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Sreedasyam A, Lovell JT, Mamidi S, Khanal S, Jenkins JW, Plott C, Bryan KB, Li Z, Shu S, Carlson J, Goodstein D, De Santiago L, Kirkbride RC, Calleja S, Campbell T, Koebernick JC, Dever JK, Scheffler JA, Pauli D, Jenkins JN, McCarty JC, Williams M, Boston L, Webber J, Udall JA, Chen ZJ, Bourland F, Stiller WN, Saski CA, Grimwood J, Chee PW, Jones DC, Schmutz J. Genome resources for three modern cotton lines guide future breeding efforts. NATURE PLANTS 2024; 10:1039-1051. [PMID: 38816498 PMCID: PMC11208153 DOI: 10.1038/s41477-024-01713-z] [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: 10/27/2023] [Accepted: 04/27/2024] [Indexed: 06/01/2024]
Abstract
Cotton (Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars ('UGA230', 'UA48' and 'CSX8308') and updating the 'TM-1' cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from 'Pima' cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.
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Affiliation(s)
- Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- DOE Joint Genome Institute, Berkeley, CA, USA.
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sameer Khanal
- Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, USA
| | - Jerry W Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Christopher Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kempton B Bryan
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Zhigang Li
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | | | | | | | - Luis De Santiago
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Ryan C Kirkbride
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | | | - Todd Campbell
- USDA-ARS, Coastal Plains Soil Water and Plant Research Center, Florence, SC, USA
| | - Jenny C Koebernick
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Jane K Dever
- Texas A&M AgriLife Research, Lubbock, TX, USA
- Pee Dee Research and Education Center, Clemson University, Florence, SC, USA
| | | | - Duke Pauli
- School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Johnie N Jenkins
- USDA-ARS, Genetics and Sustainable Agriculture Research Unit, Mississippi State, MS, USA
| | - Jack C McCarty
- USDA-ARS, Genetics and Sustainable Agriculture Research Unit, Mississippi State, MS, USA
| | - Melissa Williams
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - LoriBeth Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jenell Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Joshua A Udall
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX, USA
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Fred Bourland
- Northeast Research and Extension Center (NEREC), University of Arkansas, Keiser, AR, USA
| | - Warwick N Stiller
- CSIRO Agriculture and Food Cotton Research Unit, Narrabri, New South Wales, Australia
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Peng W Chee
- Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Tifton, GA, USA
| | - Don C Jones
- Agriculture and Environmental Research Cotton Incorporated, Cary, NC, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
- DOE Joint Genome Institute, Berkeley, CA, USA.
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Gu J, Struik PC, Evers JB, Lertngim N, Lin R, Driever SM. Quantifying differences in plant architectural development between hybrid potato (Solanum tuberosum) plants grown from two types of propagules. ANNALS OF BOTANY 2024; 133:365-378. [PMID: 38099505 PMCID: PMC11005760 DOI: 10.1093/aob/mcad194] [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: 08/15/2023] [Accepted: 12/13/2023] [Indexed: 04/11/2024]
Abstract
BACKGROUND AND AIMS Plants can propagate generatively and vegetatively. The type of propagation and the resulting propagule can influence the growth of the plants, such as plant architectural development and pattern of biomass allocation. Potato is a species that can reproduce through both types of propagation: through true botanical seeds and seed tubers. The consequences of propagule type on the plant architectural development and biomass partitioning in potatoes are not well known. We quantified architectural differences between plants grown from these two types of propagules from the same genotype, explicitly analysing branching dynamics above and below ground, and related these differences to biomass allocation patterns. METHODS A greenhouse experiment was conducted, using potato plants of the same genotype but grown from two types of propagules: true seeds and seed tubers from a plant grown from true seed (seedling tuber). Architectural traits and biomass allocation to different organs were quantified at four developmental stages. Differences between true-seed-grown and seedling-tuber-grown plants were compared at the whole-plant level and at the level of individual stems and branches, including their number, size and location on the plant. KEY RESULTS A more branched and compact architecture was produced in true-seed-grown plants compared with seedling-tuber-grown plants. The architectural differences between plants grown from true seeds and seedling tubers appeared gradually and were attributed mainly to the divergent temporal-spatial distribution of lateral branches above and below ground on the main axis. The continual production of branches in true-seed-grown plants indicated their indeterminate growth habit, which was also reflected in a slower shift of biomass allocation from above- to below-ground branches, whereas the opposite trend was found in seedling-tuber-grown plants. CONCLUSIONS In true-seed-grown plants, lateral branching was stronger and determined whole-plant architecture and plant function with regard to light interception and biomass production, compared with seedling-tuber-grown plants. This different role of branching indicates that a difference in preference between clonal and sexual reproduction might exist. The divergent branching behaviours in true-seed-grown and seedling-tuber-grown plants might be regulated by the different intensity of apical dominance, which suggests that the control of branching can depend on the propagule type.
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Affiliation(s)
- Jiahui Gu
- Centre for Crop Systems Analysis, Wageningen University & Research, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Paul C Struik
- Centre for Crop Systems Analysis, Wageningen University & Research, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Jochem B Evers
- Centre for Crop Systems Analysis, Wageningen University & Research, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Narawitch Lertngim
- Centre for Crop Systems Analysis, Wageningen University & Research, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Ruokai Lin
- Centre for Crop Systems Analysis, Wageningen University & Research, PO Box 430, 6700 AK Wageningen, The Netherlands
| | - Steven M Driever
- Centre for Crop Systems Analysis, Wageningen University & Research, PO Box 430, 6700 AK Wageningen, The Netherlands
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Baguma JK, Mukasa SB, Nuwamanya E, Alicai T, Omongo CA, Ochwo-Ssemakula M, Ozimati A, Esuma W, Kanaabi M, Wembabazi E, Baguma Y, Kawuki RS. Identification of Genomic Regions for Traits Associated with Flowering in Cassava ( Manihot esculenta Crantz). PLANTS (BASEL, SWITZERLAND) 2024; 13:796. [PMID: 38592820 PMCID: PMC10974989 DOI: 10.3390/plants13060796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/25/2024] [Accepted: 01/26/2024] [Indexed: 04/11/2024]
Abstract
Flowering in cassava (Manihot esculenta Crantz) is crucial for the generation of botanical seed for breeding. However, genotypes preferred by most farmers are erect and poor at flowering or never flower. To elucidate the genetic basis of flowering, 293 diverse cassava accessions were evaluated for flowering-associated traits at two locations and seasons in Uganda. Genotyping using the Diversity Array Technology Pty Ltd. (DArTseq) platform identified 24,040 single-nucleotide polymorphisms (SNPs) distributed on the 18 cassava chromosomes. Population structure analysis using principal components (PCs) and kinships showed three clusters; the first five PCs accounted for 49.2% of the observed genetic variation. Linkage disequilibrium (LD) estimation averaged 0.32 at a distance of ~2850 kb (kilo base pairs). Polymorphism information content (PIC) and minor allele frequency (MAF) were 0.25 and 0.23, respectively. A genome-wide association study (GWAS) analysis uncovered 53 significant marker-trait associations (MTAs) with flowering-associated traits involving 27 loci. Two loci, SNPs S5_29309724 and S15_11747301, were associated with all the traits. Using five of the 27 SNPs with a Phenotype_Variance_Explained (PVE) ≥ 5%, 44 candidate genes were identified in the peak SNP sites located within 50 kb upstream or downstream, with most associated with branching traits. Eight of the genes, orthologous to Arabidopsis and other plant species, had known functional annotations related to flowering, e.g., eukaryotic translation initiation factor and myb family transcription factor. This study identified genomic regions associated with flowering-associated traits in cassava, and the identified SNPs can be useful in marker-assisted selection to overcome hybridization challenges, like unsynchronized flowering, and candidate gene validation.
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Affiliation(s)
- Julius K. Baguma
- School of Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (S.B.M.); (E.N.); (M.O.-S.)
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Settumba B. Mukasa
- School of Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (S.B.M.); (E.N.); (M.O.-S.)
| | - Ephraim Nuwamanya
- School of Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (S.B.M.); (E.N.); (M.O.-S.)
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Titus Alicai
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Christopher Abu Omongo
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
- National Agricultural Research Organisation (NARO), Entebbe P.O. Box 295, Uganda;
| | - Mildred Ochwo-Ssemakula
- School of Agricultural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda; (S.B.M.); (E.N.); (M.O.-S.)
| | - Alfred Ozimati
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
- School of Biological Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Williams Esuma
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
- National Agricultural Research Organisation (NARO), Entebbe P.O. Box 295, Uganda;
| | - Michael Kanaabi
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Enoch Wembabazi
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
| | - Yona Baguma
- National Agricultural Research Organisation (NARO), Entebbe P.O. Box 295, Uganda;
| | - Robert S. Kawuki
- National Crops Resources Research Institute, Namulonge (NaCRRI), Kampala P.O. Box 7084, Uganda; (T.A.); (C.A.O.); (A.O.); (W.E.); (M.K.); (E.W.); (R.S.K.)
- National Agricultural Research Organisation (NARO), Entebbe P.O. Box 295, Uganda;
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Kuznetsova K, Efremova E, Dodueva I, Lebedeva M, Lutova L. Functional Modules in the Meristems: "Tinkering" in Action. PLANTS (BASEL, SWITZERLAND) 2023; 12:3661. [PMID: 37896124 PMCID: PMC10610496 DOI: 10.3390/plants12203661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND A feature of higher plants is the modular principle of body organisation. One of these conservative morphological modules that regulate plant growth, histogenesis and organogenesis is meristems-structures that contain pools of stem cells and are generally organised according to a common principle. Basic content: The development of meristems is under the regulation of molecular modules that contain conservative interacting components and modulate the expression of target genes depending on the developmental context. In this review, we focus on two molecular modules that act in different types of meristems. The WOX-CLAVATA module, which includes the peptide ligand, its receptor and the target transcription factor, is responsible for the formation and control of the activity of all meristem types studied, but it has its own peculiarities in different meristems. Another regulatory module is the so-called florigen-activated complex, which is responsible for the phase transition in the shoot vegetative meristem (e.g., from the vegetative shoot apical meristem to the inflorescence meristem). CONCLUSIONS The review considers the composition and functions of these two functional modules in different developmental programmes, as well as their appearance, evolution and use in plant breeding.
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Affiliation(s)
| | | | - Irina Dodueva
- Department of Genetics and Biotechnology, Saint Petersburg State University, Universitetskaya Emb. 7/9, 199034 Saint Petersburg, Russia; (K.K.); (E.E.); (M.L.); (L.L.)
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Zhao H, Huang X, Yang Z, Li F, Ge X. Synergistic optimization of crops by combining early maturation with other agronomic traits. TRENDS IN PLANT SCIENCE 2023; 28:1178-1191. [PMID: 37208203 DOI: 10.1016/j.tplants.2023.04.011] [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: 11/21/2022] [Revised: 04/16/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
Many newly created early maturing varieties exhibit poor stress resistance and low yield, whereas stress-resistant varieties are typically late maturing. For this reason, the polymerization of early maturity and other desired agronomic qualities requires overcoming the negative connection between early maturity, multi-resistance, and yield, which presents a formidable challenge in current breeding techniques. We review the most salient constraints of early maturity breeding in current crop planting practices and the molecular mechanisms of different maturation timeframes in diverse crops from their origin center to production areas. We explore current breeding tactics and the future direction of crop breeding and the issues that must be resolved to accomplish the polymerization of desirable traits in light of the current obstacles and limitations.
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Affiliation(s)
- Hang Zhao
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; College of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Xianzhong Huang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Chuzhou, China
| | - Zhaoen Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100 Xinjiang, China; Hainan Yazhou Bay Seed Lab, Sanya 572000, Hainan, China.
| | - Xiaoyang Ge
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou 450001, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, 831100 Xinjiang, China; Hainan Yazhou Bay Seed Lab, Sanya 572000, Hainan, China.
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Li D, Lu X, Qian D, Wang P, Tang D, Zhong Y, Shang Y, Guo H, Wang Z, Zhu G, Zhang C. Dissected Leaf 1 encodes an MYB transcription factor that controls leaf morphology in potato. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:183. [PMID: 37555965 DOI: 10.1007/s00122-023-04430-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: 03/27/2023] [Accepted: 07/24/2023] [Indexed: 08/10/2023]
Abstract
KEY MESSAGE The transcription factor StDL1 regulates dissected leaf formation in potato and the genotype frequency of recessive Stdl1/Stdl1, which results in non-dissected leaves, has increased in cultivated potatoes. Leaf morphology is a key trait of plants, influencing plant architecture, photosynthetic efficiency and yield. Potato (Solanum tuberosum L.), the third most important food crop worldwide, has a diverse leaf morphology. However, despite the recent identification of several genes regulating leaf formation in other plants, few genes involved in potato leaf development have been reported. In this study, we identified an R2R3 MYB transcription factor, Dissected Leaf 1 (StDL1), regulating dissected leaf formation in potato. A naturally occurring allele of this gene, Stdl1, confers non-dissected leaves in young seedlings. Knockout of StDL1 in a diploid potato changes the leaf morphology from dissected to non-dissected. Experiments in N. benthamiana and yeast show that StDL1 is a transcriptional activator. Notably, by calculating the genotype frequency of the Stdl1/Stdl1 in 373-potato accessions, we found that it increases significantly in cultivated potatoes. This work reveals the genetic basis of dissected leaf formation in potato and provides insights into plant leaf morphology.
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Affiliation(s)
- Dawei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xiaoyue Lu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Duoduo Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen, 518120, China
| | - Pei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Dié Tang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yang Zhong
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yi Shang
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650000, China
| | - Han Guo
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhen Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Guangtao Zhu
- Yunnan Key Laboratory of Potato Biology, The AGISCAAS-YNNU Joint Academy of Potato Sciences, Yunnan Normal University, Kunming, 650000, China.
| | - Chunzhi Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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Labadie M, Guy K, Demené MN, Caraglio Y, Heidsieck G, Gaston A, Rothan C, Guédon Y, Pradal C, Denoyes B. Spatio-temporal analysis of strawberry architecture: insights into the control of branching and inflorescence complexity. JOURNAL OF EXPERIMENTAL BOTANY 2023:7143673. [PMID: 37133320 DOI: 10.1093/jxb/erad097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 04/25/2023] [Indexed: 05/04/2023]
Abstract
Plant architecture plays a major role in flowering and therefore in crop yield. Attempts to visualize and analyse strawberry plant architecture have been few to date. Here, we developed open-source software combining two- and three-dimensional representations of plant development over time along with statistical methods to explore the variability in spatio-temporal development of plant architecture in cultivated strawberry. We applied this software to six seasonal strawberry varieties whose plants were exhaustively described monthly at the node scale. Results showed that the architectural pattern of the strawberry plant is characterized by a decrease of the module complexity between the zeroth-order module (primary crown) and higher-order modules (lateral branch crowns and extension crowns). Furthermore, for each variety, we could identify traits with a central role in determining yield, such as date of appearance and number of branches. By modeling the spatial organization of axillary meristem fate on the zeroth-order module using a hidden hybrid Markov/semi-Markov mathematical model, we further identified three zones with different probabilities of production of branch crowns, dormant buds, or stolons. This open-source software will be of value to the scientific community and breeders in studying the influence of environmental and genetic cues on strawberry architecture and yield.
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Affiliation(s)
- Marc Labadie
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140, France
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
| | - Karine Guy
- INVENIO, MIN de Brienne, 110 quai de Paludate, 33800 Bordeaux, France
| | | | - Yves Caraglio
- CIRAD, UMR AMAP and Université de Montpellier, 34398 Montpellier, France
| | - Gaetan Heidsieck
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140, France
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
| | - Amelia Gaston
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140, France
| | - Christophe Rothan
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140, France
| | - Yann Guédon
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
| | - Christophe Pradal
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- Inria and LIRMM, Univ Montpellier, CNRS, Montpellier, France
| | - Béatrice Denoyes
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140, France
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Pierik R, Fankhauser C, Strader LC, Sinha N. Architecture and plasticity: optimizing plant performance in dynamic environments. PLANT PHYSIOLOGY 2021; 187:1029-1032. [PMID: 34734285 PMCID: PMC8566305 DOI: 10.1093/plphys/kiab402] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 08/21/2021] [Indexed: 06/13/2023]
Abstract
Plasticity in plant architecture drives plant performance through dedicated molecular networks.
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Affiliation(s)
- Ronald Pierik
- Plant Ecophysiology, Department of Biology, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Christian Fankhauser
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Lucia C Strader
- Department of Biology, Duke University, Durham, North Carolina 27278, USA
| | - Neelima Sinha
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, California 95616, USA
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