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Cai Y, Zhou X, Wang C, Liu A, Sun Z, Li S, Shi X, Yang S, Guan Y, Cheng J, Wu Y, Qin R, Sun H, Zhao C, Li J, Cui F. Quantitative trait loci detection for three tiller-related traits and the effects on wheat (Triticum aestivum L.) yields. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:87. [PMID: 38512468 DOI: 10.1007/s00122-024-04589-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/23/2024] [Indexed: 03/23/2024]
Abstract
KEY MESSAGE A total of 38 putative additive QTLs and 55 pairwise putative epistatic QTLs for tiller-related traits were reported, and the candidate genes underlying qMtn-KJ-5D, a novel major and stable QTL for maximum tiller number, were characterized. Tiller-related traits play an important role in determining the yield potential of wheat. Therefore, it is important to elucidate the genetic basis for tiller number when attempting to use genetic improvement as a tool for enhancing wheat yields. In this study, a quantitative trait locus (QTL) analysis of three tiller-related traits was performed on the recombinant inbred lines (RILs) of a mapping population, referred to as KJ-RILs, that was derived from a cross between the Kenong 9204 (KN9204) and Jing 411 (J411) lines. A total of 38 putative additive QTLs and 55 pairwise putative epistatic QTLs for spike number per plant (SNPP), maximum tiller number (MTN), and ear-bearing tiller rate (EBTR) were detected in eight different environments. Among these QTLs with additive effects, three major and stable QTLs were first documented herein. Almost all but two pairwise epistatic QTLs showed minor interaction effects accounting for no more than 3.0% of the phenotypic variance. The genetic effects of two colocated major and stable QTLs, i.e., qSnpp-KJ-5D.1 and qMtn-KJ-5D, for yield-related traits were characterized. The breeding selection effect of the beneficial allele for the two QTLs was characterized, and its genetic effects on yield-related traits were evaluated. The candidate genes underlying qMtn-KJ-5D were predicted based on multi-omics data, and TraesKN5D01HG00080 was identified as a likely candidate gene. Overall, our results will help elucidate the genetic architecture of tiller-related traits and can be used to develop novel wheat varieties with high yields.
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Affiliation(s)
- Yibiao Cai
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Xiaohan Zhou
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Chenyang Wang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Aifeng Liu
- Crop Research Institute, Shandong Academy of Agricultural Science, Jinan, 250100, People's Republic of China
| | - Zhencang Sun
- Jingbo Agrochemicals Technology Co., Ltd., Binzhou, 256500, People's Republic of China
| | - Shihui Li
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Xinyao Shi
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Shuang Yang
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Yuxiang Guan
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Jiajia Cheng
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Yongzhen Wu
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Ran Qin
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Han Sun
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China
| | - Chunhua Zhao
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China.
| | - Junming Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell SignalingHebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, People's Republic of China.
| | - Fa Cui
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, College of Agriculture, Ludong University, Yantai, 264025, People's Republic of China.
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Liu P, Yin B, Liu X, Gu L, Guo J, Yang M, Zhen W. Optimizing plant spatial competition can change phytohormone content and promote tillering, thereby improving wheat yield. FRONTIERS IN PLANT SCIENCE 2023; 14:1147711. [PMID: 36993839 PMCID: PMC10040448 DOI: 10.3389/fpls.2023.1147711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/10/2023] [Indexed: 06/19/2023]
Abstract
As an important type of interplant competition, line-spacing shrinkage and row-spacing expansion (LSRE) can increase the number of tillers and improve resource utilization efficiency in wheat. Wheat tillering is closely related to various phytohormones. However, it is unclear whether LSRE regulates phytohormones and their relationship to tillering and wheat yield. This study evaluated tillering characteristics, phytohormone content in tiller nodes at the pre-winter stage, and grain yield factors for the winter wheat variety Malan1. We used a two-factor randomized block trial design with two sowing spacings of 15 cm (15RS, conventional treatment) and 7.5 cm (7.5RS, LSRE treatment) at the same density and three sowing-date groups (SD1, SD2, and SD3). LSRE significantly promoted wheat tillering and biomass at the pre-winter stage (average increases of 14.5% and 20.9% in the three sowing-date groups, respectively) and shortened the accumulated temperature required for a single tiller. Changes in the levels of phytohormones, including decreased gibberellin and indole acetic acid and increased zeatin riboside and strigolactones, were determined by high-performance liquid chromatography and were shown to be responsible for the tillering process under LSRE treatment in winter wheat. LSRE treatment can improve crop yield by increasing the number of spikes per unit area and grain weight. Our results clarified the changes in tillering and phytohormones content of winter wheat under LSRE treatment and their correlation with grain yield. This study also provides insights into the physiological mechanisms of alleviating inter-plant competition to improve crop yield.
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Affiliation(s)
- Pan Liu
- College of Agronomy, Hebei Agricultural University, Baoding, China
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
- Key Laboratory of North China Water-saving Agriculture, Ministry of Agriculture and Rural Affairs, Baoding, China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, China
| | - Baozhong Yin
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Xuejing Liu
- College of Agronomy, Hebei Agricultural University, Baoding, China
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
- Key Laboratory of North China Water-saving Agriculture, Ministry of Agriculture and Rural Affairs, Baoding, China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, China
- College of Clinical Medicine, North China University of Technology, Tangshan, China
| | - Limin Gu
- College of Agronomy, Hebei Agricultural University, Baoding, China
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
- Key Laboratory of North China Water-saving Agriculture, Ministry of Agriculture and Rural Affairs, Baoding, China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, China
| | - Jinkao Guo
- College of Agronomy, Hebei Agricultural University, Baoding, China
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
- Key Laboratory of North China Water-saving Agriculture, Ministry of Agriculture and Rural Affairs, Baoding, China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, China
- Wheat Research Center, Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuan, China
| | - Mingming Yang
- College of Agronomy, Northwest A&F University, Xianyang, China
| | - Wenchao Zhen
- College of Agronomy, Hebei Agricultural University, Baoding, China
- State Key Laboratory of North China Crop Improvement and Regulation, Baoding, China
- Key Laboratory of North China Water-saving Agriculture, Ministry of Agriculture and Rural Affairs, Baoding, China
- Key Laboratory of Crop Growth Regulation of Hebei Province, Baoding, China
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Dong C, Zhang L, Zhang Q, Yang Y, Li D, Xie Z, Cui G, Chen Y, Wu L, Li Z, Liu G, Zhang X, Liu C, Chu J, Zhao G, Xia C, Jia J, Sun J, Kong X, Liu X. Tiller Number1 encodes an ankyrin repeat protein that controls tillering in bread wheat. Nat Commun 2023; 14:836. [PMID: 36788238 PMCID: PMC9929037 DOI: 10.1038/s41467-023-36271-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Wheat (Triticum aestivum L.) is a major staple food for more than one-third of the world's population. Tiller number is an important agronomic trait in wheat, but only few related genes have been cloned. Here, we isolate a wheat mutant, tiller number1 (tn1), with much fewer tillers. We clone the TN1 gene via map-based cloning: TN1 encodes an ankyrin repeat protein with a transmembrane domain (ANK-TM). We show that a single amino acid substitution in the third conserved ankyrin repeat domain causes the decreased tiller number of tn1 mutant plants. Resequencing and haplotype analysis indicate that TN1 is conserved in wheat landraces and modern cultivars. Further, we reveal that the expression level of the abscisic acid (ABA) biosynthetic gene TaNCED3 and ABA content are significantly increased in the shoot base and tiller bud of the tn1 mutants; TN1 but not tn1 could inhibit the binding of TaPYL to TaPP2C via direct interaction with TaPYL. Taken together, we clone a key wheat tiller number regulatory gene TN1, which promotes tiller bud outgrowth probably through inhibiting ABA biosynthesis and signaling.
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Affiliation(s)
- Chunhao Dong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yuxin Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhencheng Xie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guoqing Cui
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yaoyu Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lifen Wu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhan Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guoxiang Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xueying Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cuimei Liu
- National Centre for Plant Gene Research (Beijing), Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangyao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chuan Xia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jizeng Jia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiaqiang Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Genome-Wide Association Analysis for Hybrid Breeding in Wheat. Int J Mol Sci 2022; 23:ijms232315321. [PMID: 36499647 PMCID: PMC9740285 DOI: 10.3390/ijms232315321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/24/2022] [Accepted: 11/27/2022] [Indexed: 12/12/2022] Open
Abstract
Disclosure of markers that are significantly associated with plant traits can help develop new varieties with desirable properties. This study determined the genome-wide associations based on DArTseq markers for six agronomic traits assessed in eight environments for wheat. Moreover, the association study for heterosis and analysis of the effects of markers grouped by linkage disequilibrium were performed based on mean values over all experiments. All results were validated using data from post-registration trials. GWAS revealed 1273 single nucleotide polymorphisms with biologically significant effects. Most polymorphisms were predicted to be modifiers of protein translation, with only two having a more pronounced effect. Markers significantly associated with the considered set of features were clustered within chromosomes based on linkage disequilibrium in 327 LD blocks. A GWAS for heterosis revealed 1261 markers with significant effects.
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Wu J, Xu D, Fu L, Wu L, Hao W, Li J, Dong Y, Wang F, Wu Y, He Z, Si H, Ma C, Xia X. Fine mapping of a stripe rust resistance gene YrZM175 in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2665-2673. [PMID: 35986759 DOI: 10.1007/s00122-022-04140-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/23/2022] [Indexed: 05/26/2023]
Abstract
A stripe rust resistance gene YrZM175 in Chinese wheat cultivar Zhongmai 175 was mapped to a genomic interval of 636.4 kb on chromosome arm 2AL, and a candidate gene was predicted. Stripe rust, caused by Puccinia striiformis f. sp. tritici (PST), is a worldwide wheat disease that causes large losses in production. Fine mapping and cloning of resistance genes are important for accurate marker-assisted breeding. Here, we report the fine mapping and candidate gene analysis of stripe rust resistance gene YrZM175 in a Chinese wheat cultivar Zhongmai 175. Fifteen F1, 7,325 F2 plants and 117 F2:3 lines derived from cross Avocet S/Zhongmai 175 were inoculated with PST race CYR32 at the seedling stage in a greenhouse, and F2:3 lines were also evaluated for stripe rust reaction in the field using mixed PST races. Bulked segregant RNA-seq (BSR-seq) analyses revealed 13 SNPs in the region 762.50-768.52 Mb on chromosome arm 2AL. By genome mining, we identified SNPs and InDels between the parents and contrasting bulks and mapped YrZM175 to a 0.72-cM, 636.4-kb interval spanned by YrZM175-InD1 and YrZM175-InD2 (763,452,916-764,089,317 bp) including two putative disease resistance genes based on IWGSC RefSeq v1.0. Collinearity analysis indicated similar target genomic intervals in Chinese Spring, Aegilops tauschii (2D: 647.7-650.5 Mb), Triticum urartu (2A: 750.7-752.3 Mb), Triticum dicoccoides (2A: 771.0-774.5 Mb), Triticum turgidum (2B: 784.7-788.2 Mb), and Triticum aestivum cv. Aikang 58 (2A: 776.3-778.9 Mb) and Jagger (2A: 789.3-791.7 Mb). Through collinearity analysis, sequence alignments of resistant and susceptible parents and gene expression level analysis, we predicted TRITD2Bv1G264480 from Triticum turgidum to be a candidate gene for map-based cloning of YrZM175. A gene-specific marker for TRITD2Bv1G264480 co-segregated with the resistance gene. Molecular marker analysis and stripe rust response data revealed that YrZM175 was different from genes Yr1, Yr17, Yr32, and YrJ22 located on chromosome 2A. Fine mapping of YrZM175 lays a solid foundation for functional gene analysis and marker-assisted selection for improved stripe rust resistance in wheat.
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Affiliation(s)
- Jingchun Wu
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Dengan Xu
- College of Agronomy, Qingdao Agricultural University, 700 Changcheng Road, Qingdao, 266109, Shandong province, China
| | - Luping Fu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Key Laboratory of Crop Cultivation and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, Jiangsu province, China
- Jiangsu Co-Innovation Centre for Modern Production Technology of Grain Crops, Yangzhou University, Jiangsu province, Yangzhou, 225009, China
| | - Ling Wu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, 4 Shizishan Road, Chengdu, 610011, Sichuan province, China
| | - Weihao Hao
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China
| | - Jihu Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong province, China
| | - Yan Dong
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Fengju Wang
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yuying Wu
- College of Agronomy, Henan Agricultural University, 63 Agricultural Road, Zhengzhou, 450002, Henan province, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Centre (CIMMYT) China Office c/o, CAAS, Beijing, 100081, China
| | - Hongqi Si
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China.
| | - Xianchun Xia
- College of Agronomy, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui province, China.
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
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Zhao Z, Liu Z, Zhou Y, Wang J, Zhang Y, Yu X, Wu R, Guo C, Qin A, Bawa G, Sun X. Creation of cotton mutant library based on linear electron accelerator radiation mutation. Biochem Biophys Rep 2022; 30:101228. [PMID: 35243011 PMCID: PMC8867050 DOI: 10.1016/j.bbrep.2022.101228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/21/2022] Open
Abstract
Cotton (Gossypium spp.) is one of the most important cash crops worldwide. At present, new cotton varieties are mainly produced through conventional cross breeding, which is limited by available germplasm. Although the genome of cotton has been fully sequenced, research on the function of specific genes lags behind due to the lack of sufficient genetic material. Therefore, it is very important to create a cotton mutant library to create new, higher-quality varieties and identify genes associated with the regulation of key traits. Traditional mutagenic strategies, such as physical, chemical, and site-directed mutagenesis, are relatively costly, inefficient, and difficult to perform. In this study, we used a radiation mutation method based on linear electron acceleration to mutate cotton variety 'TM-1', for which a whole-genome sequence has previously been performed, to create a high throughput cotton mutant library. Abundant phenotypic variation was observed in the progeny population for three consecutive generations, including cotton fiber color variation, plant dwarfing, significant improvement of yield traits, and increased sensitivity to Verticillium wilt. These results show that radiation mutagenesis is an effective and feasible method to create plant mutant libraries.
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Affiliation(s)
| | | | - Yaping Zhou
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Jiajing Wang
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Yixin Zhang
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Xiaole Yu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Rui Wu
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Chenxi Guo
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Aizhi Qin
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - George Bawa
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
| | - Xuwu Sun
- State Key Laboratory of Cotton Biology, State Key Laboratory of Crop Stress Adaptation and Improvement, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, 85 Minglun Street, Kaifeng, 475001, China
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Hindhaugh R, Bosch M, Donnison IS. Mechanical stimulation in wheat triggers age- and dose-dependent alterations in growth, development and grain characteristics. ANNALS OF BOTANY 2021; 128:589-603. [PMID: 34091667 PMCID: PMC8422892 DOI: 10.1093/aob/mcab070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/03/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND AND AIMS Wheat crops are exposed to a range of mechanical stimulations in their natural environment, yet we know very little about their response to such conditions. The aim of this study was to better understand the effect of mechanical stimulation on wheat growth and development, stem mechanical properties and grain measures. We focused on the following questions: (1) Does plant age affect the response to mechanical stimulation? (2) Is there a minimum threshold for the perception of mechanical stimuli? (3) Is the effect of manual brushing different to natural wind stimulation? METHODS For age- and dose-response experiments, wheat plants were grown under controlled glasshouse conditions with brushing treatments applied using a purpose-built rig. The results of the controlled experiments are compared with those from an outside experiment where wheat plants were exposed to natural wind, with or without additional brushing. Detailed phenotypic measurements were conducted and treatment effects on grain characteristics were determined using micro-computed tomography imaging. KEY RESULTS Two-week-old wheat plants were particularly sensitive to mechanical stimulation by controlled brushing treatments. Amongst others, plants exhibited a large reduction in height and grain yield, and an increase in tillers, above-ground biomass and stiffness of stem segments. Plants responded significantly to doses as small as one daily brushstroke. Outdoor experiments by and large confirmed results from controlled environment experiments. CONCLUSIONS The morphological and developmental response to mechanical brushing treatment, in relation to vegetative above-ground biomass and grain yield, is dependent on plant age as well as the dose of the treatments. This study shows that mechanical stimulation of wheat impacts on a multitude of agriculturally relevant traits and provides a much needed advancement of our understanding of wheat thigmomorphogenesis and the potential applications of mechanical conditioning to control relevant traits.
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Affiliation(s)
- Rebecca Hindhaugh
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, UK
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, UK
- For correspondence. E-mail or
| | - Iain S Donnison
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Plas Gogerddan, Aberystwyth, UK
- For correspondence. E-mail or
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Fu L, Wang Q, Li L, Lang T, Guo J, Wang S, Sun Z, Han S, Huang B, Dong W, Zhang X, Du P. Physical mapping of repetitive oligonucleotides facilitates the establishment of a genome map-based karyotype to identify chromosomal variations in peanut. BMC PLANT BIOLOGY 2021; 21:107. [PMID: 33610178 PMCID: PMC7896385 DOI: 10.1186/s12870-021-02875-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Chromosomal variants play important roles in crop breeding and genetic research. The development of single-stranded oligonucleotide (oligo) probes simplifies the process of fluorescence in situ hybridization (FISH) and facilitates chromosomal identification in many species. Genome sequencing provides rich resources for the development of oligo probes. However, little progress has been made in peanut due to the lack of efficient chromosomal markers. Until now, the identification of chromosomal variants in peanut has remained a challenge. RESULTS A total of 114 new oligo probes were developed based on the genome-wide tandem repeats (TRs) identified from the reference sequences of the peanut variety Tifrunner (AABB, 2n = 4x = 40) and the diploid species Arachis ipaensis (BB, 2n = 2x = 20). These oligo probes were classified into 28 types based on their positions and overlapping signals in chromosomes. For each type, a representative oligo was selected and modified with green fluorescein 6-carboxyfluorescein (FAM) or red fluorescein 6-carboxytetramethylrhodamine (TAMRA). Two cocktails, Multiplex #3 and Multiplex #4, were developed by pooling the fluorophore conjugated probes. Multiplex #3 included FAM-modified oligo TIF-439, oligo TIF-185-1, oligo TIF-134-3 and oligo TIF-165. Multiplex #4 included TAMRA-modified oligo Ipa-1162, oligo Ipa-1137, oligo DP-1 and oligo DP-5. Each cocktail enabled the establishment of a genome map-based karyotype after sequential FISH/genomic in situ hybridization (GISH) and in silico mapping. Furthermore, we identified 14 chromosomal variants of the peanut induced by radiation exposure. A total of 28 representative probes were further chromosomally mapped onto the new karyotype. Among the probes, eight were mapped in the secondary constrictions, intercalary and terminal regions; four were B genome-specific; one was chromosome-specific; and the remaining 15 were extensively mapped in the pericentric regions of the chromosomes. CONCLUSIONS The development of new oligo probes provides an effective set of tools which can be used to distinguish the various chromosomes of the peanut. Physical mapping by FISH reveals the genomic organization of repetitive oligos in peanut chromosomes. A genome map-based karyotype was established and used for the identification of chromosome variations in peanut following comparisons with their reference sequence positions.
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Affiliation(s)
- Liuyang Fu
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Qian Wang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Lina Li
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Tao Lang
- Institute of Biotechnology and Nuclear Technology, Sichuan Academy of Agricultural Sciences, Chengdu, 610061, Sichuan, China
| | - Junjia Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Siyu Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, 450001, Henan, China
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Ziqi Sun
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Suoyi Han
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Bingyan Huang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Wenzhao Dong
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China
| | - Xinyou Zhang
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China.
| | - Pei Du
- Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, Henan, China.
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10
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Zhao D, Yang L, Xu K, Cao S, Tian Y, Yan J, He Z, Xia X, Song X, Zhang Y. Identification and validation of genetic loci for tiller angle in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3037-3047. [PMID: 32685984 DOI: 10.1007/s00122-020-03653-6] [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: 03/20/2020] [Accepted: 07/08/2020] [Indexed: 05/26/2023]
Abstract
KEY MESSAGE Two major QTL for tiller angle were identified on chromosomes 1AL and 5DL, and TaTAC-D1 might be the candidate gene for QTA.caas-5DL. An ideal plant architecture is important for achieving high grain yield in crops. Tiller angle (TA) is an important factor influencing yield. In the present study, 266 recombinant inbred lines (RILs) derived from a cross between Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895) was used to map TA by extreme pool-genotyping and inclusive composite interval mapping (ICIM). Two quantitative trait loci (QTL) on chromosomes 1AL and 5DL were identified with reduced tiller angle alleles contributed by ZM895. QTA.caas-1AL was detected in six environments, explaining 5.4-11.2% of the phenotypic variances. The major stable QTL, QTA.caas-5DL, was identified in all eight environments, accounting for 13.8-24.8% of the phenotypic variances. The two QTL were further validated using BC1F4 populations derived from backcrosses ZM871/ZM895//ZM871 (121 lines) and ZM871/ZM895//ZM895 (175 lines). Gene TraesCS5D02G322600, located in the 5DL QTL and designated TaTAC-D1, had a SNP in the third exon with 'A' and 'G' in ZM871 and ZM895, respectively, resulting in a Thr169Ala amino acid change. A KASP marker based on this SNP was validated in two sets of germplasm, providing further evidence for the significant effects of TaTAC-D1 on TA. Thus extreme pool-genotyping can be employed to detect QTL for plant architecture traits and KASP markers tightly linked with the QTL can be used in wheat breeding programs targeting improved plant architecture.
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Affiliation(s)
- Dehui Zhao
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi province, China
| | - Li Yang
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Kaijie Xu
- Institute of Cotton Research, CAAS, 38 Huanghe Dadao, Anyang, 455000, Henan province, China
| | - Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yubing Tian
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Jun Yan
- Institute of Cotton Research, CAAS, 38 Huanghe Dadao, Anyang, 455000, Henan province, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- CIMMYT-China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xiyue Song
- College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi province, China.
| | - Yong Zhang
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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11
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Daba SD, Liu X, Aryal U, Mohammadi M. A proteomic analysis of grain yield-related traits in wheat. AOB PLANTS 2020; 12:plaa042. [PMID: 33133478 PMCID: PMC7586745 DOI: 10.1093/aobpla/plaa042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/19/2020] [Indexed: 05/13/2023]
Abstract
Grain yield, which is mainly contributed by tillering capacity as well as kernel number and weight, is the most important trait to plant breeders and agronomists. Label-free quantitative proteomics was used to analyse yield-contributing organs in wheat. These were leaf sample, tiller initiation, spike initiation, ovary and three successive kernel development stages at 5, 10 and 15 days after anthesis (DAA). We identified 3182 proteins across all samples. The largest number was obtained for spike initiation (1673), while the smallest was kernel sample at 15 DAA (709). Of the 3182 proteins, 296 of them were common to all seven organs. Organ-specific proteins ranged from 148 in ovary to 561 in spike initiation. When relative protein abundances were compared to that of leaf sample, 347 and 519 proteins were identified as differentially abundant in tiller initiation and spike initiation, respectively. When compared with ovary, 81, 35 and 96 proteins were identified as differentially abundant in kernels sampled at 5, 10 and 15 DAA, respectively. Our study indicated that two Argonaute proteins were solely expressed in spike initiation. Of the four expansin proteins detected, three of them were mainly expressed during the first 10 days of kernel development after anthesis. We also detected cell wall invertases and sucrose and starch synthases mainly during the kernel development period. The manipulation of these proteins could lead to increases in tillers, kernels per spike or final grain weight, and is worth exploring in future studies.
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Affiliation(s)
- Sintayehu D Daba
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - Xiaoqin Liu
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
| | - Uma Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA
| | - Mohsen Mohammadi
- Department of Agronomy, Purdue University, West Lafayette, IN, USA
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12
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Abid MA, Wang P, Zhu T, Liang C, Meng Z, Malik W, Guo S, Zhang R. Construction of Gossypium barbadense Mutant Library Provides Genetic Resources for Cotton Germplasm Improvement. Int J Mol Sci 2020; 21:ijms21186505. [PMID: 32899571 PMCID: PMC7554686 DOI: 10.3390/ijms21186505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 08/28/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022] Open
Abstract
Allotetraploid cotton (Gossypium hirsutum and Gossypium barbadense) are cultivated worldwide for its white fiber. For centuries, conventional breeding approaches increase cotton yield at the cost of extensive erosion of natural genetic variability. Sea Island cotton (G. barbadense) is known for its superior fiber quality, but show poor adaptability as compared to Upland cotton. Here, in this study, we use ethylmethanesulfonate (EMS) as a mutagenic agent to induce genome-wide point mutations to improve the current germplasm resources of Sea Island cotton and develop diverse breeding lines with improved adaptability and excellent economic traits. We determined the optimal EMS experimental procedure suitable for construction of cotton mutant library. At M6 generation, mutant library comprised of lines with distinguished phenotypes of the plant architecture, leaf, flower, boll, and fiber. Genome-wide analysis of SNP distribution and density in yellow leaf mutant reflected the better quality of mutant library. Reduced photosynthetic efficiency and transmission electron microscopy of yellow leaf mutants revealed the effect of induced mutations at physiological and cellular level. Our mutant collection will serve as the valuable resource for basic research on cotton functional genomics, as well as cotton breeding.
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Affiliation(s)
- Muhammad Ali Abid
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.A.A.); (P.W.); (T.Z.); (C.L.); (Z.M.); (S.G.)
| | - Peilin Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.A.A.); (P.W.); (T.Z.); (C.L.); (Z.M.); (S.G.)
| | - Tao Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.A.A.); (P.W.); (T.Z.); (C.L.); (Z.M.); (S.G.)
| | - Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.A.A.); (P.W.); (T.Z.); (C.L.); (Z.M.); (S.G.)
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.A.A.); (P.W.); (T.Z.); (C.L.); (Z.M.); (S.G.)
| | - Waqas Malik
- Genomics Lab, Department of Plant Breeding and Genetics, Bahauddin Zakariya University, Multan 60000, Pakistan;
| | - Sandui Guo
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.A.A.); (P.W.); (T.Z.); (C.L.); (Z.M.); (S.G.)
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (M.A.A.); (P.W.); (T.Z.); (C.L.); (Z.M.); (S.G.)
- Correspondence:
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13
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Liu J, Tang H, Qu X, Liu H, Li C, Tu Y, Li S, Habib A, Mu Y, Dai S, Deng M, Jiang Q, Liu Y, Chen G, Wang J, Chen G, Li W, Jiang Y, Wei Y, Lan X, Zheng Y, Ma J. A novel, major, and validated QTL for the effective tiller number located on chromosome arm 1BL in bread wheat. PLANT MOLECULAR BIOLOGY 2020; 104:173-185. [PMID: 32734417 DOI: 10.1007/s11103-020-01035-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/09/2020] [Indexed: 05/24/2023]
Abstract
A novel and major QTL for the effective tiller number was identified on chromosomal arm 1BL and validated in two genetic backgrounds The effective tiller number (ETN) substantially influences plant architecture and the wheat yield improvement. In this study, we constructed a genetic map of the 2SY (20828/SY95-71) recombinant inbred line population based on the Wheat 55K array as well as the simple sequence repeat (SSR) and Kompetitive Allele Specific PCR (KASP) markers. A comparison between the genetic and physical maps indicated the marker positions were consistent in the two maps. Additionally, we identified seven tillering-related quantitative trait locus (QTLs), including Qetn-sau-1B.1, which is a major QTL localized to a 6.17-cM interval flanked by markers AX-89635557 and AX-111544678 on chromosome 1BL. The Qetn-sau-1B.1 QTL was detected in eight environments and explained 12.12-55.71% of the phenotypic variance. Three genes associated with the ETN were detected in the physical interval of Qetn-sau-1B.1. We used a tightly linked KASP marker, KASP-AX-110129912, to further validate this QTL in two other populations with different genetic backgrounds. The results indicated that Qetn-sau-1B.1 significantly increased the ETN by up to 23.5%. The results of this study will be useful for the precise mapping and cloning of Qetn-sau-1B.1.
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Affiliation(s)
- Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shuiqing Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, 9208, Bangladesh
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shoufeng Dai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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14
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Bilgrami SS, Ramandi HD, Shariati V, Razavi K, Tavakol E, Fakheri BA, Mahdi Nezhad N, Ghaderian M. Detection of genomic regions associated with tiller number in Iranian bread wheat under different water regimes using genome-wide association study. Sci Rep 2020; 10:14034. [PMID: 32820220 PMCID: PMC7441066 DOI: 10.1038/s41598-020-69442-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 07/09/2020] [Indexed: 11/09/2022] Open
Abstract
Two of the important traits for wheat yield are tiller and fertile tiller number, both of which have been thought to increase cereal yield in favorable and unfavorable environments. A total of 6,349 single nucleotide polymorphism (SNP) markers from the 15 K wheat Infinium array were employed for genome-wide association study (GWAS) of tillering number traits, generating a physical distance of 14,041.6 Mb based on the IWGSC wheat genome sequence. GWAS analysis using Fixed and random model Circulating Probability Unification (FarmCPU) identified a total of 47 significant marker-trait associations (MTAs) for total tiller number (TTN) and fertile tiller number (FTN) in Iranian bread wheat under different water regimes. After applying a 5% false discovery rate (FDR) threshold, a total of 13 and 11 MTAs distributed on 10 chromosomes were found to be significantly associated with TTN and FTN, respectively. Linked single nucleotide polymorphisms for IWB39005 (2A) and IWB44377 (7A) were highly significantly associated (FDR < 0.01) with TTN and FTN traits. Moreover, to validate GWAS results, meta-analysis was performed and 30 meta-QTL regions were identified on 11 chromosomes. The integration of GWAS and meta-QTLs revealed that tillering trait in wheat is a complex trait which is conditioned by the combined effects of minor changes in multiple genes. The information provided by this study can enrich the currently available candidate genes and genetic resources pools, offering evidence for subsequent analysis of genetic adaptation of wheat to different climatic conditions of Iran and other countries.
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Affiliation(s)
- Sayedeh Saba Bilgrami
- Department of Plant Molecular Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.,College of Agronomy and Biotechnology, Southwest University, Beibei, 400715, Chongqing, China
| | - Hadi Darzi Ramandi
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Vahid Shariati
- Department of Plant Molecular Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Khadijeh Razavi
- Department of Plant Molecular Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| | - Elahe Tavakol
- Department of Plant Production and Genetics, Shiraz University, Shiraz, Iran
| | - Barat Ali Fakheri
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Nafiseh Mahdi Nezhad
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Mostafa Ghaderian
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Isfahan University of Technology, Isfahan, Iran
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15
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Lian X, Liu Y, Guo H, Fan Y, Wu J, Guo H, Jiao C, Tang Z, Zhang L, Fan Y, Gou Z, Zhang C, Li T, Zeng F. Ethyl methanesulfonate mutant library construction in Gossypium hirsutum L. for allotetraploid functional genomics and germplasm innovation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:858-868. [PMID: 32239588 DOI: 10.1111/tpj.14755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 03/13/2020] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
As the gene pool is exposed to both strain on land resources and a lack of diversity in elite allotetraploid cotton, the acquisition and identification of novel alleles has taken on epic importance in facilitating cotton genetic improvement and functional genomics research. Ethyl methanesulfonate (EMS) is an excellent mutagen that induces genome-wide efficient mutations to activate the mutagenic potential of plants with many advantages. The present study established, determined and verified the experimental procedure suitable for EMS-based mutant library construction as the general reference guide in allotetraploid upland cotton. This optimized method and procedure are efficient, and abundant EMS mutant libraries (approximately 12 000) in allotetraploid cotton were successfully obtained. More than 20 mutant phenotypes were observed and screened, including phenotypes of the leaf, flower, fruit, fiber and plant architecture. Through the plants mutant library, high-throughput and high-resolution melting technology-based variation evaluation detected the EMS-induced site mutation. Additionally, based on overall genome-wide mutation analyses by re-sequencing and mutant library assessment, the examination results demonstrated the ideal quality of the cotton EMS-treated mutant library constructed in this study with appropriate high mutation density and saturated genome. What is more, the collection is composed of a broad repertoire of mutants, which is the valuable resource for basic genetic research and functional genomics underlying complex allotetraploid traits, as well as cotton breeding.
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Affiliation(s)
- Xin Lian
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Yan Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Huihui Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Yijie Fan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Jianfei Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Haixia Guo
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Chengzhi Jiao
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Zhengmin Tang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Li Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Yupeng Fan
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Zhongyuan Gou
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Changyu Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Tongtong Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
| | - Fanchang Zeng
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, China
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16
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Wang N, Xie Y, Li Y, Wu S, Li S, Guo Y, Wang C. High-Resolution Mapping of the Novel Early Leaf Senescence Gene Els2 in Common Wheat. PLANTS 2020; 9:plants9060698. [PMID: 32486195 PMCID: PMC7355531 DOI: 10.3390/plants9060698] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 11/16/2022]
Abstract
Early leaf senescence negatively impacts the grain yield in wheat (Triticum aestivum L.). Induced mutants provide an important resource for mapping and cloning of genes for early leaf senescence. In our previous study, Els2, a single incomplete dominance gene, that caused early leaf senescence phenotype in the wheat mutant LF2099, had been mapped on the long arm of chromosome 2B. The objective of this study was to develop molecular markers tightly linked to the Els2 gene and construct a high-resolution map surrounding the Els2 gene. Three tightly linked single-nucleotide polymorphism (SNP) markers were obtained from the Illumina Wheat 90K iSelect SNP genotyping array and converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers. To saturate the Els2 region, the Axiom® Wheat 660K SNP array was used to screen bulked extreme phenotype DNA pools, and 9 KASP markers were developed. For fine mapping of the Els2 gene, these KASP markers and previously identified polymorphic markers were analyzed in a large F2 population of the LF2099 × Chinese Spring cross. The Els2 gene was located in a 0.24-cM genetic region flanked by the KASP markers AX-111643885 and AX-111128667, which corresponded to a physical interval of 1.61 Mb in the Chinese Spring chromosome 2BL containing 27 predicted genes with high confidence. The study laid a foundation for a map-based clone of the Els2 gene controlling the mutation phenotype and revealing the molecular regulatory mechanism of wheat leaf senescence.
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An J, Niu H, Ni Y, Jiang Y, Zheng Y, He R, Li J, Jiao Z, Zhang J, Li H, Li Q, Niu J. The miRNA-mRNA Networks Involving Abnormal Energy and Hormone Metabolisms Restrict Tillering in a Wheat Mutant dmc. Int J Mol Sci 2019; 20:E4586. [PMID: 31533225 PMCID: PMC6770018 DOI: 10.3390/ijms20184586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/14/2019] [Accepted: 09/15/2019] [Indexed: 02/07/2023] Open
Abstract
Tillers not only determine plant architecture but also influence crop yield. To explore the miRNA regulatory network restraining tiller development in a dwarf-monoculm wheat mutant (dmc) derived from Guomai 301 (wild type, WT), we employed miRNome and transcriptome integrative analysis, real-time qRT-PCR, histochemistry, and determinations of the key metabolites and photosynthesis parameters. A total of 91 differentially expressed miRNAs (DEMs) were identified between dmc and WT. Among them, 40 key DEMs targeted 45 differentially expressed genes (DEGs) including the key DEGs encode growth-regulating factors (GRF), auxin response factors (ARF), and other proteins involved in the metabolisms of hormones and carbohydrates, etc. Compared with WT, both the chlorophyll contents and the photosynthesis rate were lower in dmc. The contents of glucose, sucrose, fructose, and maltose were lower in dmc. The contents of auxin (IAA) and zeatin (ZA) were significantly lower, but gibberellin (GA) was significantly higher in the tiller tissues of dmc. This research demonstrated that the DEMs regulating hormone and carbohydrate metabolisms were important causes for dmc to not tiller. A primary miRNA-mRNA regulatory model for dmc tillering was established. The lower photosynthesis rate, insufficient energy, and abnormal hormone metabolisms restrict tillering in dmc.
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Affiliation(s)
- Junhang An
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Hao Niu
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yongjing Ni
- Shangqiu Academy of Agricultural and Forestry Sciences, Shangqiu 476000, China.
| | - Yumei Jiang
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Yongxing Zheng
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Ruishi He
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Junchang Li
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Zhixin Jiao
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Jing Zhang
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Huijuan Li
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Qiaoyun Li
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
| | - Jishan Niu
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
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Li J, Jiao Z, He R, Sun Y, Xu Q, Zhang J, Jiang Y, Li Q, Niu J. Gene Expression Profiles and microRNA Regulation Networks in Tiller Primordia, Stem Tips, and Young Spikes of Wheat Guomai 301. Genes (Basel) 2019; 10:genes10090686. [PMID: 31500166 PMCID: PMC6770858 DOI: 10.3390/genes10090686] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/07/2019] [Accepted: 08/22/2019] [Indexed: 01/26/2023] Open
Abstract
Tillering and spike differentiation are two key events for wheat (Triticum aestivum L.). A study on the transcriptomes and microRNA group profiles of wheat at the two key developmental stages will bring insight into the molecular regulation mechanisms. Guomai 301 is a representative excellent new high yield wheat cultivar in the Henan province in China. The transcriptomes and microRNA (miRNA) groups of tiller primordia (TPs), stem tips (STs), and young spikes (YSs) in Guomai 301 were compared to each other. A total of 1741 tillering specifically expressed and 281 early spikes differentiating specifically expressed differentially expressed genes (DEGs) were identified. Six major expression profile clusters of tissue-specific DEGs for the three tissues were classified by gene co-expression analysis using K-means cluster. The ribosome (ko03010), photosynthesis-antenna proteins (ko00196), and plant hormone signal transduction (ko04075) were the main metabolic pathways in TPs, STs, and YSs, respectively. Similarly, 67 TP specifically expressed and 19 YS specifically expressed differentially expressed miRNAs were identified, 65 of them were novel. The roles of 3 well known miRNAs, tae-miR156, tae-miR164, and tae-miR167a, in post-transcriptional regulation were similar to that of other researches. There were 651 significant negative miRNA-mRNA interaction pairs in TPs and YSs, involving 63 differentially expressed miRNAs (fold change > 4) and 416 differentially expressed mRNAs. Among them 12 key known miRNAs and 16 novel miRNAs were further analyzed, and miRNA-mRNA regulatory networks during tillering and early spike differentiating were established.
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Affiliation(s)
- Junchang Li
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Zhixin Jiao
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Ruishi He
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Yulong Sun
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Qiaoqiao Xu
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Jing Zhang
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Yumei Jiang
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Qiaoyun Li
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China
| | - Jishan Niu
- National Centre of Engineering and Technological Research for Wheat / Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, China.
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Wang Z, Shi H, Yu S, Zhou W, Li J, Liu S, Deng M, Ma J, Wei Y, Zheng Y, Liu Y. Comprehensive transcriptomics, proteomics, and metabolomics analyses of the mechanisms regulating tiller production in low-tillering wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2181-2193. [PMID: 31020386 DOI: 10.1007/s00122-019-03345-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
Tiller development in low-tillering wheat is related to several differentially expressed genes, proteins, and metabolites, as determined by an integrated omics approach combining transcriptome analysis, iTRAQ, and HPLC-MS on multiple NILs. Tillering is an important aspect of plant morphology that affects spike number, thereby contributing to the final crop yield. However, the mechanisms inhibiting tiller production in low-tillering wheat are poorly characterized. To investigate this aspect of wheat biology, two pairs of near-isogenic lines were developed, and an integrated omics approach combining transcriptome analysis, isobaric tags for relative and absolute quantification, and high-performance liquid chromatography-mass spectrometry were used to compare the free-tillering and low-tillering caused by an allele at Qltn.sicau-2D in wheat samples. Overall, 474 genes, 166 proteins, and 28 metabolites were identified as tillering-associated differentially expressed genes, proteins, and metabolites (DEGs, DEPs, and DEMs, respectively). Functional analysis indicated that the abundance of DEGs/DEPs/DEMs was related to lignin and cellulose metabolism, cell division, cell cycle processes, and glycerophospholipid metabolism; three transcription factor families, GRAS, GRF, and REV, might be related to the decrease in tillering in low-tillering wheat. These findings contribute to improve our understanding of the mechanisms responsible for the inhibition of tiller development in low-tillering wheat cultivars.
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Affiliation(s)
- Zhiqiang Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Haoran Shi
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Shifan Yu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Wanlin Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Jing Li
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Shihang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
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He R, Ni Y, Li J, Jiao Z, Zhu X, Jiang Y, Li Q, Niu J. Quantitative Changes in the Transcription of Phytohormone-Related Genes: Some Transcription Factors Are Major Causes of the Wheat Mutant dmc Not Tillering. Int J Mol Sci 2018; 19:ijms19051324. [PMID: 29710831 PMCID: PMC5983577 DOI: 10.3390/ijms19051324] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 04/26/2018] [Accepted: 04/26/2018] [Indexed: 01/17/2023] Open
Abstract
Tiller number is an important agronomic trait for grain yield of wheat (Triticum aestivum L.). A dwarf-monoculm wheat mutant (dmc) was obtained from cultivar Guomai 301 (wild type, WT). Here, we explored the molecular basis for the restrained tiller development of the mutant dmc. Two bulked samples of the mutant dmc (T1, T2 and T3) and WT (T4, T5 and T6) with three biological replicates were comparatively analyzed at the transcriptional level by bulked RNA sequencing (RNA-Seq). In total, 68.8 Gb data and 463 million reads were generated, 80% of which were mapped to the wheat reference genome of Chinese Spring. A total of 4904 differentially expressed genes (DEGs) were identified between the mutant dmc and WT. DEGs and their related major biological functions were characterized based on GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) categories. These results were confirmed by quantitatively analyzing the expression profiles of twelve selected DEGs via real-time qRT-PCR. The down-regulated gene expressions related to phytohormone syntheses of auxin, zeatin, cytokinin and some transcription factor (TF) families of TALE, and WOX might be the major causes of the mutant dmc, not tillering. Our work provides a foundation for subsequent tiller development research in the future.
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Affiliation(s)
- Ruishi He
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Yongjing Ni
- Shangqiu Academy of Agricultural and Forestry Sciences, Shangqiu 476000, Henan, China.
| | - Junchang Li
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Zhixin Jiao
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Xinxin Zhu
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Yumei Jiang
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Qiaoyun Li
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Jishan Niu
- National Centre of Engineering and Technological Research for Wheat/Key Laboratory of Physiological Ecology and Genetic Improvement of Food Crops in Henan Province, Henan Agricultural University, Zhengzhou 450046, Henan, China.
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Ren T, Hu Y, Tang Y, Li C, Yan B, Ren Z, Tan F, Tang Z, Fu S, Li Z. Utilization of a Wheat55K SNP Array for Mapping of Major QTL for Temporal Expression of the Tiller Number. FRONTIERS IN PLANT SCIENCE 2018; 9:333. [PMID: 29599793 PMCID: PMC5862827 DOI: 10.3389/fpls.2018.00333] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/28/2018] [Indexed: 05/19/2023]
Abstract
Maximum tiller number and productive tiller number are important traits for wheat grain yield, but research involving the temporal expression of tiller number at different quantitative trait loci (QTL) levels is limited. In the present study, a population set of 371 recombined inbred lines derived from a cross between Chuan-Nong18 and T1208 was used to construct a high-density genetic map using a Wheat55K SNP Array and to perform dynamic QTL analysis of the tiller number at four growth stages. A high-density genetic map containing 11,583 SNP markers and 59 SSR markers that spanned 4,513.95 cM and was distributed across 21 wheat chromosomes was constructed. A total of 28 single environmental QTL were identified in the recombined inbred lines population, and among these, seven QTL were stable and used for multi-environmental and dynamic analysis. These QTL were mapped to chromosomes 2D, 4A, 4D, 5A, 5D, and 7D, respectively. Each QTL explained 1.63-21.22% of the observed phenotypic variation, with an additive effect from -20.51 to 11.59. Dynamic analysis showed that cqTN-2D.2 can be detected at four growth stages of tillering, explaining 4.92-17.16% of the observed phenotypic variations and spanning 13.71 Mb (AX-109283238-AX-110544009: 82189047-95895626) according to the physical location of the flanking markers. The effects of the stable QTL were validated in the recombined inbred lines population, and the beneficial alleles could be utilized in future marker-assisted selection. Several candidate genes for MTN and PTN were predicted. The results provide a better understanding of the QTL selectively expressing the control of tiller number and will facilitate future map-based cloning. 9.17% SNP markers showed best hits to the Chinese Spring contigs. It was indicated that Wheat55K Array was efficient and valid to construct a high-density wheat genetic map.
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Affiliation(s)
- Tianheng Ren
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yangshan Hu
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Yingzi Tang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Chunsheng Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Benju Yan
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Zhenglong Ren
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Feiquan Tan
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Zongxiang Tang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Shulan Fu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Zhi Li
- College of Life Science, Sichuan Agricultural University, Ya’an, China
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Hu YS, Ren TH, Li Z, Tang YZ, Ren ZL, Yan BJ. Molecular mapping and genetic analysis of a QTL controlling spike formation rate and tiller number in wheat. Gene 2017; 634:15-21. [PMID: 28867565 DOI: 10.1016/j.gene.2017.08.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 07/21/2017] [Accepted: 08/30/2017] [Indexed: 10/18/2022]
Abstract
Spike formation rate (SR), which is based on maximum tiller number per unit area and spike number per unit area, is an important yield-related trait in wheat. Increasing the spike formation rate reduces growth competition and wastage of photosynthate from ineffective tillers. Unfortunately, research studies involving quantitative trait locus (QTL) mapping for wheat spike formation rate are limited. In the present study, a set of 371 recombinant inbreed line (RIL) population, which were derived from 1BL/LRS wheat-rye translocation lines CN18 and T1208, was analysed by simple sequence repeat (SSR) markers. Genetic analysis showed that a stable and major QTL (QSR.sicau-4D) for spike formation rate was localized to chromosome 4D and explained 18.24% and 24.48% of the observed phenotypic variance in 2015 and 2016, respectively. This QTL was closely linked to SSR marker Xcfd23, and the genetic distance between the flank markers was 3.28cM. Furthermore, QSR.sicau-4D might be a novel pleiotropic QTL, which also controlled maximum tiller number per unit area (QMTN.sicau-4D) and tiller number during pre-winter per unit area (QTNW.sicau-4D). The marker Xcfd23 associated with SR may be utilized in marker-assisted selection in wheat breeding.
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Affiliation(s)
- Yang-Shan Hu
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China
| | - Tian-Heng Ren
- Agronomy College, Sichuan Agricultural University, Chengdu 611130, Sichuan, China.
| | - Zhi Li
- Agronomy College, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Ying-Zi Tang
- Agronomy College, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Zheng-Long Ren
- Agronomy College, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Ben-Ju Yan
- College of Life Science, Sichuan Agricultural University, Ya'an 625014, Sichuan, China.
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