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Ekta, Maiti MK. Rice Big Grain1 improves grain yield in ectopically expressing rice and heterologously expressing tobacco plants. PLANT MOLECULAR BIOLOGY 2024; 114:73. [PMID: 38874648 DOI: 10.1007/s11103-024-01472-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 05/26/2024] [Indexed: 06/15/2024]
Abstract
Functional genomics through transgenesis has provided faster and more reliable methods for identifying, characterizing, and utilizing genes or quantitative trait loci linked to agronomic traits to target yield. The present study explored the role of Big Grain1 (BG1) gene of rice (Oryza sativa L.) in yield improvement of crop plants. We aimed to identify the genetic variation of OsBG1 in various indica rice cultivars by studying the allelic polymorphism of the gene, while also investigating the gene's potential to increase crop yield through the transgenic approach. Our study reports the presence of an extra 393 bp sequence having two 6 bp enhancer elements in the 3' regulatory sequence of OsBG1 in the large-grain cultivar IR64 but not in the small-grain cultivar Badshahbhog. A single copy of the OsBG1 gene in both the cultivars and a 4.1-fold higher expression of OsBG1 in IR64 than in Badshahbhog imply that the grain size is positively correlated with the level of OsBG1 expression in rice. The ectopic expression of OsBG1 under the endosperm-specific glutelin C promoter in Badshahbhog enhanced the flag leaf length, panicle weight, and panicle length by an average of 33.2%, 33.7%, and 30.5%, respectively. The length of anthers, spikelet fertility, and grain yield per plant increased in transgenic rice lines by an average of 27.5%, 8.3%, and 54.4%, respectively. Heterologous expression of OsBG1 under the constitutive 2xCaMV35S promoter improved the number of seed pods per plant and seed yield per plant in transgenic tobacco lines by an average of 2.2-fold and 2.6-fold, respectively. Improving crop yield is crucial to ensure food security and socio-economic stability, and identifying suitable genetic factor is the essential step towards this endeavor. Our findings suggest that the OsBG1 gene is a promising candidate for improving the grain yield of monocot and dicot plant systems by molecular breeding and genetic engineering.
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Affiliation(s)
- Ekta
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India
| | - Mrinal K Maiti
- Department of Bioscience and Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, India.
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Roy N, Kabir AH, Zahan N, Mouna ST, Chakravarty S, Rahman AH, Bayzid MS. Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh. PLANT DIRECT 2024; 8:e593. [PMID: 38887667 PMCID: PMC11182691 DOI: 10.1002/pld3.593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/26/2024] [Accepted: 05/02/2024] [Indexed: 06/20/2024]
Abstract
Rice genetic diversity is regulated by multiple genes and is largely dependent on various environmental factors. Uncovering the genetic variations associated with the diversity in rice populations is the key to breed stable and high yielding rice varieties. We performed genome wide association studies (GWASs) on seven rice yielding traits (grain length, grain width, grain weight, panicle length, leaf length, leaf width, and leaf angle) based on a population of 183 rice landraces of Bangladesh. Our GWASs reveal various chromosomal regions and candidate genes that are associated with different traits in Bangladeshi rice varieties. Noteworthy was the recurrent implication of chromosome 10 in all three grain-shape-related traits (grain length, grain width, and grain weight), indicating its pivotal role in shaping rice grain morphology. Our study also underscores the involvement of transposon gene families across these three traits. For leaf related traits, chromosome 10 was found to harbor regions that are significantly associated with leaf length and leaf width. The results of these association studies support previous findings as well as provide additional insights into the genetic diversity of rice. This is the first known GWAS study on various yield-related traits in the varieties of Oryza sativa available in Bangladesh-the fourth largest rice-producing country. We believe this study will accelerate rice genetics research and breeding stable high-yielding rice in Bangladesh.
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Affiliation(s)
- Nilanjan Roy
- Department of Biomedical EngineeringMilitary Institute of Science and TechnologyDhakaBangladesh
- Molecular, Cellular, and Developmental BiologyUniversity of KansasLawrenceKansasUSA
| | - Acramul Haque Kabir
- Department of Biomedical EngineeringMilitary Institute of Science and TechnologyDhakaBangladesh
- Department of Biomedical EngineeringUniversity of UtahSalt Lake CityUtahUSA
| | - Nourin Zahan
- Department of Biomedical EngineeringMilitary Institute of Science and TechnologyDhakaBangladesh
| | - Shahba Tasmiya Mouna
- Department of Biomedical EngineeringMilitary Institute of Science and TechnologyDhakaBangladesh
| | - Sakshar Chakravarty
- Department of Computer Science and EngineeringUniversity of CaliforniaRiversideCaliforniaUSA
- Department of Computer Science and EngineeringBangladesh University of Engineering and TechnologyDhakaBangladesh
| | - Atif Hasan Rahman
- Department of Computer Science and EngineeringBangladesh University of Engineering and TechnologyDhakaBangladesh
| | - Md. Shamsuzzoha Bayzid
- Department of Computer Science and EngineeringBangladesh University of Engineering and TechnologyDhakaBangladesh
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Liu M, Li Z, Kang Y, Lv J, Jin Z, Mu S, Yue H, Li L, Chen P, Li Y. A mutation in CsGME encoding GDP-mannose 3,5-epimerase results in little and wrinkled leaf in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:114. [PMID: 38678513 DOI: 10.1007/s00122-024-04600-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/13/2024] [Indexed: 05/01/2024]
Abstract
KEY MESSAGE Map-based cloning revealed that a mutation in a highly conserved amino acid of the CsGME gene encoding GDP-mannose 3,5-epimerase, causes the phenotype of little and wrinkled leaves in cucumbers. Leaf size is a critical determinant of plant architecture in cucumbers, yet only a few genes associated with this trait have been mapped or cloned. Here, we identified and characterized a mutant with little and wrinkled leaves, named lwl-1. Genetic analysis revealed that the phenotype of the lwl-1 was controlled by a single recessive gene. Through map-based cloning, the lwl-1 locus was narrowed down to a 12.22-kb region exclusively containing one fully annotated gene CsGME (CsaV3_2G004170). CsGME encodes GDP-mannose 3,5-epimerase, which is involved in the synthesis of ascorbic acid (ASA) and one of the components of pectin, RG-II. Whole-length sequencing of the 12.22 kb DNA fragment revealed the presence of only a non-synonymous mutation located in the sixth exon of CsGME in lwl-1, resulting in an amino acid alteration from Pro363 to Leu363. This mutation was unique among 118 inbred lines from cucumber natural populations. CsGME expression significantly reduced in various organs of lwl-1, accompanied by a significant decrease in ASA and pectin content in leaves. Both CsGME and Csgme proteins were localized to the cytoplasm. The mutant phenotype exhibited partial recovery after the application of exogenous boric acid. Silencing CsGME in cucumber through VIGS confirmed its role as the causal gene for lwl-1. Transcriptome profiling revealed that CsGME greatly affected the expression of genes related to the cell division process and cell plate formation. This study represents the first report to characterize and clone the CsGME in cucumber, indicating its crucial role in regulating leaf size and development.
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Affiliation(s)
- Mengying Liu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhaowei Li
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yunfeng Kang
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jinzhao Lv
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhuoshuai Jin
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Siyu Mu
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Hongzhong Yue
- Vegetable Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, Gansu, China
| | - Lixia Li
- College of Horticulture, Shanxi Agricultural University, Taigu, 030801, China
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Zhang X, Xing P, Lin C, Wang H, Bao Y, Li X. QTL mapping for the flag leaf-related traits using RILs derived from Trititrigia germplasm line SN304 and wheat cultivar Yannong15 in multiple environments. BMC PLANT BIOLOGY 2024; 24:297. [PMID: 38632517 PMCID: PMC11025246 DOI: 10.1186/s12870-024-04993-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Developing and enriching genetic resources plays important role in the crop improvement. The flag leaf affects plant architecture and contributes to the grain yield of wheat (Triticum aestivum L.). The genetic improvement of flag leaf traits faces problems such as a limited genetic basis. Among the various genetic resources of wheat, Thinopyrum intermedium has been utilized as a valuable resource in genetic improvement due to its disease resistance, large spikes, large leaves, and multiple flowers. In this study, a recombinant inbred line (RIL) population was derived from common wheat Yannong15 and wheat-Th. intermedium introgression line SN304 was used to identify the quantitative trait loci (QTL) for flag leaf-related traits. RESULTS QTL mapping was performed for flag leaf length (FLL), flag leaf width (FLW) and flag leaf area (FLA). A total of 77 QTLs were detected, and among these, 51 QTLs with positive alleles were contributed by SN304. Fourteen major QTLs for flag leaf traits were detected on chromosomes 2B, 3B, 4B, and 2D. Additionally, 28 QTLs and 8 QTLs for flag leaf-related traits were detected in low-phosphorus and drought environments, respectively. Based on major QTLs of positive alleles from SN304, we identified a pair of double-ended anchor primers mapped on chromosome 2B and amplified a specific band of Th. intermedium in SN304. Moreover, there was a major colocated QTL on chromosome 2B, called QFll/Flw/Fla-2B, which was delimited to a physical interval of approximately 2.9 Mb and contained 20 candidate genes. Through gene sequence and expression analysis, four candidate genes associated with flag leaf formation and growth in the QTL interval were identified. CONCLUSION These results promote the fine mapping of QFll/Flw/Fla-2B, which have pleiotropic effects, and will facilitate the identification of candidate genes for flag leaf-related traits. Additionally, this work provides a theoretical basis for the application of Th. intermedium in wheat breeding.
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Affiliation(s)
- Xia Zhang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong, 253023, China
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Piyi Xing
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Caicai Lin
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong, 253023, China
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Honggang Wang
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yinguang Bao
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xingfeng Li
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
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Sun Y, Jing D, Zhang J, Du L, Li C, Lan Y, Lin F, Zhou T. Yield components affected by rice black-streaked dwarf virus disease in rice cultivars with different resistance levels. Front Microbiol 2023; 14:1323569. [PMID: 38156012 PMCID: PMC10752958 DOI: 10.3389/fmicb.2023.1323569] [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: 10/18/2023] [Accepted: 11/15/2023] [Indexed: 12/30/2023] Open
Abstract
Introduction Rice black-streaked dwarf virus disease (RBSDVD) is one of the most destructive rice viral diseases, leading to severe yield losses in rice production. However, little is known about the yield-related components associated with the disease and no resistance cultivars have been successfully used in rice breeding. Methods Seven rice cultivars were analyzed in this study, including six commercial rice varieties and a new line Zhongjian No. 201 (ZJ201) containing the resistance gene OsAP47. Resistance levels of these cultivars were evaluated by artificial inoculation and yield components were collected, including panicle length (PL), spikelets per panicle (SPP), ripened grains per panicle (RGPP), as well as panicles per square meter (PPSM) and 1000-grain weight (TGW). Seed setting rate (SSR) were calculated with the data of SPP and RGPP. Results and discussion The results showed that ZJ201 displayed the highest resistance level and most of the commercial rice cultivars exhibited susceptible to RBSDVD. Yields of all the rice cultivars were significantly declined except ZJ201 and yield losses produced by RBSDVD were mainly due to the reduction of PL, SPP, RGPP, and TGW, suggesting that developments of these traits are associated with RBSDV infection. Resistant rice cultivar could reduce yield losses by maintaining normal development of these traits. Significant correlations were identified between resistance levels and the yield components except SSR and PPSM. The results provided useful clues for understanding the mechanisms of RBSDV invasion and its effect on rice production. ZJ201 was demonstrated as a resistance material that could be used in rice breeding.
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Affiliation(s)
- Yue Sun
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Dedao Jing
- Zhenjiang Institute of Agricultural Sciences of the Ning-Zhen Hilly District, Zhenjiang, Jiangsu, China
| | - Jiayuan Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Linlin Du
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Chenyang Li
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Ying Lan
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Feng Lin
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
- College of Food Science, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Tong Zhou
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu, China
- International Joint Center for Japonica Rice Research, Nanjing, Jiangsu, China
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Cheng Q, Huang S, Lin L, Zhong Q, Huang T, He H, Bian J. Genetic Analysis for the Flag Leaf Heterosis of a Super-Hybrid Rice WFYT025 Combination Using RNA-Seq. PLANTS (BASEL, SWITZERLAND) 2023; 12:2496. [PMID: 37447057 DOI: 10.3390/plants12132496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/06/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023]
Abstract
The photosynthetic capacity of flag leaf plays a key role in grain yield in rice. Nevertheless, there are few studies on the heterosis of the rice flag leaf. Therefore, this study focuses on investigating the genetic basis of heterosis for flag leaf in the indica super hybrid rice combination WFYT025 in China using a high-throughput next-generation RNA-seq strategy. We analyzed the gene expression of flag leaf in different environments and different time periods between WFYT025 and its female parent. After obtaining the gene expression profile of the flag leaf, we further investigated the gene regulatory network. Weighted gene expression network analysis (WGCNA) was used to identify the co-expressed gene sets, and a total of 5000 highly expressed genes were divided into 24 co-expression groups. In CHT025, we found 13 WRKY family transcription factors in SDGhps under the environment of early rice and 16 WRKY family genes in SDGhps of under the environment of middle rice. We found nine identical transcription factors in the two stages. Except for five reported TFs, the other four TFs might play an important role in heterosis for grain number and photosynthesis. Transcription factors such as WRKY3, WRKY68, and WRKY77 were found in both environments. To eliminate the influence of the environment, we examined the metabolic pathway with the same SDGhp (SSDGhp) in two environments. There were 312 SSDGhps in total. These SSDGhps mainly focused on the phosphorus metallic process, phosphorylation, plasma membrane, etc. These results provide resources for studying heterosis during super hybrid rice flag leaf development.
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Affiliation(s)
- Qin Cheng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shiying Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lan Lin
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qi Zhong
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Tao Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jianmin Bian
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang 330045, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
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Li Y, Tao F, Hao Y, Tong J, Xiao Y, He Z, Reynolds M. Variations in phenological, physiological, plant architectural and yield-related traits, their associations with grain yield and genetic basis. ANNALS OF BOTANY 2023; 131:503-519. [PMID: 36655618 PMCID: PMC10072080 DOI: 10.1093/aob/mcad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND AIMS Physiological and morphological traits play essential roles in wheat (Triticum aestivum) growth and development. In particular, photosynthesis is a limitation to yield. Increasing photosynthesis in wheat has been identified as an important strategy to increase yield. However, the genotypic variations and the genomic regions governing morphological, architectural and photosynthesis traits remain unexplored. METHODS Here, we conducted a large-scale investigation of the phenological, physiological, plant architectural and yield-related traits, involving 32 traits for 166 wheat lines during 2018-2020 in four environments, and performed a genome-wide association study with wheat 90K and 660K single nucleotide polymorphism (SNP) arrays. KEY RESULTS These traits exhibited considerable genotypic variations in the wheat diversity panel. Higher yield was associated with higher net photosynthetic rate (r = 0.41, P < 0.01), thousand-grain weight (r = 0.36, P < 0.01) and truncated and lanceolate shape, but shorter plant height (r = -0.63, P < 0.01), flag leaf angle (r = -0.49, P < 0.01) and spike number per square metre (r = -0.22, P < 0.01). Genome-wide association mapping discovered 1236 significant stable loci detected in the four environments among the 32 traits using SNP markers. Trait values have a cumulative effect as the number of the favourable alleles increases, and significant progress has been made in determining phenotypic values and favourable alleles over the years. Eleven elite cultivars and 14 traits associated with grain yield per plot (GY) were identified as potential parental lines and as target traits to develop high-yielding cultivars. CONCLUSIONS This study provides new insights into the phenotypic and genetic elucidation of physiological and morphological traits in wheat and their associations with GY, paving the way for discovering their underlying gene control and for developing enhanced ideotypes in wheat breeding.
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Affiliation(s)
- Yibo Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | | | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yonggui Xiao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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Narawatthana S, Phansenee Y, Thammasamisorn BO, Vejchasarn P. Multi-model genome-wide association studies of leaf anatomical traits and vein architecture in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1107718. [PMID: 37123816 PMCID: PMC10130391 DOI: 10.3389/fpls.2023.1107718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Introduction The anatomy of rice leaves is closely related to photosynthesis and grain yield. Therefore, exploring insight into the quantitative trait loci (QTLs) and alleles related to rice flag leaf anatomical and vein traits is vital for rice improvement. Methods Here, we aimed to explore the genetic architecture of eight flag leaf traits using one single-locus model; mixed-linear model (MLM), and two multi-locus models; fixed and random model circulating probability unification (FarmCPU) and Bayesian information and linkage disequilibrium iteratively nested keyway (BLINK). We performed multi-model GWAS using 329 rice accessions of RDP1 with 700K single-nucleotide polymorphisms (SNPs) markers. Results The phenotypic correlation results indicated that rice flag leaf thickness was strongly correlated with leaf mesophyll cells layer (ML) and thickness of both major and minor veins. All three models were able to identify several significant loci associated with the traits. MLM identified three non-synonymous SNPs near NARROW LEAF 1 (NAL1) in association with ML and the distance between minor veins (IVD) traits. Discussion Several numbers of significant SNPs associated with known gene function in leaf development and yield traits were detected by multi-model GWAS performed in this study. Our findings indicate that flag leaf traits could be improved via molecular breeding and can be one of the targets in high-yield rice development.
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Affiliation(s)
- Supatthra Narawatthana
- Rice Department, Thailand Rice Science Institute, Ministry of Agriculture and Cooperatives (MOAC), Suphan Buri, Thailand
- *Correspondence: Supatthra Narawatthana,
| | - Yotwarit Phansenee
- Ubon Ratchathani Rice Research Center, Rice Department, Ministry of Agriculture and Cooperatives (MOAC), Ubon Ratchathani, Thailand
| | - Bang-On Thammasamisorn
- Rice Department, Thailand Rice Science Institute, Ministry of Agriculture and Cooperatives (MOAC), Suphan Buri, Thailand
| | - Phanchita Vejchasarn
- Ubon Ratchathani Rice Research Center, Rice Department, Ministry of Agriculture and Cooperatives (MOAC), Ubon Ratchathani, Thailand
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Chen L, Xu Z, Fan X, Zhou Q, Yu Q, Liu X, Liao S, Jiang C, Lin D, Ma F, Feng B, Wang T. Genetic dissection of quantitative trait loci for flag leaf size in bread wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1047899. [PMID: 36600920 PMCID: PMC9807109 DOI: 10.3389/fpls.2022.1047899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Flag leaf size is a crucial trait influencing plant architecture and yield potential in wheat. A recombinant inbred line (RIL) population derived from the cross of W7268 and Chuanyu 12 was employed to identify quantitative trait loci (QTL) controlling flag leaf length (FLL), flag leaf width (FLW), and flag leaf area (FLA) in six environments and the best linear unbiased estimator (BLUE) datasets. Using a 55 K SNP-based genetic map, six major and stable QTL were detected with 6.33-53.12% of explained phenotypic variation. Except for QFlw.cib-4B.3, the other five major QTL were co-located within two intervals on chromosomes 2B and 2D, namely QFll/Fla.cib-2B and QFll/Flw/Fla.cib-2D, respectively. Their interactions and effects on the corresponding traits and yield-related traits were also assessed based on flanking markers. QFll/Fla.cib-2B showed pleiotropic effects on spikelet number per spike (SNS). QFlw.cib-4B.3 and QFll/Flw/Fla.cib-2D had effects on grain number per spike (GNS) and thousand-grain weight (TGW). Comparison analysis suggested that QFll/Fla.cib-2B was likely a new locus. Two candidate genes, TraesCS2B03G0222800 and TraesCS2B03G0230000, associated with leaf development within the interval of QFll/Fla.cib-2B were identified based on expression-pattern analysis, gene annotation, ortholog analysis, and sequence variation. The major QTL and markers reported here provide valuable information for understanding the genetic mechanism underlying flag leaf size as well as breeding utilization in wheat.
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Affiliation(s)
- Liangen Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qin Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Cheng Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dian Lin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fang Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
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10
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Lu Q, Yu X, Wang H, Yu Z, Zhang X, Zhao Y. Construction of ultra-high-density genetic linkage map of a sorghum-sudangrass hybrid using whole genome resequencing. PLoS One 2022; 17:e0278153. [PMID: 36445892 PMCID: PMC9707794 DOI: 10.1371/journal.pone.0278153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
The sorghum-sudangrass hybrid is a vital annual gramineous herbage. Few reports exist on its ultra-high-density genetic map. In this study, we sought to create an ultra-high-density genetic linkage map for this hybrid to strengthen its functional genomics research and genetic breeding. We used 150 sorghum-sudangrass hybrid F2 individuals and their parents (scattered ear sorghum and red hull sudangrass) for high-throughput sequencing on the basis of whole genome resequencing. In total, 1,180.66 Gb of data were collected. After identification, filtration for integrity, and partial segregation, over 5,656 single nucleotide polymorphism markers of high quality were detected. An ultra-high-density genetic linkage map was constructed using these data. The markers covered approximately 2,192.84 cM of the map with average marker intervals of 0.39 cM. The length ranged from 115.39 cM to 264.04 cM for the 10 linkage groups. Currently, this represents the first genetic linkage map of this size, number of molecular markers, density, and coverage for sorghum-sudangrass hybrid. The findings of this study provide valuable genome-level information on species evolution and comparative genomics analysis and lay the foundation for further research on quantitative trait loci fine mapping and gene cloning and marker-assisted breeding of important traits in sorghum-sudangrass hybrids.
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Affiliation(s)
- Qianqian Lu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xiaoxia Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Huiting Wang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Zhuo Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- * E-mail:
| | - Xia Zhang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Yaqi Zhao
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
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11
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Li Y, Tao F, Hao Y, Tong J, Xiao Y, He Z, Reynolds M. Wheat traits and the associated loci conferring radiation use efficiency. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:565-582. [PMID: 36004546 DOI: 10.1111/tpj.15954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 06/15/2023]
Abstract
Wheat (Triticum aestivum L.) radiation use efficiency (RUE) must be raised through crop breeding to further increase the yield potential, as the harvest index is now close to its theoretical limit. Field experiments including 209 wheat cultivars which have been widely cultivated in China since the 1940s were conducted in two growing seasons (2018-2019 and 2019-2020) to evaluate the variations of phenological, physiological, plant architectural, and yield-related traits and their contributions to RUE and to identify limiting factors for wheat yield potential. The average annual genetic gain in grain yield was 0.60% (or 45.32 kg ha-1 year-1 ; R2 = 0.44, P < 0.01), mainly attributed to the gain in RUE (r = 0.85, P < 0.01). The net photosynthetic rates were positively and closely correlated with grain RUE and grain yield, suggesting source as a limiting factor to future yield gains. Thirty-four cultivars were identified, exhibiting not only high RUE, but also traits contributing to high RUE and 11 other critical traits - of known genetic basis - as potential parents for breeding to improve yield and RUE. Our findings reveal wheat traits and the associated loci conferring RUE, which are valuable for facilitating marker-assisted breeding to improve wheat RUE and yield potential.
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Affiliation(s)
- Yibo Li
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fulu Tao
- Key Laboratory of Land Surface Pattern and Simulation, Institute of Geographic Sciences and Natural Resources Research, CAS, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jingyang Tong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yonggui Xiao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Matthew Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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12
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Sabouri H, Alegh SM, Sahranavard N, Sanchouli S. SSR Linkage Maps and Identification of QTL Controlling Morpho-Phenological Traits in Two Iranian Wheat RIL Populations. BIOTECH 2022; 11:biotech11030032. [PMID: 35997340 PMCID: PMC9397039 DOI: 10.3390/biotech11030032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/22/2022] [Accepted: 08/02/2022] [Indexed: 11/22/2022] Open
Abstract
Wheat is one of the essential grains grown in large areas. Identifying the genetic structure of agronomic and morphological traits of wheat can help to discover the genetic mechanisms of grain yield. In order to map the morpho-phenological traits, an experiment was conducted in the two cropping years of 2020 and 2021 on the university farm of the Faculty of Agriculture, GonbadKavous University. This study used two F8 populations, including 120 lines resulting from Gonbad × Zagros and Gonbad × Kuhdasht. The number of days to physiological maturity, number of days to flowering, number of germinated grains, number of tillers, number of tillers per plant, grain filling periods, plant height, peduncle length, spike length, awn length, spike weight, peduncle diameter, flag leaf length and weight, number of spikelets per spike, number of grains per spike, grain length, grain width, 1000-grain weight, biomass, grain yield, harvest index, straw-weight, and number of fertile spikelets per spike were measured. A total of 21 and 13 QTLs were identified for 11 and 13 traits in 2020 and 2021, respectively. In 2020, qGL-3D and qHI-1A were identified for grain length and harvest index on chromosomes 3D and 1A, explaining over 20% phenotypic variation, respectively. qNT-5B, qNTS-2D, and qSL-1D were identified on chromosomes 5B, 2D, and 1D with the LOD scores of 4.5, 4.13, and 3.89 in 2021, respectively.
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Affiliation(s)
- Hossein Sabouri
- Department of Plant Production, College of Agricultural Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous 4971799151, Iran
- Correspondence: (H.S.); (S.S.); Tel.: +98-911-143-8917 (H.S.); +98-911-793-0631 (S.S.)
| | - Sharifeh Mohammad Alegh
- Department of Plant Production, College of Agricultural Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous 4971799151, Iran
| | - Narges Sahranavard
- Department of Biology, College of Science, Gonbad Kavous University, Gonbad Kavous 4971799151, Iran
| | - Somayyeh Sanchouli
- Department of Plant Production, College of Agricultural Science and Natural Resources, Gonbad Kavous University, Gonbad Kavous 4971799151, Iran
- Correspondence: (H.S.); (S.S.); Tel.: +98-911-143-8917 (H.S.); +98-911-793-0631 (S.S.)
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13
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Zhao C, Liu X, Liu H, Kong W, Zhao Z, Zhang S, Wang S, Chen Y, Wu Y, Sun H, Qin R, Cui F. Fine mapping of QFlw-5B, a major QTL for flag leaf width in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2531-2541. [PMID: 35680741 DOI: 10.1007/s00122-022-04135-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 05/17/2022] [Indexed: 06/15/2023]
Abstract
A major stable QTL for flag leaf width was narrowed down to 2.5 Mb region containing two predicated putative candidate genes, and its effects on yield-related traits was characterized. Flag leaf width (FLW) is important to production in wheat. In a previous study, a major quantitative trait locus for FLW (QFlw-5B) was detected on chromosome 5B, within an interval of 6.5 cM flanked by the markers of XwPt-9103 and Xbarc142, using a mapping population of recombinant inbred lines derived from a cross between Kenong9204 (KN9204) and Jing411 (J411) (denoted as KJ-RILs). The aim of this study was to fine map QFlw-5B and characterize its genetic effects on yield-related traits. Multiple near-isogenic lines (NILs) were developed using one residual heterozygous line for QFlw-5B. Five recombinants for QFlw-5B were identified, and its location was narrowed to a 2.5 Mb region based on combined phenotypic and genotypic data analysis. This region contained 27 predicted genes, two of which were considered as the most likely candidate genes for QFlw-5B. The FLW of NIL-KN9204 was significantly higher than that of NIL-J411 across all the tested environments. Meanwhile, significant increases in plant height, grain width and 1000-grain weight were observed in NIL-KN9204 compared with that in NIL-J411. These results indicate that QFlw-5B has great potential for marker-assisted selection in wheat breeding programs designed to improve both plant architecture and yield. This study also provides a basis for the map-based cloning of QFlw-5B.
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Affiliation(s)
- Chunhua Zhao
- College of Agriculture, Ludong University, Yantai, 264025, Shandong, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants, Yantai, 264025, China
| | - Xijian Liu
- College of Agriculture, Ludong University, Yantai, 264025, Shandong, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants, Yantai, 264025, China
| | - Hongwei Liu
- College of Agriculture, Ludong University, Yantai, 264025, Shandong, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants, Yantai, 264025, China
| | - Wenchao Kong
- College of Agriculture, Ludong University, Yantai, 264025, Shandong, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants, Yantai, 264025, China
| | - Zhuochao Zhao
- College of Agriculture, Ludong University, Yantai, 264025, Shandong, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants, Yantai, 264025, China
| | - Shengren Zhang
- College of Agriculture, Ludong University, Yantai, 264025, Shandong, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants, Yantai, 264025, China
| | - Saining Wang
- College of Agriculture, Ludong University, Yantai, 264025, Shandong, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants, Yantai, 264025, China
| | | | - Yongzhen Wu
- College of Agriculture, Ludong University, Yantai, 264025, Shandong, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants, Yantai, 264025, China
| | - Han Sun
- College of Agriculture, Ludong University, Yantai, 264025, Shandong, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants, Yantai, 264025, China
| | - Ran Qin
- College of Agriculture, Ludong University, Yantai, 264025, Shandong, China.
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants, Yantai, 264025, China.
| | - Fa Cui
- College of Agriculture, Ludong University, Yantai, 264025, Shandong, China.
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants, Yantai, 264025, China.
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Wang D, Wang J, Sun W, Qiu X, Yuan Z, Yu S. Verifying the Breeding Value of A Rare Haplotype of Chalk7, GS3, and Chalk5 to Improve Grain Appearance Quality in Rice. PLANTS (BASEL, SWITZERLAND) 2022; 11:1470. [PMID: 35684243 PMCID: PMC9182975 DOI: 10.3390/plants11111470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/28/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Grain quality is a key determinant of commercial value in rice. Efficiently improving grain quality, without compromising grain yield, is a challenge in rice breeding programs. Here we report on the identification and application of a grain quality gene, Chalk7, which causes a slender shape and decreases grain chalkiness in rice. Three allele-specific markers for Chalk7, and two other grain genes (GS3 and Chalk5) were developed, and used to stack the desirable alleles at these loci. The effects of individual or combined alleles at the loci were evaluated using a set of near-isogenic lines, each containing one to three favorable alleles in a common background of an elite variety. We found that the favorable allele combination of the three loci, which rarely occurs in natural rice germplasm, greatly reduces chalky grains without negatively impacting on grain yield. The data for newly developed allele-specific markers and pre-breeding lines will facilitate the improvement of grain appearance quality in rice.
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Affiliation(s)
- Dianwen Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.W.); (W.S.); (Z.Y.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Jilin Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.W.); (W.S.); (Z.Y.)
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou 434025, China;
| | - Zhiyang Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.W.); (W.S.); (Z.Y.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (D.W.); (W.S.); (Z.Y.)
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
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15
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Wang F, Tang Z, Wang Y, Fu J, Yang W, Wang S, Wang Y, Bai T, Huang Z, Yin H, Wang Z. Leaf Mutant 7 Encoding Heat Shock Protein OsHSP40 Regulates Leaf Size in Rice. Int J Mol Sci 2022; 23:ijms23084446. [PMID: 35457263 PMCID: PMC9027358 DOI: 10.3390/ijms23084446] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/09/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023] Open
Abstract
Leaf size is an important agronomic trait directly affecting yield in rice, and thus understanding the genes determining leaf size is important in breeding. In this study, one Leaf Mutant 7 (lm7) with small leaf size was isolated using ethyl methane sulphonate (EMS) mutagenesis from the japonica Zhenggeng 1925. MutMap by whole genome resequencing of phenotypic bulks revealed that LM7 is likely located in the 133 kb region on chromosome 7 using F2 population from a cross between lm7 and wild-type (WT) Zhenggeng 1925. The candidate gene encoding heat shock protein OsHSP40 for LM7 was functionally validated. Disruption of this gene in Oshsp40 mutants significantly reduced the leaf size compared with that of WT in rice. Microscopic examination showed that OsHSP40 modulated leaf size via regulating the veins formation and cell size/cell number. Nucleotide diversity analysis indicated that a single nucleotide polymorphism (SNP) variation of C to T in the coding region of OsHSP40 may cause small leaves among rice accessions. Therefore, the natural variation of OsHSP40 contributing to leaf size might be useful for rice breeding.
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Affiliation(s)
- Fuhua Wang
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Zhengbin Tang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (Z.T.); (Z.H.)
| | - Ya Wang
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Jing Fu
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Wenbo Yang
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Shengxuan Wang
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Yuetao Wang
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Tao Bai
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
| | - Zhibo Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (Z.T.); (Z.H.)
| | - Haiqing Yin
- Institute of Cereal Crop, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (F.W.); (Y.W.); (J.F.); (W.Y.); (S.W.); (Y.W.); (T.B.)
- Correspondence: (H.Y.); (Z.W.)
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China; (Z.T.); (Z.H.)
- Correspondence: (H.Y.); (Z.W.)
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Assessment of different genotypes of wheat under late sowing condition. Heliyon 2022; 8:e08726. [PMID: 35059520 PMCID: PMC8760405 DOI: 10.1016/j.heliyon.2022.e08726] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/16/2021] [Accepted: 01/04/2022] [Indexed: 11/22/2022] Open
Abstract
The research was conducted by sowing seven genotypes of wheat which were allotted in the Farmers Field Trial kit of National Wheat Research Program, Bhairahawa, Rupandehi. This study responds to the urgency to assess wheat (Triticum aestivum L.) performance in late sowing conditions. Sowing was done on the 17th of December and heat stress was induced due to the delay in sowing. For each genotype, yield attributing characters and physiological growth stages showed up differently, and the yield obtained was not similar. Among the parameters measured, genotypes with shorter vegetative periods and longer reproductive periods thrived well in existing environmental conditions. Days to anthesis and days to maturity were major parameters for selection criterion of yield effective genotype i.e., faster the anthesis, higher the yield; slower the maturity, higher the yield. Growth stages and quantitative yield attributing parameters justified the majority of variation in yield (80.2%) whereas the remaining is expected to be environmental and nutritional factors. Vijay variety (4.06 ton/ha) out-yielded the other six genotypes while NL1193 produced the least (1.97 tons/ha). Considering Vijay best, Vijay (4.06 ton/ha) and Gautam (3.52 ton/ha) are major genotypes recommended for the cultivation in a farmer's field with the least effect of heat stress in the Terai region of Nepal.
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17
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Chen S, Liu F, Wu W, Jiang Y, Zhan K. A SNP-based GWAS and functional haplotype-based GWAS of flag leaf-related traits and their influence on the yield of bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3895-3909. [PMID: 34436627 DOI: 10.1007/s00122-021-03935-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 08/03/2021] [Indexed: 06/13/2023]
Abstract
The genetic architecture of five flag leaf morphology traits was dissected by the functional haplotype-based GWAS and a standard SNP-based GWAS in a diverse population consisting of 197 varieties. Flag leaf morphology (FLM) is a critical factor affecting plant architecture and grain yield in wheat. The genetic architecture of FLM traits has been extensively studied with QTL mapping in bi-parental populations, while few studies exploited genome-wide association studies (GWAS) in diverse populations. In this study, a panel of 197 elite and historical varieties from China was evaluated for five FLM traits including the length (FLL), width (FLW), ratio (FLR), area (FLA) and angle (FLANG) as well as yield in nine environments. Based on the phenotypic correlation between yield and FLL (-0.43), FLA (- 0.32) and FLW (0.11), an empirical FLM index combining the three FLM traits proved to be a good predictor for yield. Two GWAS approaches were applied to dissect the genetic architecture of five FLM traits with a Wheat660K SNP array. The functional haplotype-based GWAS revealed 6, 5 and 7 QTL for FLANG, FLL and FLR, respectively, whereas two QTL for FLW and one for FLR were identified by the standard SNP-based GWAS. Due to co-localization, there were 18 independent QTL and 10 of them were close to known ones. One co-localized QTL on chromosome 5A was associated with FLL, FLANG and FLR. Moreover, both GWAS approaches identified a novel QTL for FLR on chromosome 6B which was not reported in previous studies. This study provides new insights into the relationship between FLM and yield and broadens our understanding of the genetic architecture of FLM traits in wheat.
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Affiliation(s)
- Shulin Chen
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Fang Liu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Wenxue Wu
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany
| | - Kehui Zhan
- College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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18
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Management for Paddy, Oil Palm, and Pineapple Plantations in Malaysia: Current Status and Reviews. JOURNAL OF APPLIED SCIENCE & PROCESS ENGINEERING 2021. [DOI: 10.33736/jaspe.3438.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heavy rainfall causes a loss of fertiliser to the environment, and it leads to environmental issues such as eutrophication. Replenishment of fertiliser to replace the loss imposes a financial impact since frequent applications are costly and labour intensive. Therefore, investigations on proper fertiliser application in maintaining good soil pH, improving plant growth, and increasing crop yield from various plantations across Malaysia are of paramount importance. Meanwhile, limited agricultural-related studies about crop management in Malaysia have been done. This study presents a state-of-the-art review of Malaysia’s paddy, oil palm, pineapple plantations, and the existing nutrient management and fertilisation practices throughout the crop cycle. A systematic study of the existing crop management in terms of farming practices, nutrient management, and fertiliser application on the plantations of paddy, oil palm, and pineapple in Malaysia was carried out. Industry overviews for these three crop types based on past situations and future directions are also included. Recommendations on how to better manage these plantations are also outlined to promote a better understanding of the past, current, and future direction of the agricultural activities and management for principal edible crops like paddy, oil palm, and pineapple in Malaysia.
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19
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Lian Q, Fu Q, Xu Y, Hu Z, Zheng J, Zhang A, He Y, Wang C, Xu C, Chen B, Garcia-Mas J, Zhao G, Wang H. QTLs and candidate genes analyses for fruit size under domestication and differentiation in melon (Cucumis melo L.) based on high resolution maps. BMC PLANT BIOLOGY 2021; 21:126. [PMID: 33658004 PMCID: PMC7931605 DOI: 10.1186/s12870-021-02904-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Melon is a very important horticultural crop produced worldwide with high phenotypic diversity. Fruit size is among the most important domestication and differentiation traits in melon. The molecular mechanisms of fruit size in melon are largely unknown. RESULTS Two high-density genetic maps were constructed by whole-genome resequencing with two F2 segregating populations (WAP and MAP) derived from two crosses (cultivated agrestis × wild agrestis and cultivated melo × cultivated agrestis). We obtained 1,871,671 and 1,976,589 high quality SNPs that show differences between parents in WAP and MAP. A total of 5138 and 5839 recombination events generated 954 bins in WAP and 1027 bins in MAP with the average size of 321.3 Kb and 301.4 Kb respectively. All bins were mapped onto 12 linkage groups in WAP and MAP. The total lengths of two linkage maps were 904.4 cM (WAP) and 874.5 cM (MAP), covering 86.6% and 87.4% of the melon genome. Two loci for fruit size were identified on chromosome 11 in WAP and chromosome 5 in MAP, respectively. An auxin response factor and a YABBY transcription factor were inferred to be the candidate genes for both loci. CONCLUSION The high-resolution genetic maps and QTLs analyses for fruit size described here will provide a better understanding the genetic basis of domestication and differentiation, and provide a valuable tool for map-based cloning and molecular marker assisted breeding.
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Affiliation(s)
- Qun Lian
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Qiushi Fu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Yongyang Xu
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Zhicheng Hu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Jing Zheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Aiai Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Yuhua He
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Changsheng Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Shanghai, 200000, China
| | - Chuanqiang Xu
- Shenyang Agricultural University, College of Horticulture, Shenyang, 110866, China
| | - Benxue Chen
- Design Gollege, Zhoukou Normal University, Zhoukou, 466000, China
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| | - Guangwei Zhao
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
| | - Huaisong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
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20
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Cheng P, Cao LJ, Bai C, Ashikari M, Song XJ. Fine mapping and characterization of two novel quantitative trait loci for early seedling growth in rice. PLANTA 2021; 253:56. [PMID: 33527150 DOI: 10.1007/s00425-021-03576-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/21/2021] [Indexed: 06/12/2023]
Abstract
Two novel QTLs for early seedling growth in rice were fine mapped, with one of which to a 4-kb identical to the known GW6a gene, and another one to a 43-kb region that contains six candidate genes. Leaves are extremely important for plant photosynthesis: the size and shape of which determine the rate of transpiration, carbon fixation and light interception, and their robust growth at seedling stage endow crops with the ability to compete with weeds. So far, many genes for the traits have been cloned with mutants; however, identification of those quantitative trait loci (QTLs) that control early seedling growth has seldom been reported. In this study, we report the identification of two QTLs, qLBL1 and qLBL2 on the rice chromosome 6 for leaf blade length at early seedling stage. Fine mapping revealed that qLBL1 was placed into a 4-kb, and qLBL2 was delimited to a 43-kb genomic interval. We further found that LBL1 was equivalent to the known grain-size gene GW6a and the qLBL2 region contains 6 candidate genes. Genetic analysis using nearly isogenic lines and transgenic rice plants revealed that both genetic factors were positive regulators. The genetic effects were mainly due to alterations of cell division by cytological observations. RT-qPCR results showed that LBL1 was preferentially expressed in leaf blades, and consistently, histochemical staining of pGW6a::GUS plants showed that GUS signal was strong in the vascular tissues of leaf blade of seedlings. Thus, we fine mapped and characterized two QTLs for early seedling growth and provided useful information to improve crop breeding.
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Affiliation(s)
- Peng Cheng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling- Jie Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Bai
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Xian-Jun Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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21
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Lu X, Wang J, Wang Y, Wen W, Zhang Y, Du J, Zhao Y, Guo X. Genome-Wide Association Study of Maize Aboveground Dry Matter Accumulation at Seedling Stage. Front Genet 2021; 11:571236. [PMID: 33519889 PMCID: PMC7838602 DOI: 10.3389/fgene.2020.571236] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 11/30/2020] [Indexed: 11/13/2022] Open
Abstract
Dry matter accumulation and partitioning during the early phases of development could significantly affect crop growth and productivity. In this study, the aboveground dry matter (DM), the DM of different organs, and partition coefficients of a maize association mapping panel of 412 inbred lines were evaluated at the third and sixth leaf stages (V3 and V6). Further, the properties of these phenotypic traits were analyzed. Genome-wide association studies (GWAS) were conducted on the total aboveground biomass and the DM of different organs. Analysis of GWAS results identified a total of 1,103 unique candidate genes annotated by 678 significant SNPs (P value < 1.28e-6). A total of 224 genes annotated by SNPs at the top five of each GWAS method and detected by multiple GWAS methods were regarded as having high reliability. Pathway enrichment analysis was also performed to explore the biological significance and functions of these candidate genes. Several biological pathways related to the regulation of seed growth, gibberellin-mediated signaling pathway, and long-day photoperiodism were enriched. The results of our study could provide new perspectives on breeding high-yielding maize varieties.
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Affiliation(s)
- Xianju Lu
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinglu Wang
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yongjian Wang
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Weiliang Wen
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ying Zhang
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jianjun Du
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanxin Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xinyu Guo
- Beijing Key Laboratory of Digital Plant, Beijing Research Center for Information Technology in Agriculture, National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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22
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Vishnukiran T, Neeraja CN, Jaldhani V, Vijayalakshmi P, Raghuveer Rao P, Subrahmanyam D, Voleti SR. A major pleiotropic QTL identified for yield components and nitrogen content in rice (Oryza sativa L.) under differential nitrogen field conditions. PLoS One 2020; 15:e0240854. [PMID: 33079957 PMCID: PMC7575116 DOI: 10.1371/journal.pone.0240854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 10/04/2020] [Indexed: 11/22/2022] Open
Abstract
To identify the genomic regions for yield and NUE of rice genotypes and lines with promising yield under low N, a recombinant inbred population (RIL) developed between BPT5204 (a mega variety known for its quality) and PTB1 (variety with high NUE) was evaluated for consecutive wet and dry seasons under low nitrogen (LN) and recommended nitrogen (RN) field conditions. A set of 291 RILs were characterized for 24 traits related to leaf, agro-morphological, yield, N content and nitrogen use efficiency indices. More than 50 RILs were found promising with grain yield >10 g under LN. Parental polymorphism survey with 297 SSRs and selective genotyping revealed five genomic regions associated with yield under LN, which were further saturated with polymorphic SSRs. Thirteen promising SSRs were identified out of 144 marker trait associations under LN using single marker analysis. Composite interval mapping showed 37 QTL under LN with five pleiotropic QTL. A major stable pleiotropic (RM13201—RM13209) from PTB1 spanning 825.4 kb region associated with straw N % (SNP) in both treatments across seasons and yield and yield related traits in WS appears to be promising for the MAS. Another major QTL (RM13181-RM13201) was found to be associated with only relative trait parameters of biomass, grain and grain nitrogen. These two major pleiotropic QTL (RM13201-RM13209 and RM13181-RM13201) on chromosome 2 were characterized for their positive allele effect and could be deployed for the development of rice varieties with NUE.
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Affiliation(s)
- T. Vishnukiran
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - C. N. Neeraja
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
- * E-mail:
| | - V. Jaldhani
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - P. Vijayalakshmi
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - P. Raghuveer Rao
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - D. Subrahmanyam
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - S. R. Voleti
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
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23
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Knock-Down the Expression of Brassinosteroid Receptor TaBRI1 Reduces Photosynthesis, Tolerance to High Light and High Temperature Stresses and Grain Yield in Wheat. PLANTS 2020; 9:plants9070840. [PMID: 32635376 PMCID: PMC7411796 DOI: 10.3390/plants9070840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/24/2020] [Accepted: 07/01/2020] [Indexed: 12/03/2022]
Abstract
Brassinosteroid (BR)-deficient or -insensitive mutants exhibited altered plant architecture with the potential to impact yield, the underlying physiological and molecular mechanisms are still to be explored. In this study, we cloned three BR receptor homologous genes TaBRI1-A1, -B1 and -D1 from hexaploid wheat (Triticum estivum L.) and further isolated the TaBRI1-A1, TaBRI1-D1 deletion mutants from the ion beam-induced mutants of variety Xiaoyan81, TaBRI1-A1 and TaBRI1-D1 in which the expression of total receptor TaBRI1 was significantly decreased. The TaBRI1 knock-down mutants exhibited relatively erect leaves and a significant decrease in the 1000-grain weight. Further studies showed that TaBRI1 knock-down mutants showed a significant reduction in photosynthetic rate during the whole grain-filling stage. TaBRI1 knock-down plants generated by TaBRI1-A1, TaBRI1-D1 deletion or using virus-induced gene silencing exhibited the reduction in the efficiency of photosystem II (PSII) (Fv/Fm, ΦPSII and electron transport rate, ETR) especially under high light and high temperature stresses. The 24-epibrassinolide (EBR) treatment increased CO2 assimilation rate in the wild type under both normal and high light and high temperature stresses conditions, but this increasing effect was not observed in the TaBRI1 knock-down mutants. Meanwhile, the expression levels of BR biosynthetic genes including TaDWARF4, TaCPD1 and TaCPD90C1 is not decreased or decreased to a lesser extent in the TaBRI1 knock-down mutants after EBR treatment. These results suggested that TaBRI1 is required for maintaining photosynthesis and tolerance to high light and high temperature stresses both of which are important for grain yield and will be a possible engineered target to control plant photosynthesis and yields in wheat.
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24
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Wang F, Yano K, Nagamatsu S, Inari-Ikeda M, Koketsu E, Hirano K, Aya K, Matsuoka M. Genome-wide expression quantitative trait locus studies facilitate isolation of causal genes controlling panicle structure. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:266-278. [PMID: 32072700 DOI: 10.1111/tpj.14726] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 02/03/2019] [Accepted: 02/04/2020] [Indexed: 06/10/2023]
Abstract
The morphology of rice (Oryza sativa L.) panicles is an important determinant of grain yield, and elucidation of the genetic control of panicle structure is very important for fulfilling the demand for high yield in breeding programs. In a quantitative trait locus (QTL) study using 82 backcross inbred lines (BILs) derived from Koshihikari and Habataki, 68 QTLs for 25 panicle morphological traits were identified. Gene expression profiling from inflorescence meristems of BILs was obtained. A combination of phenotypic QTL (pQTL) and expression QTL (eQTL) analysis revealed co-localization between pQTLs and eQTLs, consistent with significant correlations between phenotypic traits and gene expression levels. By combining pQTL and eQTL data, two genes were identified as controlling panicle structure: OsMADS18 modulates the average length of the primary rachis and OsFTL1 has pleiotropic effects on the total number of secondary rachides, number of grains per panicle, plant height and the length of flag leaves. Phenotypes were confirmed in RNA interference knocked-down plants and overexpressor lines. The combination of pQTL and eQTL analysis could facilitate identification of genes involved in rice panicle formation.
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Affiliation(s)
- Fanmiao Wang
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Kenji Yano
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
- RIKEN Center for Advanced Intelligence Project, Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Shiro Nagamatsu
- Fukuoka Agriculture and Forestry Research Center, 587 Yoshiki, Chikushino, Fukuoka, 818-8549, Japan
| | - Mayuko Inari-Ikeda
- Department of Nutrition, School of Health and Nutrition, Tokai Gakuen University, 2-901 Nakahira, Tenpaku, Nagoya Aichi, 468-8514, Japan
| | - Eriko Koketsu
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Ko Hirano
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Koichiro Aya
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Makoto Matsuoka
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
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25
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Li L, Shi F, Wang Y, Yu X, Zhi J, Guan Y, Zhao H, Chang J, Chen M, Yang G, Wang Y, He G. TaSPL13 regulates inflorescence architecture and development in transgenic wheat (Triticum aestivum L.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 296:110516. [PMID: 32539997 DOI: 10.1016/j.plantsci.2020.110516] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/25/2020] [Accepted: 04/25/2020] [Indexed: 06/11/2023]
Abstract
The SQUAMOSA promoter-binding protein-like (SPL) proteins play vital roles in plant growth and development in rice (Oryza sative L.) and Arabidopsis thaliana (L.) Heynh. However, few studies regarding the SPL proteins have been reported in wheat. In this study, 56 TaSPLs were clustered into eight groups according to an OsSPL phylogenetic comparison analysis. The expression patterns of TaSPLs in different tissues were analysed by RNA-seq data, and partial results were confirmed by qRT-PCR. Based on the above results, genes such as TaSPL13 and TaSPL15 may be involved in spike or seed development in wheat. Multiple genes that regulate the inflorescence architecture of rice have been identified. Additionally, studies on the genes associated with spikelet development in wheat have been reported relatively rarely. Here, TaSPL13-2B was transferred into wheat cv. Bobwhite. Compared with the wild type, the transgenic lines showed significant increases in the number of florets and grains per spike, indicating that TaSPL13-2B could influence the floret development of wheat. TaSPL13-2B was transferred into rice cv. Nipponbare, which demonstrated that TaSPL13-2B can modify panicle architecture in transgenic rice, with significant increases in panicle length, the number and length of primary branches, and the number of secondary branches.
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Affiliation(s)
- Li Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, the Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Fu Shi
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, the Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Yaqiong Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, the Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Xiaofen Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, the Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Jingjing Zhi
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, the Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Yanbin Guan
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, the Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Hongyan Zhao
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, the Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, the Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Mingjie Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, the Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, the Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Yuesheng Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, the Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, the Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan 430074, China.
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26
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Yan X, Wang S, Yang B, Zhang W, Cao Y, Shi Y, Sun D, Jing R. QTL mapping for flag leaf-related traits and genetic effect of QFLW-6A on flag leaf width using two related introgression line populations in wheat. PLoS One 2020; 15:e0229912. [PMID: 32191715 PMCID: PMC7082017 DOI: 10.1371/journal.pone.0229912] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 02/17/2020] [Indexed: 11/29/2022] Open
Abstract
The flag leaf is the main organ of photosynthesis during grain-filling period of wheat, and flag leaf-related traits affect plant morphology and yield potential. In this study, two BC3F6 introgression line (IL) populations derived from the common recipient parent Lumai 14 with Jing 411 and Shaanhan 8675, respectively, were used to map quantitative trait loci (QTL) for flag leaf length (FLL), flag leaf width (FLW), flag leaf area (FLA) and chlorophyll content (CC) at flowering stage and 15 and 20 days after anthesis (DAA) in 2016–2017 (E1) and 2017–2018 (E2) two environments. A total of 14 and 15 QTLs for flag leaf-related traits were detected in Lumai 14 / Jing 411 and Lumai 14 / Shaanhan 8675 populations, respectively. Among them, Both QFLW-6A and QFLA-6A were detected in Lumai 14 / Jing 411 population under E2 and in Lumai 14 / Shaanhan 8675 population under E1 and E2 environments, respectively. QCCS2-3A from Lumai 14 / Jing 411 population and QCCS3-1A, QFLL-4A and QFLL-6A from Lumai 14 / Shaanhan 8675 population were repeatedly identified under two tested environments. Moreover, eight QTL clusters controlling flag leaf-related traits were identified, which provided a genetic basis for significant correlations in phenotype among these traits. On the other hand, positive alleles of QFLW-6A for FLW detected in two populations were derived from their donors. Eighteen lines and 44 lines carried this QTL were found in Lumai 14 / Jing 411 and Lumai 14 / Shaanhan 8675 populations, respectively. The means of FLW in these lines were wider than that of the recipient parent, Lumai 14, in two environments, suggesting that QFLW-6A played an important role for increasing FLW. The IL 124 in Lumai 14 / Jing 411 population and the IL 59 and IL 127 in Lumai 14 / Shaanhan 8675 population had five, five and four donor chromosomal segments which carried no other QTL controlling FLW than QFLW-6A, respectively. And the FLWs of these lines were significantly greater than that of Lumai 14 under two environments. So these lines and their donor parent can be regarded as potential near-isogenic lines. Further, a synteny analysis found QFLW-6A was near the 574,283,851–574,283,613 bp fragment on chromosome 6A and 10 genes were in the range of 500 kb upstream and downstream of the fragment. These results provide the basis for identification of candidate gene and map-based cloning and functional verification of the QTL.
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Affiliation(s)
- Xue Yan
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Shuguang Wang
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Bin Yang
- Wheat Research Institute, Shanxi Academy of Agricultural Sciences, Linfen, Shanxi, China
| | - Wenjun Zhang
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Yaping Cao
- Wheat Research Institute, Shanxi Academy of Agricultural Sciences, Linfen, Shanxi, China
| | - Yugang Shi
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, China
| | - Daizhen Sun
- College of Agronomy, Shanxi Agricultural University, Taigu, Shanxi, China
- * E-mail: (DS); (RJ)
| | - Ruilian Jing
- Chinese Academy of Agricultural Sciences, Institute of Crop Science, Beijing, China
- * E-mail: (DS); (RJ)
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27
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Hu J, Wang X, Zhang G, Jiang P, Chen W, Hao Y, Ma X, Xu S, Jia J, Kong L, Wang H. QTL mapping for yield-related traits in wheat based on four RIL populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:917-933. [PMID: 31897512 DOI: 10.1007/s00122-019-03515-w] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/17/2019] [Indexed: 05/24/2023]
Abstract
Eight environmentally stable QTL for grain yield-related traits were detected by four RIL populations, and two of them were validated by a natural wheat population containing 580 diverse varieties or lines. Yield and yield-related traits are important factors in wheat breeding. In this study, four RIL populations derived from the cross of one common parent Yanzhan 1 (a Chinese domesticated cultivar) and four donor parents including Hussar (a British domesticated cultivar) and three semi-wild wheat varieties in China were phenotyped for 11 yield-related traits in eight environments. An integrated genetic map containing 2009 single-nucleotide polymorphism (SNP) markers generated from a 90 K SNP array was constructed to conduct quantitative trait loci (QTL) analysis. A total of 161 QTL were identified, including ten QTL for grain yield per plant (GYP) and yield components, 49 QTL for spike-related traits, 43 QTL for flag leaf-related traits, 22 QTL for plant height (PH), and 37 QTL for heading date and flowering date. Eight environmentally stable QTL were validated in individual RIL population where the target QTL was notably detected, and six of them had a significant effect on GYP. Furthermore, Two QTL, QSPS-2A.4 and QSL-4A.1, were also validated in a natural wheat population containing 580 diverse varieties or lines, which provided valuable resources for further fine mapping and genetic improvement in yield in wheat.
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Affiliation(s)
- Junmei Hu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Xiaoqian Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Guangxu Zhang
- Lianyungang Academy of Agricultural Sciences, Lianyungang, 222000, China
| | - Peng Jiang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Wuying Chen
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Yongchao Hao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Xin Ma
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Shoushen Xu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China
| | - Jizeng Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lingrang Kong
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China.
| | - Hongwei Wang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, 271018, China.
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28
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Yang W, Feng H, Zhang X, Zhang J, Doonan JH, Batchelor WD, Xiong L, Yan J. Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives. MOLECULAR PLANT 2020; 13:187-214. [PMID: 31981735 DOI: 10.1016/j.molp.2020.01.008] [Citation(s) in RCA: 239] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 05/18/2023]
Abstract
Since whole-genome sequencing of many crops has been achieved, crop functional genomics studies have stepped into the big-data and high-throughput era. However, acquisition of large-scale phenotypic data has become one of the major bottlenecks hindering crop breeding and functional genomics studies. Nevertheless, recent technological advances provide us potential solutions to relieve this bottleneck and to explore advanced methods for large-scale phenotyping data acquisition and processing in the coming years. In this article, we review the major progress on high-throughput phenotyping in controlled environments and field conditions as well as its use for post-harvest yield and quality assessment in the past decades. We then discuss the latest multi-omics research combining high-throughput phenotyping with genetic studies. Finally, we propose some conceptual challenges and provide our perspectives on how to bridge the phenotype-genotype gap. It is no doubt that accurate high-throughput phenotyping will accelerate plant genetic improvements and promote the next green revolution in crop breeding.
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Affiliation(s)
- Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China.
| | - Hui Feng
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science/College of Agronomy, Henan Agricultural University, Zhengzhou 450002, P.R. China
| | - Jian Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - John H Doonan
- The National Plant Phenomics Centre, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | | | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, P.R. China
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Hu C, Rao J, Song Y, Chan SA, Tohge T, Cui B, Lin H, Fernie AR, Zhang D, Shi J. Dissection of flag leaf metabolic shifts and their relationship with those occurring simultaneously in developing seed by application of non-targeted metabolomics. PLoS One 2020; 15:e0227577. [PMID: 31978163 PMCID: PMC6980602 DOI: 10.1371/journal.pone.0227577] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/20/2019] [Indexed: 11/24/2022] Open
Abstract
Rice flag leaves are major source organs providing more than half of the nutrition needed for rice seed development. The dynamic metabolic changes in rice flag leaves and the detailed metabolic relationship between source and sink organs in rice, however, remain largely unknown. In this study, the metabolic changes of flag leaves in two japonica and two indica rice cultivars were investigated using non-targeted metabolomics approach. Principal component analysis (PCA) revealed that flag leaf metabolomes varied significantly depending on both species and developmental stage. Only a few of the metabolites in flag leaves displayed the same change pattern across the four tested cultivars along the process of seed development. Further association analysis found that levels of 45 metabolites in seeds that are associated with human nutrition and health correlated significantly with their levels in flag leaves. Comparison of metabolomics of flag leaves and seeds revealed that some flavonoids were specific or much higher in flag leaves while some lipid metabolites such as phospholipids were much higher in seeds. This reflected not only the function of the tissue specific metabolism but also the different physiological properties and metabolic adaptive features of these two tissues.
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Affiliation(s)
- Chaoyang Hu
- Key Laboratory of Marine Biotechnology of Zhejiang Province, Key Laboratory of Applied Marine Biotechnology of Ministry of Education, School of Marine Sciences, Ningbo University, Ningbo, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jun Rao
- Jiangxi Cancer Hospital, Nanchang, China
| | - Yue Song
- Agilent Technologies Incorporated Company, Shanghai, China
| | - Shen-An Chan
- Agilent Technologies Incorporated Company, Shanghai, China
| | - Takayuki Tohge
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Golm, Germany
| | - Bo Cui
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Lin
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Alisdair R. Fernie
- Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam, Golm, Germany
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic & Developmental Sciences, SJTU-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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30
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Ma J, Tu Y, Zhu J, Luo W, Liu H, Li C, Li S, Liu J, Ding P, Habib A, Mu Y, Tang H, Liu Y, Jiang Q, Chen G, Wang J, Li W, Pu Z, Zheng Y, Wei Y, Kang H, Chen G, Lan X. Flag leaf size and posture of bread wheat: genetic dissection, QTL validation and their relationships with yield-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:297-315. [PMID: 31628527 DOI: 10.1007/s00122-019-03458-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/10/2019] [Indexed: 05/24/2023]
Abstract
Major and environmentally stable QTL for flag leaf-related traits in wheat were identified and validated across ten environments using six populations with different genetic backgrounds. Flag leaf size and posture are two important factors of "ideotype" in wheat. Despite numerous studies on genetic analysis of flag leaf size including flag leaf length (FLL), width (FLW), area (FLA) and the ratio of length/width (FLR), few have focused on flag leaf posture including flag leaf angle (FLANG), opening angle (FLOA) and bend angle (FLBA). Further, the numbers of major, environmentally stable and verified genetic loci for flag leaf-related traits are limited. In this study, QTL for FLL, FLW, FLA, FLR, FLANG, FLOA and FLBA were identified based on a recombinant inbred line population together with values from up to ten different environments. Totally, eight major and stably expressed QTL were identified. Three co-located chromosomal intervals for seven major QTL were identified. The five major QTL QFll.sicau-5B.3 and QFll.sicau-2D.3 for FLL, QFlr.sicau-5B for FLR, QFlw.sicau-2D for FLW and QFla.sicau-2D for FLA were successfully validated by the tightly linked Kompetitive Allele Specific PCR (KASP) markers in the other five populations with different genetic backgrounds. A few genes related to leaf growth and development in intervals for these major QTL were predicated. Significant relationships between flag leaf- and yield-related traits were evidenced by analyses of Pearson correlations, conditional QTL and genetic mapping. Taken together, these results provide valuable information for understanding flag leaf size and posture of "ideotype" as well as fine mapping and breeding utilization of promising loci in bread wheat.
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Affiliation(s)
- Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Yang Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shuiqin Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Puyang Ding
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
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31
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Genetic Dissection of Seed Storability and Validation of Candidate Gene Associated with Antioxidant Capability in Rice ( Oryza sativa L.). Int J Mol Sci 2019; 20:ijms20184442. [PMID: 31505900 PMCID: PMC6770242 DOI: 10.3390/ijms20184442] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/06/2019] [Accepted: 09/08/2019] [Indexed: 11/28/2022] Open
Abstract
Seed storability, defined as the ability to remain alive during storage, is an important agronomic and physiological characteristic, but the underlying genetic mechanism remains largely unclear. Here, we report quantitative trait loci (QTLs) analyses for seed storability using a high-density single nucleotide polymorphism linkage map in the backcross recombinant inbred lines that was derived from a cross of a japonica cultivar, Nipponbare, and an indica cultivar, 9311. Seven putative QTLs were identified for seed storability under natural storage, each explaining 3.6–9.0% of the phenotypic variation in this population. Among these QTLs, qSS1 with the 9311 alleles promoting seed storability was further validated in near-isogenic line and its derived-F2 population. The other locus (qSS3.1) for seed storability colocalized with a locus for germination ability under hydrogen peroxide, which is recognized as an oxidant molecule that causes lipid damage. Transgenic experiments validated that a candidate gene (OsFAH2) resides the qSS3.1 region controlling seed storability and antioxidant capability. Overexpression of OsFAH2 that encodes a fatty acid hydroxylase reduced lipid preoxidation and increased seed storability. These findings provide new insights into the genetic and physiological bases of seed storability and will be useful for the improvement of seed storability in rice.
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Genome-wide association mapping of leaf mass traits in a Vietnamese rice landrace panel. PLoS One 2019; 14:e0219274. [PMID: 31283792 PMCID: PMC6613685 DOI: 10.1371/journal.pone.0219274] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 06/19/2019] [Indexed: 11/19/2022] Open
Abstract
Leaf traits are often strongly correlated with yield, which poses a major challenge in rice breeding. In the present study, using a panel of Vietnamese rice landraces genotyped with 21,623 single-nucleotide polymorphism markers, a genome-wide association study (GWAS) was conducted for several leaf traits during the vegetative stage. Vietnamese landraces are often poorly represented in panels used for GWAS, even though they are adapted to contrasting agrosystems and can contain original, valuable genetic determinants. A panel of 180 rice varieties was grown in pots for four weeks with three replicates under nethouse conditions. Different leaf traits were measured on the second fully expanded leaf of the main tiller, which often plays a major role in determining the photosynthetic capacity of the plant. The leaf fresh weight, turgid weight and dry weight were measured; then, from these measurements, the relative tissue weight and leaf dry matter percentage were computed. The leaf dry matter percentage can be considered a proxy for the photosynthetic efficiency per unit leaf area, which contributes to yield. By a GWAS, thirteen QTLs associated with these leaf traits were identified. Eleven QTLs were identified for fresh weight, eleven for turgid weight, one for dry weight, one for relative tissue weight and one for leaf dry matter percentage. Eleven QTLs presented associations with several traits, suggesting that these traits share common genetic determinants, while one QTL was specific to leaf dry matter percentage and one QTL was specific to relative tissue weight. Interestingly, some of these QTLs colocalize with leaf- or yield-related QTLs previously identified using other material. Several genes within these QTLs with a known function in leaf development or physiology are reviewed.
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Fu X, Xu J, Zhou M, Chen M, Shen L, Li T, Zhu Y, Wang J, Hu J, Zhu L, Gao Z, Dong G, Guo L, Ren D, Chen G, Lin J, Qian Q, Zhang G. Enhanced Expression of QTL qLL9/DEP1 Facilitates the Improvement of Leaf Morphology and Grain Yield in Rice. Int J Mol Sci 2019; 20:E866. [PMID: 30781568 PMCID: PMC6412340 DOI: 10.3390/ijms20040866] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 01/22/2023] Open
Abstract
In molecular breeding of super rice, it is essential to isolate the best quantitative trait loci (QTLs) and genes of leaf shape and explore yield potential using large germplasm collections and genetic populations. In this study, a recombinant inbred line (RIL) population was used, which was derived from a cross between the following parental lines: hybrid rice Chunyou84, that is, japonica maintainer line Chunjiang16B (CJ16); and indica restorer line Chunhui 84 (C84) with remarkable leaf morphological differences. QTLs mapping of leaf shape traits was analyzed at the heading stage under different environmental conditions in Hainan (HN) and Hangzhou (HZ). A major QTL qLL9 for leaf length was detected and its function was studied using a population derived from a single residual heterozygote (RH), which was identified in the original population. qLL9 was delimitated to a 16.17 kb region flanked by molecular markers C-1640 and C-1642, which contained three open reading frames (ORFs). We found that the candidate gene for qLL9 is allelic to DEP1 using quantitative real-time polymerase chain reaction (qRT-PCR), sequence comparison, and the clustered regularly interspaced short palindromic repeat-associated Cas9 nuclease (CRISPR/Cas9) genome editing techniques. To identify the effect of qLL9 on yield, leaf shape and grain traits were measured in near isogenic lines (NILs) NIL-qLL9CJ16 and NIL-qLL9C84, as well as a chromosome segment substitution line (CSSL) CSSL-qLL9KASA with a Kasalath introgressed segment covering qLL9 in the Wuyunjing (WYJ) 7 backgrounds. Our results showed that the flag leaf lengths of NIL-qLL9C84 and CSSL-qLL9KASA were significantly different from those of NIL-qLL9CJ16 and WYJ 7, respectively. Compared with NIL-qLL9CJ16, the spike length, grain size, and thousand-grain weight of NIL-qLL9C84 were significantly higher, resulting in a significant increase in yield of 15.08%. Exploring and pyramiding beneficial genes resembling qLL9C84 for super rice breeding could increase both the source (e.g., leaf length and leaf area) and the sink (e.g., yield traits). This study provides a foundation for future investigation of the molecular mechanisms underlying the source⁻sink balance and high-yield potential of rice, benefiting high-yield molecular design breeding for global food security.
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Affiliation(s)
- Xue Fu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jing Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Mengyu Zhou
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Minmin Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Lan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Ting Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Yuchen Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jiajia Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Guang Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jianrong Lin
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.
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Wang R, Liu Y, Isham K, Zhao W, Wheeler J, Klassen N, Hu Y, Bonman JM, Chen J. QTL identification and KASP marker development for productive tiller and fertile spikelet numbers in two high-yielding hard white spring wheat cultivars. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:135. [PMID: 30464704 DOI: 10.1007/s11032-017-0766-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/18/2018] [Indexed: 05/23/2023]
Abstract
Selecting high-yielding wheat cultivars with more productive tillers per unit area (PTN) combined with more fertile spikelets per spike (fSNS) is difficult. QTL mapping of these traits may aid understanding of this bottleneck and accelerate precision breeding for high yield via marker-assisted selection. PTN and fSNS were assessed in four to five trials from 2015 to 2017 in a doubled haploid population derived from two high-yielding cultivars "UI Platinum" and "SY Capstone." Two QTL for PTN (QPTN.uia-4A and QPTN.uia-6A) and four QTL for fSNS (QfSNS.uia-4A, QfSNS.uia-5A, QfSNS.uia-6A, and QfSNS.uia-7A) were identified. The effects of the QTL were primarily additive and, therefore, pyramiding of multiple QTL may increase PTN and fSNS. However, the two QTL for PTN were positioned in the flanking regions for the two QTL for fSNS on chromosomes 4A and 6A, respectively, suggesting either possible pleiotropic effect of the same QTL or tightly linked QTL and explaining the difficulty of selecting both high PTN and fSNS in phenotypic selection. Kompetitive allele-specific PCR (KASP) markers for all identified QTL were developed and validated in a recombinant inbred line (RIL) population derived from the same two cultivars. In addition, KASP markers for three of the QTL (QPTN.uia-6A, QfSNS.uia-6A, and QfSNS.uia-7A) were further validated in a diverse spring wheat panel, indicating their usefulness under different genetic backgrounds. These KASP markers could be used by wheat breeders to select high PTN and fSNS.
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Affiliation(s)
- Rui Wang
- 1Department of Plant Sciences, University of Idaho, Aberdeen, ID USA
| | - Yuxiu Liu
- 1Department of Plant Sciences, University of Idaho, Aberdeen, ID USA
- 2State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shanxi China
| | - Kyle Isham
- 1Department of Plant Sciences, University of Idaho, Aberdeen, ID USA
| | - Weidong Zhao
- 1Department of Plant Sciences, University of Idaho, Aberdeen, ID USA
| | - Justin Wheeler
- 1Department of Plant Sciences, University of Idaho, Aberdeen, ID USA
| | - Natalie Klassen
- 1Department of Plant Sciences, University of Idaho, Aberdeen, ID USA
| | - Yingang Hu
- 2State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shanxi China
| | - J Michael Bonman
- 3Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID USA
| | - Jianli Chen
- 1Department of Plant Sciences, University of Idaho, Aberdeen, ID USA
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Li B, Lu X, Dou J, Aslam A, Gao L, Zhao S, He N, Liu W. Construction of A High-Density Genetic Map and Mapping of Fruit Traits in Watermelon ( Citrullus Lanatus L.) Based on Whole-Genome Resequencing. Int J Mol Sci 2018; 19:ijms19103268. [PMID: 30347873 PMCID: PMC6214002 DOI: 10.3390/ijms19103268] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 12/26/2022] Open
Abstract
Watermelon (Citrullus lanatus L.) is an important horticultural crop that is grown worldwide and has a high economic value. To dissect the loci associated with important horticultural traits and to analyze the genetic and genomic information of this species, a high-density genetic map was constructed based on whole-genome resequencing (WGR), a powerful high-resolution method for single-nucleotide polymorphism (SNP) marker development, genetic map construction, and gene mapping. Resequencing of both parental lines and 126 recombinant inbred lines (RIL) resulted in the detection of 178,762 single-nucleotide polymorphism (SNP) markers in the parental lines at a sequencing depth greater than four-fold. Additionally, 2132 recombination bin markers comprising 103,029 SNP markers were mapped onto 11 linkage groups (LGs). Substantially more SNP markers were mapped to the genetic map compared with other recent studies. The total length of the linkage map was 1508.94 cM, with an average distance of 0.74 cM between adjacent bin markers. Based on this genetic map, one locus for fruit bitterness, one locus for rind color, and one locus for seed coat color with high LOD scores (58.361, 18.353, 26.852) were identified on chromosome 1, chromosome 8, and chromosome 3, respectively. These prominent loci were identified in a region of 6.16 Mb, 2.07 Mb, and 0.37 Mb, respectively. On the basis of current research, the high-density map and mapping results will provide a valuable tool for identifying candidate genes, map-based gene cloning, comparative mapping, and marker-assisted selection (MAS) in watermelon breeding.
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Affiliation(s)
- Bingbing Li
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Xuqiang Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Junling Dou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Ali Aslam
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Lei Gao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Shengjie Zhao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Nan He
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
| | - Wenge Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.
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36
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Li F, Wen W, He Z, Liu J, Jin H, Cao S, Geng H, Yan J, Zhang P, Wan Y, Xia X. Genome-wide linkage mapping of yield-related traits in three Chinese bread wheat populations using high-density SNP markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1903-1924. [PMID: 29858949 DOI: 10.1007/s00122-018-3122-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 05/24/2018] [Indexed: 05/19/2023]
Abstract
We identified 21 new and stable QTL, and 11 QTL clusters for yield-related traits in three bread wheat populations using the wheat 90 K SNP assay. Identification of quantitative trait loci (QTL) for yield-related traits and closely linked molecular markers is important in order to identify gene/QTL for marker-assisted selection (MAS) in wheat breeding. The objectives of the present study were to identify QTL for yield-related traits and dissect the relationships among different traits in three wheat recombinant inbred line (RIL) populations derived from crosses Doumai × Shi 4185 (D × S), Gaocheng 8901 × Zhoumai 16 (G × Z) and Linmai 2 × Zhong 892 (L × Z). Using the available high-density linkage maps previously constructed with the wheat 90 K iSelect single nucleotide polymorphism (SNP) array, 65, 46 and 53 QTL for 12 traits were identified in the three RIL populations, respectively. Among them, 34, 23 and 27 were likely to be new QTL. Eighteen common QTL were detected across two or three populations. Eleven QTL clusters harboring multiple QTL were detected in different populations, and the interval 15.5-32.3 cM around the Rht-B1 locus on chromosome 4BS harboring 20 QTL is an important region determining grain yield (GY). Thousand-kernel weight (TKW) is significantly affected by kernel width and plant height (PH), whereas flag leaf width can be used to select lines with large kernel number per spike. Eleven candidate genes were identified, including eight cloned genes for kernel, heading date (HD) and PH-related traits as well as predicted genes for TKW, spike length and HD. The closest SNP markers of stable QTL or QTL clusters can be used for MAS in wheat breeding using kompetitive allele-specific PCR or semi-thermal asymmetric reverse PCR assays for improvement of GY.
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Affiliation(s)
- Faji Li
- College of Agronomy, Xinjiang Agricultural University, Ürümqi, 830052, Xinjiang, China
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Weie Wen
- College of Agronomy, Xinjiang Agricultural University, Ürümqi, 830052, Xinjiang, China
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Jindong Liu
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Hui Jin
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- Sino-Russia Agricultural Scientific and Technological Cooperation Center, Heilongjiang Academy of Agricultural Sciences, 368 Xuefu Street, Harbin, 150086, Heilongjiang, China
| | - Shuanghe Cao
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Hongwei Geng
- College of Agronomy, Xinjiang Agricultural University, Ürümqi, 830052, Xinjiang, China
| | - Jun Yan
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), 38 Huanghe Street, Anyang, 455000, Henan, China
| | - Pingzhi Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, 40 Nongke South Street, Hefei, 230001, Anhui, China
| | - Yingxiu Wan
- Crop Research Institute, Anhui Academy of Agricultural Sciences, 40 Nongke South Street, Hefei, 230001, Anhui, China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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Liu K, Xu H, Liu G, Guan P, Zhou X, Peng H, Yao Y, Ni Z, Sun Q, Du J. QTL mapping of flag leaf-related traits in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:839-849. [PMID: 29359263 PMCID: PMC5852184 DOI: 10.1007/s00122-017-3040-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 12/11/2017] [Indexed: 05/04/2023]
Abstract
QTL controlling flag leaf length, flag leaf width, flag leaf area and flag leaf angle were mapped in wheat. This study aimed to advance our understanding of the genetic mechanisms underlying morphological traits of the flag leaves of wheat (Triticum aestivum L.). A recombinant inbred line (RIL) population derived from ND3331 and the Tibetan semi-wild wheat Zang1817 was used to identify quantitative trait loci (QTLs) controlling flag leaf length (FLL), flag leaf width (FLW), flag leaf area (FLA), and flag leaf angle (FLANG). Using an available simple sequence repeat genetic linkage map, 23 putative QTLs for FLL, FLW, FLA, and FLANG were detected on chromosomes 1B, 2B, 3A, 3D, 4B, 5A, 6B, 7B, and 7D. Individual QTL explained 4.3-68.52% of the phenotypic variance in different environments. Four QTLs for FLL, two for FLW, four for FLA, and five for FLANG were detected in at least two environments. Positive alleles of 17 QTLs for flag leaf-related traits originated from ND3331 and 6 originated from Zang1817. QTLs with pleiotropic effects or multiple linked QTL were also identified on chromosomes 1B, 4B, and 5A; these are potential target regions for fine-mapping and marker-assisted selection in wheat breeding programs.
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Affiliation(s)
- Kaiye Liu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Hao Xu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Gang Liu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Panfeng Guan
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
| | - Xueyao Zhou
- High School Attached to Captain Normal University, Beijing, 100048, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China
- Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China
- Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinkun Du
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing, 100193, China.
- Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing, 100193, China.
- Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
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Tang X, Gong R, Sun W, Zhang C, Yu S. Genetic dissection and validation of candidate genes for flag leaf size in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:801-815. [PMID: 29218376 DOI: 10.1007/s00122-017-3036-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 12/01/2017] [Indexed: 05/17/2023]
Abstract
Two major loci with functional candidate genes were identified and validated affecting flag leaf size, which offer desirable genes to improve leaf architecture and photosynthetic capacity in rice. Leaf size is a major determinant of plant architecture and yield potential in crops. However, the genetic and molecular mechanisms regulating leaf size remain largely elusive. In this study, quantitative trait loci (QTLs) for flag leaf length and flag leaf width in rice were detected with high-density single nucleotide polymorphism genotyping of a chromosomal segment substitution line (CSSL) population, in which each line carries one or a few chromosomal segments from the japonica cultivar Nipponbare in a common background of the indica variety Zhenshan 97. In total, 14 QTLs for flag leaf length and nine QTLs for flag leaf width were identified in the CSSL population. Among them, qFW4-2 for flag leaf width was mapped to a 37-kb interval, with the most likely candidate gene being the previously characterized NAL1. Another major QTL for both flag leaf width and length was delimited by substitution mapping to a small region of 13.5 kb that contains a single gene, Ghd7.1. Mutants of Ghd7.1 generated using CRISPR/CAS9 approach showed reduced leaf size. Allelic variation analyses also validated Ghd7.1 as a functional candidate gene for leaf size, photosynthetic capacity and other yield-related traits. These results provide useful genetic information for the improvement of leaf size and yield in rice breeding programs.
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Affiliation(s)
- Xinxin Tang
- National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rong Gong
- National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chaopu Zhang
- National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Wuhan, 430070, China.
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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Alqudah AM, Youssef HM, Graner A, Schnurbusch T. Natural variation and genetic make-up of leaf blade area in spring barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:873-886. [PMID: 29350248 PMCID: PMC5852197 DOI: 10.1007/s00122-018-3053-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 01/04/2018] [Indexed: 05/02/2023]
Abstract
KEY MESSAGE GWAS analysis for leaf blade area (LA) revealed intriguing genomic regions associated with putatively novel QTL and known plant stature-related phytohormone and sugar-related genes. Despite long-standing studies in the morpho-physiological characters of leaf blade area (LA) in cereal crops, advanced genetic studies to explore its natural variation are lacking. The importance of modifying LA in improving cereal grain yield and the genes controlling leaf traits have been well studied in rice but not in temperate cereals. To better understand the natural genetic variation of LA at four developmental stages, main culm LA was measured from 215 worldwide spring barleys including 92 photoperiod-sensitive accessions [PHOTOPERIOD RESPONSE LOCUS 1 (Ppd-H1)] and 123 accessions with reduced photoperiod sensitivity (ppd-H1) locus under controlled greenhouse conditions (long-day; 16/8 h; ~ 20/~ 16 °C day/night). The LA of Ppd-H1-carrying accessions was always smaller than in ppd-H1-carrying accessions. We found that nine SNPs from the Ppd-H1 gene were present in the collection of which marker 9 (M9; G/T in the CCT-domain) showed the most significant and consistent effect on LA at all studied developmental stages. Genome-wide association scans (GWAS) showed that the accessions carrying the ppd-H1 allele T/M9 (late heading) possessed more genetic variation in LA than the Ppd-H1 group carrying G/M9 (early heading). Several QTL with major effects on LA variation were found close to plant stature-related heading time, phytohormone- and sugar-related genes. The results provide evidence that natural variation of LA is an important source for improving grain yield, adaptation and canopy architecture of temperate cereals.
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Affiliation(s)
- Ahmad M Alqudah
- HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, OT Gatersleben, 06466, Seeland, Germany.
| | - Helmy M Youssef
- HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, OT Gatersleben, 06466, Seeland, Germany
- Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Andreas Graner
- Research Group Genome Diversity, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, OT Gatersleben, 06466, Seeland, Germany
| | - Thorsten Schnurbusch
- HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, OT Gatersleben, 06466, Seeland, Germany.
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Yin C, Li H, Zhao Z, Wang Z, Liu S, Chen L, Liu X, Tian Y, Ma J, Xu L, Zhang D, Zhu S, Li D, Wan J, Wang J. Genetic dissection of top three leaf traits in rice using progenies from a japonica × indica cross. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2017; 59:866-880. [PMID: 28875589 DOI: 10.1111/jipb.12597] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/04/2017] [Indexed: 05/17/2023]
Abstract
The size of the top three leaves of rice plants is strongly associated with yield; thus, it is important to consider quantitative traits representing leaf size (e.g., length and width) when breeding novel rice varieties. It is challenging to measure such traits on a large scale in the field, and little is known about the genetic factors that determine the size of the top three leaves. In the present study, a population of recombinant inbred lines (RILs) and reciprocal single chromosomal segment substitution lines (SSSLs) derived from the progeny of a japonica Asominori × indica IR24 cross were grown under four diverse environmental conditions. Six morphological traits associated with leaf size were measured, namely length and flag leaf, length and flag, second and third leaves. In the RIL population, 49 QTLs were identified that clustered in 30 genomic region. Twenty-three of these QTLs were confirmed in the SSSL population. A comparison with previously reported genes/QTLs revealed eight novel genomic regions that contained uncharacterized ORFs associated with leaf size. The QTLs identified in this study can be used for marker-assisted breeding and for fine mapping of novel genetic elements controlling leaf size in rice.
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Affiliation(s)
- Changbin Yin
- The National Key Facility for Crop Gene Resources and Genetic Improvement, and Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huihui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement, and Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhigang Zhao
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiquan Wang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Shijia Liu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China
| | - Liangming Chen
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi Liu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunlu Tian
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China
| | - Juan Ma
- The National Key Facility for Crop Gene Resources and Genetic Improvement, and Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lidong Xu
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Research Center of Jiangsu Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China
| | - Dashuang Zhang
- Rice Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Susong Zhu
- Rice Research Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Danting Li
- Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Jianmin Wan
- The National Key Facility for Crop Gene Resources and Genetic Improvement, and Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiankang Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, and Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Yang D, Liu Y, Cheng H, Chang L, Chen J, Chai S, Li M. Genetic dissection of flag leaf morphology in wheat (Triticum aestivum L.) under diverse water regimes. BMC Genet 2016; 17:94. [PMID: 27352616 PMCID: PMC4924301 DOI: 10.1186/s12863-016-0399-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/16/2016] [Indexed: 11/10/2022] Open
Abstract
Background Morphological traits related to flag leaves are determinant traits influencing plant architecture and yield potential in wheat (Triticum aestivum L.). However, little is known regarding their genetic controls under drought stress. One hundred and twenty F8-derived recombinant inbred lines from a cross between two common wheat cultivars Longjian 19 and Q9086 were developed to identify quantitative trait loci (QTLs) and to dissect the genetic bases underlying flag leaf width, length, area, length to width ratio and basal angle under drought stress and well-watered conditions consistent over four environments. Results A total of 55 additive and 51 pairs of epistatic QTLs were identified on all 21 chromosomes except 6D, among which additive loci were highly concentrated in a few of same or adjacent marker intervals in individual chromosomes. Two specific marker intervals of Xwmc694-Xwmc156 on chromosome 1B and Xbarc1072-Xwmc272 on chromosome 2B were co-located by additive QTLs for four tested traits. Twenty additive loci were repeatedly detected in more than two environments, suggestive of stable A-QTLs. A majority of QTLs involved significant additive and epistatic effects, as well as QTL × environment interactions (QEIs). Of these, 72.7 % of additive QEIs and 80 % of epistatic QEIs were related to drought stress with significant genetic effects decreasing phenotypic values. By contrast, additive and QEIs effects contributed more phenotypic variation than epistatic effects. Conclusions Flag leaf morphology in wheat was predominantly controlled by additive and QEIs effects, where more QEIs effects occurred in drought stress and depressed phenotypic performances. Several QTL clusters indicated tight linkage or pleiotropy in the inheritance of these traits. Twenty stable QTLs for flag leaf morphology are potentially useful for the genetic improvement of drought tolerance in wheat through QTL pyramiding.
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Affiliation(s)
- Delong Yang
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuan Liu
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Hongbo Cheng
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Lei Chang
- School of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jingjing Chen
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shouxi Chai
- School of Agronomy, Gansu Agricultural University, Lanzhou, 730070, China
| | - Mengfei Li
- Gansu Provincial Key Lab of Aridland Crop Science/School of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
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Ci D, Song Y, Du Q, Tian M, Han S, Zhang D. Variation in genomic methylation in natural populations of Populus simonii is associated with leaf shape and photosynthetic traits. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:723-37. [PMID: 26552881 DOI: 10.1093/jxb/erv485] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA methylation, one of the best-studied types of chromatin modification, suppresses the expression of transposable elements, pseudogenes, repetitive sequences, and individual genes. However, the extent and variation of genome-wide DNA methylation in natural populations of plants remain relatively unknown. To investigate variation in DNA methylation and whether this variation associates with important plant traits, including leaf shape and photosynthesis, 20 413 DNA methylation sites were examined in a poplar association population (505 individuals) using methylation-sensitive amplification polymorphism (MSAP) technology. Calculation of epi-population structure and kinships assigned individuals into subsets (K=3), revealing that the natural population of P. simonii consists of three subpopulations. Population epigenetic distance and geographic distance showed a significant correlation (r=0.4688, P<0.001), suggesting that environmental factors may affect epigenetics. Single-marker approaches were also used to identify significant marker-trait associations, which found 1087 high-confidence DNA methylation markers associated with different phenotypic traits explaining ~5-15% of the phenotypic variance. Among these loci, 147 differentially methylated fragments were obtained by sequencing, representing 130 candidate genes. Expression analysis of six candidate genes indicated that these genes might play important roles in leaf development and regulation of photosynthesis. This study provides association analysis to study the effects of DNA methylation on plant development and these data indicate that epigenetics bridges environmental and genetic factors in affecting plant growth and development.
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Affiliation(s)
- Dong Ci
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Yuepeng Song
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Min Tian
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Shuo Han
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing 100083, P. R. China
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Lu Q, Zhang M, Niu X, Wang S, Xu Q, Feng Y, Wang C, Deng H, Yuan X, Yu H, Wang Y, Wei X. Genetic variation and association mapping for 12 agronomic traits in indica rice. BMC Genomics 2015; 16:1067. [PMID: 26673149 PMCID: PMC4681178 DOI: 10.1186/s12864-015-2245-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 11/25/2015] [Indexed: 01/13/2023] Open
Abstract
Background Increasing rice (Oryza sativa L.) yield is a crucial challenge for modern agriculture. The ideal plant architecture is considered to be critical to enhance rice yield. Elite plant morphological traits should include compact plant type, short stature, few unproductive tillers, thick and sturdy stems and erect leaves. To reveal the genetic variations of important morphological traits, 523 germplasm accessions were genotyped using the Illumina custom-designed array containing 5,291 single nucleotide polymorphisms (SNPs) and phenotyped in two independent environments. Genome-wide association studies were performed to uncover the genotypic and phenotypic variations using a mixed linear model. Results In total, 126 and 172 significant loci were identified and these loci explained an average of 34.45 % and 39.09 % of the phenotypic variance in two environments, respectively, and 16 of 298 (~5.37 %) loci were detected across the two environments. For the 16 loci, 423 candidate genes were predicted in a 200-kb region (±100 kb of the peak SNP). Expression-level analyses identified four candidate genes as the most promising regulators of tiller angle. Known (NAL1 and Rc) and new significant loci showed pleiotropy and gene linkage. In addition, a long genome region covering ~1.6 Mb on chromosome 11 was identified, which may be critical for rice leaf architecture because of a high association with flag leaf length and the ratio of flag leaf length and width. The pyramid effect of the elite alleles indicated that these significant loci could be beneficial for rice plant architecture improvements in the future. Finally, 37 elite varieties were chosen as breeding donors for further rice plant architectural modifications. Conclusions This study detected multiple novel loci and candidate genes related to rice morphological traits, and the work demonstrated that genome-wide association studies are powerful strategies for uncovering the genetic variations of complex traits and identifying candidate genes in rice, even though the linkage disequilibrium decayed slowly in self-pollinating species. Future research will focus on the biological validation of the candidate genes, and elite varieties will also be of interest in genome selection and breeding by design. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2245-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qing Lu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Mengchen Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Xiaojun Niu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China. .,College of Agricultural Sciences, Shanxi Agricultural University, Taigu, 030801, China.
| | - Shan Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Qun Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Yue Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Caihong Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Hongzhong Deng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Xiaoping Yuan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Hanyong Yu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Yiping Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Xinghua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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Zhang B, Ye W, Ren D, Tian P, Peng Y, Gao Y, Ruan B, Wang L, Zhang G, Guo L, Qian Q, Gao Z. Genetic analysis of flag leaf size and candidate genes determination of a major QTL for flag leaf width in rice. RICE (NEW YORK, N.Y.) 2015; 8:39. [PMID: 26054240 PMCID: PMC4883130 DOI: 10.1186/s12284-014-0039-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 12/16/2014] [Indexed: 05/17/2023]
Abstract
BACKGROUND Flag leaf is the most essential organ for photosynthesis in rice and its size plays an important role in rice breeding for ideal plant-type. Flag leaf size affect photosynthesis to a certain extent, thereby influencing rice production. Several genes controlling leaf size and shape have been identified with mutants. Although a number of quantitative trait loci (QTLs) for leaf size and shape have been detected on 12 chromosomes with different populations of rice, few of them were cloned. RESULTS The pair-wise correlation analysis was conducted on length, width and length-width ratio of the flag leaf, and yield per plant in the core recombinant inbred lines of Liang-You-Pei-Jiu (LYP9) developed in Hainan and Hangzhou. There were significant correlations among the three flag leaf size and shape traits. Interestingly, a positive correlation was found between flag leaf width and yield per plant. Based on the high-resolution linkage map we constructed before, 43 QTLs were detected for three flag leaf size and shape traits and yield per plant, among which 31 QTLs were unreported so far. Seven QTLs were identified common in two environments. And qFLW7.2, a new major QTL for flag leaf width, was fine mapped within 27.1 kb region on chromosome 7. Both qFLW7.2 and qPY7 were located in the interval of 45.30 ~ 53.34 cM on chromosome 7, which coincided with the relationship between yield per plant (PY) and flag leaf width (FLW). CONCLUSION qFLW7.2, which explained 14% of the phenotypic variation, increased flag leaf width with 93-11 allele. Two candidate genes were selected based on sequence variation and expression difference between two parents, which facilitated further QTL cloning and molecular breeding in super rice.
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Affiliation(s)
- Bin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Weijun Ye
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Peng Tian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Youlin Peng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Yang Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Banpu Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Li Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Tiyuchang Road 359, Hangzhou, 310006 China
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Huang Y, Kong Z, Wu X, Cheng R, Yu D, Ma Z. Characterization of three wheat grain weight QTLs that differentially affect kernel dimensions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2437-45. [PMID: 26334548 DOI: 10.1007/s00122-015-2598-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 08/16/2015] [Indexed: 05/25/2023]
Abstract
The QGw.nau - 2D, QGw.nau - 4B and QGw.nau - 5A intervals were investigated for their effects on weight, length, width, and thickness of kernels and their differential roles in determining kernel size and shape were demonstrated. Grain weight (GW) contributes greatly to wheat yield and is directly related to kernel size and shape. Although over 100 quantitative trait loci (QTLs) for GW have been reported in the literatures, few have been well characterized for their association with kernel traits. In this study, three GW QTLs identified in elite cultivar 'Nanda2419' ('Mentana'), including QGw.nau-2D, QGw.nau-4B and QGw.nau-5A, were investigated through near isogenic line (NIL) development and evaluation. NILs for all three QTLs and one NIL with both QGw.nau-4B and QGw.nau-5A were developed with the help of marker-assisted selection after two to three generations of backcross using cultivar 'Wangshuibai' as the recurrent parent. One NIL with QGw.nau-4B in the background of cultivar 'Wenmai6' was also obtained. In four different field trials, these NILs consistently produced heavier kernels than the recurrent parents. QGw.nau-4B showed the largest effect on GW; its presence resulted in 0.4-0.5 g increase of hundred-grain weight, depending on genetic backgrounds. QGw.nau-4B and QGw.nau-5A functioned additively in conditioning GW. These three QTL intervals showed pleiotropic effects on, or close linkage with genes for, spike length, plant height and flag leaf width, respectively, and acted differentially in determining the kernel dimensions that are the major GW determinants. They all conditioned wider kernels with QGw.nau-5A displaying the largest effect. QGw.nau-4B and QGw.nau-5A also conditioned thicker kernels but had opposite effects on kernel length. This study demonstrated that marker-assisted selection is effective for GW improvement. The availability of GW NILs could facilitate cloning of GW genes and unraveling of kernel development mechanisms.
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Affiliation(s)
- Yulong Huang
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhongxin Kong
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xinyi Wu
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ruiru Cheng
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Dong Yu
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhengqiang Ma
- The Applied Plant Genomics Laboratory of Crop Genomics and Bioinformatics Centre, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Yang W, Guo Z, Huang C, Wang K, Jiang N, Feng H, Chen G, Liu Q, Xiong L. Genome-wide association study of rice (Oryza sativa L.) leaf traits with a high-throughput leaf scorer. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5605-15. [PMID: 25796084 PMCID: PMC4585412 DOI: 10.1093/jxb/erv100] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Leaves are the plant's solar panel and food factory, and leaf traits are always key issues to investigate in plant research. Traditional methods for leaf trait measurement are time-consuming. In this work, an engineering prototype has been established for high-throughput leaf scoring (HLS) of a large number of Oryza sativa accessions. The mean absolute per cent of errors in traditional measurements versus HLS were below 5% for leaf number, area, shape, and colour. Moreover, HLS can measure up to 30 leaves per minute. To demonstrate the usefulness of HLS in dissecting the genetic bases of leaf traits, a genome-wide association study (GWAS) was performed for 29 leaf traits related to leaf size, shape, and colour at three growth stages using HLS on a panel of 533 rice accessions. Nine associated loci contained known leaf-related genes, such as Nal1 for controlling the leaf width. In addition, a total of 73, 123, and 177 new loci were detected for traits associated with leaf size, colour, and shape, respectively. In summary, after evaluating the performance with a large number of rice accessions, the combination of GWAS and high-throughput leaf phenotyping (HLS) has proven a valuable strategy to identify the genetic loci controlling rice leaf traits.
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Affiliation(s)
- Wanneng Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, PR China College of Engineering, Huazhong Agricultural University, Wuhan 430070, PR China Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Zilong Guo
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, PR China
| | - Chenglong Huang
- College of Engineering, Huazhong Agricultural University, Wuhan 430070, PR China Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ke Wang
- College of Engineering, Huazhong Agricultural University, Wuhan 430070, PR China Agricultural Bioinformatics Key Laboratory of Hubei Province, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ni Jiang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, PR China
| | - Hui Feng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, PR China
| | - Guoxing Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China
| | - Qian Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan 430074, PR China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, PR China
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Wu B, Mao D, Liu T, Li Z, Xing Y. Two quantitative trait loci for grain yield and plant height on chromosome 3 are tightly linked in coupling phase in rice. MOLECULAR BREEDING 2015; 35:156. [PMID: 0 DOI: 10.1007/s11032-015-0345-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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48
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Sun W, Zhou Q, Yao Y, Qiu X, Xie K, Yu S. Identification of genomic regions and the isoamylase gene for reduced grain chalkiness in rice. PLoS One 2015; 10:e0122013. [PMID: 25790260 PMCID: PMC4366167 DOI: 10.1371/journal.pone.0122013] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 02/09/2015] [Indexed: 11/18/2022] Open
Abstract
Grain chalkiness is an important grain quality related to starch granules in the endosperm. A high percentage of grain chalkiness is a major problem because it diminishes grain quality in rice. Here, we report quantitative trait loci identification for grain chalkiness using high-throughput single nucleotide polymorphism genotyping of a chromosomal segment substitution line population in which each line carried one or a few introduced japonica cultivar Nipponbare segments in the genetic background of the indica cultivar ZS97. Ten quantitative trait loci regions were commonly identified for the percentage of grain chalkiness and the degree of endosperm chalkiness. The allelic effects at nine of these quantitative trait loci reduced grain chalkiness. Furthermore, a quantitative trait locus (qPGC8-2) on chromosome 8 was validated in a chromosomal segment substitution line-derived segregation population, and had a stable effect on chalkiness in a multiple-environment evaluation of the near-isogenic lines. Residing on the qPGC8-2 region, the isoamylase gene (ISA1) was preferentially expressed in the endosperm and revealed some nucleotide polymorphisms between two varieties, Nipponbare and ZS97. Transgenic lines with suppression of ISA1 by RNA interference produced grains with 20% more chalkiness than the control. The results support that the gene may underlie qPGC8-2 for grain chalkiness. The multiple-environment trials of the near-isogenic lines also show that combination of the favorable alleles such as the ISA1 gene for low chalkiness and the GS3 gene for long grains considerably improved grain quality of ZS97, which proves useful for grain quality improvement in rice breeding programs.
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Affiliation(s)
- Wenqian Sun
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qiaoling Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yue Yao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianjin Qiu
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Kun Xie
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, Wuhan, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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49
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Bargsten JW, Nap JP, Sanchez-Perez GF, van Dijk ADJ. Prioritization of candidate genes in QTL regions based on associations between traits and biological processes. BMC PLANT BIOLOGY 2014; 14:330. [PMID: 25492368 PMCID: PMC4274756 DOI: 10.1186/s12870-014-0330-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/10/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Elucidation of genotype-to-phenotype relationships is a major challenge in biology. In plants, it is the basis for molecular breeding. Quantitative Trait Locus (QTL) mapping enables to link variation at the trait level to variation at the genomic level. However, QTL regions typically contain tens to hundreds of genes. In order to prioritize such candidate genes, we show that we can identify potentially causal genes for a trait based on overrepresentation of biological processes (gene functions) for the candidate genes in the QTL regions of that trait. RESULTS The prioritization method was applied to rice QTL data, using gene functions predicted on the basis of sequence- and expression-information. The average reduction of the number of genes was over ten-fold. Comparison with various types of experimental datasets (including QTL fine-mapping and Genome Wide Association Study results) indicated both statistical significance and biological relevance of the obtained connections between genes and traits. A detailed analysis of flowering time QTLs illustrates that genes with completely unknown function are likely to play a role in this important trait. CONCLUSIONS Our approach can guide further experimentation and validation of causal genes for quantitative traits. This way it capitalizes on QTL data to uncover how individual genes influence trait variation.
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Affiliation(s)
- Joachim W Bargsten
- />Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- />Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands
- />Laboratory for Plant Breeding, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Jan-Peter Nap
- />Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- />Netherlands Bioinformatics Centre (NBIC), Nijmegen, The Netherlands
| | - Gabino F Sanchez-Perez
- />Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- />Laboratory of Bioinformatics, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Aalt DJ van Dijk
- />Applied Bioinformatics, Bioscience, Plant Sciences Group, Wageningen University and Research Centre, Wageningen, The Netherlands
- />Biometris, Wageningen University and Research Centre, Wageningen, The Netherlands
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50
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Lim JH, Yang HJ, Jung KH, Yoo SC, Paek NC. Quantitative trait locus mapping and candidate gene analysis for plant architecture traits using whole genome re-sequencing in rice. Mol Cells 2014; 37:149-60. [PMID: 24599000 PMCID: PMC3935628 DOI: 10.14348/molcells.2014.2336] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 12/21/2013] [Accepted: 12/23/2013] [Indexed: 11/27/2022] Open
Abstract
Plant breeders have focused on improving plant architecture as an effective means to increase crop yield. Here, we identify the main-effect quantitative trait loci (QTLs) for plant shape-related traits in rice (Oryza sativa) and find candidate genes by applying whole genome re-sequencing of two parental cultivars using next-generation sequencing. To identify QTLs influencing plant shape, we analyzed six traits: plant height, tiller number, panicle diameter, panicle length, flag leaf length, and flag leaf width. We performed QTL analysis with 178 F7 recombinant in-bred lines (RILs) from a cross of japonica rice line 'SNUSG1' and indica rice line 'Milyang23'. Using 131 molecular markers, including 28 insertion/deletion markers, we identified 11 main- and 16 minor-effect QTLs for the six traits with a threshold LOD value > 2.8. Our sequence analysis identified fifty-four candidate genes for the main-effect QTLs. By further comparison of coding sequences and meta-expression profiles between japonica and indica rice varieties, we finally chose 15 strong candidate genes for the 11 main-effect QTLs. Our study shows that the whole-genome sequence data substantially enhanced the efficiency of polymorphic marker development for QTL fine-mapping and the identification of possible candidate genes. This yields useful genetic resources for breeding high-yielding rice cultivars with improved plant architecture.
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Affiliation(s)
- Jung-Hyun Lim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
| | - Hyun-Jung Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
| | - Ki-Hong Jung
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 446-701,
Korea
| | - Soo-Cheul Yoo
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
| | - Nam-Chon Paek
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 151-921,
Korea
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