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Colleoni PE, van Es SW, Winkelmolen T, Immink RGH, van Esse GW. Flowering time genes branching out. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4195-4209. [PMID: 38470076 PMCID: PMC11263490 DOI: 10.1093/jxb/erae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/11/2024] [Indexed: 03/13/2024]
Abstract
Plants are sessile by nature, and as such they have evolved to sense changes in seasonality and their surrounding environment, and adapt to these changes. One prime example of this is the regulation of flowering time in angiosperms, which is precisely timed by the coordinated action of two proteins: FLOWERING LOCUS T (FT) and TERMINAL FLOWER 1 (TFL1). Both of these regulators are members of the PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN (PEBP) family of proteins. These regulatory proteins do not interact with DNA themselves, but instead interact with transcriptional regulators, such as FLOWERING LOCUS D (FD). FT and TFL1 were initially identified as key regulators of flowering time, acting through binding with FD; however, PEBP family members are also involved in shaping plant architecture and development. In addition, PEBPs can interact with TCP transcriptional regulators, such as TEOSINTE BRANCHED 1 (TB1), a well-known regulator of plant architecture, and key domestication-related genes in many crops. Here, we review the role of PEBPs in flowering time, plant architecture, and development. As these are also key yield-related traits, we highlight examples from the model plant Arabidopsis as well as important food and feed crops such as, rice, barley, wheat, tomato, and potato.
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Affiliation(s)
- Pierangela E Colleoni
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Sam W van Es
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Ton Winkelmolen
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - Richard G H Immink
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
- Bioscience, Wageningen Plant Research, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
| | - G Wilma van Esse
- Laboratory of Molecular Biology, Wageningen University and Research, 6708 PB, Wageningen, The Netherlands
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2
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Li J, Li J, Cheng X, Yang Z, Pang Y, Wang C, Wu J, Ji W, Chen X, Zhao J. The addition of Psathyrostachys Huashanica Keng 6Ns large segment chromosomes has positive impact on stripe rust resistance and plant spikelet number of common wheat. BMC PLANT BIOLOGY 2024; 24:685. [PMID: 39026182 PMCID: PMC11256485 DOI: 10.1186/s12870-024-05395-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 07/09/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Developing novel germplasm by using wheat wild related species is an effective way to rebuild the wheat resource bank. The Psathyrostachys huashanica Keng (P. huashanica, 2n = 2x = 14, NsNs) is regarded as a superior species to improve wheat breeding because of its multi-resistance, early maturation and numerous tiller traits. Introducing genetic components of P. huashanica into the common wheat background is the most important step in achieving the effective use. Therefore, the cytogenetic characterization and influence of the introgressed P. huashanica large segment chromosomes in the wheat background is necessary to be explored. RESULTS In this study, we characterized a novel derived line, named D88-2a, a progeny of the former characterized wheat-P. huashanica partial amphiploid line H8911 (2n = 7x = 49, AABBDDNs). Cytological identification showed that the chromosomal composition of D88-2a was 2n = 44 = 22II, indicating the addition of exogenous chromosomes. Genomic in situ hybridization demonstrated that the supernumerary chromosomes were a pair of homologues from the P. huashanica and could be stably inherited in the common wheat background. Molecular markers and 15 K SNP array indicated that the additional chromosomes were derived from the sixth homoeologous group (i.e., 6Ns) of P. huashanica. Based on the distribution of the heterozygous single-nucleotide polymorphism sites and fluorescence in situ hybridization karyotype of each chromosome, this pair of additional chromosomes was confirmed as P. huashanica 6Ns large segment chromosomes, which contained the entire short arm and the proximal centromere portion of the long arm. In terms of the agronomic traits, the addition line D88-2a exhibited enhanced stripe rust resistance, improved spike characteristics and increased protein content than its wheat parent line 7182. CONCLUSIONS The new wheat germplasm D88-2a is a novel cytogenetically stable wheat-P. huashanica 6Ns large segment addition line, and the introgressed large segment alien chromosome has positive impact on plant spikelet number and stripe rust resistance. Thus, this germplasm can be used for genetic improvement of cultivated wheat and the study of functional alien chromosome segment.
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Affiliation(s)
- Jiaojiao Li
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Jiachuang Li
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Xueni Cheng
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zujun Yang
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610000, China
| | - Yuhui Pang
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Chunping Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Jun Wu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wanquan Ji
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xinhong Chen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Jixin Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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3
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Huang Y, Schnurbusch T. The Birth and Death of Floral Organs in Cereal Crops. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:427-458. [PMID: 38424062 DOI: 10.1146/annurev-arplant-060223-041716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Florets of cereal crops are the basic reproductive organs that produce grains for food or feed. The birth of a floret progresses through meristem initiation and floral organ identity specification and maintenance. During these processes, both endogenous and external cues can trigger a premature floral organ death, leading to reproductive failure. Recent advances in different cereal crops have identified both conserved and distinct regulators governing the birth of a floret. However, the molecular underpinnings of floral death are just beginning to be understood. In this review, we first provide a general overview of the current findings in the field of floral development in major cereals and outline different forms of floral deaths, particularly in the Triticeae crops. We then highlight the importance of vascular patterning and photosynthesis in floral development and reproductive success and argue for an expanded knowledge of floral birth-death balance in the context of agroecology.
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Affiliation(s)
- Yongyu Huang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, Germany; ,
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Seeland, Germany; ,
- Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
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4
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Liao S, Xu Z, Fan X, Zhou Q, Liu X, Jiang C, Ma F, Wang Y, Wang T, Feng B. Identification and validation of two major QTL for grain number per spike on chromosomes 2B and 2D in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:147. [PMID: 38834870 DOI: 10.1007/s00122-024-04652-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/16/2024] [Indexed: 06/06/2024]
Abstract
KEY MESSAGE Major QTL for grain number per spike were identified on chromosomes 2B and 2D. Haplotypes and candidate genes of QGns.cib-2B.1 were analyzed. Grain number per spike (GNS) is one of the main components of wheat yield. Genetic dissection of their regulatory factors is essential to improve the yield potential. In present study, a recombinant inbred line population comprising 180 lines developed from the cross between a high GNS line W7268 and a cultivar Chuanyu12 was employed to identify quantitative trait loci (QTL) associated with GNS across six environments. Two major QTL, QGns.cib-2B.1 and QGns.cib-2D.1, were detected in at least four environments with the phenotypic variations of 12.99-27.07% and 8.50-13.79%, respectively. And significant interactions were observed between the two major QTL. In addition, QGns.cib-2B.1 is a QTL cluster for GNS, grain number per spikelet and fertile tiller number, and they were validated in different genetic backgrounds using Kompetitive Allele Specific PCR (KASP) markers. QGns.cib-2B.1 showed pleotropic effects on other yield-related traits including plant height, spike length, and spikelet number per spike, but did not significantly affect thousand grain weight which suggested that it might be potentially applicable in breeding program. Comparison analysis suggested that QGns.cib-2B.1 might be a novel QTL. Furthermore, haplotype analysis of QGns.cib-2B.1 indicated that it is a hot spot of artificial selection during wheat improvement. Based on the expression patterns, gene annotation, orthologs analysis and sequence variations, the candidate genes of QGns.cib-2B.1 were predicted. Collectively, the major QTL and KASP markers reported here provided a wealth of information for the genetic basis of GNS and grain yield improvement.
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Affiliation(s)
- Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cheng Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fang Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanlin Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
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5
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Gauley A, Pasquariello M, Yoshikawa GV, Alabdullah AK, Hayta S, Smedley MA, Dixon LE, Boden SA. Photoperiod-1 regulates the wheat inflorescence transcriptome to influence spikelet architecture and flowering time. Curr Biol 2024; 34:2330-2343.e4. [PMID: 38781956 PMCID: PMC11149547 DOI: 10.1016/j.cub.2024.04.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/08/2024] [Accepted: 04/11/2024] [Indexed: 05/25/2024]
Abstract
Photoperiod insensitivity has been selected by breeders to help adapt crops to diverse environments and farming practices. In wheat, insensitive alleles of Photoperiod-1 (Ppd-1) relieve the requirement of long daylengths to flower by promoting expression of floral promoting genes early in the season; however, these alleles also limit yield by reducing the number and fertility of grain-producing florets through processes that are poorly understood. Here, we performed transcriptome analysis of the developing inflorescence using near-isogenic lines that contain either photoperiod-insensitive or null alleles of Ppd-1, during stages when spikelet number is determined and floret development initiates. We report that Ppd-1 influences the stage-specific expression of genes with roles in auxin signaling, meristem identity, and protein turnover, and analysis of differentially expressed transcripts identified bZIP and ALOG transcription factors, namely PDB1 and ALOG1, which regulate flowering time and spikelet architecture. These findings enhance our understanding of genes that regulate inflorescence development and introduce new targets for improving yield potential.
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Affiliation(s)
- Adam Gauley
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Marianna Pasquariello
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Guilherme V Yoshikawa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Hartley Grove, Glen Osmond, SA 5064, Australia
| | - Abdul Kader Alabdullah
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Sadiye Hayta
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Mark A Smedley
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK
| | - Laura E Dixon
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Scott A Boden
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Hartley Grove, Glen Osmond, SA 5064, Australia.
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6
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Li M, Jiao Y. Cereal genetics: Novel modulators of spikelet number and flowering time. Curr Biol 2024; 34:R528-R530. [PMID: 38834023 DOI: 10.1016/j.cub.2024.04.071] [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: 06/06/2024]
Abstract
The spikelet is the unit component of the spike and the site of grain production in Triticeae crops. Two new studies revealed that plant-specific transcription factors ALOG1 and PDB1 participate in modulating spikelet number and flowering time in barley and wheat.
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Affiliation(s)
- Mingjiu Li
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Shandong, China.
| | - Yuling Jiao
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Shandong, China; School of Life Sciences, State Key Laboratory for Protein and Plant Gene Research, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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7
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Jiang G, Koppolu R, Rutten T, Hensel G, Lundqvist U, Tandron Moya YA, Huang Y, Rajaraman J, Poursarebani N, von Wirén N, Kumlehn J, Mascher M, Schnurbusch T. Non-cell-autonomous signaling associated with barley ALOG1 specifies spikelet meristem determinacy. Curr Biol 2024; 34:2344-2358.e5. [PMID: 38781954 DOI: 10.1016/j.cub.2024.04.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/18/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Inflorescence architecture and crop productivity are often tightly coupled in our major cereal crops. However, the underlying genetic mechanisms controlling cereal inflorescence development remain poorly understood. Here, we identified recessive alleles of barley (Hordeum vulgare L.) HvALOG1 (Arabidopsis thaliana LSH1 and Oryza G1) that produce non-canonical extra spikelets and fused glumes abaxially to the central spikelet from the upper-mid portion until the tip of the inflorescence. Notably, we found that HvALOG1 exhibits a boundary-specific expression pattern that specifically excludes reproductive meristems, implying the involvement of previously proposed localized signaling centers for branch regulation. Importantly, during early spikelet formation, non-cell-autonomous signals associated with HvALOG1 expression may specify spikelet meristem determinacy, while boundary formation of floret organs appears to be coordinated in a cell-autonomous manner. Moreover, barley ALOG family members synergistically modulate inflorescence morphology, with HvALOG1 predominantly governing meristem maintenance and floral organ development. We further propose that spatiotemporal redundancies of expressed HvALOG members specifically in the basal inflorescence may be accountable for proper patterning of spikelet formation in mutant plants. Our research offers new perspectives on regulatory signaling roles of ALOG transcription factors during the development of reproductive meristems in cereal inflorescences.
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Affiliation(s)
- Guojing Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Goetz Hensel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | | | - Yudelsy Antonia Tandron Moya
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Yongyu Huang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Jeyaraman Rajaraman
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Naser Poursarebani
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstr. 3, 06466 Seeland, Germany; Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany.
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8
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Yoshikawa GV, Boden SA. Finding the right balance: The enduring role of florigens during cereal inflorescence development and their influence on fertility. CURRENT OPINION IN PLANT BIOLOGY 2024; 79:102539. [PMID: 38599051 DOI: 10.1016/j.pbi.2024.102539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 02/23/2024] [Accepted: 03/23/2024] [Indexed: 04/12/2024]
Abstract
Flowering is a vital process in a plant's lifecycle and variation for flowering-time has helped cereals adapt to diverse environments. Much cereal research has focused on understanding how flowering signals, or florigens, regulate the floral transition and timing of ear emergence. However, flowering genes also perform an enduring role during inflorescence development, with genotypes that elicit a weaker flowering signal producing more elaborately branched inflorescences with extra floret-bearing spikelets. While this outcome indicates that variable expression of flowering genes could boost yield potential, further analysis has shown that dampened florigen levels can compromise fertility, negating the benefit of extra grain-producing sites. Here, we discuss ways that florigens contribute to early and late inflorescence development, including their influence on branch/spikelet architecture and fertility. We propose that a deeper understanding of the role for florigens during inflorescence development could be used to balance the effects of florigens throughout flowering to improve productivity.
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Affiliation(s)
- Guilherme V Yoshikawa
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia
| | - Scott A Boden
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA, 5064, Australia.
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9
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Romero JM, Serrano-Bueno G, Camacho-Fernández C, Vicente MH, Ruiz MT, Pérez-Castiñeira JR, Pérez-Hormaeche J, Nogueira FTS, Valverde F. CONSTANS, a HUB for all seasons: How photoperiod pervades plant physiology regulatory circuits. THE PLANT CELL 2024; 36:2086-2102. [PMID: 38513610 PMCID: PMC11132886 DOI: 10.1093/plcell/koae090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 02/07/2024] [Accepted: 02/28/2024] [Indexed: 03/23/2024]
Abstract
How does a plant detect the changing seasons and make important developmental decisions accordingly? How do they incorporate daylength information into their routine physiological processes? Photoperiodism, or the capacity to measure the daylength, is a crucial aspect of plant development that helps plants determine the best time of the year to make vital decisions, such as flowering. The protein CONSTANS (CO) constitutes the central regulator of this sensing mechanism, not only activating florigen production in the leaves but also participating in many physiological aspects in which seasonality is important. Recent discoveries place CO in the center of a gene network that can determine the length of the day and confer seasonal input to aspects of plant development and physiology as important as senescence, seed size, or circadian rhythms. In this review, we discuss the importance of CO protein structure, function, and evolutionary mechanisms that embryophytes have developed to incorporate annual information into their physiology.
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Affiliation(s)
- Jose M Romero
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, 41012 Seville, Spain
| | - Gloria Serrano-Bueno
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, 41012 Seville, Spain
| | - Carolina Camacho-Fernández
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, 41012 Seville, Spain
- Universidad Politécnica de Valencia, Vicerrectorado de Investigación, 46022 Valencia, Spain
| | - Mateus Henrique Vicente
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), University of São Paulo (USP), Piracicaba, 13418-900 São Paulo, Brazil
| | - M Teresa Ruiz
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
| | - J Román Pérez-Castiñeira
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
- Department of Plant Biochemistry and Molecular Biology, Universidad de Sevilla, 41012 Seville, Spain
| | - Javier Pérez-Hormaeche
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
| | - Fabio T S Nogueira
- Laboratory of Molecular Genetics of Plant Development, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ), University of São Paulo (USP), Piracicaba, 13418-900 São Paulo, Brazil
| | - Federico Valverde
- Plant Development Group - Institute for Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones Científicas, Universidad de Sevilla, 41092 Seville, Spain
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10
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Ai G, He C, Bi S, Zhou Z, Liu A, Hu X, Liu Y, Jin L, Zhou J, Zhang H, Du D, Chen H, Gong X, Saeed S, Su H, Lan C, Chen W, Li Q, Mao H, Li L, Liu H, Chen D, Kaufmann K, Alazab KF, Yan W. Dissecting the molecular basis of spike traits by integrating gene regulatory networks and genetic variation in wheat. PLANT COMMUNICATIONS 2024; 5:100879. [PMID: 38486454 PMCID: PMC11121755 DOI: 10.1016/j.xplc.2024.100879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/25/2024] [Accepted: 03/11/2024] [Indexed: 04/30/2024]
Abstract
Spike architecture influences both grain weight and grain number per spike, which are the two major components of grain yield in bread wheat (Triticum aestivum L.). However, the complex wheat genome and the influence of various environmental factors pose challenges in mapping the causal genes that affect spike traits. Here, we systematically identified genes involved in spike trait formation by integrating information on genomic variation and gene regulatory networks controlling young spike development in wheat. We identified 170 loci that are responsible for variations in spike length, spikelet number per spike, and grain number per spike through genome-wide association study and meta-QTL analyses. We constructed gene regulatory networks for young inflorescences at the double ridge stage and the floret primordium stage, in which the spikelet meristem and the floret meristem are predominant, respectively, by integrating transcriptome, histone modification, chromatin accessibility, eQTL, and protein-protein interactome data. From these networks, we identified 169 hub genes located in 76 of the 170 QTL regions whose polymorphisms are significantly associated with variation in spike traits. The functions of TaZF-B1, VRT-B2, and TaSPL15-A/D in establishment of wheat spike architecture were verified. This study provides valuable molecular resources for understanding spike traits and demonstrates that combining genetic analysis and developmental regulatory networks is a robust approach for dissection of complex traits.
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Affiliation(s)
- Guo Ai
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Siteng Bi
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ziru Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ankui Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanyan Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Liujie Jin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - JiaCheng Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Heping Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Dengxiang Du
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Gong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Sulaiman Saeed
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome, Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Hao Liu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität Zu Berlin, 10115 Berlin, Germany
| | - Khaled F Alazab
- Plant Research Department, Nuclear Research Center, Egyptian Atomic Energy Authority, Cairo 13759, Egypt
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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11
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Makhoul M, Schlichtermann RH, Ugwuanyi S, Weber SE, Voss-Fels KP, Stahl A, Zetzsche H, Wittkop B, Snowdon RJ, Obermeier C. Novel PHOTOPERIOD-1 gene variants associate with yield-related and root-angle traits in European bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:125. [PMID: 38727862 PMCID: PMC11087350 DOI: 10.1007/s00122-024-04634-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/20/2024] [Indexed: 05/13/2024]
Abstract
KEY MESSAGE PHOTOPERIOD-1 homoeologous gene copies play a pivotal role in regulation of flowering time in wheat. Here, we show that their influence also extends to spike and shoot architecture and even impacts root development. The sequence diversity of three homoeologous copies of the PHOTOPERIOD-1 gene in European winter wheat was analyzed by Oxford Nanopore amplicon-based multiplex sequencing and molecular markers in a panel of 194 cultivars representing breeding progress over the past 5 decades. A strong, consistent association with an average 8% increase in grain yield was observed for the PpdA1-Hap1 haplotype across multiple environments. This haplotype was found to be linked in 51% of cultivars to the 2NS/2AS translocation, originally introduced from Aegilops ventricosa, which leads to an overestimation of its effect. However, even in cultivars without the 2NS/2AS translocation, PpdA1-Hap1 was significantly associated with increased grain yield, kernel per spike and kernel per m2 under optimal growth conditions, conferring a 4% yield advantage compared to haplotype PpdA1-Hap4. In contrast to Ppd-B1 and Ppd-D1, the Ppd-A1 gene exhibits novel structural variations and a high number of SNPs, highlighting the evolutionary changes that have occurred in this region over the course of wheat breeding history. Additionally, cultivars carrying the photoperiod-insensitive Ppd-D1a allele not only exhibit earlier heading, but also deeper roots compared to those with photoperiod-sensitive alleles under German conditions. PCR and KASP assays have been developed that can be effectively employed in marker-assisted breeding programs to introduce these favorable haplotypes.
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Affiliation(s)
- Manar Makhoul
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | | | - Samson Ugwuanyi
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Sven E Weber
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Kai P Voss-Fels
- Institute for Grapevine Breeding, Hochschule Geisenheim University, Geisenheim, Germany
| | - Andreas Stahl
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Holger Zetzsche
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, Quedlinburg, Germany
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Christian Obermeier
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany.
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12
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Zhang L, Zhou H, Fu X, Zhou N, Liu M, Bai S, Zhao X, Cheng R, Li S, Zhang D. Identification and map-based cloning of an EMS-induced mutation in wheat gene TaSP1 related to spike architecture. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:119. [PMID: 38709271 DOI: 10.1007/s00122-024-04621-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
KEY MESSAGE A candidate gene TaSP1 related to spike shape was cloned, and the gene-specific marker was developed to efficiently track the superior haplotype in common wheat. Spike shape, an important factor that affects wheat grain yield, is mainly defined by spike length (SPL), spikelet number (SPN), and compactness. Zhoumai32 mutant 1160 (ZM1160), a mutant obtained from ethyl methane sulfonate (EMS) treatment of hexaploid wheat variety Zhoumai32, was used to identify and clone the candidate gene that conditioned the spike shape. Genetic analysis of an F2 population derived from a cross of ZM1160 and Bainong207 suggested that the compact spike shape in ZM1160 was controlled by a single recessive gene, and therefore, the mutated gene was designated as Tasp1. With polymorphic markers identified through bulked segregant analysis (BSA), the gene was mapped to a 2.65-cM interval flanked by markers YZU0852 and MIS46239 on chromosome 7D, corresponding to a 0.42-Mb physical interval of Chinese spring (CS) reference sequences (RefSeq v1.0). To fine map TaSP1, 15 and seven recombinants were, respectively, screened from 1599 and 1903 F3 plants derived from the heterozygous F2 plants. Finally, TaSP1 was delimited to a 21.9 Kb (4,870,562 to 4,892,493 bp) Xmis48123-Xmis48104 interval. Only one high-confidence gene TraesCS7D02G010200 was annotated in this region, which encodes an unknown protein with a putative vWA domain. Quantitative reverse transcription PCR (qRT-PCR) analysis showed that TraesCS7D02G010200 was mainly expressed in the spike. Haplotype analysis of 655 wheat cultivars using the candidate gene-specific marker Xg010200p2 identified a superior haplotype TaSP1b with longer spike and more spikelet number. TaSP1 is beneficial to the improvement in wheat spike shape.
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Affiliation(s)
- Lin Zhang
- School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Huidan Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agricultural Sciences, Henan University, Kaifeng, 475001, Henan, China
| | - Xian Fu
- School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Niuniu Zhou
- School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Mengjie Liu
- School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Shenglong Bai
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agricultural Sciences, Henan University, Kaifeng, 475001, Henan, China
| | - Xinpeng Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agricultural Sciences, Henan University, Kaifeng, 475001, Henan, China
| | - Ruiru Cheng
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agricultural Sciences, Henan University, Kaifeng, 475001, Henan, China.
| | - Suoping Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agricultural Sciences, Henan University, Kaifeng, 475001, Henan, China.
| | - Dale Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agricultural Sciences, Henan University, Kaifeng, 475001, Henan, China.
- The Zhongzhou Laboratory for Integrative Biology, Zhengzhou, 450000, Henan, China.
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13
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Wu L, Li G, Li D, Dong C, Zhang X, Zhang L, Yang Z, Kong X, Xia C, Chen J, Liu X. Identification and functional analysis of a chromosome 2D fragment harboring TaFPF1 gene with the potential for yield improvement using a late heading wheat mutant. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:92. [PMID: 38568320 DOI: 10.1007/s00122-024-04593-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024]
Abstract
KEY MESSAGE A chromosome fragment influencing wheat heading and grain size was identified using mapping of m406 mutant. The study of TaFPF1 in this fragment provides more insights into wheat yield improvement. In recent years, wheat production has faced formidable challenges driven by rapid population growth and climate change, emphasizing the importance of improving specific agronomic traits such as heading date, spike length, and grain size. To identify potential genes for improving these traits, we screened a wheat EMS mutant library and identified a mutant, designated m406, which exhibited a significantly delayed heading date compared to the wild-type. Intriguingly, the mutant also displayed significantly longer spike and larger grain size. Genetic analysis revealed that a single recessive gene was responsible for the delayed heading. Surprisingly, a large 46.58 Mb deletion at the terminal region of chromosome arm 2DS in the mutant was identified through fine mapping and fluorescence in situ hybridization. Thus, the phenotypes of the mutant m406 are controlled by a group of linked genes. This deletion encompassed 917 annotated high-confidence genes, including the previously studied wheat genes Ppd1 and TaDA1, which could affect heading date and grain size. Multiple genes in this region probably contribute to the phenotypes of m406. We further investigated the function of TaFPF1 using gene editing. TaFPF1 knockout mutants showed delayed heading and increased grain size. Moreover, we identified the direct upstream gene of TaFPF1 and investigated its relationship with other important flowering genes. Our study not only identified more genes affecting heading and grain development within this deleted region but also highlighted the potential of combining these genes for improvement of wheat traits.
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Affiliation(s)
- Lifen Wu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, Sichuan, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chunhao Dong
- 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
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, Sichuan, China
| | - Xiuying Kong
- 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.
| | - Jingtang Chen
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China.
| | - Xu Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding, 071001, Hebei, China.
- 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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14
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Lin Y, Zhou S, Yang W, Han B, Liang X, Zhang Y, Zhang J, Han H, Guo B, Liu W, Yang X, Li X, Li L. Chromosomal mapping of a major genetic locus from Agropyron cristatum chromosome 6P that influences grain number and spikelet number in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:82. [PMID: 38489037 DOI: 10.1007/s00122-024-04584-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/03/2024] [Indexed: 03/17/2024]
Abstract
KEY MESSAGE A novel locus on Agropyron cristatum chromosome 6P that increases grain number and spikelet number was identified in wheat-A. cristatum derivatives and across 3 years. Agropyron cristatum (2n = 4x = 28, PPPP), which has the characteristics of high yield with multiple flowers and spikelets, is a promising gene donor for wheat high-yield improvement. Identifying the genetic loci and genes that regulate yield could elucidate the genetic variations in yield-related traits and provide novel gene sources and insights for high-yield wheat breeding. In this study, cytological analysis and molecular marker analysis revealed that del10a and del31a were wheat-A. cristatum chromosome 6P deletion lines. Notably, del10a carried a segment of the full 6PS and 6PL bin (1-13), while del31a carried a segment of the full 6PS and 6PL bin (1-8). The agronomic characterization and genetic population analysis confirmed that the 6PL bin (9-13) brought about an increase in grain number per spike (average increase of 10.43 grains) and spikelet number per spike (average increase of 3.67) over the three growing seasons. Furthermore, through resequencing, a multiple grain number locus was mapped to the physical interval of 593.03-713.89 Mb on chromosome 6P of A. cristatum Z559. The RNA-seq analysis revealed the expression of 537 genes in the del10a young spike tissue, with the annotation indicating that 16 of these genes were associated with grain number and spikelet number. Finally, a total of ten A. cristatum-specific molecular markers were developed for this interval. In summary, this study presents novel genetic material that is useful for high-yield wheat breeding initiatives to meet the challenge of global food security through enhanced agricultural production.
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Affiliation(s)
- Yida Lin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Shenghui Zhou
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Wenjing Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Bing Han
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Xuezhong Liang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Yuxin Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Jinpeng Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Haiming Han
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Baojin Guo
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Weihua Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Xinming Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Xiuquan Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Lihui Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China.
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100, China.
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15
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Lin X, Xu Y, Wang D, Yang Y, Zhang X, Bie X, Gui L, Chen Z, Ding Y, Mao L, Zhang X, Lu F, Zhang X, Uauy C, Fu X, Xiao J. Systematic identification of wheat spike developmental regulators by integrated multi-omics, transcriptional network, GWAS, and genetic analyses. MOLECULAR PLANT 2024; 17:438-459. [PMID: 38310351 DOI: 10.1016/j.molp.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/29/2023] [Accepted: 01/30/2024] [Indexed: 02/05/2024]
Abstract
The spike architecture of wheat plays a crucial role in determining grain number, making it a key trait for optimization in wheat breeding programs. In this study, we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages, revealing coordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering transition. We constructed a core transcriptional regulatory network (TRN) that drives wheat spike formation and experimentally validated a multi-layer regulatory module involving TaSPL15, TaAGLG1, and TaFUL2. By integrating the TRN with genome-wide association studies, we identified 227 transcription factors, including 42 with known functions and 185 with unknown functions. Further investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time, such as TaMYC2-A1, TaMYB30-A1, and TaWRKY37-A1. Of particular interest, TaMYB30-A1, downstream of and repressed by WFZP, was found to regulate fertile spikelet number. Notably, the excellent haplotype of TaMYB30-A1, which contains a C allele at the WFZP binding site, was enriched during wheat breeding improvement in China, leading to improved agronomic traits. Finally, we constructed a free and open access Wheat Spike Multi-Omic Database (http://39.98.48.156:8800/#/). Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development, with practical value for wheat breeding.
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Affiliation(s)
- Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongxin Xu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongzhi Wang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xiaoyu Zhang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomin Bie
- Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Lixuan Gui
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan 610000, China
| | - Zhongxu Chen
- Department of Life Science, Tcuni Inc., Chengdu, Sichuan 610000, China
| | - Yiliang Ding
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Long Mao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xueyong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Fei Lu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, CAS, Beijing 100101, China
| | - Xiansheng Zhang
- Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Xiangdong Fu
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, CAS, Beijing 100101, China.
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16
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Sakuma S, Yamashita Y, Suzuki T, Nasuda S. A Catalog of GNI-A1 Genes That Regulate Floret Fertility in a Diverse Bread Wheat Collection. PLANTS (BASEL, SWITZERLAND) 2024; 13:330. [PMID: 38337864 PMCID: PMC10857310 DOI: 10.3390/plants13030330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Modifying inflorescence architecture improves grain number and grain weight in bread wheat (Triticum aestivum). Allelic variation in Grain Number Increase 1 (GNI-A1) genes, encoding a homeodomain leucine zipper class I transcription factor, influences grain number and yield. However, allelic information about GNI-A1 in diverse germplasms remains limited. Here, we investigated GNI-A1 alleles in a panel of 252 diverse bread wheat accessions (NBRP core collection and HRO breeder's panel) by target resequencing. Cultivars carrying the reduced-function allele (105Y) were predominant in the NBRP panel, whereas the 105N functional allele was the major type in the HRO panel. Cultivars with the 105Y allele were distributed in Asian landraces but not in European genotypes. Association analysis demonstrated that floret fertility, together with grain size, were improved in cultivars in the NBRP core collection carrying the 105Y allele. These results imply that different alleles of GNI-A1 have been locally selected, with the 105Y allele selected in East Asia and the 105N allele selected in Europe.
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Affiliation(s)
- Shun Sakuma
- Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
| | - Yoko Yamashita
- Central Agricultural Experiment Station, Hokkaido Research Organization, Naganuma, Hokkaido 069-1395, Japan; (Y.Y.); (T.S.)
| | - Takako Suzuki
- Central Agricultural Experiment Station, Hokkaido Research Organization, Naganuma, Hokkaido 069-1395, Japan; (Y.Y.); (T.S.)
| | - Shuhei Nasuda
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan;
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17
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Jiang C, Xu Z, Fan X, Zhou Q, Ji G, Liao S, Wang Y, Ma F, Zhao Y, Wang T, Feng B. Genetic dissection of major QTL for grain number per spike on chromosomes 5A and 6A in bread wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2024; 14:1305547. [PMID: 38259947 PMCID: PMC10800429 DOI: 10.3389/fpls.2023.1305547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/08/2023] [Indexed: 01/24/2024]
Abstract
Grain number per spike (GNS) is a crucial component of grain yield and plays a significant role in improving wheat yield. To identify quantitative trait loci (QTL) associated with GNS, a recombinant inbred line (RIL) population derived from the cross of Zhongkemai 13F10 and Chuanmai 42 was employed to conduct QTL mapping across eight environments. Based on the bulked segregant exome sequencing (BSE-Seq), genomic regions associated with GNS were detected on chromosomes 5A and 6A. According to the constructed genetic maps, two major QTL QGns.cib-5A (LOD = 4.35-8.16, PVE = 8.46-14.43%) and QGns.cib-6A (LOD = 3.82-30.80, PVE = 5.44-12.38%) were detected in five and four environments, respectively. QGns.cib-6A is a QTL cluster for other seven yield-related traits. QGns.cib-5A and QGns.cib-6A were further validated using linked Kompetitive Allele Specific PCR (KASP) markers in different genetic backgrounds. QGns.cib-5A exhibited pleiotropic effects on productive tiller number (PTN), spike length (SL), fertile spikelet number per spike (FSN), and ratio of grain length to grain width (GL/GW) but did not significantly affect thousand grain weight (TGW). Haplotype analysis revealed that QGns.cib-5A and QGns.cib-6A were the targets of artificial selection during wheat improvement. Candidate genes for QGns.cib-5A and QGns.cib-6A were predicted by analyzing gene annotation, spatiotemporal expression patterns, and orthologous and sequence differences. These findings will be valuable for fine mapping and map-based cloning of genes underlying QGns.cib-5A and QGns.cib-6A.
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Affiliation(s)
- Cheng Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- College of Life Sciences, Sichuan University, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guangsi Ji
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanlin Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fang Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yun Zhao
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- The Innovative of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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18
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Zhang Y, Shen C, Shi J, Shi J, Zhang D. Boosting Triticeae crop grain yield by manipulating molecular modules to regulate inflorescence architecture: insights and knowledge from other cereal crops. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:17-35. [PMID: 37935244 DOI: 10.1093/jxb/erad386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
One of the challenges for global food security is to reliably and sustainably improve the grain yield of cereal crops. One solution is to modify the architecture of the grain-bearing inflorescence to optimize for grain number and size. Cereal inflorescences are complex structures, with determinacy, branching patterns, and spikelet/floret growth patterns that vary by species. Recent decades have witnessed rapid advancements in our understanding of the genetic regulation of inflorescence architecture in rice, maize, wheat, and barley. Here, we summarize current knowledge on key genetic factors underlying the different inflorescence morphologies of these crops and model plants (Arabidopsis and tomato), focusing particularly on the regulation of inflorescence meristem determinacy and spikelet meristem identity and determinacy. We also discuss strategies to identify and utilize these superior alleles to optimize inflorescence architecture and, ultimately, improve crop grain yield.
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Affiliation(s)
- Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
- School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5064, Australia
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19
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Abbai R, Golan G, Longin CFH, Schnurbusch T. Grain yield trade-offs in spike-branching wheat can be mitigated by elite alleles affecting sink capacity and post-anthesis source activity. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:88-102. [PMID: 37739800 PMCID: PMC10735541 DOI: 10.1093/jxb/erad373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Introducing variations in inflorescence architecture, such as the 'Miracle-Wheat' (Triticum turgidum convar. compositum (L.f.) Filat.) with a branching spike, has relevance for enhancing wheat grain yield. However, in the spike-branching genotypes, the increase in spikelet number is generally not translated into grain yield advantage because of reduced grains per spikelet and grain weight. Here, we investigated if such trade-offs might be a function of source-sink strength by using 385 recombinant inbred lines developed by intercrossing the spike-branching landrace TRI 984 and CIRNO C2008, an elite durum (T. durum L.) cultivar; they were genotyped using the 25K array. Various plant and spike architectural traits, including flag leaf, peduncle, and spike senescence rate, were phenotyped under field conditions for 2 consecutive years. On chromosome 5AL, we found a new modifier QTL for spike branching, branched headt3 (bht-A3), which was epistatic to the previously known bht-A1 locus. Besides, bht-A3 was associated with more grains per spikelet and a delay in flag leaf senescence rate. Importantly, favourable alleles, viz. bht-A3 and grain protein content (gpc-B1) that delayed senescence, are required to improve grain number and grain weight in the spike-branching genotypes. In summary, achieving a balanced source-sink relationship might minimize grain yield trade-offs in Miracle-Wheat.
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Affiliation(s)
- Ragavendran Abbai
- Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466 Seeland, Germany
| | - Guy Golan
- Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466 Seeland, Germany
| | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstr. 21, 70599 Stuttgart, Germany
| | - Thorsten Schnurbusch
- Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, 06466 Seeland, Germany
- Martin Luther University Halle-Wittenberg, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, 06120 Halle, Germany
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20
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Si Y, Tian S, Niu J, Yu Z, Ma S, Lu Q, Wu H, Ling HQ, Zheng S. Dissection and validation of a promising QTL controlling spikelet number on 5B in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:240. [PMID: 37930446 DOI: 10.1007/s00122-023-04488-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023]
Abstract
KEY MESSAGE Five environmentally stable QTLs for spikelet number per spike and days to heading were identified using a high-genetic map containing 95,444 SNPs, among which QSns.ucas-5B was validated using residual heterozygous line at multiple environments. Spikelet number per spike (SNS) and days to heading (DTH) play pivotal roles in the improvement of wheat yield. In this study, a high-density genetic map for a recombinant inbred lines (RILs) population derived from Zhengnong 17 (ZN17) and Yangbaimai (YBM) was constructed using 95,444 single-nucleotide polymorphism (SNP) markers from the Wheat660K SNP array. Our study identified a total of five environmentally stable QTLs for SNS and DTH, one of which was named QSns.ucas-5B, with a physical interval of approximately 545.4-552.1 Mb on the 5BL chromosome arm. Importantly, the elite haplotype within QSns.ucas-5B showed a consistent and positive effect on SNS, grain number and weight per spike, without extending the days to heading. These findings provide a foundation for future efforts to map and clone the gene(s) responsible for QSns.ucas-5B and further indicate the potential application of the developed and validated InDel marker of QSns.ucas-5B for molecular breeding purposes, aimed at improving wheat grain yield.
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Affiliation(s)
- Yaoqi Si
- 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
| | - Shuiquan Tian
- 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
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianqing Niu
- 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
| | - Zhongqing Yu
- National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China
| | - Shengwei Ma
- 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
| | - Qiao Lu
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huilan Wu
- 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
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Qing Ling
- 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.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Shusong 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.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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21
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Qiao P, Li X, Liu D, Lu S, Zhi L, Rysbekova A, Chen L, Hu YG. Mining novel genomic regions and candidate genes of heading and flowering dates in bread wheat by SNP- and haplotype-based GWAS. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:76. [PMID: 37873506 PMCID: PMC10587053 DOI: 10.1007/s11032-023-01422-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a global staple crop vital for human nutrition. Heading date (HD) and flowering date (FD) are critical traits influencing wheat growth, development, and adaptability to diverse environmental conditions. A comprehensive study were conducted involving 190 bread wheat accessions to unravel the genetic basis of HD and FD using high-throughput genotyping and multi-environment field trials. Seven independent quantitative trait loci (QTLs) were identified to be significantly associated with HD and FD using two GWAS methods, which explained a proportion of phenotypic variance ranging from 1.43% to 9.58%. Notably, QTLs overlapping with known vernalization genes Vrn-D1 were found, validating their roles in regulating flowering time. Moreover, novel QTLs on chromosome 2A, 5B, 5D, and 7B associated with HD and FD were identified. The effects of these QTLs on HD and FD were confirmed in an additional set of 74 accessions across different environments. An increase in the frequency of alleles associated with early flowering in cultivars released in recent years was also observed, suggesting the influence of molecular breeding strategies. In summary, this study enhances the understanding of the genetic regulation of HD and FD in bread wheat, offering valuable insights into crop improvement for enhanced adaptability and productivity under changing climatic conditions. These identified QTLs and associated markers have the potential to improve wheat breeding programs in developing climate-resilient varieties to ensure food security. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01422-z.
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Affiliation(s)
- Pengfang Qiao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi China
| | - Xuan Li
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi China
| | - Dezheng Liu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi China
| | - Shan Lu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi China
| | - Lei Zhi
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi China
| | - Aiman Rysbekova
- S. Seifullin Kazakh Agro-Technical University, Astana, Kazakhstan
| | - Liang Chen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi China
| | - Yin-gang Hu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi China
- State Key Laboratory of Crop Stress Biology for Arid Areas, Institute of Water-saving Agriculture in Arid Areas of China, Northwest A&F University, Yangling, Shaanxi China
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22
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Luo X, Yang Y, Lin X, Xiao J. Deciphering spike architecture formation towards yield improvement in wheat. J Genet Genomics 2023; 50:835-845. [PMID: 36907353 DOI: 10.1016/j.jgg.2023.02.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/12/2023]
Abstract
Wheat is the most widely grown crop globally, providing 20% of the daily consumed calories and protein content around the world. With the growing global population and frequent occurrence of extreme weather caused by climate change, ensuring adequate wheat production is essential for food security. The architecture of the inflorescence plays a crucial role in determining the grain number and size, which is a key trait for improving yield. Recent advances in wheat genomics and gene cloning techniques have improved our understanding of wheat spike development and its applications in breeding practices. Here, we summarize the genetic regulation network governing wheat spike formation, the strategies used for identifying and studying the key factors affecting spike architecture, and the progress made in breeding applications. Additionally, we highlight future directions that will aid in the regulatory mechanistic study of wheat spike determination and targeted breeding for grain yield improvement.
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Affiliation(s)
- Xumei Luo
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiman Yang
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Xuelei Lin
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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23
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Glenn P, Woods DP, Zhang J, Gabay G, Odle N, Dubcovsky J. Wheat bZIPC1 interacts with FT2 and contributes to the regulation of spikelet number per spike. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:237. [PMID: 37906302 PMCID: PMC10618405 DOI: 10.1007/s00122-023-04484-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: 08/01/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023]
Abstract
KEY MESSAGE The wheat transcription factor bZIPC1 interacts with FT2 and affects spikelet and grain number per spike. We identified a natural allele with positive effects on these two economically important traits. Loss-of-function mutations and natural variation in the gene FLOWERING LOCUS T2 (FT2) in wheat have previously been shown to affect spikelet number per spike (SNS). However, while other FT-like wheat proteins interact with bZIP-containing transcription factors from the A-group, FT2 does not interact with any of them. In this study, we used a yeast-two-hybrid screen with FT2 as bait and identified a grass-specific bZIP-containing transcription factor from the C-group, designated here as bZIPC1. Within the C-group, we identified four clades including wheat proteins that show Y2H interactions with different sets of FT-like and CEN-like encoded proteins. bZIPC1 and FT2 expression partially overlap in the developing spike, including the inflorescence meristem. Combined loss-of-function mutations in bZIPC-A1 and bZIPC-B1 (bzipc1) in tetraploid wheat resulted in a drastic reduction in SNS with a limited effect on heading date. Analysis of natural variation in the bZIPC-B1 (TraesCS5B02G444100) region revealed three major haplotypes (H1-H3), with the H1 haplotype showing significantly higher SNS, grain number per spike and grain weight per spike than both the H2 and H3 haplotypes. The favorable effect of the H1 haplotype was also supported by its increased frequency from the ancestral cultivated tetraploids to the modern tetraploid and hexaploid wheat varieties. We developed markers for the two non-synonymous SNPs that differentiate the bZIPC-B1b allele in the H1 haplotype from the ancestral bZIPC-B1a allele present in all other haplotypes. These diagnostic markers are useful tools to accelerate the deployment of the favorable bZIPC-B1b allele in pasta and bread wheat breeding programs.
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Affiliation(s)
- Priscilla Glenn
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Daniel P Woods
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Junli Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Gilad Gabay
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Natalie Odle
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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24
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Liu Y, Chen J, Yin C, Wang Z, Wu H, Shen K, Zhang Z, Kang L, Xu S, Bi A, Zhao X, Xu D, He Z, Zhang X, Hao C, Wu J, Gong Y, Yu X, Sun Z, Ye B, Liu D, Zhang L, Shen L, Hao Y, Ma Y, Lu F, Guo Z. A high-resolution genotype-phenotype map identifies the TaSPL17 controlling grain number and size in wheat. Genome Biol 2023; 24:196. [PMID: 37641093 PMCID: PMC10463835 DOI: 10.1186/s13059-023-03044-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most wheat genome-wide association studies (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain number per spikelet have been reported due to sensitivity of this trait to variable environments. RESULTS We perform a large-scale GWAS using approximately 40 million filtered SNPs for 27 spike morphology traits. We detect 132,086 significant marker-trait associations and the associated SNP markers are located within 590 associated peaks. We detect additional and stronger peaks by dividing spike morphology into sub-traits relative to GWAS results of spike morphology traits. We propose that the genetic dissection of spike morphology is a powerful strategy to detect signals for grain yield traits in wheat. The GWAS results reveal that TaSPL17 positively controls grain size and number by regulating spikelet and floret meristem development, which in turn leads to enhanced grain yield per plant. The haplotypes at TaSPL17 indicate geographical differentiation, domestication effects, and breeding selection. CONCLUSION Our study provides valuable resources for genetic improvement of spike morphology and a fast-forward genetic solution for candidate gene detection and cloning in wheat.
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Affiliation(s)
- Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - He Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiliang Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Lipeng Kang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Song Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Aoyue Bi
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Xuebo Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Daxing Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, Beijing, 100081, China
| | - Xueyong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Chenyang Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yan Gong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xuchang Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiwen Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Botao Ye
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danni Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lili Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Fei Lu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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25
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Zhou J, Li W, Yang Y, Xie X, Liu J, Liu Y, Tang H, Deng M, Xu Q, Jiang Q, Chen G, Qi P, Jiang Y, Chen G, He Y, Ren Y, Tang L, Gou L, Zheng Y, Wei Y, Ma J. A promising QTL QSns.sau-MC-3D.1 likely superior to WAPO1 for the number of spikelets per spike of wheat shows no adverse effects on yield-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:181. [PMID: 37550493 DOI: 10.1007/s00122-023-04429-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/24/2023] [Indexed: 08/09/2023]
Abstract
KEY MESSAGE A likely new locus QSns.sau-MC-3D.1 associated with SNS showing no negative effect on yield-related traits compared to WAPO1 was identified and validated in various genetic populations under multiple environments. The number of spikelets per spike (SNS) is one of the crucial factors determining wheat yield. Thus, improving our understanding of the genes that regulate SNS could help develop wheat varieties with higher yield. In this study, a recombinant inbred line (RIL) population (MC) containing 198 lines derived from a cross between msf and Chuannong 16 (CN16) was used to construct a genetic linkage map using the GenoBaits Wheat 16 K Panel. The genetic map contained 5,991 polymorphic SNP markers spanning 2,813.25 cM. A total of twelve QTL for SNS were detected, and two of them, i.e., QSns.sau-MC-3D.1 and QSns.sau-MC-7A, were stably expressed. QSns.sau-MC-3D.1 had high LOD values ranging from 4.99 to 11.06 and explained 9.71-16.75% of the phenotypic variation. Comparison of QSns.sau-MC-3D.1 with previously reported SNS QTL suggested that it is likely a novel one, and two kompetitive allele-specific PCR (KASP) markers were further developed. The positive effect of QSns.sau-MC-3D.1 was also validated in three biparental populations and a diverse panel containing 388 Chinese wheat accessions. Genetic analysis indicated that WHEAT ORTHOLOG OFAPO1 (WAPO1) was a candidate gene for QSns.sau-MC-7A. Pyramiding of QSns.sau-MC-3D.1 and WAP01 had a great additive effect increasing SNS by 7.10%. Correlation analysis suggested that QSns.sau-MC-3D.1 was likely independent of effective tiller number, plant height, spike length, anthesis date, and thousand kernel weight. However, the H2 haplotype of WAPO1 may affect effective tiller number and plant height. These results indicated that utilization of QSns.sau-MC-3D.1 should be given priority for wheat breeding. Geographical distribution analysis showed that the positive allele of QSns.nsau-MC-3D.1 was dominant in most wheat-producing regions of China, and it has been positively selected among modern cultivars released in China since the 1940s. Gene prediction, qRT-PCR analysis, and sequence alignment suggested that TraesCS3D03G0216800 may be the candidate gene of QSns.nsau-MC-3D.1. Taken together, these results enrich our understanding of the genetic basis of wheat SNS and will be useful for fine mapping and cloning of the gene underlying QSns.sau-MC-3D.1.
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Affiliation(s)
- Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaoyao Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xinlin Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanling Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yuanjiang He
- Mianyang Academy of Agricultural Science, Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, China
| | - Yong Ren
- Mianyang Academy of Agricultural Science, Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, China
| | - Liwei Tang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Lulu Gou
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
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Han J, Liu Y, Shen Y, Zhang D, Li W. Transcriptome Dynamics during Spike Differentiation of Wheat Reveal Amazing Changes in Cell Wall Metabolic Regulators. Int J Mol Sci 2023; 24:11666. [PMID: 37511426 PMCID: PMC10380499 DOI: 10.3390/ijms241411666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/12/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
Coordinated cell proliferation and differentiation result in the complex structure of the inflorescence in wheat. It exhibits unique differentiation patterns and structural changes at different stages, which have attracted the attention of botanists studying the dynamic regulation of its genes. Our research aims to understand the molecular mechanisms underlying the regulation of spike development genes at different growth stages. We conducted RNA-Seq and qRT-PCR evaluations on spikes at three stages. Our findings revealed that genes associated with the cell wall and carbohydrate metabolism showed high expression levels between any two stages throughout the entire process, suggesting their regulatory role in early spike development. Furthermore, through transgenic experiments, we elucidated the role of the cell wall regulator gene in spike development regulation. These research results contribute to identifying essential genes associated with the morphology and development of wheat spike tissue.
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Affiliation(s)
- Junjie Han
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832000, China
| | - Yichen Liu
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832000, China
| | - Yiting Shen
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832000, China
| | - Donghai Zhang
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832000, China
| | - Weihua Li
- College of Agriculture, The Key Laboratory of Oasis Eco-Agriculture, Xinjiang Production and Construction Group, Shihezi University, Shihezi 832000, China
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27
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Wang M, Lu J, Liu R, Li Y, Ao D, Wu Y, Zhang L. Identification and validation of a major quantitative trait locus for spike length and compactness in the wheat ( Triticum aestivum L.) line Chuanyu12D7. FRONTIERS IN PLANT SCIENCE 2023; 14:1186183. [PMID: 37469784 PMCID: PMC10353862 DOI: 10.3389/fpls.2023.1186183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/12/2023] [Indexed: 07/21/2023]
Abstract
Spike length (SL) and spike compactness (SC) are crucial traits related to wheat (Triticum aestivum L.) yield potential. In this study, a backcrossed inbred lines (BILs) population segregating for SL/SC was developed by using a commercial variety chuanyu25 as recurrent parent and a backbone parent Chuanyu12D7. Bulked segregant analysis (BSA) combined with the Wheat 660K SNP array was performed to conduct quantitative trait locus (QTL) mapping. A major and stable SL/SC QTL (designated as QSl/Sc.cib-2D.1) was identified on chromosome 2DS, explaining 45.63-59.72% of the phenotypic variation. QSl/Sc.cib-2D.1 was mapped to a 102.29-Kb interval by flanking SNPs AX-110276364 and AX-111593853 using a BC4F2:3 population. Since QSl/Sc.cib-2D.1 is linked to the Rht8 gene, their additive effects on plant type and spike type were analysed. Remarkably, the superior allele of QSl/Sc.cib-2D.1 combined with Rht8 can increase SL and TGW, and decrese SC without any apparent trade-offs in other yield-related traits. In addition, the closely linked kompetitive allele-specific PCR (KASP) markers of this locus were developed for marker-assisted selection (MAS) breeding. Four genes within the physical interval were considered as potential candidates based on expression patterns as well as orthologous gene functions. These results laid the foundation for map-based cloning of the gene(s) underlying QSl/Sc.cib-2D.1 and its potential application in wheat ideotype breeding.
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Affiliation(s)
- Mingxiu Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- Department of Agriculture, Forestry and Food Engineering of Yibin University, Yibin, China
| | - Yunfang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Donghui Ao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yu Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Lei Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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28
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Ning S, Li S, Xu K, Liu D, Ma L, Ma C, Hao M, Zhang L, Chen W, Zhang B, Jiang Y, Huang L, Chen X, Jiang B, Yuan Z, Liu D. Development and Characterization of Near-Isogenic Lines Derived from Synthetic Wheat Revealing the 2 kb Insertion in the PPD-D1 Gene Responsible for Heading Delay and Grain Number Improvement. Int J Mol Sci 2023; 24:10834. [PMID: 37446014 DOI: 10.3390/ijms241310834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Spikelet number and grain number per spike are two crucial and correlated traits for grain yield in wheat. Photoperiod-1 (Ppd-1) is a key regulator of inflorescence architecture and spikelet formation in wheat. In this study, near-isogenic lines derived from the cross of a synthetic hexaploid wheat and commercial cultivars generated by double top-cross and two-phase selection were evaluated for the number of days to heading and other agronomic traits. The results showed that heading time segregation was conferred by a single incomplete dominant gene PPD-D1, and the 2 kb insertion in the promoter region was responsible for the delay in heading. Meanwhile, slightly delayed heading plants and later heading plants obviously have advantages in grain number and spikelet number of the main spike compared with early heading plants. Utilization of PPD-D1 photoperiod sensitivity phenotype as a potential means to increase wheat yield potential.
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Affiliation(s)
- Shunzong Ning
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shengke Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Kai Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Dongmei Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunfang Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenjie Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Bo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Yun Jiang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
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29
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Li Y, Xiong H, Guo H, Zhou C, Fu M, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Wang C, Irshad A, Liu L, Fang Z. Fine mapping and genetic analysis identified a C 2H 2-type zinc finger as a candidate gene for heading date regulation in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:140. [PMID: 37243757 DOI: 10.1007/s00122-023-04363-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 04/08/2023] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE A minor-effect QTL, Qhd.2AS, that affects heading date in wheat was mapped to a genomic interval of 1.70-Mb on 2AS, and gene analysis indicated that the C2H2-type zinc finger protein gene TraesCS2A02G181200 is the best candidate for Qhd.2AS. Heading date (HD) is a complex quantitative trait that determines the regional adaptability of cereal crops, and identifying the underlying genetic elements with minor effects on HD is important for improving wheat production in diverse environments. In this study, a minor QTL for HD that we named Qhd.2AS was detected on the short arm of chromosome 2A by Bulked Segregant Analysis and validated in a recombinant inbred population. Using a segregating population of 4894 individuals, Qhd.2AS was further delimited to an interval of 0.41 cM, corresponding to a genomic region spanning 1.70 Mb (from 138.87 to 140.57 Mb) that contains 16 high-confidence genes based on IWGSC RefSeq v1.0. Analyses of sequence variations and gene transcription indicated that TraesCS2A02G181200, which encodes a C2H2-type zinc finger protein, is the best candidate gene for Qhd.2AS that influences HD. Screening a TILLING mutant library identified two mutants with premature stop codons in TraesCS2A02G181200, both of which exhibited a delay in HD of 2-4 days. Additionally, variations in its putative regulatory sites were widely present in natural accession, and we also identified the allele which was positively selected during wheat breeding. Epistatic analyses indicated that Qhd.2AS-mediated HD variation is independent of VRN-B1 and environmental factors. Phenotypic investigation of homozygous recombinant inbred lines (RILs) and F2:3 families showed that Qhd.2AS has no negative effect on yield-related traits. These results provide important cues for refining HD and therefore improving yield in wheat breeding programs and will deepen our understanding of the genetic regulation of HD in cereal plants.
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Affiliation(s)
- Yuting Li
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongchun Xiong
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijun Guo
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chunyun Zhou
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meiyu Fu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongdun Xie
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Linshu Zhao
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiayu Gu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shirong Zhao
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuping Ding
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaojie Wang
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ahsan Irshad
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Luxiang Liu
- National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Zhengwu Fang
- MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China.
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30
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Yi X, Ye Y, Wang J, Li Z, Li J, Chen Y, Chen G, Ma J, Pu Z, Peng Y, Qi P, Liu Y, Jiang Q, Wang J, Wei Y, Zheng Y, Li W. Identification and validation of two major QTLs for spikelet number per spike in wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1144486. [PMID: 37235013 PMCID: PMC10208070 DOI: 10.3389/fpls.2023.1144486] [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: 01/14/2023] [Accepted: 03/23/2023] [Indexed: 05/28/2023]
Abstract
The total number of spikelets (TSPN) and the number of fertile spikelets (FSPN) affect the final number of grains per spikelet in wheat. This study constructed a high-density genetic map using 55K single nucleotide polymorphism (SNP) arrays from a population of 152 recombinant inbred lines (RIL) from crossing the wheat accessions 10-A and B39. Twenty-four quantitative trait loci (QTLs) for TSPN and 18 QTLs for FSPN were localized based on the phenotype in 10 environments in 2019-2021. Two major QTLs, QTSPN/QFSPN.sicau-2D.4 (34.43-47.43 Mb) and QTSPN/QFSPN.sicau-2D.5(32.97-34.43 Mb), explained 13.97%-45.90% of phenotypic variation. Linked kompetitive allele-specific PCR (KASP) markers further validated these two QTLs and revealed that QTSPN.sicau-2D.4 had less effect on TSPN than QTSPN.sicau-2D.5 in 10-A×BE89 (134 RILs) and 10-A×Chuannong 16 (192 RILs) populations, and one population of Sichuan wheat (233 accessions). The alleles combination haplotype 3 with the allele from 10-A of QTSPN/QFSPN.sicau-2D.5 and the allele from B39 of QTSPN.sicau-2D.4 resulted in the highest number of spikelets. In contrast, the allele from B39 for both loci resulted in the lowest number of spikelets. Using bulk-segregant analysis-exon capture sequencing, six SNP hot spots that included 31 candidate genes were identified in the two QTLs. We identified Ppd-D1a from B39 and Ppd-D1d from 10-A and further analyzed Ppd-D1 variation in wheat. These results identified loci and molecular markers with potential utility for wheat breeding and laid a foundation for further fine mapping and cloning of the two loci.
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Affiliation(s)
- Xiaoyu Yi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yingtong Ye
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jinhui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhen Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiamin Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuqi Chen
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuanying Peng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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31
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Slafer GA, Casas AM, Igartua E. Sense in sensitivity: difference in the meaning of photoperiod-insensitivity between wheat and barley. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad128. [PMID: 37021554 DOI: 10.1093/jxb/erad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Indexed: 06/19/2023]
Abstract
The description of long photoperiod sensitivity in wheat and barley is a cause of confusion for researchers working in these crops, usually accustomed to free exchange of physiological and genetic knowledge of such similar crops. Indeed, wheat and barley scientists customarily quote studies of either crop species when researching one of them. Among their numerous similarities the main gene controlling that response is the same in both crops (PPD1; PPD-H1 in barley and PPD-D1 in hexaploid wheat). However, the photoperiod responses are different: (i) the main dominant allele inducing shorter time to anthesis is the insensitive allele in wheat (Ppd-D1a) but the sensitive allele in barley (Ppd-H1) (i.e. sensitivity to photoperiod produces opposite effects on time to heading in wheat and barley), (ii) the main "insensitive" allele in wheat, Ppd-D1a, does confer insensitivity, whilst that of barley reduces the sensitivity but still responds to photoperiod. The different behaviour of PPD1 genes in wheat and barley is put in a common framework based on the similarities and differences of the molecular bases of their mutations, which include polymorphism at gene expression levels, copy number variation, and sequence of coding regions. This common perspective sheds light on a source on confusion for cereal researchers, and prompts us to recommend accounting for the photoperiod sensitivity status of the plant materials when doing research on genetic control of phenology. Finally, we provide advice to facilitate the management of natural PPD1 diversity in breeding programs and suggest targets for further modification through gene editing, based on mutual knowledge on the two crops.
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Affiliation(s)
- Gustavo A Slafer
- Department of Crop and Forest Sciences University of Lleida and AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25198 Lleida, Spain
- ICREA, Catalonian Institution for Research and Advanced Studies, Spain
| | - Ana M Casas
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD, CSIC, Avda. Montañana 1005, E-50059 Zaragoza, Spain
| | - Ernesto Igartua
- Department of Genetics and Plant Production, Aula Dei Experimental Station, EEAD, CSIC, Avda. Montañana 1005, E-50059 Zaragoza, Spain
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Basu U, Parida SK. The developmental dynamics in cool season legumes with focus on chickpea. PLANT MOLECULAR BIOLOGY 2023; 111:473-491. [PMID: 37016106 DOI: 10.1007/s11103-023-01340-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
Chickpea is one of the most widely consumed grain legume world-wide. Advances in next-generation sequencing and genomics tools have led to genetic dissection and identification of potential candidate genes regulating agronomic traits in chickpea. However, the developmental particularities and its potential in reforming the yield and nutritional value remain largely unexplored. Studies in crops such as rice, maize, tomato and pea have highlighted the contribution of key regulator of developmental events in yield related traits. A comprehensive knowledge on the development aspects of a crop can pave way for new vistas to explore. Pea and Medicago are the close relatives of genus Cicer and the basic developmental events in these legumes are similar. However, there are some distinct developmental features in chickpea which hold potential for future crop improvement endeavours. The global chickpea germplasm encompasses wide range of diversities in terms of morphology at both vegetative and reproductive stages. There is an immediate need for understanding the genetic and molecular basis of this diversity and utilizing them for the yield contributing trait improvement. The review discusses some of the key developmental events which have potential in yield enhancement and the lessons which can be learnt from model legumes in this regard.
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Affiliation(s)
- Udita Basu
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, P.O. Box: 10531, New Delhi, 110067, India
| | - Swarup K Parida
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, P.O. Box: 10531, New Delhi, 110067, India.
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Jiang C, Xu Z, Fan X, Zhou Q, Ji G, Chen L, Yu Q, Liao S, Zhao Y, Feng B, Wang T. Identification and validation of quantitative trait loci for fertile spikelet number per spike and grain number per fertile spikelet in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:69. [PMID: 36952062 DOI: 10.1007/s00122-023-04297-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/26/2022] [Indexed: 06/18/2023]
Abstract
A major and stable QTL for fertile spikelet number per spike and grain number per fertile spikelet identified in a 4.96-Mb interval on chromosome 2A was validated in different genetic backgrounds. Fertile spikelet number per spike (FSN) and grain number per fertile spikelet (GNFS) contribute greatly to wheat yield improvement. To detect quantitative trait loci (QTL) associated with FSN and GNFS, we used a recombinant inbred line population crossed by Zhongkemai 13F10 and Chuanmai 42 in eight environments. Two Genomic regions associated with FSN were detected on chromosomes 2A and 6A using bulked segregant exome sequencing analysis. After the genetic linkage maps were constructed, four QTL QFsn.cib-2A, QFsn.cib-6A, QGnfs.cib-2A and QGnfs.cib-6A were identified in three or more environments. Among them, two major QTL QFsn.cib-2A (LOD = 4.67-9.34, PVE = 6.66-13.05%) and QGnfs.cib-2A (LOD = 5.27-11.68, PVE = 7.95-16.71%) were detected in seven and six environments, respectively. They were co-located in the same region, namely QFsn/Gnfs.cib-2A. The developed linked Kompetitive Allele Specific PCR (KASP) markers further validated this QTL in a different genetic background. QFsn/Gnfs.cib-2A showed pleiotropic effects on grain number per spike (GNS) and spike compactness (SC), and had no effect on grain weight. Since QFsn/Gnfs.cib-2A might be a new locus, it and the developed KASP markers can be used in wheat breeding. According to haplotype analysis, QFsn/Gnfs.cib-2A was identified as a target of artificial selection during wheat improvement. Based on haplotype analysis, sequence differences, spatiotemporal expression patterns, and gene annotation, the potential candidate genes for QFsn/Gnfs.cib-2A were predicted. These results provide valuable information for fine mapping and cloning gene(s) underlying QFsn/Gnfs.cib-2A.
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Affiliation(s)
- Cheng Jiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- College of Life Sciences, Sichuan University, Chengdu, 610064, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Guangsi Ji
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liangen Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qin Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yun Zhao
- College of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Sakuma S, Koppolu R. Form follows function in Triticeae inflorescences. BREEDING SCIENCE 2023; 73:46-56. [PMID: 37168815 PMCID: PMC10165339 DOI: 10.1270/jsbbs.22085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 12/21/2022] [Indexed: 05/13/2023]
Abstract
Grass inflorescences produce grains, which are directly connected to our food. In grass crops, yields are mainly affected by grain number and weight; thus, understanding inflorescence shape is crucially important for cereal crop breeding. In the last two decades, several key genes controlling inflorescence shape have been elucidated, thanks to the availability of rich genetic resources and powerful genomics tools. In this review, we focus on the inflorescence architecture of Triticeae species, including the major cereal crops wheat and barley. We summarize recent advances in our understanding of the genetic basis of spike branching, and spikelet and floret development in the Triticeae. Considering our changing climate and its impacts on cereal crop yields, we also discuss the future orientation of research.
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Affiliation(s)
- Shun Sakuma
- Faculty of Agriculture, Tottori University, Tottori 680-8553, Japan
- Corresponding authors (e-mail: and )
| | - Ravi Koppolu
- Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
- Corresponding authors (e-mail: and )
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Errum A, Rehman N, Uzair M, Inam S, Ali GM, Khan MR. CRISPR/Cas9 editing of wheat Ppd-1 gene homoeologs alters spike architecture and grain morphometric traits. Funct Integr Genomics 2023; 23:66. [PMID: 36840774 DOI: 10.1007/s10142-023-00989-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/26/2023]
Abstract
Mutations in Photoperiod-1 (Ppd-1) gene are known to modify flowering time and yield in wheat. We cloned TaPpd-1 from wheat and found high similarity among the three homoeologs of TaPpd-1. To clarify the characteristics of TaPpd-1 homoeologs in different photoperiod conditions for inflorescence architecture and yield, we used CRISPR/Cas9 system to generate Tappd-1 mutant plants by simultaneous modification of the three homoeologs of wheat Ppd-1. Tappd-1 mutant plants showed no off-target mutations. Four T0-edited lines under short-day length and three lines under long-day length conditions with the mutation frequency of 25% and 21%, respectively. These putative transgenic plants of all the lines were self-fertilized and generated T1 and T2 progenies and were evaluated by phenotypic and expression analysis. Results demonstrated that simultaneously edited TaPpd-1- A1, B1, and D1 homoeologs gene copies in T2_SDL-8-4, T2_SDL-4-5, T2_SDL-3-9, and T2_LDL-10-9 showed similar spike inflorescence, flowering time, and significantly increase in 1000-grain weight, grain area, grain width, grain length, plant height, and spikelets per spike due to mutation in both alleles of Ppd-B1 and Ppd-D1 homoeologs but only spike length was decreased in T2_SDL-8-4, T2_SDL-4-5, and T2_LDL-13-3 mutant lines due to mutation in both alleles of Ppd-A1 homoeolog under both conditions. Our results indicate that all TaPpd1 gene homoeologs influence wheat spike development by affecting both late flowering and earlier flowering but single mutant TaPpd-A1 homoeolog affect lowest as compared to the combination with double mutants of TaPpd-B1 and TaPpd-D1, TaPpd-A1 and TaPpd-B1, and TaPpd-A1 and TaPpd-D1 homoeologs for yield enhancement. Our findings further raised the idea that the relative expression of the various genomic copies of TaPpd-1 homoeologs may have an impact on the spike inflorescence architecture and grain morphometric features in wheat cultivars.
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Affiliation(s)
- Aliya Errum
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
- PARC Institute of Advanced Studies in Agriculture (PIASA), Islamabad, Pakistan
| | - Nazia Rehman
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | - Safeena Inam
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan
| | | | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology (NIGAB), National Agricultural Research Centre (NARC), Park Road, Islamabad, 45500, Pakistan.
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Horváth Á, Kiss T, Berki Z, Horváth ÁD, Balla K, Cseh A, Veisz O, Karsai I. Effects of genetic components of plant development on yield-related traits in wheat ( Triticum aestivum L.) under stress-free conditions. FRONTIERS IN PLANT SCIENCE 2023; 13:1070410. [PMID: 36844908 PMCID: PMC9945125 DOI: 10.3389/fpls.2022.1070410] [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: 10/14/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
The dynamics of plant development not only has an impact on ecological adaptation but also contributes to the realization of genetically determined yield potentials in various environments. Dissecting the genetic determinants of plant development becomes urgent due to the global climate change, which can seriously affect and even disrupt the locally adapted developmental patterns. In order to determine the role plant developmental loci played in local adaptation and yield formation, a panel of 188 winter and facultative wheat cultivars from diverse geographic locations were characterized with the 15K Illumina Single Nucleotide Polymorphism (SNP) chip and functional markers of several plant developmental genes and included into a multiseason field experiment. Genome-wide association analyses were conducted on five consecutive developmental phases spanning from the first node appearance to full heading together with various grain yield-related parameters. The panel was balanced for the PPD-D1 photoperiod response gene, which facilitated the analyses in the two subsets of photoperiod-insensitive and -sensitive genotypes in addition to the complete panel. PPD-D1 was the single highest source, explaining 12.1%-19.0% of the phenotypic variation in the successive developmental phases. In addition, 21 minor developmental loci were identified, each one explaining only small portions of the variance, but, together, their effects amounted to 16.6%-50.6% of phenotypic variance. Eight loci (2A_27, 2A_727, 4A_570, 5B_315, 5B_520, 6A_26, 7A_1-(VRN-A3), and 7B_732) were independent of PPD-D1. Seven loci were only detectable in the PPD-D1-insensitive genetic background (1A_539, 1B_487, 2D_649, 4A_9, 5A_584-(VRN-A1), 5B_571-(VRN-B1), and 7B_3-(VRN-B3)), and six loci were only detectable in the sensitive background, specifically 2A_740, 2D_25, 3A_579, 3B_414, 7A_218, 7A_689, and 7B_538. The combination of PPD-D1 insensitivity and sensitivity with the extremities of early or late alleles in the corresponding minor developmental loci resulted in significantly altered and distinct plant developmental patterns with detectable outcomes on some yield-related traits. This study examines the possible significance of the above results in ecological adaptation.
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Affiliation(s)
- Ádám Horváth
- Agricultural Institute, Centre of Agriculture, Eötvös Loránd Research Network (ELKH), Martonvásár, Hungary
| | - Tibor Kiss
- Agricultural Institute, Centre of Agriculture, Eötvös Loránd Research Network (ELKH), Martonvásár, Hungary
- Food and Wine Research Institute, Eszterházy Károly Catholic University, Eger, Hungary
| | - Zita Berki
- Agricultural Institute, Centre of Agriculture, Eötvös Loránd Research Network (ELKH), Martonvásár, Hungary
| | - Ádám D. Horváth
- Agricultural Institute, Centre of Agriculture, Eötvös Loránd Research Network (ELKH), Martonvásár, Hungary
| | - Krisztina Balla
- Agricultural Institute, Centre of Agriculture, Eötvös Loránd Research Network (ELKH), Martonvásár, Hungary
| | - András Cseh
- Agricultural Institute, Centre of Agriculture, Eötvös Loránd Research Network (ELKH), Martonvásár, Hungary
| | - Ottó Veisz
- Agricultural Institute, Centre of Agriculture, Eötvös Loránd Research Network (ELKH), Martonvásár, Hungary
| | - Ildikó Karsai
- Agricultural Institute, Centre of Agriculture, Eötvös Loránd Research Network (ELKH), Martonvásár, Hungary
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Slafer GA, Foulkes MJ, Reynolds MP, Murchie EH, Carmo-Silva E, Flavell R, Gwyn J, Sawkins M, Griffiths S. A 'wiring diagram' for sink strength traits impacting wheat yield potential. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:40-71. [PMID: 36334052 PMCID: PMC9786893 DOI: 10.1093/jxb/erac410] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 11/04/2022] [Indexed: 05/17/2023]
Abstract
Identifying traits for improving sink strength is a bottleneck to increasing wheat yield. The interacting processes determining sink strength and yield potential are reviewed and visualized in a set of 'wiring diagrams', covering critical phases of development (and summarizing known underlying genetics). Using this framework, we reviewed and assembled the main traits determining sink strength and identified research gaps and potential hypotheses to be tested for achieving gains in sink strength. In pre-anthesis, grain number could be increased through: (i) enhanced spike growth associated with optimized floret development and/or a reduction in specific stem-internode lengths and (ii) improved fruiting efficiency through an accelerated rate of floret development, improved partitioning between spikes, or optimized spike cytokinin levels. In post-anthesis, grain, sink strength could be augmented through manipulation of grain size potential via ovary size and/or endosperm cell division and expansion. Prospects for improving spike vascular architecture to support all rapidly growing florets, enabling the improved flow of assimilate, are also discussed. Finally, we considered the prospects for enhancing grain weight realization in relation to genetic variation in stay-green traits as well as stem carbohydrate remobilization. The wiring diagrams provide a potential workspace for breeders and crop scientists to achieve yield gains in wheat and other field crops.
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Affiliation(s)
| | | | - Matthew P Reynolds
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mexico, El Batan, Texcoco, Mexico
| | - Erik H Murchie
- Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire LE12 5RD, UK
| | | | - Richard Flavell
- International Wheat Yield Partnership, 1500 Research Parkway, College Station, TX 77843, USA
| | - Jeff Gwyn
- International Wheat Yield Partnership, 1500 Research Parkway, College Station, TX 77843, USA
| | - Mark Sawkins
- International Wheat Yield Partnership, 1500 Research Parkway, College Station, TX 77843, USA
| | - Simon Griffiths
- John Innes Centre, Norwich Research Park, Colney Ln, Norwich NR4 7UH, UK
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Trevaskis B, Harris FAJ, Bovill WD, Rattey AR, Khoo KHP, Boden SA, Hyles J. Advancing understanding of oat phenology for crop adaptation. FRONTIERS IN PLANT SCIENCE 2022; 13:955623. [PMID: 36311119 PMCID: PMC9614419 DOI: 10.3389/fpls.2022.955623] [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: 05/29/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
Oat (Avena sativa) is an annual cereal grown for forage, fodder and grain. Seasonal flowering behaviour, or phenology, is a key contributor to the success of oat as a crop. As a species, oat is a vernalization-responsive long-day plant that flowers after winter as days lengthen in spring. Variation in both vernalization and daylength requirements broadens adaptation of oat and has been used to breed modern cultivars with seasonal flowering behaviours suited to different regions, sowing dates and farming practices. This review examines the importance of variation in oat phenology for crop adaptation. Strategies to advance understanding of the genetic basis of oat phenology are then outlined. These include the potential to transfer knowledge from related temperate cereals, particularly wheat (Triticum aestivum) and barley (Hordeum vulgare), to provide insights into the potential molecular basis of variation in oat phenology. Approaches that use emerging genomic resources to directly investigate the molecular basis of oat phenology are also described, including application of high-resolution genome-wide diversity surveys to map genes linked to variation in flowering behaviour. The need to resolve the contribution of individual phenology genes to crop performance by developing oat genetic resources, such as near-isogenic lines, is emphasised. Finally, ways that deeper knowledge of oat phenology can be applied to breed improved varieties and to inform on-farm decision-making are outlined.
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Affiliation(s)
- Ben Trevaskis
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food Business Unit, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | - Felicity A. J. Harris
- Department of Primary Industries, Pine Gully Road, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW, Australia
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - William D. Bovill
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food Business Unit, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
| | | | - Kelvin H. P. Khoo
- School of Agriculture, Food & Wine, Faculty of Sciences, Waite Research Institute, University of Adelaide, Urrbrae, Adelaide, SA, Australia
| | - Scott A. Boden
- School of Agriculture, Food & Wine, Faculty of Sciences, Waite Research Institute, University of Adelaide, Urrbrae, Adelaide, SA, Australia
| | - Jessica Hyles
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food Business Unit, Black Mountain Science and Innovation Park, Canberra, ACT, Australia
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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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40
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McSteen P, Kellogg EA. Molecular, cellular, and developmental foundations of grass diversity. Science 2022; 377:599-602. [PMID: 35926032 DOI: 10.1126/science.abo5035] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Humans have cultivated grasses for food, feed, beverages, and construction materials for millennia. Grasses also dominate the landscape in vast parts of the world, where they have adapted morphologically and physiologically, diversifying to form ~12,000 species. Sequences of hundreds of grass genomes show that they are essentially collinear; nonetheless, not all species have the same complement of genes. Here, we focus on the molecular, cellular, and developmental bases of grain yield and dispersal-traits that are essential for domestication. Distinct genes, networks, and pathways were selected in different crop species, reflecting underlying genomic diversity. With increasing genomic resources becoming available in nondomesticated species, we anticipate advances in coming years that illuminate the ecological and economic success of the grasses.
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Affiliation(s)
- Paula McSteen
- Division of Biological Sciences, Bond Life Sciences Center, Interdisciplinary Plant Group, University of Missouri, 1201 Rollins Street, Columbia, MO 65211, USA
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Wang Y, Du F, Wang J, Wang K, Tian C, Qi X, Lu F, Liu X, Ye X, Jiao Y. Improving bread wheat yield through modulating an unselected AP2/ERF gene. NATURE PLANTS 2022; 8:930-939. [PMID: 35851621 DOI: 10.1038/s41477-022-01197-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Crop breeding heavily relies on natural genetic variation. However, additional new variations are desired to meet the increasing human demand. Inflorescence architecture determines grain number per spike, a major determinant of bread wheat (Triticum aestivum L.) yield. Here, using Brachypodium distachyon as a wheat proxy, we identified DUO-B1, encoding an APETALA2/ethylene response factor (AP2/ERF) transcription factor, regulating spike inflorescence architecture in bread wheat. Mutations of DUO-B1 lead to mild supernumerary spikelets, increased grain number per spike and, importantly, increased yield under field conditions without affecting other major agronomic traits. DUO-B1 suppresses cell division and promotes the expression of BHt/WFZP, whose mutations could lead to branched 'miracle-wheat'. Pan-genome analysis indicated that DUO-B1 has not been utilized in breeding, and holds promise to increase wheat yield further.
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Affiliation(s)
- Yuange Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Fei Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jian Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Ke Wang
- National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Caihuan Tian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xiaoquan Qi
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fei Lu
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xigang Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Xingguo Ye
- National Key Facility of Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, China.
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, China.
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Zhang J, Tang Y, Pu X, Qiu X, Wang J, Li T, Yang Z, Zhou Y, Chang Y, Liang J, Zhang H, Deng G, Long H. Genetic and transcriptomic dissection of an artificially induced paired spikelets mutant of wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2543-2554. [PMID: 35695919 DOI: 10.1007/s00122-022-04137-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Morphological, genetic and transcriptomic characterizations of an EMS-induced wheat paired spikelets (PS) mutant were performed. A novel qualitative locus WPS1 on chromosome 1D was identified. Grain yield of wheat is significantly associated with inflorescence or spike architecture. However, few genes related to wheat spike development have been identified and their underlying mechanisms are largely unknown. In this study, we characterized an ethyl methanesulfonate (EMS)-induced wheat mutant, wheat paired spikelets 1 (wps1). Unlike a single spikelet that usually develops at each node of rachis, a secondary spikelet appeared below the primary spikelet at most of the rachis nodes of wps1. The microscope observation showed that the secondary spikelet initiated later than the primary spikelet. Genetic analysis suggested that the PS of wps1 is controlled by a single dominant nuclear gene, designated WHEAT PAIRED SPIKELETS 1 (WPS1). Further RNA-seq based bulked segregant analysis and molecular marker mapping localized WPS1 in an interval of 208.18-220.92 Mb on the chromosome arm 1DL, which is different to known genes related to spike development in wheat. By using wheat omics data, TraesCS1D02G155200 encoding a HD-ZIP III transcription factor was considered as a strong candidate gene for WPS1. Transcriptomic analysis indicated that PS formation in wps1 is associated with auxin-related pathways and may be regulated by networks involving TB1, Ppd1, FT1, VRN1, etc. This study laid the solid foundation for further validation of the causal gene of WPS1 and explored its regulatory mechanism in PS formation and inflorescence development, which may benefit to kernel yield improvement of wheat based on optimization or design of spike architecture in the future.
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Affiliation(s)
- Juanyu Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yanyan Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xi Pu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Xuebing Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Jinhui Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Tao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Zhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yao Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China
| | - Yuxiao Chang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, Guangdong, China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China.
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43
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Zhong J, Kong F. The control of compound inflorescences: insights from grasses and legumes. TRENDS IN PLANT SCIENCE 2022; 27:564-576. [PMID: 34973922 DOI: 10.1016/j.tplants.2021.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/16/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
A major challenge in biology is to understand how organisms have increased developmental complexity during evolution. Inflorescences, with remarkable variation in branching systems, are a fitting model to understand architectural complexity. Inflorescences bear flowers that may become fruits and/or seeds, impacting crop productivity and species fitness. Great advances have been achieved in understanding the regulation of complex inflorescences, particularly in economically and ecologically important grasses and legumes. Surprisingly, a synthesis is still lacking regarding the common or distinct principles underlying the regulation of inflorescence complexity. Here, we synthesize the similarities and differences in the regulation of compound inflorescences in grasses and legumes, and propose that the emergence of novel higher-order repetitive modules is key to the evolution of inflorescence complexity.
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Affiliation(s)
- Jinshun Zhong
- School of Life Sciences, South China Agricultural University, Wushan Street 483, Guangzhou 510642, China; Institute for Plant Genetics, Heinrich-Heine University, Universitätsstraße 1, D-40225 Düsseldorf, Germany; Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Köln, Germany; Cluster of Excellence on Plant Sciences, 'SMART Plants for Tomorrow's Needs', Heinrich-Heine University, Universitätsstraße 1, D-40225 Düsseldorf, Germany.
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China.
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44
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Dixon LE, Pasquariello M, Badgami R, Levin KA, Poschet G, Ng PQ, Orford S, Chayut N, Adamski NM, Brinton J, Simmonds J, Steuernagel B, Searle IR, Uauy C, Boden SA. MicroRNA-resistant alleles of HOMEOBOX DOMAIN-2 modify inflorescence branching and increase grain protein content of wheat. SCIENCE ADVANCES 2022; 8:eabn5907. [PMID: 35544571 PMCID: PMC9094671 DOI: 10.1126/sciadv.abn5907] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/25/2022] [Indexed: 05/26/2023]
Abstract
Plant and inflorescence architecture determine the yield potential of crops. Breeders have harnessed natural diversity for inflorescence architecture to improve yields, and induced genetic variation could provide further gains. Wheat is a vital source of protein and calories; however, little is known about the genes that regulate the development of its inflorescence. Here, we report the identification of semidominant alleles for a class III homeodomain-leucine zipper transcription factor, HOMEOBOX DOMAIN-2 (HB-2), on wheat A and D subgenomes, which generate more flower-bearing spikelets and enhance grain protein content. These alleles increase HB-2 expression by disrupting a microRNA 165/166 complementary site with conserved roles in plants; higher HB-2 expression is associated with modified leaf and vascular development and increased amino acid supply to the inflorescence during grain development. These findings enhance our understanding of genes that control wheat inflorescence development and introduce an approach to improve the nutritional quality of grain.
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Affiliation(s)
- Laura E. Dixon
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Marianna Pasquariello
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Roshani Badgami
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Kara A. Levin
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Gernot Poschet
- Centre of Organismal Studies (COS), University of Heidelberg, Heidelberg 69120, Germany
| | - Pei Qin Ng
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Simon Orford
- Germplasm Resources Unit, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Noam Chayut
- Germplasm Resources Unit, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Nikolai M. Adamski
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jemima Brinton
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - James Simmonds
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Burkhard Steuernagel
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Iain R. Searle
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Scott A. Boden
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia
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45
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DeWitt N, Guedira M, Murphy JP, Marshall D, Mergoum M, Maltecca C, Brown-Guedira G. A network modeling approach provides insights into the environment-specific yield architecture of wheat. Genetics 2022; 221:6583185. [PMID: 35536185 PMCID: PMC9252273 DOI: 10.1093/genetics/iyac076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/01/2022] [Indexed: 11/12/2022] Open
Abstract
Wheat (Triticum aestivum) yield is impacted by a diversity of developmental processes which interact with the environment during plant growth. This complex genetic architecture complicates identifying quantitative trait loci (QTL) that can be used to improve yield. Trait data collected on individual processes or components of yield have simpler genetic bases and can be used to model how QTL generate yield variation. The objectives of this experiment were to identify QTL affecting spike yield, evaluate how their effects on spike yield proceed from effects on component phenotypes, and to understand how the genetic basis of spike yield variation changes between environments. A 358 F5:6 RIL population developed from the cross of LA-95135 and SS-MPV-57 was evaluated in two replications at five locations over the 2018 and 2019 seasons. The parents were two soft red winter wheat cultivars differing in flowering, plant height, and yield component characters. Data on yield components and plant growth were used to assemble a structural equation model (SEM) to characterize the relationships between QTL, yield components and overall spike yield. The effects of major QTL on spike yield varied by environment, and their effects on total spike yield were proportionally smaller than their effects on component traits. This typically resulted from contrasting effects on component traits, where an increase in traits associated with kernel number was generally associated with a decrease in traits related to kernel size. In all, the complete set of identified QTL was sufficient to explain most of the spike yield variation observed within each environment. Still, the relative importance of individual QTL varied dramatically. Path analysis based on coefficients estimated through SEM demonstrated that these variations in effects resulted from both different effects of QTL on phenotypes and environment-by-environment differences in the effects of phenotypes on one another, providing a conceptual model for yield genotype-by-environment interactions in wheat.
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Affiliation(s)
- Noah DeWitt
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA 27695.,USDA-ARS SEA,Plant Science Research, Raleigh, NC, USA 27695
| | - Mohammed Guedira
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA 27695
| | - J Paul Murphy
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA 27695
| | - David Marshall
- USDA-ARS SEA,Plant Science Research, Raleigh, NC, USA 27695
| | - Mohamed Mergoum
- Department of Crop and Soil Sciences, University of Georgia, Athens, 30602, GA, USA
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, USA 27695
| | - Gina Brown-Guedira
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, USA 27695.,USDA-ARS SEA,Plant Science Research, Raleigh, NC, USA 27695
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46
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Reynolds MP, Slafer GA, Foulkes JM, Griffiths S, Murchie EH, Carmo-Silva E, Asseng S, Chapman SC, Sawkins M, Gwyn J, Flavell RB. A wiring diagram to integrate physiological traits of wheat yield potential. NATURE FOOD 2022; 3:318-324. [PMID: 37117579 DOI: 10.1038/s43016-022-00512-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 04/30/2023]
Abstract
As crop yields are pushed closer to biophysical limits, achieving yield gains becomes increasingly challenging and will require more insight into deterministic pathways to yields. Here, we propose a wiring diagram as a platform to illustrate the interrelationships of the physiological traits that impact wheat yield potential and to serve as a decision support tool for crop scientists. The wiring diagram is based on the premise that crop yield is a function of photosynthesis (source), the investment of assimilates into reproductive organs (sinks) and the underlying processes that enable expression of both. By illustrating these linkages as coded wires, the wiring diagram can show connections among traits that may not have been apparent, and can inform new research hypotheses and guide crosses designed to accumulate beneficial traits and alleles in breeding. The wiring diagram can also serve to create an ever-richer common point of reference for refining crop models in the future.
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Affiliation(s)
| | - Gustavo Ariel Slafer
- Catalonian Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
- Center for Research in Agrotechnology (AGROTECNIO), Lleida, Spain.
- University of Lleida, Lleida, Spain.
| | | | | | | | | | | | | | - Mark Sawkins
- International Wheat Yield Partnership (IWYP), College Station, TX, USA
- Texas A&M AgriLife Research, Weslaco, TX, USA
| | - Jeff Gwyn
- International Wheat Yield Partnership (IWYP), College Station, TX, USA
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47
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Chen Z, Ke W, He F, Chai L, Cheng X, Xu H, Wang X, Du D, Zhao Y, Chen X, Xing J, Xin M, Guo W, Hu Z, Su Z, Liu J, Peng H, Yao Y, Sun Q, Ni Z. A single nucleotide deletion in the third exon of FT-D1 increases the spikelet number and delays heading date in wheat (Triticum aestivum L.). PLANT BIOTECHNOLOGY JOURNAL 2022; 20:920-933. [PMID: 34978137 PMCID: PMC9055817 DOI: 10.1111/pbi.13773] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/02/2021] [Accepted: 12/24/2021] [Indexed: 05/31/2023]
Abstract
The spikelet number and heading date are two crucial and correlated traits for yield in wheat. Here, a quantitative trait locus (QTL) analysis was conducted in F8 recombinant inbred lines (RILs) derived from crossing two common wheats with different spikelet numbers. A total of 15 stable QTL influencing total spikelet number (TSN) and heading date (HD) were detected. Notably, FT-D1, a well-known flowering time gene in wheat, was located within the finely mapped interval of a major QTL on 7DS (QTsn/Hd.cau-7D). A causal indel of one G in the third exon of FT-D1 was significantly associated with total spikelet number and heading date. Consistently, CRISPR/Cas9 mutant lines with homozygous mutations in FT-D1 displayed an increase in total spikelet number and heading date when compared with wild type. Moreover, one simple and robust marker developed according to the polymorphic site of FT-D1 revealed that this one G indel had been preferentially selected to adapt to different environments. Collectively, these data provide further insights into the genetic basis of spikelet number and heading date, and the diagnostic marker of FT-D1 will be useful for marker-assisted pyramiding in wheat breeding.
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Affiliation(s)
- Zhaoyan Chen
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Wensheng Ke
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Fei He
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Lingling Chai
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJCIC‐MCPCIC‐MCPNanjing Agricultural UniversityNanjingChina
| | - Huanwen Xu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Xiaobo Wang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Dejie Du
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Yidi Zhao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Xiyong Chen
- Hebei Crop Genetic Breeding LaboratoryInstitute of Cereal and Oil CropsHebei Academy of Agriculture and Forestry SciencesShijiazhuangChina
| | - Jiewen Xing
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Zhenqi Su
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Jie Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE)Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijingChina
- National Plant Gene Research CentreBeijingChina
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48
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Zhang C, Chang W, Li X, Yang B, Zhang L, Xiao Z, Li J, Lu K. Transcriptome and Small RNA Sequencing Reveal the Mechanisms Regulating Harvest Index in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:855486. [PMID: 35444672 PMCID: PMC9014204 DOI: 10.3389/fpls.2022.855486] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Harvest index (HI), the ratio of harvested seed weight to total aboveground biomass weight, is an economically critical value reflecting the convergence of complex agronomic traits. HI values in rapeseed (Brassica napus) remain much lower than in other major crops, and the underlying regulatory network is largely unknown. In this study, we performed mRNA and small RNA sequencing to reveal the mechanisms shaping HI in B. napus during the seed-filling stage. A total of 8,410 differentially expressed genes (DEGs) between high-HI and low-HI accessions in four tissues (silique pericarp, seed, leaves, and stem) were identified. Combining with co-expression network, 72 gene modules were identified, and a key gene BnaSTY46 was found to participate in retarded establishment of photosynthetic capacity to influence HI. Further research found that the genes involved in circadian rhythms and response to stimulus may play important roles in HI and that their transcript levels were modulated by differentially expressed microRNAs (DEMs), and we identified 903 microRNAs (miRNAs), including 46 known miRNAs and 857 novel miRNAs. Furthermore, transporter activity-related genes were critical to enhancing HI in good cultivation environments. Of 903 miRNAs, we found that the bna-miR396-Bna.A06SRp34a/Bna.A01EMB3119 pair may control the seed development and the accumulation of storage compounds, thus contributing to higher HI. Our findings uncovered the underlying complex regulatory network behind HI and offer potential approaches to rapeseed improvement.
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Affiliation(s)
- Chao Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Oil Research Institute of Guizhou Province, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Wei Chang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xiaodong Li
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Bo Yang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Liyuan Zhang
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Zhongchun Xiao
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jiana Li
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Kun Lu
- Chongqing Rapeseed Engineering Research Center, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
- Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
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49
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Katz A, Byrne P, Reid S, Bratschun S, Haley S, Pearce S. Identification and validation of a QTL for spikelet number on chromosome arm 6BL of common wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:17. [PMID: 37309457 PMCID: PMC10248590 DOI: 10.1007/s11032-022-01288-7] [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: 07/30/2021] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
To provide food security for a growing world population, it will be necessary to increase yields of staple crops such as wheat (Triticum aestivum L.). Yield is a complex, polygenic trait influenced by grain weight and number, which are negatively correlated with one another. Spikelet number is an important determinant of grain number, but allelic variants impacting its expression are often associated with heading date, constraining their use in wheat germplasm that must be adapted for specific environments. Identification and characterization of genetic variants affecting spikelet number will increase selection efficiency through their deployment in breeding programs. In this study, a quantitative trait locus (QTL) on chromosome arm 6BL for spikelet number was identified and validated using an association mapping panel, a recombinant inbred line population, and seven derived heterogeneous inbred families. The superior allele, QSn.csu-6Bb, was associated with an increase of 0.248 to 0.808 spikelets per spike across multiple environments that varied for mean spikelet number. Despite epistatic interactions between QSn.csu-6B and three other loci (WAPO-A1, VRN-D3, and PPD-B1), genotypes with a greater number of superior alleles at these loci consistently exhibit higher spikelet number. The frequency of superior alleles at these loci varies among winter wheat varieties adapted to different latitudes of the US Great Plains, revealing opportunities for breeders to select for increased spikelet number using simple molecular markers. This work lays the foundation for the positional cloning of the genetic variant underlying the QSn.csu-6B QTL to strengthen our understanding of spikelet number determination in wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01288-7.
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Affiliation(s)
- Andrew Katz
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Patrick Byrne
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Scott Reid
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Sarah Bratschun
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Scott Haley
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Stephen Pearce
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
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50
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Koppolu R, Jiang G, Milner SG, Muqaddasi QH, Rutten T, Himmelbach A, Guo Y, Stein N, Mascher M, Schnurbusch T. The barley mutant multiflorus2.b reveals quantitative genetic variation for new spikelet architecture. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:571-590. [PMID: 34773464 PMCID: PMC8866347 DOI: 10.1007/s00122-021-03986-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/26/2021] [Indexed: 05/26/2023]
Abstract
Spikelet indeterminacy and supernumerary spikelet phenotypes in barley multiflorus2.b mutant show polygenic inheritance. Genetic analysis of multiflorus2.b revealed major QTLs for spikelet determinacy and supernumerary spikelet phenotypes on 2H and 6H chromosomes. Understanding the genetic basis of yield forming factors in small grain cereals is of extreme importance, especially in the wake of stagnation of further yield gains in these crops. One such yield forming factor in these cereals is the number of grain-bearing florets produced per spikelet. Wild-type barley (Hordeum vulgare L.) spikelets are determinate structures, and the spikelet axis (rachilla) degenerates after producing single floret. In contrast, the rachilla of wheat (Triticum ssp.) spikelets, which are indeterminate, elongates to produce up to 12 florets. In our study, we characterized the barley spikelet determinacy mutant multiflorus2.b (mul2.b) that produced up to three fertile florets on elongated rachillae of lateral spikelets. Apart from the lateral spikelet indeterminacy (LS-IN), we also characterized the supernumerary spikelet phenotype in the central spikelets (CS-SS) of mul2.b. Through our phenotypic and genetic analyses, we identified two major QTLs on chromosomes 2H and 6H, and two minor QTLs on 3H for the LS-IN phenotype. For, the CS-SS phenotype, we identified one major QTL on 6H, and a minor QTL on 5H chromosomes. Notably, the 6H QTLs for CS-SS and LS-IN phenotypes co-located with each other, potentially indicating that a single genetic factor might regulate both phenotypes. Thus, our in-depth phenotyping combined with genetic analyses revealed the quantitative nature of the LS-IN and CS-SS phenotypes in mul2.b, paving the way for cloning the genes underlying these QTLs in the future.
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Affiliation(s)
- Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany.
| | - Guojing Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
| | - Sara G Milner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
| | - Quddoos H Muqaddasi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
- BASF Agricultural Solutions GmbH, Am Schwabeplan 8, OT Gatersleben, 06466, Seeland, Germany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
| | - Yu Guo
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
- Department of Crop Sciences, Center of Integrated Breeding Research (CiBreed), Georg-August-University, 37075, Göttingen, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Correns Strasse 3, OT Gatersleben, 06466, Seeland, Germany.
- Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany.
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