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Dwivedi SL, Heslop-Harrison P, Amas J, Ortiz R, Edwards D. Epistasis and pleiotropy-induced variation for plant breeding. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38875130 DOI: 10.1111/pbi.14405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 05/07/2024] [Accepted: 05/24/2024] [Indexed: 06/16/2024]
Abstract
Epistasis refers to nonallelic interaction between genes that cause bias in estimates of genetic parameters for a phenotype with interactions of two or more genes affecting the same trait. Partitioning of epistatic effects allows true estimation of the genetic parameters affecting phenotypes. Multigenic variation plays a central role in the evolution of complex characteristics, among which pleiotropy, where a single gene affects several phenotypic characters, has a large influence. While pleiotropic interactions provide functional specificity, they increase the challenge of gene discovery and functional analysis. Overcoming pleiotropy-based phenotypic trade-offs offers potential for assisting breeding for complex traits. Modelling higher order nonallelic epistatic interaction, pleiotropy and non-pleiotropy-induced variation, and genotype × environment interaction in genomic selection may provide new paths to increase the productivity and stress tolerance for next generation of crop cultivars. Advances in statistical models, software and algorithm developments, and genomic research have facilitated dissecting the nature and extent of pleiotropy and epistasis. We overview emerging approaches to exploit positive (and avoid negative) epistatic and pleiotropic interactions in a plant breeding context, including developing avenues of artificial intelligence, novel exploitation of large-scale genomics and phenomics data, and involvement of genes with minor effects to analyse epistatic interactions and pleiotropic quantitative trait loci, including missing heritability.
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Affiliation(s)
| | - Pat Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Department of Genetics and Genome Biology, Institute for Environmental Futures, University of Leicester, Leicester, UK
| | - Junrey Amas
- Centre for Applied Bioinformatics, School of Biological Sciences, University of Western Australia, Perth, WA, Australia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - David Edwards
- Centre for Applied Bioinformatics, School of Biological Sciences, University of Western Australia, Perth, WA, Australia
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Huang L, Tang J, Zhu B, Chen G, Chen L, Bu S, Zhu H, Liu Z, Li Z, Meng L, Liu G, Wang S. QTL epistasis plays a role of homeostasis on heading date in rice. Sci Rep 2024; 14:373. [PMID: 38172169 PMCID: PMC10764746 DOI: 10.1038/s41598-023-50786-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/25/2023] [Indexed: 01/05/2024] Open
Abstract
If there was no gene interaction, the gene aggregation effect would increase infinitely with the increase of gene number. Epistasis avoids the endless accumulation of gene effects, playing a role of homeostasis. To confirm the role, QTL epistases were analyzed by four single-segment substitution lines with heading date QTLs in this paper. We found that QTLs of three positive effects and one negative effect generated 62.5% negative dual QTL epistatic effects and 57.7% positive triple QTL epistatic effects, forming the relationship "positive QTLs-negative one order interactions-positive two order interactions". In this way, the aggregation effect of QTLs was partially neutralized by the opposite epistatic effect sum. There also were two exceptions, QTL OsMADS50 and gene Hd3a-2 were always with consistent effect directions with their epistases, implying they could be employed in pyramiding breeding with different objectives. This study elucidated the mechanism of epistatic interactions among four QTLs and provided valuable genetic resources for improving heading date in rice.
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Affiliation(s)
- Lilong Huang
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Jichun Tang
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200, People's Republic of China
| | - Bihuang Zhu
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Guodong Chen
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Leyi Chen
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Suhong Bu
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Haitao Zhu
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Zupei Liu
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Zhan Li
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Lijun Meng
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, 528200, People's Republic of China.
| | - Guifu Liu
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
| | - Shaokui Wang
- Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
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Shen S, Xu S, Wang M, Ma T, Chen N, Wang J, Zheng H, Yang L, Zou D, Xin W, Liu H. BSA-Seq for the Identification of Major Genes for EPN in Rice. Int J Mol Sci 2023; 24:14838. [PMID: 37834285 PMCID: PMC10573429 DOI: 10.3390/ijms241914838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/16/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Improving rice yield is one of the most important food issues internationally. It is an undeniable goal of rice breeding, and the effective panicle number (EPN) is a key factor determining rice yield. Increasing the EPN in rice is a major way to increase rice yield. Currently, the main quantitative trait locus (QTL) for EPN in rice is limited, and there is also limited research on the gene for EPN in rice. Therefore, the excavation and analysis of major genes related to EPN in rice is of great significance for molecular breeding and yield improvement. This study used japonica rice varieties Dongfu 114 and Longyang 11 to construct an F5 population consisting of 309 individual plants. Two extreme phenotypic pools were constructed by identifying the EPN of the population, and QTL-seq analysis was performed to obtain three main effective QTL intervals for EPN. This analysis also helped to screen out 34 candidate genes. Then, EPN time expression pattern analysis was performed on these 34 genes to screen out six candidate genes with higher expression levels. Using a 3K database to perform haplotype analysis on these six genes, we selected haplotypes with significant differences in EPN. Finally, five candidate genes related to EPN were obtained.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Wei Xin
- Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education/College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.S.); (S.X.); (M.W.); (T.M.); (N.C.); (J.W.); (H.Z.); (L.Y.); (D.Z.)
| | - Hualong Liu
- Key Laboratory of Germplasm Enhancement and Physiology & Ecology of Food Crop in Cold Region, Ministry of Education/College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (S.S.); (S.X.); (M.W.); (T.M.); (N.C.); (J.W.); (H.Z.); (L.Y.); (D.Z.)
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Han Z, Lei X, Sha H, Liu J, Zhang C, Wang J, Zheng H, Zou D, Fang J. Adaptation to high latitudes through a novel allele of Hd3a strongly promoting heading date in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:141. [PMID: 37247094 DOI: 10.1007/s00122-023-04391-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/20/2023] [Indexed: 05/30/2023]
Abstract
KEY MESSAGE A novel Hd3a allele strongly promoting rice heading date was identified, and it functions through florigen activation complex (FAC) and was selected during the spread of rice cultivation to high-latitude areas. Heading date is a critical agronomic trait for rice that determines the utilization of light and temperature conditions and thereby affects grain yield. Rice is a short day (SD) plant, and its photoperiodic information is processed by complex pathways and integrated by florigens to control flowering. In this study, we identified a novel allele for the florigen gene Heading date 3a (Hd3a), characterized by a C435G substitution in its coding region, by a genome-wide association study (GWAS) approach in a panel of 199 high-latitude japonica rice varieties. The C435G substitution induces plants to flower 10 days earlier in high-latitude area (long day condition). Then, we mutated C435 to G in Hd3a by prime editing and found the point mutation plants flowered 12 days earlier. Further molecular experiments showed the novel Hd3a protein can interact with GF14b protein and increase the expression of OsMADS14, the output gene of florigen activation complex (FAC). Molecular signatures of selection indicated that the novel Hd3a allele was selected during the process of rice cultivation expansion into high-latitude areas. Collectively, these results provide new insights into heading date regulation in high-latitude areas and advance improvements to rice adaptability to enhance crop yield.
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Affiliation(s)
- Zhongmin Han
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Xiangliang Lei
- Jiangxi Agricultural University/Fuzhou Institute of Agricultural Science, Nanchang, China
| | - Hanjing Sha
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Jia Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Chuanzhong Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jun Fang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
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Li Y, Xiong H, Guo H, Zhou C, Fu M, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Wang C, Irshad A, Liu L, Fang Z. Fine mapping and genetic analysis identified a C 2H 2-type zinc finger as a candidate gene for heading date regulation in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:140. [PMID: 37243757 DOI: 10.1007/s00122-023-04363-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/08/2023] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE A minor-effect QTL, Qhd.2AS, that affects heading date in wheat was mapped to a genomic interval of 1.70-Mb on 2AS, and gene analysis indicated that the C2H2-type zinc finger protein gene TraesCS2A02G181200 is the best candidate for Qhd.2AS. Heading date (HD) is a complex quantitative trait that determines the regional adaptability of cereal crops, and identifying the underlying genetic elements with minor effects on HD is important for improving wheat production in diverse environments. In this study, a minor QTL for HD that we named Qhd.2AS was detected on the short arm of chromosome 2A by Bulked Segregant Analysis and validated in a recombinant inbred population. Using a segregating population of 4894 individuals, Qhd.2AS was further delimited to an interval of 0.41 cM, corresponding to a genomic region spanning 1.70 Mb (from 138.87 to 140.57 Mb) that contains 16 high-confidence genes based on IWGSC RefSeq v1.0. Analyses of sequence variations and gene transcription indicated that TraesCS2A02G181200, which encodes a C2H2-type zinc finger protein, is the best candidate gene for Qhd.2AS that influences HD. Screening a TILLING mutant library identified two mutants with premature stop codons in TraesCS2A02G181200, both of which exhibited a delay in HD of 2-4 days. Additionally, variations in its putative regulatory sites were widely present in natural accession, and we also identified the allele which was positively selected during wheat breeding. Epistatic analyses indicated that Qhd.2AS-mediated HD variation is independent of VRN-B1 and environmental factors. Phenotypic investigation of homozygous recombinant inbred lines (RILs) and F2:3 families showed that Qhd.2AS has no negative effect on yield-related traits. These results provide important cues for refining HD and therefore improving yield in wheat breeding programs and will deepen our understanding of the genetic regulation of HD in cereal plants.
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Affiliation(s)
- Yuting Li
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongchun Xiong
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijun Guo
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunyun Zhou
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meiyu Fu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongdun Xie
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linshu Zhao
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiayu Gu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shirong Zhao
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuping Ding
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaojie Wang
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ahsan Irshad
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luxiang Liu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Zhengwu Fang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China.
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Liu C, Wang T, Chen H, Ma X, Jiao C, Cui D, Han B, Li X, Jiao A, Ruan R, Xue D, Wang Y, Han L. Genomic footprints of Kam Sweet Rice domestication indicate possible migration routes of the Dong people in China and provide resources for future rice breeding. MOLECULAR PLANT 2023; 16:415-431. [PMID: 36578210 DOI: 10.1016/j.molp.2022.12.020] [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: 07/17/2022] [Revised: 11/22/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
The Dong people are one of China's 55 recognized ethnic minorities, but there has been a long-standing debate about their origins. In this study, we performed whole-genome resequencing of Kam Sweet Rice (KSR), a valuable, rare, and ancient rice landrace unique to the Dong people. Through comparative genomic analyses of KSR and other rice landraces from south of the Yangtze River Basin in China, we provide evidence that the ancestors of the Dong people likely originated from the southeast coast of China at least 1000 years ago. Alien introgression and admixture in KSR demonstrated multiple migration events in the history of the Dong people. Genomic footprints of domestication demonstrated characteristics of KSR that arose from artificial selection and geographical adaptation by the Dong people. The key genes GS3, Hd1, and DPS1 (related to agronomic traits) and LTG1 and MYBS3 (related to cold tolerance) were identified as domestication targets, reflecting crop improvement and changes in the geographical environment of the Dong people during migration. A genome-wide association study revealed a candidate yield-associated gene, Os01g0923300, a specific haplotype in KSR that is important for regulating grain number per panicle. RNA-sequencing and quantitative reverse transcription-PCR results showed that this gene was more highly expressed in KSR than in ancestral populations, indicating that it may have great value in increasing yield potential in other rice accessions. In summary, our work develops a novel approach for studying human civilization and migration patterns and provides valuable genomic datasets and resources for future breeding of high-yield and climate-resilient rice varieties.
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Affiliation(s)
- Chunhui Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Tianyi Wang
- Smartgenomics Technology Institute, Tianjin 301700, China
| | - Huicha Chen
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang 550025, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengzhi Jiao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaobing Li
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang 550025, China
| | - Aixia Jiao
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang 550025, China
| | - Renchao Ruan
- Institute of Crop Germplasm Resources, Guizhou Academy of Agricultural Sciences, Guiyang 550025, China
| | - Dayuan Xue
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China
| | - Yanjie Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Sanchez DL, Samonte SOP, Alpuerto JBB, Croaker PA, Morales KY, Yang Y, Wilson LT, Tabien RE, Yan Z, Thomson MJ, Septiningsih EM. Phenotypic variation and genome-wide association studies of main culm panicle node number, maximum node production rate, and degree-days to heading in rice. BMC Genomics 2022; 23:390. [PMID: 35606708 PMCID: PMC9125873 DOI: 10.1186/s12864-022-08629-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 05/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Grain yield is a complex trait that results from interaction between underlying phenotypic traits and climatic, edaphic, and biotic variables. In rice, main culm panicle node number (MCPNN; the node number on which the panicle is borne) and maximum node production rate (MNPR; the number of leaves that emerge per degree-day > 10°C) are primary phenotypic plant traits that have significant positive direct effects on yield-related traits. Degree-days to heading (DDTH), which has a significant positive effect on grain yield, is influenced by the interaction between MCPNN and MNPR. The objective of this research is to assess the phenotypic variation of MCPNN, MNPR, and DDTH in a panel of diverse rice accessions, determine regions in the rice genome associated with these traits using genome-wide association studies (GWAS), and identify putative candidate genes that control these traits. Results Considerable variation was observed for the three traits in a 220-genotype diverse rice population. MCPNN ranged from 8.1 to 20.9 nodes in 2018 and from 9.9 to 21.0 nodes in 2019. MNPR ranged from 0.0097 to 0.0214 nodes/degree day > 10°C in 2018 and from 0.0108 to 0.0193 nodes/degree-day > 10°C in 2019. DDTH ranged from 713 to 2,345 degree-days > 10°C in 2018 and from 778 to 2,404 degree-days > 10°C in 2019. Thirteen significant (P < 2.91 x 10-7) trait-single nucleotide polymorphism (SNP) associations were identified using the multilocus mixed linear model for GWAS. Significant associations between MCPNN and three SNPs in chromosome 2 (S02_12032235, S02_11971745, and S02_12030176) were detected with both the 2018 and best linear unbiased prediction (BLUP) datasets. Nine SNPs in chromosome 6 (S06_1970442, S06_2310856, S06_2550351, S06_1968653, S06_2296852, S06_1968680, S06_1968681, S06_1970597, and S06_1970602) were significantly associated with MNPR in the 2019 dataset. One SNP in chromosome 11 (S11_29358169) was significantly associated with the DDTH in the BLUP dataset. Conclusions This study identifies SNP markers that are putatively associated with MCPNN, MNPR, and DDTH. Some of these SNPs were located within or near gene models, which identify possible candidate genes involved in these traits. Validation of the putative candidate genes through expression and gene editing analyses are necessary to confirm their roles in regulating MCPNN, MNPR, and DDTH. Identifying the underlying genetic basis for primary phenotypic traits MCPNN and MNPR could lead to the development of fast and efficient approaches for their estimation, such as marker-assisted selection and gene editing, which is essential in increasing breeding efficiency and enhancing grain yield in rice. On the other hand, DDTH is a resultant variable that is highly affected by nitrogen and water management, plant density, and several other factors. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08629-y.
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Affiliation(s)
- Darlene L Sanchez
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA.
| | | | - Jasper Benedict B Alpuerto
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA.,Bayer Research and Development Services (Bayer Crop Science), Chesterfield, Missouri, 63017, USA
| | - Peyton A Croaker
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Karina Y Morales
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, 77843, USA
| | - Yubin Yang
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Lloyd T Wilson
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Rodante E Tabien
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Zongbu Yan
- Texas A&M AgriLife Research Center at Beaumont, Beaumont, Texas, 77713, USA
| | - Michael J Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, 77843, USA
| | - Endang M Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, 77843, USA
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Prakash S, Rai R, Zamzam M, Ahmad O, Peesapati R, Vijayraghavan U. OsbZIP47 Is an Integrator for Meristem Regulators During Rice Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2022; 13:865928. [PMID: 35498659 PMCID: PMC9044032 DOI: 10.3389/fpls.2022.865928] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
Stem cell homeostasis by the WUSCHEL-CLAVATA (WUS-CLV) feedback loop is generally conserved across species; however, its links with other meristem regulators can be species-specific, rice being an example. We characterized the role of rice OsbZIP47 in vegetative and reproductive development. The knockdown (KD) transgenics showed meristem size abnormality and defects in developmental progression. The size of the shoot apical meristem (SAM) in 25-day OsbZIP47KD plants was increased as compared to the wild-type (WT). Inflorescence of KD plants showed reduced rachis length, number of primary branches, and spikelets. Florets had defects in the second and third whorl organs and increased organ number. OsbZIP47KD SAM and panicles had abnormal expression for CLAVATA peptide-like signaling genes, such as FON2-LIKE CLE PROTEIN1 (FCP1), FLORAL ORGAN NUMBER 2 (FON2), and hormone pathway genes, such as cytokinin (CK) ISOPENTEYLTRANSFERASE1 (OsIPT1), ISOPENTEYLTRANSFERASE 8 (OsIPT8), auxin biosynthesis OsYUCCA6, OsYUCCA7 and gibberellic acid (GA) biosynthesis genes, such as GRAIN NUMBER PER PANICLE1 (GNP1/OsGA20OX1) and SHORTENED BASAL INTERNODE (SBI/OsGA2ox4). The effects on ABBERANT PANICLE ORGANIZATION1 (APO1), OsMADS16, and DROOPING LEAF (DL) relate to the second and third whorl floret phenotypes in OsbZIP47KD. Protein interaction assays showed OsbZIP47 partnerships with RICE HOMEOBOX1 (OSH1), RICE FLORICULA/LEAFY (RFL), and OsMADS1 transcription factors. The meta-analysis of KD panicle transcriptomes in OsbZIP47KD, OsMADS1KD, and RFLKD transgenics, combined with global OSH1 binding sites divulge potential targets coregulated by OsbZIP47, OsMADS1, OSH1, and RFL. Further, we demonstrate that OsbZIP47 redox status affects its DNA binding affinity to a cis element in FCP1, a target locus. Taken together, we provide insights on OsbZIP47 roles in SAM development, inflorescence branching, and floret development.
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Cheng YC, Li G, Yin M, Adegoke TV, Wang YF, Tong XH, Zhang J, Ying JZ. Verification and dissection of one quantitative trait locus for grain size and weight on chromosome 1 in rice. Sci Rep 2021; 11:18252. [PMID: 34521909 PMCID: PMC8440748 DOI: 10.1038/s41598-021-97622-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 08/23/2021] [Indexed: 11/09/2022] Open
Abstract
Grain size and weight are the key traits determining rice quality and yield and are mainly controlled by quantitative trait loci (QTL). In this study, one minor QTL that was previously mapped in the marker interval of JD1009-JD1019 using the Huanghuazhan/Jizi1560 (HHZ/JZ1560) recombinant inbred line (RIL) population, qTGW1-2, was validated to regulate grain size and weight across four rice-growing seasons using twenty-one near isogenic line (NIL)-F2 populations. The twenty-one populations were in two types of genetic background that were derived from the same parents HHZ and JZ1560. Twelve F9, F10 or F11 NIL-F2 populations with the sequential residual heterozygous regions covering JD1009-RM6840 were developed from one residual heterozygote (RH) in the HHZ/JZ1560 RIL population, and the remaining nine BC3F3, BC3F4 or BC3F5 NIL-F2 populations with the sequential residual heterozygous regions covering JD1009-RM6840 were constructed through consecutive backcrosses to the recurrent parent HHZ followed with marker assistant selection in each generation. Based on the QTL analysis of these genetic populations, qTGW1-2 was successfully confirmed to control grain length, width and weight and further dissected into two QTLs, qTGW1-2a and qTGW1-2b, which were respectively narrowed down to the marker intervals of JD1139-JD1127 (~ 978.2-kb) and JD1121-JD1102 (~ 54.8-kb). Furthermore, the two types of NIL-F2 populations were proved to be able to decrease the genetic background noise and increase the detection power of minor QTL. These results provided an important basis for further map-based cloning and molecular design breeding with the two QTLs in rice.
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Affiliation(s)
- Yi-Chen Cheng
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Guan Li
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Man Yin
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Tosin Victor Adegoke
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yi-Feng Wang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiao-Hong Tong
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jian Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Jie-Zheng Ying
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China. .,State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Zhejiang Province, China.
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10
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Cai M, Zhu S, Wu M, Zheng X, Wang J, Zhou L, Zheng T, Cui S, Zhou S, Li C, Zhang H, Chai J, Zhang X, Jin X, Cheng Z, Zhang X, Lei C, Ren Y, Lin Q, Guo X, Zhao L, Wang J, Zhao Z, Jiang L, Wang H, Wan J. DHD4, a CONSTANS-like family transcription factor, delays heading date by affecting the formation of the FAC complex in rice. MOLECULAR PLANT 2021; 14:330-343. [PMID: 33246053 DOI: 10.1016/j.molp.2020.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/03/2020] [Accepted: 11/18/2020] [Indexed: 05/21/2023]
Abstract
Heading date (or flowering time) is one of the most important agronomic traits in rice, influencing its regional adaptability and crop yield. Many major-effect genes for rice heading date have been identified, but in practice they are difficult to be used for rice molecular breeding because of their dramatic effects on heading date. Genes with minor effects on heading date, which are more desirable for fine-tuning flowering time without significant yield penalty, were seldom reported. In this study, we identified a new minor-effect heading date repressor, Delayed Heading Date 4 (DHD4). The dhd4 mutant shows a slightly earlier flowering phenotype without a notable yield penalty compared with wild-type plants under natural long-day conditions. DHD4 encodes a CONSTANS-like transcription factor localized in the nucleus. Molecular, biochemical, and genetic assays show that DHD4 can compete with 14-3-3 to interact with OsFD1, thus affecting the formation of the Hd3a-14-3-3-OsFD1 tri-protein FAC complex, resulting in reduced expression of OsMADS14 and OsMADS15, and ultimately delaying flowering. Taken together, these results shed new light on the regulation of flowering time in rice and provide a promising target for fine-tuning flowering time to improve the regional adaptability of rice.
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Affiliation(s)
- Maohong Cai
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Mingming Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiachang Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Liang Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Tianhui Zheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Song Cui
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Shirong Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huan Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Juntao Chai
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyue Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Jin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lei Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhichao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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11
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Chen Z, Shen Z, Xu L, Zhao D, Zou Q. Regulator Network Analysis of Rice and Maize Yield-Related Genes. Front Cell Dev Biol 2021; 8:621464. [PMID: 33425929 PMCID: PMC7793993 DOI: 10.3389/fcell.2020.621464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 11/12/2020] [Indexed: 11/13/2022] Open
Abstract
Rice and maize are the principal food crop species worldwide. The mechanism of gene regulation for the yield of rice and maize is still the research focus at present. Seed size, weight and shape are important traits of crop yield in rice and maize. Most members of three gene families, APETALA2/ethylene response factor, auxin response factors and MADS, were identified to be involved in yield traits in rice and maize. Analysis of molecular regulation mechanisms related to yield traits provides theoretical support for the improvement of crop yield. Genetic regulatory network analysis can provide new insights into gene families with the improvement of sequencing technology. Here, we analyzed the evolutionary relationships and the genetic regulatory network for the gene family members to predicted genes that may be involved in yield-related traits in rice and maize. The results may provide some theoretical and application guidelines for future investigations of molecular biology, which may be helpful for developing new rice and maize varieties with high yield traits.
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Affiliation(s)
- Zheng Chen
- School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen, China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Zijie Shen
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Lei Xu
- School of Electronic and Communication Engineering, Shenzhen Polytechnic, Shenzhen, China
| | - Da Zhao
- School of Applied Chemistry and Biological Technology, Shenzhen Polytechnic, Shenzhen, China.,Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China
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12
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Wei H, Wang X, Xu H, Wang L. Molecular basis of heading date control in rice. ABIOTECH 2020; 1:219-232. [PMID: 36304129 PMCID: PMC9590479 DOI: 10.1007/s42994-020-00019-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/06/2020] [Indexed: 01/25/2023]
Abstract
Flowering time is of great significance for crop reproduction, yield, and regional adaptability, which is intricately regulated by various environmental cues and endogenous signals. Genetic approaches in Arabidopsis have revealed the elaborate underlying mechanisms of sensing the dynamic change of photoperiod via a coincidence between light signaling and circadian clock, the cellular time keeping system, to precisely control photoperiodic flowering time, and many other signaling pathways including internal hormones and external temperature cues. Extensive studies in rice (Oryza sativa.), one of the short-day plants (SDP), have uncovered the multiple major genetic components in regulating heading date, and revealed the underlying mechanisms for regulating heading date. Here we summarize the current progresses on the molecular basis for rice heading date control, especially focusing on the integration mechanism between photoperiod and circadian clock, and epigenetic regulation and heading procedures in response to abiotic stresses.
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Affiliation(s)
- Hua Wei
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xiling Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Hang Xu
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093 China.,University of Chinese Academy of Sciences, Beijing, 100049 China
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13
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Molla KA, Karmakar S, Molla J, Bajaj P, Varshney RK, Datta SK, Datta K. Understanding sheath blight resistance in rice: the road behind and the road ahead. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:895-915. [PMID: 31811745 PMCID: PMC7061877 DOI: 10.1111/pbi.13312] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/15/2019] [Accepted: 11/22/2019] [Indexed: 05/03/2023]
Abstract
Rice sheath blight disease, caused by the basidiomycetous necrotroph Rhizoctonia solani, became one of the major threats to the rice cultivation worldwide, especially after the adoption of high-yielding varieties. The pathogen is challenging to manage because of its extensively broad host range and high genetic variability and also due to the inability to find any satisfactory level of natural resistance from the available rice germplasm. It is high time to find remedies to combat the pathogen for reducing rice yield losses and subsequently to minimize the threat to global food security. The development of genetic resistance is one of the alternative means to avoid the use of hazardous chemical fungicides. This review mainly focuses on the effort of better understanding the host-pathogen relationship, finding the gene loci/markers imparting resistance response and modifying the host genome through transgenic development. The latest development and trend in the R. solani-rice pathosystem research with gap analysis are provided.
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Affiliation(s)
- Kutubuddin A. Molla
- ICAR‐National Rice Research InstituteCuttackIndia
- Laboratory of Translational Research on Transgenic CropsDepartment of BotanyUniversity of CalcuttaKolkataIndia
- The Huck Institute of the Life SciencesThe Pennsylvania State UniversityUniversity ParkPAUSA
- Department of Plant Pathology and Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - Subhasis Karmakar
- Laboratory of Translational Research on Transgenic CropsDepartment of BotanyUniversity of CalcuttaKolkataIndia
| | - Johiruddin Molla
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Prasad Bajaj
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB)International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Swapan K. Datta
- Laboratory of Translational Research on Transgenic CropsDepartment of BotanyUniversity of CalcuttaKolkataIndia
| | - Karabi Datta
- Laboratory of Translational Research on Transgenic CropsDepartment of BotanyUniversity of CalcuttaKolkataIndia
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14
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Zhu Y, Ye J, Zhan J, Zheng X, Zhang J, Shi J, Wang X, Liu G, Wang H. Validation and Characterization of a Seed Number Per Silique Quantitative Trait Locus qSN.A7 in Rapeseed ( Brassica napus L.). FRONTIERS IN PLANT SCIENCE 2020; 11:68. [PMID: 32153604 PMCID: PMC7047150 DOI: 10.3389/fpls.2020.00068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
Seed number is a key character/trait tightly related to the plant fitness/evolution and crop domestication/improvement. The seed number per silique (SNPS) shows a huge variation from several to more than 30, however the underlying regulatory mechanisms are poorly known, which has hindered its improvement. To answer this question, several representative lines with extreme SNPS were previously subjected to systematic genetic and cytological analyses. The results showed that the natural variation of seed number per silique is mainly controlled by maternal and embryonic genotype, which are co-determined by ovule number per ovary, fertile ovule ratio, ovule fertilization rate, and fertilized ovule development rate. More importantly, we also mapped two repeatable quantitative trait loci (QTLs) for SNPS using the F2:3 population derived from Zhongshuang11 and No. 73290, of which the major QTL qSN.A6 has been fine-mapped. In the current study, the near-isogenic lines (NILs) of qSN.A7 were successfully developed by the successive backcross of F1 with Zhongshuang11. First, the effect of qSN.A7 was validated by evaluating the SNPS of two types of homozygous NILs from BC3F2 population, which showed a significant difference of 2.23 on average. Then, qSN.A7 was successfully fine-mapped from the original 4.237 to 1.389 Mb, using a BC4F2 segregating population of 2,551 individuals. To further clarify the regulatory mechanism of qSN.A7, the two types of homologous NILs were subjected to genetic and cytological analyses. The results showed that the difference in SNPS between the two homologous NILs was determined by the embryonic genotypic effect. Highly accordant with this, no significant difference was observed in ovule number per ovary, ovule fertility, fertilization rate, and pollen fertility between the two homologous NILs. Therefore, the regulatory mechanism of qSN.A7 is completely different from the cloned qSS.C9 and qSN.A6. These results will advance the understanding of SNPS and facilitate gene cloning and molecular breeding in Brassica napus.
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Affiliation(s)
| | | | | | | | | | - Jiaqin Shi
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministryof Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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15
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Zhang ZH, Zhu YJ, Wang SL, Fan YY, Zhuang JY. Importance of the Interaction between Heading Date Genes Hd1 and Ghd7 for Controlling Yield Traits in Rice. Int J Mol Sci 2019; 20:ijms20030516. [PMID: 30691093 PMCID: PMC6387254 DOI: 10.3390/ijms20030516] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/20/2019] [Accepted: 01/23/2019] [Indexed: 12/29/2022] Open
Abstract
Appropriate flowering time is crucial for successful grain production, which relies on not only the action of individual heading date genes, but also the gene-by-gene interactions. In this study, influences of interaction between Hd1 and Ghd7 on flowering time and yield traits were analyzed using near isogenic lines derived from a cross between indica rice cultivars ZS97 and MY46. In the non-functional ghd7ZS97 background, the functional Hd1ZS97 allele promoted flowering under both the natural short-day (NSD) conditions and natural long-day (NLD) conditions. In the functional Ghd7MY46 background, Hd1ZS97 remained to promote flowering under NSD conditions, but repressed flowering under NLD conditions. For Ghd7, the functional Ghd7MY46 allele repressed flowering under both conditions, which was enhanced in the functional Hd1ZS97 background under NLD conditions. With delayed flowering, spikelet number and grain weight increased under both conditions, but spikelet fertility and panicle number fluctuated. Rice lines carrying non-functional hd1MY46 and functional Ghd7MY46 alleles had the highest grain yield under both conditions. These results indicate that longer growth duration for a larger use of available temperature and light does not always result in higher grain production. An optimum heading date gene combination needs to be carefully selected for maximizing grain yield in rice.
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Affiliation(s)
- Zhen-Hua Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Yu-Jun Zhu
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Shi-Lin Wang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Ye-Yang Fan
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China.
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16
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Zhong H, Kong W, Gong Z, Fang X, Deng X, Liu C, Li Y. Evolutionary Analyses Reveal Diverged Patterns of SQUAMOSA Promoter Binding Protein-Like ( SPL) Gene Family in Oryza Genus. FRONTIERS IN PLANT SCIENCE 2019; 10:565. [PMID: 31139200 PMCID: PMC6517846 DOI: 10.3389/fpls.2019.00565] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/15/2019] [Indexed: 05/07/2023]
Abstract
The SPL (SQUAMOSA promoter binding protein-like) gene family is one of the plant-specific transcription factor families and controls a considerable number of biological functions, including floral development, phytohormone signaling, and toxin resistance. However, the evolutionary patterns and driving forces of SPL genes in the Oryza genus are still not well-characterized. In this study, we investigated a total of 105 SPL genes from six AA genome Oryza representative species (O. barthii, O. glumipatula, O. nivara, O. rufipogon, O. glaberrima, and O. sativa). Phylogenetic and motif analyses indicated that SPL proteins could be divided into two distinct lineages (I and II), and further studies showed lineage II consisted of three clades (IIA, IIB, and IIC). We found that clade I had comparable structural features with clade IIA, whereas genes in clade IIC displayed intrinsic differences, such as lower exon numbers and the presence of miR156 regulation elements. Nineteen orthologous groups of OsSPLs in Oryza were also identified, and most exons within those genes maintained constant length, whereas length of intron changed relatively. All groups were constrained by stronger purifying selection and diversified continually including alterative gene number, intron length, and miR156 regulation. Subsequently, cis-acting element analyses revealed the potential role of SPLs in wild rice, which might participate in light-responsive, phytohormone response, and plant growth and development. Our results shed light on that different evolutionary rates and duplication events might result in divergent evolutionary patterns in each lineage of SPL genes, providing a guide in exploring diverse function in the rice gene family among six closely related Oryza species.
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17
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Hu Z, Cao L, Sun X, Zhu Y, Zhang T, Jiang L, Liu Y, Dong S, Sun D, Yang J, He H, Luo X. Fine mapping of a major quantitative trait locus, qgnp7(t), controlling grain number per panicle in African rice ( Oryza glaberrima S.). BREEDING SCIENCE 2018; 68:606-613. [PMID: 30697122 PMCID: PMC6345233 DOI: 10.1270/jsbbs.18084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 09/18/2018] [Indexed: 06/09/2023]
Abstract
Grain number per panicle is a major component of rice yield that is typically controlled by many quantitative trait loci (QTLs). The identification of genes controlling grain number per panicle in rice would be valuable for the breeding of high-yielding rice. The Oryza glaberrima chromosome segment substitution line 9IL188 had significantly smaller panicles compared with the recurrent parent 9311. QTL analysis in an F2 population derived from a cross between 9IL188 and 9311 revealed that qgnp7(t), a major QTL located on the short arm of chromosome 7, was responsible for this phenotypic variation. Fine mapping was conducted using a large F3 population containing 2250 individuals that were derived from the F2 heterozygous plants. Additionally, plant height, panicle length, and grain number per panicle of the key F4 recombinant families were examined. Through two-step substitution mapping, qgnp7(t) was finally localized to a 41 kb interval in which eight annotated genes were identified according to available sequence annotation databases. Phenotypic evaluation of near isogenic lines (NIL-qgnp7 and NIL-qGNP7) indicated that qgnp7(t) has pleiotropic effects on rice plant architecture and panicle structure. In addition, yield estimation of NILs indicated that qGNP7(t) derived from 9311 is the favorable allele. Our results provide a foundation for isolating qgnp7(t). Markers flanking this QTL will be a useful tool for the marker-assisted selection of favorable alleles in O. glaberrima improvement programs.
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Affiliation(s)
- Zejun Hu
- Group of Crop Genetics and Breeding, Jiangxi Agricultural University,
Nanchang 330045,
China
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University,
Shanghai 200433,
China
| | - Liming Cao
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences,
Shanghai 201403,
China
| | - Xuejun Sun
- Group of Crop Genetics and Breeding, Jiangxi Agricultural University,
Nanchang 330045,
China
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University,
Shanghai 200433,
China
| | - Yu Zhu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University,
Shanghai 200433,
China
| | - Tianyu Zhang
- Deng Jia Bu Rice Foundation Seed Farm of Jiangxi Province,
Yujiang 335200,
China
| | - Lin Jiang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University,
Shanghai 200433,
China
| | - Yahui Liu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University,
Shanghai 200433,
China
| | - Siqing Dong
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University,
Shanghai 200433,
China
| | - Dayun Sun
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University,
Shanghai 200433,
China
| | - Jingshui Yang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University,
Shanghai 200433,
China
| | - Haohua He
- Group of Crop Genetics and Breeding, Jiangxi Agricultural University,
Nanchang 330045,
China
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University,
Shanghai 200433,
China
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18
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Dong Q, Zhang ZH, Wang LL, Zhu YJ, Fan YY, Mou TM, Ma LY, Zhuang JY. Dissection and fine-mapping of two QTL for grain size linked in a 460-kb region on chromosome 1 of rice. RICE (NEW YORK, N.Y.) 2018; 11:44. [PMID: 30073424 PMCID: PMC6081826 DOI: 10.1186/s12284-018-0236-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/13/2018] [Indexed: 05/05/2023]
Abstract
BACKGROUND Grain size is a key determinant of grain weight and a trait having critical influence on grain quality in rice. While increasing evidences are shown for the importance of minor-effect QTL in controlling complex traits, the attention has not been given to grain size until recently. In previous studies, five QTL having small effects for grain size were resolved on the long arm of chromosome 1 using populations derived from indica rice cross Zhenshan 97///Zhenshan 97//Zhenshan 97/Milyang 46. One of them, qTGW1.2c that was located in a 2.1-Mb region, was targeted for fine-mapping in the present study. RESULTS Firstly, the qTGW1.2c region was narrowed down into 1.1 Mb by determining genotypes of the cross-over regions using polymorphic markers newly developed. Then, one BC2F9 plant that was only heterozygous in the updated QTL region was identified. A total of 12 populations in generations from BC2F11:12 to BC2F15:16 were derived and used for QTL mapping. Two QTL linked in a 460-kb region were separated. The qGS1-35.2 was delimited into a 57.7-kb region, containing six annotated genes of which five showed nucleotide polymorphisms between the two parental lines. Quantitative real-time PCR detected expression differences between near isogenic lines for qGS1-35.2 at three of the six annotated genes. This QTL affected grain length and width with opposite allelic directions, exhibiting significant effect on ratio of grain length to width but showing little influence on yield traits. The other QTL, qGW1-35.5, was located within a 125.5-kb region and found to primarily control grain width and consequently affect grain weight. CONCLUSIONS Our work lays a foundation for cloning of two minor QTL for grain size that have potential application in rice breeding. The qGS1-35.2 could be used to modify grain appearance quality without yield penalty because it affects grain shape but hardly influences grain yield, while qGW1-35.5 offers a new gene recourse for enhancing grain yield since it contributes to grain size and grain weight simultaneously.
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Affiliation(s)
- Qing Dong
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- State Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhen-Hua Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lin-Lin Wang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yu-Jun Zhu
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- State Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Ye-Yang Fan
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Tong-Min Mou
- State Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Liang-Yong Ma
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.
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Chen JY, Zhang HW, Zhang HL, Ying JZ, Ma LY, Zhuang JY. Natural variation at qHd1 affects heading date acceleration at high temperatures with pleiotropism for yield traits in rice. BMC PLANT BIOLOGY 2018; 18:112. [PMID: 29879910 PMCID: PMC5992824 DOI: 10.1186/s12870-018-1330-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/24/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Rice is highly sensitive to temperature fluctuations. Recently, the frequent occurrence of high temperature stress has heavily influenced rice production. Proper heading date in specific environmental conditions could ensure high grain yield. Rice heading greatly depends on the accurate measurement of environmental changes, particularly in day length and temperature. In contrary to the detailed understanding of the photoperiod pathway, little has been known about how temperature regulates the genetic control of rice heading. RESULTS Near isogenic lines that were segregated for qHd1, were developed from a cross between indica rice varieties Zhenshan 97 (ZS97) and Milyang 46 (MY46). Using a five sowing-date experiment in the paddy field, we observed the involvement of qHd1 in temperature responses. With the gradual increase of temperature from Trial I to V, heading date of MY46 homozygotes continued to decrease for about 5 d per trial from 76 to 58 d, while that of ZS97 homozygotes was promoted at the same rate from Trial I to III and then stabilized at 69 d. This thermal response was confirmed in a temperature-gradient experiment conducted in the phytotron. It is also found that tolerance of the ZS97 allele to heading acceleration at high temperature was associated with higher grain weight that resulted in higher grain yield. Then, by qRT-PCR and RNA-seq, we found the pathway OsMADS51-Ehd1-RFT1/Hd3a underlying the qHd1-mediated floral response to temperature. By sequence comparison, OsMADS51 for qHd1 displayed a 9.5-kb insertion in the 1st intron of the ZS97 allele compared to the MY46 allele. Furthermore, this large insertion is commonly found in major early-season indica rice varieties, but not in the middle- and late-season ones, which corresponds to the requirement for high-temperature tolerance during the heading and grain-filling stages of early-season rice. CONCLUSIONS Beneficial alleles at qHd1 confer tolerance to high temperatures at the heading and grain-filling stages, playing a significant role in the eco-geographical adaptation of early-season indica rice during modern breeding. These results, together with the underlying OsMADS51-Ehd1-RFT1/Hd3a floral pathway, provide valuable information for better understanding the molecular mechanism of temperature responsive regulation of heading date and yield traits in rice.
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Affiliation(s)
- Jun-Yu Chen
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
| | - Hong-Wei Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
| | - Hua-Li Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
| | - Jie-Zheng Ying
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
| | - Liang-Yong Ma
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006 China
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20
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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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Yu M, Cao LL, Yang YX, Guan LL, Gou LL, Shu XY, Huang J, Liu D, Zhang H, Hou DB. Genetic diversity and marker–trait association analysis for agronomic traits in Aconitum carmichaelii Debeaux. BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1355747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Ma Yu
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Ling-Li Cao
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Yu-Xia Yang
- Laboratory of Genetic Resources, Institute of Traditional Chinese Medicine Resources and Cultivation, Sichuan Academy of Traditional Chinese Medicine Sciences, Chengdu, Sichuan, PR China
| | - Ling-Liang Guan
- Department of Genetic Breeding, Chinese Academy of Tropical Agricultural Sciences (CATAS), Tropical Crops Genetic Resources Institute, Danzhou, PR China
| | - Lu-Lu Gou
- Department of Genetic Breeding, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, PR China
| | - Xiao-Yan Shu
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Jing Huang
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Dan Liu
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Hong Zhang
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
| | - Da-Bin Hou
- Department of Agronomy, School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, PR China
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22
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Rice Flowering Locus T 1 plays an important role in heading date influencing yield traits in rice. Sci Rep 2017; 7:4918. [PMID: 28687802 PMCID: PMC5501849 DOI: 10.1038/s41598-017-05302-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 05/26/2017] [Indexed: 12/26/2022] Open
Abstract
Important role of flowering genes in enhancing grain productivity in rice has become well recognized for a number of key genes regulating the florigen production, but little has been known for the two florigen genes themselves. In this study, pleiotropism of Rice Flowering Locus T 1 (RFT1), one of the two florigen genes in rice, was firstly evaluated using near isogenic lines (NILs) carrying RFT1 alleles from the indica rice cultivars Zhenshan 97 (ZS97) and Milyang 46, respectively, and then determined by transformation of the RFT1ZS97 allele into a japonica rice variety, Zhonghua 11. The RFT1ZS97 allele was shown to delay heading and increase plant height, grain weight, grain number and grain yield, indicating that RFT1 plays an important role in the growth and development of rice. This study has also validated the potential of using a new type of genetic resource, sequential residual heterozygotes (SeqRHs), for QTL fine-mapping. A step-by-step approach was employed for SeqRHs identification, NIL development and QTL fine-mapping. The heterozygous segments and candidate QTL regions were gradually narrowed down. Eventually, the QTL region was delimited to a 1.7 kb region containing a single gene.
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23
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Sun B, Zhan XD, Lin ZC, Wu WX, Yu P, Zhang YX, Sun LP, Cao LY, Cheng SH. Fine mapping and candidate gene analysis of qHD5, a novel major QTL with pleiotropism for yield-related traits in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:247-258. [PMID: 27677631 DOI: 10.1007/s00122-016-2787-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 09/12/2016] [Indexed: 06/06/2023]
Abstract
A major QTL for heading date, qHD5, was fine-mapped to a 52.59-kb region on the short arm of rice chromosome 5. Heading date (HD) is one of the most important traits that enables rice to adapt to seasonal differences and specific growth conditions in diverse growing regions. In this study, a major-effect quantitative trait locus (QTL), qHD5, was resolved as a single Medelian factor that causes NIL(BG1) and NIL(XLJ) (two near-isogenic lines (NILs) used in our study) to have at a minimum of 10-day difference in HD under both long-day and short-day conditions in rice. qHD5 was initially mapped to a 309.52-kb genomic region in our previous study. Here, using an advanced BC4F3 population and map-based cloning, we further narrowed the location of qHD5 to a 52.59-kb region between the H71 and RD502 markers. Sequence analysis revealed that Os05g03040, which putatively encodes an AP2 (APETALA2) transcription factor, has six single nucleotide polymorphisms (SNPs) between NIL(BG1) and NIL(XLJ). On this basis, this gene was concluded to be the most probable candidate gene for qHD5. Our results also showed that Hd3a, RFT1, Hd1, Ehd1, and Ghd7 were differentially expressed in the two NILs. Moreover, qHD5 was found to affect yield-related traits such as flag leaf width, flag leaf length, branch number, and 1000-grain weight.
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Affiliation(s)
- Bin Sun
- Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiao-Deng Zhan
- Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Ze-Chuan Lin
- Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Wei-Xun Wu
- Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Ping Yu
- Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Ying-Xin Zhang
- Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lian-Ping Sun
- Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Li-Yong Cao
- Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Shi-Hua Cheng
- Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
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Zhang ZH, Cao LY, Chen JY, Zhang YX, Zhuang JY, Cheng SH. Effects of Hd2 in the presence of the photoperiod-insensitive functional allele of Hd1 in rice. Biol Open 2016; 5:1719-1726. [PMID: 27797723 PMCID: PMC5155538 DOI: 10.1242/bio.021071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The role of photoperiod sensitivity (PS) of flowering genes have become well recognized in rice, whereas little attention has been drawn to the non-PS component of these genes, especially to their influence on gene-by-gene interactions. Rice populations in which the photoperiod-sensitive allele at Hd1 has become insensitive to photoperiod but continued to affect heading date (HD) were used in this study to fine-map a quantitative trait locus (QTL) for HD and analyze its genetic relationship to Hd1. The QTL was delimitated to a 96.3-kb region on the distal end of the long arm of chromosome 7. Sequence comparison revealed that this QTL is identical to Hd2. In the near-isogenic line (NIL) populations analyzed, Hd1 and Hd2 were shown to be photoperiod insensitive and have pleiotropic effects for HD, plant height and yield traits. The two genes were found to largely act additively in regulating HD and yield traits. The results indicate that non-PS components of flowering genes involved in photoperiod response play an important role in controlling flowering time and grain yield in rice, which should allow breeders to better manipulate pleiotropic genes for balancing adaptability and high-yielding accumulation. Summary: We show that photoperiod-insensitive components of alleles of Hd1 and Hd2 play an important role in balancing ecological adaptability and high-yield accumulation in rice.
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Affiliation(s)
- Zhen-Hua Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Li-Yong Cao
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Jun-Yu Chen
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Ying-Xin Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shi-Hua Cheng
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
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Zhang HW, Fan YY, Zhu YJ, Chen JY, Yu SB, Zhuang JY. Dissection of the qTGW1.1 region into two tightly-linked minor QTLs having stable effects for grain weight in rice. BMC Genet 2016; 17:98. [PMID: 27363861 PMCID: PMC4929766 DOI: 10.1186/s12863-016-0410-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 06/24/2016] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Most agronomical traits of crop species are complex traits controlled by multiple genes and affected by environmental factors. While considerable efforts have been made to fine-map and clone major quantitative trait loci (QTLs) for yield-related traits in rice, it is not until recently that the attention has been paid to minor QTLs. Following previous dissection of QTLs for grain weight and grain size in a 12-Mb interval on the long arm of chromosome 1 in rice, this study targeted at one putative QTL region for a more precise mapping and for analyzing the genotype-by-environment interaction of minor QTLs. RESULTS Four BC2F10 plants of the indica rice cross ZS97///ZS97//ZS97/MY46 were selected. They carried overlapped heterozygous segments that jointly covered the entire putative region for qTGW1.1 detected previously. Four sets of near isogenic lines (NILs) were developed from selfing progenies of the four plants. Each NIL set consisted of 32 ZS97 homozygous lines and 32 MY46 homozygous lines that differed in the corresponding heterozygous region. They were grown in two locations having distinct ecological conditions and measured for 1000-grain weight, grain length and grain width. Two QTLs were separated in an 835.2-kb interval flanked by DNA markers Wn28447 and RM11569. They both showed consistent effects across the two environments. The qTGW1.1a located within the 120.4-kb interval Wn28447 - RM11543 significantly affect all the three traits with the enhancing allele derived from ZS97, showing a stronger influence on grain weight than on grain length and width. The qTGW1.1b located in the 521.8-kb interval RM11554 - RM11569 significantly affect grain weight and length with the enhancing allele derived from MY46, having a stronger influence on grain length than on grain weight. Consistent performance of the two QTLs was confirmed in a validation experiment using five NIL-F2 populations segregated for either qTGW1.1a or qTGW1.1b. CONCLUSION Separation of closely-linked QTLs having small effects is achievable in the absence of major-QTL segregation. Minor QTLs for complex traits could act consistently in diverse environments, offering the potential of pyramiding beneficial alleles of multiple minor QTLs through marker-assisted selection.
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Affiliation(s)
- Hong-Wei Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.,State Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Ye-Yang Fan
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yu-Jun Zhu
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jun-Yu Chen
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Si-Bin Yu
- State Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie-Yun Zhuang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.
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