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Zhang A, Zhao T, Hu X, Zhou Y, An Y, Pei H, Sun D, Sun G, Li C, Ren X. Identification of QTL underlying the main stem related traits in a doubled haploid barley population. FRONTIERS IN PLANT SCIENCE 2022; 13:1063988. [PMID: 36531346 PMCID: PMC9751491 DOI: 10.3389/fpls.2022.1063988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Lodging reduces grain yield in cereal crops. The height, diameter and strength of stem are crucial for lodging resistance, grain yield, and photosynthate transport in barley. Understanding the genetic basis of stem benefits barley breeding. Here, we evaluated 13 stem related traits after 28 days of heading in a barley DH population in two consecutive years. Significant phenotypic correlations between lodging index (LI) and other stem traits were observed. Three mapping methods using the experimental data and the BLUP data, detected 27 stable and major QTLs, and 22 QTL clustered regions. Many QTLs were consistent with previously reported traits for grain filling rate, internodes, panicle and lodging resistance. Further, candidate genes were predicted for stable and major QTLs and were associated with plant development and adverse stress in the transition from vegetative stage to reproductive stage. This study provided potential genetic basis and new information for exploring barley stem morphology, and laid a foundation for map-based cloning and further fine mapping of these QTLs.
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Affiliation(s)
- Anyong Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Ting Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xue Hu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yu Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yue An
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Haiyi Pei
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Genlou Sun
- Department of Biology, Saint Mary’s University, Halifax, NS, Canada
| | - Chengdao Li
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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Bretani G, Shaaf S, Tondelli A, Cattivelli L, Delbono S, Waugh R, Thomas W, Russell J, Bull H, Igartua E, Casas AM, Gracia P, Rossi R, Schulman AH, Rossini L. Multi-environment genome -wide association mapping of culm morphology traits in barley. FRONTIERS IN PLANT SCIENCE 2022; 13:926277. [PMID: 36212331 PMCID: PMC9539552 DOI: 10.3389/fpls.2022.926277] [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: 04/22/2022] [Accepted: 07/28/2022] [Indexed: 06/16/2023]
Abstract
In cereals with hollow internodes, lodging resistance is influenced by morphological characteristics such as internode diameter and culm wall thickness. Despite their relevance, knowledge of the genetic control of these traits and their relationship with lodging is lacking in temperate cereals such as barley. To fill this gap, we developed an image analysis-based protocol to accurately phenotype culm diameters and culm wall thickness across 261 barley accessions. Analysis of culm trait data collected from field trials in seven different environments revealed high heritability values (>50%) for most traits except thickness and stiffness, as well as genotype-by-environment interactions. The collection was structured mainly according to row-type, which had a confounding effect on culm traits as evidenced by phenotypic correlations. Within both row-type subsets, outer diameter and section modulus showed significant negative correlations with lodging (<-0.52 and <-0.45, respectively), but no correlation with plant height, indicating the possibility of improving lodging resistance independent of plant height. Using 50k iSelect SNP genotyping data, we conducted multi-environment genome-wide association studies using mixed model approach across the whole panel and row-type subsets: we identified a total of 192 quantitative trait loci (QTLs) for the studied traits, including subpopulation-specific QTLs and 21 main effect loci for culm diameter and/or section modulus showing effects on lodging without impacting plant height. Providing insights into the genetic architecture of culm morphology in barley and the possible role of candidate genes involved in hormone and cell wall-related pathways, this work supports the potential of loci underpinning culm features to improve lodging resistance and increase barley yield stability under changing environments.
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Affiliation(s)
- Gianluca Bretani
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Salar Shaaf
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Stefano Delbono
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - William Thomas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Hazel Bull
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Ernesto Igartua
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Ana M. Casas
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Pilar Gracia
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Roberta Rossi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Alan H. Schulman
- Viikki Plant Sciences Centre, Natural Resources Institue (LUKE), HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
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Pu X, Tang Y, Zhang M, Li T, Qiu X, Zhang J, Wang J, Li L, Yang Z, Su Y, Zhang H, Liang J, Yu M, Tang Y, Deng G, Long H. Identification and candidate gene mining of HvSS1, a novel qualitative locus on chromosome 6H, regulating the uppermost internode elongation in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2481-2494. [PMID: 33942136 DOI: 10.1007/s00122-021-03837-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/13/2021] [Indexed: 05/27/2023]
Abstract
A novel qualitative locus regulating the uppermost internode elongation of barley was identified and mapped on 6H, and the candidate gene mining was performed by employing various barley genomic resources. The stem of grass crops, such as barley and wheat, is composed of several interconnected internodes. The extent of elongation of these internodes determines stem height, and hence lodging, canopy architecture, and grain yield. The uppermost internode (UI) is the last internode to elongate. Its elongation contributes largely to stem height and facilitates spike exsertion, which is crucial for final grain yield. Despite the molecular mechanism underlying regulation of UI elongation was extensively investigated in rice, little is known in barley. In this study, we characterized a barley spontaneous mutant, Sheathed Spike 1 (SS1), showing significantly shortened UI and sheathed spike (SS). The extension of UI parenchyma cell in SS1 was significantly suppressed. Exogenous hormone treatments and RNA-seq analysis indicated that the suppression of UI elongation is possibly related to insufficient content of endogenous bioactive gibberellin. Genetic analysis showed that SS1 is possibly controlled by a qualitative dominant nuclear factor. Bulked segregant analysis and further molecular marker mapping identified a novel major locus, HvSS1, in a recombination cold spot expanding 173.44-396.33 Mb on chromosome 6H. The candidate gene mining was further conducted by analyzing sequence differences, spatiotemporal expression patterns, and variant distributions of genes in the candidate interval by employing various barley genomic resources of worldwide collections of barley accessions. This study made insight into genetic control of UI elongation in barley and laid a solid foundation for further gene cloning and functional characterization. The results obtained here also provided valuable information for similar research in wheat.
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Affiliation(s)
- Xi Pu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yanyan Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Meihao Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Tao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xvebing Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Juanyu Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jinhui Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Lilan Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Zhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yan Su
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yawei Tang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, People's Republic of China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China.
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Hu X, Zuo J, Wang J, Liu L, Sun G, Li C, Ren X, Sun D. Multi-Locus Genome-Wide Association Studies for 14 Main Agronomic Traits in Barley. FRONTIERS IN PLANT SCIENCE 2018; 9:1683. [PMID: 30524459 PMCID: PMC6257129 DOI: 10.3389/fpls.2018.01683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/29/2018] [Indexed: 05/02/2023]
Abstract
The agronomic traits, including morphological and yield component traits, are important in barley breeding programs. In order to reveal the genetic foundation of agronomic traits of interest, in this study 122 doubled haploid lines from a cross between cultivars "Huaai 11" (six-rowed and dwarf) and "Huadamai 6" (two-rowed) were genotyped by 9680 SNPs and phenotyped 14 agronomic traits in 3 years, and the two datasets were used to conduct multi-locus genome-wide association studies. As a result, 913 quantitative trait nucleotides (QTNs) were identified by five multi-locus GWAS methods to be associated with the above 14 traits and their best linear unbiased predictions. Among these QTNs and their adjacent genes, 39 QTNs (or QTN clusters) were repeatedly detected in various environments and methods, and 10 candidate genes were identified from gene annotation. Nineteen QTNs and two genes (sdw1/denso and Vrs1) were previously reported, and eight candidate genes need to be further validated. The Vrs1 gene, controlling the number of rows in the spike, was found to be associated with spikelet number of main spike, spikelet number per plant, grain number per plant, grain number per spike, and 1,000 grain weight in multiple environments and by multi-locus GWAS methods. Therefore, the above results evidenced the feasibility and reliability of genome-wide association studies in doubled haploid population, and the QTNs and their candidate genes detected in this study are useful for marker-assisted selection breeding, gene cloning, and functional identification in barley.
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Affiliation(s)
- Xin Hu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Guiyang College of Traditional Chinese Medicine, Guiyang, China
| | - Jianfang Zuo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jibin Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lipan Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, NS, Canada
| | - Chengdao Li
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, China
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Xifeng Ren
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, China
- *Correspondence: Dongfa Sun
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Shah AN, Tanveer M, Rehman AU, Anjum SA, Iqbal J, Ahmad R. Lodging stress in cereal—effects and management: an overview. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2017; 24:5222-5237. [PMID: 0 DOI: 10.1007/s11356-016-8237-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/09/2016] [Indexed: 05/04/2023]
Affiliation(s)
- Adnan Noor Shah
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Mohsin Tanveer
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Atique Ur Rehman
- Department of Agronomy, Bahauddin Zakariya University, Multan, Pakistan
| | | | - Javaid Iqbal
- Ghazi University, Dera Ghazi Khan, Punjab, 32200, Pakistan
| | - Riaz Ahmad
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
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6
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Yadav S, Singh UM, Naik SM, Venkateshwarlu C, Ramayya PJ, Raman KA, Sandhu N, Kumar A. Molecular Mapping of QTLs Associated with Lodging Resistance in Dry Direct-Seeded Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1431. [PMID: 28871266 PMCID: PMC5567065 DOI: 10.3389/fpls.2017.01431] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/03/2017] [Indexed: 05/04/2023]
Abstract
Dry direct-seeded rice (DSR) is an alternative crop establishment method with less water and labor requirement through mechanization. It provides better opportunities for a second crop during the cropping season and therefore, a feasible alternative system to transplanted lowland rice. However, lodging is one of the major constraints in attaining high yield in DSR. Identification of QTLs for lodging resistance and their subsequent use in improving varieties under DSR will be an efficient breeding strategy to address the problem. In order to map the QTLs associated with lodging resistance, a set of 253 BC3F4 lines derived from a backcross between Swarna and Moroberekan were evaluated in two consecutive years. A total of 12 QTLs associated with lodging resistance traits [culm length (qCL), culm diameter (qCD), and culm strength (qCS)] were mapped on chromosomes 1, 2, 6, and 7 using 193 polymorphic SNP markers. Two major and consistent effect QTLs, namely qCD1.1 (with R2 of 10%) and qCS1.1 (with R2 of 14%) on chromosome 1 with id1003559 being the peak SNP marker (flanking markers; id1001973-id1006772) were identified as a common genomic region associated with important lodging resistance traits. In silico analysis revealed the presence of Gibberellic Acid 3 beta-hydroxylase along with 34 other putative candidate genes in the marker interval region of id1001973-id1006772. The positive alleles for culm length, culm diameter, and culm strength were contributed by the upland adaptive parent Moroberekan. Our results identified significant positive correlation between lodging related traits (culm length diameter and strength) and grain yield under DSR, indicating the role of lodging resistant traits in grain yield improvement under DSR. Deployment of the identified alleles influencing the culm strength and culm diameter in marker assisted introgression program may facilitate the lodging resistance under DSR.
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Affiliation(s)
- Shailesh Yadav
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
- International Rice Research InstituteMetro Manila, Philippines
| | - Uma M Singh
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Shilpa M Naik
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Challa Venkateshwarlu
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Perumalla J Ramayya
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - K Anitha Raman
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Nitika Sandhu
- International Rice Research InstituteMetro Manila, Philippines
| | - Arvind Kumar
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
- International Rice Research InstituteMetro Manila, Philippines
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Makkar HPS. Smart livestock feeding strategies for harvesting triple gain – the desired outcomes in planet, people and profit dimensions: a developing country perspective. ANIMAL PRODUCTION SCIENCE 2016. [DOI: 10.1071/an15557] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Of the total greenhouse gas emission from the livestock sector, 45% relates to feed production and processing. Enteric methane (35%), land-use change (9%) and manure nitrous oxide and manure methane together (9.5%) are the other sources of greenhouse gas emissions, which to a large extent depend on feed types. Inefficient use of feeds reduces profitability. Increasing future feed demand and food-feed-fuel competition have environmental and social impacts. The growth for demand in livestock products comes with social, economic and environmental challenges. This paper argues that the efficient utilisation of feed resources and application of appropriate feeding strategies are vital for strengthening the three conventional pillars of sustainability (environment, social and economic). Towards this end, it identifies and explores a series of promising innovations and practices in feed production and feeding including balanced and phased feeding; increase in the quality and level of use of forages in diets; reduction in use of grains; harvesting forages when nutrient availability per unit of land is maximum; targeted mineral feeding; reduction in feed losses; use of straw-based densified feed blocks; better recycling of human food wastes and human-inedible food components to feed; new business models for production and use of urea-ammoniated straws, urea-molasses blocks, forages and silages in smallholder farms; and use of underutilised locally available feed crops linked with strengthening of seed development and distribution infrastructure. The development of simple tools and on-site assays for correcting nutritional imbalances also offers interesting opportunities. Collection of data on feed availability at the national level, and generation of sound chemical composition and nutritional value data of feeds, are a prerequisite to innovate. The focus of the discussion will be on low-input livestock systems in developing world. A large number of livestock are found in such systems and small improvements can have high global impact. In addition to the technological aspects, policy and institutional building options required to realise large impact are also discussed.
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Wang J, Yang J, Jia Q, Zhu J, Shang Y, Hua W, Zhou M. A new QTL for plant height in barley (Hordeum vulgare L.) showing no negative effects on grain yield. PLoS One 2014; 9:e90144. [PMID: 24587247 PMCID: PMC3938599 DOI: 10.1371/journal.pone.0090144] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 01/27/2014] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION Reducing plant height has played an important role in improving crop yields. The success of a breeding program relies on the source of dwarfing genes. For a dwarfing or semi-dwarfing gene to be successfully used in a breeding program, the gene should have minimal negative effects on yield and perform consistently in different environments. METHODS In this study, 182 doubled haploid lines, generated from a cross between TX9425 and Naso Nijo, were grown in six different environments to identify quantitative trait loci (QTL) controlling plant height and investigate QTL × environments interaction. RESULTS A QTL for plant was identified on 7H. This QTL showed no significant effects on other agronomic traits and yield components and consistently expressed in the six environments. A sufficient allelic effect makes it possible for this QTL to be successfully used in breeding programs.
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Affiliation(s)
- Junmei Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Jianming Yang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Qiaojun Jia
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Jinghuan Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Yi Shang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Wei Hua
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture and School of Land and Food, University of Tasmania, Kings Meadows, Tasmania, Australia
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Wang N, Ning S, Pourkheirandish M, Honda I, Komatsuda T. An alternative mechanism for cleistogamy in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2753-2762. [PMID: 23925483 DOI: 10.1007/s00122-013-2169-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 07/12/2013] [Indexed: 06/02/2023]
Abstract
Cleistogamy in barley is genetically determined by the presence of the recessive allele cly1, but the dominant allele at the linked locus Cly2 is epistatic over cly1. Although the molecular basis for cly1 action is well understood, that of Cly2 is not. Here we show that anther non-extrusion can occur not just when the lodicules fail to expand adequately (a trait which is fully determined by the allelic state at the cly1 locus), but by the premature timing of anthesis before the spike has emerged from the boot. The transcription of HvAP2 at cly1 is unaffected by the timing of anthesis. Where this occurs prematurely, by the time that the spike has emerged from the boot, the lodicules have already become shrunken and have lost the capacity to push the lemma and palea apart. Premature anthesis appears to be governed by a dominant gene, probably Cly2. Of the three phases of development of a non-cleistogamous barley floret (spike emergence from the boot, floret gaping induced by lodicule expansion and anther extrusion), genetic variation is available regarding at least the former two.
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Affiliation(s)
- Ning Wang
- National Institute of Agrobiological Sciences, Plant Genome Research Unit, Tsukuba, Ibaraki, 305-8602, Japan
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10
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Kuczyńska A, Surma M, Adamski T, Mikołajczak K, Krystkowiak K, Ogrodowicz P. Effects of the semi-dwarfing sdw1/denso gene in barley. J Appl Genet 2013; 54:381-90. [PMID: 23975516 PMCID: PMC3825292 DOI: 10.1007/s13353-013-0165-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 07/31/2013] [Accepted: 08/01/2013] [Indexed: 01/01/2023]
Abstract
Recent advances in cereal genomics have made it possible to analyse the architecture of cereal genomes and their expressed components, leading to an increase in our knowledge of those genes that are associated with the key agronomical traits. Presently, use of a dwarfing gene in breeding process is crucial for the development of modern cultivars. In barley, more than 30 types of dwarfs or semi-dwarfs have been hitherto described. However, only a few of them have been successfully used in barley breeding programs. Both breeding and molecular mapping experiments were undertaken to enhance and evaluate the performance of semi-dwarf barley lines. The semi-dwarfing cultivars had improved lodging resistance and a higher harvest index. There have been a lot of investigations that have contributed new information to our basic understanding of the mechanisms underlying growth regulations in barley. This paper reviews semi-dwarfing genes in barley in general and special attention is paid to mapping of the sdw1/denso locus, changes in protein abundance and associations of the semi-dwarfness with gibberellins.
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Affiliation(s)
- Anetta Kuczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland,
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Yu GT, Horsley RD, Zhang B, Franckowiak JD. A new semi-dwarfing gene identified by molecular mapping of quantitative trait loci in barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:853-61. [PMID: 20069416 DOI: 10.1007/s00122-009-1216-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Accepted: 11/03/2009] [Indexed: 05/07/2023]
Abstract
Semi-dwarfing genes have been widely used in spring barley (Hordeum vulgare L.) breeding programs in many parts of the world, but the success in developing barley cultivars with semi-dwarfing genes has been limited in North America. Exploiting new semi-dwarfing genes may help in solving this dilemma. A recombinant inbred line population was developed by crossing ZAU 7, a semi-dwarf cultivar from China, to ND16092, a tall breeding line from North Dakota. To identify quantitative trait loci (QTL) controlling plant height, a linkage map comprised of 111 molecular markers was constructed. Simple interval mapping was performed for each of the eight environments. A consistent QTL for plant height was found on chromosome 7HL. This QTL is not associated with maturity and rachis internode length. We suggest the provisional name Qph-7H for this QTL. Qph-7H from ZAU 7 reduced plant height to about 3/4 of normal; thus, Qph-7H is considered a semi-dwarfing gene. Other QTLs for plant height were found, but their expression was variable across the eight environments tested.
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Affiliation(s)
- Guo Tai Yu
- Department of Entomology, North Dakota State University, Fargo, ND 58105, USA.
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Shahinnia F, Ebrahim Sayed-Tabatabaei B, Sato K, Pourkheirandish M, Komatsuda T. Mapping of QTL for intermedium spike on barley chromosome 4H using EST-based markers. BREEDING SCIENCE 2009. [PMID: 0 DOI: 10.1270/jsbbs.59.383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Affiliation(s)
- Fahimeh Shahinnia
- Plant Genome Research Unit, National Institute of Agrobiological Sciences (NIAS)
- Department of Agronomy and Plant Breeding, Isfahan University of Technology
- Present address: Department of Gene Bank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)
| | | | - Kazuhiro Sato
- Research Institute for Bioresources, Okayama University
| | | | - Takao Komatsuda
- Plant Genome Research Unit, National Institute of Agrobiological Sciences (NIAS)
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Jones N, Ougham H, Thomas H, Pašakinskienė I. Markers and mapping revisited: finding your gene. THE NEW PHYTOLOGIST 2009; 183:935-966. [PMID: 19594696 DOI: 10.1111/j.1469-8137.2009.02933.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
This paper is an update of our earlier review (Jones et al., 1997, Markers and mapping: we are all geneticists now. New Phytologist 137: 165-177), which dealt with the genetics of mapping, in terms of recombination as the basis of the procedure, and covered some of the first generation of markers, including restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), simple sequence repeats (SSRs) and quantitative trait loci (QTLs). In the intervening decade there have been numerous developments in marker science with many new systems becoming available, which are herein described: cleavage amplification polymorphism (CAP), sequence-specific amplification polymorphism (S-SAP), inter-simple sequence repeat (ISSR), sequence tagged site (STS), sequence characterized amplification region (SCAR), selective amplification of microsatellite polymorphic loci (SAMPL), single nucleotide polymorphism (SNP), expressed sequence tag (EST), sequence-related amplified polymorphism (SRAP), target region amplification polymorphism (TRAP), microarrays, diversity arrays technology (DArT), single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE) and methylation-sensitive PCR. In addition there has been an explosion of knowledge and databases in the area of genomics and bioinformatics. The number of flowering plant ESTs is c. 19 million and counting, with all the opportunity that this provides for gene-hunting, while the survey of bioinformatics and computer resources points to a rapid growth point for future activities in unravelling and applying the burst of new information on plant genomes. A case study is presented on tracking down a specific gene (stay-green (SGR), a post-transcriptional senescence regulator) using the full suite of mapping tools and comparative mapping resources. We end with a brief speculation on how genome analysis may progress into the future of this highly dynamic arena of plant science.
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Affiliation(s)
- Neil Jones
- IBERS, Aberystwyth University, Edward Llwyd Building, Penglais Campus, Aberystwyth, Ceredigion SY23 3DA, UK
| | - Helen Ougham
- IBERS, Aberystwyth University, Gogerddan Campus, Aberystwyth, Ceredigion SY23 3EB, UK
| | - Howard Thomas
- IBERS, Aberystwyth University, Edward Llwyd Building, Penglais Campus, Aberystwyth, Ceredigion SY23 3DA, UK
| | - Izolda Pašakinskienė
- Botanical Garden of Vilnius University, Kairenu 43, LT-10239 Vilnius, Lithuania
- Faculty of Natural Sciences, Department of Botany and Genetics, MK Čiurlionio g. 21, LT-03101 Vilnius, Lithuania
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