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Zhou P, Liu Y, Yang M, Yan H. Genome-Wide Association Study Uncovers Genomic Regions Associated with Coleoptile Length in a Worldwide Collection of Oat. Genes (Basel) 2024; 15:411. [PMID: 38674348 PMCID: PMC11049438 DOI: 10.3390/genes15040411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/24/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
The length of coleoptile is crucial for determining the sowing depth of oats in low-precipitation regions, which is significant for oat breeding programs. In this study, a diverse panel of 243 oat accessions was used to explore coleoptile length in two independent experiments. The panel exhibited significant variation in coleoptile length, ranging from 4.66 to 8.76 cm. Accessions from Africa, America, and the Mediterranean region displayed longer coleoptile lengths than those from Asia and Europe. Genome-wide association studies (GWASs) using 26,196 SNPs identified 34 SNPs, representing 32 quantitative trait loci (QTLs) significantly associated with coleoptile length. Among these QTLs, six were consistently detected in both experiments, explaining 6.43% to 10.07% of the phenotypic variation. The favorable alleles at these stable loci additively increased coleoptile length, offering insights for pyramid breeding. Gene Ontology (GO) analysis of the 350 candidate genes underlying the six stable QTLs revealed significant enrichment in cell development-related processes. Several phytochrome-related genes, including auxin transporter-like protein 1 and cytochrome P450 proteins, were found within these QTLs. Further validation of these loci will enhance our understanding of coleoptile length regulation. This study provides new insights into the genetic architecture of coleoptile length in oats.
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Affiliation(s)
| | | | | | - Honghai Yan
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (P.Z.)
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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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Zhao X, Li J, Niu Y, Hossain Z, Gao X, Bai X, Mao T, Qi G, He F. Exogenous Serotonin (5-HT) Promotes Mesocotyl and Coleoptile Elongation in Maize Seedlings under Deep-Seeding Stress through Enhancing Auxin Accumulation and Inhibiting Lignin Formation. Int J Mol Sci 2023; 24:17061. [PMID: 38069387 PMCID: PMC10707020 DOI: 10.3390/ijms242317061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/27/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
Serotonin (5-HT), an indoleamine compound, has been known to mediate many physiological responses of plants under environmental stress. The deep-seeding (≥20 cm) of maize seeds is an important cultivation strategy to ensure seedling emergence and survival under drought stress. However, the role of 5-HT in maize deep-seeding tolerance remains unexplored. Understanding the mechanisms and evaluating the optimal concentration of 5-HT in alleviating deep-seeding stress could benefit maize production. In this study, two maize inbred lines were treated with or without 5-HT at both sowing depths of 20 cm and 3 cm, respectively. The effects of different concentrations of 5-HT on the growth phenotypes, physiological metabolism, and gene expression of two maize inbred lines were examined at the sowing depths of 20 cm and 3 cm. Compared to the normal seedling depth of 3 cm, the elongation of the mesocotyl (average elongation 3.70 cm) and coleoptile (average elongation 0.58 cm), secretion of indole-3-acetic acid (IAA; average increased 3.73 and 0.63 ng g-1 FW), and hydrogen peroxide (H2O2; average increased 1.95 and 0.63 μM g-1 FW) in the mesocotyl and coleoptile were increased under 20 cm stress, with a concomitant decrease in lignin synthesis (average decreased 0.48 and 0.53 A280 g-1). Under 20 cm deep-seeding stress, the addition of 5-HT activated the expression of multiple genes of IAA biosynthesis and signal transduction, including Zm00001d049601, Zm00001d039346, Zm00001d026530, and Zm00001d049659, and it also stimulated IAA production in both the mesocotyl and coleoptile of maize seedlings. On the contrary, 5-HT suppressed the expression of genes for lignin biosynthesis (Zm00001d016471, Zm00001d005998, Zm00001d032152, and Zm00001d053554) and retarded the accumulation of H2O2 and lignin, resulting in the elongation of the mesocotyl and coleoptile of maize seedlings. A comprehensive evaluation analysis showed that the optimum concentration of 5-HT in relieving deep-seeding stress was 2.5 mg/L for both inbred lines, and 5-HT therefore could improve the seedling emergence rate and alleviate deep-seeding stress in maize seedlings. These findings could provide a novel strategy for improving maize deep-seeding tolerance, thus enhancing yield potential under drought and water stress.
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Affiliation(s)
- Xiaoqiang Zhao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiayao Li
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Yining Niu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Zakir Hossain
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK S9H 3X2, Canada;
| | - Xiquan Gao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaodong Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Taotao Mao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Guoxiang Qi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
| | - Fuqiang He
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China; (X.Z.); (J.L.); (X.B.); (T.M.); (G.Q.); (F.H.)
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Sakhale SA, Yadav S, Clark LV, Lipka AE, Kumar A, Sacks EJ. Genome-wide association analysis for emergence of deeply sown rice ( Oryza sativa) reveals novel aus-specific phytohormone candidate genes for adaptation to dry-direct seeding in the field. FRONTIERS IN PLANT SCIENCE 2023; 14:1172816. [PMID: 37377815 PMCID: PMC10291202 DOI: 10.3389/fpls.2023.1172816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, an understanding of the genomic regions and underlying genes that confer emergence in deeply sown dry-DSR would be highly advantageous. A combined diversity panel of 470 rice accessions (RDP1 plus aus subset of 3K RGP) was evaluated with 2.9 million single nucleotide polymorphisms (SNPs) to identify associations with dry-DSR traits in the field and component traits in a controlled-environment experiment. Using genome-wide association study (GWAS) analyses, we identified 18 unique QTLs on chromosomes 1, 2, 4, 5, 6, 7, 9, 10, and 11, explaining phenotypic variance ranging from 2.6% to 17.8%. Three QTLs, namely, qSOE-1.1, qEMERG-AUS-1.2, and qEMERG-AUS-7.1, were co-located with previously reported QTLs for mesocotyl length. Among the identified QTLs, half were associated with the emergence of aus, and six were unique to the aus genetic group. Based on functional annotation, we identified eleven compelling candidate genes that primarily regulate phytohormone pathways such as cytokinin, auxin, gibberellic acid, and jasmonic acid. Prior studies indicated that these phytohormones play a critical role in mesocotyl length under deep sowing. This study provides new insight into the importance of aus and indica as desirable genetic resources to mine favorable alleles for deep-sowing tolerance in rice. The candidate genes and marker-tagged desirable alleles identified in this study should benefit rice breeding programs directly.
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Affiliation(s)
- Sandeep A. Sakhale
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
- International Rice Research Institute (IRRI), Los Baños, Philippines
- International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India
| | - Shailesh Yadav
- International Rice Research Institute (IRRI), Los Baños, Philippines
- Africa Rice Center (AfricaRice), Abidjan, Côte d’Ivoire
| | - Lindsay V. Clark
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
- Seattle Children’s Research Institute, Seattle, WA, United States
| | - Alexander E. Lipka
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Arvind Kumar
- International Rice Research Institute (IRRI), Los Baños, Philippines
- International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India
| | - Erik J. Sacks
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
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Xu D, Hao Q, Yang T, Lv X, Qin H, Wang Y, Jia C, Liu W, Dai X, Zeng J, Zhang H, He Z, Xia X, Cao S, Ma W. Impact of "Green Revolution" gene Rht-B1b on coleoptile length of wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1147019. [PMID: 36938052 PMCID: PMC10017974 DOI: 10.3389/fpls.2023.1147019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Wheat coleoptile is a sheath-like structure that helps to deliver the first leaf from embryo to the soil surface. Here, a RIL population consisting of 245 lines derived from Zhou 8425B × Chinese Spring cross was genotyped by the high-density Illumina iSelect 90K assay for coleoptile length (CL) QTL mapping. Three QTL for CL were mapped on chromosomes 2BL, 4BS and 4DS. Of them, two major QTL QCL.qau-4BS and QCL.qau-4DS were detected, which could explain 9.1%-22.2% of the phenotypic variances across environments on Rht-B1 and Rht-D1 loci, respectively. Several studies have reported that Rht-B1b may reduce the length of wheat CL but no study has been carried out at molecular level. In order to verify that the Rht-B1 gene is the functional gene for the 4B QTL, an overexpression line Rht-B1b-OE and a CRISPR/SpCas9 line Rht-B1b-KO were studied. The results showed that Rht-B1b overexpression could reduce the CL, while loss-of-function of Rht-B1b would increase the CL relative to that of the null transgenic plants (TNL). To dissect the underlying regulatory mechanism of Rht-B1b on CL, comparative RNA-Seq was conducted between Rht-B1b-OE and TNL. Transcriptome profiles revealed a few key pathways involving the function of Rht-B1b in coleoptile development, including phytohormones, circadian rhythm and starch and sucrose metabolism. Our findings may facilitate wheat breeding for longer coleoptiles to improve seedling early vigor for better penetration through the soil crust in arid regions.
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Affiliation(s)
- Dengan Xu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Qianlin Hao
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Tingzhi Yang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Xinru Lv
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Huimin Qin
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Yalin Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Chenfei Jia
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Wenxing Liu
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Xuehuan Dai
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Jianbin Zeng
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Hongsheng Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuanghe Cao
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wujun Ma
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
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Schierenbeck M, Alqudah AM, Thabet SG, Lohwasser U, Simón MR, Börner A. Association mapping unravels the genetics controlling seedling drought stress tolerance in winter wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1061845. [PMID: 36818842 PMCID: PMC9933780 DOI: 10.3389/fpls.2023.1061845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Drought is a major constraint in wheat (Triticum aestivum L.) grain yield. The present work aimed to identify quantitative trait nucleotides (QTNs)/ candidate genes influencing drought tolerance-related traits at the seedling stage in 261 accessions of a diverse winter wheat panel. Seeds from three consecutive years were exposed to polyethylene glycol 12% (PEG-6000) and a control treatment (distilled water). The Farm-CPU method was used for the association analysis with 17,093 polymorphic SNPs. PEG treatment reduced shoot length (SL) (-36.3%) and root length (RL) (-11.3%) compared with control treatments, while the coleoptile length (CL) was increased by 11% under drought conditions, suggesting that it might be considered as an indicator of stress-tolerance. Interestingly, we revealed 70 stable QTN across 17 chromosomes. Eight QTNs related to more than one trait were detected on chromosomes 1B, 2A (2), 2B, 2D, 4B, 7A, and 7B and located nearby or inside candidate genes within the linkage disequilibrium (LD) interval. For instance, the QTN on chromosome 2D is located inside the gene TraesCS2D02G133900 that controls the variation of CL_S and SL_C. The allelic variation at the candidate genes showed significant influence on the associated traits, demonstrating their role in controlling the natural variation of multi-traits of drought stress tolerance. The gene expression of these candidate genes under different stress conditions validates their biological role in stress tolerance. Our findings offer insight into understanding the genetic factors and diverse mechanisms in response to water shortage conditions that are important for wheat improvement and adaptation at early developmental stages.
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Affiliation(s)
- Matías Schierenbeck
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Seeland, Germany
- Cereals, Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina
- CONICET CCT La Plata, La Plata, Argentina
| | - Ahmad M. Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha, Qatar
| | - Samar G. Thabet
- Department of Botany, Faculty of Science, Fayoum University, Fayoum, Egypt
| | - Ulrike Lohwasser
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Seeland, Germany
| | - María Rosa Simón
- Cereals, Faculty of Agricultural Sciences and Forestry, National University of La Plata, La Plata, Argentina
- CONICET CCT La Plata, La Plata, Argentina
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Seeland, Germany
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Zeng Z, Guo C, Yan X, Song J, Wang C, Xu X, Hao Y. QTL mapping and KASP marker development for seed vigor related traits in common wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:994973. [PMID: 36247615 PMCID: PMC9563228 DOI: 10.3389/fpls.2022.994973] [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: 07/15/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Seed vigor is an important parameter of seed quality, and identification of seed vigor related genes can provide an important basis for highly efficient molecular breeding in wheat. In the present study, a doubled haploid (DH) population with 174 lines derived from a cross between Yangmai16 and Zhongmai 895 was used to evaluate 10 seed vigor related traits in Luoyang during the 2018-2019 cropping season and in Mengjin and Luoning Counties during 2019-2020 cropping season for three environments. Quantitative trait locus (QTL) mapping of 10 seed vigor related traits in the DH population resulted in the discovery/identification of 28 QTLs on chromosomes 2B, 3D, 4B, 4D, 5A, 5B, 6A, 6B, 6D, 7A and 7D, explaining 3.6-23.7% of the phenotypic variances. Among them, one QTL cluster for shoot length, root length and vigor index was mapped between AX-89421921 and Rht-D1_SNP on chromosome 4D in the physical intervals of 18.78-19.29 Mb (0.51 Mb), explaining 9.2-20.5% of the phenotypic variances. Another QTL for these traits was identified at the physical position 185.74 Mb on chromosome 5B, which was flanked by AX-111465230 and AX-109519938 and accounted for 8.0-13.3% of the phenotypic variances. Two QTLs for shoot length, shoot fresh weight and shoot dry weight were identified in the marker intervals of AX-109384026-AX-111120402 and AX-111651800-AX-94443918 on chromosomes 6A and 6B, explaining 8.2-11.7% and 3.6-10.3% of the phenotypic variance, respectively; both alleles for increasing phenotypic values were derived from Yangmai 16. We also developed the KASP markers for the QTL cluster QVI.haust-4D.1/QSL.haust-4D/QRL.haust-4D, and validated in an international panel of 135 wheat accessions. The germplasm, genes and KASP markers were developed for breeders to improve wheat varieties with seed vigor related traits.
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Affiliation(s)
- Zhankui Zeng
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
- The Shennong Laboratory, Zhengzhou, China
| | - Cheng Guo
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Xuefang Yan
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
| | - Junqiao Song
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
- The Shennong Laboratory, Zhengzhou, China
| | - Chunping Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
- The Shennong Laboratory, Zhengzhou, China
| | - Xiaoting Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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Wei N, Zhang S, Liu Y, Wang J, Wu B, Zhao J, Qiao L, Zheng X, Wang J, Zheng J. Genome-wide association study of coleoptile length with Shanxi wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:1016551. [PMID: 36212294 PMCID: PMC9532578 DOI: 10.3389/fpls.2022.1016551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
In arid and semi-arid regions, coleoptile length is a vital agronomic trait for wheat breeding. The coleoptile length determines the maximum depth that seeds can be sown, and it is critical for establishment of the crop. Therefore, identifying loci associated with coleoptile length in wheat is essential. In the present study, 282 accessions from Shanxi Province representing wheat breeding for the Loess Plateau were grown under three experimental conditions to study coleoptile length. The results of phenotypic variation indicated that drought stress and light stress could lead to shortening of coleoptile length. Under drought stress the growth rate of environmentally sensitive cultivars decreased more than insensitive cultivars. The broad-sense heritability (H 2) of BLUP (best linear unbiased prediction) under various conditions showed G × E interaction for coleoptile length but was mainly influenced by heredity. Correlation analysis showed that correlation between plant height-related traits and coleoptile length was significant in modern cultivars whereas it was not significant in landraces. A total of 45 significant marker-trait associations (MTAs) for coleoptile length in the three conditions were identified using the 3VmrMLM (3 Variance-component multi-locus random-SNP-effect Mixed Linear Model) and MLM (mixed linear model). In total, nine stable genetic loci were identified via 3VmrMLM under the three conditions, explaining 2.94-7.79% of phenotypic variation. Five loci on chromosome 2B, 3A, 3B, and 5B have not been reported previously. Six loci had additive effects toward increasing coleoptile length, three of which are novel. Molecular markers for the loci with additive effects on coleoptile length can be used to breed cultivars with long coleoptiles.
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Affiliation(s)
- Naicui Wei
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - ShengQuan Zhang
- Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ye Liu
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Jie Wang
- School of Life Sciences, Shanxi University, Taiyuan, China
| | - Bangbang Wu
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jiajia Zhao
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ling Qiao
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Xingwei Zheng
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Juanling Wang
- School of Life Sciences, Shanxi University, Taiyuan, China
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jun Zheng
- School of Life Sciences, Shanxi University, Taiyuan, China
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
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Vukasovic S, Alahmad S, Christopher J, Snowdon RJ, Stahl A, Hickey LT. Dissecting the Genetics of Early Vigour to Design Drought-Adapted Wheat. FRONTIERS IN PLANT SCIENCE 2022; 12:754439. [PMID: 35046971 PMCID: PMC8763316 DOI: 10.3389/fpls.2021.754439] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
Due to the climate change and an increased frequency of drought, it is of enormous importance to identify and to develop traits that result in adaptation and in improvement of crop yield stability in drought-prone regions with low rainfall. Early vigour, defined as the rapid development of leaf area in early developmental stages, is reported to contribute to stronger plant vitality, which, in turn, can enhance resilience to erratic drought periods. Furthermore, early vigour improves weed competitiveness and nutrient uptake. Here, two sets of a multi-reference nested association mapping (MR-NAM) population of bread wheat (Triticum aestivum ssp. aestivum L.) were used to investigate early vigour in a rain-fed field environment for 3 years, and additionally assessed under controlled conditions in a greenhouse experiment. The normalised difference vegetation index (NDVI) calculated from red/infrared light reflectance was used to quantify early vigour in the field, revealing a correlation (p < 0.05; r = 0.39) between the spectral measurement and the length of the second leaf. Under controlled environmental conditions, the measured projected leaf area, using a green-pixel counter, was also correlated to the leaf area of the second leaf (p < 0.05; r = 0.38), as well as to the recorded biomass (p < 0.01; r = 0.71). Subsequently, genetic determination of early vigour was tested by conducting a genome-wide association study (GWAS) for the proxy traits, revealing 42 markers associated with vegetation index and two markers associated with projected leaf area. There are several quantitative trait loci that are collocated with loci for plant developmental traits including plant height on chromosome 2D (log10 (P) = 3.19; PVE = 0.035), coleoptile length on chromosome 1B (-log10 (P) = 3.24; PVE = 0.112), as well as stay-green and vernalisation on chromosome 5A (-log10 (P) = 3.14; PVE = 0.115).
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Affiliation(s)
- Stjepan Vukasovic
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Samir Alahmad
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Jack Christopher
- Leslie Research Facility, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Toowoomba, QLD, Australia
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Giessen, Germany
| | - Andreas Stahl
- Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Julius Kühn-Institute, Quedlinburg, Germany
| | - Lee T. Hickey
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD, Australia
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Francki MG, Stainer GS, Walker E, Rebetzke GJ, Stefanova KT, French RJ. Phenotypic Evaluation and Genetic Analysis of Seedling Emergence in a Global Collection of Wheat Genotypes ( Triticum aestivum L.) Under Limited Water Availability. FRONTIERS IN PLANT SCIENCE 2021; 12:796176. [PMID: 35003185 PMCID: PMC8739788 DOI: 10.3389/fpls.2021.796176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The challenge in establishing an early-sown wheat crop in southern Australia is the need for consistently high seedling emergence when sowing deep in subsoil moisture (>10 cm) or into dry top-soil (4 cm). However, the latter is strongly reliant on a minimum soil water availability to ensure successful seedling emergence. This study aimed to: (1) evaluate 233 Australian and selected international wheat genotypes for consistently high seedling emergence under limited soil water availability when sown in 4 cm of top-soil in field and glasshouse (GH) studies; (2) ascertain genetic loci associated with phenotypic variation using a genome-wide association study (GWAS); and (3) compare across loci for traits controlling coleoptile characteristics, germination, dormancy, and pre-harvest sprouting. Despite significant (P < 0.001) environment and genotype-by-environment interactions within and between field and GH experiments, eight genotypes that included five cultivars, two landraces, and one inbred line had consistently high seedling emergence (mean value > 85%) across nine environments. Moreover, 21 environment-specific quantitative trait loci (QTL) were detected in GWAS analysis on chromosomes 1B, 1D, 2B, 3A, 3B, 4A, 4B, 5B, 5D, and 7D, indicating complex genetic inheritance controlling seedling emergence. We aligned QTL for known traits and individual genes onto the reference genome of wheat and identified 16 QTL for seedling emergence in linkage disequilibrium with coleoptile length, width, and cross-sectional area, pre-harvest sprouting and dormancy, germination, seed longevity, and anthocyanin development. Therefore, it appears that seedling emergence is controlled by multifaceted networks of interrelated genes and traits regulated by different environmental cues.
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Affiliation(s)
- Michael G. Francki
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Grantley S. Stainer
- Department of Primary Industries and Regional Development, Merredin, WA, Australia
| | - Esther Walker
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Gregory J. Rebetzke
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Canberra, ACT, Australia
| | - Katia T. Stefanova
- Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Robert J. French
- Department of Primary Industries and Regional Development, Merredin, WA, Australia
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Chen F, Ji X, Bai M, Zhuang Z, Peng Y. Network Analysis of Different Exogenous Hormones on the Regulation of Deep Sowing Tolerance in Maize Seedlings. FRONTIERS IN PLANT SCIENCE 2021; 12:739101. [PMID: 34925395 PMCID: PMC8674439 DOI: 10.3389/fpls.2021.739101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 11/12/2021] [Indexed: 06/14/2023]
Abstract
The planting method of deep sowing can make the seeds make full use of water in deep soil, which is considered to be an effective way to respond to drought stress. However, deep sowing will affect the growth and development of maize (Zea mays L.) at seedling stage. To better understand the response of maize to deep sowing stress and the mechanism of exogenous hormones [Gibberellin (GA3), Brassinolide (BR), Strigolactone (SL)] alleviates the damaging effects of deep-sowing stress, the physiological and transcriptome expression profiles of seedlings of deep sowing sensitive inbred line Zi330 and the deep-tolerant inbred line Qi319 were compared under deep sowing stress and the conditions of exogenous hormones alleviates stress. The results showed that mesocotyl elongated significantly after both deep sowing stress and application of exogenous hormones, and its elongation was mainly through elongation and expansion of cell volume. Hormone assays revealed no significant changes in zeatin (ZT) content of the mesocotyl after deep sowing and exogenous hormone application. The endogenous GA3 and auxin (IAA) contents in the mesocotyl of the two inbred lines increased significantly after the addition of exogenous GA3, BR, and SL under deep sowing stress compared to deep sowing stress, while BR and SL decreased significantly. Transcriptome analysis showed that the deep seeding stress was alleviated by GA3, BR, and SLs, the differentially expressed genes (DEGs) mainly included cellulose synthase, expansin and glucanase, oxidase, lignin biosynthesis genes and so on. We also found that protein phosphatase 2C and GA receptor GID1 enhanced the ability of resist deep seeding stress in maize by participating in the abscisic acid (ABA) and the GA signaling pathway, respectively. In addition, we identified two gene modules that were significantly related to mesocotyl elongation, and identified some hub genes that were significantly related to mesocotyl elongation by WGCNA analysis. These genes were mainly involved in transcription regulation, hydrolase activity, protein binding and plasma membrane. Our results from this study may provide theoretical basis for determining the maize deep seeding tolerance and the mechanism by which exogenous hormones regulates deep seeding tolerance.
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12
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Luo Q, Hu P, Yang G, Li H, Liu L, Wang Z, Li B, Li Z, Zheng Q. Mapping QTL for seedling morphological and physiological traits under normal and salt treatments in a RIL wheat population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2991-3011. [PMID: 34095960 DOI: 10.1007/s00122-021-03872-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/25/2021] [Indexed: 06/12/2023]
Abstract
The genetic basis of 27 seedling traits under normal and salt treatments was fully analyzed in a RIL wheat population, and seven QTL intervals were validated in two other genetic populations. Soil salinity seriously constrains wheat (Triticum aestivum L.) production globally by influencing its growth and development. To explore the genetic basis of salt tolerance in wheat, a recombinant inbred line (RIL) population derived from a cross between high-yield wheat cultivar Zhongmai 175 (ZM175) and salt-tolerant cultivar Xiaoyan 60 (XY60) was used to map QTL for seedling traits under normal and salt treatments based on a high-density genetic linkage map. A total of 158 stable additive QTL for 27 morphological and physiological traits were identified and distributed on all wheat chromosomes except 3A and 4D. They explained 2.35-46.43% of the phenotypic variation with a LOD score range of 2.61-40.38. The alleles from XY60 increased corresponding traits for 100 QTL, while the alleles from ZM175 had positive effects for the other 58 QTL. Nearly half of the QTL (78/158) were mapped in nine QTL clusters on chromosomes 2A, 2B, 2D, 4B, 5A, 5B, 5D, and 7D (2), respectively. To prove the reliability and potentiality in molecular marker-assisted selection (MAS), seven QTL intervals were validated in two other genetic populations. Besides additive QTL, 94 pairs of loci were detected with significant epistatic effect and 20 QTL were found to interact with treatment. This study provides a full elucidation of the genetic basis of seedling traits (especially root system-related traits) associated with salt tolerance in wheat, and the developed kompetitive allele-specific PCR markers closely linked to stable QTL would supply strong supports to MAS in salt-tolerant wheat breeding.
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Affiliation(s)
- Qiaoling Luo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pan Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guotang Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongwei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liqin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zishan Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bin Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhensheng Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qi Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Ullah S, Bramley H, Mahmood T, Trethowan R. Implications of emmer (Triticum dicoccon Schrank) introgression on bread wheat response to heat stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110738. [PMID: 33568290 DOI: 10.1016/j.plantsci.2020.110738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/29/2020] [Accepted: 10/30/2020] [Indexed: 06/12/2023]
Abstract
Wheat is sensitive to heat stress, particularly during grain filling, and this reduces grain yield. Ancestral wheat species, such as emmer wheat (Triticum dicoccon Schrank), represent potential sources of new genetic diversity for traits that may impact wheat responses to heat stress. However, the diversity available in emmer wheat has only been explored superficially. Recently developed emmer derived hexaploid wheat genotypes were evaluated for physiological, phenological and agronomic traits in a multi-environment, multi-season strategy. The emmer-based hexaploid lines were developed from crosses and backcrosses to 9 hexaploid recurrent parents and these genotypes and 7 commercial cultivars were evaluated under two times of sowing (E1 and E2) in the field for three consecutive years (2014-2016). The materials were genotyped using a 90 K SNP platform and these data used to estimate the contribution of emmer wheat to the progeny. Significant phenotypic and genetic variation for traits were observed. Higher temperature during reproductive development and grain filling reduced trait expression. Emmer progeny with greater trait values than their recurrent parents and commercial cultivars in both environments were found. Derivatives with higher physiological trait values yielded well in both environments; as indicated by the clustering of genotypes. The emmer wheat parent contributed between 1 and 43 % of the genome of the emmer-based hexaploid progeny, and progeny with greater emmer contribution had superior trait values in both environments. These results showed a positive effect of direct emmer introgression on wheat performance under heat stress. Mitigation of high temperature stress through the introgression of favorable alleles from wheat close relatives into modern wheat cultivars is possible.
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Affiliation(s)
- Smi Ullah
- The University of Sydney, School of Life and Environmental Sciences, Plant Breeding Institute and Sydney Institute of Agriculture, Narrabri 2390, NSW, Australia; Australian Grain Technologies Pty Ltd, Roseworthy 5371, SA, Australia.
| | - Helen Bramley
- The University of Sydney, School of Life and Environmental Sciences, Plant Breeding Institute and Sydney Institute of Agriculture, Narrabri 2390, NSW, Australia
| | - Tariq Mahmood
- The University of Sydney, School of Life and Environmental Sciences, Plant Breeding Institute and Sydney Institute of Agriculture, Cobbitty 2570, NSW, Australia
| | - Richard Trethowan
- The University of Sydney, School of Life and Environmental Sciences, Plant Breeding Institute and Sydney Institute of Agriculture, Narrabri 2390, NSW, Australia; The University of Sydney, School of Life and Environmental Sciences, Plant Breeding Institute and Sydney Institute of Agriculture, Cobbitty 2570, NSW, Australia
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14
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Merrick LF, Burke AB, Zhang Z, Carter AH. Comparison of Single-Trait and Multi-Trait Genome-Wide Association Models and Inclusion of Correlated Traits in the Dissection of the Genetic Architecture of a Complex Trait in a Breeding Program. FRONTIERS IN PLANT SCIENCE 2021; 12:772907. [PMID: 35154175 PMCID: PMC8831792 DOI: 10.3389/fpls.2021.772907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/29/2021] [Indexed: 05/06/2023]
Abstract
Unknown genetic architecture makes it difficult to characterize the genetic basis of traits and associated molecular markers because of the complexity of small effect quantitative trait loci (QTLs), environmental effects, and difficulty in phenotyping. Seedling emergence of wheat (Triticum aestivum L.) from deep planting, has a poorly understood genetic architecture, is a vital factor affecting stand establishment and grain yield, and is historically correlated with coleoptile length. This study aimed to dissect the genetic architecture of seedling emergence while accounting for correlated traits using one multi-trait genome-wide association study (MT-GWAS) model and three single-trait GWAS (ST-GWAS) models. The ST-GWAS models included one single-locus model [mixed-linear model (MLM)] and two multi-locus models [fixed and random model circulating probability unification (FarmCPU) and Bayesian information and linkage-disequilibrium iteratively nested keyway (BLINK)]. We conducted GWAS using two populations. The first population consisted of 473 varieties from a diverse association mapping panel phenotyped from 2015 to 2019. The second population consisted of 279 breeding lines phenotyped in 2015 in Lind, WA, with 40,368 markers. We also compared the inclusion of coleoptile length and markers associated with reduced height as covariates in our ST-GWAS models. ST-GWAS found 107 significant markers across 19 chromosomes, while MT-GWAS found 82 significant markers across 14 chromosomes. The FarmCPU and BLINK models, including covariates, were able to identify many small effect markers while identifying large effect markers on chromosome 5A. By using multi-locus model breeding, programs can uncover the complex nature of traits to help identify candidate genes and the underlying architecture of a trait, such as seedling emergence.
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15
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Puttamadanayaka S, Harikrishna, Balaramaiah M, Biradar S, Parmeshwarappa SV, Sinha N, Prasad SVS, Mishra PC, Jain N, Singh PK, Singh GP, Prabhu KV. Mapping genomic regions of moisture deficit stress tolerance using backcross inbred lines in wheat (Triticum aestivum L.). Sci Rep 2020; 10:21646. [PMID: 33303897 PMCID: PMC7729395 DOI: 10.1038/s41598-020-78671-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/13/2020] [Indexed: 11/24/2022] Open
Abstract
Identification of markers associated with major physiological and yield component traits under moisture deficit stress conditions in preferred donor lines paves the way for marker-assisted selection (MAS). In the present study, a set of 183 backcross inbred lines (BILs) derived from the cross HD2733/2*C306 were genotyped using 35K Axiom genotyping array and SSR markers. The multi-trait, multi-location field phenotyping of BILs was done at three locations covering two major wheat growing zones of India, north-western plains zone (NWPZ) and central zone (CZ) under varying moisture regimes. A linkage map was constructed using 705 SNPs and 86 SSR polymorphic markers. A total of 43 genomic regions and QTL × QTL epistatic interactions were identified for 14 physiological and yield component traits, including NDVI, chlorophyll content, CT, CL, PH, GWPS, TGW and GY. Chromosomes 2A, 5D, 5A and 4B harbors greater number of QTLs for these traits. Seven Stable QTLs were identified across environment for DH (QDh.iari_6D), GWPS (QGWPS.iari_5B), PH (QPh.iari_4B-2, QPh.iari_4B-3) and NDVI (QNdvi1.iari_5D, QNdvi3.iari_5A). Nine genomic regions identified carrying major QTLs for CL, NDVI, RWC, FLA, PH, TGW and biomass explaining 10.32–28.35% of the phenotypic variance. The co-segregation of QTLs of physiological traits with yield component traits indicate the pleiotropic effects and their usefulness in the breeding programme. Our findings will be useful in dissecting genetic nature and marker-assisted selection for moisture deficit stress tolerance in wheat.
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Affiliation(s)
| | - Harikrishna
- ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India.
| | - Manu Balaramaiah
- ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - Sunil Biradar
- ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | | | - Nivedita Sinha
- ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - S V Sai Prasad
- ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
| | - P C Mishra
- Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur, Madhya Pradesh, 482 004, India
| | - Neelu Jain
- ICAR-Indian Agricultural Research Institute, New Delhi, 110 012, India
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16
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Khadka K, Raizada MN, Navabi A. Recent Progress in Germplasm Evaluation and Gene Mapping to Enable Breeding of Drought-Tolerant Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:1149. [PMID: 32849707 PMCID: PMC7417477 DOI: 10.3389/fpls.2020.01149] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/15/2020] [Indexed: 05/02/2023]
Abstract
There is a need to increase wheat productivity to meet the food demands of the ever-growing human population. However, accelerated development of high yielding varieties is hindered by drought, which is worsening due to climate change. In this context, germplasm diversity is central to the development of drought-tolerant wheat. Extensive collections of these genetic resources are conserved in national and international genebanks. In addition to phenotypic assessments, the use of advanced molecular techniques (e.g., genotype by sequencing) to identify quantitative trait loci (QTLs) for drought tolerance related traits is useful for genome- and marker-assisted selection based approaches. Therefore, to assist wheat breeders at a critical time, we searched the recent peer-reviewed literature (2011-current), first, to identify wheat germplasm observed to be useful genetic sources for drought tolerance, and second, to report QTLs associated with drought tolerance. Though many breeders limit the parents used in breeding programs to a familiar core collection, the results of this review show that larger germplasm collections have been sources of useful genes for drought tolerance in wheat. The review also demonstrates that QTLs for drought tolerance in wheat are associated with diverse physio-morphological traits, at different growth stages. Here, we also briefly discuss the potential of genome engineering/editing to improve drought tolerance in wheat. The use of CRISPR-Cas9 and other gene-editing technologies can be used to fine-tune the expression of genes controlling drought adaptive traits, while high throughput phenotyping (HTP) techniques can potentially accelerate the selection process. These efforts are empowered by wheat researcher consortia.
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Affiliation(s)
- Kamal Khadka
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
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17
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Bazzer SK, Kaler AS, Ray JD, Smith JR, Fritschi FB, Purcell LC. Identification of quantitative trait loci for carbon isotope ratio (δ 13C) in a recombinant inbred population of soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2141-2155. [PMID: 32296861 DOI: 10.1007/s00122-020-03586-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/31/2020] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE QTL analysis identified 16 QTLs, grouped in eight loci on seven soybean chromosomes that were associated with carbon isotope ratio (δ13C) in a biparental recombinant inbred population. Drought is a major limitation to soybean yield, and the frequency of drought stress is likely to increase under future climatic scenarios. Water use efficiency (WUE) is associated with drought tolerance, and carbon isotope ratio (δ13C) is positively correlated with WUE. In this study, 196 F6-derived recombinant inbred lines from a cross of PI 416997 (high WUE) × PI 567201D (low WUE) were evaluated in four environments to identify genomic regions associated with δ13C. There were positive correlations of δ13C values between different environments (0.67 ≤ r ≤ 0.78). Genotype, environment, and genotype × environment interactions had significant effects on δ13C. Narrow sense heritability of δ13C was 90% when estimated across environments. There was a total of 16 QTLs on seven chromosomes with individual QTLs explaining between 2.5 and 29.9% of the phenotypic variation and with additive effects ranging from 0.07 to 0.22‰. These 16 QTLs likely identified eight loci based on their overlapping confidence intervals. Of these eight loci, two loci on chromosome 20 (Gm20) were detected in at least three environments and were considered as stable QTLs. Additive QTLs on Gm20 showed epistatic interactions with 10 QTLs present across nine chromosomes. Five QTLs were identified across environments and showed significant QTL × environment interactions. These findings demonstrate that additive QTLs and QTL × QTL interactions play significant roles in genetic control of the δ13C trait. Markers flanking identified QTLs may facilitate marker-assisted selection to accumulate desirable QTLs to improve WUE and drought tolerance in soybean.
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Affiliation(s)
- Sumandeep K Bazzer
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA
| | - Avjinder S Kaler
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA
| | - Jeffery D Ray
- Agricultural Research Service, Crop Genetics Research Unit, USDA, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - James R Smith
- Agricultural Research Service, Crop Genetics Research Unit, USDA, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - Felix B Fritschi
- Division of Plant Sciences, University of Missouri, 1-13 Agriculture Building, Columbia, MO, 65211, USA
| | - Larry C Purcell
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72704, USA.
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18
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Ma J, Lin Y, Tang S, Duan S, Wang Q, Wu F, Li C, Jiang X, Zhou K, Liu Y. A Genome-Wide Association Study of Coleoptile Length in Different Chinese Wheat Landraces. FRONTIERS IN PLANT SCIENCE 2020; 11:677. [PMID: 32582239 PMCID: PMC7287122 DOI: 10.3389/fpls.2020.00677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/29/2020] [Indexed: 05/26/2023]
Abstract
From the perspective of wheat yield improvement, the coleoptile is vital for successful crop establishment, and long coleoptile lengths (CLs) are preferred in wheat-growing regions where deep planting is practiced. To determine the genetic basis of CL, we performed a genome-wide association study on a set of 707 Chinese wheat landraces using 18,594 single-nucleotide polymorphisms and 38,678 diversity array technology sequencing markers. We accordingly detected a total of 29 significant markers [-log10 (P) > 4.76] distributed on chromosomes 2B, 2D, 3A, 4A, 5A, 6A, 6B, 6D, and 7B. Based on linkage disequilibrium decay distance, we identified a total of 17 quantitative trait loci associated with CL, among which QCl.sicau-6B.2, located at 508.17-509.26 Mb on chromosome 6B, was recognized as a novel major locus. We subsequently developed a high-resolution melt marker for QCl.sicau-6B.2, which was validated in an F 2 : 3 population. Our findings provide important insights into the genetic mechanisms underlying coleoptile growth and could be applied to marker-assisted wheat selection.
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Affiliation(s)
- Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yu Lin
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Si Tang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shuonan Duan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Qing Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Fangkun Wu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Caixia Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaojun Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Kunyu Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
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Sidhu JS, Singh D, Gill HS, Brar NK, Qiu Y, Halder J, Al Tameemi R, Turnipseed B, Sehgal SK. Genome-Wide Association Study Uncovers Novel Genomic Regions Associated With Coleoptile Length in Hard Winter Wheat. Front Genet 2020; 10:1345. [PMID: 32117410 PMCID: PMC7025573 DOI: 10.3389/fgene.2019.01345] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/09/2019] [Indexed: 01/13/2023] Open
Abstract
Successful seedling establishment depends on the optimum depth of seed placement especially in drought-prone conditions, providing an opportunity to exploit subsoil water and increase winter survival in winter wheat. Coleoptile length is a key determinant for the appropriate depth at which seed can be sown. Thus, understanding the genetic basis of coleoptile length is necessary and important for wheat breeding. We conducted a genome-wide association study (GWAS) using a diverse panel of 298 winter wheat genotypes to dissect the genetic architecture of coleoptile length. We identified nine genomic regions associated with the coleoptile length on seven different chromosomes. Of the nine genomic regions, five have been previously reported in various studies, including one mapped to previously known Rht-B1 region. Three novel quantitative trait loci (QTLs), QCL.sdsu-2AS, QCL.sdsu-4BL, and QCL.sdsu-5BL were identified in our study. QCL.sdsu-5BL has a large substitution effect which is comparable to Rht-B1's effect and could be used to compensate for the negative effect of Rht-B1 on coleoptile length. In total, the nine QTLs explained 59% of the total phenotypic variation. Cultivars 'Agate' and 'MT06103' have the longest coleoptile length and interestingly, have favorable alleles at nine and eight coleoptile loci, respectively. These lines could be a valuable germplasm for longer coleoptile breeding. Gene annotations in the candidate regions revealed several putative proteins of specific interest including cytochrome P450-like, expansins, and phytochrome A. The QTLs for coleoptile length linked to single-nucleotide polymorphism (SNP) markers reported in this study could be employed in marker-assisted breeding for longer coleoptile in wheat. Thus, our study provides valuable insights into the genetic and molecular regulation of the coleoptile length in winter wheat.
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Affiliation(s)
- Jagdeep Singh Sidhu
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Dilkaran Singh
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, United States
| | - Harsimardeep Singh Gill
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Navreet Kaur Brar
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Yeyan Qiu
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Jyotirmoy Halder
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Rami Al Tameemi
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Brent Turnipseed
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
| | - Sunish Kumar Sehgal
- Department of Agronomy, Horticulture & Plant Science, South Dakota State University, Brookings, SD, United States
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Bovill WD, Hyles J, Zwart AB, Ford BA, Perera G, Phongkham T, Brooks BJ, Rebetzke GJ, Hayden MJ, Hunt JR, Spielmeyer W. Increase in coleoptile length and establishment by Lcol-A1, a genetic locus with major effect in wheat. BMC PLANT BIOLOGY 2019; 19:332. [PMID: 31357930 PMCID: PMC6664495 DOI: 10.1186/s12870-019-1919-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/02/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Good establishment is important for rapid leaf area development in wheat crops. Poor establishment results in fewer, later-emerging plants, reduced leaf area and tiller number. In addition, poorly established crops suffer from increased soil moisture loss through evaporation and greater competition from weeds while fewer spikes are produced which can reduce grain yield. By protecting the emerging first leaf, the coleoptile is critical for achieving good establishment, and its length and interaction with soil physical properties determine the ability of a cultivar to emerge from depth. RESULTS Here we characterise a locus on chromosome 1AS, that increases coleoptile length in wheat, which we designate as Lcol-A1. We identified Lcol-A1 by bulked-segregant analysis and used a Halberd-derived population to fine map the gene to a 2 cM region, equivalent to 7 Mb on the IWGSC genome reference sequence of Chinese Spring (RefSeqv1.0). By sowing recently released cultivars and near-isogenic lines in the field at both conventional and deep sowing depths, we confirmed that Locl-A1 was associated with increased emergence from depth in the presence and absence of conventional dwarfing genes. Flanking markers IWB58229 and IWA710 were developed to assist breeders to select for long coleoptile wheats. CONCLUSIONS Increased coleoptile length is sought in many global wheat production areas to improve crop emergence. The identification of the gene Lcol-A1, together with tools to allow wheat breeders to track the gene, will enable improvements to be made for this important trait.
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Affiliation(s)
- William D. Bovill
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT 2601 Australia
| | - Jessica Hyles
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT 2601 Australia
| | | | - Brett A. Ford
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT 2601 Australia
| | - Geetha Perera
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT 2601 Australia
| | - Tanya Phongkham
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT 2601 Australia
| | - Brenton J. Brooks
- CSIRO Agriculture and Food, P.O. Box 1700, Canberra, ACT 2601 Australia
| | | | - Matthew J. Hayden
- Agriculture Victoria Research, AgriBio Centre for AgriBiosciences, Bundoora, VIC 3086 Australia
| | - James R. Hunt
- Department of Animal, Plant and Soil Sciences, AgriBio Centre for AgriBiosciences, La Trobe University, Bundoora, VIC 3086 Australia
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21
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Hassan FSC, Solouki M, Fakheri BA, Nezhad NM, Masoudi B. Mapping QTLs for physiological and biochemical traits related to grain yield under control and terminal heat stress conditions in bread wheat ( Triticum aestivum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:1231-1243. [PMID: 30425437 PMCID: PMC6214426 DOI: 10.1007/s12298-018-0590-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 07/02/2018] [Accepted: 07/24/2018] [Indexed: 05/04/2023]
Abstract
In order to detect genomic regions with different effects for some of the physiological and biochemical traits of wheat, four experiments were conducted at Research Farm of Agricultural and Natural Resources Research Center of Zabol in 2015-2016 and 2016-2017 growing seasons. The experiments were carried out using four alpha lattice designs with two replications under non-stress and terminal heat stress conditions. Plant materials used in this study included 167 recombinant inbred lines and their parents ('SeriM82' and 'Babax'). Six traits including grain yield (GY), proline content (PRO), water soluble carbohydrates (WSC), maximum efficiency of photosystem II (Fv/Fm), cytoplasmic membrane stability (CMS) and chlorophyll content (CHL) were evaluated. Genetic linkage map consisted of 211 AFLP marker, 120 SSR marker and 144 DArT markers with 1864 cm length and 4.4 cm mean distance. QTL analysis was carried out using a mixed-model-based composite interval mapping (MCIM) method. By the combined analysis of normal phenotypic values, 27 additive QTLs and five pairs of epistatic effects were identified for studied traits, among which two additive and one epistatic QTL showed significant QTL × environment interactions. By the combined analysis of stress phenotypic values, a total of 26 QTLs with additive effects and 5 epistatic QTLs were detected, among which one additive and one epistatic QTL showed QTL × environment interactions. Six QTLs with major effects (QGY-2B, QGY-2D, QPro-5B, QWSC-4A, QFv/Fm-6A and QCMS-4B), which were common between two conditions could be useful for marker-assisted selection (MAS) in order to develop heat tolerant and high-performance wheat varieties.
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Affiliation(s)
- Faramarz Sohrabi Chah Hassan
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, P.O. Box 98615-538, Zabol, 9861335856 Iran
| | - Mahmood Solouki
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, P.O. Box 98615-538, Zabol, 9861335856 Iran
| | - Barat Ali Fakheri
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, P.O. Box 98615-538, Zabol, 9861335856 Iran
| | - Nafiseh Mahdi Nezhad
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, P.O. Box 98615-538, Zabol, 9861335856 Iran
| | - Bahram Masoudi
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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22
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Lucas SJ, Salantur A, Yazar S, Budak H. High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis. Funct Integr Genomics 2017; 17:667-685. [PMID: 28550605 DOI: 10.1007/s10142-017-0563-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 11/24/2022]
Abstract
Durum wheat (Triticum turgidum var. durum Desf.) is a major world crop that is grown primarily in areas of the world that experience periodic drought, and therefore, breeding climate-resilient durum wheat is a priority. High-throughput single nucleotide polymorphism (SNP) genotyping techniques have greatly increased the power of linkage and association mapping analyses for bread wheat, but as yet there is no durum wheat-specific platform available. In this study, we evaluate the new 384HT Wheat Breeders Array for its usefulness in tetraploid wheat breeding by genotyping a breeding population of F6 hybrids, derived from multiple crosses between T. durum cultivars and wild and cultivated emmer wheat accessions. Using a combined linkage and association mapping approach, we generated a genetic map including 1345 SNP markers, and identified markers linked to 6 QTLs for coleoptile length (2), heading date (1), anthocyanin accumulation (1) and osmotic stress tolerance (2). We also developed a straightforward approach for combining genetic data from multiple families of limited size that will be useful for evaluating and mapping pre-existing breeding material.
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Affiliation(s)
- Stuart J Lucas
- SU Nanotechnology Research and Application Centre, Sabanci University, 34956, Tuzla, İstanbul, Turkey.
| | - Ayten Salantur
- Breeding and Genetics, Field Crops Central Research Institute, Ankara, Turkey
| | - Selami Yazar
- Breeding and Genetics, Field Crops Central Research Institute, Ankara, Turkey
| | - Hikmet Budak
- Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey. .,412 Leon Johnson Hall, Cereal Genomics Lab, Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, USA.
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23
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Valliyodan B, Ye H, Song L, Murphy M, Shannon JG, Nguyen HT. Genetic diversity and genomic strategies for improving drought and waterlogging tolerance in soybeans. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1835-1849. [PMID: 27927997 DOI: 10.1093/jxb/erw433] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Drought and its interaction with high temperature are the major abiotic stress factors affecting soybean yield and production stability. Ongoing climate changes are anticipated to intensify drought events, which will further impact crop production and food security. However, excessive water also limits soybean production. The success of soybean breeding programmes for crop improvement is dependent on the extent of genetic variation present in the germplasm base. Screening for natural genetic variation in drought- and flooding tolerance-related traits, including root system architecture, water and nitrogen-fixation efficiency, and yield performance indices, has helped to identify the best resources for genetic studies in soybean. Genomic resources, including whole-genome sequences of diverse germplasms, millions of single-nucleotide polymorphisms, and high-throughput marker genotyping platforms, have expedited gene and marker discovery for translational genomics in soybean. This review highlights the current knowledge of the genetic diversity and quantitative trait loci associated with root system architecture, canopy wilting, nitrogen-fixation ability, and flooding tolerance that contributes to the understanding of drought- and flooding-tolerance mechanisms in soybean. Next-generation mapping approaches and high-throughput phenotyping will facilitate a better understanding of phenotype-genotype associations and help to formulate genomic-assisted breeding strategies, including genomic selection, in soybean for tolerance to drought and flooding stress.
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Affiliation(s)
- Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - Heng Ye
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - Li Song
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - MacKensie Murphy
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
| | - J Grover Shannon
- Division of Plant Sciences, University of Missouri-Fisher Delta Research Center, Portageville, MO 63873, USA
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA
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24
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Sabiel SAI, Huang S, Hu X, Ren X, Fu C, Peng J, Sun D. SNP-based association analysis for seedling traits in durum wheat ( Triticum turgidum L. durum (Desf.)). BREEDING SCIENCE 2017; 67:83-94. [PMID: 28588384 PMCID: PMC5445962 DOI: 10.1270/jsbbs.16074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 10/26/2016] [Indexed: 06/07/2023]
Abstract
In the present study, 150 accessions of worldwide originated durum wheat germplasm (Triticum turgidum spp. durum) were observed for major seedling traits and their growth. The accessions were evaluated for major seedling traits under controlled conditions of hydroponics at the 13th, 20th, 27th and 34th day-after germination. Biomass traits were measured at the 34th day-after germination. Correlation analysis was conducted among the seedling traits and three field traits at maturity, plant height, grain weight and 1000-grain weight observed in four consecutive years. Associations of the measured seedling traits and SNP markers were analyzed based on the mixed linear model (MLM). The results indicated that highly significant genetic variation and robust heritability were found for the seedling and field mature traits. In total, 259 significant associations were detected for all the traits and four growth stages. The phenotypic variation explained (R2) by a single SNP marker is higher than 10% for most (84%) of the significant SNP markers. Forty-six SNP markers associated with multiple traits, indicating non-neglectable pleiotropy in seedling stage. The associated SNP markers could be helpful for genetic analysis of seedling traits, and marker-assisted breeding of new wheat varieties with strong seedling vigor.
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Affiliation(s)
- Salih A. I. Sabiel
- College of Plant Science and Technology, Huazhong Agricultural University,
Wuhan Hubei, 430070,
China
- Plant Breeding Program, Agricultural Research Corporation,
Wad Medani, P. O. Box 126,
Sudan
| | - Sisi Huang
- College of Plant Science and Technology, Huazhong Agricultural University,
Wuhan Hubei, 430070,
China
| | - Xin Hu
- College of Plant Science and Technology, Huazhong Agricultural University,
Wuhan Hubei, 430070,
China
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University,
Wuhan Hubei, 430070,
China
| | - Chunjie Fu
- Life Science and Technology Center of China National Seed Group Co., Ltd., and the State Key Laboratory of Crop Breeding Technology Innovation and Integration,
Wuhan, Hubei, 430206,
China
| | - Junhua Peng
- Life Science and Technology Center of China National Seed Group Co., Ltd., and the State Key Laboratory of Crop Breeding Technology Innovation and Integration,
Wuhan, Hubei, 430206,
China
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University,
Wuhan Hubei, 430070,
China
- Hubei Collaborative Innovation Center for Grain Industry,
Jingzhou, Hubei, 434025,
China
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25
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QTL Analysis for Drought Tolerance in Wheat: Present Status and Future Possibilities. AGRONOMY-BASEL 2017. [DOI: 10.3390/agronomy7010005] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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26
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Lou X, Li X, Li A, Pu M, Shoaib M, Liu D, Sun J, Zhang A, Yang W. The 160 bp Insertion in the Promoter of Rht-B1i Plays a Vital Role in Increasing Wheat Height. FRONTIERS IN PLANT SCIENCE 2016; 7:307. [PMID: 27014327 PMCID: PMC4792873 DOI: 10.3389/fpls.2016.00307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 02/27/2016] [Indexed: 05/10/2023]
Abstract
The extensive use of two alleles (Rht-B1b and Rht-D1b) at the Rht-1 locus in wheat allowed dramatic increases in yields, triggering the so-called "Green Revolution." Here, we found that a new natural allelic variation (Rht-B1i) containing a single missense SNP (A614G) in the coding region significantly increased plant height against the genetic background of both Rht-D1a (11.68%) and Rht-D1b (7.89%). To elucidate the molecular mechanism of Rht-B1i, we investigated the promoter region. Sequence analysis showed that the Rht-B1i promoter could be divided into two classes depending on the presence or absence of a specific 160 bp insertion: Rht-B1i-1 (with the 160 bp insertion) and Rht-B1i-2 (without the 160 bp insertion). The promoter of Rht-B1i-1 contained 32 more possible cis-acting elements than Rht-B1a, including a unique auxin response element AUXREPSIAA4. Quantitative RT-PCR analysis indicated that the 160 bp insertion is likely to promote the transcription of the Rht-B1i-1 gene. The coleoptile lengths of wheat varieties treated with IAA, GA3, and IAA/GA3, combined with the histochemical staining of transgenic Arabidopsis containing the Rht-B1i-1 promoter, showed that the height-increasing effect of Rht-B1i-1 may be due to the synergistic action of IAA and GA3. These results augment our understanding of the regulatory mechanisms of Rht-1 in wheat and provide new genetic resources for wheat improvement.
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Affiliation(s)
- Xueyuan Lou
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- Graduate University of Chinese Academy of SciencesBeijing, China
| | - Xin Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Aixia Li
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- Graduate University of Chinese Academy of SciencesBeijing, China
| | - Mingyu Pu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- Graduate University of Chinese Academy of SciencesBeijing, China
| | - Muhammad Shoaib
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Dongcheng Liu
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Jiazhu Sun
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
| | - Aimin Zhang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- The Collaborative Innovation Center for Grain Crops in Henan, Henan Agricultural UniversityZhengzhou, China
- *Correspondence: Aimin Zhang, ; Wenlong Yang,
| | - Wenlong Yang
- The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijing, China
- *Correspondence: Aimin Zhang, ; Wenlong Yang,
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Ryan PR, Liao M, Delhaize E, Rebetzke GJ, Weligama C, Spielmeyer W, James RA. Early vigour improves phosphate uptake in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:7089-100. [PMID: 26320241 PMCID: PMC4765783 DOI: 10.1093/jxb/erv403] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Quantitative trait loci (QTLs) for shoot biomass were identified in wheat grown on a soil high in total phosphorus (P) but low in plant-available P. The two populations screened included recombinant inbred lines (RILs) from Chuan-Mai 18/Vigour 18 and doubled-haploid lines from Kukri/Janz. Glasshouse-grown plants were harvested at the five-leaf stage. Seven QTLs for shoot biomass were identified in the RILs, with the largest on chromosome 7A accounting for 7.4% of the phenotypic variance. RILs from the upper tail had larger embryos than RILs from the lower tail. Tail lines were then grown in non-limiting P and the results indicated that early vigour and the capacity to access P contributed to the initial distribution. The influence of early vigour on P nutrition was examined further with advanced vigour lines (AVLs). The AVLs accumulated more shoot biomass, maintained lower shoot P concentrations, and showed greater P-acquisition efficiency than Vigour 18. Nine QTLs for shoot biomass were identified in the Kukri/Janz population. Two on chromosomes 4B and 4D accounted for 24.8% of the variance. Candidates underlying these QTLs are the Rht genes. We confirmed the influence of these genes using near-isogenic lines with different Rht alleles. The dwarf and semi-dwarf alleles affected shoot and root biomass at high and low P but not the efficiency of P acquisition. We conclude that early vigour contributed to the distributions in both populations. Early vigour can increase plant growth at suboptimal P and some sources can also improve the efficiency of P acquisition.
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Affiliation(s)
- Peter R Ryan
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
| | - Mingtan Liao
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
| | | | | | | | | | - Richard A James
- CSIRO Agriculture, GPO Box 1600, Canberra ACT 2601, Australia
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28
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Acuña‐Galindo MA, Mason RE, Subramanian NK, Hays DB. Meta‐Analysis of Wheat QTL Regions Associated with Adaptation to Drought and Heat Stress. CROP SCIENCE 2015; 55:477-492. [PMID: 0 DOI: 10.2135/cropsci2013.11.0793] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Affiliation(s)
- M. Andrea Acuña‐Galindo
- Dep. of Crop, Soil, and Environmental SciencesUniv. of Arkansas115 Plant Sciences BuildingFayettevilleAR72701
| | - R. Esten Mason
- Dep. of Crop, Soil, and Environmental SciencesUniv. of Arkansas115 Plant Sciences BuildingFayettevilleAR72701
| | - Nithya K. Subramanian
- Dep. of Crop, Soil, and Environmental SciencesUniv. of Arkansas115 Plant Sciences BuildingFayettevilleAR72701
| | - Dirk B. Hays
- Dep. of Soil and Crop SciencesTexas A&M UniversityCollege StationTX77843
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29
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Conditional and unconditional QTL mapping of drought-tolerance-related traits of wheat seedling using two related RIL populations. J Genet 2014; 92:213-31. [PMID: 23970077 DOI: 10.1007/s12041-013-0253-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
For discovering the quantitative trait loci (QTLs) contributing to early seedling growth and drought tolerance during germination, conditional and unconditional analyses of 12 traits of wheat seedlings: coleoptile length, seedling height, longest root length, root number, seedling fresh weight, stem and leaves fresh weight, root fresh weight, seedling dry weight, stem and leaves dry weight, root dry weight, root to shoot fresh weight ratio, root-to-shoot dry weight ratio, were conducted under two water conditions using two F8:9 recombinant inbred line (RIL) populations. The results of unconditional analysis are as follows: 88 QTLs accounting for 3.33-77.01% of the phenotypic variations were detected on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5A, 5B, 5D, 6A, 6B, 6D, 7A, 7B and 7D. Among these QTLs, 19 were main-effect QTLs with a contribution rate greater than 10%. The results of the conditional QTL analysis of 12 traits under osmotic stress on normal water conditions were as follows: altogether 22 QTLs concerned with drought tolerance were detected on chromosomes 1B, 2A, 2B, 3B, 4A, 5D, 6A, 6D, 7B, and 7D. Of these QTLs, six were main-effect QTLs. These 22 QTLs were all special loci directly concerned with drought tolerance and most of them could not be detected by unconditional analysis. The finding of these QTLs has an important significance for fine-mapping technique, map-based cloning, and molecular marker-assisted selection of early seedling traits, such as growth and drought tolerance.
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Narayanan S, Mohan A, Gill KS, Prasad PVV. Variability of root traits in spring wheat germplasm. PLoS One 2014; 9:e100317. [PMID: 24945438 PMCID: PMC4063797 DOI: 10.1371/journal.pone.0100317] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 05/25/2014] [Indexed: 11/20/2022] Open
Abstract
Root traits influence the amount of water and nutrient absorption, and are important for maintaining crop yield under drought conditions. The objectives of this research were to characterize variability of root traits among spring wheat genotypes and determine whether root traits are related to shoot traits (plant height, tiller number per plant, shoot dry weight, and coleoptile length), regions of origin, and market classes. Plants were grown in 150-cm columns for 61 days in a greenhouse under optimal growth conditions. Rooting depth, root dry weight, root: shoot ratio, and shoot traits were determined for 297 genotypes of the germplasm, Cultivated Wheat Collection (CWC). The remaining root traits such as total root length and surface area were measured for a subset of 30 genotypes selected based on rooting depth. Significant genetic variability was observed for root traits among spring wheat genotypes in CWC germplasm or its subset. Genotypes Sonora and Currawa were ranked high, and genotype Vandal was ranked low for most root traits. A positive relationship (R2 ≥ 0.35) was found between root and shoot dry weights within the CWC germplasm and between total root surface area and tiller number; total root surface area and shoot dry weight; and total root length and coleoptile length within the subset. No correlations were found between plant height and most root traits within the CWC germplasm or its subset. Region of origin had significant impact on rooting depth in the CWC germplasm. Wheat genotypes collected from Australia, Mediterranean, and west Asia had greater rooting depth than those from south Asia, Latin America, Mexico, and Canada. Soft wheat had greater rooting depth than hard wheat in the CWC germplasm. The genetic variability identified in this research for root traits can be exploited to improve drought tolerance and/or resource capture in wheat.
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Affiliation(s)
- Sruthi Narayanan
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
| | - Amita Mohan
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Kulvinder S. Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - P. V. Vara Prasad
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
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QTL mapping for germination of seeds obtained from previous wheat generation under drought. Open Life Sci 2014. [DOI: 10.2478/s11535-013-0273-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
AbstractThe QTLs controlling germination and early seedling growth were mapped using seeds acquired from mapping population and parental lines of Chinese Spring and SQ1 grown under water-limited conditions, severe drought (SDr) and well-watered plants (C). Germination ability was determined by performing a standard germination test based on the quantification of the germination percentage (GP24) of seeds incubated for 24 h at 25°C in the dark. Early seedling growth was evaluated on the basis of the length of the root and leaf at the 6th day of the experiment. QTLs were identified by composite interval mapping method using Windows QTLCartographer 2.5 software. For the traits studied, a total of thirty eight additive QTLs were identified. Seventeen QTLs were mapped in C on chromosomes: 1A, 2A, 7A, 1B, 2B, 3B, 4B, 5B, 6B, 7B, 2D, 3D, 4D and 6D, while twenty one QTLs were identified in SDr on chromosomes: 1A, 2A, 5A, 2B, 3B, 4B, 5B, 6B, 7B, 3D, 5D and 6D. Most of the QTLs for GP and early leaf growth parameters were clustered on chromosome 4B (associated with the Rht-B1 marker) both in C and SDr plants. The results indicate the complex and polygenic nature of germination.
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Rebetzke GJ, Verbyla AP, Verbyla KL, Morell MK, Cavanagh CR. Use of a large multiparent wheat mapping population in genomic dissection of coleoptile and seedling growth. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:219-30. [PMID: 24151921 DOI: 10.1111/pbi.12130] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2013] [Revised: 08/19/2013] [Accepted: 08/22/2013] [Indexed: 05/18/2023]
Abstract
Identification of alleles towards the selection for improved seedling vigour is a key objective of many wheat breeding programmes. A multiparent advanced generation intercross (MAGIC) population developed from four commercial spring wheat cultivars (cvv. Baxter, Chara, Westonia and Yitpi) and containing ca. 1000 F(2) -derived, F(6:7) RILs was assessed at two contrasting soil temperatures (12 and 20 °C) for shoot length and coleoptile characteristics length and thickness. Narrow-sense heritabilities were high for coleoptile and shoot length (h(2) = 0.68-0.70), indicating a strong genetic basis for the differences among progeny. Genotypic variation was large, and distributions of genotype means were approximately Gaussian with evidence for transgressive segregation for all traits. A number of significant QTL were identified for all early growth traits, and these were commonly repeatable across the different soil temperatures. The largest negative effects on coleoptile lengths were associated with Rht-B1b (-8.2%) and Rht-D1b (-10.9%) dwarfing genes varying in the population. Reduction in coleoptile length with either gene was particularly large at the warmer soil temperature. Other large QTL for coleoptile length were identified on chromosomes 1A, 2B, 4A, 5A and 6B, but these were relatively smaller than allelic effects at the Rht-B1 and Rht-D1 loci. A large coleoptile length effect allele (a = 5.3 mm at 12 °C) was identified on chromosome 1AS despite the relatively shorter coleoptile length of the donor Yitpi. Strong, positive genetic correlations for coleoptile and shoot lengths (r(g) = 0.85-0.90) support the co-location of QTL for these traits and suggest a common physiological basis for both. The multiparent population has enabled the identification of promising shoot and coleoptile QTL despite the potential for the confounding of large effect dwarfing gene alleles present in the commercial parents. The incidence of these alleles in commercial wheat breeding programmes should facilitate their ready implementation in selection of varieties with improved establishment and early growth.
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Affiliation(s)
- Greg J Rebetzke
- CSIRO Plant Industry, Canberra, ACT, Australia; CSIRO Food Futures Flagship, Canberra, ACT, Australia
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Hathorn A, Chapman S, Dieters M. Simulated breeding with QU-GENE graphical user interface. Methods Mol Biol 2014; 1145:131-142. [PMID: 24816665 DOI: 10.1007/978-1-4939-0446-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Comparing the efficiencies of breeding methods with field experiments is a costly, long-term process. QU-GENE is a highly flexible genetic and breeding simulation platform capable of simulating the performance of a range of different breeding strategies and for a continuum of genetic models ranging from simple to complex. In this chapter we describe some of the basic mechanics behind the QU-GENE user interface and give a simplified example of how it works.
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Affiliation(s)
- Adrian Hathorn
- CSIRO Plant Industry, 306 Carmody Rd, St. Lucia, QLD, Australia
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Yang Z, Xin D, Liu C, Jiang H, Han X, Sun Y, Qi Z, Hu G, Chen Q. Identification of QTLs for seed and pod traits in soybean and analysis for additive effects and epistatic effects of QTLs among multiple environments. Mol Genet Genomics 2013; 288:651-67. [PMID: 24022198 DOI: 10.1007/s00438-013-0779-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 08/27/2013] [Indexed: 01/10/2023]
Abstract
Soybean seed and pod traits are important yield components. Selection for high yield style in seed and pod along with agronomic traits is a goal of many soybean breeders. The intention of this study was to identify quantitative trait loci (QTL) underlying seed and pod traits in soybean among eleven environments in China. 147 recombinant inbred lines were advanced through single-seed-descent method. The population was derived from a cross between Charleston (an American high yield soybean cultivar) and DongNong594 (a Chinese high yield soybean cultivar). A total of 157 polymorphic simple sequence repeat markers were used to construct a genetic linkage map. The phenotypic data of seed and pod traits [number of one-seed pod, number of two-seed pod, number of three-seed pod, number of four-seed pod, number of (two plus three)-seed pod, number of (three plus four)-seed pod, seed weight per plant, number of pod per plant] were recorded in eleven environments. In the analysis of single environment, fourteen main effect QTLs were identified. In the conjoint analysis of multiple environments, twenty-four additive QTLs were identified, and additive QTLs by environments interactions (AE) were evaluated and analyzed at the same time among eleven environments; twenty-three pairs of epistatic QTLs were identified, and epistasis (additive by additive) by environments interactions (AAE) were also analyzed and evaluated among eleven environments. Comparing the results of identification between single environment mapping and multiple environments conjoint mapping, three main effect QTLs with positive additive values and another three main effect QTLs with negative additive values, had no interactions with all environments, supported that these QTLs could be used in molecular assistant breeding in the future. These different effect QTLs could supply a good foundation to the gene clone and molecular asisstant breeding of soybean seed and pod traits.
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Mohan A, Schillinger WF, Gill KS. Wheat seedling emergence from deep planting depths and its relationship with coleoptile length. PLoS One 2013; 8:e73314. [PMID: 24019916 PMCID: PMC3760894 DOI: 10.1371/journal.pone.0073314] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Accepted: 07/18/2013] [Indexed: 11/18/2022] Open
Abstract
Successful stand establishment is prerequisite for optimum crop yields. In some low-precipitation zones, wheat (Triticum aestivum L.) is planted as deep as 200 mm below the soil surface to reach adequate soil moisture for germination. To better understand the relationship of coleoptile length and other seed characteristics with emergence from deep planting (EDP), we evaluated 662 wheat cultivars grown around the world since the beginning of the 20(th) century. Coleoptile length of collection entries ranged from 34 to 114 mm. A specialized field EDP test showed dramatic emergence differences among cultivars ranging from 0-66% by 21 days after planting (DAP). Less than 1% of entries had any seedlings emerged by 7 DAP and 43% on day 8. A wide range of EDP within each coleoptile length class suggests the involvement of genes other than those controlling coleoptile length. Emergence was correlated with coleoptile length, but some lines with short coleoptiles ranked among the top emergers. Coleoptiles longer than 90 mm showed no advantage for EDP and may even have a negative effect. Overall, coleoptile length accounted for only 28% of the variability in emergence among entries; much lower than the 60% or greater reported in previous studies. Seed weight had little correlation with EDP. Results show that EDP is largely controlled by yet poorly understood mechanisms other than coleoptile length.
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Affiliation(s)
- Amita Mohan
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - William F. Schillinger
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
| | - Kulvinder S. Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, United States of America
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Zhang H, Cui F, Wang L, Li J, Ding A, Zhao C, Bao Y, Yang Q, Wang H. Conditional and unconditional QTL mapping of drought-tolerance-related traits of wheat seedling using two related RIL populations. J Genet 2013. [PMID: 23970077 DOI: 10.1007/s12041‐013‐0253‐z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For discovering the quantitative trait loci (QTLs) contributing to early seedling growth and drought tolerance during germination, conditional and unconditional analyses of 12 traits of wheat seedlings: coleoptile length, seedling height, longest root length, root number, seedling fresh weight, stem and leaves fresh weight, root fresh weight, seedling dry weight, stem and leaves dry weight, root dry weight, root to shoot fresh weight ratio, root-to-shoot dry weight ratio, were conducted under two water conditions using two F8:9 recombinant inbred line (RIL) populations. The results of unconditional analysis are as follows: 88 QTLs accounting for 3.33-77.01% of the phenotypic variations were detected on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5A, 5B, 5D, 6A, 6B, 6D, 7A, 7B and 7D. Among these QTLs, 19 were main-effect QTLs with a contribution rate greater than 10%. The results of the conditional QTL analysis of 12 traits under osmotic stress on normal water conditions were as follows: altogether 22 QTLs concerned with drought tolerance were detected on chromosomes 1B, 2A, 2B, 3B, 4A, 5D, 6A, 6D, 7B, and 7D. Of these QTLs, six were main-effect QTLs. These 22 QTLs were all special loci directly concerned with drought tolerance and most of them could not be detected by unconditional analysis. The finding of these QTLs has an important significance for fine-mapping technique, map-based cloning, and molecular marker-assisted selection of early seedling traits, such as growth and drought tolerance.
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Affiliation(s)
- Hong Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Taian Subcenter of National Wheat Improvement Center, College of Agronomy, Shandong Agricultural University, Taian 271018, People's Republic of China
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37
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Tuberosa R. Phenotyping for drought tolerance of crops in the genomics era. Front Physiol 2012; 3:347. [PMID: 23049510 PMCID: PMC3446691 DOI: 10.3389/fphys.2012.00347] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 08/09/2012] [Indexed: 12/11/2022] Open
Abstract
Improving crops yield under water-limited conditions is the most daunting challenge faced by breeders. To this end, accurate, relevant phenotyping plays an increasingly pivotal role for the selection of drought-resilient genotypes and, more in general, for a meaningful dissection of the quantitative genetic landscape that underscores the adaptive response of crops to drought. A major and universally recognized obstacle to a more effective translation of the results produced by drought-related studies into improved cultivars is the difficulty in properly phenotyping in a high-throughput fashion in order to identify the quantitative trait loci that govern yield and related traits across different water regimes. This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars.
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Affiliation(s)
- Roberto Tuberosa
- Department of Agroenvironmental Science and Technology, University of BolognaBologna, Italy
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38
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Zorić M, Dodig D, Kobiljski B, Quarrie S, Barnes J. Population structure in a wheat core collection and genomic loci associated with yield under contrasting environments. Genetica 2012; 140:259-75. [PMID: 22968391 DOI: 10.1007/s10709-012-9677-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 08/28/2012] [Indexed: 10/27/2022]
Abstract
A set of 96 winter wheat accessions sampled from a variety of geographic origins, including cultivars and breeding lines, were characterized with 46 genome-wide SSR loci for genetic diversity and population structure. The genetic diversity within these accessions was examined using a genetic distance-based and a model-based clustering method. The model-based analysis identified an underlying population structure comprising of four distinct sub-populations which corresponded well with distance-based groupings. Information on the population structure is taken into account in an association mapping study of grain yield from a 3-years field trial incorporating fully irrigated, rainfed and drought stress treatments. A total of 21 marker-grain yield associations (P < 0.01) were identified with nine SSR markers. Most associations were detected only in one to three environments (treatment/year combination), with an average R ( 2 ) value around 13 %. However, marker gwm484 (on chromosome 2D) was associated with yield in six environments, including irrigated, rainfed and drought stress treatments, suggesting it could be used to improve grain yield across a range of environments. Variation in grain yield at this locus was associated with earliness, early vigour, kernels per spikelet and harvest index. Microsatellite locus psp3200 (on chromosome 6D) was associated with yield in dry and hot environments, which was related to earliness, early vigour, productive tillering and total biomass per plant. Partial least squares regression, with nine environmental factors, showed that precipitation from tillering to maturity was the main environmental factor causing marker × environment associations for grain yield.
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Affiliation(s)
- Miroslav Zorić
- Institute of Field and Vegetative Crops, Maksima Gorkog 30, Novi Sad, Serbia.
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39
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Molnar SJ, Chapados JT, Satheeskumar S, Wight CP, Bancroft B, Orr W, Luckert DE, Kibite S. Comparative mapping of the oat Dw6/dw6 dwarfing locus using NILs and association with vacuolar proton ATPase subunit H. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1115-25. [PMID: 22307555 DOI: 10.1007/s00122-011-1773-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 12/15/2011] [Indexed: 05/12/2023]
Abstract
Seven pairs of oat near-isogenic lines (NILs) (Kibite in Crop Sci 41:277-278, 2001) contrasting for the Dw6 dwarfing gene were used to test for correlation between tall/dwarf phenotype and polymorphic genotype using restriction fragment length polymorphism (RFLP) and other molecular markers selected from the Kanota × Ogle (K×O) (Wight et al. in Genome 46:28-47, 2003) and Terra × Marion (De Koeyer et al. in Theor Appl Genet 108:1285-1298, 2004) recombination maps. This strategy located the Dw6/dw6 locus to a small chromosomal region on K×O linkage group (LG) KO33, near or at a putative RFLP locus aco245z. Aco245z and other tightly linked flanking markers have potential for use in marker-assisted selection (MAS), and PCR-based markers were developed from several of these. RFLP genotyping of the Dw6 NILs indicated that 13 of the 14 individual lines were homogeneously maternal or paternal for a large genomic region near Dw6/dw6, an unexpected result for NILs. The cDNA clone aco245 codes for a vacuolar proton ATPase subunit H, a potential candidate gene for Dw6. Vacuolar proton ATPase enzymes have a central role in plant growth and development and a mutation in subunit C is responsible for the det3 dwarfing mutation in Arabidopsis thaliana (Schumacher et al. in Genes Dev 13:3259-3270, 1999). Aco245 affords the potential of designing highly precise diagnostic markers for MAS for Dw6. The Dw6 NILs have potential utility to investigate the role of vacuolar proton ATPases in growth and development in plants.
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Affiliation(s)
- Stephen J Molnar
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Central Experimental Farm, 960 Carling Ave., Ottawa, ON, K1A 0C6, Canada.
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Zhang H, Ma P, Zhao Z, Zhao G, Tian B, Wang J, Wang G. Mapping QTL controlling maize deep-seeding tolerance-related traits and confirmation of a major QTL for mesocotyl length. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:223-32. [PMID: 22057118 DOI: 10.1007/s00122-011-1700-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 09/07/2011] [Indexed: 05/10/2023]
Abstract
Deep-seeding tolerant seeds can emerge from deep soil where the moisture is suitable for seed germination. Breeding deep-seeding tolerant cultivars is becoming increasingly important in arid and semi-arid regions. To dissect the quantitative trait loci (QTL) controlling deep-seeding tolerance traits, we selected a tolerant maize inbred line 3681-4 and crossed it with the elite inbred line-X178 to generate an F(2) population and the derivative F(2:3) families. A molecular linkage map composed of 179 molecular markers was constructed, and 25 QTL were detected including 10 QTL for sowing at 10 cm depth and 15 QTL for sowing at 20 cm depth. The QTL analysis results confirmed that deep-seeding tolerance was mainly caused by mesocotyl elongation and also revealed considerable overlap among QTL for different traits. To confirm a major QTL on chromosome 10 for mesocotyl length measured at 20 cm depth, we selected and self-pollinated a BC(3)F(2) plant that was heterozygous at the markers around the target QTL and homozygous at other QTL to generate a BC(3)F(3) population. We found that this QTL explained more phenotypic variance in the BC(3)F(3) population than that in the F(2) population, which laid the foundation for fine mapping and NIL (near-isogenic line) construction.
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Affiliation(s)
- Hongwei Zhang
- State Key Laboratory of Agrobiotechnology and National Center for Plant Gene Research (Beijing), China Agricultural University, Beijing, 100193, China.
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Borràs-Gelonch G, Rebetzke GJ, Richards RA, Romagosa I. Genetic control of duration of pre-anthesis phases in wheat (Triticum aestivum L.) and relationships to leaf appearance, tillering, and dry matter accumulation. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:69-89. [PMID: 21920907 PMCID: PMC3245455 DOI: 10.1093/jxb/err230] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The duration of pre-anthesis developmental phases is of interest in breeding for improved adaptation and yield potential in temperate cereals. Yet despite numerous studies on the genetic control of anthesis (flowering) time and floral initiation, little is known about the genetic control of other pre-anthesis phases. Furthermore, little is known about the effect that changes in the duration of pre-anthesis phases could have on traits related to leaf appearance and tillering, or dry matter accumulation before terminal spikelet initiation (TS). The genetic control of the leaf and spikelet initiation phase (LS; from sowing to TS), the stem elongation phase (SE; from TS to anthesis), and, within the latter, from TS to flag leaf appearance and from then to anthesis, was studied in two doubled-haploid, mapping bread wheat populations, Cranbrook × Halberd and CD87 × Katepwa, in two field experiments (ACT and NSW, Australia). The lengths of phases were estimated from measurements of both TS and the onset of stem elongation. Dry weight per plant before TS, rate of leaf appearance, tillering rate, maximum number of tillers and number of leaves, and dry weight per plant at TS were also estimated in the Cranbrook × Halberd population. More genomic regions were identified for the length of the different pre-anthesis phases than for total time to anthesis. Although overall genetic correlations between LS and SE were significant and positive, independent genetic variability between LS and SE, and several quantitative trait loci (QTLs) with different effects on both phases were found in the two populations. Several of these QTLs (which did not seem to coincide with reported major genes) could be of interest for breeding purposes since they were only significant for either LS or SE. There was no relationship between LS and the rate of leaf appearance. LS was strongly and positively correlated with dry weight at TS but only slightly negatively correlated with early vigour (dry weight before TS). Despite significant genetic correlations between LS and some tillering traits, shortening LS so as to lengthen SE without modifying total time to anthesis would not necessarily reduce tillering capacity, as QTLs for tillering traits did not coincide with those QTLs significant only for LS or SE. Therefore, the study of different pre-anthesis phases is relevant for a better understanding of genetic factors regulating developmental time and may offer new tools for fine-tuning it in breeding for both adaptability and yield potential.
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Affiliation(s)
- Gisela Borràs-Gelonch
- Department of Crop and Forest Sciences, University of Lleida, and Centre UdL-IRTA, Alcalde Rovira Roure, 191, 25198 Lleida, Catalonia, Spain.
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42
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LIU XL, CHANG XP, LI RZ, JING RL. Mapping QTLs for Seminal Root Architecture and Coleoptile Length in Wheat. ZUOWU XUEBAO 2011. [DOI: 10.3724/sp.j.1006.2011.00381] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Reynolds M, Manes Y, Izanloo A, Langridge P. Phenotyping approaches for physiological breeding and gene discovery in wheat. ANNALS OF APPLIED BIOLOGY 2009. [PMID: 0 DOI: 10.1111/j.1744-7348.2009.00351.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
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Wang J, Chapman SC, Bonnett DG, Rebetzke GJ. Simultaneous selection of major and minor genes: use of QTL to increase selection efficiency of coleoptile length of wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:65-74. [PMID: 19360392 DOI: 10.1007/s00122-009-1017-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2008] [Accepted: 03/17/2009] [Indexed: 05/27/2023]
Abstract
Plant breeders simultaneously select for qualitative traits controlled by one or a small number of major genes, as well as for polygenic traits controlled by multiple genes that may be detected as quantitative trait loci (QTL). In this study, we applied computer simulation to investigate simultaneous selection for alleles at both major and minor gene (as QTL) loci in breeding populations of two wheat parental lines, HM14BS and Sunstate. Loci targeted for selection included six major genes affecting plant height, disease resistance, and grain quality, plus 6 known and 11 "unidentified" QTL affecting coleoptile length (CL). Parental line HM14BS contributed the target alleles at two of the major gene loci, while parental line Sunstate contributed target alleles at four loci. The parents have similar plant height, but HM14BS has a longer coleoptile, a desirable attribute for deep sowing in rainfed environments. Including the wild-type allele at the major reduced-height locus Rht-D1, HM14BS was assumed to have 13 QTL for increased CL, and Sunstate four; these assumptions being derived from mapping studies and empirical data from an actual HM14BS/Sunstate population. Simulation indicated that compared to backcross populations, a single biparental F(1) cross produced the highest frequency of target genotypes (six desired alleles at major genes plus desired QTL alleles for long CL). From 1,000 simulation runs, an average of 2.4 individuals with the target genotype were present in unselected F(1)-derived doubled haploid (DH) or recombinant inbred line (RIL) populations of size 200. A selection scheme for the six major genes increased the number of target individuals to 19.1, and additional marker-assisted selection (MAS) for CL increased the number to 23.0. Phenotypic selection (PS) of CL outperformed MAS in this study due to the high heritability of CL, incompletely linked markers for known QTL, and the existence of unidentified QTL. However, a selection scheme combining MAS and PS was equally as efficient as PS and would result in net savings in production and time to delivery of long coleoptile wheats containing the six favorable alleles.
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Affiliation(s)
- Jiankang Wang
- Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement and CIMMYT China, Chinese Academy of Agricultural Sciences, Beijing, China.
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Reynolds M, Foulkes MJ, Slafer GA, Berry P, Parry MAJ, Snape JW, Angus WJ. Raising yield potential in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:1899-918. [PMID: 19363203 DOI: 10.1093/jxb/erp016] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Recent advances in crop research have the potential to accelerate genetic gains in wheat, especially if co-ordinated with a breeding perspective. For example, improving photosynthesis by exploiting natural variation in Rubisco's catalytic rate or adopting C(4) metabolism could raise the baseline for yield potential by 50% or more. However, spike fertility must also be improved to permit full utilization of photosynthetic capacity throughout the crop life cycle and this has several components. While larger radiation use efficiency will increase the total assimilates available for spike growth, thereby increasing the potential for grain number, an optimized phenological pattern will permit the maximum partitioning of the available assimilates to the spikes. Evidence for underutilized photosynthetic capacity during grain filling in elite material suggests unnecessary floret abortion. Therefore, a better understanding of its physiological and genetic basis, including possible signalling in response to photoperiod or growth-limiting resources, may permit floret abortion to be minimized for a more optimal source:sink balance. However, trade-offs in terms of the partitioning of assimilates to competing sinks during spike growth, to improve root anchorage and stem strength, may be necessary to prevent yield losses as a result of lodging. Breeding technologies that can be used to complement conventional approaches include wide crossing with members of the Triticeae tribe to broaden the wheat genepool, and physiological and molecular breeding strategically to combine complementary traits and to identify elite progeny more efficiently.
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Affiliation(s)
- Matthew Reynolds
- International Maize and Wheat Improvement Centre (CIMMYT) Int. Apdo. Postal 6-641, 06600 México, DF, Mexico.
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Reynolds M, Tuberosa R. Translational research impacting on crop productivity in drought-prone environments. CURRENT OPINION IN PLANT BIOLOGY 2008; 11:171-9. [PMID: 18329330 DOI: 10.1016/j.pbi.2008.02.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 01/31/2008] [Accepted: 02/08/2008] [Indexed: 05/19/2023]
Abstract
Conventional breeding for drought-prone environments (DPE) has been complemented by using exotic germplasm to extend crop gene pools and physiological approaches that consider water uptake (WU), water-use efficiency (WUE), and harvest index (HI) as drivers of yield. Drivers are associated with proxy genetic markers, such as carbon-isotope discrimination for WUE, canopy temperature for WU, and anthesis-silking interval for HI in maize. Molecular markers associated with relevant quantitative trait loci are being developed. WUE has also been increased through combining understanding of root-to-shoot signaling with deficit irrigation. Impacts in DPE will be accelerated by combining proven technologies with promising new strategies such as marker-assisted selection, and genetic transformation, as well as conservation agriculture that can increase WU while averting soil degradation.
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Affiliation(s)
- Matthew Reynolds
- International Maize and Wheat Improvement Center CIMMYT, Int. AP 6-641, 06600 México, DF, Mexico.
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Mapping QTLs with epistatic effects and QTL × environment interactions for plant height using a doubled haploid population in cultivated wheat. J Genet Genomics 2008; 35:119-27. [DOI: 10.1016/s1673-8527(08)60017-x] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2007] [Revised: 11/20/2007] [Accepted: 11/21/2007] [Indexed: 11/18/2022]
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