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Hong Y, Zhang M, Zhu J, Zhang Y, Lv C, Guo B, Wang F, Xu R. Genome-wide association studies reveal novel loci for grain size in two-rowed barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:58. [PMID: 38407646 DOI: 10.1007/s00122-024-04562-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 01/24/2024] [Indexed: 02/27/2024]
Abstract
KEY MESSAGE SNP-based and InDel-based GWAS on multi-environment data identified genomic regions associated with barley grain size. Barley yield and quality are greatly influenced by grain size. Improving barley grain size in breeding programs requires knowledge of genetic loci and alleles in germplasm resources. In this study, a collection of 334 worldwide two-rowed barley accessions with extensive genetic diversity was evaluated for grain size including grain length (GL), grain width (GW), and thousand-grain weight (TGW) across six independent field trials. Significant differences were observed in genotype and environments for all measured traits. SNP- and InDel-based GWAS were applied to dissect the genetic architecture of grain size with an SLAF-seq strategy. Two approaches using the FarmCPU model revealed 38 significant marker-trait associations (MTAs) with PVE ranging from 0.01% to 20.68%. Among these MTAs, five were on genomic regions where no previously reported QTL for grain size. Superior alleles of TGW-associated SNP233060 and GL-associated InDel11006 exhibited significantly higher levels of phenotype. The significant MTAs could be used in marker-assisted selection breeding.
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Affiliation(s)
- Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Juan Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yuhang Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Chao Lv
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Baojian Guo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Feifei Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education / Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding / Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops / Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
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Yang H, Luo L, Li Y, Li H, Zhang X, Zhang K, Zhu S, Li X, Li Y, Wan Y, Liu F. Fine mapping of qAHPS07 and functional studies of AhRUVBL2 controlling pod size in peanut (Arachis hypogaea L.). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1785-1798. [PMID: 37256840 PMCID: PMC10440995 DOI: 10.1111/pbi.14076] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 04/18/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023]
Abstract
Cultivated peanut (Arachis hypogaea L.) is an important oil and cash crop. Pod size is one of the major traits determining yield and commodity characteristic of peanut. Fine mapping of quantitative trait locus (QTL) and identification of candidate genes associated with pod size are essential for genetic improvement and molecular breeding of peanut varieties. In this study, a major QTL related to pod size, qAHPS07, was fine mapped to a 36.46 kb interval on chromosome A07 using F2 , recombinant inbred line (RIL) and secondary F2 populations. qAHPS07 explained 38.6%, 23.35%, 37.48%, 25.94% of the phenotypic variation for single pod weight (SPW), pod length (PL), pod width (PW) and pod shell thickness (PST), respectively. Whole genome resequencing and gene expression analysis revealed that a RuvB-like 2 protein coding gene AhRUVBL2 was the most likely candidate for qAHPS07. Overexpression of AhRUVBL2 in Arabidopsis led to larger seeds and plants than the wild type. AhRUVBL2-silenced peanut seedlings represented small leaves and shorter main stems. Three haplotypes were identified according to three SNPs in the promoter of AhRUVBL2 among 119 peanut accessions. Among them, SPW, PW and PST of accessions carrying Hap_ATT represent 17.6%, 11.2% and 26.3% higher than those carrying Hap_GAC,respectively. In addition, a functional marker of AhRUVBL2 was developed. Taken together, our study identified a key functional gene of peanut pod size, which provides new insights into peanut pod size regulation mechanism and offers practicable markers for the genetic improvement of pod size-related traits in peanut breeding.
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Affiliation(s)
- Hui Yang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Lu Luo
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Yuying Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Huadong Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Xiurong Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Kun Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Suqing Zhu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Xuanlin Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Yingjie Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Yongshan Wan
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
| | - Fengzhen Liu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop BiologyCollege of Agronomy, Shandong Agricultural UniversityTai'anChina
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Hong Y, Zhang M, Xu R. Genetic Localization and Homologous Genes Mining for Barley Grain Size. Int J Mol Sci 2023; 24:ijms24054932. [PMID: 36902360 PMCID: PMC10003025 DOI: 10.3390/ijms24054932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/27/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
Grain size is an important agronomic trait determining barley yield and quality. An increasing number of QTLs (quantitative trait loci) for grain size have been reported due to the improvement in genome sequencing and mapping. Elucidating the molecular mechanisms underpinning barley grain size is vital for producing elite cultivars and accelerating breeding processes. In this review, we summarize the achievements in the molecular mapping of barley grain size over the past two decades, highlighting the results of QTL linkage analysis and genome-wide association studies. We discuss the QTL hotspots and predict candidate genes in detail. Moreover, reported homologs that determine the seed size clustered into several signaling pathways in model plants are also listed, providing the theoretical basis for mining genetic resources and regulatory networks of barley grain size.
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Affiliation(s)
- Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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Qin D, Liu G, Liu R, Wang C, Xu F, Xu Q, Ling Y, Dong G, Peng Y, Ge S, Guo G, Dong J, Li C. Positional cloning identified HvTUBULIN8 as the candidate gene for round lateral spikelet (RLS) in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:7. [PMID: 36656367 PMCID: PMC9852219 DOI: 10.1007/s00122-023-04272-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Map-based cloning, subcellular localization, virus-induced-gene-silencing and transcriptomic analysis reveal HvTUB8 as a candidate gene with pleiotropic effects on barley spike and leaf development via ethylene and chlorophyll metabolism. Barley lateral spikelet morphology and grain shape play key roles in grain physical quality and yield. Several genes and QTLs for these traits have been cloned or fine mapped previously. Here, we report the phenotypic and genotypic analysis of a barley mutant with round lateral spikelet (rls) from cv. Edamai 934. rls had round lateral spikelet, short but round grain, shortened awn, thick glume and dark green leaves. Histocytologic and ultrastructural analysis revealed that the difference of grain shape of rls was caused by change of cell arrangement in glume, and the dark leaf color resulted from enlarged chloroplast. HvTUBULIN8 (HvTUB8) was identified as the candidate gene for rls by combination of RNA-Seq, map-based-cloning, virus-induced-gene-silencing (VIGS) and protein subcellular location. A single G-A substitution at the third exon of HvTUB8 resulted in change of Cysteine 354 to tyrosine. Furthermore, the mutant isoform Hvtub8 could be detected in both nucleus and cytoplasm, whereas the wild-type protein was only in cytoplasm and granular organelles of wheat protoplasts. Being consistent with the rare phenotype, the "A" allele of HvTUB8 was only detected in rls, but not in a worldwide barley germplasm panel with 400 accessions. VIGS confirmed that HvTUB8 was essential to maintain spike integrity. RNA-Seq results suggested that HvTUB8 may control spike morphogenesis via ethylene homeostasis and signaling, and control leaf color through chlorophyll metabolism. Collectively, our results support HvTUB8 as a candidate gene for barley spike and leaf morphology and provide insight of a novel mechanism of it in barley development.
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Affiliation(s)
- Dandan Qin
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Gang Liu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Rui Liu
- Wuhan Polytechnic University, Wuhan, 430023, Hubei, China
| | - Chunchao Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fuchao Xu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Qing Xu
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, Guangdong, China
| | - Guoqing Dong
- Wuhan Polytechnic University, Wuhan, 430023, Hubei, China
| | - Yanchun Peng
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Shuangtao Ge
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Ganggang Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Dong
- Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
- Key Laboratory for Crop Molecular, Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, 430064, Hubei, China
| | - Chengdao Li
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Western Australia, WA, 6150, Australia.
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Shrestha A, Cosenza F, van Inghelandt D, Wu PY, Li J, Casale FA, Weisweiler M, Stich B. The double round-robin population unravels the genetic architecture of grain size in barley. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:7344-7361. [PMID: 36094852 PMCID: PMC9730814 DOI: 10.1093/jxb/erac369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
Grain number, size and weight primarily determine the yield of barley. Although the genes regulating grain number are well studied in barley, the genetic loci and the causal gene for sink capacity are poorly understood. Therefore, the primary objective of our work was to dissect the genetic architecture of grain size and weight in barley. We used a multi-parent population developed from a genetic cross between 23 diverse barley inbreds in a double round-robin design. Seed size-related parameters such as grain length, grain width, grain area and thousand-grain weight were evaluated in the HvDRR population comprising 45 recombinant inbred line sub-populations. We found significant genotypic variation for all seed size characteristics, and observed 84% or higher heritability across four environments. The quantitative trait locus (QTL) detection results indicate that the genetic architecture of grain size is more complex than previously reported. In addition, both cultivars and landraces contributed positive alleles at grain size QTLs. Candidate genes identified using genome-wide variant calling data for all parental inbred lines indicated overlapping and potential novel regulators of grain size in cereals. Furthermore, our results indicated that sink capacity was the primary determinant of grain weight in barley.
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Affiliation(s)
- Asis Shrestha
- Institute for Quantitative Genetics and Genomics of Plants, Biology Department, Heinrich Heine University, Dusseldorf, Germany
| | - Francesco Cosenza
- Institute for Quantitative Genetics and Genomics of Plants, Biology Department, Heinrich Heine University, Dusseldorf, Germany
| | - Delphine van Inghelandt
- Institute for Quantitative Genetics and Genomics of Plants, Biology Department, Heinrich Heine University, Dusseldorf, Germany
| | - Po-Ya Wu
- Institute for Quantitative Genetics and Genomics of Plants, Biology Department, Heinrich Heine University, Dusseldorf, Germany
| | - Jinquan Li
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Federico A Casale
- Institute for Quantitative Genetics and Genomics of Plants, Biology Department, Heinrich Heine University, Dusseldorf, Germany
| | - Marius Weisweiler
- Institute for Quantitative Genetics and Genomics of Plants, Biology Department, Heinrich Heine University, Dusseldorf, Germany
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Niu Y, Chen T, Zheng Z, Zhao C, Liu C, Jia J, Zhou M. A new major QTL for flag leaf thickness in barley (Hordeum vulgare L.). BMC PLANT BIOLOGY 2022; 22:305. [PMID: 35751018 PMCID: PMC9229122 DOI: 10.1186/s12870-022-03694-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Carbohydrate accumulation of photosynthetic organs, mainly leaves, are the primary sources of grain yield in cereals. The flag leaf plays a vital role in seed development, which is probably the most neglected morphological characteristic during traditional selection processes. RESULTS In this experiment, four flag leaf morphological traits and seven yield-related traits were investigated in a DH population derived from a cross between a wild barley and an Australian malting barley cultivar. Flag leaf thickness (FLT) showed significantly positive correlations with grain size. Four QTL, located on chromosomes 1H, 2H, 3H, and 5H, respectively, were identified for FLT. Among them, a major QTL was located on chromosome 3H with a LOD value of 18.4 and determined 32% of the phenotypic variation. This QTL showed close links but not pleiotropism to the previously reported semi-dwarf gene sdw1 from the cultivated barley. This QTL was not reported before and the thick leaf allele from the wild barley could provide a useful source for improving grain yield through breeding. CONCLUSIONS Our results also provided valuable evidence that source traits and sink traits in barley are tightly connected and suggest further improvement of barley yield potential with enhanced and balanced source and sink relationships by exploiting potentialities of the wild barley resources. Moreover, this study will provide a novel sight on understanding the evolution and development of leaf morphology in barley and improving barley production by rewilding for lost superior traits during plant evolution.
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Affiliation(s)
- Yanan Niu
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, 7250, Prospect, TAS, Australia
| | - Tianxiao Chen
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, 7250, Prospect, TAS, Australia
| | - Zhi Zheng
- CSIRO Agriculture and Food, 4067, St Lucia, QLD, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, 7250, Prospect, TAS, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, 4067, St Lucia, QLD, Australia
| | - Jizeng Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Private Bag 1375, 7250, Prospect, TAS, Australia.
- College of Agronomy, Shanxi Agricultural University, 030801, Taigu, China.
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Kong D, Xu J, Wang L, Wang H, You E, Li X, Chen T, Shen Y. Combined RNA-seq and Phenotype Analysis Reveals a Potential Molecular Mechanism of the Difference in Grain Size of Naked Barley From the Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:822607. [PMID: 35185989 PMCID: PMC8847792 DOI: 10.3389/fpls.2022.822607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
To understand the molecular mechanism controlling the size of barley grains, a number of traits were analyzed and RNA-seq was conducted on grains of two barley materials with a significant difference in thousand-grain weight (TGW) after flowering. The trait dataset delineates the dynamic changes in grain size after flowering, and it provides an understanding of the source of the difference in TGW. By comparing the transcripts of barley grains at several stages after flowering, we identified the gene expression characteristics and significantly enriched pathways in each stage. At the early stage of grain development, genes involved in fatty acid metabolism, plant hormone signal transduction, and pathways involved in cytoskeleton formation were significantly upregulated. At the later stage of grain development, genes involved in starch synthesis, glucose metabolism, and other pathways were significantly upregulated. Further, we used weighted gene coexpression network analysis (WGCNA) and correlation analysis of trait datasets to identify the coexpressed gene modules significantly associated with traits, such as grain length (GL), grain width (GW), and dry weight (DW). After comparing the modules with the differentially expressed gene (DEG) set, 12 candidate genes were selected, and among these, four genes were homologous to genes that regulate grain size in rice and other plants. The combined analysis identified many potential key regulatory factors that may control barley grain size and yield potential, thus providing new insights into the molecular mechanism of barley grain size.
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Affiliation(s)
- Doudou Kong
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Jinqing Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Lei Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Handong Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - En You
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xiaolan Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Tongrui Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Yuhu Shen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai-Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, China
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8
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The effect of exogenous spermine application on some biochemichal and molecular properties in hordeum vulgare l. under both normal and drought stress. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00967-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Sun Y, Lyu M, Han H, Zhou S, Lu Y, Liu W, Yang X, Li X, Zhang J, Liu X, Li L. Identification and fine mapping of alien fragments associated with enhanced grain weight from Agropyron cristatum chromosome 7P in common wheat backgrounds. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3759-3772. [PMID: 34355268 DOI: 10.1007/s00122-021-03927-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
An enhanced grain weight locus from Agropyron cristatum chromosome 7P was verified in two wheat backgrounds, localized to the 7PS1-2 region. Novel translocation lines with this locus were evaluated. Agropyron cristatum is a wild relative of wheat that harbours elite genes for wheat improvement. The wheat-A. cristatum 7P disomic addition line II-5-1 exhibits high grain weight. Here, to dissect the genetic basis of grain weight contributed by A. cristatum chromosome 7P in wheat backgrounds, four segregated populations of the addition line were developed and evaluated in two wheat backgrounds. The results showed that A. cristatum chromosome 7P can stably and significantly increase the grain weight by approximately 2 g, mainly by increasing grain length at different grain weight levels of the wheat background. The locus for increased grain weight from chromosome 7P shows dominant inheritance independent of the wheat background. Moreover, two deletion lines and 23 translocation lines were identified by cytological methods and molecular markers, and an enlarged chromosome 7P bin map was constructed with 158 STS markers and 40 bin intervals. With the genetic populations of these deletion and translocation lines, the genetic locus of increased grain weight was narrowed down to bin 7PS1-2. Two translocation lines (7PT-A18 and 7PT-B4) with smaller 7P chromosomal segments exhibited an increase in grain weight, grain length and grain width simultaneously. These translocation lines carrying the 7PS1-2 chromosomal fragment will be valuable genetic resources for wheat grain weight improvement. Collectively, this study uncovers the grain weight locus from chromosome 7P and provides novel pre-breeding lines with enhanced grain weight.
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Affiliation(s)
- Yangyang Sun
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mingjie Lyu
- 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
| | - Shenghui Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yuqing Lu
- 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
| | - 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
| | - Jinpeng Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xu Liu
- 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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Wang J, Wu X, Yue W, Zhao C, Yang J, Zhou M. Identification of QTL for barley grain size. PeerJ 2021; 9:e11287. [PMID: 33986999 PMCID: PMC8088763 DOI: 10.7717/peerj.11287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/25/2021] [Indexed: 01/22/2023] Open
Abstract
Background Barley grain size is one of the key factors determining storage capacity during grain filling. Large, well-filled grains also have a high malt extract potential. Grain size is a complex quantitative trait and can be easily affected by environmental factors thus the identification of genes controlling the trait and the use of molecular markers linked to the genes in breeding program is the most effective way of improving grain size. Methods Grain sizes of 188 doubled-haploid (DH) lines derived from the cross of a Japanese malting barley variety (Naso Nijo) and a Chinese feed barley variety (TX9425) were obtained from three different sites in two consecutive years. The average data were used for identifying QTL for grain size. Results A total of four significant QTL were identified for grain length (GL) and three for grain width (GW). The two major GL QTL are located at similar positions to the QTL for malt extract on 2H and uzu gene on 3H, respectively. However, the GL QTL on 2H is more likely a different one from the malt extract QTL as most of the candidate genes are located outside the fine mapped QTL region for malt extract. The GL QTL on 3H is closely linked with uzu gene but not due to a pleiotropic effect of uzu. The three QTL for grain width on 1H, 2H and 5H, respectively, were located at same position to those for GL.
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Affiliation(s)
- Junmei Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaojian Wu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wenhao Yue
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS, Australia
| | - Jianming Yang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS, Australia
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Fang Y, Zhang X, Zhang X, Tong T, Zhang Z, Wu G, Hou L, Zheng J, Niu C, Li J, Wang W, Wang H, Xue D. A High-Density Genetic Linkage Map of SLAFs and QTL Analysis of Grain Size and Weight in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2020; 11:620922. [PMID: 33424912 PMCID: PMC7793689 DOI: 10.3389/fpls.2020.620922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 11/26/2020] [Indexed: 05/12/2023]
Abstract
Grain size is an important agronomic trait determines yield in barley, and a high-density genetic map is helpful to accurately detect quantitative trait loci (QTLs) related to grain traits. Using specific-locus amplified fragment sequencing (SLAF-seq) technology, a high-density genetic map was constructed with a population of 134 recombinant inbred lines (RILs) deriving from a cross between Golden Promise (GP) and H602, which contained 12,635 SLAFs with 26,693 SNPs, and spanned 896.74 cM with an average interval of 0.07 cM on seven chromosomes. Based on the map, a total of 16 QTLs for grain length (GL), grain width and thousand-grain weight were detected on 1H, 2H, 4H, 5H, and 6H. Among them, a major QTL locus qGL1, accounting for the max phenotypic variance of 16.7% was located on 1H, which is a new unreported QTL affecting GL. In addition, the other two QTLs, qGL5 and qTGW5, accounting for the max phenotypic variances of 20.7 and 21.1%, respectively, were identified in the same region, and sequencing results showed they are identical to HvDep1 gene. These results indicate that it is a feasible approach to construct a high-quality genetic map for QTL mapping by using SLAF markers, and the detected major QTLs qGL1, qGL5, and qTGW5 are useful for marker-assisted selection (MAS) of grain size in barley breeding.
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Affiliation(s)
- Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaoqin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xian Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Tao Tong
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ziling Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Gengwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Linlin Hou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Junjun Zheng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Chunyu Niu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Jia Li
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Wenjia Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Hua Wang,
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Dawei Xue,
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