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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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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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Begović L, Abičić I, Lalić A, Lepeduš H, Cesar V, Leljak-Levanić D. Lignin synthesis and accumulation in barley cultivars differing in their resistance to lodging. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 133:142-148. [PMID: 30419464 DOI: 10.1016/j.plaphy.2018.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/24/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Since lignin greatly affects stem strength, which is an important agronomical trait, understanding the relationship between lodging resistance and lignin synthesis is important in barley breeding and selection processes. The aim of the study was to reveal the connection between physiological aspects of lignin synthesis and genetic background of barley cultivars with different lodging phenotype. Three barley cultivars Astor, Scarlett and Jaran were compared by measuring lignin, cellulose and total soluble phenolics content, phenylalanine ammonia-lyase activity (PAL) and expression of cinnamoyl-CoA reductase (CCR) and cinnamyl-alcohol dehydrogenase (CAD) in three lower internodes at flowering and grain filling stage. To assess their genetic background simple sequence repeats (SSR) markers, connected to lodging resistance and plant height, were analyzed. Compared to lodging susceptible cultivars Scarlett and Jaran, a lodging resistant cultivar Astor revealed different dynamics of lignin synthesis and deposition, showing higher PAL activity and total soluble phenolics content as well as higher expression of CCR and CAD genes in the second internode at grain filling stage. Analysis of SSR markers associated with quantitative trait loci (QTL) for lodging resistance revealed that Astor discriminates from Scarlett and Jaran by marker Bmag337 connected with elongation of the second internode. Lignification process is under a strong influence of genotype and environmental factors which determine lignin synthesis dynamics and deposition of lignin in the cell walls of barley.
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Affiliation(s)
- Lidija Begović
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Ulica Cara Hadrijana 8/A, HR-31000, Osijek, Croatia.
| | - Ivan Abičić
- Agricultural Institute Osijek, Južno Predgrađe 3, HR-31000, Osijek, Croatia.
| | - Alojzije Lalić
- Agricultural Institute Osijek, Južno Predgrađe 3, HR-31000, Osijek, Croatia.
| | - Hrvoje Lepeduš
- Faculty of Humanities and Social Sciences, Josip Juraj Strossmayer University of Osijek, Lorenza Jägera 9, HR-31000, Osijek, Croatia.
| | - Vera Cesar
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Ulica Cara Hadrijana 8/A, HR-31000, Osijek, Croatia.
| | - Dunja Leljak-Levanić
- Division of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102A, HR-10000, Zagreb, Croatia.
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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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Wang Q, Sun G, Ren X, Wang J, Du B, Li C, Sun D. Detection of QTLs for seedling characteristics in barley (Hordeum vulgare L.) grown under hydroponic culture condition. BMC Genet 2017; 18:94. [PMID: 29115942 PMCID: PMC5678765 DOI: 10.1186/s12863-017-0562-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 10/30/2017] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Seedling characteristics play significant roles in the growth and development of barley (Hordeum vulgare L.), including stable stand establishment, water and nutrients uptake, biotic resistance and abiotic stresses, and can influence yield and quality. However, the genetic mechanisms underlying seedling characteristics in barley are largely unknown and little research has been done. In the present work, 21 seedling-related characteristics are assessed in a barley double haploid (DH) population, grown under hydroponic conditions. Of them, leaf age (LAG), shoot height (SH), maximum root length (MRL), main root number (MRN) and seedling fresh weight (SFW) were investigated at the 13th, 20th, 27th, and 34th day after germination. The objectives were to identify quantitative trait loci (QTLs) underlying these seedling characteristics using a high-density linkage map and to reveal the QTL expression pattern by comparing the QTLs among four different seedling growth stages. RESULTS A total of 70 QTLs were distributed over all chromosomes except 4H, and, individually, accounted for 5.01%-77.78% of phenotypic variation. Out of the 70 detected QTLs, 23 showed a major effect on 14 seedling-related characteristics. Ten co-localized chromosomal regions on 2H (five regions), 3H (two regions) and 7H (three regions) involved 39 QTLs (55.71%), each simultaneously influenced more than one trait. Meanwhile, 9 co-localized genomic regions involving 22 QTLs for five seedling characteristics (LAG, SH, MRL, MRN and SFW) at the 13th, 20th, 27th and 34th day-old seedling were common for two or more growth stages of seedling. QTL in the vicinity of Vrs1 locus on chromosome 2H with the favorable alleles from Huadamai 6 was found to have the largest main effects on multiple seedling-related traits. CONCLUSIONS Six QTL cluster regions associated with 16 seedling-related characteristics were observed on chromosome 2H, 3H and 7H. The majority of the 29 regions identified for five seedling characteristics were selectively expressed at different developmental stages. The genetic effects of 9 consecutive expression regions displayed different developmental influences at different developmental stages. These findings enhanced our understanding of a genetic basis underlying seedling characteristics in barley. Some QTLs detected here could be used for marker-assisted selection (MAS) in barley breeding.
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Affiliation(s)
- Qifei Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Genlou Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- Biology Department, Saint Mary’s University, 923 Robie Street, Halifax, NS B3H 3C3 Canada
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Jibin Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Binbin Du
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Chengdao Li
- Department of Agriculture & Food/Agricultural Research Western Australia, 3 Baron-Hay Court, South Perth, WA 6155 Australia
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, Hubei 434025 China
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SNP-based high density genetic map and mapping of btwd1 dwarfing gene in barley. Sci Rep 2016; 6:31741. [PMID: 27530597 PMCID: PMC4987670 DOI: 10.1038/srep31741] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 07/26/2016] [Indexed: 11/08/2022] Open
Abstract
A high-density linkage map is a valuable tool for functional genomics and breeding. A newly developed sequence-based marker technology, restriction site associated DNA (RAD) sequencing, has been proven to be powerful for the rapid discovery and genotyping of genome-wide single nucleotide polymorphism (SNP) markers and for the high-density genetic map construction. The objective of this research was to construct a high-density genetic map of barley using RAD sequencing. 1894 high-quality SNP markers were developed and mapped onto all seven chromosomes together with 68 SSR markers. These 1962 markers constituted a total genetic length of 1375.8 cM and an average of 0.7 cM between adjacent loci. The number of markers within each linkage group ranged from 209 to 396. The new recessive dwarfing gene btwd1 in Huaai 11 was mapped onto the high density linkage maps. The result showed that the btwd1 is positioned between SNP marks 7HL_6335336 and 7_249275418 with a genetic distance of 0.9 cM and 0.7 cM on chromosome 7H, respectively. The SNP-based high-density genetic map developed and the dwarfing gene btwd1 mapped in this study provide critical information for position cloning of the btwd1 gene and molecular breeding of barley.
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