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Abstract
Plants bred or engineered to be short can stand up better to windstorms. They could also boost yields and benefit the environment.
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Wu Q, Liu Y, Huang J. CRISPR-Cas9 Mediated Mutation in OsPUB43 Improves Grain Length and Weight in Rice by Promoting Cell Proliferation in Spikelet Hull. Int J Mol Sci 2022; 23:ijms23042347. [PMID: 35216463 PMCID: PMC8877319 DOI: 10.3390/ijms23042347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 12/27/2022] Open
Abstract
Grain weight, a crucial trait that determines the grain yield in rice, is influenced by grain size. Although a series of regulators that control grain size have been identified in rice, the mechanisms underlying grain development are not yet well understood. In this study, we identified OsPUB43, a U-box E3 ubiquitin ligase, as an important negative regulator determining the gain size and grain weight in rice. Phenotypes of large grain are observed in ospub43 mutants, whereas overexpression of OsPUB43 results in short grains. Scanning electron microscopy analysis reveals that OsPUB43 modulates the grain size mainly by inhibiting cell proliferation in the spikelet hull. The OsPUB43 protein is localized in the cytoplasm and nucleus. The ospub43 mutants display high sensitivity to exogenous BR, while OsPUB43-OE lines are hyposensitive to BR. Furthermore, the transient transcriptional activity assay shows that OsBZR1 can activate the expression of OsPUB43. Collectively, our results indicate that OsPUB43 negatively controls the gain size by modulating the expression of BR-responsive genes as well as MADS-box genes that are required for lemma/palea specification, suggesting that OsPUB43 has a potential valuable application in the enlargement of grain size in rice.
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Li T, Deng G, Su Y, Yang Z, Tang Y, Wang J, Zhang J, Qiu X, Pu X, Yang W, Li J, Liu Z, Zhang H, Liang J, Yu M, Wei Y, Long H. Genetic dissection of quantitative trait loci for grain size and weight by high-resolution genetic mapping in bread wheat (Triticum aestivum L.). Theor Appl Genet 2022; 135:257-271. [PMID: 34647130 DOI: 10.1007/s00122-021-03964-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/29/2021] [Indexed: 06/13/2023]
Abstract
Six major QTLs for wheat grain size and weight were identified on chromosomes 4A, 4B, 5A and 6A across multiple environments, and were validated in different genetic backgrounds. Grain size and weight are crucial components of wheat yield. Dissection of their genetic control is thus essential for the improvement of yield potential in wheat breeding. We used a doubled haploid (DH) population to detect quantitative trait loci (QTLs) for grain width (GW), grain length (GL), and thousand grain weight (TGW) in five environments. Six major QTLs, QGw.cib-4B.2, QGl.cib-4A, QGl.cib-5A.1, QGl.cib-6A, QTgw.cib-4B, and QTgw.cib-5A, were consistently identified in at least three individual environments and in best linear unbiased prediction (BLUP) datasets, and explained 5.65-34.06% of phenotypic variation. QGw.cib-4B.2, QTgw.cib-4B, QGl.cib-5A.1 and QGl.cib-6A had no effect on grain number per spike (GNS). In addition to QGl.cib-4A, the other major QTLs were further validated by using Kompetitive Allele Specific PCR (KASP) markers in different genetic backgrounds. Moreover, significant interactions between the three major GL QTLs and two major TGW QTLs were observed. Comparison analysis showed that QGl.cib-5A.1 and QGl.cib-6A are likely new loci. Notably, QGw.cib-4B.2 and QTgw.cib-4B were co-located on chromosome 4B and improved TGW by increasing only GW, unlike nearby or overlapped loci reported previously. Three genes associated with grain development within the QGw.cib-4B.2/QTgw.cib-4B interval were identified by searches on sequence similarity, spatial expression patterns, and orthologs. The major QTLs and KASP markers reported here will be useful for elucidating the genetic architecture of grain size and weight and for developing new wheat cultivars with high and stable yield.
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Affiliation(s)
- Tao Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yan Su
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Zhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yanyan Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Jinhui Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Juanyu Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xvebing Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xi Pu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, China.
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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Zhou L, Zhu C, Fang X, Liu H, Zhong S, Li Y, Liu J, Song Y, Jian X, Lin Z. Gene duplication drove the loss of awn in sorghum. Mol Plant 2021; 14:1831-1845. [PMID: 34271177 DOI: 10.1016/j.molp.2021.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/18/2021] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
Loss of the awn in some cereals, including sorghum, is a key transition during cereal domestication or improvement that has facilitated grain harvest and storage. The genetic basis of awn loss in sorghum during domestication or improvement remains unknown. Here, we identified the awn1 gene encoding a transcription factor with the ALOG domain that is responsible for awn loss during sorghum domestication or improvement. awn1 arose from a gene duplication on chromosome 10 that translocated to chromosome 3, recruiting a new promoter from the neighboring intergenic region filled with "noncoding DNA" and recreating the first exon and intron. awn1 acquired high expression after duplication and represses the elongation of awns in domesticated sorghum. Comparative mapping revealed high collinearity at the awn1 paralog locus on chromosome 10 across cereals, and awn growth and development were successfully reactivated on the rice spikelet by inactivating the rice awn1 ortholog. RNA-seq and DAP-seq revealed that as a transcriptional repressor, AWN1 bound directly to a motif in the regulatory regions of three MADS genes related to flower development and two genes, DL and LKS2, involved in awn development. AWN1 downregulates the expression of these genes, thereby repressing awn elongation. The preexistence of regulatory elements in the neighboring intergenic region of awn1 before domestication implicates that noncoding DNA may serve as a treasure trove for evolution during sorghum adaptation to a changing world. Taken together, our results suggest that gene duplication can rapidly drive the evolution of gene regulatory networks in plants.
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Affiliation(s)
- Leina Zhou
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Can Zhu
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Xiaojian Fang
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Hangqin Liu
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Shuyang Zhong
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Yan Li
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Jiacheng Liu
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Yang Song
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Xing Jian
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China
| | - Zhongwei Lin
- National Maize Improvement Center, Center for Crop Functional Genomics and Molecular Breeding, Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, Laboratory of Crop Heterosis and Utilization, China Agricultural University, Beijing 100193, China.
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Dwiningsih Y, Kumar A, Thomas J, Ruiz C, Alkahtani J, Al-hashimi A, Pereira A. Identification of Genomic Regions Controlling Chalkiness and Grain Characteristics in a Recombinant Inbred Line Rice Population Based on High-Throughput SNP Markers. Genes (Basel) 2021; 12:1690. [PMID: 34828295 PMCID: PMC8625982 DOI: 10.3390/genes12111690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 10/18/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022] Open
Abstract
Rice (Oryza sativa L.) is the primary food for half of the global population. Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbred line (RIL) population from a japonica/indica cross based on high-throughput SNP markers and to provide a strategy for improving rice quality. The RIL population used was derived from a cross of "Kaybonnet (KBNT lpa)" and "ZHE733" named the K/Z RIL population, consisting of 198 lines. A total of 4133 SNP markers were used to identify quantitative trait loci (QTLs) with higher resolution and to identify more accurate candidate genes. The characteristics measured included grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC). QTL analysis was performed using QTL IciMapping software. Continuous distributions and transgressive segregations of all the traits were observed, suggesting that the traits were quantitatively inherited. A total of twenty-eight QTLs and ninety-two candidate genes related to rice grain characteristics were identified. This genetic information is important to develop rice varieties of high quality.
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Affiliation(s)
- Yheni Dwiningsih
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (Y.D.); (A.K.); (J.T.); (C.R.)
| | - Anuj Kumar
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (Y.D.); (A.K.); (J.T.); (C.R.)
| | - Julie Thomas
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (Y.D.); (A.K.); (J.T.); (C.R.)
| | - Charles Ruiz
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (Y.D.); (A.K.); (J.T.); (C.R.)
| | - Jawaher Alkahtani
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (J.A.); (A.A.-h.)
| | - Abdulrahman Al-hashimi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia; (J.A.); (A.A.-h.)
| | - Andy Pereira
- Department of Crop, Soil and Environmental Sciences, University of Arkansas, Fayetteville, AR 72701, USA; (Y.D.); (A.K.); (J.T.); (C.R.)
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Beena R, Kirubakaran S, Nithya N, Manickavelu A, Sah RP, Abida PS, Sreekumar J, Jaslam PM, Rejeth R, Jayalekshmy VG, Roy S, Manju RV, Viji MM, Siddique KHM. Association mapping of drought tolerance and agronomic traits in rice (Oryza sativa L.) landraces. BMC Plant Biol 2021; 21:484. [PMID: 34686134 PMCID: PMC8539776 DOI: 10.1186/s12870-021-03272-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/29/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Asian cultivars were predominantly represented in global rice panel selected for sequencing and to identify novel alleles for drought tolerance. Diverse genetic resources adapted to Indian subcontinent were not represented much in spite harboring useful alleles that could improve agronomic traits, stress resilience and productivity. These rice accessions are valuable genetic resource in developing rice varieties suited to different rice ecosystem that experiences varying drought stress level, and at different crop stages. A core collection of rice germplasm adapted to Southwestern Indian peninsular genotyped using SSR markers and characterized by contrasting water regimes to associate genomic regions for physiological, root traits and yield related traits. Genotyping-By-Sequencing of selected accessions within the diverse panel revealed haplotype variation in genic content within genomic regions mapped for physiological, morphological and root traits. RESULTS Diverse rice panel (99 accessions) were evaluated in field and measurements on plant physiological, root traits and yield related traits were made over five different seasons experiencing varying drought stress intensity at different crop stages. Traits like chlorophyll stability index, leaf rolling, days to 50% flowering, chlorophyll content, root volume and root biomass were identified as best predictors of grain yield under stress. Association mapping revealed genetic variation among accessions and revealed 14 genomic targets associated with different physiological, root and plant production traits. Certain accessions were found to have beneficial allele to improve traits, plant height, root length and spikelet fertility, that contribute to the grain yield under stress. Genomic characterization of eleven accessions revealed haplotype variation within key genomic targets on chromosomes 1, 4, 6 and 11 for potential use as molecular markers to combine drought avoidance and tolerance traits. Genes mined within the genomic QTL intervals identified were prioritized based on tissue specific expression level in publicly available rice transcriptome data. CONCLUSION The genetic and genomic resources identified will enable combining traits with agronomic value to optimize yield under stress and hasten trait introgression into elite cultivars. Alleles associated with plant height, specific leaf area, root length from PTB8 and spikelet fertility and grain weight from PTB26 can be harnessed in future rice breeding program.
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Affiliation(s)
- Radha Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | | | - Narayanan Nithya
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Alagu Manickavelu
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala India
| | - Rameshwar Prasad Sah
- Indian Council of Agricultural Research (ICAR)-Central Rice Research Institute, currently named National Rice Research Institute (NRRI), Cuttack, Odisha India
| | - Puthenpeedikal Salim Abida
- Regional Agricultural Research Station, Pattambi, Kerala Agricultural University, Palakkad, Kerala India
| | - Janardanan Sreekumar
- Indian Council of Agricultural Research (ICAR)-Central Tuber Crops Research Institute, Sreekaryam, Thiruvananthapuram, Kerala India
| | | | - Rajendrakumar Rejeth
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Vijayalayam Gengamma Jayalekshmy
- Department of Plant Breeding and Genetics, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Stephen Roy
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Ramakrishnan Vimala Manju
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
| | - Mariasoosai Mary Viji
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agricultural University, Thiruvananthapuram, Kerala India
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Qiao J, Jiang H, Lin Y, Shang L, Wang M, Li D, Fu X, Geisler M, Qi Y, Gao Z, Qian Q. A novel miR167a-OsARF6-OsAUX3 module regulates grain length and weight in rice. Mol Plant 2021; 14:1683-1698. [PMID: 34186219 DOI: 10.1016/j.molp.2021.06.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 05/26/2021] [Accepted: 06/25/2021] [Indexed: 05/02/2023]
Abstract
Grain size is one of the most important factors that control rice yield, as it is associated with grain weight (GW). To date, dozens of rice genes that regulate grain size have been isolated; however, the regulatory mechanism underlying GW control is not fully understood. Here, the quantitative trait locus qGL5 for grain length (GL) and GW was identified in recombinant inbred lines of 9311 and Nipponbare (NPB) and fine mapped to a candidate gene, OsAUX3. Sequence variations between 9311 and NPB in the OsAUX3 promoter and loss of function of OsAUX3 led to higher GL and GW. RNA sequencing, gene expression quantification, dual-luciferase reporter assays, chromatin immunoprecipitation-quantitative PCR, and yeast one-hybrid assays demonstrated that OsARF6 is an upstream transcription factor regulating the expression of OsAUX3. OsARF6 binds directly to the auxin response elements of the OsAUX3 promoter, covering a single-nucleotide polymorphism site between 9311 and NPB/Dongjin/Hwayoung, and thereby controls GL by altering longitudinal expansion and auxin distribution/content in glume cells. Furthermore, we showed that miR167a positively regulate GL and GW by directing OsARF6 mRNA silencing. Taken together, our study reveals that a novel miR167a-OsARF6-OsAUX3 module regulates GL and GW in rice, providing a potential target for the improvement of rice yield.
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Affiliation(s)
- Jiyue Qiao
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China; State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Hongzhen Jiang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Yuqing Lin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dongming Li
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, University of Chinese Academy of Sciences, 100049, China
| | - Markus Geisler
- Department of Biology, University of Fribourg, Rue Albert-Gockel 3, CH-1700 Fribourg, Switzerland
| | - Yanhua Qi
- Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010000, China; State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China.
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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Duan P, Li Y. Size matters: G protein signaling is crucial for grain size control in rice. Mol Plant 2021; 14:1618-1620. [PMID: 34411726 DOI: 10.1016/j.molp.2021.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/07/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Affiliation(s)
- Penggen Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100039, China.
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Jung WJ, Lee YJ, Kang CS, Seo YW. Identification of genetic loci associated with major agronomic traits of wheat (Triticum aestivum L.) based on genome-wide association analysis. BMC Plant Biol 2021; 21:418. [PMID: 34517837 PMCID: PMC8436466 DOI: 10.1186/s12870-021-03180-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/11/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Bread wheat (Triticum aestivum L.) is one of the most widely consumed cereal crops, but its complex genome makes it difficult to investigate the genetic effect on important agronomic traits. Genome-wide association (GWA) analysis is a useful method to identify genetic loci controlling complex phenotypic traits. With the RNA-sequencing based gene expression analysis, putative candidate genes governing important agronomic trait can be suggested and also molecular markers can be developed. RESULTS We observed major quantitative agronomic traits of wheat; the winter survival rate (WSR), days to heading (DTH), days to maturity (DTM), stem length (SL), spike length (SPL), awn length (AL), liter weight (LW), thousand kernel weight (TKW), and the number of seeds per spike (SPS), of 287 wheat accessions from diverse country origins. A significant correlation was observed between the observed traits, and the wheat genotypes were divided into three subpopulations according to the population structure analysis. The best linear unbiased prediction (BLUP) values of the genotypic effect for each trait under different environments were predicted, and these were used for GWA analysis based on a mixed linear model (MLM). A total of 254 highly significant marker-trait associations (MTAs) were identified, and 28 candidate genes closely located to the significant markers were predicted by searching the wheat reference genome and RNAseq data. Further, it was shown that the phenotypic traits were significantly affected by the accumulation of favorable or unfavorable alleles. CONCLUSIONS From this study, newly identified MTA and putative agronomically useful genes will help to study molecular mechanism of each phenotypic trait. Further, the agronomically favorable alleles found in this study can be used to develop wheats with superior agronomic traits.
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Affiliation(s)
- Woo Joo Jung
- Department of Plant Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Yong Jin Lee
- Department of Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Chon-Sik Kang
- National Institute of Crop Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Yong Weon Seo
- Department of Plant Biotechnology, Korea University, Seoul, 02841, South Korea.
- Department of Biotechnology, Korea University, Seoul, 02841, South Korea.
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Schierenbeck M, Alqudah AM, Lohwasser U, Tarawneh RA, Simón MR, Börner A. Genetic dissection of grain architecture-related traits in a winter wheat population. BMC Plant Biol 2021; 21:417. [PMID: 34507551 PMCID: PMC8431894 DOI: 10.1186/s12870-021-03183-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 08/20/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND The future productivity of wheat (T. aestivum L.) as the most grown crop worldwide is of utmost importance for global food security. Thousand kernel weight (TKW) in wheat is closely associated with grain architecture-related traits, e.g. kernel length (KL), kernel width (KW), kernel area (KA), kernel diameter ratio (KDR), and factor form density (FFD). Discovering the genetic architecture of natural variation in these traits, identifying QTL and candidate genes are the main aims of this study. Therefore, grain architecture-related traits in 261 worldwide winter accessions over three field-year experiments were evaluated. RESULTS Genome-wide association analysis using 90K SNP array in FarmCPU model revealed several interesting genomic regions including 17 significant SNPs passing false discovery rate threshold and strongly associated with the studied traits. Four of associated SNPs were physically located inside candidate genes within LD interval e.g. BobWhite_c5872_589 (602,710,399 bp) found to be inside TraesCS6A01G383800 (602,699,767-602,711,726 bp). Further analysis reveals the four novel candidate genes potentially involved in more than one grain architecture-related traits with a pleiotropic effects e.g. TraesCS6A01G383800 gene on 6A encoding oxidoreductase activity was associated with TKW and KA. The allelic variation at the associated SNPs showed significant differences betweeen the accessions carying the wild and mutated alleles e.g. accessions carying C allele of BobWhite_c5872_589, TraesCS6A01G383800 had significantly higher TKW than the accessions carying T allele. Interestingly, these genes were highly expressed in the grain-tissues, demonstrating their pivotal role in controlling the grain architecture. CONCLUSIONS These results are valuable for identifying regions associated with kernel weight and dimensions and potentially help breeders in improving kernel weight and architecture-related traits in order to increase wheat yield potential and end-use quality.
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Affiliation(s)
- Matías Schierenbeck
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr 3, D-06466, Seeland, Germany.
- Cereals, Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina.
- CONICET CCT La Plata. La Plata, Buenos Aires, Argentina.
| | - Ahmad M Alqudah
- Department of Agroecology, Aarhus University at Flakkebjerg, Forsøgsvej 1, 4200, Slagelse, Denmark.
| | - Ulrike Lohwasser
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr 3, D-06466, Seeland, Germany
| | - Rasha A Tarawneh
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr 3, D-06466, Seeland, Germany
| | - María Rosa Simón
- Cereals, Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina
- CONICET CCT La Plata. La Plata, Buenos Aires, Argentina
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstr 3, D-06466, Seeland, Germany
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11
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Wu T, Ali A, Wang J, Song J, Fang Y, Zhou T, Luo Y, Zhang H, Chen X, Liao Y, Liu Y, Xu P, Wu X. A homologous gene of OsREL2/ASP1, ASP-LSL regulates pleiotropic phenotype including long sterile lemma in rice. BMC Plant Biol 2021; 21:390. [PMID: 34418975 PMCID: PMC8379857 DOI: 10.1186/s12870-021-03163-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Panicle is a harvesting organ of rice, and its morphology and development are closely associated with grain yield. The current study was carried on a mutant screened through an EMS (ethyl-methane sulphonate) mutagenized population of a Japonica cultivar Kitaake (WT). RESULTS A mutant, named as asp-lsl (aberrant spikelet-long sterile lemma), showed a significant decrease in plant height, number of tillers, thousand-grains weight, seed setting rate, spikelet length, kernel length and effective number of grains per panicle as compared to WT. Asp-lsl showed a pleiotropic phenotype coupled with the obvious presence of a long sterile lemma. Cross-sections of lemma showed an increase in the cell volume rather than the number of cells. Genetic segregation analysis revealed its phenotypic trait is controlled by a single recessive nuclear gene. Primary and fine mapping indicated that candidate gene controlling the phenotype of asp-lsl was located in an interval of 212 kb on the short arm of chromosome 8 between RM22445 and RM22453. Further sequencing and indels markers analysis revealed LOC_Os08g06480 harbors a single base substitution (G→A), resulting in a change of 521st amino acid(Gly→Glu. The homology comparison and phylogenetic tree analysis revealed mutation was occurred in a highly conserved domain and had a high degree of similarity in Arabidopsis, corn, and sorghum. The CRISPR/Cas9 mutant line of ASP-LSL produced a similar phenotype as that of asp-lsl. Subcellular localization of ASP-LSL revealed that its protein is localized in the nucleus. Relative expression analysis revealed ASP-LSL was preferentially expressed in panicle, stem, and leaves. The endogenous contents of GA, CTK, and IAA were found significantly decreased in asp-lsl as compared to WT. CONCLUSIONS Current study presents the novel phenotype of asp-lsl and also validate the previously reported function of OsREL2 (ROMOSA ENHANCER LOCI2), / ASP1(ABERRANT SPIKELET AND PANICLE 1).
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Affiliation(s)
- Tingkai Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Asif Ali
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Jinhao Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Jiahe Song
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yongqiong Fang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Tingting Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yi Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Hongyu Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Xiaoqiong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yongxiang Liao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Yutong Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Peizhou Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Xianjun Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, 611130, Chengdu, China.
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12
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Hu Y, Zhang Z. GridFree: a python package of imageanalysis for interactive grain counting and measuring. Plant Physiol 2021; 186:2239-2252. [PMID: 34618106 PMCID: PMC8331130 DOI: 10.1093/plphys/kiab226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/20/2021] [Indexed: 06/13/2023]
Abstract
Grain characteristics, including kernel length, kernel width, and thousand kernel weight, are critical component traits for grain yield. Manual measurements and counting are expensive, forming the bottleneck for dissecting these traits' genetic architectures toward ultimate yield improvement. High-throughput phenotyping methods have been developed by analyzing images of kernels. However, segmenting kernels from the image background and noise artifacts or from other kernels positioned in close proximity remain as challenges. In this study, we developed a software package, named GridFree, to overcome these challenges. GridFree uses an unsupervised machine learning approach, K-Means, to segment kernels from the background by using principal component analysis on both raw image channels and their color indices. GridFree incorporates users' experiences as a dynamic criterion to set thresholds for a divide-and-combine strategy that effectively segments adjacent kernels. When adjacent multiple kernels are incorrectly segmented as a single object, they form an outlier on the distribution plot of kernel area, length, and width. GridFree uses the dynamic threshold settings for splitting and merging. In addition to counting, GridFree measures kernel length, width, and area with the option of scaling with a reference object. Evaluations against existing software programs demonstrated that GridFree had the smallest error on counting seeds for multiple crop species. GridFree was implemented in Python with a friendly graphical user interface to allow users to easily visualize the outcomes and make decisions, which ultimately eliminates time-consuming and repetitive manual labor. GridFree is freely available at the GridFree website (https://zzlab.net/GridFree).
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Affiliation(s)
- Yang Hu
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
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13
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Huang X, Hilscher J, Stoger E, Christou P, Zhu C. Modification of cereal plant architecture by genome editing to improve yields. Plant Cell Rep 2021; 40:953-978. [PMID: 33559722 DOI: 10.1007/s00299-021-02668-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/22/2021] [Indexed: 06/12/2023]
Abstract
We summarize recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement. Plant architecture is defined as the three-dimensional organization of the entire plant. Shoot architecture refers to the structure and organization of the aboveground components of a plant, reflecting the developmental patterning of stems, branches, leaves and inflorescences/flowers. Root system architecture is essentially determined by four major shape parameters-growth, branching, surface area and angle. Interest in plant architecture has arisen from the profound impact of many architectural traits on agronomic performance, and the genetic and hormonal regulation of these traits which makes them sensitive to both selective breeding and agronomic practices. This is particularly important in staple crops, and a large body of literature has, therefore, accumulated on the control of architectural phenotypes in cereals, particularly rice due to its twin role as one of the world's most important food crops as well as a model organism in plant biology and biotechnology. These studies have revealed many of the molecular mechanisms involved in the regulation of tiller/axillary branching, stem height, leaf and flower development, root architecture and the grain characteristics that ultimately help to determine yield. The advent of genome editing has made it possible, for the first time, to introduce precise mutations into cereal crops to optimize their architecture and close in on the concept of the ideotype. In this review, we consider recent genome editing studies that have focused on the examination (or reexamination) of plant architectural phenotypes in cereals and the modification of these traits for crop improvement.
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Affiliation(s)
- Xin Huang
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
| | - Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 33, 1180, Vienna, Austria
| | - Paul Christou
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Passeig Lluís Companys 23, 08010, Barcelona, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio Center, Av. Alcalde Rovira Roure, 191, 25198, Lleida, Spain.
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14
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Sharma M, Gangurde SS, Salgotra RK, Kumar B, Singh AK, Pandey MK. Genetic mapping for grain quality and yield-attributed traits in Basmati rice using SSR-based genetic map. J Biosci 2021; 46:50. [PMID: 34148873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rice grain shape and nutritional quality traits have high economic value for commercial production of rice and largely determine the market price, besides influencing the global food demand for high-quality rice. Detection, mapping and exploitation of quantitative trait loci (QTL) associated with kernel elongation and grain quality in Basmati rice is considered as an efficient strategy for improving the kernel elongation and grain quality trait in rice varieties. Genetic information in rice for most of these traits is scanty and needed interventions through the use of molecular markers. A recombinant inbred lines (RIL) population consisting of 130 lines generated from the cross involving Basmati 370, a superior quality Basmati variety and Pusa Basmati 1121, a Basmati derived variety were used to map the QTLs for 9 important grain quality and yield related traits. Correlation studies showed that various components of yield show a significant positive relationship with grain yield. A genetic map was constructed using 70 polymorphic simple sequence repeat (SSR) markers spanning a genetic distance of 689.3 cM distributed over 12 rice chromosomes. Significant variation was observed and showed transgressive segregation for grain quality traits in RIL population. A total of 20 QTLs were identified associated with nine yield and quality traits. Epistatic interactions were also identified for grain quality related traits indicating complex genetic nature inheritance. Therefore, the identified QTLs and flanking marker information could be utilized in the marker-assisted selection to improve kernel elongation and nutritional grain quality traits in rice varieties.
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Affiliation(s)
- Madhvi Sharma
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology, Chatha, Jammu 180 009, India
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15
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Sengupta S, Bhattacharya S, Karmakar A, Ghosh S, Sarkar SN, Gangopadhyay G, Datta K, Datta SK. RNAi-mediated down-regulation of ITPK-2 enhanced inorganic phosphorus and minerals in the transgenic rice. J Biosci 2021; 46:32. [PMID: 33859067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phytic acid or Myo-inositol hexakisphosphate is an essential compound for the rice plants. It remains in the form of phytate, a mixed salt of different mineral cations, in the seeds. The phytate breaks down during germination and provides the inorganic phosphorus and mineral ions to the seedlings. However, humans do not get the benefit of those essential ions from rice consumption due to the absence of phytase in the gut. We envisaged down-regulating ITPK, the gene behind the phytic acid biosynthesis so that its low amount would facilitate a greater amount of free mineral ions in the endosperm. Since there are six homologues of rice ITPK, we studied their expression in seeds. Additionally, we undertook an in-silico analysis of the homologous proteins. Considering the results, we selected ITPK-2 for its RNAi-mediated embryo-specific down-regulation to obtain the low phytate rice. We obtained a 37% reduction of phytic acid content accompanied by a nearly three-fold enhancement of inorganic phosphorus in the transgenic seeds. Additionally, the iron and zinc content increased in polished rice grains compared to the wild type. The results also showed that reduced phytic acid content did not affect the germination potential and seedling growth of the transgenic rice.
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16
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Ahn E, Odvody G, Prom LK, Magill C. Leaf angle distribution in Johnsongrass, leaf thickness in sorghum and Johnsongrass, and association with response to Colletotrichum sublineola. Sci Rep 2020; 10:22320. [PMID: 33339866 PMCID: PMC7749152 DOI: 10.1038/s41598-020-79473-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 12/03/2020] [Indexed: 11/10/2022] Open
Abstract
Basal leaf angle distribution was surveyed in twenty-one Johnsongrass cultivars near the end of the vegetative stage. The angles increased from the top to the bottom leaves, and compared to cultivated grain sorghums, the average angle was larger in Johnsongrass. When basal leaf angle distribution data were correlated with pathogenicity test data from excised-leaf assays for three isolates of Colletotrichum sublineola, the results showed a weak positive correlation between basal leaf angle and pathogenicity level in Johnsongrass. In order to investigate a protective role of leaf thickness to C. sublineola, leaf thickness was measured in three sorghum cultivars and one Johnsongrass cultivar at the 8-leaf-stage. Leaf thickness near the apex, near the base, and half-way between the two points were measured in the top four leaves of each plant. Thickness of leaf blade and midrib were recorded separately. Using an excised-leaf-assay, the three points were inoculated with C. sublineola, and pathogenicity level was recorded 4-days-post-inoculation. Results showed strong negative correlations between leaf midrib thickness and pathogenicity level in sorghum and Johnsongrass but not in leaf blades.
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Affiliation(s)
- Ezekiel Ahn
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA
| | - Gary Odvody
- Texas A&M AgriLife Research, Corpus Christi, TX, USA
| | - Louis K Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.
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17
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Nkhata W, Shimelis H, Melis R, Chirwa R, Mzengeza T, Mathew I, Shayanowako A. Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers. PLoS One 2020; 15:e0243238. [PMID: 33338076 PMCID: PMC7748271 DOI: 10.1371/journal.pone.0243238] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 11/18/2020] [Indexed: 11/19/2022] Open
Abstract
Knowledge of genetic diversity in plant germplasm and the relationship between genetic factors and phenotypic expression is vital for crop improvement. This study's objectives were to understand the extent of genetic diversity and population structure in 60 common bean genotypes from East and Southern Africa. The common bean genotypes exhibited significant (p<0.05) levels of variability for traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield per hectare in kilograms (GYD). About 47.82 per cent of the variation among the genotypes was explained by seven principal components (PC) associated with the following agronomic traits: NPP, NFF (nodes to first flower), DTF, GH (growth habit) and GYD. The SNP markers revealed mean gene diversity and polymorphic information content values of 0.38 and 0.25, respectively, which suggested the presence of considerable genetic variation among the assessed genotypes. Analysis of molecular variance showed that 51% of the genetic variation were between the gene pools, while 49% of the variation were within the gene pools. The genotypes were delineated into two distinct groups through the population structure, cluster and phylogenetic analyses. Genetically divergent genotypes such as DRK57, MW3915, NUA59, and VTTT924/4-4 with high yield and agronomic potential were identified, which may be useful for common bean improvement.
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Affiliation(s)
- Wilson Nkhata
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Hussein Shimelis
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Rob Melis
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Rowland Chirwa
- International Centre for Tropical Agriculture, Chitedze Agricultural Research Station, Lilongwe, Malawi
| | - Tenyson Mzengeza
- Department of Agricultural Research Service, Chitedze Agricultural Research Station, Lilongwe, Malawi
| | - Isack Mathew
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Admire Shayanowako
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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18
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Mantilla-Perez MB, Bao Y, Tang L, Schnable PS, Salas-Fernandez MG. Toward "Smart Canopy" Sorghum: Discovery of the Genetic Control of Leaf Angle Across Layers. Plant Physiol 2020; 184:1927-1940. [PMID: 33093232 PMCID: PMC7723111 DOI: 10.1104/pp.20.00632] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/09/2020] [Indexed: 05/15/2023]
Abstract
A "smart canopy" ideotype has been proposed with leaves being upright at the top and more horizontal toward the bottom of the plant to maximize light interception and conversion efficiencies, and thus increasing yield. The genetic control of leaf angle has, to date, been studied on one or two leaves, or data have been merged from multiple leaves to generate average values. This approach has limited our understanding of the diversity of leaf angles across layers and their genetic control. Genome-wide association studies and quantitative trait loci mapping studies in sorghum (Sorghum bicolor) were performed using layer-specific angle data collected manually and via high-throughput phenotyping strategies. The observed distribution of angles in indoor and field settings is opposite to the ideotype. Several genomic regions were associated with leaf angle within layers or across the canopy. The expression of the brassinosteroid-related transcription factor BZR1/BES1 and the auxin-transporter Dwarf3 were found to be highly correlated with the distribution of angles at different layers. The application of a brassinosteroid biosynthesis inhibitor could not revert the undesirable overall angle distribution. These discoveries demonstrate that the exploitation of layer-specific quantitative trait loci/genes will be instrumental to reversing the natural angle distribution in sorghum according to the "smart canopy" ideotype.
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Affiliation(s)
| | - Yin Bao
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa 50011
| | - Lie Tang
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, Iowa 50011
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Ntakirutimana F, Xie W. Unveiling the Actual Functions of Awns in Grasses: From Yield Potential to Quality Traits. Int J Mol Sci 2020; 21:ijms21207593. [PMID: 33066600 PMCID: PMC7589186 DOI: 10.3390/ijms21207593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 12/25/2022] Open
Abstract
Awns, which are either bristles or hair-like outgrowths of lemmas in the florets, are one of the typical morphological characteristics of grass species. These stiff structures contribute to grain dispersal and burial and fend off animal predators. However, their phenotypic and genetic associations with traits deciding potential yield and quality are not fully understood. Awns appear to improve photosynthesis, provide assimilates for grain filling, thus contributing to the final grain yield, especially under temperature- and water-stress conditions. Long awns, however, represent a competing sink with developing kernels for photosynthates, which can reduce grain yield under favorable conditions. In addition, long awns can hamper postharvest handling, storage, and processing activities. Overall, little is known about the elusive role of awns, thus, this review summarizes what is known about the effect of awns on grain yield and biomass yield, grain nutritional value, and forage-quality attributes. The influence of awns on the agronomic performance of grasses seems to be associated with environmental and genetic factors and varies in different stages of plant development. The contribution of awns to yield traits and quality features previously documented in major cereal crops, such as rice, barley, and wheat, emphasizes that awns can be targeted for yield and quality improvement and may advance research aimed at identifying the phenotypic effects of morphological traits in grasses.
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20
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Kiseleva AA, Leonova IN, Pshenichnikova TA, Salina EA. Dissection of novel candidate genes for grain texture in Russian wheat varieties. Plant Mol Biol 2020; 104:219-233. [PMID: 32617826 DOI: 10.1007/s11103-020-01025-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Antonina A Kiseleva
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090.
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090.
| | - Irina N Leonova
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090
| | - Tatyana A Pshenichnikova
- The Federal State Budgetary Institution of Science Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090
| | - Elena A Salina
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, Russia, 630090
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Kumar A, Daware A, Kumar A, Kumar V, Gopala Krishnan S, Mondal S, Patra BC, Singh AK, Tyagi AK, Parida SK, Thakur JK. Genome-wide analysis of polymorphisms identified domestication-associated long low-diversity region carrying important rice grain size/weight quantitative trait loci. Plant J 2020; 103:1525-1547. [PMID: 32432802 DOI: 10.1111/tpj.14845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 05/01/2020] [Accepted: 05/12/2020] [Indexed: 05/02/2023]
Abstract
Rice grain size and weight are major determinants of grain quality and yield and so have been under rigorous selection since domestication. However, the genetic basis for contrasting grain size/weight trait among Indian germplasms and their association with domestication-driven evolution is not well understood. In this study, two long (LGG) and two short grain (SGG) genotypes were resequenced. LGG (LGR and PB 1121) differentiated from SGG (Sonasal and Bindli) by 504 439 single nucleotide polymorphisms (SNPs) and 78 166 insertion-and-deletion polymorphisms. The LRK gene cluster was different and a truncation mutation in the LRK8 kinase domain was associated with LGG. Phylogeny with 3000 diverse rice accessions revealed that the four sequenced genotypes belonged to the japonica group and were at the edge of the clades indicating them to be the potential source of genetic diversity available in Indian rice germplasm. Six SNPs were significantly associated with grain size/weight and the top four of these could be validated in mapping a population, suggesting this study as a valuable resource for high-throughput genotyping. A contiguous long low-diversity region (LDR) of approximately 6 Mb carrying a major grain weight quantitative trait loci (harbouring OsTOR gene) was identified on Chromosome 5. This LDR was identified as an evolutionary important site with significant positive selection and multiple selection sweeps, and showed association with many domestication-related traits, including grain size/weight. The aus population retained more allelic variations in the LDR than the japonica and indica populations, suggesting it to be one of the divergence loci. All the data and analyses can be accessed from the RiceSzWtBase database.
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Affiliation(s)
- Angad Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Arvind Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vinay Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Subhasish Mondal
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Bhaskar C Patra
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, 753006, India
| | - Ashok K Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Thakur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
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22
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Navrotskyi S, Belamkar V, Baenziger PS, Rose DJ. Insights into the Genetic Architecture of Bran Friability and Water Retention Capacity, Two Important Traits for Whole Grain End-Use Quality in Winter Wheat. Genes (Basel) 2020; 11:E838. [PMID: 32717821 PMCID: PMC7466047 DOI: 10.3390/genes11080838] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 11/16/2022] Open
Abstract
Bran friability (particle size distribution after milling) and water retention capacity (WRC) impact wheat bran functionality in whole grain milling and baking applications. The goal of this study was to identify genomic regions and underlying genes that may be responsible for these traits. The Hard Winter Wheat Association Mapping Panel, which comprised 299 lines from breeding programs in the Great Plains region of the US, was used in a genome-wide association study. Bran friability ranged from 34.5% to 65.9% (median, 51.1%) and WRC ranged from 159% to 458% (median, 331%). Two single-nucleotide polymorphisms (SNPs) on chromosome 5D were significantly associated with bran friability, accounting for 11-12% of the phenotypic variation. One of these SNPs was located within the Puroindoline-b gene, which is known for influencing endosperm texture. Two SNPs on chromosome 4A were tentatively associated with WRC, accounting for 4.6% and 4.4% of phenotypic variation. The favorable alleles at the SNP sites were present in only 15% (friability) and 34% (WRC) of lines, indicating a need to develop new germplasm for these whole-grain end-use quality traits. Validation of these findings in independent populations will be useful for breeding winter wheat cultivars with improved functionality for whole grain food applications.
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Affiliation(s)
- Sviatoslav Navrotskyi
- Department of Food Science & Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Vikas Belamkar
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
| | - P. Stephen Baenziger
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
| | - Devin J. Rose
- Department of Food Science & Technology, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA;
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23
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Wang GJ, Wang Y, Ying JZ, Song XJ. Identification of qLG2, qLG8, and qWG2 as novel quantitative trait loci for grain shape and the allelic analysis in cultivated rice. Planta 2020; 252:18. [PMID: 32671480 DOI: 10.1007/s00425-020-03420-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Three novel QTLs for grain shape were genetically fine mapped, with two of which to a 250-kb target interval on rice chromosome 2 that contains fourteen candidate genes. Grain shape (grain length, width, and thickness) determines crop yield and grain quality. However, the trait is regulated by numerous naturally occurring quantitative trait loci (QTLs) and the underlying mechanism remains largely unknown. Here, we report the genetic mapping of three new QTLs, qLG2, qWG2, and qLG8 that each exerts a semi-dominant effect on grain shape in cultivated rice. These QTLs were validated using populations derived from the corresponding chromosome segment substitution lines (CSSLs), and were further delimited to small genomic intervals in progeny testing experiments. Especially, qLG2/qWG2 was placed into an about 250-kb genomic candidate region, and 14 predicted ORFs localized within the interval. We also evaluated the individual and pyramiding genetic effect(s) of these QTL(s) using the corresponding nearly isogenic lines, and found that they have additive effects on the traits. Collectively, these findings provided useful information as a tool to improve grain shape in crop breeding programs and established foundations for future QTL cloning.
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Affiliation(s)
- Gao-Jie Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie-Zheng Ying
- National Key Laboratory of Rice Biology and Chinese Center of Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xian-Jun Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Chinese Academy of Sciences, No. 20 Nanxincun, Xiangshan, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, China.
- The Innovative Academy of Seed Design, The Chinese Academy of Sciences, Beijing, China.
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24
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Sakamoto L, Kajiya-Kanegae H, Noshita K, Takanashi H, Kobayashi M, Kudo T, Yano K, Tokunaga T, Tsutsumi N, Iwata H. Comparison of shape quantification methods for genomic prediction, and genome-wide association study of sorghum seed morphology. PLoS One 2019; 14:e0224695. [PMID: 31751371 PMCID: PMC6872133 DOI: 10.1371/journal.pone.0224695] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/18/2019] [Indexed: 11/19/2022] Open
Abstract
Seed shape is an important agronomic trait with continuous variation among genotypes. Therefore, the quantitative evaluation of this variation is highly important. Among geometric morphometrics methods, elliptic Fourier analysis and semi-landmark analysis are often used for the quantification of biological shape variations. Elliptic Fourier analysis is an approximation method to treat contours as a waveform. Semi-landmark analysis is a method of superimposed points in which the differences of multiple contour positions are minimized. However, no detailed comparison of these methods has been undertaken. Moreover, these shape descriptors vary when the scale and direction of the contour and the starting point of the contour trace change. Thus, these methods should be compared with respect to the standardization of the scale and direction of the contour and the starting point of the contour trace. In the present study, we evaluated seed shape variations in a sorghum (Sorghum bicolor Moench) germplasm collection to analyze the association between shape variations and genome-wide single-nucleotide polymorphisms by genomic prediction (GP) and genome-wide association studies (GWAS). In our analysis, we used all possible combinations of three shape description methods and eight standardization procedures for the scale and direction of the contour as well as the starting point of the contour trace; these combinations were compared in terms of GP accuracy and the GWAS results. We compared the shape description methods (elliptic Fourier descriptors and the coordinates of superposed pseudo-landmark points) and found that principal component analysis of their quantitative descriptors yielded similar results. Different scaling and direction standardization procedures caused differences in the principal component scores, average shape, and the results of GP and GWAS.
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Affiliation(s)
- Lisa Sakamoto
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
- JSPS Research Fellow, Tokyo, Japan
| | | | - Koji Noshita
- Department of Biology, Kyushu University, Fukuoka, Japan
- PRESTO, JST, Saitama, Japan
| | - Hideki Takanashi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | | | - Toru Kudo
- Faculty of Agriculture, Meiji University, Kanagawa, Japan
| | - Kentaro Yano
- Faculty of Agriculture, Meiji University, Kanagawa, Japan
| | | | - Nobuhiro Tsutsumi
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Hiroyoshi Iwata
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
- * E-mail:
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25
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Tian P, Liu J, Mou C, Shi C, Zhang H, Zhao Z, Lin Q, Wang J, Wang J, Zhang X, Guo X, Cheng Z, Zhu S, Ren Y, Lei C, Wang H, Wan J. GW5-Like, a homolog of GW5, negatively regulates grain width, weight and salt resistance in rice. J Integr Plant Biol 2019; 61:1171-1185. [PMID: 30450718 DOI: 10.1111/jipb.12745] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/09/2018] [Indexed: 05/23/2023]
Abstract
Grain size is an important determinant of yield potential in crops. We previously demonstrated that natural mutations in the regulatory sequences of qSW5/GW5 confer grain width diversity in rice. However, the biological function of a GW5 homolog, named GW5-Like (GW5L), remains unknown. In this study, we report on GW5L knockout mutants in Kitaake, a japonica cultivar (cv.) considered to have a weak gw5 variant allele that confers shorter and wider grains. GW5L is evenly expressed in various tissues, and its protein product is localized to the plasma membrane. Biochemical assays verified that GW5L functions in a similar fashion to GW5. It positively regulates brassinosteroid (BR) signaling through repression of the phosphorylation activity of GSK2. Genetic data show that GW5L overexpression in either Kitaake or a GW5 knockout line, Kasaorf3 (indica cv. Kasalath background), causes more slender, longer grains relative to the wild-type. We also show that GW5L could confer salt stress resistance through an association with calmodulin protein OsCaM1-1. These findings identify GW5L as a negative regulator of both grain size and salt stress tolerance, and provide a potential target for breeders to improve grain yield and salt stress resistance in rice.
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Affiliation(s)
- Peng Tian
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Jiafan Liu
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Changling Mou
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cuilan Shi
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Huan Zhang
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhichao Zhao
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Qibing Lin
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Jie Wang
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Jiulin Wang
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Xin Zhang
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Xiuping Guo
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Zhijun Cheng
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Shanshan Zhu
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Yulong Ren
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Cailin Lei
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Haiyang Wang
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
| | - Jianmin Wan
- Institute of Crop Sciences, the Chinese Academy of Agriculture Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Beijing, 100081, China
- Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing, 210095, China
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26
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Zhang Z, Han H, Liu W, Song L, Zhang J, Zhou S, Yang X, Li X, Li L. Deletion mapping and verification of an enhanced-grain number per spike locus from the 6PL chromosome arm of Agropyron cristatum in common wheat. Theor Appl Genet 2019; 132:2815-2827. [PMID: 31309244 DOI: 10.1007/s00122-019-03390-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 07/05/2019] [Indexed: 06/10/2023]
Abstract
An enhanced-grain number per spike locus from Agropyron cristatum 6PL was mapped onto 6PL (0.27-0.51) via deletion mapping, and its effect was further verified by evaluating a newly created translocation line. Agropyron cristatum (2n = 4x = 28, PPPP) is an important wild relative of common wheat and carries many desirable yield-related traits. The wheat-A. cristatum 6P disomic addition line 4844-12 exhibited high grain number per spike (GNS), high spikelet number per spike (SNS), and high kernel number per spikelet (KNS). In this study, five A. cristatum 6P deletion lines, five wheat-A. cristatum 6P translocation lines, and genetic populations of these lines were used to map the enhanced-GNS locus from A. cristatum chromosome 6P, which were genotyped via genomic in situ hybridization, fluorescence in situ hybridization, or molecular markers. According to the evaluation of the agronomic traits in four growing seasons (2014-2015, 2015-2016, 2016-2017, and 2017-2018), we found that the deletion lines and the translocation lines carrying the long arm of A. cristatum chromosome 6P (6PL) exhibited high GNS, SNS, and KNS, and the enhanced-GNS locus was ultimately mapped onto 6PL (0.27-0.51). To verify the localization results, we created a new translocation line WAT650a (T5BL•5BS-6PL) that carried 6PL (0.35-0.42); this line exhibited higher GNS and SNS than the recipient parent Fukuhokomugi (Fukuho). Collectively, the enhanced-GNS locus of A. cristatum 6PL can be important for improving yield traits in common wheat; the translocation lines with the enhanced-GNS locus can serve as novel and valuable germplasm resources for wheat breeding.
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Affiliation(s)
- Zhi Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Haiming Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weihua Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liqiang Song
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology of Sciences, Shijiazhuang, 050022, China
| | - Jinpeng Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shenghui Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinming Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiuquan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lihui Li
- 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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27
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Kumar A, Mantovani EE, Simsek S, Jain S, Elias EM, Mergoum M. Genome wide genetic dissection of wheat quality and yield related traits and their relationship with grain shape and size traits in an elite × non-adapted bread wheat cross. PLoS One 2019; 14:e0221826. [PMID: 31532783 PMCID: PMC6750600 DOI: 10.1371/journal.pone.0221826] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/15/2019] [Indexed: 12/21/2022] Open
Abstract
The genetic gain in yield and quality are two major targets of wheat breeding programs around the world. In this study, a high density genetic map consisting of 10,172 SNP markers identified a total of 43 genomic regions associated with three quality traits, three yield traits and two agronomic traits in hard red spring wheat (HRSW). When compared with six grain shape and size traits, the quality traits showed mostly independent genetic control (~18% common loci), while the yield traits showed moderate association (~53% common loci). Association of genomic regions for grain area (GA) and thousand-grain weight (TGW), with yield suggests that targeting an increase in GA may help enhancing wheat yield through an increase in TGW. Flour extraction (FE), although has a weak positive phenotypic association with grain shape and size, they do not share any common genetic loci. A major contributor to plant height was the Rht8 locus and the reduced height allele was associated with significant increase in grains per spike (GPS) and FE, and decrease in number of spikes per square meter and test weight. Stable loci were identified for almost all the traits. However, we could not find any QTL in the region of major known genes like GPC-B1, Ha, Rht-1, and Ppd-1. Epistasis also played an important role in the genetics of majority of the traits. In addition to enhancing our knowledge about the association of wheat quality and yield with grain shape and size, this study provides novel loci, genetic information and pre-breeding material (combining positive alleles from both parents) to enhance the cultivated gene pool in wheat germplasm. These resources are valuable in facilitating molecular breeding for wheat quality and yield improvement.
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Affiliation(s)
- Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States of America
| | - Eder E. Mantovani
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States of America
| | - Senay Simsek
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States of America
| | - Shalu Jain
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States of America
| | - Elias M. Elias
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States of America
| | - Mohamed Mergoum
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States of America
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28
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Nomura T, Arakawa N, Yamamoto T, Ueda T, Adachi S, Yonemaru JI, Abe A, Takagi H, Yokoyama T, Ookawa T. Next generation long-culm rice with superior lodging resistance and high grain yield, Monster Rice 1. PLoS One 2019; 14:e0221424. [PMID: 31437205 PMCID: PMC6705783 DOI: 10.1371/journal.pone.0221424] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/06/2019] [Indexed: 12/30/2022] Open
Abstract
During late 1960s Green Revolution, researchers utilized semidwarf 1 (sd1) to improve the yield and lodging resistance in rice (Oryza sativa L.). However, sd1 has a negative effect to culm strength and biomass production. To increase yield dramatically in 21th century, development of next generation long-culm rice for non-lodging and high grain yield independent of sd1 has been needed. The present study developed Monster Rice 1, a long-culm and heavy-panicle type of rice line and compared it with Takanari, a high-yielding semidwarf rice variety about yield and lodging resistance associated traits. Brown rice yield and bending moment at breaking of the basal elongated internode were higher in Monster Rice 1 than those in Takanari due to a large number of spikelets per panicle and thicker culm. Furthermore, to identify QTLs with superior alleles for these traits, QTL and haplotype analyses were performed using F2 population and recombinant inbred lines derived from a cross between Monster Rice 1 and Takanari. The results from this study suggest that long-culm and heavy-panicle type of rice with a superior lodging resistance by culm strength can perform its high yield potential by using these identified QTLs contributing yield and lodging resistance.
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Affiliation(s)
- Tomohiro Nomura
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Naoya Arakawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Toshio Yamamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Tadamasa Ueda
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | | | - Akira Abe
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Hiroki Takagi
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Tadashi Yokoyama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
- * E-mail:
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29
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Golan G, Ayalon I, Perry A, Zimran G, Ade-Ajayi T, Mosquna A, Distelfeld A, Peleg Z. GNI-A1 mediates trade-off between grain number and grain weight in tetraploid wheat. Theor Appl Genet 2019; 132:2353-2365. [PMID: 31079164 DOI: 10.1007/s00122-019-03358-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/02/2019] [Indexed: 05/19/2023]
Abstract
Wild emmer allele of GNI-A1 ease competition among developing grains through the suppression of floret fertility and increase grain weight in tetraploid wheat. Grain yield is a highly polygenic trait determined by the number of grains per unit area, as well as by grain weight. In wheat, grain number and grain weight are usually negatively correlated. Yet, the genetic basis underlying trade-off between the two is mostly unknown. Here, we fine-mapped a grain weight QTL using wild emmer introgressions in a durum wheat background and showed that grain weight is associated with the GNI-A1 gene, a regulator of floret fertility. In-depth characterization of grain number and grain weight indicated that suppression of distal florets by the wild emmer GNI-A1 allele increases weight of proximal grains in basal and central spikelets due to alteration in assimilate distribution. Re-sequencing of GNI-A1 in tetraploid wheat demonstrated the rich allelic repertoire of the wild emmer gene pool, including a rare allele which was present in two gene copies and contained a nonsynonymous mutation in the C-terminus of the protein. Using an F2 population generated from a cross between wild emmer accessions Zavitan, which carries the rare allele, and TTD140, we demonstrated that this unique polymorphism is associated with grain weight, independent of grain number. Moreover, we showed, for the first time, that GNI-A1 proteins are transcriptional activators and that selection targeted compromised activity of the protein. Our findings expand the knowledge of the genetic basis underlying trade-off between key yield components and may contribute to breeding efforts for enhanced grain yield.
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Affiliation(s)
- Guy Golan
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, 7610001, Rehovot, Israel
| | - Idan Ayalon
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, 7610001, Rehovot, Israel
| | - Aviad Perry
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, 7610001, Rehovot, Israel
| | - Gil Zimran
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, 7610001, Rehovot, Israel
| | - Toluwanimi Ade-Ajayi
- School of Plant Sciences and Food Security, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Assaf Mosquna
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, 7610001, Rehovot, Israel
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, P.O. Box 12, 7610001, Rehovot, Israel.
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30
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Zhao Y, Xie P, Guan P, Wang Y, Li Y, Yu K, Xin M, Hu Z, Yao Y, Ni Z, Sun Q, Xie C, Peng H. Btr1-A Induces Grain Shattering and Affects Spike Morphology and Yield-Related Traits in Wheat. Plant Cell Physiol 2019; 60:1342-1353. [PMID: 30994893 DOI: 10.1093/pcp/pcz050] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/21/2019] [Indexed: 06/09/2023]
Abstract
Spike brittleness represents an important domestication trait in crops. Although the brittle rachis of wild wheat was cloned, however, the molecular mechanism underlying spike brittleness is yet to be elucidated. Here, we identified a single dominant brittle rachis gene Br-Ab on chromosome arm 3AbS using an F2 population of diploid wheat and designated Btr1-Ab. Sequence analysis of the Btr1-A gene in 40 diploid wheat accessions, 80 tetraploid wheat accessions and 38 hexaploid wheat accessions showed that two independent mutations (Ala119Thr for diploid and Gly97* for polyploids) in the Btr1-A coding region resulting in the nonbrittle rachis allele. Overexpression of Btr1-Ab in nonbrittle hexaploid wheat led to brittle rachis in transgenic plants. RNA-Seq analysis revealed that Btr1-A represses the expression of cell wall biosynthesis genes during wheat rachis development. In addition, we found that Btr1-A can modify spike morphology and reduce threshability, grain size and thousand grain weight in transgenic wheat. These results demonstrated that Btr1-A reduces cell wall synthesis in rachis nodes, resulting in natural spikelet shattering, and that the transition from Btr1-A to btr1-A during wheat domestication had profound effects on evolution of spike morphology and yield-related traits.
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Affiliation(s)
- Yue Zhao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
- These authors contributed equally to this work
| | - Peng Xie
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
- These authors contributed equally to this work
| | - Panfeng Guan
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
- These authors contributed equally to this work
| | - Yongfa Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Yinghui Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Kuohai Yu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Chaojie Xie
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, PR China
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Tong X, Wang Y, Sun A, Bello BK, Ni S, Zhang J. Notched Belly Grain 4, a Novel Allele of Dwarf 11, Regulates Grain Shape and Seed Germination in Rice (Oryza sativa L.). Int J Mol Sci 2018; 19:ijms19124069. [PMID: 30558382 PMCID: PMC6321642 DOI: 10.3390/ijms19124069] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/03/2018] [Accepted: 12/04/2018] [Indexed: 12/19/2022] Open
Abstract
Notched belly grain (NBG) is a type of deformed grain shape that has been associated with inferior appearance and tastes in rice. NBG is coordinated by both environments and genetics. In this study, we report on the first map-based cloning of an NBG gene on chromosome 4, denoted NBG4, which is a novel allele of Dwarf 11 encoding a cytochrome P450 (CYP724B1) involved in brassinosteroid (BR) biosynthesis. A 10-bp deletion in the 7th exon knocked down the level of the NBG4 transcript and shifted the reading frame of the resulting protein. In addition to the dwarf and clustered panicle as previously reported in the allelic mutants, nbg4 grains also displayed retarded germination and NBG due to the physical constraint of deformed hulls caused by abnormal hull elongation. NBG4 is constitutively expressed with the highest level of expression in immature inflorescences. In all, 2294 genes were differentially expressed in nbg4 and wild-type (WT), and evidence is presented that NBG4 regulates OsPPS-2, OsPRA2, OsYUCCA1, sped1-D, and Dwarf that play critical roles in determining plant architecture, panicle development, and seed germination. This study demonstrated that NBG4 is a key node in the brassinosteroid-mediated regulation of rice grain shape.
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Affiliation(s)
- Xiaohong Tong
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Yifeng Wang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Aiqun Sun
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Babatunde Kazeem Bello
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Shen Ni
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
| | - Jian Zhang
- State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou 311400, China.
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32
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Ma Y, Yang X, Huan X, Gao Y, Wang W, Li Z, Ma Z, Perry L, Sun G, Jiang L, Jin G, Lu H. Multiple indicators of rice remains and the process of rice domestication: A case study in the lower Yangtze River region, China. PLoS One 2018; 13:e0208104. [PMID: 30507965 PMCID: PMC6277086 DOI: 10.1371/journal.pone.0208104] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 11/11/2018] [Indexed: 11/18/2022] Open
Abstract
The process of rice domestication has been studied for decades based on changing morphological characteristics in assemblages of both macroremains, such as charred seeds and spikelet bases, and microremains, such as phytoliths, esp. bulliform and double-peaked phytoliths. The applicability of these indicators in determining if a specific assemblage is wild or domesticated, however, is rarely discussed. To understand the significance of these indicators in the determination of domestication, we collected 38 archaeological samples from eight Neolithic sites, dating from 10-2ka BP, in the lower Yangtze River region to analyze and compare the changes of these different indicators over eight thousand years. The data demonstrate that the comprehensive analysis of multiple indicators may be the best method to study the process of rice domestication developed thus far. An assemblage of rice remains can be identified as domesticated forms if they meet the following criteria simultaneously: 1) the proportion of domesticated-type bulliform phytoliths is more than 73%; and 2) the proportion of domesticated-type rice spikelet bases is higher than 75%. Furthermore, we found that each indicator tends to change steadily and gradually over time, and each stabilized at a different time, suggesting that the characteristics of domesticated rice developed slowly and successively. Changes of multiple indicators during the period between 10,000-2,000 yr BP indicate that the process of rice domestication in the lower Yangtze River region lasted as long as ca. 6,000 years during the Neolithic, and can be divided into three stages with the turning points in the middle Hemudu-late Majiabang culture (6,500-5,800yr BP) and the late Liangzhu culture (4,600-4,300yr BP).
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Affiliation(s)
- Yongchao Ma
- School of Archaeology and Museology, Peking University, Beijing, China
| | - Xiaoyan Yang
- Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- * E-mail:
| | - Xiujia Huan
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
| | - Yu Gao
- School of Archaeology and Museology, Peking University, Beijing, China
- Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Weiwei Wang
- Department of Archaeology and Natural History, Australian National University, Canberra, Australia
| | - Zhao Li
- School of Archaeology and Ancient History, University of Leicester, Leicester, United Kingdom
| | - Zhikun Ma
- School of Cultural Heritage, Northwest University, Xi’an, China
| | - Linda Perry
- The Foundation for Archaeobotanical Research in Microfossils, Fairfax, United States of America
- Department of Anthropology, George Washington University, Washington, DC, United States of America
| | - Guoping Sun
- Zhejiang Provincial Institute of Cultural Relics and Archaeology, Hangzhou, China
| | - Leping Jiang
- Zhejiang Provincial Institute of Cultural Relics and Archaeology, Hangzhou, China
| | - Guiyun Jin
- Institute for Cultural Heritage, Shandong University, Jinan, China
| | - Houyuan Lu
- Key Laboratory of Cenozoic Geology and Environment, Institute of Geology and Geophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Tibetan Plateau Earth Science, Chinese Academy of Sciences, Beijing, China
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Wei H, Zhao Y, Xie Y, Wang H. Exploiting SPL genes to improve maize plant architecture tailored for high-density planting. J Exp Bot 2018; 69:4675-4688. [PMID: 29992284 DOI: 10.1093/jxb/ery258] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 07/09/2018] [Indexed: 05/04/2023]
Abstract
Maize (Zea mays ssp. mays) is an agronomically important crop and also a classical genetic model for studying the regulation of plant architecture formation, which is a critical determinant of grain yield. Since the 1930s, increasing planting density has been a major contributing factor to the >7-fold increase in maize grain yield per unit land area in the USA, which is accompanied by breeding and utilization of cultivars characterized by high-density-tolerant plant architecture, including decreased ear height, lodging resistance, more upright leaves, reduced tassel branch number, and reduced anthesis-silking interval (ASI). Recent studies demonstrated that phytochrome-mediated red/far-red light signaling pathway and the miR156/SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) regulatory module co-ordinately regulate the shade avoidance response and diverse aspects of plant architecture in responding to shading in Arabidopsis. The maize genome contains 30 ZmSPL genes, and 18 of them are predicted as direct targets of zma-miR156s. Accumulating evidence indicates that ZmSPL genes play important roles in regulating maize flowering time, plant/ear height, tilling, leaf angle, tassel and ear architecture, and grain size and shape. Finally, we discuss ways to exploit maize SPL genes and downstream targets for improving maize plant architecture tailored for high-density planting.
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Affiliation(s)
- Hongbin Wei
- School of Life Sciences, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
| | - Yongping Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yurong Xie
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haiyang Wang
- School of Life Sciences, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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34
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Xia D, Zhou H, Liu R, Dan W, Li P, Wu B, Chen J, Wang L, Gao G, Zhang Q, He Y. GL3.3, a Novel QTL Encoding a GSK3/SHAGGY-like Kinase, Epistatically Interacts with GS3 to Produce Extra-long Grains in Rice. Mol Plant 2018; 11:754-756. [PMID: 29567448 DOI: 10.1016/j.molp.2018.03.006] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 02/27/2018] [Accepted: 03/07/2018] [Indexed: 05/22/2023]
Affiliation(s)
- Duo Xia
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Rongjia Liu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Wenhan Dan
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Pingbo Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Bian Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Junxiao Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lingqiang Wang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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Ying JZ, Ma M, Bai C, Huang XH, Liu JL, Fan YY, Song XJ. TGW3, a Major QTL that Negatively Modulates Grain Length and Weight in Rice. Mol Plant 2018; 11:750-753. [PMID: 29567450 DOI: 10.1016/j.molp.2018.03.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 03/04/2018] [Accepted: 03/07/2018] [Indexed: 05/23/2023]
Affiliation(s)
- Jie-Zheng Ying
- National Key Laboratory of Rice Biology and Chinese Center of Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Ming Ma
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Beijing 100093, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Bai
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Beijing 100093, China; Graduate University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xue-Hui Huang
- College of Life and Environment Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Jian-Li Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Beijing 100093, China
| | - Ye-Yang Fan
- National Key Laboratory of Rice Biology and Chinese Center of Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Xian-Jun Song
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, the Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Beijing 100093, China.
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36
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Radchuk V, Tran V, Radchuk R, Diaz-Mendoza M, Weier D, Fuchs J, Riewe D, Hensel G, Kumlehn J, Munz E, Heinzel N, Rolletschek H, Martinez M, Borisjuk L. Vacuolar processing enzyme 4 contributes to maternal control of grain size in barley by executing programmed cell death in the pericarp. New Phytol 2018; 218:1127-1142. [PMID: 28836669 DOI: 10.1111/nph.14729] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 06/25/2017] [Indexed: 05/12/2023]
Abstract
The angiosperm embryo and endosperm are limited in space because they grow inside maternal seed tissues. The elimination of cell layers of the maternal seed coat by programmed cell death (PCD) could provide space and nutrition to the filial organs. Using the barley (Hordeum vulgare L.) seed as a model, we elucidated the role of vacuolar processing enzyme 4 (VPE4) in cereals by using an RNAi approach and targeting the enzymatic properties of the recombinant protein. A comparative characterization of transgenic versus wild-type plants included transcriptional and metabolic profiling, flow cytometry, histology and nuclear magnetic imaging of grains. The recombinant VPE4 protein exhibited legumain and caspase-1 properties in vitro. Pericarp disintegration was delayed in the transgenic grains. Although the VPE4 gene and enzymatic activity was decreased in the early developing pericarp, storage capacity and the size of the endosperm and embryo were reduced in the mature VPE4-repressed grains. The persistence of the pericarp in the VPE4-affected grains constrains endosperm and embryo growth and leads to transcriptional reprogramming, perturbations in signalling and adjustments in metabolism. We conclude that VPE4 expression executes PCD in the pericarp, which is required for later endosperm filling, and argue for a role of PCD in maternal control of seed size in cereals.
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Affiliation(s)
- Volodymyr Radchuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Van Tran
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Ruslana Radchuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Mercedes Diaz-Mendoza
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Campus Montegancedo, Pozuelo de Alarcon, Madrid, 28223, Spain
| | - Diana Weier
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Joerg Fuchs
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - David Riewe
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Goetz Hensel
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Eberhard Munz
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Nicolas Heinzel
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Hardy Rolletschek
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
| | - Manuel Martinez
- Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM), Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (INIA), Campus Montegancedo, Pozuelo de Alarcon, Madrid, 28223, Spain
| | - Ljudmilla Borisjuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany
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37
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Xie Q, Li N, Yang Y, Lv Y, Yao H, Wei R, Sparkes DL, Ma Z. Pleiotropic effects of the wheat domestication gene Q on yield and grain morphology. Planta 2018; 247:1089-1098. [PMID: 29353419 DOI: 10.1007/s00425-018-2847-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/12/2018] [Indexed: 06/07/2023]
Abstract
Transformation from q to Q during wheat domestication functioned outside the boundary of threshability to increase yield, grains m-2, grain weight and roundness, but to reduce grains per spike/spikelet. Mutation of the Q gene, well-known affecting wheat spike structure, represents a key domestication step in the formation of today's free-threshing, economically important wheats. In a previous study, multiple yield components and spike characteristics were associated with the Q gene interval in the bread wheat 'Forno' × European spelt 'Oberkulmer' recombinant inbred line population. Here, we reported that this interval was also associated with grain yield, grains m-2, grain morphology, and spike dry weight at anthesis. To clarify the roles of Q in agronomic trait performance, a functional marker for the Q gene was developed. Analysis of allelic effects showed that the bread wheat Q allele conferred free-threshing habit, soft glumes, and short and compact spikes compared with q. In addition, the Q allele contributed to higher grain yield, more grains m-2, and higher thousand grain weight, whereas q contributed to more grains per spike/spikelet likely resulting from increased preanthesis spike growth. For grain morphology, the Q allele was associated with reduced ratio of grain length to height, indicating a rounder grain. These results are supported by analysis of four Q mutant lines in the Chinese Spring background. Therefore, the transition from q to Q during wheat domestication had profound effects on grain yield and grain shape evolution as well, being a consequence of pleiotropy.
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Affiliation(s)
- Quan Xie
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Na Li
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yang Yang
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yulong Lv
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Hongni Yao
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Rong Wei
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Debbie L Sparkes
- Division of Plant and Crop Sciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Zhengqiang Ma
- The Applied Plant Genomics Laboratory, Crop Genomics and Bioinformatics Center, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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38
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Shee CN, Lemenager RP, Schoonmaker JP. Feeding dried distillers grains with solubles to lactating beef cows: impact of excess protein and fat on post-weaning progeny growth, glucose tolerance and carcass traits. Animal 2018; 12:750-756. [PMID: 28835301 DOI: 10.1017/s1751731117002099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Feeding dried distillers grains with solubles (DDGS), a feed high in fat and protein, to lactating beef cows can alter milk production and composition, resulting in improved pre-weaning growth of progeny. This alteration in milk profile may consequently alter the growth and carcass composition of the offspring after weaning. Therefore, Angus×Simmental steers (n=48) whose dams were fed one of two diets supplemented with either DDGS or soybean meal (CON) from calving to mid-lactation were placed in a feedlot to determine the effects of maternal nutrition during lactation on progeny development and carcass composition. Cow-calf pairs were allotted to two treatments at birth based on cow and calf BW, breed and age. Maternal diets were isocaloric (3.97 MJ/kg NEg) and consisted of rye hay supplemented with DDGS at 1% of BW (19.4% CP; 8.76% fat) or rye hay and corn silage supplemented with CON (11.7% CP; 2.06% fat). After conclusion of the treatments at 129 days postpartum, cow-calf pairs were comingled and managed as one group until weaning at 219 days postpartum. Steers were then transitioned to a common diet composed of 60% DDGS, 34% corn silage and 6% vitamin/mineral supplement and were placed indoors in individual pens with slatted floors. An intravenous glucose tolerance test (IVGTT) was performed 134 days after feedlot entry on 16 steers (CON, n=7; DDGS, n=9) to determine the effect of maternal diet on glucose and insulin sensitivity. Steers were slaughtered at a target BW of 645 kg. Categorical and continuous data were analyzed using the GLIMMIX and MIXED procedures of SAS, respectively. Steers from DDGS dams tended to be heavier on day 85 of feedlot finishing (P=0.09) compared with steers from CON dams. However, there were no differences in final weight, average daily gain, dry matter intake or efficiency (gain:feed, P⩾0.18). Maternal treatments did not affect progeny days on feed (P=0.15), despite a mean difference of 9 days in favor of DDGS. Glucose and insulin concentrations and area under the curve of progeny as measured by IVGTT were not affected by maternal diet (P⩾0.16). Maternal DDGS supplementation decreased marbling score (P=0.04), but did not influence carcass grading percentage or any other carcass characteristic (P⩾0.17).
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Affiliation(s)
- C N Shee
- Department of Animal Science,Purdue University,915 W. State St.,West Lafayette,IN 47907,USA
| | - R P Lemenager
- Department of Animal Science,Purdue University,915 W. State St.,West Lafayette,IN 47907,USA
| | - J P Schoonmaker
- Department of Animal Science,Purdue University,915 W. State St.,West Lafayette,IN 47907,USA
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Gong J, Miao J, Zhao Y, Zhao Q, Feng Q, Zhan Q, Cheng B, Xia J, Huang X, Yang S, Han B. Dissecting the Genetic Basis of Grain Shape and Chalkiness Traits in Hybrid Rice Using Multiple Collaborative Populations. Mol Plant 2017; 10:1353-1356. [PMID: 28803900 DOI: 10.1016/j.molp.2017.07.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 07/14/2017] [Accepted: 07/27/2017] [Indexed: 05/28/2023]
Affiliation(s)
- Junyi Gong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Jiashun Miao
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Zhao
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qiang Zhao
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qi Feng
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Qilin Zhan
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Benyi Cheng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Junhui Xia
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Xuehui Huang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Shihua Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China.
| | - Bin Han
- National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
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You C, Chen L, He H, Wu L, Wang S, Ding Y, Ma C. iTRAQ-based proteome profile analysis of superior and inferior Spikelets at early grain filling stage in japonica Rice. BMC Plant Biol 2017; 17:100. [PMID: 28592253 PMCID: PMC5463490 DOI: 10.1186/s12870-017-1050-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/29/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Large-panicle rice varieties often fail to achieve their yield potential due to poor grain filling of late-flowering inferior spikelets (IS). The physiological and molecular mechanisms of poor IS grain filling, and whether an increase in assimilate supply could regulate protein abundance and consequently improve IS grain filling for japonica rice with large panicles is still partially understood. RESULTS A field experiment was performed with two spikelet removal treatments at anthesis in the large-panicle japonica rice line W1844, including removal of the top 1/3 of spikelets (T1) and removal of the top 2/3 of spikelets (T2), with no spikelet removal as a control (T0). The size, weight, setting rate, and grain filling rate of IS were significantly increased after spikelet removing. The biological functions of the differentially expressed proteins (DEPs) between superior and inferior spikelets as well as the response of IS to the removal of superior spikelets (SS) were investigated by using iTRAQ at 10 days post anthesis. A total of 159, 87, and 28 DEPs were identified from group A (T0-SS/T0-IS), group B (T0-SS/T2-IS), and group C (T2-IS/T0-IS), respectively. Among these, 104, 63, and 22 proteins were up-regulated, and 55, 24, and 6 proteins were down-regulated, respectively. Approximately half of these DEPs were involved in carbohydrate metabolism (sucrose-to-starch metabolism and energy metabolism) and protein metabolism (protein synthesis, folding, degradation, and storage). CONCLUSIONS Reduced endosperm cell division and decreased activities of key enzymes associated with sucrose-starch metabolism and nitrogen metabolism are mainly attributed to the poor sink strength of IS. In addition, due to weakened photosynthesis and respiration, IS are unable to obtain a timely supply of materials and energy after fertilization, which might be resulted in the stagnation of IS development. Finally, an increased abundance of 14-3-3 protein in IS could be involved in the inhibition of starch synthesis. The removal of SS contributed to transfer of assimilates to IS and enhanced enzymatic activities of carbon metabolism (sucrose synthase, starch branching enzyme, soluble starch synthase, and pullulanase) and nitrogen metabolism (aspartate amino transferase and alanine amino transferase), promoting starch and protein synthesis in IS. In addition, improvements in energy metabolism (greater abundance of pyrophosphate-fructose 6-phosphate 1-phosphotransferase) might be played a vital role in inducing the initiation of grain filling. These results collectively demonstrate that carbohydrate supply is the main cause of poor IS grain filling.
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Affiliation(s)
- Cuicui You
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Lin Chen
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Haibing He
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Liquan Wu
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
| | - Shaohua Wang
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 People’s Republic of China
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 People’s Republic of China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Hefei, 230036 People’s Republic of China
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Wu W, Liu X, Wang M, Meyer RS, Luo X, Ndjiondjop MN, Tan L, Zhang J, Wu J, Cai H, Sun C, Wang X, Wing RA, Zhu Z. A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nat Plants 2017; 3:17064. [PMID: 28481332 DOI: 10.1038/nplants.2017.64] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/04/2017] [Indexed: 05/04/2023]
Abstract
Grain size is one of the most important components of grain yield and selecting large seeds has been a main target during plant domestication. Surprisingly, the grain of African cultivated rice (Oryza glaberrima Steud.) typically is smaller than that of its progenitor, Oryza barthii. Here we report the cloning and characterization of a quantitative trait locus, GL4, controlling the grain length on chromosome 4 in African rice, which regulates longitudinal cell elongation of the outer and inner glumes. Interestingly, GL4 also controls the seed shattering phenotype like its orthologue SH4 gene in Asian rice. Our data show that a single-nucleotide polymorphism (SNP) mutation in the GL4 gene resulted in a premature stop codon and led to small seeds and loss of seed shattering during African rice domestication. These results provide new insights into diverse domestication practices in African rice, and also pave the way for enhancing crop yield to meeting the challenge of cereal demand in West Africa.
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Affiliation(s)
- Wenguang Wu
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Xiaoyun Liu
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Muhua Wang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | | | - Lubin Tan
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Jianzhong Wu
- Advanced Genomics Breeding Section, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8602, Japan
| | - Hongwei Cai
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Chuanqing Sun
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Xiangkun Wang
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
- International Rice Research Institute, T.T. Chang Genetic Resources Centre, Los Baños, Laguna, Philippines
| | - Zuofeng Zhu
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
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42
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Wu W, Liu X, Wang M, Meyer RS, Luo X, Ndjiondjop MN, Tan L, Zhang J, Wu J, Cai H, Sun C, Wang X, Wing RA, Zhu Z. A single-nucleotide polymorphism causes smaller grain size and loss of seed shattering during African rice domestication. Nat Plants 2017; 3:17064. [PMID: 28481332 DOI: 10.1038/nplants.2017.1064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 04/04/2017] [Indexed: 05/23/2023]
Abstract
Grain size is one of the most important components of grain yield and selecting large seeds has been a main target during plant domestication. Surprisingly, the grain of African cultivated rice (Oryza glaberrima Steud.) typically is smaller than that of its progenitor, Oryza barthii. Here we report the cloning and characterization of a quantitative trait locus, GL4, controlling the grain length on chromosome 4 in African rice, which regulates longitudinal cell elongation of the outer and inner glumes. Interestingly, GL4 also controls the seed shattering phenotype like its orthologue SH4 gene in Asian rice. Our data show that a single-nucleotide polymorphism (SNP) mutation in the GL4 gene resulted in a premature stop codon and led to small seeds and loss of seed shattering during African rice domestication. These results provide new insights into diverse domestication practices in African rice, and also pave the way for enhancing crop yield to meeting the challenge of cereal demand in West Africa.
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Affiliation(s)
- Wenguang Wu
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Xiaoyun Liu
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Muhua Wang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Rachel S Meyer
- Department of Ecology and Evolutionary Biology, University of California Los Angeles, Los Angeles, California 90095, USA
| | - Xiaojin Luo
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | | | - Lubin Tan
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Jianzhong Wu
- Advanced Genomics Breeding Section, Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8602, Japan
| | - Hongwei Cai
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Chuanqing Sun
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
- State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing 100193, China
| | - Xiangkun Wang
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
- International Rice Research Institute, T.T. Chang Genetic Resources Centre, Los Baños, Laguna, Philippines
| | - Zuofeng Zhu
- National Centre for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China
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43
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Duan P, Xu J, Zeng D, Zhang B, Geng M, Zhang G, Huang K, Huang L, Xu R, Ge S, Qian Q, Li Y. Natural Variation in the Promoter of GSE5 Contributes to Grain Size Diversity in Rice. Mol Plant 2017; 10:685-694. [PMID: 28366824 DOI: 10.1016/j.molp.2017.03.009] [Citation(s) in RCA: 171] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 05/20/2023]
Abstract
The utilization of natural genetic variation greatly contributes to improvement of important agronomic traits in crops. Understanding the genetic basis for natural variation of grain size can help breeders develop high-yield rice varieties. In this study, we identify a previously unrecognized gene, named GSE5, in the qSW5/GW5 locus controlling rice grain size by combining the genome-wide association study with functional analyses. GSE5 encodes a plasma membrane-associated protein with IQ domains, which interacts with the rice calmodulin protein, OsCaM1-1. We found that loss of GSE5 function caused wide and heavy grains, while overexpression of GSE5 resulted in narrow grains. We showed that GSE5 regulates grain size predominantly by influencing cell proliferation in spikelet hulls. Three major haplotypes of GSE5 (GSE5, GSE5DEL1+IN1, and GSE5DEL2) in cultivated rice were identified based on the deletion/insertion type in its promoter region. We demonstrated that a 950-bp deletion (DEL1) in indica varieties carrying the GSE5DEL1+IN1 haplotype and a 1212-bp deletion (DEL2) in japonica varieties carrying the GSE5DEL2 haplotype associated with decreased expression of GSE5, resulting in wide grains. Further analyses indicate that wild rice accessions contain all three haplotypes of GSE5, suggesting that the GSE5 haplotypes present in cultivated rice are likely to have originated from different wild rice accessions during rice domestication. Taken together, our results indicate that the previously unrecognized GSE5 gene in the qSW5/GW5 locus, which is widely utilized by rice breeders, controls grain size, and reveal that natural variation in the promoter region of GSE5 contributes to grain size diversity in rice.
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Affiliation(s)
- Penggen Duan
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Jinsong Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Baolan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Mufan Geng
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China
| | - Guozheng Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China; University of Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Ke Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China; University of Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Luojiang Huang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China; University of Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Ran Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
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44
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Lin Z, Zhang X, Wang Z, Jiang Y, Liu Z, Alexander D, Li G, Wang S, Ding Y. Metabolomic analysis of pathways related to rice grain chalkiness by a notched-belly mutant with high occurrence of white-belly grains. BMC Plant Biol 2017; 17:39. [PMID: 28166731 PMCID: PMC5294873 DOI: 10.1186/s12870-017-0985-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 01/25/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Grain chalkiness is a highly undesirable trait deleterious to rice appearance and milling quality. The physiological and molecular foundation of chalkiness formation is still partially understood, because of the complex interactions between multiple genes and growing environments. RESULTS We report the untargeted metabolomic analysis of grains from a notched-belly mutant (DY1102) with high percentage of white-belly, which predominantly occurs in the bottom part proximal to the embryo. Metabolites in developing grains were profiled on the composite platforms of UPLC/MS/MS and GC/MS. Sampling times were 5, 10, 15, and 20 days after anthesis, the critical time points for chalkiness formation. A total of 214 metabolites were identified, covering most of the central metabolic pathways and partial secondary pathways including amino acids, carbohydrates, lipids, cofactors, peptides, nucleotides, phytohormones, and secondary metabolites. A comparison of the bottom chalky part and the upper translucent part of developing grains of DY1102 resulted in 180 metabolites related to chalkiness formation. CONCLUSIONS Generally, in comparison to the translucent upper part, the chalky endosperm had lower levels of metabolites regarding carbon and nitrogen metabolism for synthesis of storage starch and protein, which was accompanied by perturbation of pathways participating in scavenging of reactive oxygen species, osmorugulation, cell wall synthesis, and mineral ion homeostasis. Based on these results, metabolic mechanism of chalkiness formation is discussed, with the role of embryo highlighted.
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Affiliation(s)
- Zhaomiao Lin
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Crops Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350013 People’s Republic of China
| | - Xincheng Zhang
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Zunxin Wang
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Yutong Jiang
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Zhenghui Liu
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing, 210095 People’s Republic of China
| | | | - Ganghua Li
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Shaohua Wang
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural University/Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095 People’s Republic of China
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45
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Abstract
Plant organs, such as seeds, are primary sources of food for both humans and animals. Seed size is one of the major agronomic traits that have been selected in crop plants during their domestication. Legume seeds are a major source of dietary proteins and oils. Here, we report a conserved role for the BIG SEEDS1 (BS1) gene in the control of seed size and weight in the model legume Medicago truncatula and the grain legume soybean (Glycine max). BS1 encodes a plant-specific transcription regulator and plays a key role in the control of the size of plant organs, including seeds, seed pods, and leaves, through a regulatory module that targets primary cell proliferation. Importantly, down-regulation of BS1 orthologs in soybean by an artificial microRNA significantly increased soybean seed size, weight, and amino acid content. Our results provide a strategy for the increase in yield and seed quality in legumes.
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Affiliation(s)
- Liangfa Ge
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK 73401
| | - Jianbin Yu
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Hongliang Wang
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK 73401
| | - Diane Luth
- Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, IA 50011
- Department of Agronomy, Iowa State University, Ames, IA 50011
| | - Guihua Bai
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
- Hard Winter Wheat Genetics Research Unit, Agricultural Research Service, United States Department of Agriculture, Manhattan, KS 66506
| | - Kan Wang
- Center for Plant Transformation, Plant Sciences Institute, Iowa State University, Ames, IA 50011
- Department of Agronomy, Iowa State University, Ames, IA 50011
| | - Rujin Chen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK 73401;
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McCormick RF, Truong SK, Mullet JE. 3D Sorghum Reconstructions from Depth Images Identify QTL Regulating Shoot Architecture. Plant Physiol 2016; 172:823-834. [PMID: 27528244 PMCID: PMC5047103 DOI: 10.1104/pp.16.00948] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/11/2016] [Indexed: 05/18/2023]
Abstract
Dissecting the genetic basis of complex traits is aided by frequent and nondestructive measurements. Advances in range imaging technologies enable the rapid acquisition of three-dimensional (3D) data from an imaged scene. A depth camera was used to acquire images of sorghum (Sorghum bicolor), an important grain, forage, and bioenergy crop, at multiple developmental time points from a greenhouse-grown recombinant inbred line population. A semiautomated software pipeline was developed and used to generate segmented, 3D plant reconstructions from the images. Automated measurements made from 3D plant reconstructions identified quantitative trait loci for standard measures of shoot architecture, such as shoot height, leaf angle, and leaf length, and for novel composite traits, such as shoot compactness. The phenotypic variability associated with some of the quantitative trait loci displayed differences in temporal prevalence; for example, alleles closely linked with the sorghum Dwarf3 gene, an auxin transporter and pleiotropic regulator of both leaf inclination angle and shoot height, influence leaf angle prior to an effect on shoot height. Furthermore, variability in composite phenotypes that measure overall shoot architecture, such as shoot compactness, is regulated by loci underlying component phenotypes like leaf angle. As such, depth imaging is an economical and rapid method to acquire shoot architecture phenotypes in agriculturally important plants like sorghum to study the genetic basis of complex traits.
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Affiliation(s)
- Ryan F McCormick
- Interdisciplinary Program in Genetics and Biochemistry and Biophysics Department, Texas A&M University, College Station, Texas 77843
| | - Sandra K Truong
- Interdisciplinary Program in Genetics and Biochemistry and Biophysics Department, Texas A&M University, College Station, Texas 77843
| | - John E Mullet
- Interdisciplinary Program in Genetics and Biochemistry and Biophysics Department, Texas A&M University, College Station, Texas 77843
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47
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Feng Y, Lu Q, Zhai R, Zhang M, Xu Q, Yang Y, Wang S, Yuan X, Yu H, Wang Y, Wei X. Genome wide association mapping for grain shape traits in indica rice. Planta 2016; 244:819-30. [PMID: 27198135 PMCID: PMC5018019 DOI: 10.1007/s00425-016-2548-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/06/2016] [Indexed: 05/20/2023]
Abstract
Using genome-wide association mapping, 47 SNPs within 27 significant loci were identified for four grain shape traits, and 424 candidate genes were predicted from public database. Grain shape is a key determinant of grain yield and quality in rice (Oryza sativa L.). However, our knowledge of genes controlling rice grain shape remains limited. Genome-wide association mapping based on linkage disequilibrium (LD) has recently emerged as an effective approach for identifying genes or quantitative trait loci (QTL) underlying complex traits in plants. In this study, association mapping based on 5291 single nucleotide polymorphisms (SNPs) was conducted to identify significant loci associated with grain shape traits in a global collection of 469 diverse rice accessions. A total of 47 SNPs were located in 27 significant loci for four grain traits, and explained ~44.93-65.90 % of the phenotypic variation for each trait. In total, 424 candidate genes within a 200 kb extension region (±100 kb of each locus) of these loci were predicted. Of them, the cloned genes GS3 and qSW5 showed very strong effects on grain length and grain width in our study. Comparing with previously reported QTLs for grain shape traits, we found 11 novel loci, including 3, 3, 2 and 3 loci for grain length, grain width, grain length-width ratio and thousand grain weight, respectively. Validation of these new loci would be performed in the future studies. These results revealed that besides GS3 and qSW5, multiple novel loci and mechanisms were involved in determining rice grain shape. These findings provided valuable information for understanding of the genetic control of grain shape and molecular marker assistant selection (MAS) breeding in rice.
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Affiliation(s)
- Yue Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Qing Lu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Rongrong Zhai
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, Zhejiang, China
| | - Mengchen Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Qun Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Yaolong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Shan Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Xiaoping Yuan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Hanyong Yu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Yiping Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China
| | - Xinghua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, Zhejiang, China.
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48
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Si L, Chen J, Huang X, Gong H, Luo J, Hou Q, Zhou T, Lu T, Zhu J, Shangguan Y, Chen E, Gong C, Zhao Q, Jing Y, Zhao Y, Li Y, Cui L, Fan D, Lu Y, Weng Q, Wang Y, Zhan Q, Liu K, Wei X, An K, An G, Han B. OsSPL13 controls grain size in cultivated rice. Nat Genet 2016. [PMID: 26950093 DOI: 10.1038/ng3518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
Abstract
Although genetic diversity has a cardinal role in domestication, abundant natural allelic variations across the rice genome that cause agronomically important differences between diverse varieties have not been fully explored. Here we implement an approach integrating genome-wide association testing with functional analysis on grain size in a diverse rice population. We report that a major quantitative trait locus, GLW7, encoding the plant-specific transcription factor OsSPL13, positively regulates cell size in the grain hull, resulting in enhanced rice grain length and yield. We determine that a tandem-repeat sequence in the 5' UTR of OsSPL13 alters its expression by affecting transcription and translation and that high expression of OsSPL13 is associated with large grains in tropical japonica rice. Further analysis indicates that the large-grain allele of GLW7 in tropical japonica rice was introgressed from indica varieties under artificial selection. Our study demonstrates that new genes can be effectively identified on the basis of genome-wide association data.
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Affiliation(s)
- Lizhen Si
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiaying Chen
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xuehui Huang
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Hao Gong
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jianghong Luo
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qingqing Hou
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Taoying Zhou
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Tingting Lu
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jingjie Zhu
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yingying Shangguan
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Erwang Chen
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chengxiang Gong
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qiang Zhao
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yufeng Jing
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan Zhao
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan Li
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lingling Cui
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Danlin Fan
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yiqi Lu
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qijun Weng
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yongchun Wang
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qilin Zhan
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Kunyan Liu
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xinghua Wei
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Kyungsook An
- Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Gynheung An
- Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea
| | - Bin Han
- National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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Qiu X, Pang Y, Yuan Z, Xing D, Xu J, Dingkuhn M, Li Z, Ye G. Genome-Wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm. PLoS One 2015; 10:e0145577. [PMID: 26714258 PMCID: PMC4694703 DOI: 10.1371/journal.pone.0145577] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 12/04/2015] [Indexed: 11/18/2022] Open
Abstract
Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding.
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Affiliation(s)
- Xianjin Qiu
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Yunlong Pang
- Institute of Crop Science/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhihua Yuan
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Danying Xing
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education/College of Agriculture, Yangtze University, Jingzhou 434025, China
| | - Jianlong Xu
- Institute of Crop Science/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Institute of Breeding & Innovation, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Michael Dingkuhn
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- CIRAD, UMR AGAP, F-34398 Montpellier, France
| | - Zhikang Li
- Institute of Crop Science/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guoyou Ye
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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50
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Zhang J, Yin B, Xie Y, Li J, Yang Z, Zhang G. Legume-Cereal Intercropping Improves Forage Yield, Quality and Degradability. PLoS One 2015; 10:e0144813. [PMID: 26672990 PMCID: PMC4687681 DOI: 10.1371/journal.pone.0144813] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 11/24/2015] [Indexed: 11/18/2022] Open
Abstract
Intercropping legume with cereal is an extensively applied planting pattern in crop cultivation. However, forage potential and the degradability of harvested mixtures from intercropping system remain unclear. To investigate the feasibility of applying an intercropping system as a forage supply source to ruminants, two consecutive experiments (experiments 1 and 2) involving a field cultivation trial and a subsequent in vivo degradable experiment were conducted to determine the forage production performance and the ruminally degradable characteristics of a harvested mixture from an alfalfa/corn-rye intercropping system. In experiment 1, the intercropping system was established by alternating alfalfa and corn or rye with a row ratio of 5:2. Dry matter (DM) and nutrient yields were determined. In experiment 2, forages harvested from the different treatments were used as feedstuff to identify nutrient degradation kinetics and distribution of components between the rapidly degradable (a), potentially degradable (b) and the degradation rate constant (c) of 'b' fraction by in sacco method in Small-Tail Han wether Sheep. The intercropping system of alfalfa and corn-rye provided higher forage production performance with net increases of 9.52% and 34.81% in DM yield, 42.13% and 16.74% in crude protein (CP) yield, 25.94% and 69.99% in degradable DM yield, and 16.96% and 5.50% in degradable CP yield than rotation and alfalfa sole cropping systems, respectively. In addition, the harvest mixture from intercropping system also had greater 'a' fraction, 'b' fraction, 'c' values, and effective degradability (E value) of DM and CP than corn or rye hay harvested from rotation system. After 48-h exposure to rumen microbes, intercropping harvest materials were degraded to a higher extent than separately degraded crop stems from the sole system as indicated by visual microscopic examination with more tissues disappeared. Thus, the intercropping of alfalfa and corn-rye exhibited a greater forage production potential, and could be applied as forage supply source for ruminants. The improved effective degradability of harvest mixture material could be attributed to greater degradable components involving the rapidly degradable fractions (a), potentially degradable (b) fractions, and degradable rate constant
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Affiliation(s)
- Jie Zhang
- College of Animal Sciences and Technology, Shandong Agricultural University, Tai-an, Shandong 271018, P. R. China
| | - Binjie Yin
- College of Animal Sciences and Technology, Shandong Agricultural University, Tai-an, Shandong 271018, P. R. China
| | - Yuhuai Xie
- College of Animal Sciences and Technology, Shandong Agricultural University, Tai-an, Shandong 271018, P. R. China
| | - Jing. Li
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Peking University, Beijing 100871, P. R. China
| | - Zaibin Yang
- College of Animal Sciences and Technology, Shandong Agricultural University, Tai-an, Shandong 271018, P. R. China
| | - Guiguo Zhang
- College of Animal Sciences and Technology, Shandong Agricultural University, Tai-an, Shandong 271018, P. R. China
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Peking University, Beijing 100871, P. R. China
- * E-mail:
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