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Chen B, Hou Y, Huo Y, Zeng Z, Hu D, Mao X, Zhong C, Xu Y, Tang X, Gao X, Ma J, Chen G. QTL Mapping of Yield, Agronomic, and Nitrogen-Related Traits in Barley ( Hordeum vulgare L.) under Low Nitrogen and Normal Nitrogen Treatments. PLANTS (BASEL, SWITZERLAND) 2024; 13:2137. [PMID: 39124255 PMCID: PMC11314459 DOI: 10.3390/plants13152137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/28/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]
Abstract
Improving low nitrogen (LN) tolerance in barley (Hordeum vulgare L.) increases global barley yield and quality. In this study, a recombinant inbred line (RIL) population crossed between "Baudin × CN4079" was used to conduct field experiments on twenty traits of barley yield, agronomy, and nitrogen(N)-related traits under LN and normal nitrogen (NN) treatments for two years. This study identified seventeen QTL, comprising eight QTL expressed under both LN and NN treatments, eight LN-specific QTL, and one NN-specific QTL. The localized C2 cluster contained QTL controlling yield, agronomic, and N-related traits. Of the four novel QTL, the expression of the N-related QTL Qstna.sau-5H and Qnhi.sau-5H was unaffected by N treatment. Qtgw.sau-2H for thousand-grain weight, Qph.sau-3H for plant height, Qsl.sau-7H for spike length, and Qal.sau-7H for awn length were identified to be the four stable expression QTL. Correlation studies revealed a significant negative correlation between grain N content and harvest index (p < 0.01). These results are essential for barley marker-assisted selection (MAS) breeding.
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Affiliation(s)
- Bingjie Chen
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (B.C.); (Y.H.); (Y.H.); (Z.Z.); (D.H.); (X.M.); (Y.X.); (X.T.); (X.G.)
| | - Yao Hou
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (B.C.); (Y.H.); (Y.H.); (Z.Z.); (D.H.); (X.M.); (Y.X.); (X.T.); (X.G.)
| | - Yuanfeng Huo
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (B.C.); (Y.H.); (Y.H.); (Z.Z.); (D.H.); (X.M.); (Y.X.); (X.T.); (X.G.)
| | - Zhaoyong Zeng
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (B.C.); (Y.H.); (Y.H.); (Z.Z.); (D.H.); (X.M.); (Y.X.); (X.T.); (X.G.)
| | - Deyi Hu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (B.C.); (Y.H.); (Y.H.); (Z.Z.); (D.H.); (X.M.); (Y.X.); (X.T.); (X.G.)
| | - Xingwu Mao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (B.C.); (Y.H.); (Y.H.); (Z.Z.); (D.H.); (X.M.); (Y.X.); (X.T.); (X.G.)
| | - Chengyou Zhong
- College of Economics, Hunan Agricultural University, Changsha 410125, China;
| | - Yinggang Xu
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (B.C.); (Y.H.); (Y.H.); (Z.Z.); (D.H.); (X.M.); (Y.X.); (X.T.); (X.G.)
| | - Xiaoyan Tang
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (B.C.); (Y.H.); (Y.H.); (Z.Z.); (D.H.); (X.M.); (Y.X.); (X.T.); (X.G.)
| | - Xuesong Gao
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (B.C.); (Y.H.); (Y.H.); (Z.Z.); (D.H.); (X.M.); (Y.X.); (X.T.); (X.G.)
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China;
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China; (B.C.); (Y.H.); (Y.H.); (Z.Z.); (D.H.); (X.M.); (Y.X.); (X.T.); (X.G.)
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Gao S, Su Z, Ma J, Ma J, Liu C, Li H, Zheng Z. Identification of a novel and plant height-independent QTL for coleoptile length in barley and validation of its effect using near isogenic lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:53. [PMID: 38381194 PMCID: PMC10881613 DOI: 10.1007/s00122-024-04561-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 01/24/2024] [Indexed: 02/22/2024]
Abstract
KEY MESSAGE This study reported the identification and validation of novel QTL conferring coleoptile length in barley and predicted candidate genes underlying the largest effect QTL based on orthologous analysis and comparison of the whole genome assemblies for both parental genotypes of the mapping population. Coleoptile length (CL) is one of the most important agronomic traits in cereal crops due to its direct influence on the optimal depth for seed sowing which facilitates better seedling establishment. Varieties with longer coleoptiles are preferred in drought-prone areas where less moisture maintains at the top layer of the soil. Compared to wheat, genetic study on coleoptile length is limited in barley. Here, we reported a study on detecting the genomic regions associated with CL in barley by assessing a population consisting of 201 recombinant inbred lines. Four putative QTL conferring CL were consistently identified on chromosomes 1H, 5H, 6H, and 7H in each of the trials conducted. Of these QTL, the two located on chromosomes 5H and 6H (designated as Qcl.caf-5H and Qcl.caf-6H) are likely novel and Qcl.caf-5H showed the most significant effect explaining up to 30.9% of phenotypic variance with a LOD value of 15.1. To further validate the effect of this putative QTL, five pairs of near isogenic lines (NILs) were then developed and assessed. Analysis of the NILs showed an average difference of 21.0% in CL between the two isolines. Notably, none of the other assessed morphological characteristics showed consistent differences between the two isolines for each pair of the NILs. Candidate genes underlying the Qcl.caf-5H locus were also predicted by employing orthologous analysis and comparing the genome assemblies for both parental genotypes of the mapping population in the present study. Taken together, these findings expand our understanding on genetic basis of CL and will be indicative for further gene cloning and functional analysis underly this locus in barley.
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Affiliation(s)
- Shang Gao
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China
| | - Zhouyang Su
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS, 7205, Australia
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Chunji Liu
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia
| | - Huihui Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, 572024, Hainan, China.
| | - Zhi Zheng
- CSIRO Agriculture and Food, 306 Carmody Road, St Lucia, QLD, 4067, Australia.
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Su Z, Gao S, Zheng Z, Stiller J, Hu S, McNeil MD, Shabala S, Zhou M, Liu C. Transcriptomic insights into shared responses to Fusarium crown rot infection and drought stresses in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:34. [PMID: 38286831 PMCID: PMC10824894 DOI: 10.1007/s00122-023-04537-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/27/2023] [Indexed: 01/31/2024]
Abstract
KEY MESSAGE Shared changes in transcriptomes caused by Fusarium crown rot infection and drought stress were investigated based on a single pair of near-isogenic lines developed for a major locus conferring tolerance to both stresses. Fusarium crown rot (FCR) is a devastating disease in many areas of cereal production worldwide. It is well-known that drought stress enhances FCR severity but possible molecular relationship between these two stresses remains unclear. To investigate their relationships, we generated several pairs of near isogenic lines (NILs) targeting a locus conferring FCR resistance on chromosome 2D in bread wheat. One pair of these NILs showing significant differences between the two isolines for both FCR resistance and drought tolerance was used to investigate transcriptomic changes in responsive to these two stresses. Our results showed that the two isolines likely deployed different strategies in dealing with the stresses, and significant differences in expressed gene networks exist between the two time points of drought stresses evaluated in this study. Nevertheless, results from analysing Gene Ontology terms and transcription factors revealed that similar regulatory frameworks were activated in coping with these two stresses. Based on the position of the targeted locus, changes in expression following FCR infection and drought stresses, and the presence of non-synonymous variants between the two isolines, several candidate genes conferring resistance or tolerance to these two types of stresses were identified. The NILs generated, the large number of DEGs with single-nucleotide polymorphisms detected between the two isolines, and the candidate genes identified would be invaluable in fine mapping and cloning the gene(s) underlying the targeted locus.
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Affiliation(s)
- Zhouyang Su
- CSIRO Agriculture and Food, St Lucia, QLD, 4067, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS, 7250, Australia
| | - Shang Gao
- CSIRO Agriculture and Food, St Lucia, QLD, 4067, Australia
| | - Zhi Zheng
- CSIRO Agriculture and Food, St Lucia, QLD, 4067, Australia
| | - Jiri Stiller
- CSIRO Agriculture and Food, St Lucia, QLD, 4067, Australia
| | - Shuwen Hu
- CSIRO Agriculture and Food, St Lucia, QLD, 4067, Australia
| | | | - Sergey Shabala
- School of Biological Sciences, University of Western Australia, Crawley, WA, 6009, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, 5280, Guangdong, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS, 7250, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, St Lucia, QLD, 4067, Australia.
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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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Huang B, Wu W, Hong Z. Genetic Loci Underlying Awn Morphology in Barley. Genes (Basel) 2021; 12:genes12101613. [PMID: 34681007 PMCID: PMC8535194 DOI: 10.3390/genes12101613] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/03/2021] [Accepted: 10/09/2021] [Indexed: 11/28/2022] Open
Abstract
Barley awns are highly active in photosynthesis and account for 30–50% of grain weight in barley. They are diverse in length, ranging from long to awnless, and in shape from straight to hooded or crooked. Their diversity and importance have intrigued geneticists for several decades. A large collection of awnness mutants are available—over a dozen of them have been mapped on chromosomes and a few recently cloned. Different awnness genes interact with each other to produce diverse awn phenotypes. With the availability of the sequenced barley genome and application of new mapping and gene cloning strategies, it will now be possible to identify and clone more awnness genes. A better understanding of the genetic basis of awn diversity will greatly facilitate development of new barley cultivars with improved yield, adaptability and sustainability.
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Affiliation(s)
- Biguang Huang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Fujian Collegiate Key Laboratory of Applied Plant Genetics, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
| | - Weiren Wu
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Z.H.)
| | - Zonglie Hong
- Department of Plant Sciences, University of Idaho, Moscow, ID 83844, USA
- Correspondence: (W.W.); (Z.H.)
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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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Genetic Interactions of Awnness Genes in Barley. Genes (Basel) 2021; 12:genes12040606. [PMID: 33924025 PMCID: PMC8073869 DOI: 10.3390/genes12040606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/08/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
Awns are extending structures from lemmas in grasses and are very active in photosynthesis, contributing directly to the filling of the developing grain. Barley (Hordeum vulgare L.) awns are highly diverse in shape and length and are known to be controlled by multiple awn-related genes. The genetic effects of these genes on awn diversity and development in barley are multiplexed and include complementary effect, cumulative effect, duplicate effect, recessive epistasis, dominant epistasis, and inhibiting effect, each giving a unique modified Mendelian ratio of segregation. The complexity of gene interactions contributes to the awn diversity in barley. Excessive gene interactions create a challenging task for genetic mapping and specific strategies have to be developed for mapping genes with specific interactive effects. Awn gene interactions can occur at different levels of gene expression, from the transcription factor-mediated gene transcription to the regulation of enzymes and metabolic pathways. A better understanding of gene interactions will greatly facilitate deciphering the genetic mechanisms underlying barley awn diversity and development.
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Ntakirutimana F, Xie W. Unveiling the Actual Functions of Awns in Grasses: From Yield Potential to Quality Traits. Int J Mol Sci 2020; 21:ijms21207593. [PMID: 33066600 PMCID: PMC7589186 DOI: 10.3390/ijms21207593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 12/25/2022] Open
Abstract
Awns, which are either bristles or hair-like outgrowths of lemmas in the florets, are one of the typical morphological characteristics of grass species. These stiff structures contribute to grain dispersal and burial and fend off animal predators. However, their phenotypic and genetic associations with traits deciding potential yield and quality are not fully understood. Awns appear to improve photosynthesis, provide assimilates for grain filling, thus contributing to the final grain yield, especially under temperature- and water-stress conditions. Long awns, however, represent a competing sink with developing kernels for photosynthates, which can reduce grain yield under favorable conditions. In addition, long awns can hamper postharvest handling, storage, and processing activities. Overall, little is known about the elusive role of awns, thus, this review summarizes what is known about the effect of awns on grain yield and biomass yield, grain nutritional value, and forage-quality attributes. The influence of awns on the agronomic performance of grasses seems to be associated with environmental and genetic factors and varies in different stages of plant development. The contribution of awns to yield traits and quality features previously documented in major cereal crops, such as rice, barley, and wheat, emphasizes that awns can be targeted for yield and quality improvement and may advance research aimed at identifying the phenotypic effects of morphological traits in grasses.
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Understanding Mechanisms of Salinity Tolerance in Barley by Proteomic and Biochemical Analysis of Near-Isogenic Lines. Int J Mol Sci 2020; 21:ijms21041516. [PMID: 32098451 PMCID: PMC7073193 DOI: 10.3390/ijms21041516] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 12/13/2022] Open
Abstract
Salt stress is one of the major environmental factors impairing crop production. In our previous study, we identified a major QTL for salinity tolerance on chromosome 2H on barley (Hordeum vulgare L.). For further investigation of the mechanisms responsible for this QTL, two pairs of near-isogenic lines (NILs) differing in this QTL were developed. Sensitive NILs (N33 and N53) showed more severe damage after exposure to 300 mM NaCl than tolerant ones (T46 and T66). Both tolerant NILs maintained significantly lower Na+ content in leaves and much higher K+ content in the roots than sensitive lines under salt conditions, thus indicating the presence of a more optimal Na+/K+ ratio in plant tissues. Salinity stress caused significant accumulation of H2O2, MDA, and proline in salinity-sensitive NILs, and a greater enhancement in antioxidant enzymatic activities at one specific time or tissues in tolerant lines. One pair of NILs (N33 and T46) were used for proteomic studies using two-dimensional gel electrophoresis. A total of 53 and 51 differentially expressed proteins were identified through tandem mass spectrometry analysis in the leaves and roots, respectively. Proteins which are associated with photosynthesis, reactive oxygen species (ROS) scavenging, and ATP synthase were found to be specifically upregulated in the tolerant NIL. Proteins identified in this study can serve as a useful resource with which to explore novel candidate genes for salinity tolerance in barley.
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Gao S, Zheng Z, Powell J, Habib A, Stiller J, Zhou M, Liu C. Validation and delineation of a locus conferring Fusarium crown rot resistance on 1HL in barley by analysing transcriptomes from multiple pairs of near isogenic lines. BMC Genomics 2019; 20:650. [PMID: 31412765 PMCID: PMC6694680 DOI: 10.1186/s12864-019-6011-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 07/31/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Fusarium crown rot (FCR) is a chronic and severe disease in cereal production in semi-arid regions worldwide. A putative quantitative trait locus conferring FCR resistance, Qcrs.cpi-1H, had previously been mapped on the long arm of chromosome 1H in barley. RESULTS In this study, five pairs of near-isogenic lines (NILs) targeting the 1HL locus were developed. Analysing the NILs found that the resistant allele at Qcrs.cpi-1H significantly reduced FCR severity. Transcriptomic analysis was then conducted against three of the NIL pairs, which placed the Qcrs.cpi-1H locus in an interval spanning about 11 Mbp. A total of 56 expressed genes bearing single nucleotide polymorphisms (SNPs) were detected in this interval. Five of them contain non-synonymous SNPs. These results would facilitate detailed mapping as well as cloning gene(s) underlying the resistance locus. CONCLUSION NILs developed in this study and the transcriptomic sequences obtained from them did not only allow the validation of the resistance locus Qcrs.cpi-1H and the identification of candidate genes underlying its resistance, they also allowed the delineation of the resistance locus and the development of SNPs markers which formed a solid base for detailed mapping as well as cloning gene(s) underlying the locus.
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Affiliation(s)
- Shang Gao
- CSIRO Agriculture and Food, St Lucia, Queensland 4067 Australia
- School of Land and Food and Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
| | - Zhi Zheng
- CSIRO Agriculture and Food, St Lucia, Queensland 4067 Australia
| | - Jonathan Powell
- CSIRO Agriculture and Food, St Lucia, Queensland 4067 Australia
| | - Ahsan Habib
- CSIRO Agriculture and Food, St Lucia, Queensland 4067 Australia
- School of Land and Food and Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, 9208 Bangladesh
| | - Jiri Stiller
- CSIRO Agriculture and Food, St Lucia, Queensland 4067 Australia
| | - Meixue Zhou
- School of Land and Food and Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
| | - Chunji Liu
- CSIRO Agriculture and Food, St Lucia, Queensland 4067 Australia
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Ijaz B, Zhao N, Kong J, Hua J. Fiber Quality Improvement in Upland Cotton ( Gossypium hirsutum L.): Quantitative Trait Loci Mapping and Marker Assisted Selection Application. FRONTIERS IN PLANT SCIENCE 2019; 10:1585. [PMID: 31921240 PMCID: PMC6917639 DOI: 10.3389/fpls.2019.01585] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/12/2019] [Indexed: 05/17/2023]
Abstract
Genetic improvement in fiber quality is one of the main challenges for cotton breeders. Fiber quality traits are controlled by multiple genes and are classified as complex quantitative traits, with a negative relationship with yield potential, so the genetic gain is low in traditional genetic improvement by phenotypic selection. The availability of Gossypium genomic sequences facilitates the development of high-throughput molecular markers, quantitative trait loci (QTL) fine mapping and gene identification, which helps us to validate candidate genes and to use marker assisted selection (MAS) on fiber quality in breeding programs. Based on developments of high density linkage maps, QTLs fine mapping, marker selection and omics, we have performed trait dissection on fiber quality traits in diverse populations of upland cotton. QTL mapping combined with multi-omics approaches such as, RNA sequencing datasets to identify differentially expressed genes have benefited the improvement of fiber quality. In this review, we discuss the application of molecular markers, QTL mapping and MAS for fiber quality improvement in upland cotton.
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Affiliation(s)
- Babar Ijaz
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Nan Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding/Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- *Correspondence: Jinping Hua,
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12
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Zhang XW, Jiang QT, Wei YM, Liu C. Inheritance analysis and mapping of quantitative trait loci (QTL) controlling individual anthocyanin compounds in purple barley (Hordeum vulgare L.) grains. PLoS One 2017; 12:e0183704. [PMID: 28832657 PMCID: PMC5568277 DOI: 10.1371/journal.pone.0183704] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/09/2017] [Indexed: 11/19/2022] Open
Abstract
Anthocyanin-rich barley can have great potential in promoting human health and in developing nutraceuticals and functional foods. As different anthocyanin compounds have different antioxidant activities, breeding cultivars with pre-designed anthocyanin compositions could be highly desirable. Working toward this possibility, we assessed and reported for the first time the genetic control of individual anthocyanin compounds in barley. Of the ten anthocyanins assessed, two, peonidin-3-glucoside (P3G) and cyanidin-3-glucoside (C3G), were major components in the purple pericarp barley genotype RUSSIA68. Quantitative trait locus (QTL) mapping showed that both anthocyanin compounds were the interactive products of two loci, one located on chromosome arm 2HL and the other on 7HS. However, the two different anthocyanin components seem to be controlled by different interactions between the two loci. The effects of the 7HS locus on P3G and C3G were difficult to detect without removing the effect of the 2HL locus. At least one copy of the 2HL alleles from the purple pericarp parent was required for the synthesis of P3G. This does not seem to be the case for the production of C3G which was produced in each of all the different allele combinations between the two loci. Typical maternal effect was also observed in the inheritance of purple pericarp grains in barley. The varied values of different compounds, coupled with their different genetic controls, highlight the need for targeting individual anthocyanins in crop breeding and food processing.
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Affiliation(s)
- Xiao-Wei Zhang
- CSIRO Agriculture & Food, St Lucia, Queensland, Australia
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Qian-Tao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Yu-Ming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Chunji Liu
- CSIRO Agriculture & Food, St Lucia, Queensland, Australia
- * E-mail:
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13
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Xu P, Gao J, Cao Z, Chee PW, Guo Q, Xu Z, Paterson AH, Zhang X, Shen X. Fine mapping and candidate gene analysis of qFL-chr1, a fiber length QTL in cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1309-1319. [PMID: 28361363 DOI: 10.1007/s00122-017-2890-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 03/02/2017] [Indexed: 05/20/2023]
Abstract
A fiber length QTL, qFL-chr1, was fine mapped to a 0.9 cM interval of cotton chromosome 1. Two positional candidate genes showed positive correlation between gene expression level and fiber length. Prior analysis of a backcross-self mapping population derived from a cross between Gossypium hirsutum L. and G. barbadense L. revealed a QTL on chromosome 1 associated with increased fiber length (qFL-chr1), which was confirmed in three independent populations of near-isogenic introgression lines (NIILs). Here, a single NIIL, R01-40-08, was used to develop a large population segregating for the target region. Twenty-two PCR-based polymorphic markers used to genotype 1672 BC4F2 plants identified 432 recombinants containing breakpoints in the target region. Substitution mapping using 141 informative recombinants narrowed the position of qFL-chr1 to a 1.0-cM interval between SSR markers MUSS084 and CIR018. To exclude possible effects of non-target introgressions on fiber length, different heterozygous BC4F3 plants introgressed between SSR markers NAU3384 and CGR5144 were selected to develop sub-NILs. The qFL-chr1 was further mapped at 0.9-cM interval between MUSS422 and CIR018 by comparisons of sub-NIL phenotype, and increased fiber length by ~1 mm. The 2.38-Mb region between MUSS422 and CIR018 in G. barbadense contained 19 annotated genes. Expression levels of two of these genes, GOBAR07705 (encoding 1-aminocyclopropane-1-carboxylate synthase) and GOBAR25992 (encoding amino acid permease), were positively correlated with fiber length in a small F2 population, supporting these genes as candidates for qFL-chr1.
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Affiliation(s)
- Peng Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, People's Republic of China
- The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Jin Gao
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, People's Republic of China
- The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Zhibin Cao
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, People's Republic of China
- The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Peng W Chee
- Molecular Cotton Breeding Laboratory, University of Georgia, Tifton, GA, 3179, USA
| | - Qi Guo
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, People's Republic of China
- The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Zhenzhen Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, People's Republic of China
- The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30602, USA
| | - Xianggui Zhang
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, People's Republic of China
- The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Xinlian Shen
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, People's Republic of China.
- The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China.
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14
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Liller CB, Walla A, Boer MP, Hedley P, Macaulay M, Effgen S, von Korff M, van Esse GW, Koornneef M. Fine mapping of a major QTL for awn length in barley using a multiparent mapping population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:269-281. [PMID: 27734096 PMCID: PMC5263209 DOI: 10.1007/s00122-016-2807-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/29/2016] [Indexed: 05/18/2023]
Abstract
Awn length was mapped using a multiparent population derived from cv. Morex and four wild accessions. One QTL was fine mapped and candidate genes were identified in NILs by RNA-seq. Barley awns are photosynthetically active and contribute to grain yield. Awn length is variable among both wild and cultivated barley genotypes and many mutants with alterations in awn length have been identified. Here, we used a multiparent mapping population derived from cv. Morex and four genetically diverse wild barley lines to detect quantitative trait loci (QTLs) for awn length. Twelve QTLs, distributed over the barley genome, were identified with the most significant one located on chromosome arm 7HL (QTL AL7.1). The effect of AL7.1 was confirmed using near isogenic lines (NILs) and fine-mapped in two independent heterogeneous inbred families to a < 0.9 cM interval. With exception of a small effect on grain width, no other traits such as plant height or flowering time were affected by AL7.1. Variant calling on transcripts obtained from RNA sequencing reads in NILs was used to narrow down the list of candidate genes located in the interval. This data may be used for further characterization and unravelling of the mechanisms underlying natural variation in awn length.
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Affiliation(s)
- Corinna B Liller
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Agatha Walla
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
- Institute of Plant Genetics, Heinrich Heine University Duesseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
- Cluster of Excellence in Plant Sciences (CEPLAS), Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40255, Düsseldorf, Germany
| | - Martin P Boer
- Biometris, Plant Research International, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Pete Hedley
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Malcolm Macaulay
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland, UK
| | - Sieglinde Effgen
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Maria von Korff
- Institute of Plant Genetics, Heinrich Heine University Duesseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany.
- Cluster of Excellence in Plant Sciences (CEPLAS), Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40255, Düsseldorf, Germany.
| | - G Wilma van Esse
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
- Cluster of Excellence in Plant Sciences (CEPLAS), Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40255, Düsseldorf, Germany.
| | - Maarten Koornneef
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany.
- Cluster of Excellence in Plant Sciences (CEPLAS), Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40255, Düsseldorf, Germany.
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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Ma J, Du G, Li X, Zhang C, Guo J. A major locus controlling malondialdehyde content under water stress is associated with Fusarium crown rot resistance in wheat. Mol Genet Genomics 2015; 290:1955-62. [PMID: 25939503 DOI: 10.1007/s00438-015-1053-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 04/21/2015] [Indexed: 10/23/2022]
Abstract
Malondialdehyde (MDA) is a naturally occurring product of lipid peroxidation and the level of MDA in plant is often used as a parameter to evaluate the damage to plants' cells due to stress. Plant with lower amounts of MDA under drought conditions is generally considered as more tolerant to drought. In this study, a population of recombinant inbred lines was used to map the quantitative trait locus (QTLs) that controlled MDA content under well-watered condition (WW) and water deficit (WD) condition. A major QTL, designated as Qheb.mda-3B, was detected on the long arm of chromosome 3B. Based on interval mapping analysis, Qheb.mda-3B explained 31.5 and 39.0 % of the phenotypic variance under WW and WD conditions, respectively. Qheb.mda-3B was located in the same interval as a previously identified QTL (Qcrs.cpi-3B) that controlled resistance to Fusarium crown rot (FCR), a fungal disease caused by Fusarium species. Three pairs of near-isogenic lines (NILs) previously developed for Qcrs.cpi-3B were found to show significant differences in MDA content under WD condition. These results suggested that same set of genes is likely to be involved in drought tolerance and FCR resistance in wheat.
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Affiliation(s)
- Jun Ma
- School of Plant Biology, The University of Western Australia, Perth, WA, 6009, Australia.,CSIRO Agriculture Flagship, 306 Carmody Road, Brisbane, QLD, 4067, Australia
| | - Guangyue Du
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Department of Plant Genetics and Breeding, Agricultural University of Hebei, 071001, Baoding, Hebei, China
| | - Xihuan Li
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Department of Plant Genetics and Breeding, Agricultural University of Hebei, 071001, Baoding, Hebei, China
| | - Caiying Zhang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Department of Plant Genetics and Breeding, Agricultural University of Hebei, 071001, Baoding, Hebei, China.
| | - Jinkao Guo
- Shijiazhuang Academy of Agriculture and Forestry Sciences, 479 Shengli North Avenue, 050021, Shijiazhuang, China.
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16
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Wang J, Yang J, Zhang Q, Zhu J, Jia Q, Hua W, Shang Y, Li C, Zhou M. Mapping a major QTL for malt extract of barley from a cross between TX9425 × Naso Nijo. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:943-52. [PMID: 25773294 DOI: 10.1007/s00122-015-2481-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/09/2015] [Indexed: 05/02/2023]
Abstract
One major QTL-controlling malt extract was identified on 2H, based on the data from four different environments and a large number of DH lines, determining 48% of phenotypic variation. This QTL is of a high value for marker-assisted selection. Improving malting quality traits is one of the major breeding objectives for barley breeding programmes. Among different quality traits, malt extract is one of the most important, determining the yield of beer production. The use of molecular markers linked to loci affecting the quality traits can greatly improve selection efficiency. However, the discovery of closely linked markers relies on not only the availability of the loci, but the accuracy of phenotyping. In this experiment, 188 doubled-haploid lines derived from the cross between a Japanese malting barley and a Chinese feed barley were grown in four different environments (two sites × 2 years). Different quality traits were determined and used to map QTL for these traits. Several QTLs were identified for different quality traits. One major QTL-controlling malt extract was identified on 2H and determined 48% of phenotypic variation with the closest marker of GBM1121. This QTL was consistently expressed in all four environments and is of a high value for marker-assisted selection in malting barley breeding.
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Affiliation(s)
- Junmei Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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17
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Fan Y, Shabala S, Ma Y, Xu R, Zhou M. Using QTL mapping to investigate the relationships between abiotic stress tolerance (drought and salinity) and agronomic and physiological traits. BMC Genomics 2015; 16:43. [PMID: 25651931 PMCID: PMC4320823 DOI: 10.1186/s12864-015-1243-8] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 01/15/2015] [Indexed: 11/24/2022] Open
Abstract
Background Drought and salinity are two major abiotic stresses that severely limit barley production worldwide. Physiological and genetic complexity of these tolerance traits has significantly slowed the progress of developing stress-tolerant cultivars. Marker-assisted selection (MAS) may potentially overcome this problem. In the current research, seventy two double haploid (DH) lines from a cross between TX9425 (a Chinese landrace variety with superior drought and salinity tolerance) and a sensitive variety, Franklin were used to identify quantitative trait loci (QTL) for drought and salinity tolerance, based on a range of developmental and physiological traits. Results Two QTL for drought tolerance (leaf wilting under drought stress) and one QTL for salinity tolerance (plant survival under salt stress) were identified from this population. The QTL on 2H for drought tolerance determined 42% of phenotypic variation, based on three independent experiments. This QTL was closely linked with a gene controlling ear emergency. The QTL on 5H for drought tolerance was less affected by agronomic traits and can be effectively used in breeding programs. A candidate gene for this QTL on 5H was identified based on the draft barley genome sequence. The QTL for proline accumulation, under both drought and salinity stresses, were located on different positions to those for drought and salinity tolerance, indicating no relationship with plant tolerance to either of these stresses. Conclusions Using QTL mapping, the relationships between QTL for agronomic and physiological traits and plant drought and salinity tolerance were studied. A new QTL for drought tolerance which was not linked to any of the studied traits was identified. This QTL can be effectively used in breeding programs. It was also shown that proline accumulation under stresses was not necessarily linked with drought or salinity tolerance based on methods of phenotyping used in this experiment. The use of proline content in breeding programs can also be limited by the accuracy of phenotyping. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1243-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yun Fan
- University of Tasmania, P.O. Box 46, Kings Meadows, TAS 7249, Australia.
| | - Sergey Shabala
- University of Tasmania, P.O. Box 46, Kings Meadows, TAS 7249, Australia.
| | - Yanling Ma
- University of Tasmania, P.O. Box 46, Kings Meadows, TAS 7249, Australia.
| | - Rugen Xu
- Barley Research Institution of Yangzhou University, Yangzhou, 225009, China.
| | - Meixue Zhou
- University of Tasmania, P.O. Box 46, Kings Meadows, TAS 7249, Australia.
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18
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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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19
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Chen G, Yan W, Liu Y, Wei Y, Zhou M, Zheng YL, Manners JM, Liu C. The non-gibberellic acid-responsive semi-dwarfing gene uzu affects Fusarium crown rot resistance in barley. BMC PLANT BIOLOGY 2014; 14:22. [PMID: 24418007 PMCID: PMC3898025 DOI: 10.1186/1471-2229-14-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/08/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND Studies in Arabidopsis show that DELLA genes may differentially affect responses to biotrophic and necrophic pathogens. A recent report based on the study of DELLA-producing reduced height (Rht) genes in wheat and barley also hypothesized that DELLA genes likely increased susceptibility to necrotrophs but increased resistance to biotrophs. RESULTS Effects of uzu, a non-GA (gibberellic acid)-responsive semi-dwarfing gene, on Fusarium crown rot (FCR) resistance in barley were investigated. Fifteen pairs of near isogenic lines for this gene were generated and assessed under two different temperature regimes. Similar to its impacts on plant height, the semi-dwarfing gene uzu also showed larger effects on FCR severity in the high temperature regime when compared with that in the low temperature regime. CONCLUSIONS Results from this study add to the growing evidence showing that the effects of plant height on Fusarium resistances are unlikely related to DELLA genes but due to direct or indirect effects of height difference per se. The interaction between these two characteristics highlights the importance of understanding relationships between resistance and other traits of agronomic importance as the value of a resistance gene could be compromised if it dramatically affects plant development and morphology.
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Affiliation(s)
- Guangdeng Chen
- CSIRO Plant Industry, 306 Carmody Road, St Lucia QLD 4067, Australia
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
- Institute of Ecological and Environmental Sciences, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Wei Yan
- CSIRO Plant Industry, 306 Carmody Road, St Lucia QLD 4067, Australia
- Institute of Food Crops, Jiangsu Academy of Agricultural Science, 50 Zhongling Street, Nanjing 210014, China
| | - Yaxi Liu
- CSIRO Plant Industry, 306 Carmody Road, St Lucia QLD 4067, Australia
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture and School of Agricultural Science, University of Tasmania, P.O. Box 46, Kings Meadows, Tasmania 7250, Australia
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - John M Manners
- CSIRO Plant Industry, 306 Carmody Road, St Lucia QLD 4067, Australia
| | - Chunji Liu
- CSIRO Plant Industry, 306 Carmody Road, St Lucia QLD 4067, Australia
- School of Plant Biology, The University of Western Australia, Perth, WA 6009, Australia
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20
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Chen GD, Liu YX, Wei YM, McIntyre CL, Zhou MX, Zheng YL, Liu CJ. Major QTL for Fusarium crown rot resistance in a barley landrace. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2511-20. [PMID: 23824201 DOI: 10.1007/s00122-013-2151-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 06/20/2013] [Indexed: 05/09/2023]
Abstract
Fusarium crown rot (FCR) is a serious cereal disease in semi-arid regions worldwide. In assisting the effort of breeding cultivars with enhanced resistance, we identified several barley genotypes with high levels of FCR resistance. One of these genotypes, AWCS079 which is a barley landrace originating from Japan, was investigated by developing and assessing three populations of recombinant inbred lines. Two QTL, one located on the long arm of chromosome 1H (designated as Qcrs.cpi-1H) and the other on 3HL (designated as Qcrs.cpi-3H), were found to be responsible for the FCR resistance of this genotype. Qcrs.cpi-1H is novel as no other FCR loci have been reported on this chromosome arm. Qcrs.cpi-3H co-located with a reduced height (Rht) locus and the effectiveness of the former was significantly affected by the latter. The total phenotypic variance explained by these two QTL was over 60 %. Significant effects were detected for each of the QTL in each of the three populations assessed. The existence of these loci with major effects should not only facilitate breeding and exploitation of FCR-resistant barley cultivars but also their further characterization based on fine mapping and map-based gene cloning.
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Affiliation(s)
- G D Chen
- CSIRO Plant Industry, 306 Carmody Road, St Lucia, QLD, 4067, Australia
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21
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Chen G, Liu Y, Ma J, Zheng Z, Wei Y, McIntyre CL, Zheng YL, Liu C. A novel and major quantitative trait locus for fusarium crown rot resistance in a genotype of Wild Barley (Hordeum spontaneum L.). PLoS One 2013; 8:e58040. [PMID: 23536780 PMCID: PMC3594225 DOI: 10.1371/journal.pone.0058040] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 01/29/2013] [Indexed: 11/24/2022] Open
Abstract
Fusarium crown rot (FCR), caused by various Fusarium species, is a destructive disease of cereal crops in semiarid regions worldwide. As part of our contribution to the development of Fusarium resistant cultivars, we identified several novel sources of resistance by systematically assessing barley genotypes representing different geographical origins and plant types. One of these sources of resistance was investigated in this study by generating and analysing two populations of recombinant inbred lines. A major locus conferring FCR resistance, designated as Qcrs.cpi-4H, was detected in one of the populations (mapping population) and the effects of the QTL was confirmed in the other population. The QTL was mapped to the distal end of chromosome arm 4HL and it is effective against both of the Fusarium isolates tested, one F. pseudograminearum and the other F. graminearum. The QTL explains up to 45.3% of the phenotypic variance. As distinct from an earlier report which demonstrated co-locations of loci conferring FCR resistance and plant height in barley, a correlation between these two traits was not detected in the mapping population. However, as observed in a screen of random genotypes, an association between FCR resistance and plant growth rate was detected and a QTL controlling the latter was detected near the Qcrs.cpi-4H locus in the mapping population. Existing data indicate that, although growth rate may affect FCR resistance, different genes at this locus are likely involved in controlling these two traits.
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Affiliation(s)
- Guangdeng Chen
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Queensland, Australia
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Yaxi Liu
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Queensland, Australia
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Jun Ma
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Queensland, Australia
- School of Plant Biology, The University of Western Australia, Perth, Western Australia, Australia
| | - Zhi Zheng
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Queensland, Australia
- School of Plant Biology, The University of Western Australia, Perth, Western Australia, Australia
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - C. Lynne McIntyre
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Queensland, Australia
| | - You-Liang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, China
| | - Chunji Liu
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Plant Industry, St Lucia, Queensland, Australia
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