 yields and 4 quality traits, are compiled and assessed for drought resistance using the drought resistance coefficient (DRC) and membership function value of drought resistance (MFVD). Genome-wide association studies, linkage analysis, and bulked segregant analysis are combined to analyze the DR-related QTL. A total of 121 significant QTL are identified by DRC and MFVD of the 8 traits. CRISPR/Cas9 and virus-induced gene silencing techniques verified DRR1 and DRT1 as pivotal genes in regulating drought resistant of cotton, with hap3-79 exhibiting greater drought resistance than hapE22 concerning DRR1 and DRT1. Moreover, 14 markers with superior yield and fiber quality are selected for drought treatment. This study offers valuable insights into yield and fiber quality variations between G. hirsutum and G. barbadense amid drought, providing crucial theoretical and technological backing for developing cotton varieties resilient to drought, with high yield and superior fiber quality.
Collapse
Affiliation(s)
- Bei Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenhao Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fengjiao Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Pengkai Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhilin Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dandan Yue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Bing Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Yu Yu
- Cotton Institute, Xinjiang Academy of Agriculture and Reclamation Science, Shihezi, 832000, China
| | - Yanqin Wang
- College of Life Sciences, Tarim University, Alar, 843300, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| |
Collapse
|
2
|
Zhao X, Xu Z, Chen Y, Du Y, Li M, Huang B, Ge Y, Gu M, Tang S, Liu Q, Zhang H. Development of introgression lines and mapping of qGW2, a novel QTL that confers grain width, in rice ( Oryza sativa L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:10. [PMID: 38298743 PMCID: PMC10825081 DOI: 10.1007/s11032-024-01453-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/19/2024] [Indexed: 02/02/2024]
Abstract
Rice grain size is a key determinant of both grain yield and quality. Identification of favorable alleles for use in rice breeding may help to meet the demand for increased yield. In this study, we developed a set of 210 introgression lines (ILs) by using indica variety Huanghuazhan as the donor parent and erect-panicle japonica rice variety Wuyujing3R as the recurrent parent. A total of 133 ILs were selected for high-throughput sequencing. Using specific-locus amplified fragment (SLAF) sequencing technology, 10,103 high-quality SLAF labels evenly distributed on 12 chromosomes were obtained and selected for subsequent analysis. Using a high-density map, quantitative trait locus (QTL) mapping of grain size-related traits was performed, and a total of 38 QTLs were obtained in two environments. Furthermore, qGW2, a novel QTL that controls grain width on chromosome 2, was validated and delimited to a region of 309 kb via substitution mapping. These findings provide new genetic material and a basis for future fine mapping and cloning of favorable QTLs. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01453-0.
Collapse
Affiliation(s)
- Xiangqiang Zhao
- School of Life Sciences, Nantong University, Nantong, 226019 Jiangsu China
| | - Zuopeng Xu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - YiBo Chen
- Guangdong Academy of Agricultural Sciences, Rice Research Institute, Guangzhou, 510640 Guangdong China
| | - Yuanyue Du
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Meng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Benxi Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Yongshen Ge
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
| | - Minghong Gu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Shuzhu Tang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Honggen Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou, 225009 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| |
Collapse
|
3
|
Singh G, Kaur N, Khanna R, Kaur R, Gudi S, Kaur R, Sidhu N, Vikal Y, Mangat GS. 2Gs and plant architecture: breaking grain yield ceiling through breeding approaches for next wave of revolution in rice ( Oryza sativa L.). Crit Rev Biotechnol 2024; 44:139-162. [PMID: 36176065 DOI: 10.1080/07388551.2022.2112648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 07/10/2022] [Accepted: 07/27/2022] [Indexed: 11/03/2022]
Abstract
Rice is a principal food crop for more than half of the global population. Grain number and grain weight (2Gs) are the two complex traits controlled by several quantitative trait loci (QTLs) and are considered the most critical components for yield enhancement in rice. Novel molecular biology and QTL mapping strategies can be utilized in dissecting the complex genetic architecture of these traits. Discovering the valuable genes/QTLs associated with 2Gs traits hidden in the rice genome and utilizing them in breeding programs may bring a revolution in rice production. Furthermore, the positional cloning and functional characterization of identified genes and QTLs may aid in understanding the molecular mechanisms underlying the 2Gs traits. In addition, knowledge of modern genomic tools aids the understanding of the nature of plant and panicle architecture, which enhances their photosynthetic activity. Rice researchers continue to combine important yield component traits (including 2Gs for the yield ceiling) by utilizing modern breeding tools, such as marker-assisted selection (MAS), haplotype-based breeding, and allele mining. Physical co-localization of GW7 (for grain weight) and DEP2 (for grain number) genes present on chromosome 7 revealed the possibility of simultaneous introgression of these two genes, if desirable allelic variants were found in the single donor parent. This review article will reveal the genetic nature of 2Gs traits and use this knowledge to break the yield ceiling by using different breeding and biotechnological tools, which will sustain the world's food requirements.
Collapse
Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navdeep Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Renu Khanna
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rupinder Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Navjot Sidhu
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - G S Mangat
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| |
Collapse
|
4
|
Nguyen HTL, Suetsugu S, Nakamura Y, Demeter Z, Zheng SH, Fujita D. Identification and characterization of stable QTLs for vascular bundle number at the panicle neck in rice ( Oryza sativa L.). BREEDING SCIENCE 2023; 73:365-372. [PMID: 38106512 PMCID: PMC10722095 DOI: 10.1270/jsbbs.23013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/11/2023] [Indexed: 12/19/2023]
Abstract
A large vascular bundle number (VBN) in the panicle neck in rice (Oryza sativa L.) is related to the ability to transport assimilates from stem and leaf to reproductive organs during seed maturation. Several quantitative trait loci (QTLs) for VBN have been identified by using segregating populations derived from a cross between indica and japonica rice cultivars. However, the detailed location, effect, and interaction of QTLs for VBN were not understood well. Here, to elucidate the genetic basis of VBN, we identified three stable QTLs for VBN-qVBN5, qVBN6 and qVBN11-by using 71 recombinant inbred lines derived from a cross between indica 'IR24' and japonica 'Asominori'. We confirmed their positions and characterized their effects by using chromosome segment substitution lines (CSSLs) with an 'IR24' genetic background. qVBN6 had the most substantial effect on VBN, followed by qVBN11 and qVBN5. We developed pyramided lines carrying two QTLs for VBN to estimate their interaction. The combination of qVBN6 and qVBN11 accumulated VBN negatively in the pyramided lines owing to the independent actions of each QTL. The QTLs detected for VBN will enhance our understanding of genetic mechanisms of VBN and can be used in rice breeding.
Collapse
Affiliation(s)
- Ha Thi Le Nguyen
- The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-8580, Japan
- Forest Science Institute of South Vietnam, 1 Pham Van Hai, Tan Binh District, Ho Chi Minh City, Viet Nam
| | - Shizuka Suetsugu
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Yuna Nakamura
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Zita Demeter
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Shao-Hui Zheng
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| | - Daisuke Fujita
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga 840-8502, Japan
| |
Collapse
|
5
|
Xu G, Deng K, Yu J, Li Q, Li L, Xiang A, Ling Y, Zhang C, Zhao F. Genetic Effects Analysis of QTLs for Rice Grain Size Based on CSSL-Z403 and Its Dissected Single and Dual-Segment Substitution Lines. Int J Mol Sci 2023; 24:12013. [PMID: 37569388 PMCID: PMC10418668 DOI: 10.3390/ijms241512013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Rice chromosomal segment substitution lines (CSSLs) are ideal materials for studying quantitative traits such as grain size. Here, a rice large-grain CSSL-Z403 was identified among progeny of the recipient Xihui18 and the donor Jinhui35 based on molecular marker-assisted selection. Z403 carried 10 substitution segments with average length of 3.01 Mb. Then, a secondary F2 population derived from a cross between Xihui18 and Z403 was used to map quantitative trait loci (QTL) for grain size. Six QTLs distributed on chromosomes 5, 6, 7, 9 and 12 were detected. Finally four single-segment substitution lines (SSSLs) and two dual-segment substitution lines (DSSLs) carrying these target QTLs were constructed, and 10 novel QTLs were identified by four SSSLs. The large grain of Z403 was controlled at least by qGWT5, qGWT7, qGWT9 and qGWT12, and its grain weight was influenced through grain length QTL such as qGL5, qGL6, qGL9 and qGL12, as well as grain width QTL such as qGW5, qGW7, qGW9 and qGW12. Among 16 QTLs, four QTLs including qGL6, etc., might be novel compared with the reported documents. Again, positive or less negative epistatic effects between two non-allelic QTLs (additive effect > 0) may assist screening the genotype with larger grain size in further selection.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Fangming Zhao
- Rice Research Institute, Academy of Agricultural Science, Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing 400715, China; (G.X.)
| |
Collapse
|
6
|
Nagata K, Nonoue Y, Matsubara K, Mizobuchi R, Ono N, Shibaya T, Ebana K, Ogiso-Tanaka E, Tanabata T, Sugimoto K, Taguchi-Shiobara F, Yonemaru JI, Uga Y, Fukuda A, Ueda T, Yamamoto SI, Yamanouchi U, Takai T, Ikka T, Kondo K, Hoshino T, Yamamoto E, Adachi S, Sun J, Kuya N, Kitomi Y, Iijima K, Nagasaki H, Shomura A, Mizubayashi T, Kitazawa N, Hori K, Ando T, Yamamoto T, Fukuoka S, Yano M. Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice. BREEDING SCIENCE 2023; 73:332-342. [PMID: 37840983 PMCID: PMC10570878 DOI: 10.1270/jsbbs.23006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/12/2023] [Indexed: 10/17/2023]
Abstract
Many agronomic traits that are important in rice breeding are controlled by multiple genes. The extensive time and effort devoted so far to identifying and selecting such genes are still not enough to target multiple agronomic traits in practical breeding in Japan because of a lack of suitable plant materials in which to efficiently detect and validate beneficial alleles from diverse genetic resources. To facilitate the comprehensive analysis of genetic variation in agronomic traits among Asian cultivated rice, we developed 12 sets of chromosome segment substitution lines (CSSLs) with the japonica background, 11 of them in the same genetic background, using donors representing the genetic diversity of Asian cultivated rice. Using these materials, we overviewed the chromosomal locations of 1079 putative QTLs for seven agronomic traits and their allelic distribution in Asian cultivated rice through multiple linear regression analysis. The CSSLs will allow the effects of putative QTLs in the highly homogeneous japonica background to be validated.
Collapse
Affiliation(s)
- Kazufumi Nagata
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yasunori Nonoue
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuki Matsubara
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ritsuko Mizobuchi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Nozomi Ono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Taeko Shibaya
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kaworu Ebana
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Eri Ogiso-Tanaka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Takanari Tanabata
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuhiko Sugimoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Fumio Taguchi-Shiobara
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Jun-ichi Yonemaru
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yusaku Uga
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Atsunori Fukuda
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tadamasa Ueda
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shin-ichi Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Utako Yamanouchi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Toshiyuki Takai
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Takashi Ikka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Katsuhiko Kondo
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tomoki Hoshino
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Eiji Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shunsuke Adachi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Jian Sun
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Noriyuki Kuya
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yuka Kitomi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ken Iijima
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hideki Nagasaki
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ayahiko Shomura
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tatsumi Mizubayashi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Noriyuki Kitazawa
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kiyosumi Hori
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tsuyu Ando
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Toshio Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shuichi Fukuoka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Masahiro Yano
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| |
Collapse
|
7
|
Zhao N, Yuan R, Usman B, Qin J, Yang J, Peng L, Mackon E, Liu F, Qin B, Li R. Detection of QTLs Regulating Six Agronomic Traits of Rice Based on Chromosome Segment Substitution Lines of Common Wild Rice ( Oryza rufipogon Griff.) and Mapping of qPH1.1 and qLMC6.1. Biomolecules 2022; 12:biom12121850. [PMID: 36551278 PMCID: PMC9775987 DOI: 10.3390/biom12121850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Wild rice is a primary source of genes that can be utilized to generate rice cultivars with advantageous traits. Chromosome segment substitution lines (CSSLs) are consisting of a set of consecutive and overlapping donor chromosome segments in a recipient's genetic background. CSSLs are an ideal genetic population for mapping quantitative traits loci (QTLs). In this study, 59 CSSLs from the common wild rice (Oryza rufipogon Griff.) accession DP15 under the indica rice cultivar (O. sativa L. ssp. indica) variety 93-11 background were constructed through multiple backcrosses and marker-assisted selection (MAS). Through high-throughput whole genome re-sequencing (WGRS) of parental lines, 12,565 mapped InDels were identified and designed for polymorphic molecular markers. The 59 CSSLs library covered 91.72% of the genome of common wild rice accession DP15. The DP15-CSSLs displayed variation in six economic traits including grain length (GL), grain width (GW), thousand-grain weight (TGW), grain length-width ratio (GLWR), plant height (PH), and leaf margin color (LMC), which were finally attributed to 22 QTLs. A homozygous CSSL line and a purple leave margin CSSL line were selected to construct two secondary genetic populations for the QTLs mapping. Thus, the PH-controlling QTL qPH1.1 was mapped to a region of 4.31-Mb on chromosome 1, and the LMC-controlling QTL qLMC6.1 was mapped to a region of 370-kb on chromosome 6. Taken together, these identified novel QTLs/genes from common wild rice can potentially promote theoretical knowledge and genetic applications to rice breeders worldwide.
Collapse
Affiliation(s)
- Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ruizhi Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Babar Usman
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jiaming Qin
- Maize Research Institute, Guangxi Academy of Agricultural Science, Nanning 530007, China
| | - Jinlian Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Liyun Peng
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- Correspondence:
| |
Collapse
|
8
|
Identification of QTLs for Heat Tolerance at the Flowering Stage Using Chromosome Segment Substitution Lines in Rice. Genes (Basel) 2022; 13:genes13122248. [PMID: 36553515 PMCID: PMC9777623 DOI: 10.3390/genes13122248] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/24/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022] Open
Abstract
High temperature is a major stress in rice production. Although considerable progress has been made in investigating heat tolerance (HT) in rice, the genetic basis of HT at the heading stage remains largely unknown. In this study, a novel set of chromosome segment substitution lines (CSSLs) consisting of 113 lines derived from a heat-resistant indica variety N22 and a heat-sensitive indica variety 9311 was developed and used for the analysis of the genetic basis of HT. The heat sensitivity index (HSI) calculated based on seed-setting rates under natural and high-temperature environments was used to evaluate the influence of HT at the rice heading stage. In total, five quantitative trait loci (QTLs) associated with HT were detected based on seed-setting rate (SSR) evaluation; these were named qSSR6-1, qSSR7-1, qSSR8-1, qSSR9-1 and qSSR11-1 located on chromosomes 6, 7, 8, 9 and 11, respectively. Heat-tolerant alleles of the QTLs were all derived from N22. Among them, qSSR9-1 overlapped with QTLs identified previously, while the remaining QTLs were found novel. In particular, qSSR7-1 explained a high phenotypic variation of 26.35% with a LOD score of 10.75, thus deserved to be further validated. These findings will increase our understanding of the genetic mechanism underlying HT and facilitate the breeding of heat-tolerant rice varieties.
Collapse
|
9
|
Gong H, Han B. Genetic introgression between different groups reveals the differential process of Asian cultivated rice. Sci Rep 2022; 12:17662. [PMID: 36271113 PMCID: PMC9587041 DOI: 10.1038/s41598-022-22674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 10/18/2022] [Indexed: 01/18/2023] Open
Abstract
The Asian cultivated rice consists of two major subspecies: indica and japonica. There are already many reports about the existence of genetic introgression between the two subspecies. They propose some possible introgression-related genes from the comparison of population parameters. This study uses the genome-wide variation data of Asia cultivated rice to investigate their genetic introgression on the whole genome level. We detect a total of 13 significantly high introgression loci between the tropical japonica and indica populations. Two different methods are used to identify the genetic introgression regions. For most of the detected introgression regions, they generally get consistent results. Some previously known introgression genes are detected in the identified introgression loci, such as heat resistance gene TT1 and GLW7. The biological functions for these genetic introgression regions are annotated by the published QTL mapping results. We find that genetic introgression plays a vital role in the determination of both the phenotype and the domestication process of different groups. Our study also provides useful information and resources for the study of rice gene function and the domestication process.
Collapse
Affiliation(s)
- Hao Gong
- grid.411411.00000 0004 0644 5457School of Life Science, Huizhou University, Huizhou, 516007 China
| | - Bin Han
- grid.9227.e0000000119573309National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233 China
| |
Collapse
|
10
|
Wittern LM, Barrero JM, Bovill WD, Verbyla KL, Hughes T, Swain SM, Steed G, Webb AAR, Gardner K, Greenland A, Jacobs J, Frohberg C, Schmidt RC, Cavanagh C, Rohde A, Davey MW, Hannah MA. Overexpression of the WAPO-A1 gene increases the number of spikelets per spike in bread wheat. Sci Rep 2022; 12:14229. [PMID: 35987959 PMCID: PMC9392761 DOI: 10.1038/s41598-022-18614-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/16/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractTwo homoeologous QTLs for number of spikelets per spike (SPS) were mapped on chromosomes 7AL and 7BL using two wheat MAGIC populations. Sets of lines contrasting for the QTL on 7AL were developed which allowed for the validation and fine mapping of the 7AL QTL and for the identification of a previously described candidate gene, WHEAT ORTHOLOG OF APO1 (WAPO1). Using transgenic overexpression in both a low and a high SPS line, we provide a functional validation for the role of this gene in determining SPS also in hexaploid wheat. We show that the expression levels of this gene positively correlate with SPS in multiple MAGIC founder lines under field conditions as well as in transgenic lines grown in the greenhouse. This work highlights the potential use of WAPO1 in hexaploid wheat for further yield increases. The impact of WAPO1 and SPS on yield depends on other genetic and environmental factors, hence, will require a finely balanced expression level to avoid the development of detrimental pleiotropic phenotypes.
Collapse
|
11
|
Zhang B, Ma L, Wu B, Xing Y, Qiu X. Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:863789. [PMID: 35557720 PMCID: PMC9087921 DOI: 10.3389/fpls.2022.863789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/01/2022] [Indexed: 05/14/2023]
Abstract
The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.
Collapse
Affiliation(s)
- Bo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou, China
| |
Collapse
|
12
|
Li G, Cheng Y, Yin M, Yang J, Ying J, Zhu C. Detection of QTLs for panicle-related traits using an indica × japonica recombinant inbred line population in rice. PeerJ 2021; 9:e12504. [PMID: 34909275 PMCID: PMC8638570 DOI: 10.7717/peerj.12504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/26/2021] [Indexed: 11/20/2022] Open
Abstract
Background The panicle is the most important organ in rice, and all the panicle-related traits are correlated with rice grain yield. Understanding the underlying genetic mechanisms controlling panicle development is very important for improving rice production. Methods Nine panicle-related traits including heading date, panicle length, number of primary branches, number of secondary branches, number of grains per panicle, number of panicles per plant, number of filled grains per plant, seed-setting rate, and grain yield per plant were investigated. To map the quantitative trait loci (QTLs) for the nine panicle-related traits, a PCR-based genetic map with 208 markers (including 121 simple sequence repeats and 87 InDels) and a high-density linkage map with 18,194 single nucleotide polymorphism (SNP) markers were both used. Results Using a recombinant inbred line population derived from an indica variety Huanghuazhan and a japonica line Jizi 1560, a total of 110 and 112 QTLs were detected for panicle-related traits by PCR-based genetic map and by high-density linkage map, respectively. Most of the QTLs were clustered on chromosomes 1, 2, 3, 6, and 7 while no QTLs were detected on chromosome 10. Almost all the QTLs with LOD values of more than 5.0 were repeatedly detected, indicating the accuracy of the two methods and the stability of the QTL effects. No genes for panicle-related traits have been previously reported in most of these regions. QTLs found in JD1006-JD1007 and RM1148-RM5556 with high LOD and additive values deserved further research. The results of this study are beneficial for marker-assisted breeding and provide research foundation for further fine-mapping and cloning of these QTLs for panicle-related traits.
Collapse
Affiliation(s)
- Guan Li
- School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang, Jiangxi Province, China.,China National Rice Research Institute, Hangzhou, Zhejiang Province, China
| | - Yichen Cheng
- China National Rice Research Institute, Hangzhou, Zhejiang Province, China
| | - Man Yin
- China National Rice Research Institute, Hangzhou, Zhejiang Province, China
| | - Jinyu Yang
- China National Rice Research Institute, Hangzhou, Zhejiang Province, China
| | - Jiezheng Ying
- China National Rice Research Institute, Hangzhou, Zhejiang Province, China
| | - Changlan Zhu
- School of Agricultural Sciences, Jiangxi Agricultural University, Nanchang, Jiangxi Province, China
| |
Collapse
|
13
|
Mao F, Wang Z, Zheng Y, Tang S, Luo X, Xiong T, Yan S. Fine mapping of a heading date QTL, Se16(t), under extremely long day conditions in rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:70. [PMID: 37309360 PMCID: PMC10236121 DOI: 10.1007/s11032-021-01263-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 11/03/2021] [Indexed: 06/14/2023]
Abstract
Heading date (flowering time) is a key trait that determines the yield and the adaptability of rice varieties. In the past 20 years, a number of genetic studies have been carried out to elucidate the genetic control of rice heading date, and many important genes have been cloned. These genes were identified under natural day (ND) conditions; however, little is known about the heading behavior under extreme day-length conditions. In this study, we identified a japonica variety, Sasanishiki, that showed sensitivity to extremely long days (ELD). Its heading date was significantly delayed for about 20 days under artificial ELD conditions that were achieved by setting a light emitting diode (LED) lamp beside a paddy field. We found that the late heading phenotype of Sasanishiki was induced when the day length was more than 14.75 h, and the LED light intensity was above 2 µmol m-2 s-1. Genetic analysis revealed that the photoperiod sensitivity of Sasanishiki was controlled by a dominant locus, temporarily named Se16(t). It was fine mapped to a 30.4-kb interval on chromosome 3, containing five predicted genes, including PHYC, a phytochrome encoding gene of rice. Our findings provide new information on the heading date under ELD conditions in rice. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01263-8.
Collapse
Affiliation(s)
- Fangming Mao
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Zhiquan Wang
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Yiyun Zheng
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Shusheng Tang
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Xin Luo
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Tao Xiong
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Song Yan
- Rice National Engineering Laboratory (Nanchang), Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| |
Collapse
|
14
|
Fukuda A, Hirose T, Hashida Y, Aoki N, Nagano AJ. Selection of transcripts related to low-temperature tolerance using RNA sequencing from F 2 plants between japonica and indica rice (Oryza sativa L.) cultivars. FUNCTIONAL PLANT BIOLOGY : FPB 2021; 48:984-993. [PMID: 34112311 DOI: 10.1071/fp21088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/21/2021] [Indexed: 06/12/2023]
Abstract
At low temperatures (18°C), seedlings of an indica rice (Oryza sativa L.) cultivar Kasalath showed symptoms of chlorosis, although the leaves of a japonica cultivar Arroz da Terra remained green. In this study, transcripts related to the chlorophyll content of rice seedlings grown at 18°C were investigated using RNA-sequencing (RNA-Seq) data for F2 crosses between cultivars Arroz da Terra and Kasalath, as well as their parental cultivars. Differential expression analysis revealed that gene ontology terms related to 'photosynthesis' were significantly enriched in lowly expressed genes at 18°C than at 25°C in Kasalath. However, the gene ontology terms related to 'response to stress' were significantly enriched in highly expressed genes at 18°C than at 25°C in Kasalath. When the F2 plants were grown at 18°C, their chlorophyll contents varied. Transcripts with expression levels related to chlorophyll content were statistically selected using RNA-Seq data from 21 F2 plants. In regression models, frequently selected genes included four photosynthetic and two stress-responsive genes. The expression values of four photosynthetic and two stress-responsive genes in high-frequency selected genes were significantly correlated with chlorophyll content not only in plants analysed using RNA-Seq but also in 95 F2 plants.
Collapse
Affiliation(s)
- Akari Fukuda
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan; and Corresponding author.
| | - Tatsuro Hirose
- Faculty of Agriculture, Takasaki University of Health and Welfare, Takasaki, Gunma, Japan
| | - Yoichi Hashida
- Faculty of Agriculture, Takasaki University of Health and Welfare, Takasaki, Gunma, Japan
| | - Naohiro Aoki
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | | |
Collapse
|
15
|
Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species. PLANTS 2021; 10:plants10040725. [PMID: 33917982 PMCID: PMC8068336 DOI: 10.3390/plants10040725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [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.
Collapse
|
16
|
Yoneyama S, Maeda K, Sadamori A, Saitoh S, Tsuda M, Azuma T, Nagano A, Tomiyama T, Matsumoto T. Construction of a genetic linkage map and detection of quantitative trait locus for the ergothioneine content in tamogitake mushroom ( Pleurotus cornucopiae var. citrinopileatus). MYCOSCIENCE 2021; 62:71-80. [PMID: 37090022 PMCID: PMC9157747 DOI: 10.47371/mycosci.2020.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/05/2020] [Accepted: 11/08/2020] [Indexed: 11/16/2022]
Abstract
Developing high-content strains of L-ergothioneine (EGT), an antioxidant amino acid, is an important breeding target for tamogitake mushroom, Pleurotus cornucopiae var. citrinopileatus. We constructed a genetic linkage map based on segregation analysis of markers in 105 F1 progenies. The loci of 245 markers, including 10 AFLP markers, 195 Rad markers, 2 mating type factors, and 38 gene markers, were mapped. The map contained 12 linkage groups with a total genetic distance of 906.8 cM, and an average marker interval of 4.0 cM. The population from crossing between tester monokaryon and F1 progenies was used to characterize quantitative trait loci (QTL) for EGT content. With composite interval mapping (CIM) method, QTL of EGT content were found to be located in linkage group 10, having a Logarithm of the odds (LOD) score of 2.53 with a 10.1% contribution rate. Moreover, a single nucleotide polymorphism (SNP), A/T, was identified in a gene region of the genome in the neighborhood where the QTL peak existed. This SNP genotype was in good agreement with the EGT phenotypes of each strain in the both QTL population and wild population. Thus, this SNP would have great potential value to use the marker-assisted selection (MAS) for this mushroom with high EGT content.
Collapse
Affiliation(s)
- Shozo Yoneyama
- Forest Products Research Institute, Hokkaido Research Organization
| | - Kaede Maeda
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University
| | - Ayuka Sadamori
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University
| | - Sayaka Saitoh
- Forest Products Research Institute, Hokkaido Research Organization
| | - Mayumi Tsuda
- Forest Products Research Institute, Hokkaido Research Organization
| | - Tomonori Azuma
- Forest Products Research Institute, Hokkaido Research Organization
| | | | | | - Teruyuki Matsumoto
- Fungus/Mushroom Resource and Research Center, Faculty of Agriculture, Tottori University
| |
Collapse
|
17
|
Yuan R, Zhao N, Usman B, Luo L, Liao S, Qin Y, Nawaz G, Li R. Development of Chromosome Segment Substitution Lines (CSSLs) Derived from Guangxi Wild Rice ( Oryza rufipogon Griff.) under Rice ( Oryza sativa L.) Background and the Identification of QTLs for Plant Architecture, Agronomic Traits and Cold Tolerance. Genes (Basel) 2020; 11:E980. [PMID: 32842674 PMCID: PMC7564255 DOI: 10.3390/genes11090980] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 11/16/2022] Open
Abstract
Common wild rice contains valuable resources of novel alleles for rice improvement. It is well known that genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) ais a powerful tool for fine mapping of quantitative traits, new gene discovery and marker-assisted breeding. In this study, 132 CSSLs were developed from a cultivated rice (Oryza sativa) cultivar (93-11) and common wild rice (Oryza rufipogon Griff. DP30) by selfing-crossing, backcrossing and marker-assisted selection (MAS). Based on the high-throughput sequencing of the 93-11 and DP30, 285 pairs of Insertion-deletions (InDel) markers were selected with an average distance of 1.23 Mb. The length of this DP30-CSSLs library was 536.4 cM. The coverage rate of substitution lines cumulatively overlapping the whole genome of DP30 was about 91.55%. DP30-CSSLs were used to analyze the variation for 17 traits leading to the detection of 36 quantitative trait loci (QTLs) with significant phenotypic effects. A cold-tolerant line (RZ) was selected to construct a secondary mapping F2 population, which revealed that qCT2.1 is in the 1.7 Mb region of chromosome 2. These CSSLs may, therefore, provide powerful tools for genome wide large-scale gene discovery in wild rice. This research will also facilitate fine mapping and cloning of QTLs and genome-wide study of wild rice. Moreover, these CSSLs will provide a foundation for rice variety improvement.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (R.Y.); (N.Z.); (B.U.); (L.L.); (S.L.); (Y.Q.); (G.N.)
| |
Collapse
|
18
|
Kumar A, Sandhu N, Venkateshwarlu C, Priyadarshi R, Yadav S, Majumder RR, Singh VK. Development of introgression lines in high yielding, semi-dwarf genetic backgrounds to enable improvement of modern rice varieties for tolerance to multiple abiotic stresses free from undesirable linkage drag. Sci Rep 2020; 10:13073. [PMID: 32753648 PMCID: PMC7403580 DOI: 10.1038/s41598-020-70132-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/01/2020] [Indexed: 12/16/2022] Open
Abstract
Occurrence of multiple abiotic stresses in a single crop season has become more frequent than before. Most of the traditional donors possessing tolerance to abiotic stresses are tall, low-yielding with poor grain quality. To facilitate efficient use of complex polygenic traits in rice molecular breeding research, we undertook development of introgression lines in background of high-yielding, semi-dwarf varieties with good grain quality. The study reports the development and evaluations of over 25,000 introgression lines in eleven elite rice genetic backgrounds for improvement of yield under multiple abiotic-stresses such as drought, flood, high/low temperature. The developed introgression lines within each genetic background are near isogenic/recombinant inbred lines to their recipient recurrent parent with 50 to 98% background recovery and additionally carry QTLs/genes for abiotic stresses. The multiple-stress tolerant pyramided breeding lines combining high yield under normal situation and good yield under moderate to severe reproductive-stage drought, semi-dwarf plant type with good grain quality traits have been developed. The introgression lines in dwarf backgrounds open new opportunity to improve other varieties without any linkage drag as well as facilitate cloning of QTLs, identification and functional characterization of candidate genes, mechanisms associated with targeted QTLs and the genetic networks underlying complex polygenic traits.
Collapse
Affiliation(s)
- Arvind Kumar
- International Rice Research Institute, Metro Manila, Philippines. .,IRRI South Asia Regional Centre (ISARC), Varanasi, Uttar Pradesh, India.
| | - Nitika Sandhu
- International Rice Research Institute, Metro Manila, Philippines.,Punjab Agricultural University, Ludhiana, India
| | - Challa Venkateshwarlu
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Rahul Priyadarshi
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India.,International Rice Research Institute, Guwahati, Assam, India
| | - Shailesh Yadav
- International Rice Research Institute, Metro Manila, Philippines
| | | | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| |
Collapse
|
19
|
Gouda G, Gupta MK, Donde R, Mohapatra T, Vadde R, Behera L. Marker-assisted selection for grain number and yield-related traits of rice ( Oryza sativa L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:885-898. [PMID: 32377039 PMCID: PMC7196572 DOI: 10.1007/s12298-020-00773-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 05/11/2023]
Abstract
Continuous rise in the human population has resulted in an upsurge in food demand, which in turn demand grain yield enhancement of cereal crops, including rice. Rice yield is estimated via the number of tillers, grain number per panicles, and the number of spikes present per panicle. Marker-assisted selection (MAS) serve as one of the best ways to introduce QTLs/gene associated with yield in the rice plant. MAS has also been employed effectively in dissecting several other complex agricultural traits, for instance, drought, cold tolerance, salinity, etc. in rice plants. Thus, in this review, authors attempted to collect information about various genes/QTLs associated with high yield, including grain number, in rice and how different scheme of MAS can be employed to introduce them in rice (Oryza sativa L.) plant, which in turn will enhance rice yield. Information obtained to date suggest that, numerous QTLs, e.g., Gn1a, Dep1, associated with grain number and yield-related traits, have been identified either via mapping or cloning approaches. These QTLs have been successfully introduced into rice plants using various schemes of MAS for grain yield enhancement in rice. However, sometimes, MAS does not perform well in breeding, which might be due to lack of resources, skilled labors, reliable markers, and high costs associated with MAS. Thus, by overcoming these problems, we can enhance the application of MAS in plant breeding, which, in turn, may help us in increasing yield, which subsequently may help in bridging the gap between demand and supply of food for the continuously growing population.
Collapse
Affiliation(s)
- Gayatri Gouda
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | - Manoj Kumar Gupta
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh 516 005 India
| | - Ravindra Donde
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| | - Trilochan Mohapatra
- Secretary (DARE) and Director General (ICAR), Government of India, New Delhi, India
| | - Ramakrishna Vadde
- Department of Biotechnology and Bioinformatics, Yogi Vemana University, Kadapa, Andhra Pradesh 516 005 India
| | - Lambodar Behera
- ICAR-National Rice Research Institute, Cuttack, Odisha 753 006 India
| |
Collapse
|
20
|
A single segment substitution line population for identifying traits relevant to drought tolerance and avoidance. Genomics 2019; 114:476-481. [PMID: 31678150 DOI: 10.1016/j.ygeno.2019.10.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 11/22/2022]
Abstract
A population of chromosome segment substitution lines was developed using KDML105 as the recurrent parent and one of DH212 (IR68586-F2-CA-143) or DH103 (IR68586-F2-CA-31) as the donor parent. The donor parents are part of a doubled haploid population from a cross between CT9993, an upland japonica accession, and IR62266, a lowland indica accession. Multiple QTL that are relevant to drought avoidance, drought tolerance and yield traits under drought stress were mapped in this doubled haploid population and the segments selected for the chromosome segment substitution lines were chosen to capture these QTL. The chromosome segment substitution line population was phenotyped under irrigated and mild drought stress conditions, which identified that many yield traits under drought stress had been introduced into the chromosome segment substitution lines.
Collapse
|
21
|
Detection of QTL for panicle architecture in $$\hbox {F}_{2}$$ population of rice. J Genet 2019. [DOI: 10.1007/s12041-019-1088-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
22
|
Fujino K, Obara M, Ikegaya T. Establishment of adaptability to the northern-limit of rice production. Mol Genet Genomics 2019; 294:729-737. [PMID: 30874890 DOI: 10.1007/s00438-019-01542-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/23/2019] [Indexed: 10/27/2022]
Abstract
The domestication of cultivated crops from their wild relatives narrowed down their genetic diversity in a bottleneck effect. Subsequently, the cultivation areas of crops have expanded all over the world into various environmental conditions from the original area along with human migration after domestication. Here, we demonstrated the genetic changes in the adaptation of rice to Hokkaido (41°2-45°3N latitude), Japan, from the tropics of their origin in Asian cultivated rice, Oryza sativa L. Although cultivated rice originated from the tropics, Hokkaido is one of the northern-limits of rice cultivation worldwide. Population genomics focusing on the local populations showed the varieties had genetically distinct classes with limited genetic diversity. In addition, some varieties in the class carried unique genotypes for flowering time, exhibiting extremely early flowering time. Certain mutations in unique genotypes can split off the varieties that are able to grow in Hokkaido. Furthermore, the changes in the genotype for flowering time during rice cultivation in Hokkaido demonstrated novel combinations of genes for flowering time owing to the intensive artificial selection on natural variation and rice breeding programs to achieve stable rice production in Hokkaido.
Collapse
Affiliation(s)
- Kenji Fujino
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, 062-8555, Japan.
| | - Mari Obara
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, 062-8555, Japan
| | - Tomohito Ikegaya
- Hokkaido Agricultural Research Center, National Agricultural Research Organization, Sapporo, 062-8555, Japan
| |
Collapse
|
23
|
Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S. Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1-25. [PMID: 30483819 DOI: 10.1007/s00122-018-3219-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/24/2018] [Indexed: 05/27/2023]
Abstract
CSSLs are a complete library of introgression lines with chromosomal segments of usually a distant genotype in an adapted background and are valuable genetic resources for basic and applied research on improvement of complex traits. Chromosome segment substitution lines (CSSLs) are genetic stocks representing the complete genome of any genotype in the background of a cultivar as overlapping segments. Ideally, each CSSL has a single chromosome segment from the donor with a maximum recurrent parent genome recovered in the background. CSSL development program requires population-wide backcross breeding and genome-wide marker-assisted selection followed by selfing. Each line in a CSSL library has a specific marker-defined large donor segment. CSSLs are evaluated for any target phenotype to identify lines significantly different from the parental line. These CSSLs are then used to map quantitative trait loci (QTLs) or causal genes. CSSLs are valuable prebreeding tools for broadening the genetic base of existing cultivars and harnessing the genetic diversity from the wild- and distant-related species. These are resources for genetic map construction, mapping QTLs, genes or gene interactions and their functional analysis for crop improvement. In the last two decades, the utility of CSSLs in identification of novel genomic regions and QTL hot spots influencing a wide range of traits has been well demonstrated in food and commercial crops. This review presents an overview of how CSSLs are developed, their status in major crops and their use in genomic studies and gene discovery.
Collapse
Affiliation(s)
- Divya Balakrishnan
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Malathi Surapaneni
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sukumar Mesapogu
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sarla Neelamraju
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India.
| |
Collapse
|
24
|
Mulsanti IW, Yamamoto T, Ueda T, Samadi AF, Kamahora E, Rumanti IA, Thanh VC, Adachi S, Suzuki S, Kanekatsu M, Hirasawa T, Ookawa T. Finding the superior allele of japonica-type for increasing stem lodging resistance in indica rice varieties using chromosome segment substitution lines. RICE 2018; 11:25. [PMID: 29671092 PMCID: PMC5906422 DOI: 10.1186/s12284-018-0216-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 04/04/2018] [Indexed: 05/04/2023]
|
25
|
Okada S, Onogi A, Iijima K, Hori K, Iwata H, Yokoyama W, Suehiro M, Yamasaki M. Identification of QTLs for rice grain size using a novel set of chromosomal segment substitution lines derived from Yamadanishiki in the genetic background of Koshihikari. BREEDING SCIENCE 2018; 68:210-218. [PMID: 29875604 PMCID: PMC5982188 DOI: 10.1270/jsbbs.17112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/13/2017] [Indexed: 05/20/2023]
Abstract
Grain size is important for brewing-rice cultivars, but the genetic basis for this trait is still unclear. This paper aims to identify QTLs for grain size using novel chromosomal segment substitution lines (CSSLs) harboring chromosomal segments from Yamadanishiki, an excellent sake-brewing rice, in the genetic background of Koshihikari, a cooking cultivar. We developed a set of 49 CSSLs. Grain length (GL), grain width (GWh), grain thickness (GT), 100-grain weight (GWt) and days to heading (DTH) were evaluated, and a CSSL-QTL analysis was conducted. Eighteen QTLs for grain size and DTH were identified. Seven (qGL11, qGWh5, qGWh10, qGWt6-2, qGWt10-2, qDTH3, and qDTH6) that were detected in F2 and recombinant inbred lines (RILs) from Koshihikari/Yamadanishiki were validated, suggesting that they are important for large grain size and heading date in Yamadanishiki. Additionally, QTL reanalysis for GWt showed that qGWt10-2 was only detected in early-flowering RILs, while qGWt5 (in the same region as qGWh5) was only detected in late-flowering RILs, suggesting that these QTLs show different responses to the environment. Our study revealed that grain size in the Yamadanishiki cultivar is determined by a complex genetic mechanism. These findings could be useful for the breeding of both cooking and brewing rice.
Collapse
Affiliation(s)
- Satoshi Okada
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University,
Kasai, Hyogo 675-2103,
Japan
| | - Akio Onogi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
Yayoi, Bunkyo-Ku, Tokyo 113-8657,
Japan
| | - Ken Iijima
- Institute of Crop Science, National Agriculture and Food Research Organization,
Tsukuba, Ibaraki 305-8518,
Japan
| | - Kiyosumi Hori
- Institute of Crop Science, National Agriculture and Food Research Organization,
Tsukuba, Ibaraki 305-8518,
Japan
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
Yayoi, Bunkyo-Ku, Tokyo 113-8657,
Japan
| | - Wakana Yokoyama
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University,
Kasai, Hyogo 675-2103,
Japan
| | - Miki Suehiro
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University,
Kasai, Hyogo 675-2103,
Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University,
Kasai, Hyogo 675-2103,
Japan
- Corresponding author (e-mail: )
| |
Collapse
|
26
|
Jang S, Lee Y, Lee G, Seo J, Lee D, Yu Y, Chin JH, Koh HJ. Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice. BMC Genet 2018; 19:5. [PMID: 29334899 PMCID: PMC5769279 DOI: 10.1186/s12863-017-0591-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/20/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Balancing panicle-related traits such as panicle length and the numbers of primary and secondary branches per panicle, is key to improving the number of spikelets per panicle in rice. Identifying genetic information contributes to a broader understanding of the roles of gene and provides candidate alleles for use as DNA markers. Discovering relations between panicle-related traits and sequence variants allows opportunity for molecular application in rice breeding to improve the number of spikelets per panicle. RESULTS In total, 142 polymorphic sites, which constructed 58 haplotypes, were detected in coding regions of ten panicle development gene and 35 sequence variants in six genes were significantly associated with panicle-related traits. Rice cultivars were clustered according to their sequence variant profiles. One of the four resultant clusters, which contained only indica and tong-il varieties, exhibited the largest average number of favorable alleles and highest average number of spikelets per panicle, suggesting that the favorable allele combination found in this cluster was beneficial in increasing the number of spikelets per panicle. CONCLUSIONS Favorable alleles identified in this study can be used to develop functional markers for rice breeding programs. Furthermore, stacking several favorable alleles has the potential to substantially improve the number of spikelets per panicle in rice.
Collapse
Affiliation(s)
- Su Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Yunjoo Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Gileung Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jeonghwan Seo
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Dongryung Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Yoye Yu
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Joong Hyoun Chin
- Graduate School of Integrated Bioindustry, Sejong University, 209, Neungdong-ro, Gwangjin-gu, Seoul, 05006, South Korea.
| | - Hee-Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
| |
Collapse
|
27
|
Zhu S, Huang R, Wai HP, Xiong H, Shen X, He H, Yan S. Mapping quantitative trait loci for heat tolerance at the booting stage using chromosomal segment substitution lines in rice. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:817-825. [PMID: 29158631 PMCID: PMC5671447 DOI: 10.1007/s12298-017-0465-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/15/2017] [Accepted: 08/25/2017] [Indexed: 05/21/2023]
Abstract
High temperature stress is a major obstacle in rice productivity. Considerable progress has been made on studying heat tolerance (HT) at different stages. However, the genetic basis of HT at the booting stage is poorly understood. In this study, we analyzed the morphological features of a heat-sensitive japonica cultivar Sasanishiki under natural high temperature stress at the booting stage. The anthers became smaller and the number, and fertility, of pollen grains were decreased significantly. As a result, there was a dramatic reduction in spikelet fertility. In contrast, the indica cultivar Habataki showed high HT and normal spikelet fertility under high temperature stress. Additonally, a set of chromosome segment substitution lines, derived from Sasanishiki and Habataki, were evaluated for HT related quantitative trait loci (QTLs) across two environments in the natural field. A total of 12 QTLs associated with HT were detected, of which, 5 were identified in two environments, and 7 in one environment. Furthermore, one of the major-effect QTLs (qHTB3-3) detected on the long arm of chromosome 3, was confirmed using overlapping substituted lines. qHTB3-3 was finally mapped between the two markers RM3525 and 3-M95, approximately 2.8 Mb apart. These findings and further gene cloning of qHTB3-3 will help us better understand the molecular control of HT in rice, and may contribute to the development of high HT rice varieties.
Collapse
Affiliation(s)
- Shan Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
- Rice National Engineering Laboratory (Nanchang), Nanchang Sub-center, National Rice Improvement Center, Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Renliang Huang
- Rice National Engineering Laboratory (Nanchang), Nanchang Sub-center, National Rice Improvement Center, Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Hnin Pwint Wai
- Rice National Engineering Laboratory (Nanchang), Nanchang Sub-center, National Rice Improvement Center, Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
- Biotechnology Research Department, Department of Research and Innovation, Ministry of Education (Ministry of Science and Technology), Kyaukse, 05151 Myanmar
| | - Hongliang Xiong
- Rice National Engineering Laboratory (Nanchang), Nanchang Sub-center, National Rice Improvement Center, Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Xianhua Shen
- Rice National Engineering Laboratory (Nanchang), Nanchang Sub-center, National Rice Improvement Center, Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 China
| | - Song Yan
- Rice National Engineering Laboratory (Nanchang), Nanchang Sub-center, National Rice Improvement Center, Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang, 330200 China
| |
Collapse
|
28
|
Kumar J, Gupta DS, Gupta S, Dubey S, Gupta P, Kumar S. Quantitative trait loci from identification to exploitation for crop improvement. PLANT CELL REPORTS 2017; 36:1187-1213. [PMID: 28352970 DOI: 10.1007/s00299-017-2127-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/09/2017] [Indexed: 05/24/2023]
Abstract
Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.
Collapse
Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sunanda Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sonali Dubey
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Priyanka Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat-Institutes, B.P. 6299, Rabat, Morocco
| |
Collapse
|
29
|
Sasaki K, Fujita D, Koide Y, Lumanglas PD, Gannaban RB, Tagle AG, Obara M, Fukuta Y, Kobayashi N, Ishimaru T. Fine mapping of a quantitative trait locus for spikelet number per panicle in a new plant type rice and evaluation of a near-isogenic line for grain productivity. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2693-2702. [PMID: 28582550 PMCID: PMC5853308 DOI: 10.1093/jxb/erx128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 04/13/2017] [Indexed: 05/20/2023]
Abstract
Total spikelet number per panicle (TSN) is one of the determinants of grain productivity in rice (Oryza sativa L.). In this study, we attempted to detect quantitative trait loci (QTLs) for TSN in the introgression lines with high TSN, derived from the cross of Indica Group variety IR 64 with new plant type lines. Two QTLs were detected on the long arm of chromosome 12: qTSN12.1 in the BC4F2 population of YTH63/IR 64 and qTSN12.2 in the BC4F3 population of YTH83/IR 64. TSN of the main tiller was significantly higher in near-isogenic lines (NILs) for qTSN12.1 (IR 64-NIL1; 188.6) and for qTSN12.2 (IR 64-NIL12; 199.4) than in IR 64 (141.2), owing to a significant increase in both primary and secondary branch numbers. These results suggest the critical function of these QTLs in the promotion of rachis branching at the panicle formation stage. Fine mapping of qTSN12.2 revealed six candidate genes in a 92-kb region of the Nipponbare reference genome sequence between flanking markers RM28746 and RM28753. Detailed phenotyping of agronomic traits of IR 64-NIL12 carrying qTSN12.2 showed drastic changes in plant architecture: this line had lower panicle number, longer culm, and longer and wider leaves compared with IR 64. Percentage of fertility and 1000-grain weight tended to be greater, and grain yield per square meter was also greater in IR 64-NIL12 than in IR 64. The newly identified QTLs will be useful for genetic improvement of the yield potential of Indica Group varieties. The markers tightly linked to qTSN12.2 are available for marker-assisted breeding.
Collapse
Affiliation(s)
- Kazuhiro Sasaki
- Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Ibaraki, Japan
- International Rice Research Institute (IRRI), DA, Metro Manila, Philippines
- Graduate School of Agricultural and Life Sciences, Institute of Sustainable Agro-ecosystem Services (ISAS), The University of Tokyo, Midoricho, Nishitokyo, Tokyo, Japan
| | - Daisuke Fujita
- Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Ibaraki, Japan
- International Rice Research Institute (IRRI), DA, Metro Manila, Philippines
- Faculty of Agriculture, Saga University, Honjo-machi, Saga, Japan
| | - Yohei Koide
- Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Ibaraki, Japan
- International Rice Research Institute (IRRI), DA, Metro Manila, Philippines
- Research Faculty of Agriculture, Hokkaido University, Kita-9 Nishi-9, Kita-ku, Sapporo, Japan
| | | | - Ritchel B Gannaban
- International Rice Research Institute (IRRI), DA, Metro Manila, Philippines
| | - Analiza G Tagle
- International Rice Research Institute (IRRI), DA, Metro Manila, Philippines
| | - Mitsuhiro Obara
- Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Ibaraki, Japan
| | - Yoshimichi Fukuta
- Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Ibaraki, Japan
| | - Nobuya Kobayashi
- Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Ibaraki, Japan
- International Rice Research Institute (IRRI), DA, Metro Manila, Philippines
- National Institute of Crop Science (NICS), NARO, Kannondai, Tsukuba, Ibaraki, Japan
| | - Tsutomu Ishimaru
- Japan International Research Center for Agricultural Sciences (JIRCAS), Ohwashi, Tsukuba, Ibaraki, Japan
- International Rice Research Institute (IRRI), DA, Metro Manila, Philippines
- Central Region Agricultural Research Center (CARC), National Agriculture and Food Research Organization (NARO), Inada, Joetsu, Niigata, Japan
- Correspondence:
| |
Collapse
|
30
|
Sun Z, Yin X, Ding J, Yu D, Hu M, Sun X, Tan Y, Sheng X, Liu L, Mo Y, Ouyang N, Jiang B, Yuan G, Duan M, Yuan D, Fang J. QTL analysis and dissection of panicle components in rice using advanced backcross populations derived from Oryza Sativa cultivars HR1128 and 'Nipponbare'. PLoS One 2017; 12:e0175692. [PMID: 28422981 PMCID: PMC5396889 DOI: 10.1371/journal.pone.0175692] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/29/2017] [Indexed: 02/04/2023] Open
Abstract
Panicle traits are among the most important agronomic characters which directly relate to yield in rice. Grain number (GN), panicle length (PL), primary branch number (PBN), and secondary branch number (SBN) are the major components of rice panicle structure, and are all controlled by quantitative trait loci (QTLs). In our research, four advanced backcross overlapping populations (BIL152, BIL196a, BIL196b, and BIL196b-156) carrying introgressed segments from chromosome 6 were derived from an indica/japonica cross that used the super-hybrid rice restorer line HR1128 and the international sequenced japonica cultivar ‘Nipponbare’ as the donor and recurrent parents, respectively. The four panicle traits, GN, PL, PBN, and SBN, were evaluated for QTL effects using the inclusive composite interval mapping (ICIM) method in populations over two years at two sites. Results showed that a total of twelve QTLs for GN, PL, PBN, and SBN were detected on chromosome 6. Based on marker loci physical positions, the QTLs were found to be tightly linked to three important chromosomal intervals described as RM7213 to RM19962, RM20000 to RM20210, and RM412 to RM20595. Three QTLs identified in this study, PL6-5, PBN6-1, and PBN6-2, were found to be novel compared with previous studies. A major QTL (PL6-5) for panicle length was detected in all four populations at two locations, and its position was narrowed down to a 1.3Mb region on chromosome 6. Near isogenic lines (NILs) carrying PL6-5 will be developed for fine mapping of the QTL, and our results will provide referable information for gene excavation of panicle components in rice.
Collapse
Affiliation(s)
- Zhizhong Sun
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Xiaoling Yin
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
| | - Jia Ding
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Dong Yu
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Miao Hu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
| | - Xuewu Sun
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Yanning Tan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Xiabing Sheng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Ling Liu
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
| | - Yi Mo
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
| | - Ning Ouyang
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
| | - Beibei Jiang
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
| | - Guilong Yuan
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
| | - Meijuan Duan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
- Long Ping Branch, Graduate School of Hunan University, Changsha, Hunan, China
- * E-mail: (JF); (DYY); (MD)
| | - Dingyang Yuan
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, Hunan, China
- Hunan Academy of Agricultural Sciences, Changsha, Hunan, China
- * E-mail: (JF); (DYY); (MD)
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan, China
- * E-mail: (JF); (DYY); (MD)
| |
Collapse
|
31
|
Surapaneni M, Balakrishnan D, Mesapogu S, Addanki KR, Yadavalli VR, Tripura Venkata VGN, Neelamraju S. Identification of Major Effect QTLs for Agronomic Traits and CSSLs in Rice from Swarna/ Oryza nivara Derived Backcross Inbred Lines. FRONTIERS IN PLANT SCIENCE 2017; 8:1027. [PMID: 28690618 PMCID: PMC5480306 DOI: 10.3389/fpls.2017.01027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/29/2017] [Indexed: 05/04/2023]
Abstract
Backcross inbred lines (BILs) derived from elite x wild crosses are very useful for basic studies and breeding. The aim of this study was to map quantitative trait loci (QTLs) associated with yield and related traits and to identify chromosomal segment substitution lines (CSSLs) from unselected BC2F8 BILs of Swarna/Oryza nivara IRGC81848. In all, 94 BILs were field evaluated in 2 years (wet seasons, 2014 and 2015) for nine traits; days to 50% flowering, days to maturity (DM), plant height (PH), number of tillers, number of productive tillers, panicle weight, yield per plant, bulk yield, and biomass. BILs were genotyped using 111 polymorphic simple sequence repeats distributed across the genome. Fifteen QTLs including 10 novel QTLs were identified using composite interval mapping, Inclusive composite interval mapping and multiple interval mapping (MIM). O. nivara alleles were trait-enhancing in 26% of QTLs. Only 3 of 15 QTLs were also reported previously in BC2F2 of the same cross. These three included the two major effect QTLs for DM and PH detected in both years with 13 and 20% phenotypic variance. Further, a set of 74 CSSLs was identified using CSSL Finder and 22 of these showed significantly higher values than Swarna for five yield traits. CSSLs, 220S for panicle weight and 10-2S with consistent high yield in both years are worthy of large scale field evaluation. The major QTLs and 22 significantly different CSSLs are a useful resource for rice improvement and dissecting yield related traits.
Collapse
|
32
|
Gichuhi E, Himi E, Takahashi H, Zhu S, Doi K, Tsugane K, Maekawa M. Identification of QTLs for yield-related traits in RILs derived from the cross between pLIA-1 carrying Oryza longistaminata chromosome segments and Norin 18 in rice. BREEDING SCIENCE 2016; 66:720-733. [PMID: 28163588 PMCID: PMC5282759 DOI: 10.1270/jsbbs.16083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/01/2016] [Indexed: 05/04/2023]
Abstract
To improve rice yield, a wide genetic pool is necessary. It is therefore important to explore wild rice relatives. Oryza longistaminata is a distantly related wild rice relative that carries the AA genome. Its potential for improving agronomic traits is not well studied. Introgression line (pLIA-1) that carries Oryza longistaminata's chromosome segments, showed high performance in yield-related traits under non-fertilized conditions. Therefore, to illustrate Oryza longistaminata's potential for improving yield-related traits, RILs from the F1 of a cross between pLIA-1 and Norin 18 were developed and QTL analysis was done using the RAD-Seq method. In total, 36 QTLs for yield-related traits were identified on chromosomes 1, 2, 3, 5, 6, 7, 8, 10, and 11. Clusters of QTLs for strongly correlated traits were also identified on chromosomes 1, 3, 6, and 8. Phenotypic data from recombinant plants for chromosomes 1 and 8 QTL clusters revealed that the pLIA-1 genotype on chromosome 1 region was more important for panicle-related traits and a combination of pLIA-1 genotypes on chromosomes 1 and 8 showed a favorable phenotype under non-fertilized conditions. These results suggest that Oryza longistaminata's chromosome segments carry important alleles that can be used to improve yield-related traits of rice.
Collapse
Affiliation(s)
- Emily Gichuhi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan; Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Eiko Himi
- Institute of Plant Science and Resources, Okayama University , Kurashiki, Okayama 710-0046 , Japan
| | - Hidekazu Takahashi
- Graduate School of Bioresource Sciences, Akita Prefectural University , Akita 010-0195 , Japan
| | - Sinhao Zhu
- Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya, Aichi 464-8601 , Japan
| | - Kazuyuki Doi
- Graduate School of Bioagricultural Sciences, Nagoya University , Nagoya, Aichi 464-8601 , Japan
| | - Kazuo Tsugane
- National Institute for Basic Biology , Okazaki, Aichi 444-8585 , Japan
| | - Masahiko Maekawa
- Institute of Plant Science and Resources, Okayama University , Kurashiki, Okayama 710-0046 , Japan
| |
Collapse
|
33
|
Ookawa T, Aoba R, Yamamoto T, Ueda T, Takai T, Fukuoka S, Ando T, Adachi S, Matsuoka M, Ebitani T, Kato Y, Mulsanti IW, Kishii M, Reynolds M, Piñera F, Kotake T, Kawasaki S, Motobayashi T, Hirasawa T. Precise estimation of genomic regions controlling lodging resistance using a set of reciprocal chromosome segment substitution lines in rice. Sci Rep 2016; 6:30572. [PMID: 27465821 PMCID: PMC4964586 DOI: 10.1038/srep30572] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 07/04/2016] [Indexed: 01/30/2023] Open
Abstract
Severe lodging has occurred in many improved rice varieties after the recent strong typhoons in East and Southeast Asian countries. The indica variety Takanari possesses strong culm characteristics due to its large section modulus, which indicates culm thickness, whereas the japonica variety Koshihikari is subject to substantial bending stress due to its thick cortical fibre tissue. To detect quantitative trait loci (QTLs) for lodging resistance and to eliminate the effects of genetic background, we used reciprocal chromosome segment substitution lines (CSSLs) derived from a cross between Koshihikari and Takanari. The oppositional effects of QTLs for section modulus were confirmed in both genetic backgrounds on chromosomes 1, 5 and 6, suggesting that these QTLs are not affected by the genetic background and are controlled independently by a single factor. The candidate region of a QTL for section modulus included SD1. The section modulus of NIL-sd1 was lower than that of Koshihikari, whereas the section modulus of NIL-SD1 was higher than that of Takanari. This result indicated that those regions regulate the culm thickness. The reciprocal effects of the QTLs for cortical fibre tissue thickness were confirmed in both genetic backgrounds on chromosome 9 using CSSLs.
Collapse
Affiliation(s)
- Taiichiro Ookawa
- Institute of Agriculture, Graduate School, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Ryo Aoba
- Institute of Agriculture, Graduate School, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Toshio Yamamoto
- NARO Agrogenomics Research Center, Tsukuba, Ibaraki 305-8602, Japan
| | - Tadamasa Ueda
- NARO Agrogenomics Research Center, Tsukuba, Ibaraki 305-8602, Japan
| | - Toshiyuki Takai
- Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan
| | - Shuichi Fukuoka
- NARO Agrogenomics Research Center, Tsukuba, Ibaraki 305-8602, Japan
| | - Tsuyu Ando
- NARO Agrogenomics Research Center, Tsukuba, Ibaraki 305-8602, Japan
| | - Shunsuke Adachi
- Institute of Agriculture, Graduate School, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Makoto Matsuoka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Takeshi Ebitani
- Agricultural Research Institute, Toyama Agricultural, Forestry &Fisheries Research Center, Toyama, Toyama 939-8153, Japan
| | - Yoichiro Kato
- International Rice Research Institute, Los Banos, Philippines
| | - Indria Wahyu Mulsanti
- Institute of Agriculture, Graduate School, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Masahiro Kishii
- International Maize and Wheat Improvement Center, Texcoco, 56237, Mexico
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center, Texcoco, 56237, Mexico
| | - Francisco Piñera
- International Maize and Wheat Improvement Center, Texcoco, 56237, Mexico
| | - Toshihisa Kotake
- Graduate School of Science and Engineering, Saitama University, Saitama 338-8570, Japan
| | - Shinji Kawasaki
- Department of Plant Physiology, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Takashi Motobayashi
- Institute of Agriculture, Graduate School, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Tadashi Hirasawa
- Institute of Agriculture, Graduate School, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| |
Collapse
|
34
|
Zhang HW, Fan YY, Zhu YJ, Chen JY, Yu SB, Zhuang JY. Dissection of the qTGW1.1 region into two tightly-linked minor QTLs having stable effects for grain weight in rice. BMC Genet 2016; 17:98. [PMID: 27363861 PMCID: PMC4929766 DOI: 10.1186/s12863-016-0410-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/24/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Most agronomical traits of crop species are complex traits controlled by multiple genes and affected by environmental factors. While considerable efforts have been made to fine-map and clone major quantitative trait loci (QTLs) for yield-related traits in rice, it is not until recently that the attention has been paid to minor QTLs. Following previous dissection of QTLs for grain weight and grain size in a 12-Mb interval on the long arm of chromosome 1 in rice, this study targeted at one putative QTL region for a more precise mapping and for analyzing the genotype-by-environment interaction of minor QTLs. RESULTS Four BC2F10 plants of the indica rice cross ZS97///ZS97//ZS97/MY46 were selected. They carried overlapped heterozygous segments that jointly covered the entire putative region for qTGW1.1 detected previously. Four sets of near isogenic lines (NILs) were developed from selfing progenies of the four plants. Each NIL set consisted of 32 ZS97 homozygous lines and 32 MY46 homozygous lines that differed in the corresponding heterozygous region. They were grown in two locations having distinct ecological conditions and measured for 1000-grain weight, grain length and grain width. Two QTLs were separated in an 835.2-kb interval flanked by DNA markers Wn28447 and RM11569. They both showed consistent effects across the two environments. The qTGW1.1a located within the 120.4-kb interval Wn28447 - RM11543 significantly affect all the three traits with the enhancing allele derived from ZS97, showing a stronger influence on grain weight than on grain length and width. The qTGW1.1b located in the 521.8-kb interval RM11554 - RM11569 significantly affect grain weight and length with the enhancing allele derived from MY46, having a stronger influence on grain length than on grain weight. Consistent performance of the two QTLs was confirmed in a validation experiment using five NIL-F2 populations segregated for either qTGW1.1a or qTGW1.1b. CONCLUSION Separation of closely-linked QTLs having small effects is achievable in the absence of major-QTL segregation. Minor QTLs for complex traits could act consistently in diverse environments, offering the potential of pyramiding beneficial alleles of multiple minor QTLs through marker-assisted selection.
Collapse
Affiliation(s)
- Hong-Wei Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.,State Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Ye-Yang Fan
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yu-Jun Zhu
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jun-Yu Chen
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Si-Bin Yu
- State Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.
| |
Collapse
|
35
|
Zhao L, Lei J, Huang Y, Zhu S, Chen H, Huang R, Peng Z, Tu Q, Shen X, Yan S. Mapping quantitative trait loci for heat tolerance at anthesis in rice using chromosomal segment substitution lines. BREEDING SCIENCE 2016; 66:358-66. [PMID: 27436945 PMCID: PMC4902453 DOI: 10.1270/jsbbs.15084] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 01/18/2016] [Indexed: 05/04/2023]
Abstract
To study the genetic basis of heat tolerance at anthesis, a set of chromosome segment substitution lines (CSSLs) derived from Sasanishiki (japonica ssp. heat susceptible) and Habataki (indica spp. heat tolerant) were used for analysis across three high temperature environments. Spikelet fertility (SF), daily flowering time (DFT) and pollen shedding level (PSL) under high temperature (HT) were assessed. Eleven related QTLs were detected, of which, two QTLs qSF (ht) 2 and qSF (ht) 4.2 for spikelet fertility were identified on chromosomes 2 and 4. Four QTLs qDFT3, qDFT8, qDFT10.1 and qDFT11 for daily flowering time were detected on chromosomes 3, 8, 10 and 11. The other five QTLs qPSL (ht) 1, qPSL (ht) 4.1, qPSL (ht) 5, qPSL (ht) 7 and qPSL (ht) 10.2 on chromosomes 1, 4, 5, 7 and 10, respectively, were found had effects both on spikelet fertility and pollen shedding level. Of the 11 QTLs, 8 were overlapped with QTLs reported by others, 3 QTLs qPSL (ht) 4.1, qPSL (ht) 7 and qPSL (ht) 10.2 identified in this study were novel. The stability of qPSL (ht) 4.1 was further verified at different temperatures, which could be used to improve the pollen shedding and pollen growth on stigma for rice heat-tolerance breeding.
Collapse
Affiliation(s)
- Lei Zhao
- Rice National Engineering Laboratory (Nanchang), Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences,
Nanchang 330200,
China
- College of Agronomy, Jiangxi Agricultural University,
Nanchang 330045,
China
- Key Laboratory of Agriculture Responding to Climate Change,
Nanchang 30045,
China
| | - Jianguo Lei
- Rice National Engineering Laboratory (Nanchang), Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences,
Nanchang 330200,
China
- College of Agronomy, Jiangxi Agricultural University,
Nanchang 330045,
China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education,
Nanchang 330045,
China
| | - Yingjin Huang
- College of Agronomy, Jiangxi Agricultural University,
Nanchang 330045,
China
- Key Laboratory of Agriculture Responding to Climate Change,
Nanchang 30045,
China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education,
Nanchang 330045,
China
| | - Shan Zhu
- Rice National Engineering Laboratory (Nanchang), Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences,
Nanchang 330200,
China
- College of Agronomy, Jiangxi Agricultural University,
Nanchang 330045,
China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education,
Nanchang 330045,
China
| | - Hongping Chen
- Rice National Engineering Laboratory (Nanchang), Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences,
Nanchang 330200,
China
| | - Renliang Huang
- Rice National Engineering Laboratory (Nanchang), Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences,
Nanchang 330200,
China
| | - Zhiqin Peng
- Rice National Engineering Laboratory (Nanchang), Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences,
Nanchang 330200,
China
- College of Agronomy, Jiangxi Agricultural University,
Nanchang 330045,
China
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education,
Nanchang 330045,
China
| | - Qinghua Tu
- Rice National Engineering Laboratory (Nanchang), Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences,
Nanchang 330200,
China
- Jiangxi Seed Administration,
Jiangxi Province 30046,
China
| | - Xianhua Shen
- Rice National Engineering Laboratory (Nanchang), Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences,
Nanchang 330200,
China
| | - Song Yan
- Rice National Engineering Laboratory (Nanchang), Jiangxi Provincial Key Laboratory of Rice Physiology and Genetics, Rice Research Institute, Jiangxi Academy of Agricultural Sciences,
Nanchang 330200,
China
- Corresponding author (e-mail: )
| |
Collapse
|
36
|
Tang W, Wu T, Ye J, Sun J, Jiang Y, Yu J, Tang J, Chen G, Wang C, Wan J. SNP-based analysis of genetic diversity reveals important alleles associated with seed size in rice. BMC PLANT BIOLOGY 2016; 16:93. [PMID: 27095382 PMCID: PMC4837510 DOI: 10.1186/s12870-016-0779-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/13/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Single-nucleotide polymorphisms (SNPs) have become the genetic markers of choice in various genetic, ecological, and evolutionary studies. Genotyping-by-sequencing (GBS) is a next-generation-sequencing based method that takes advantage of reduced representation to enable high-throughput genotyping using a large number of SNP markers. RESULTS In the present study, the distribution of non-redundant SNPs in the parents of 12 rice recombination line populations was evaluated through GBS. A total of 45 Gigabites of nucleotide sequences conservatively provided satisfactory genotyping of rice SNPs. By assembling to the genomes of reference genomes of japonica Nipponbare, we detected 22,682 polymorphic SNPs that may be utilized for QTL/gene mapping with the Recombinant Inbred Lines (RIL) populations derived from these parental lines. Meanwhile, we identified polymorphic SNPs with large effects on protein-coding and miRNA genes. To validate the effect of the polymorphic SNPs, we further investigated a SNP (chr4:28,894,757) at the miRNA binding site in the 3'-UTR region of the locus Os4g48460, which is associated with rice seed size. Os4g48460 encodes a putative cytochrome P450, CYP704A3. Direct degradation of the 3'-UTR of the CYP704A3 gene by a miRNA (osa-miRf10422-akr) was validated by in planta mRNA degradation assay. We also showed that rice seeds of longer lengths may be produced by downregulating CYP704A3 via RNAi. CONCLUSIONS Our study has identified the genome-wide SNPs by GBS of the parental varieties of RIL populations and identified CYP704A3, a miRNA-regulated gene that is responsible for rice seed length.
Collapse
Affiliation(s)
- Weijie Tang
- />State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095 Nanjing, China
- />Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Tingting Wu
- />State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jian Ye
- />State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Juan Sun
- />State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095 Nanjing, China
| | - Yue Jiang
- />State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jun Yu
- />State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095 Nanjing, China
| | - Jianpeng Tang
- />State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095 Nanjing, China
| | - Gaoming Chen
- />State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095 Nanjing, China
| | - Chunming Wang
- />State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095 Nanjing, China
- />Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, China
| | - Jianmin Wan
- />State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 210095 Nanjing, China
- />National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| |
Collapse
|
37
|
Rebolledo MC, Peña AL, Duitama J, Cruz DF, Dingkuhn M, Grenier C, Tohme J. Combining Image Analysis, Genome Wide Association Studies and Different Field Trials to Reveal Stable Genetic Regions Related to Panicle Architecture and the Number of Spikelets per Panicle in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:1384. [PMID: 27703460 PMCID: PMC5029283 DOI: 10.3389/fpls.2016.01384] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 08/30/2016] [Indexed: 05/19/2023]
Abstract
Number of spikelets per panicle (NSP) is a key trait to increase yield potential in rice (O. sativa). The architecture of the rice inflorescence which is mainly determined by the length and number of primary (PBL and PBN) and secondary (SBL and SBN) branches can influence NSP. Although several genes controlling panicle architecture and NSP in rice have been identified, there is little evidence of (i) the genetic control of panicle architecture and NSP in different environments and (ii) the presence of stable genetic associations with panicle architecture across environments. This study combines image phenotyping of 225 accessions belonging to a genetic diversity array of indica rice grown under irrigated field condition in two different environments and Genome Wide Association Studies (GWAS) based on the genotyping of the diversity panel, providing 83,374 SNPs. Accessions sown under direct seeding in one environement had reduced Panicle Length (PL), NSP, PBN, PBL, SBN, and SBL compared to those established under transplanting in the second environment. Across environments, NSP was significantly and positively correlated with PBN, SBN and PBL. However, the length of branches (PBL and SBL) was not significantly correlated with variables related to number of branches (PBN and SBN), suggesting independent genetic control. Twenty- three GWAS sites were detected with P ≤ 1.0E-04 and 27 GWAS sites with p ≤ 5.9E-04. We found 17 GWAS sites related to NSP, 10 for PBN and 11 for SBN, 7 for PBL and 11 for SBL. This study revealed new regions related to NSP, but only three associations were related to both branching number (PBN and SBN) and NSP. Two GWAS sites associated with SBL and SBN were stable across contrasting environments and were not related to genes previously reported. The new regions reported in this study can help improving NSP in rice for both direct seeded and transplanted conditions. The integrated approach of high-throughput phenotyping, multi-environment field trials and GWAS has the potential to dissect complex traits, such as NSP, into less complex traits and to match single nucleotide polymorphisms with relevant function under different environments, offering a potential use for molecular breeding.
Collapse
Affiliation(s)
- Maria C. Rebolledo
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
- *Correspondence: Maria C. Rebolledo
| | - Alexandra L. Peña
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
| | - Jorge Duitama
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
| | - Daniel F. Cruz
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
| | - Michael Dingkuhn
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
- Agricultural Research for Development - CIRAD, Unités Mixtes de Recherche - Amélioration Génétique et Adaptation des PlantesMontpellier, France
| | - Cecile Grenier
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
- Agricultural Research for Development - CIRAD, Unités Mixtes de Recherche - Amélioration Génétique et Adaptation des PlantesMontpellier, France
| | - Joe Tohme
- Agrobiodiversity, International Center for Tropical AgriculturePalmira, Colombia
| |
Collapse
|
38
|
Yamamoto T, Suzuki T, Suzuki K, Adachi S, Sun J, Yano M, Ookawa T, Hirasawa T. Detection of QTL for exudation rate at ripening stage in rice and its contribution to hydraulic conductance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:270-277. [PMID: 26566844 DOI: 10.1016/j.plantsci.2015.08.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/16/2015] [Accepted: 08/22/2015] [Indexed: 06/05/2023]
Abstract
Dry matter production of crops is determined by how much light they intercept and how efficiently they use it for carbon fixation; i.e., photosynthesis. The high-yielding rice cultivar, Akenohoshi, maintains a high photosynthetic rate in the middle of the day owing to its high hydraulic conductance in comparison with the elite commercial rice cultivar, Koshihikari. We developed 94 recombinant inbred lines derived from Akenohoshi and Koshihikari and measured their exudation rate to calculate hydraulic conductance to osmotic water transport in a paddy field. A quantitative trait locus (QTL) for exudation rate was detected on the long arm of chromosome 2 at the heading and ripening stages. We developed chromosome segment substitution lines which carried Akenohoshi segments in the Koshihikari genetic background, and measured hydraulic conductance to both osmotic and passive water transport. The QTL was confirmed to be located within a region of about 4.2Mbp on the distal end of long arm of chromosome 2. The Akenohoshi allele increased root surface area and hydraulic conductance, but didn't increase hydraulic conductivity of a plant.
Collapse
Affiliation(s)
- Toshio Yamamoto
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Tadafumi Suzuki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Kenji Suzuki
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Shunsuke Adachi
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan; Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan; NARO Institute of Crop Science, Tsukuba, Ibaraki, 305-8518, Japan
| | - Jian Sun
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan
| | - Masahiro Yano
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan; NARO Institute of Crop Science, Tsukuba, Ibaraki, 305-8518, Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Tadashi Hirasawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| |
Collapse
|
39
|
Nagata K, Ando T, Nonoue Y, Mizubayashi T, Kitazawa N, Shomura A, Matsubara K, Ono N, Mizobuchi R, Shibaya T, Ogiso-Tanaka E, Hori K, Yano M, Fukuoka S. Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross. BREEDING SCIENCE 2015; 65:308-18. [PMID: 26366113 PMCID: PMC4542931 DOI: 10.1270/jsbbs.65.308] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 05/29/2015] [Indexed: 05/18/2023]
Abstract
Grain shape is an important trait for improving rice yield. A number of quantitative trait loci (QTLs) for this trait have been identified by using primary F2 mapping populations and recombinant inbred lines, in which QTLs with a small effect are harder to detect than they would be in advanced generations. In this study, we developed two advanced mapping populations (chromosome segment substitution lines [CSSLs] and BC4F2 lines consisting of more than 2000 individuals) in the genetic backgrounds of two improved cultivars: a japonica cultivar (Koshihikari) with short, round grains, and an indica cultivar (IR64) with long, slender grains. We compared the ability of these materials to reveal QTLs for grain shape with that of an F2 population. Only 8 QTLs for grain length or grain width were detected in the F2 population, versus 47 in the CSSL population and 65 in the BC4F2 population. These results strongly suggest that advanced mapping populations can reveal QTLs for agronomic traits under complicated genetic control, and that DNA markers linked with the QTLs are useful for choosing superior allelic combinations to enhance grain shape in the Koshihikari and IR64 genetic backgrounds.
Collapse
Affiliation(s)
- Kazufumi Nagata
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Tsuyu Ando
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Yasunori Nonoue
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries,
446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854,
Japan
| | - Tatsumi Mizubayashi
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Noriyuki Kitazawa
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Ayahiko Shomura
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kazuki Matsubara
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Nozomi Ono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries,
446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854,
Japan
| | - Ritsuko Mizobuchi
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Taeko Shibaya
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Eri Ogiso-Tanaka
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Kiyosumi Hori
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Masahiro Yano
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Shuichi Fukuoka
- National Institute of Agrobiological Sciences,
2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
- Corresponding author (e-mail: )
| |
Collapse
|
40
|
Ozone-Induced Rice Grain Yield Loss Is Triggered via a Change in Panicle Morphology That Is Controlled by ABERRANT PANICLE ORGANIZATION 1 Gene. PLoS One 2015; 10:e0123308. [PMID: 25923431 PMCID: PMC4414449 DOI: 10.1371/journal.pone.0123308] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/03/2015] [Indexed: 11/25/2022] Open
Abstract
Rice grain yield is predicted to decrease in the future because of an increase in tropospheric ozone concentration. However, the underlying mechanisms are unclear. Here, we investigated the responses to ozone of two rice (Oryza Sativa L.) cultivars, Sasanishiki and Habataki. Sasanishiki showed ozone-induced leaf injury, but no grain yield loss. By contrast, Habataki showed grain yield loss with minimal leaf injury. A QTL associated with grain yield loss caused by ozone was identified in Sasanishiki/Habataki chromosome segment substitution lines and included the ABERRANT PANICLE ORGANIZATION 1 (APO1) gene. The Habataki allele of the APO1 locus in a near-isogenic line also resulted in grain yield loss upon ozone exposure, suggesting APO1 involvement in ozone-induced yield loss. Only a few differences in the APO1 amino acid sequences were detected between the cultivars, but the APO1 transcript level was oppositely regulated by ozone exposure: i.e., it increased in Sasanishiki and decreased in Habataki. Interestingly, the levels of some phytohormones (jasmonic acid, jasmonoyl-L-isoleucine, and abscisic acid) known to be involved in attenuation of ozone-induced leaf injury tended to decrease in Sasanishiki but to increase in Habataki upon ozone exposure. These data indicate that ozone-induced grain yield loss in Habataki is caused by a reduction in the APO1 transcript level through an increase in the levels of phytohormones that reduce leaf damage.
Collapse
|
41
|
Arbelaez JD, Moreno LT, Singh N, Tung CW, Maron LG, Ospina Y, Martinez CP, Grenier C, Lorieux M, McCouch S. Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015; 35:81. [PMID: 25705117 PMCID: PMC4328105 DOI: 10.1007/s11032-015-0276-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/29/2015] [Indexed: 05/04/2023]
Abstract
Two populations of interspecific introgression lines (ILs) in a common recurrent parent were developed for use in pre-breeding and QTL mapping. The ILs were derived from crosses between cv Curinga, a tropical japonica upland cultivar, and two different wild donors, Oryza meridionalis Ng. accession (W2112) and Oryza rufipogon Griff. accession (IRGC 105491). The lines were genotyped using genotyping-by-sequencing (GBS) and SSRs. The 32 Curinga/O. meridionalis ILs contain 76.73 % of the donor genome in individual introgressed segments, and each line has an average of 94.9 % recurrent parent genome. The 48 Curinga/O. rufipogon ILs collectively contain 97.6 % of the donor genome with an average of 89.9 % recurrent parent genome per line. To confirm that these populations were segregating for traits of interest, they were phenotyped for pericarp color in the greenhouse and for four agronomic traits-days to flowering, plant height, number of tillers, and number of panicles-in an upland field environment. Seeds from these IL libraries and the accompanying GBS datasets are publicly available and represent valuable genetic resources for exploring the genetics and breeding potential of rice wild relatives.
Collapse
Affiliation(s)
- Juan D. Arbelaez
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853-1901 USA
| | - Laura T. Moreno
- School of Botany, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Namrata Singh
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853-1901 USA
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, 106 Taiwan
| | - Lyza G. Maron
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853-1901 USA
| | - Yolima Ospina
- Rice Program, International Center for Tropical Agriculture (CIAT), AA6713 Cali, Colombia
| | - César P. Martinez
- Rice Program, International Center for Tropical Agriculture (CIAT), AA6713 Cali, Colombia
| | | | - Mathias Lorieux
- DIADE Research Unit, Institut de Recherche Pour le Développement, 34394 Montpellier Cedex 5, France
- Rice Genetics and Genomics Laboratory, International Center for Tropical Agriculture (CIAT), AA6713 Cali, Colombia
| | - Susan McCouch
- Department of Plant Breeding and Genetics, Cornell University, 162 Emerson Hall, Ithaca, NY 14853-1901 USA
| |
Collapse
|
42
|
Matsuda F, Nakabayashi R, Yang Z, Okazaki Y, Yonemaru JI, Ebana K, Yano M, Saito K. Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 81:13-23. [PMID: 25267402 PMCID: PMC4309412 DOI: 10.1111/tpj.12681] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 09/19/2014] [Accepted: 09/19/2014] [Indexed: 05/18/2023]
Abstract
Plants produce structurally diverse secondary (specialized) metabolites to increase their fitness for survival under adverse environments. Several bioactive compounds for new drugs have been identified through screening of plant extracts. In this study, genome-wide association studies (GWAS) were conducted to investigate the genetic architecture behind the natural variation of rice secondary metabolites. GWAS using the metabolome data of 175 rice accessions successfully identified 323 associations among 143 single nucleotide polymorphisms (SNPs) and 89 metabolites. The data analysis highlighted that levels of many metabolites are tightly associated with a small number of strong quantitative trait loci (QTLs). The tight association may be a mechanism generating strains with distinct metabolic composition through the crossing of two different strains. The results indicate that one plant species produces more diverse phytochemicals than previously expected, and plants still contain many useful compounds for human applications.
Collapse
Affiliation(s)
- Fumio Matsuda
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University1-5 Yamadaoka, Suita, Osaka, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Zhigang Yang
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan
| | - Jun-ichi Yonemaru
- National Institute of Agrobiological Sciences2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Kaworu Ebana
- National Institute of Agrobiological Sciences2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Masahiro Yano
- National Institute of Agrobiological Sciences2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba UniversityInohana 1-8-1, Chuo-ku, Chiba, Japan
- *For correspondence (e-mail )
| |
Collapse
|
43
|
Kim DM, Lee HS, Kwon SJ, Fabreag ME, Kang JW, Yun YT, Chung CT, Ahn SN. High-density mapping of quantitative trait loci for grain-weight and spikelet number in rice. RICE (NEW YORK, N.Y.) 2014; 7:14. [PMID: 26055996 PMCID: PMC4884038 DOI: 10.1186/s12284-014-0014-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 07/14/2014] [Indexed: 05/14/2023]
Abstract
BACKGROUND High grain yield is one of the most important traits requiring improvement in rice breeding programs. Consequently, the genetic basis of spikelets per panicle (SPP) and grain weight (TGW) have received much research focus because of their importance in rice yield. RESULTS In this study, IL28, which is a near isogenic line (NIL) developed by introgressing chromosomal segments of the cultivar 'Moroberekan' into the cultivar 'Ilpumbyeo', showed a significant increase in the number of spikelets per panicle (SPP) and 1,000-grain weight (TGW) compared to the recurrent parent, Ilpumbyeo. Quantitative trait locus (QTL) analysis in 243 F2 plants derived from a cross between IL28 and Ilpumbyeo indicated that both qSPP6 and qTGW6 are located in the interval RM3430-RM20580. Following substitution mapping with 50 F3:4:5 lines, qSPP6 was mapped to a 429-kb interval between RM20521 and InDel-1, while qTGW6 was mapped to a 37.85-kb interval between InDel-1 and SNP--3 based on the japonica genome sequence. This result indicates that qSPP6 and qTGW6 are different genes. Yield trials with substitution lines indicated that lines harboring the homozygous Moroberekan segment at both the qSPP6 and qTGW6 region showed significantly higher grain yield than Ilpumbyeo. CONCLUSION Because the Moroberekan alleles for SPP and TGW have been shown to be beneficial in the genetic background of Ilpumbyeo, both the qSPP6 and qTGW6 alleles might prove valuable in improving rice yields. Closely linked SSR markers are expected to facilitate the cloning of genes that underlie these QTLs, as well as with marker-assisted selection for variation in SPP and TGW in rice breeding programs.
Collapse
Affiliation(s)
- Dong-Min Kim
- />Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, 305-764 South Korea
- />Present address: Department of Variety Testing, Korea Seed & Variety Service, Ministry of Agriculture, Food and Rural Affairs, Kimcheon, 740-220 South Korea
| | - Hyun-Sook Lee
- />Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, 305-764 South Korea
| | - Soo-Jin Kwon
- />National Academy of Agricultural Science, Rural Development Administration, Suweon, 441-707 South Korea
| | - Mark Edward Fabreag
- />Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, 305-764 South Korea
| | - Ju-Won Kang
- />Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, 305-764 South Korea
| | - Yeo-Tae Yun
- />Chungnam Agricultural Research and Extension Services, Yesan, 340-861 South Korea
| | - Chong-Tae Chung
- />Chungnam Agricultural Research and Extension Services, Yesan, 340-861 South Korea
| | - Sang-Nag Ahn
- />Department of Agronomy, College of Agriculture & Life Sciences, Chungnam National University, Daejeon, 305-764 South Korea
| |
Collapse
|
44
|
Takai T, Ikka T, Kondo K, Nonoue Y, Ono N, Arai-Sanoh Y, Yoshinaga S, Nakano H, Yano M, Kondo M, Yamamoto T. Genetic mechanisms underlying yield potential in the rice high-yielding cultivar Takanari, based on reciprocal chromosome segment substitution lines. BMC PLANT BIOLOGY 2014; 14:295. [PMID: 25404368 PMCID: PMC4243286 DOI: 10.1186/s12870-014-0295-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 10/17/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND Increasing rice yield potential is a major objective in rice breeding programs, given the need for meeting the demands of population growth, especially in Asia. Genetic analysis using genomic information and high-yielding cultivars can facilitate understanding of the genetic mechanisms underlying rice yield potential. Chromosome segment substitution lines (CSSLs) are a powerful tool for the detection and precise mapping of quantitative trait loci (QTLs) that have both large and small effects. In addition, reciprocal CSSLs developed in both parental cultivar backgrounds may be appropriate for evaluating gene activity, as a single factor or in epistatic interactions. RESULTS We developed reciprocal CSSLs derived from a cross between Takanari (one of the most productive indica cultivars) and a leading japonica cultivar, Koshihikari; both the cultivars were developed in Japan. Forty-one CSSLs covered most of the Takanari genome in the Koshihikari background and 39 CSSLs covered the Koshihikari genome in the Takanari background. Using the reciprocal CSSLs, we conducted yield trials under canopy conditions in paddy fields. While no CSSLs significantly exceeded the recurrent parent cultivar in yield, genetic analysis detected 48 and 47 QTLs for yield and its components in the Koshihikari and Takanari backgrounds, respectively. A number of QTLs showed a trade-off, in which the allele with increased sink-size traits (spikelet number per panicle or per square meter) was associated with decreased ripening percentage or 1000-grain weight. These results indicate that increased sink size is not sufficient to increase rice yield in both backgrounds. In addition, most QTLs were detected in either one of the two genetic backgrounds, suggesting that these loci may be under epistatic control with other gene(s). CONCLUSIONS We demonstrated that the reciprocal CSSLs are a useful tool for understanding the genetic mechanisms underlying yield potential in the high-yielding rice cultivar Takanari. Our results suggest that sink-size QTLs in combination with QTLs for source strength or translocation capacity, as well as careful attention to epistatic interactions, are necessary for increasing rice yield. Thus, our findings provide a foundation for developing rice cultivars with higher yield potential in future breeding programs.
Collapse
Affiliation(s)
- Toshiyuki Takai
- />NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518 Japan
- />National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 Japan
| | - Takashi Ikka
- />National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 Japan
| | - Katsuhiko Kondo
- />National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 Japan
| | - Yasunori Nonoue
- />Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | - Nozomi Ono
- />Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854 Japan
| | | | | | - Hiroshi Nakano
- />NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518 Japan
| | - Masahiro Yano
- />National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 Japan
| | - Motohiko Kondo
- />NARO Institute of Crop Science, Tsukuba, Ibaraki 305-8518 Japan
| | - Toshio Yamamoto
- />National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602 Japan
| |
Collapse
|
45
|
Jahani M, Nematzadeh G, Dolatabadi B, Hashemi SH, Mohammadi-Nejad G. Identification and validation of functional markers in a global rice collection by association mapping. Genome 2014; 57:355-62. [PMID: 25243661 DOI: 10.1139/gen-2014-0044] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Recent results indicate that marker-assisted selection is an effective approach to reduce the cost and to improve the efficacy and accuracy of selection in plant breeding. This study was conducted to identify and validate molecular markers linked to important breeding traits by association mapping. The association was evaluated between 81 molecular markers (STS, SSR, Indel, CAPS, and PCR-based SNP) and 15 morphological traits in a global panel of 100 rice (Oryza sativa) accessions. The population structure analysis identified three main subpopulations. Obvious kinship relationships were also detected between the rice accessions. Association analysis was performed based on the mixed linear model by considering population structure and family relatedness. In addition, the false discovery rate method was used to correct the multiple testing. A total of 47 marker-trait associations were identified, including 22 markers for 14 traits. Among all, the polymorphism at the loci DDR-GL was highly associated with grain characters (grain length, grain width, and length/width ratio). In addition, marker RM3148 was responsible for five important traits simultaneously. Results demonstrated that such informative markers can be very useful for rice breeding programs using marker-assisted selection. Moreover, the diverse populations of rice accessions are a valuable resource for association mapping of morphological traits.
Collapse
Affiliation(s)
- Mojtaba Jahani
- a Department of Agronomy and Plant Breeding, Faculty of Agriculture, Shahid Bahonar University of Kerman, P.O. Box 76169-133, Kerman, Iran
| | | | | | | | | |
Collapse
|
46
|
Crowell S, Falcão AX, Shah A, Wilson Z, Greenberg AJ, McCouch SR. High-Resolution Inflorescence Phenotyping Using a Novel Image-Analysis Pipeline, PANorama. PLANT PHYSIOLOGY 2014; 165:479-495. [PMID: 24696519 PMCID: PMC4044845 DOI: 10.1104/pp.114.238626] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/01/2014] [Indexed: 05/19/2023]
Abstract
Variation in inflorescence development is an important target of selection for numerous crop species, including many members of the Poaceae (grasses). In Asian rice (Oryza sativa), inflorescence (panicle) architecture is correlated with yield and grain-quality traits. However, many rice breeders continue to use composite phenotypes in selection pipelines, because measuring complex, branched panicles requires a significant investment of resources. We developed an open-source phenotyping platform, PANorama, which measures multiple architectural and branching phenotypes from images simultaneously. PANorama automatically extracts skeletons from images, allows users to subdivide axes into individual internodes, and thresholds away structures, such as awns, that normally interfere with accurate panicle phenotyping. PANorama represents an improvement in both efficiency and accuracy over existing panicle imaging platforms, and flexible implementation makes PANorama capable of measuring a range of organs from other plant species. Using high-resolution phenotypes, a mapping population of recombinant inbred lines, and a dense single-nucleotide polymorphism data set, we identify, to our knowledge, the largest number of quantitative trait loci (QTLs) for panicle traits ever reported in a single study. Several areas of the genome show pleiotropic clusters of panicle QTLs, including a region near the rice Green Revolution gene SEMIDWARF1. We also confirm that multiple panicle phenotypes are distinctly different among a small collection of diverse rice varieties. Taken together, these results suggest that clusters of small-effect QTLs may be responsible for varietal or subpopulation-specific panicle traits, representing a significant opportunity for rice breeders selecting for yield performance across different genetic backgrounds.
Collapse
Affiliation(s)
- Samuel Crowell
- Department of Plant Biology (S.C., S.R.M.) and Department of Plant Breeding and Genetics (A.X.F., A.S., Z.W., A.J.G., S.R.M.), Cornell University, Ithaca, New York 14853; andDepartment of Information Systems Institute of Computing, University of Campinas, CEP 13083-852 Sao Paulo, Brazil (A.X.F.)
| | - Alexandre X Falcão
- Department of Plant Biology (S.C., S.R.M.) and Department of Plant Breeding and Genetics (A.X.F., A.S., Z.W., A.J.G., S.R.M.), Cornell University, Ithaca, New York 14853; andDepartment of Information Systems Institute of Computing, University of Campinas, CEP 13083-852 Sao Paulo, Brazil (A.X.F.)
| | - Ankur Shah
- Department of Plant Biology (S.C., S.R.M.) and Department of Plant Breeding and Genetics (A.X.F., A.S., Z.W., A.J.G., S.R.M.), Cornell University, Ithaca, New York 14853; andDepartment of Information Systems Institute of Computing, University of Campinas, CEP 13083-852 Sao Paulo, Brazil (A.X.F.)
| | - Zachary Wilson
- Department of Plant Biology (S.C., S.R.M.) and Department of Plant Breeding and Genetics (A.X.F., A.S., Z.W., A.J.G., S.R.M.), Cornell University, Ithaca, New York 14853; andDepartment of Information Systems Institute of Computing, University of Campinas, CEP 13083-852 Sao Paulo, Brazil (A.X.F.)
| | - Anthony J Greenberg
- Department of Plant Biology (S.C., S.R.M.) and Department of Plant Breeding and Genetics (A.X.F., A.S., Z.W., A.J.G., S.R.M.), Cornell University, Ithaca, New York 14853; andDepartment of Information Systems Institute of Computing, University of Campinas, CEP 13083-852 Sao Paulo, Brazil (A.X.F.)
| | - Susan R McCouch
- Department of Plant Biology (S.C., S.R.M.) and Department of Plant Breeding and Genetics (A.X.F., A.S., Z.W., A.J.G., S.R.M.), Cornell University, Ithaca, New York 14853; andDepartment of Information Systems Institute of Computing, University of Campinas, CEP 13083-852 Sao Paulo, Brazil (A.X.F.)
| |
Collapse
|
47
|
Adachi S, Baptista LZ, Sueyoshi T, Murata K, Yamamoto T, Ebitani T, Ookawa T, Hirasawa T. Introgression of two chromosome regions for leaf photosynthesis from an indica rice into the genetic background of a japonica rice. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2049-56. [PMID: 24591053 PMCID: PMC3991736 DOI: 10.1093/jxb/eru047] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Increases in rates of individual leaf photosynthesis (P n) are critical for future increases of rice yields. A previous study, using introgression lines derived from a cross between indica cultivar Habataki, with one of the highest recorded values of P n, and the Japanese elite cultivar Koshihikari, identified four QTLs (qCAR4, qCAR5, qCAR8, and qCAR11) that affect P n. The present study examined the combined effect of qCAR4 and qCAR8 on P n in the genetic background of Koshihikari. The pyramided near-isogenic line NIL(qCAR4+qCAR8) showed higher P n than both NIL(qCAR4) and NIL(qCAR8), equivalent to that of Habataki despite being due to only two out of the four QTLs. The high P n of NIL(qCAR4+qCAR8) may be attributable to the high leaf nitrogen content, which may have been inherited from NIL(qCAR4), to the large hydraulic conductance due to the large root surface area from NIL(qCAR4), and to the high hydraulic conductivity from NIL(qCAR8). It might be also attributable to high mesophyll conductance, which may have been inherited from NIL(qCAR4). The induction of mesophyll conductance and the high leaf nitrogen content and high hydraulic conductivity could not be explained in isolation from the Koshihikari background. These results suggest that QTL pyramiding is a useful approach in rice breeding aimed at increasing P n.
Collapse
Affiliation(s)
- Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu 183–8509, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Kawaguchi 332-0012, Japan
- National Institute of Agrobiological Sciences, Tsukuba 305–8602, Japan
| | - Leticia Z. Baptista
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu 183–8509, Japan
| | - Tomohiro Sueyoshi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu 183–8509, Japan
| | - Kazumasa Murata
- Toyama Prefectural Agricultural, Forestry and Fisheries Research Center, Toyama 939–8153, Japan
| | - Toshio Yamamoto
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, Kawaguchi 332-0012, Japan
| | - Takeshi Ebitani
- Toyama Prefectural Agricultural, Forestry and Fisheries Research Center, Toyama 939–8153, Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu 183–8509, Japan
| | - Tadashi Hirasawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu 183–8509, Japan
- * To whom correspondence should be addressed. E-mail:
| |
Collapse
|
48
|
Furuta T, Uehara K, Angeles-Shim RB, Shim J, Ashikari M, Takashi T. Development and evaluation of chromosome segment substitution lines (CSSLs) carrying chromosome segments derived from Oryza rufipogon in the genetic background of Oryza sativa L. BREEDING SCIENCE 2014; 63:468-75. [PMID: 24757386 PMCID: PMC3949583 DOI: 10.1270/jsbbs.63.468] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 11/25/2013] [Indexed: 05/04/2023]
Abstract
The wild relatives of rice (Oryza sativa L.) are useful sources of alleles that have evolved to adapt in diverse environments around the world. Oryza rufipogon, the known progenitor of the cultivated rice, harbors genes that have been lost in cultivated varieties through domestication or evolution. This makes O. rufipogon an ideal source of value-added traits that can be utilized to improve the existing rice cultivars. To explore the potential of the rice progenitor as a genetic resource for improving O. sativa, 33 chromosome segment substitution lines (CSSLs) of O. rufipogon (W0106) in the background of the elite japonica cultivar Koshihikari were developed and evaluated for several agronomic traits. Over 90% of the entire genome was introgressed from the donor parent into the CSSLs. A total of 99 putative QTLs were detected, of which 15 were identified as major effective QTLs that have significantly large effects on the traits examined. Among the 15 major effective QTLs, a QTL on chromosome 10 showed a remarkable positive effect on the number of grains per panicle. Comparison of the putative QTLs identified in this study and previous studies indicated a wide genetic diversity between O. rufipogon accessions.
Collapse
Affiliation(s)
- Tomoyuki Furuta
- Bioscience and Biotechnology Center, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
| | - Kanako Uehara
- Bioscience and Biotechnology Center, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
| | - Rosalyn B. Angeles-Shim
- Bioscience and Biotechnology Center, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
| | - Junghyun Shim
- Bioscience and Biotechnology Center, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University,
Chikusa, Nagoya, Aichi 464-8601,
Japan
| | - Tomonori Takashi
- STAY GREEN Co., Ltd.,
2-1-5 Kazusa-Kamatari, Kisarazu, Chiba 292-0818,
Japan
- Corresponding author (e-mail: )
| |
Collapse
|
49
|
QTL mapping and correlation analysis for 1000-grain weight and percentage of grains with chalkiness in rice. J Genet 2013; 92:281-7. [DOI: 10.1007/s12041-013-0267-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
50
|
Zuo S, Yin Y, Pan C, Chen Z, Zhang Y, Gu S, Zhu L, Pan X. Fine mapping of qSB-11(LE), the QTL that confers partial resistance to rice sheath blight. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1257-72. [PMID: 23423653 DOI: 10.1007/s00122-013-2051-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 01/19/2013] [Indexed: 05/22/2023]
Abstract
Sheath blight (SB), caused by Rhizoctonia solani kühn, is one of the most serious global rice diseases. No major resistance genes to SB have been identified so far. All discovered loci are quantitative resistance to rice SB. The qSB-11(LE) resistance quantitative trait locus (QTL) has been previously reported on chromosome 11 of Lemont (LE). In this study, we report the precise location of qSB-11 (LE) . We developed a near isogenic line, NIL-qSB11(TQ), by marker-assisted selection that contains susceptible allele(s) from Teqing (TQ) at the qSB-11 locus in the LE genetic background. NIL-qSB11(TQ) shows higher susceptibility to SB than LE in both field and greenhouse tests, suggesting that this region of LE contains a QTL contributing to SB resistance. In order to eliminate the genetic background effects and increase the accuracy of phenotypic evaluation, a total of 112 chromosome segment substitution lines (CSSLs) with the substituted segment specific to the qSB-11 (LE) region were produced as the fine mapping population. The genetic backgrounds and morphological characteristics of these CSSLs are similar to those of the recurrent parent LE. The donor TQ chromosomal segments in these CSSL lines contiguously overlap to bridge the qSB-11 (LE) region. Through artificial inoculation, all CSSLs were evaluated for resistance to SB in the field in 2005. For the recombinant lines, their phenotypes were evaluated in the field for another 3 years and during the final year were also evaluated in a controlled greenhouse environment, showing a consistent phenotype in SB resistance across years and conditions. After comparing the genotypic profile of each CSSL with its phenotype, we are able to localize qSB-11 (LE) to the region defined by two cleaved-amplified polymorphic sequence markers, Z22-27C and Z23-33C covering 78.871 kb, based on the rice reference genome. Eleven putative genes were annotated within this region and three of them were considered the most likely candidates. The results of this study will greatly facilitate the cloning of the genes responsible for qSB-11 (LE) and marker-assisted breeding to incorporate qSB-11 (LE) into other rice cultivars.
Collapse
Affiliation(s)
- Shimin Zuo
- Key Lab of Plant Functional Genomics, Ministry of Education, Yangzhou University, Yangzhou 225009, People's Republic of China.
| | | | | | | | | | | | | | | |
Collapse
|