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Rychel-Bielska S, Bielski W, Surma A, Annicchiarico P, Belter J, Kozak B, Galek R, Harzic N, Książkiewicz M. A GWAS study highlights significant associations between a series of indels in a FLOWERING LOCUS T gene promoter and flowering time in white lupin (Lupinus albus L.). BMC PLANT BIOLOGY 2024; 24:722. [PMID: 39075363 PMCID: PMC11285409 DOI: 10.1186/s12870-024-05438-1] [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: 02/13/2023] [Accepted: 07/19/2024] [Indexed: 07/31/2024]
Abstract
BACKGROUND White lupin (Lupinus albus L.) is a high-protein Old World grain legume with remarkable food and feed production interest. It is sown in autumn or early spring, depending on the local agroclimatic conditions. This study aimed to identify allelic variants associated with vernalization responsiveness, in order to improve our knowledge of legume flowering regulatory pathways and develop molecular selection tools for the desired phenology as required for current breeding and adaptation to the changing climate. RESULTS Some 120 white lupin accessions originating from a wide range of environments of Europe, Africa, and Asia were phenotyped under field conditions in three environments with different intensities of vernalization, namely, a Mediterranean and a subcontinental climate sites of Italy under autumn sowing, and a suboceanic climate site of France under spring sowing. Two hundred sixty-two individual genotypes extracted from them were phenotyped in a greenhouse under long-day photoperiod without vernalization. Phenology data, and marker data generated by Diversity Arrays Technology sequencing (DArT-seq) and by PCR-based screening targeting published quantitative trait loci (QTLs) from linkage map and newly identified insertion/deletion polymorphisms in the promoter region of the FLOWERING LOCUS T homolog, LalbFTc1 gene (Lalb_Chr14g0364281), were subjected to a genome-wide association study (GWAS). Population structure followed differences in phenology and isolation by distance pattern. The GWAS highlighted numerous loci significantly associated with flowering time, including four LalbFTc1 gene promoter deletions: 2388 bp and 2126 bp deletions at the 5' end, a 264 bp deletion in the middle and a 28 bp deletion at the 3' end of the promoter. Besides LalbFTc1 deletions, this set contained DArT-seq markers that matched previously published major QTLs in chromosomes Lalb_Chr02, Lalb_Chr13 and Lalb_Chr16, and newly discovered QTLs in other chromosomes. CONCLUSIONS This study highlighted novel QTLs for flowering time and validated those already published, thereby providing novel evidence on the convergence of FTc1 gene functional evolution into the vernalization pathway in Old World lupin species. Moreover, this research provided the set of loci specific for extreme phenotypes (the earliest or the latest) awaiting further implementation in marker-assisted selection for spring- or winter sowing.
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Affiliation(s)
- Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 24A, Wrocław, 50-363, Poland
| | - Wojciech Bielski
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, Poznan, 60-632, Poland
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznań, 60-479, Poland
| | - Anna Surma
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznań, 60-479, Poland
| | - Paolo Annicchiarico
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture, Viale Piacenza 29, Lodi, 26900, Italy
| | - Jolanta Belter
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznań, 60-479, Poland
| | - Bartosz Kozak
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 24A, Wrocław, 50-363, Poland
| | - Renata Galek
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 24A, Wrocław, 50-363, Poland
| | - Nathalie Harzic
- Cérience, 1 Allée de la Sapinière, Saint Sauvant, 86600, France
| | - Michał Książkiewicz
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznań, 60-479, Poland.
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2
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Feng L, Teng F, Li N, Zhang JC, Zhang BJ, Tsai SN, Yue XL, Gu LF, Meng GH, Deng TQ, Tong SW, Wang CM, Li Y, Shi W, Zeng YL, Jiang YM, Yu W, Ngai SM, An LZ, Lam HM, He JX. A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and drought-tolerance mechanisms. PLANT COMMUNICATIONS 2024; 5:100891. [PMID: 38561965 PMCID: PMC11287142 DOI: 10.1016/j.xplc.2024.100891] [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: 09/02/2023] [Revised: 02/26/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
Plants that grow in extreme environments represent unique sources of stress-resistance genes and mechanisms. Ammopiptanthus mongolicus (Leguminosae) is a xerophytic evergreen broadleaf shrub native to semi-arid and desert regions; however, its drought-tolerance mechanisms remain poorly understood. Here, we report the assembly of a reference-grade genome for A. mongolicus, describe its evolutionary history within the legume family, and examine its drought-tolerance mechanisms. The assembled genome is 843.07 Mb in length, with 98.7% of the sequences successfully anchored to the nine chromosomes of A. mongolicus. The genome is predicted to contain 47 611 protein-coding genes, and 70.71% of the genome is composed of repetitive sequences; these are dominated by transposable elements, particularly long-terminal-repeat retrotransposons. Evolutionary analyses revealed two whole-genome duplication (WGD) events at 130 and 58 million years ago (mya) that are shared by the genus Ammopiptanthus and other legumes, but no species-specific WGDs were found within this genus. Ancestral genome reconstruction revealed that the A. mongolicus genome has undergone fewer rearrangements than other genomes in the legume family, confirming its status as a "relict plant". Transcriptomic analyses demonstrated that genes involved in cuticular wax biosynthesis and transport are highly expressed, both under normal conditions and in response to polyethylene glycol-induced dehydration. Significant induction of genes related to ethylene biosynthesis and signaling was also observed in leaves under dehydration stress, suggesting that enhanced ethylene response and formation of thick waxy cuticles are two major mechanisms of drought tolerance in A. mongolicus. Ectopic expression of AmERF2, an ethylene response factor unique to A. mongolicus, can markedly increase the drought tolerance of transgenic Arabidopsis thaliana plants, demonstrating the potential for application of A. mongolicus genes in crop improvement.
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Affiliation(s)
- Lei Feng
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China; Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Fei Teng
- BGI-Shenzhen Tech Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Na Li
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Jia-Cheng Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Bian-Jiang Zhang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Sau-Na Tsai
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Xiu-Le Yue
- School of Life Sciences and Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou 730030, China
| | - Li-Fei Gu
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Guang-Hua Meng
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Tian-Quan Deng
- BGI-Shenzhen Tech Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Suk-Wah Tong
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Chun-Ming Wang
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Yan Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
| | - Wei Shi
- BGI-Shenzhen Tech Co., Ltd., Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Yong-Lun Zeng
- State Key Laboratory of Plant Diversity and Specialty Crops, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yue-Ming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Weichang Yu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Sai-Ming Ngai
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China
| | - Li-Zhe An
- School of Life Sciences and Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou 730030, China; State Key Laboratory of Efficient Production of Forest Resources, Beijing Forestry University, Beijing 100083, China.
| | - Hon-Ming Lam
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China.
| | - Jun-Xian He
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong, China.
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Ye D, Xie M, Liu T, Huang H, Zhang X, Yu H, Zheng Z, Wang Y, Tang Y, Li T. Physiological and molecular responses in phosphorus-hyperaccumulating Polygonum species to high phosphorus exposure. PLANT, CELL & ENVIRONMENT 2024; 47:2475-2490. [PMID: 38567814 DOI: 10.1111/pce.14895] [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: 09/05/2023] [Revised: 02/16/2024] [Accepted: 03/11/2024] [Indexed: 06/06/2024]
Abstract
Phosphorus (P)-hyperaccumulators for phytoextraction from P-polluted areas generally show rapid growth and accumulate large amounts of P without any toxicity symptom, which depends on a range of physiological processes and gene expression patterns that have never been explored. We investigated growth, leaf element concentrations, P fractions, photosynthetic traits, and leaf metabolome and transcriptome response in amphibious P-hyperaccumulators, Polygonum hydropiper and P. lapathifolium, to high-P exposure (5 mmol L-1), with 0.05 mmol L-1 as the control. Under high-P exposure, both species demonstrated good growth, allocating more P to metabolite P and inorganic P (Pi) accompanied by high potassium and calcium. The expression of a cluster of unigenes associated with photosynthesis was maintained or increased in P. lapathifolium, explaining the increase in net photosynthetic rate and the rapid growth under high-P exposure. Metabolites of trehalose metabolism, including trehalose 6-phosphate and trehalose, were sharply increased in both species by the high-P exposure, in line with the enhanced expression of associated unigenes, indicating that trehalose metabolic pathway was closely related to high-P tolerance. These findings elucidated the physiological and molecular responses involved in the photosynthesis and trehalose metabolism in P-hyperaccumulators to high-P exposure, and provides potential regulatory pathways to improve the P-phytoextraction capability.
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Affiliation(s)
- Daihua Ye
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Min Xie
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tao Liu
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huagang Huang
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xizhou Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Haiying Yu
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zicheng Zheng
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yongdong Wang
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu Tang
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tingxuan Li
- College of Resources, Sichuan Agricultural University, Chengdu, Sichuan, China
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4
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Luo B, Zhang G, Yu T, Zhang C, Yang G, Luo X, Zhang S, Guo J, Zhang H, Zheng H, Tang Z, Li Q, Lan Y, Ma P, Nie Z, Zhang X, Liu D, Wu L, Gao D, Gao S, Su S, Guo J, Gao S. Genome-wide association studies dissect low-phosphorus stress response genes underling field and seedling traits in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:172. [PMID: 38935162 DOI: 10.1007/s00122-024-04681-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Phosphorus (P) is an essential element for plant growth, and its deficiency can cause decreased crop yield. This study systematically evaluated the low-phosphate (Pi) response traits in a large population at maturity and seedling stages, and explored candidate genes and their interrelationships with specific traits. The results revealed a greater sensitivity of seedling maize to low-Pi stress compared to that at maturity stage. The phenotypic response patterns to low-Pi stress at different stages were independent. Chlorophyll content was found to be a potential indicator for screening low-Pi-tolerant materials in the field. A total of 2900 and 1446 significantly associated genes at the maturity and seedling stages were identified, respectively. Among these genes, 972 were uniquely associated with maturity traits, while 330 were specifically detected at the seedling stage under low-Pi stress. Moreover, 768 and 733 genes were specifically associated with index values (low-Pi trait/normal-Pi trait) at maturity and seedling stage, respectively. Genetic network diagrams showed that the low-Pi response gene Zm00001d022226 was specifically associated with multiple primary P-related traits under low-Pi conditions. A total of 963 out of 2966 genes specifically associated with traits under low-Pi conditions or index values were found to be induced by low-Pi stress. Notably, ZmSPX4.1 and ZmSPX2 were sharply up-regulated in response to low-Pi stress across different lines or tissues. These findings advance our understanding of maize's response to low-Pi stress at different developmental stages, shedding light on the genes and pathways implicated in this response.
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Affiliation(s)
- Bowen Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, Sichuan, China
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Guidi Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Ting Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Chong Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Guohui Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Xianfu Luo
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Shuhao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Jianyong Guo
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Haiying Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Hao Zheng
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zirui Tang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qile Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yuzhou Lan
- Department of Plant Breeding, The Swedish University of Agricultural Sciences, P.O. Box 190, 23422, Lomma, Sweden
| | - Peng Ma
- Mianyang Academy of Agricultural Sciences, Mianyang, 621023, Sichuan, China
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang, China
| | - Zhi Nie
- Sichuan Academy of Agricultural Sciences, Biotechnology and Nuclear Technology Research Institute, Chengdu, China
| | - Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Dan Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Ling Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Duojiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Shiqiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China
| | - Shunzong Su
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jia Guo
- Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shibin Gao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130, Sichuan, China.
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130, Sichuan, China.
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5
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Bhat MA, Mishra AK, Shah SN, Bhat MA, Jan S, Rahman S, Baek KH, Jan AT. Soil and Mineral Nutrients in Plant Health: A Prospective Study of Iron and Phosphorus in the Growth and Development of Plants. Curr Issues Mol Biol 2024; 46:5194-5222. [PMID: 38920984 PMCID: PMC11201952 DOI: 10.3390/cimb46060312] [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: 04/09/2024] [Revised: 05/17/2024] [Accepted: 05/19/2024] [Indexed: 06/27/2024] Open
Abstract
Plants being sessile are exposed to different environmental challenges and consequent stresses associated with them. With the prerequisite of minerals for growth and development, they coordinate their mobilization from the soil through their roots. Phosphorus (P) and iron (Fe) are macro- and micronutrient; P serves as an important component of biological macromolecules, besides driving major cellular processes, including photosynthesis and respiration, and Fe performs the function as a cofactor for enzymes of vital metabolic pathways. These minerals help in maintaining plant vigor via alterations in the pH, nutrient content, release of exudates at the root surface, changing dynamics of root microbial population, and modulation of the activity of redox enzymes. Despite this, their low solubility and relative immobilization in soil make them inaccessible for utilization by plants. Moreover, plants have evolved distinct mechanisms to cope with these stresses and coregulate the levels of minerals (Fe, P, etc.) toward the maintenance of homeostasis. The present study aims at examining the uptake mechanisms of Fe and P, and their translocation, storage, and role in executing different cellular processes in plants. It also summarizes the toxicological aspects of these minerals in terms of their effects on germination, nutrient uptake, plant-water relationship, and overall yield. Considered as an important and indispensable component of sustainable agriculture, a separate section covers the current knowledge on the cross-talk between Fe and P and integrates complete and balanced information of their effect on plant hormone levels.
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Affiliation(s)
- Mujtaba Aamir Bhat
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, J&K, India; (M.A.B.); (S.N.S.); (M.A.B.); (S.J.)
| | - Awdhesh Kumar Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | - Sheezma Nazir Shah
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, J&K, India; (M.A.B.); (S.N.S.); (M.A.B.); (S.J.)
| | - Mudasir Ahmad Bhat
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, J&K, India; (M.A.B.); (S.N.S.); (M.A.B.); (S.J.)
| | - Saima Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, J&K, India; (M.A.B.); (S.N.S.); (M.A.B.); (S.J.)
| | - Safikur Rahman
- Department of Botany, Munshi Singh College, BR Ambedkar Bihar University, Muzaffarpur 845401, Bihar, India;
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri 185234, J&K, India; (M.A.B.); (S.N.S.); (M.A.B.); (S.J.)
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6
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Zhong Q, Liang S. Phosphorus balancing for optimal crop yields. NATURE FOOD 2024; 5:277-278. [PMID: 38671233 DOI: 10.1038/s43016-024-00970-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Affiliation(s)
- Qiumeng Zhong
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, P.R. China
| | - Sai Liang
- Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, Key Laboratory for City Cluster Environmental Safety and Green Development of the Ministry of Education, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, P.R. China.
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7
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Fang C, Jiang N, Teresi SJ, Platts AE, Agarwal G, Niederhuth C, Edger PP, Jiang J. Dynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry. Nat Commun 2024; 15:2491. [PMID: 38509076 PMCID: PMC10954716 DOI: 10.1038/s41467-024-46861-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.
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Affiliation(s)
- Chao Fang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA
| | - Adrian E Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Gaurav Agarwal
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Chad Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, 48824, USA.
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
- Michigan State University AgBioResearch, East Lansing, MI, 48824, USA.
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Luo J, Chen Z, Huang R, Wu Y, Liu C, Cai Z, Dong R, Arango J, Rao IM, Schultze-Kraft R, Liu G, Liu P. Multi-omics analysis reveals the roles of purple acid phosphatases in organic phosphorus utilization by the tropical legume Stylosanthes guianensis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:729-746. [PMID: 37932930 DOI: 10.1111/tpj.16526] [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: 01/03/2022] [Accepted: 10/23/2023] [Indexed: 11/08/2023]
Abstract
Stylo (Stylosanthes guianensis) is a tropical legume known for its exceptional tolerance to low phosphate (Pi), a trait believed to be linked to its high acid phosphatase (APase) activity. Previous studies have observed genotypic variations in APase activity in stylo; however, the gene encoding the crucial APase responsible for this variation remains unidentified. In this study, transcriptomic and proteomic analyses were employed to identify eight Pi starvation-inducible (PSI) APases belonging to the purple APase (PAP) family in the roots of stylo and seven in the leaves. Among these PSI-PAPs, SgPAP7 exhibited a significantly positive correlation in its expression levels with the activities of both internal APase and root-associated APase across 20 stylo genotypes under low-Pi conditions. Furthermore, the recombinant SgPAP7 displayed high catalytic activity toward adenosine 5'-diphosphate (ADP) and phosphoenolpyruvate (PEP) in vitro. Overexpression (OE) of SgPAP7 in Arabidopsis facilitated exogenous organic phosphorus utilization. Moreover, SgPAP7 OE lines showed lower shoot ADP and PEP levels than the wild type, implying that SgPAP7 is involved in the catabolism and recycling of endogenous ADP and PEP, which could be beneficial for plant growth in low-Pi soils. In conclusion, SgPAP7 is a key gene with a major role in stylo adaptation to low-Pi conditions by facilitating the utilization of both exogenous and endogenous organic phosphorus sources. It may also function as a PEP phosphatase involved in a glycolytic bypass pathway that minimizes the need for adenylates and Pi. Thus, SgPAP7 could be a promising target for improving tolerance of crops to low-Pi availability.
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Affiliation(s)
- Jiajia Luo
- Tropical Crops Genetic Resources Institute & National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Zhijian Chen
- Tropical Crops Genetic Resources Institute & National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Rui Huang
- Tropical Crops Genetic Resources Institute & National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Yuanhang Wu
- College of Tropical Crops & College of Forestry, Hainan University, Haikou, 570228, China
| | - Chun Liu
- Tropical Crops Genetic Resources Institute & National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
- College of Tropical Crops & College of Forestry, Hainan University, Haikou, 570228, China
| | - Zeping Cai
- College of Tropical Crops & College of Forestry, Hainan University, Haikou, 570228, China
| | - Rongshu Dong
- Tropical Crops Genetic Resources Institute & National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Jacobo Arango
- Alliance of Bioversity International and International Center for Tropical Agriculture, Cali, 763537, Colombia
| | - Idupulapati Madhusudana Rao
- Alliance of Bioversity International and International Center for Tropical Agriculture, Cali, 763537, Colombia
| | - Rainer Schultze-Kraft
- Alliance of Bioversity International and International Center for Tropical Agriculture, Cali, 763537, Colombia
| | - Guodao Liu
- Tropical Crops Genetic Resources Institute & National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Pandao Liu
- Tropical Crops Genetic Resources Institute & National Key Laboratory for Tropical Crop Breeding, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
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Dou T, Gao F, Zhu J, Wang Z, Yang X, Hao Y, Song N, An S, Yin X, Liu X. Evolutionary analysis and biological characterization of a novel alphabaculovirus isolated from Mythimna separata. J Gen Virol 2024; 105. [PMID: 38376497 DOI: 10.1099/jgv.0.001958] [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] [Indexed: 02/21/2024] Open
Abstract
Baculoviruses are insect-specific pathogens. Novel baculovirus isolates provide new options for the biological control of pests. Therefore, research into the biological characteristics of newly isolated baculoviruses, including accurate classification and nomenclature, is important. In this study, a baculovirus was isolated from Mythimna separata and its complete genome sequence was determined by next-generation sequencing. The double-stranded DNA genome was 153 882 bp in length, encoding 163 open reading frames. The virus was identified as a variant of Mamestra brassicae multiple nucleopolyhedrovirus (MbMNPV) and designated Mamestra brassicae multiple nucleopolyhedrovirus CHN1 (MbMNPV-CHN1) according to ultrastructural analysis, genome comparison and phylogenetic analysis. Phylogenetic inference placed MbMNPV-CHN1 in a clade containing isolates of MacoNPV-A, MacoNPV-B and MbMNPV, which we have designated the Mb-McNPV group. The genomes of isolates in the Mb-McNPV group exhibited a high degree of collinearity with relatively minor differences in the content of annotated open reading frames. The development of codon usage bias in the Mb-McNPV group was affected mainly by natural selection. MbMNPV-CHN1 shows high infectivity against seven species of Lepidoptera. The yield of MbMNPV-CHN1 in the fourth- and fifth-instar M. separata larvae was 6.25×109-1.23×1010 OBs/cadaver. Our data provide insights into the classification, host range and virulence differences among baculoviruses of the Mb-McNPV group, as well as a promising potential new baculoviral insecticide.
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Affiliation(s)
- Tao Dou
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Futao Gao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Junhua Zhu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Zihao Wang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Xifa Yang
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Youwu Hao
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
| | - Shiheng An
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
| | - Xinming Yin
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
| | - Xiangyang Liu
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
- Henan Engineering Laboratory of Pest Biological Control, Zhengzhou 450046, PR China
- NanoAgro CenterCollege of Plant Protection, Henan Agricultural University, Zhengzhou 450046, PR China
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10
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Wang R, Funayama-Noguchi S, Xiong Z, Staudinger C, Wasaki J. Phosphorus absorption kinetics and exudation strategies of roots developed by three lupin species to tackle P deficiency. PLANTA 2023; 259:29. [PMID: 38133691 DOI: 10.1007/s00425-023-04307-9] [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: 07/21/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023]
Abstract
MAIN CONCLUSION Different lupin species exhibited varied biomass, P allocation, and physiological responses to P-deprivation. White and yellow lupins had higher carboxylate exudation rates, while blue lupin showed the highest phosphatase activity. White lupin (Lupinus albus) can produce specialized root structures, called cluster roots, which are adapted to low-phosphorus (P) soil. Blue lupin (L. angustifolius) and yellow lupin (L. luteus), which are two close relatives of white lupin, do not produce cluster roots. This study characterized plant responses to nutrient limitation by analyzing biomass accumulation and P distribution, absorption kinetics and root exudation in white, blue, and yellow lupins. Plants were grown in hydroponic culture with (64 µM NaH2PO4) or without P for 31 days. Under P limitation, more biomass was allocated to roots to improve P absorption. Furthermore, the relative growth rate of blue lupin showed the strongest inhibition. Under + P conditions, the plant total-P contents of blue lupin and yellow lupin were higher than that of white lupin. To elucidate the responses of lupins via the perspective of absorption kinetics and secretion analysis, blue and yellow lupins were confirmed to have stronger affinity and absorption capacity for orthophosphate after P-deprivation cultivation, whereas white lupin and yellow lupin had greater ability to secrete organic acids. The exudation of blue lupin had higher acid phosphatase activity. This study elucidated that blue lupin was more sensitive to P-scarcity stress and yellow had the greater tolerance of P-deficient condition than either of the other two lupin species. The three lupin species have evolved different adaptation strategies to cope with P deficiency.
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Affiliation(s)
- Ruixin Wang
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima, 739-8521, Japan
| | - Sachiko Funayama-Noguchi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo, 113-8657, Japan
| | - Zilin Xiong
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima, 739-8521, Japan
| | - Christiana Staudinger
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima, 739-8521, Japan
- Department of Crop Sciences, University of Natural Resources and Life Sciences (BOKU), Konrad Lorenz Str. 24, 3430, Tulln, Austria
| | - Jun Wasaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima, 739-8521, Japan.
- Seto Inland Sea Carbon Neutral Research Center, Hiroshima University, Higashi-Hiroshima, Japan.
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11
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Zhang K, Zhang L, Cui Y, Yang Y, Wu J, Liang J, Li X, Zhang X, Zhang Y, Guo Z, Zhang L, Chen S, Ruan J, Freeling M, Wang X, Cheng F. The lack of negative association between TE load and subgenome dominance in synthesized Brassica allotetraploids. Proc Natl Acad Sci U S A 2023; 120:e2305208120. [PMID: 37816049 PMCID: PMC10589682 DOI: 10.1073/pnas.2305208120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/01/2023] [Indexed: 10/12/2023] Open
Abstract
Polyploidization is important to the evolution of plants. Subgenome dominance is a distinct phenomenon associated with most allopolyploids. A gene on the dominant subgenome tends to express to higher RNA levels in all organs as compared to the expression of its syntenic paralogue (homoeolog). The mechanism that underlies the formation of subgenome dominance remains unknown, but there is evidence for the involvement of transposon/DNA methylation density differences nearby the genes of parents as being causal. The subgenome with lower density of transposon and methylation near genes is positively associated with subgenome dominance. Here, we generated eight generations of allotetraploid progenies from the merging of parental genomes Brassica rapa and Brassica oleracea. We found that transposon/methylation density differ near genes between the parental (rapa:oleracea) existed in the wide hybrid, persisted in the neotetraploids (the synthetic Brassica napus), but these neotetraploids expressed no expected subgenome dominance. This absence of B. rapa vs. B. oleracea subgenome dominance is particularly significant because, while there is no negative relationship between transposon/methylation level and subgenome dominance in the neotetraploids, the more ancient parental subgenomes for all Brassica did show differences in transposon/methylation densities near genes and did express, in the same samples of cells, biased gene expression diagnostic of subgenome dominance. We conclude that subgenome differences in methylated transposon near genes are not sufficient to initiate the biased gene expressions defining subgenome dominance. Our result was unexpected, and we suggest a "nuclear chimera" model to explain our data.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Lingkui Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Yinan Cui
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
- Chengde Academy of Agriculture and Forestry Sciences, Chengde067032, China
| | - Yinqing Yang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Jian Wu
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Jianli Liang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Xing Li
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Xin Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Yiyue Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Zhongwei Guo
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Lei Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Shumin Chen
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Jue Ruan
- 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, Shenzhen518120, China
| | - Michael Freeling
- Department of Plant and Microbial Biology, University of California, Berkeley, CA94720-3102
| | - Xiaowu Wang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing100081, China
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12
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Sun M, Zheng C, Feng W, Shao J, Pang C, Li P, Dong H. Low soil available phosphorus level reduces cotton fiber length via osmoregulation. FRONTIERS IN PLANT SCIENCE 2023; 14:1254103. [PMID: 37662180 PMCID: PMC10471804 DOI: 10.3389/fpls.2023.1254103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/01/2023] [Indexed: 09/05/2023]
Abstract
Introduction Phosphorus (P) deficiency hinders cotton (Gossypium hirustum L.) growth and development, seriously affecting lint yield and fiber quality. However, it is still unclear how P fertilizer affects fiber length. Methods Therefore, a two-year (2019-2020) pool-culture experiment was conducted using the split-plot design, with two cotton cultivars (CCRI-79; low-P tolerant and SCRC-28; low-P sensitive) as the main plot. Three soil available phosphorus (AP) contents (P0: 3 ± 0.5, P1: 6 ± 0.5, and P2 (control) with 15 ± 0.5 mg kg-1) were applied to the plots, as the subplot, to investigate the impact of soil AP content on cotton fiber elongation and length. Results Low soil AP (P0 and P1) decreased the contents of the osmotically active solutes in the cotton fibers, including potassium ions (K+), malate, soluble sugar, and sucrose, by 2.2-10.2%, 14.4-47.3%, 8.7-24.5%, and 10.1-23.4%, respectively, inhibiting the vacuoles from facilitating fiber elongation through osmoregulation. Moreover, soil AP deficiency also reduced the activities of enzymes participated in fiber elongation (plasma membrane H+-ATPase (PM-H+-ATPase), vacuole membrane H+-ATPase (V-H+-ATPase), vacuole membrane H+-translocating inorganic pyrophosphatase (V-H+-PPase), and phosphoenolpyruvate carboxylase (PEPC)). The PM-H+-ATPase, V-H+-ATPase, V-H+-PPase, and PEPC were reduced by 8.4-33.0%, 7.0-33.8%, 14.1-38.4%, and 16.9-40.2%, respectively, inhibiting the transmembrane transport of the osmotically active solutes and acidified conditions for fiber cell wall, thus limiting the fiber elongation. Similarly, soil AP deficiency reduced the fiber length by 0.6-3.0 mm, mainly due to the 3.8-16.3% reduction of the maximum velocity of fiber elongation (VLmax). Additionally, the upper fruiting branch positions (FB10-11) had higher VLmax and longer fiber lengths under low soil AP. Discussion Cotton fibers with higher malate content and V-H+-ATPase and V-H+-PPase activities yielded longer fibers. And the malate and soluble sugar contents and V-H+-ATPase and PEPC activities in the SCRC-28's fiber were more sensitive to soil AP deficiency in contrast to those of CCRI-79, possibly explaining the SCRC-28 fiber length sensitivity to low soil AP.
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Affiliation(s)
- Miao Sun
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Cangsong Zheng
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Weina Feng
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jingjing Shao
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Pengcheng Li
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Helin Dong
- State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji, China
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13
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Zhang S, Liu J, Shi L, Wang Q, Zhang P, Wang H, Liu J, Li H, Li L, Li X, Huang L, Qin P. Identification of core genes associated with different phosphorus levels in quinoa seedlings by weighted gene co-expression network analysis. BMC Genomics 2023; 24:399. [PMID: 37454047 DOI: 10.1186/s12864-023-09507-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Quinoa is a highly nutritious and novel crop that is resistant to various abiotic stresses. However, its growth and development is restricted due to its limited utilization of soil phosphorus. Studies on the levels of phosphorus in quinoa seedlings are limited; therefore, we analyzed transcriptome data from quinoa seedlings treated with different concentrations of phosphorus. RESULTS To identify core genes involved in responding to various phosphorus levels, the weighted gene co-expression network analysis method was applied. From the 12,085 expressed genes, an analysis of the gene co-expression network was done. dividing the expressed genes into a total of twenty-five different modules out of which two modules were strongly correlated with phosphorus levels. Subsequently we identified five core genes that correlated strongly either positively or negatively with the phosphorus levels. Gene ontology and assessments of the Kyoto Encyclopedia of Genes and Genomes have uncovered important biological processes and metabolic pathways that are involved in the phosphorus level response. CONCLUSIONS We discovered crucial new core genes that encode proteins from various transcription factor families, such as MYB, WRKY, and ERF, which are crucial for abiotic stress resistance. This new library of candidate genes associated with the phosphorus level responses in quinoa seedlings will help in breeding varieties that are tolerant to phosphorus levels.
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Affiliation(s)
- Shan Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jian Liu
- Institute of Agricultural Sciences of the Lixiache District, Yangzhou, 225007, China
| | - Lian Shi
- Yuxi Academy of Agricultural Sciences, Yuxi, 653100, China
| | - Qianchao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Hongxin Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Hanxue Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Li Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Xinyi Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Liubin Huang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.
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14
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Pahuja S, Bheri M, Bisht D, Pandey GK. Calcium signalling components underlying NPK homeostasis: potential avenues for exploration. Biochem J 2023; 480:1015-1034. [PMID: 37418287 DOI: 10.1042/bcj20230156] [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: 04/23/2023] [Revised: 06/06/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023]
Abstract
Plants require the major macronutrients, nitrogen (N), phosphorus (P) and potassium (K) for normal growth and development. Their deficiency in soil directly affects vital cellular processes, particularly root growth and architecture. Their perception, uptake and assimilation are regulated by complex signalling pathways. To overcome nutrient deficiencies, plants have developed certain response mechanisms that determine developmental and physiological adaptations. The signal transduction pathways underlying these responses involve a complex interplay of components such as nutrient transporters, transcription factors and others. In addition to their involvement in cross-talk with intracellular calcium signalling pathways, these components are also engaged in NPK sensing and homeostasis. The NPK sensing and homeostatic mechanisms hold the key to identify and understand the crucial players in nutrient regulatory networks in plants under both abiotic and biotic stresses. In this review, we discuss calcium signalling components/pathways underlying plant responses to NPK sensing, with a focus on the sensors, transporters and transcription factors involved in their respective signalling and homeostasis.
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Affiliation(s)
- Sonam Pahuja
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Malathi Bheri
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Diksha Bisht
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Girdhar K Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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15
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Zhu X, Xu W, Liu B, Zhan Y, Xia T. Adaptation of high-efficiency CRISPR/Cas9-based multiplex genome editing system in white lupin by using endogenous promoters. PHYSIOLOGIA PLANTARUM 2023; 175:e13976. [PMID: 37616014 DOI: 10.1111/ppl.13976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/21/2023] [Accepted: 07/10/2023] [Indexed: 08/25/2023]
Abstract
White lupin (Lupinus albus L.) is an important crop with high phosphorus (P) use efficiency; however, technologies for its functional genomic and molecular analyses are limited. Cluster regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) (CRISPR/Cas9) system has been applied to gene editing and function genomics in many crops, but its application in white lupin has not been well documented. Here, we adapted the CRISPR/Cas9-based multiplex genome editing system by using the native U3/U6 and ubiquitin (UBQ) promoters to drive sgRNAs and Cas9. Two target sites (T1 and T2) within the Lalb_Chr05g0223881 gene, encoding a putative trehalase, were selected to validate its efficacy in white lupin based on the Agrobacterium rhizogenes-mediated transformation. We found that the T0 hairy roots were efficiently mutated at T1 and T2 with a frequency of 6.25%-35% and 50%-92.31%, respectively. The mutation types include nucleotide insertion, deletion, substitution, and complicated variant. Simultaneous mutations of the two targets were also observed with a range of 6.25%-35%. The combination of LaU6.6 promoter for sgRNA and LaUBQ12 promoter for Cas9 generated the highest frequency of homozygous/biallelic mutations at 38.46%. In addition, the target-sgRNA sequence also contributes to the editing efficiency of the CRISPR/Cas9 system in white lupin. In conclusion, our results expand the toolbox of the CRISPR/Cas9 system and benefit the basic research in white lupin.
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Affiliation(s)
- Xiaoqi Zhu
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resource and Environment, Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Weifeng Xu
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resource and Environment, Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bowen Liu
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resource and Environment, Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yujie Zhan
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resource and Environment, Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Tianyu Xia
- Joint International Research Laboratory of Water and Nutrient in Crop and College of Resource and Environment, Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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16
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Xie B, Chen Y, Zhang Y, An X, Li X, Yang A, Kang G, Zhou J, Cheng C. Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of apple dwarfing rootstock root morphogenesis under nitrogen and/or phosphorus deficient conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1120777. [PMID: 37404544 PMCID: PMC10315683 DOI: 10.3389/fpls.2023.1120777] [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: 12/10/2022] [Accepted: 05/16/2023] [Indexed: 07/06/2023]
Abstract
Nitrogen (N) and phosphorus (P) are essential phytomacronutrients, and deficiencies in these two elements limit growth and yield in apple (Malus domestica Borkh.). The rootstock plays a key role in the nutrient uptake and environmental adaptation of apple. The objective of this study was to investigate the effects of N and/or P deficiency on hydroponically-grown dwarfing rootstock 'M9-T337' seedlings, particularly the roots, by performing an integrated physiological, transcriptomics-, and metabolomics-based analyses. Compared to N and P sufficiency, N and/or P deficiency inhibited aboveground growth, increased the partitioning of total N and total P in roots, enhanced the total number of tips, length, volume, and surface area of roots, and improved the root-to-shoot ratio. P and/or N deficiency inhibited NO3 - influx into roots, and H+ pumps played a important role in the response to P and/or N deficiency. Conjoint analysis of differentially expressed genes and differentially accumulated metabolites in roots revealed that N and/or P deficiency altered the biosynthesis of cell wall components such as cellulose, hemicellulose, lignin, and pectin. The expression of MdEXPA4 and MdEXLB1, two cell wall expansin genes, were shown to be induced by N and/or P deficiency. Overexpression of MdEXPA4 enhanced root development and improved tolerance to N and/or P deficiency in transgenic Arabidopsis thaliana plants. In addition, overexpression of MdEXLB1 in transgenic Solanum lycopersicum seedlings increased the root surface area and promoted acquisition of N and P, thereby facilitating plant growth and adaptation to N and/or P deficiency. Collectively, these results provided a reference for improving root architecture in dwarfing rootstock and furthering our understanding of integration between N and P signaling pathways.
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Affiliation(s)
- Bin Xie
- Key Laboratory of Mineral Nutrition and Efficient Fertilization for Deciduous Fruits, Liaoning Province/Key Laboratory of Fruit Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs/Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Yanhui Chen
- Key Laboratory of Mineral Nutrition and Efficient Fertilization for Deciduous Fruits, Liaoning Province/Key Laboratory of Fruit Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs/Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Yanzhen Zhang
- Key Laboratory of Mineral Nutrition and Efficient Fertilization for Deciduous Fruits, Liaoning Province/Key Laboratory of Fruit Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs/Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Xiuhong An
- Research Center for Agricultural Engineering Technology of Mountain District of Hebei/Mountainous Areas Research Institute, Hebei Agricultural University, Baoding, Hebei, China
| | - Xin Li
- Key Laboratory of Mineral Nutrition and Efficient Fertilization for Deciduous Fruits, Liaoning Province/Key Laboratory of Fruit Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs/Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - An Yang
- Key Laboratory of Mineral Nutrition and Efficient Fertilization for Deciduous Fruits, Liaoning Province/Key Laboratory of Fruit Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs/Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Guodong Kang
- Key Laboratory of Mineral Nutrition and Efficient Fertilization for Deciduous Fruits, Liaoning Province/Key Laboratory of Fruit Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs/Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Jiangtao Zhou
- Key Laboratory of Mineral Nutrition and Efficient Fertilization for Deciduous Fruits, Liaoning Province/Key Laboratory of Fruit Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs/Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Cungang Cheng
- Key Laboratory of Mineral Nutrition and Efficient Fertilization for Deciduous Fruits, Liaoning Province/Key Laboratory of Fruit Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs/Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
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17
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Kong X, Zhang Y, Wang Z, Bao S, Feng Y, Wang J, Yu Z, Long F, Xiao Z, Hao Y, Gao X, Li Y, Ding Y, Wang J, Lei T, Xu C, Wang J. Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae. HORTICULTURE RESEARCH 2023; 10:uhad073. [PMID: 37303613 PMCID: PMC10251138 DOI: 10.1093/hr/uhad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/10/2023] [Indexed: 06/13/2023]
Abstract
An ancient hexaploidization event in the most but not all Asteraceae plants, may have been responsible for shaping the genomes of many horticultural, ornamental, and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth. However, the duplication process of this hexaploidy, as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization, are still poorly understood. We analyzed 11 genomes from 10 genera in Asteraceae, and redated the Asteraceae common hexaploidization (ACH) event ~70.7-78.6 million years ago (Mya) and the Asteroideae specific tetraploidization (AST) event ~41.6-46.2 Mya. Moreover, we identified the genomic homologies generated from the ACH, AST and speciation events, and constructed a multiple genome alignment framework for Asteraceae. Subsequently, we revealed biased fractionations between the paleopolyploidization produced subgenomes, suggesting the ACH and AST both are allopolyplodization events. Interestingly, the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae. Furthermore, we reconstructed ancestral Asteraceae karyotype (AAK) that has 9 paleochromosomes, and revealed a highly flexible reshuffling of Asteraceae paleogenome. Of specific significance, we explored the genetic diversity of Heat Shock Transcription Factors (Hsfs) associated with recursive whole-genome polyploidizations, gene duplications, and paleogenome reshuffling, and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae. Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae, and is helpful for further communication and exploration of the diversification of plant families and phenotypes.
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Affiliation(s)
| | | | | | | | - Yishan Feng
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Jiaqi Wang
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Zijian Yu
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Feng Long
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Zejia Xiao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Xintong Gao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yinfeng Li
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yue Ding
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
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18
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Chen H, Guo M, Dong S, Wu X, Zhang G, He L, Jiao Y, Chen S, Li L, Luo H. A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity. PLANT COMMUNICATIONS 2023; 4:100516. [PMID: 36597358 DOI: 10.1016/j.xplc.2023.100516] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 12/14/2022] [Accepted: 12/31/2022] [Indexed: 05/11/2023]
Abstract
Artemisia argyi Lévl. et Vant., a perennial Artemisia herb with an intense fragrance, is widely used in traditional medicine in China and many other Asian countries. Here, we present a chromosome-scale genome assembly of A. argyi comprising 3.89 Gb assembled into 17 pseudochromosomes. Phylogenetic and comparative genomic analyses revealed that A. argyi underwent a recent lineage-specific whole-genome duplication (WGD) event after divergence from Artemisia annua, resulting in two subgenomes. We deciphered the diploid ancestral genome of A. argyi, and unbiased subgenome evolution was observed. The recent WGD led to a large number of duplicated genes in the A. argyi genome. Expansion of the terpene synthase (TPS) gene family through various types of gene duplication may have greatly contributed to the diversity of volatile terpenoids in A. argyi. In particular, we identified a typical germacrene D synthase gene cluster within the expanded TPS gene family. The entire biosynthetic pathways of germacrenes, (+)-borneol, and (+)-camphor were elucidated in A. argyi. In addition, partial deletion of the amorpha-4,11-diene synthase (ADS) gene and loss of function of ADS homologs may have resulted in the lack of artemisinin production in A. argyi. Our study provides new insights into the genome evolution of Artemisia and lays a foundation for further improvement of the quality of this important medicinal plant.
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Affiliation(s)
- Hongyu Chen
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Miaoxian Guo
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Shuting Dong
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xinling Wu
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Guobin Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian 271018, China; College of Agronomy, Shandong Agricultural University, Taian 271018, China
| | - Liu He
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Shilin Chen
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China.
| | - Li Li
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY 14853, USA; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Hongmei Luo
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China.
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19
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Chen Y, Fang T, Su H, Duan S, Ma R, Wang P, Wu L, Sun W, Hu Q, Zhao M, Sun L, Dong X. A reference-grade genome assembly for Astragalus mongholicus and insights into the biosynthesis and high accumulation of triterpenoids and flavonoids in its roots. PLANT COMMUNICATIONS 2023; 4:100469. [PMID: 36307985 PMCID: PMC10030368 DOI: 10.1016/j.xplc.2022.100469] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 09/18/2022] [Accepted: 10/23/2022] [Indexed: 05/04/2023]
Abstract
Astragalus membranaceus var. mongholicus (AMM), a member of the Leguminosae, is one of the most important medicinal plants worldwide. The dried roots of AMM have a wide range of pharmacological effects and are a traditional Chinese medicine. Here, we report the first chromosome-level reference genome of AMM, comprising nine pseudochromosomes with a total size of 1.47 Gb and 27 868 protein-encoding genes. Comparative genomic analysis reveals that AMM has not experienced an independent whole-genome duplication (WGD) event after the WGD event shared by the Papilionoideae species. Analysis of long terminal repeat retrotransposons suggests a recent burst of these elements at approximately 0.13 million years ago, which may explain the large size of the AMM genome. Multiple gene families involved in the biosynthesis of triterpenoids and flavonoids were expanded, and our data indicate that tandem duplication has been the main driver for expansion of these families. Among the expanded families, the phenylalanine ammonia-lyase gene family was primarily expressed in the roots of AMM, suggesting their roles in the biosynthesis of phenylpropanoid compounds. The functional versatility of 2,3-oxidosqualene cyclase genes in cluster III may play a critical role in the diversification of triterpenoids in AMM. Our findings provide novel insights into triterpenoid and flavonoid biosynthesis and can facilitate future research on the genetics and medical applications of AMM.
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Affiliation(s)
- Yi Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ting Fang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - He Su
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou 510120, China
| | - Sifei Duan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ruirui Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ping Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Lin Wu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Wenbin Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Qichen Hu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Meixia Zhao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Lianjun Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Xuehui Dong
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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20
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Cai Z, Zhao X, Zhou C, Fang T, Liu G, Luo J. Genome-Wide Mining of the Tandem Duplicated Type III Polyketide Synthases and Their Expression, Structure Analysis of Senna tora. Int J Mol Sci 2023; 24:ijms24054837. [PMID: 36902267 PMCID: PMC10003783 DOI: 10.3390/ijms24054837] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Senna tora is one of the homologous crops used as a medicinal food containing an abundance of anthraquinones. Type III polyketide synthases (PKSs) are key enzymes that catalyze polyketide formation; in particular, the chalcone synthase-like (CHS-L) genes are involved in anthraquinone production. Tandem duplication is a fundamental mechanism for gene family expansion. However, the analysis of the tandem duplicated genes (TDGs) and the identification and characterization of PKSs have not been reported for S. tora. Herein, we identified 3087 TDGs in the S. tora genome; the synonymous substitution rates (Ks) analysis indicated that the TDGs had recently undergone duplication. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the type III PKSs were the most enriched TDGs involved in the biosynthesis of the secondary metabolite pathways, as evidenced by 14 tandem duplicated CHS-L genes. Subsequently, we identified 30 type III PKSs with complete sequences in the S. tora genome. Based on the phylogenetic analysis, the type III PKSs were classified into three groups. The protein conserved motifs and key active residues showed similar patterns in the same group. The transcriptome analysis showed that the chalcone synthase (CHS) genes were more highly expressed in the leaves than in the seeds in S. tora. The transcriptome and qRT-PCR analysis showed that the CHS-L genes had a higher expression in the seeds than in other tissues, particularly seven tandem duplicated CHS-L2/3/5/6/9/10/13 genes. The key active-site residues and three-dimensional models of the CHS-L2/3/5/6/9/10/13 proteins showed slight variation. These results indicated that the rich anthraquinones in S. tora seeds might be ascribed to the PKSs' expansion from tandem duplication, and the seven key CHS-L2/3/5/6/9/10/13 genes provide candidate genes for further research. Our study provides an important basis for further research on the regulation of anthraquinones' biosynthesis in S. tora.
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Affiliation(s)
- Zeping Cai
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou 570228, China
| | - Xingkun Zhao
- College of Tropical Crops & College of Life Sciences, Hainan University, Haikou 570228, China
| | - Chaoye Zhou
- College of Tropical Crops & College of Life Sciences, Hainan University, Haikou 570228, China
| | - Ting Fang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou 570228, China
| | - Guodao Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (G.L.); (J.L.)
| | - Jiajia Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Correspondence: (G.L.); (J.L.)
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21
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Marcolungo L, Vincenzi L, Ballottari M, Cecchin M, Cosentino E, Mignani T, Limongi A, Ferraris I, Orlandi M, Rossato M, Delledonne M. Structural Refinement by Direct Mapping Reveals Assembly Inconsistencies near Hi-C Junctions. PLANTS (BASEL, SWITZERLAND) 2023; 12:320. [PMID: 36679033 PMCID: PMC9861903 DOI: 10.3390/plants12020320] [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: 11/30/2022] [Revised: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
High-throughput chromosome conformation capture (Hi-C) is widely used for scaffolding in de novo assembly because it produces highly contiguous genomes, but its indirect statistical approach can introduce connection errors. We employed optical mapping (Bionano Genomics) as an orthogonal scaffolding technology to assess the structural solidity of Hi-C reconstructed scaffolds. Optical maps were used to assess the correctness of five de novo genome assemblies based on long-read sequencing for contig generation and Hi-C for scaffolding. Hundreds of inconsistencies were found between the reconstructions generated using the Hi-C and optical mapping approaches. Manual inspection, exploiting raw long-read sequencing data and optical maps, confirmed that several of these conflicts were derived from Hi-C joining errors. Such misjoins were widespread, involved the connection of both small and large contigs, and even overlapped annotated genes. We conclude that the integration of optical mapping data after, not before, Hi-C-based scaffolding, improves the quality of the assembly and limits reconstruction errors by highlighting misjoins that can then be subjected to further investigation.
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Affiliation(s)
- Luca Marcolungo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Leonardo Vincenzi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Matteo Ballottari
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Michela Cecchin
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | | | - Thomas Mignani
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Antonina Limongi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Irene Ferraris
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Matteo Orlandi
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
- Genartis srl, Via IV Novembre 24, 37126 Verona, Italy
| | - Massimo Delledonne
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
- Genartis srl, Via IV Novembre 24, 37126 Verona, Italy
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22
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Liang L, Zhang J, Xiao J, Li X, Xie Y, Tan H, Song X, Zhu L, Xue X, Xu L, Zhou P, Ran J, Sun B, Huang Z, Tang Y, Lin L, Sun G, Lai Y, Li H. Genome and pan-genome assembly of asparagus bean ( Vigna unguiculata ssp. sesquipedialis) reveal the genetic basis of cold adaptation. FRONTIERS IN PLANT SCIENCE 2022; 13:1059804. [PMID: 36589110 PMCID: PMC9802904 DOI: 10.3389/fpls.2022.1059804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Asparagus bean (Vigna unguiculata ssp. sesquipedialis) is an important cowpea subspecies. We assembled the genomes of Ningjiang 3 (NJ, 550.31 Mb) and Dubai bean (DB, 564.12 Mb) for comparative genomics analysis. The whole-genome duplication events of DB and NJ occurred at 64.55 and 64.81 Mya, respectively, while the divergence between soybean and Vigna occurred in the Paleogene period. NJ genes underwent positive selection and amplification in response to temperature and abiotic stress. In species-specific gene families, NJ is mainly enriched in response to abiotic stress, while DB is primarily enriched in respiration and photosynthesis. We established the pan-genomes of four accessions (NJ, DB, IT97K-499-35 and Xiabao II) and identified 20,336 (70.5%) core genes present in all the accessions, 6,507 (55.56%) variable genes in two individuals, and 2,004 (6.95%) unique genes. The final pan genome is 616.35 Mb, and the core genome is 399.78 Mb. The variable genes are manifested mainly in stress response functions, ABC transporters, seed storage, and dormancy control. In the pan-genome sequence variation analysis, genes affected by presence/absence variants were enriched in biological processes associated with defense responses, immune system processes, signal transduction, and agronomic traits. The results of the present study provide genetic data that could facilitate efficient asparagus bean genetic improvement, especially in producing cold-adapted asparagus bean.
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Affiliation(s)
- Le Liang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jianwei Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiachang Xiao
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaomei Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan, Chengdu, China
| | - Yongdong Xie
- Institute for Processing and Storage of Agricultural Products, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Huaqiang Tan
- Horticulture Research Institute, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Xueping Song
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Zhu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinru Xue
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Linyu Xu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peihan Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jianzhao Ran
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhi Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yi Tang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lijin Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guochao Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunsun Lai
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huanxiu Li
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
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23
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Aslam MM, Pueyo JJ, Pang J, Yang J, Chen W, Chen H, Waseem M, Li Y, Zhang J, Xu W. Root acid phosphatases and rhizobacteria synergistically enhance white lupin and rice phosphorus acquisition. PLANT PHYSIOLOGY 2022; 190:2449-2465. [PMID: 36066452 PMCID: PMC9706455 DOI: 10.1093/plphys/kiac418] [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: 05/09/2022] [Accepted: 08/05/2022] [Indexed: 05/11/2023]
Abstract
The rhizosheath is a belowground area that acts as a communication hub at the root-soil interface to promote water and nutrient acquisition. Certain crops, such as white lupin (Lupinus albus), acquire large amounts of phosphorus (P), owing partially to exudation of acid phosphatases (APases). Plant growth-promoting rhizobacteria also increase soil P availability. However, potential synergistic effects of root APases and rhizosheath-associated microbiota on P acquisition require further research. In this study, we investigated the roles of root purple APases (PAPs) and plant growth-promoting rhizobacteria in rhizosheath formation and P acquisition under conditions of soil drying (SD) and P treatment (+P: soil with P fertilizer; -P: soil without fertilizer). We expressed purple acid phosphatase12 (LaPAP12) in white lupin and rice (Oryza sativa) plants and analyzed the rhizosheath-associated microbiome. Increased or heterologous LaPAP12 expression promoted APase activity and rhizosheath formation, resulting in increased P acquisition mainly under SD-P conditions. It also increased the abundance of members of the genus Bacillus in the rhizosheath-associated microbial communities of white lupin and rice. We isolated a phosphate-solubilizing, auxin-producing Bacillus megaterium strain from the rhizosheath of white lupin and used this to inoculate white lupin and rice plants. Inoculation promoted rhizosheath formation and P acquisition, especially in plants with increased LaPAP12 expression and under SD-P conditions, suggesting a functional role of the bacteria in alleviating P deficit stress via rhizosheath formation. Together, our results suggest a synergistic enhancing effect of LaPAP12 and plant growth-promoting rhizobacteria on rhizosheath formation and P acquisition under SD-P conditions.
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Affiliation(s)
- Mehtab Muhammad Aslam
- Joint International Research Laboratory of Water and Nutrient in Crops, Haixia Institute of Ecology and Environmental Engineering, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Department of Biology, Hong Kong Baptist University, Hong Kong
- State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong
| | - José J Pueyo
- Institute of Agricultural Sciences, ICA-CSIC, Madrid 28006, Spain
| | - Jiayin Pang
- School of Agriculture and Environment, UWA Institute of Agriculture, University of Western Australia, Perth, Western Australia 6009, Australia
| | - Jinyong Yang
- Joint International Research Laboratory of Water and Nutrient in Crops, Haixia Institute of Ecology and Environmental Engineering, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiguo Chen
- Joint International Research Laboratory of Water and Nutrient in Crops, Haixia Institute of Ecology and Environmental Engineering, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hao Chen
- Joint International Research Laboratory of Water and Nutrient in Crops, Haixia Institute of Ecology and Environmental Engineering, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Muhammad Waseem
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Ying Li
- College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong
- State Key Laboratory of Agrobiotechnology, Chinese University of Hong Kong, Hong Kong
| | - Weifeng Xu
- Joint International Research Laboratory of Water and Nutrient in Crops, Haixia Institute of Ecology and Environmental Engineering, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Zhang H, Mascher M, Abbo S, Jayakodi M. Advancing Grain Legumes Domestication and Evolution Studies with Genomics. PLANT & CELL PHYSIOLOGY 2022; 63:1540-1553. [PMID: 35534441 PMCID: PMC9680859 DOI: 10.1093/pcp/pcac062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 06/14/2023]
Abstract
Grain legumes were domesticated in parallel with cereals in several regions of the world and formed the economic basis of early farming cultures. Since then, legumes have played a vital role in human and animal diets and in fostering agrobiodiversity. Increasing grain legume cultivation will be crucial to safeguard nutritional security and the resilience of agricultural ecosystems across the globe. A better understanding of the molecular underpinnings of domestication and crop evolution of grain legumes may be translated into practical approaches in modern breeding programs to stabilize yield, which is threatened by evolving pathogens and changing climates. During recent decades, domestication research in all crops has greatly benefited from the fast progress in genomic technologies. Yet still, many questions surrounding the domestication and diversification of legumes remain unanswered. In this review, we assess the potential of genomic approaches in grain legume research. We describe the centers of origin and the crucial domestication traits of grain legumes. In addition, we survey the effect of domestication on both above-ground and below-ground traits that have economic importance. Finally, we discuss open questions in grain legume domestication and diversification and outline how to bridge the gap between the preservation of historic crop diversity and their utilization in modern plant breeding.
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Affiliation(s)
- Hailin Zhang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, Leipzig 04103, Germany
| | - Shahal Abbo
- The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
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25
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Jha UC, Nayyar H, von Wettberg EJB, Naik YD, Thudi M, Siddique KHM. Legume Pangenome: Status and Scope for Crop Improvement. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11223041. [PMID: 36432770 PMCID: PMC9696634 DOI: 10.3390/plants11223041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 05/31/2023]
Abstract
In the last decade, legume genomics research has seen a paradigm shift due to advances in genome sequencing technologies, assembly algorithms, and computational genomics that enabled the construction of high-quality reference genome assemblies of major legume crops. These advances have certainly facilitated the identification of novel genetic variants underlying the traits of agronomic importance in many legume crops. Furthermore, these robust sequencing technologies have allowed us to study structural variations across the whole genome in multiple individuals and at the species level using 'pangenome analysis.' This review updates the progress of constructing pangenome assemblies for various legume crops and discusses the prospects for these pangenomes and how to harness the information to improve various traits of economic importance through molecular breeding to increase genetic gain in legumes and tackle the increasing global food crisis.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research, Kanpur 208024, India
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 160014, India
| | - Eric J. B. von Wettberg
- Department and Plant and Soil Science, Gund Institute for the Environment, The University of Vermont, Burlington, VT 05405, USA
| | - Yogesh Dashrath Naik
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa 848125, India
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa 848125, India
- Shandong Academy of Agricultural Sciences, Jinan 250100, China
- Department of Agricultural Biotechnology and Molecular Biology, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
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26
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Sun C, Sun N, Ou Y, Gong B, Jin C, Shi Q, Lin X. Phytomelatonin and plant mineral nutrition. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:5903-5917. [PMID: 35767844 DOI: 10.1093/jxb/erac289] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 06/29/2022] [Indexed: 05/27/2023]
Abstract
Plant mineral nutrition is critical for agricultural productivity and for human nutrition; however, the availability of mineral elements is spatially and temporally heterogeneous in many ecosystems and agricultural landscapes. Nutrient imbalances trigger intricate signalling networks that modulate plant acclimation responses. One signalling agent of particular importance in such networks is phytomelatonin, a pleiotropic molecule with multiple functions. Evidence indicates that deficiencies or excesses of nutrients generally increase phytomelatonin levels in certain tissues, and it is increasingly thought to participate in the regulation of plant mineral nutrition. Alterations in endogenous phytomelatonin levels can protect plants from oxidative stress, influence root architecture, and influence nutrient uptake and efficiency of use through transcriptional and post-transcriptional regulation; such changes optimize mineral nutrient acquisition and ion homeostasis inside plant cells and thereby help to promote growth. This review summarizes current knowledge on the regulation of plant mineral nutrition by melatonin and highlights how endogenous phytomelatonin alters plant responses to specific mineral elements. In addition, we comprehensively discuss how melatonin influences uptake and transport under conditions of nutrient shortage.
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Affiliation(s)
- Chengliang Sun
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, PR China
| | - Nan Sun
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, PR China
| | - Yiqun Ou
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, PR China
| | - Biao Gong
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, PR China
| | - Chongwei Jin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, PR China
| | - Qinghua Shi
- College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, PR China
| | - Xianyong Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, PR China
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Garg G, Kamphuis LG, Bayer PE, Kaur P, Dudchenko O, Taylor CM, Frick KM, Foley RC, Gao L, Aiden EL, Edwards D, Singh KB. A pan-genome and chromosome-length reference genome of narrow-leafed lupin (Lupinus angustifolius) reveals genomic diversity and insights into key industry and biological traits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1252-1266. [PMID: 35779281 PMCID: PMC9544533 DOI: 10.1111/tpj.15885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/15/2022] [Accepted: 06/23/2022] [Indexed: 06/02/2023]
Abstract
Narrow-leafed lupin (NLL; Lupinus angustifolius) is a key rotational crop for sustainable farming systems, whose grain is high in protein content. It is a gluten-free, non-genetically modified, alternative protein source to soybean (Glycine max) and as such has gained interest as a human food ingredient. Here, we present a chromosome-length reference genome for the species and a pan-genome assembly comprising 55 NLL lines, including Australian and European cultivars, breeding lines and wild accessions. We present the core and variable genes for the species and report on the absence of essential mycorrhizal associated genes. The genome and pan-genomes of NLL and its close relative white lupin (Lupinus albus) are compared. Furthermore, we provide additional evidence supporting LaRAP2-7 as the key alkaloid regulatory gene for NLL and demonstrate the NLL genome is underrepresented in classical NLR disease resistance genes compared to other sequenced legume species. The NLL genomic resources generated here coupled with previously generated RNA sequencing datasets provide new opportunities to fast-track lupin crop improvement.
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Affiliation(s)
- Gagan Garg
- CSIRO Agriculture and FoodFloreatWA6014Australia
| | - Lars G. Kamphuis
- CSIRO Agriculture and FoodFloreatWA6014Australia
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWA6009Australia
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWA6102Australia
| | - Philipp E. Bayer
- The School of Biological SciencesUniversity of Western AustraliaCrawleyWA6009Australia
| | - Parwinder Kaur
- School of Agriculture and Environment, University of Western AustraliaCrawleyWA6009Australia
| | - Olga Dudchenko
- Center for Genome Architecture, Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
- Center for Theoretical Biological PhysicsRice UniversityHoustonTX77005USA
| | - Candy M. Taylor
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWA6009Australia
- School of Agriculture and Environment, University of Western AustraliaCrawleyWA6009Australia
| | - Karen M. Frick
- CSIRO Agriculture and FoodFloreatWA6014Australia
- Section for Plant Biochemistry and Copenhagen Plant Science Centre, Department of Plant and Environmental SciencesUniversity of CopenhagenFrederiksbergDenmark
| | | | | | - Erez Lieberman Aiden
- School of Agriculture and Environment, University of Western AustraliaCrawleyWA6009Australia
- Center for Genome Architecture, Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
- Center for Theoretical Biological PhysicsRice UniversityHoustonTX77005USA
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTechPudongChina
- Broad Institute of MIT and HarvardCambridgeMAUSA
| | - David Edwards
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWA6009Australia
- The School of Biological SciencesUniversity of Western AustraliaCrawleyWA6009Australia
| | - Karam B. Singh
- CSIRO Agriculture and FoodFloreatWA6014Australia
- UWA Institute of AgricultureUniversity of Western AustraliaCrawleyWA6009Australia
- Centre for Crop and Disease ManagementCurtin UniversityBentleyWA6102Australia
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28
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Plewiński P, Rychel-Bielska S, Kozak B, Maureira-Butler IJ, Iqbal MM, Nelson MN, Książkiewicz M. FLOWERING LOCUS T indel variants confer vernalization-independent and photoperiod-insensitive flowering of yellow lupin ( Lupinus luteus L.). HORTICULTURE RESEARCH 2022; 9:uhac180. [PMID: 36338848 PMCID: PMC9627521 DOI: 10.1093/hr/uhac180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023]
Abstract
Ongoing climate change has considerably reduced the seasonal window for crop vernalization, concurrently expanding cultivation area into northern latitudes with long-day photoperiod. To address these changes, cool season legume breeders need to understand molecular control of vernalization and photoperiod. A key floral transition gene integrating signals from these pathways is the Flowering locus T (FT). Here, a recently domesticated grain legume, yellow lupin (Lupinus luteus L.), was explored for potential involvement of FT homologues in abolition of vernalization and photoperiod requirements. Two FTa (LlutFTa1a and LlutFTa1b) and FTc (LlutFTc1 and LlutFTc2) homologues were identified and sequenced for two contrasting parents of a reference recombinant inbred line (RIL) population, an early-flowering cultivar Wodjil and a late-flowering wild-type P28213. Large deletions were detected in the 5' promoter regions of three FT homologues. Quantitative trait loci were identified for flowering time and vernalization response in the RIL population and in a diverse panel of wild and domesticated accessions. A 2227 bp deletion found in the LlutFTc1 promoter was linked with early phenology and vernalization independence, whereas LlutFTa1a and LlutFTc2 indels with photoperiod responsiveness. Comparative mapping highlighted convergence of FTc1 indel evolution in two Old World lupin species, addressing both artificial selection during domestication and natural adaptation to short season environmental conditions. We concluded that rapid flowering in yellow lupin is associated with the de-repression of the LlutFTc1 homologue from the juvenile phase, putatively due to the elimination of all binding sites in the promoter region for the AGAMOUS-like 15 transcription factor.
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Affiliation(s)
- Piotr Plewiński
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Bartosz Kozak
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Iván J Maureira-Butler
- Instituto de Producción y Sanidad Vegetal, Facultad de Ciencias Agrarias y Alimentarias, Universidad Austral de Chile, Valdivia, Chile
| | - Muhammad Munir Iqbal
- Centre for Plant Genetics and Breeding, The University of Western Australia, Perth, 6009, WA, Australia
- Genomics WA, Joint initiative of Telethon Kids Institute, Harry Perkins Institute of Medical Research and The University of Western Australia, QEII campus, Nedlands, 6009, Western Australia, Australia
| | - Matthew N Nelson
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia
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29
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Chapman MA, He Y, Zhou M. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security. THE NEW PHYTOLOGIST 2022; 234:1583-1597. [PMID: 35318683 PMCID: PMC9994440 DOI: 10.1111/nph.18021] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/22/2022] [Indexed: 04/14/2023]
Abstract
Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.
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Affiliation(s)
- Mark A. Chapman
- Biological SciencesUniversity of SouthamptonLife Sciences Building 85, Highfield CampusSouthamptonSO17 1BJUK
| | - Yuqi He
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
| | - Meiliang Zhou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesRoom 405, National Crop Gene Bank BuildingZhongguancun South Street No. 12Haidian DistrictBeijing100081China
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30
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Lei W, Wang Z, Cao M, Zhu H, Wang M, Zou Y, Han Y, Wang D, Zheng Z, Li Y, Liu B, Ru D. Chromosome-level genome assembly and characterization of Sophora Japonica. DNA Res 2022; 29:6573451. [PMID: 35466378 PMCID: PMC9154292 DOI: 10.1093/dnares/dsac009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/07/2022] [Indexed: 11/18/2022] Open
Abstract
Sophora japonica is a medium-size deciduous tree belonging to Leguminosae family and famous for its high ecological, economic and medicinal value. Here, we reveal a draft genome of S. japonica, which was ∼511.49 Mb long (contig N50 size of 17.34 Mb) based on Illumina, Nanopore and Hi-C data. We reliably assembled 110 contigs into 14 chromosomes, representing 91.62% of the total genome, with an improved N50 size of 31.32 Mb based on Hi-C data. Further investigation identified 271.76 Mb (53.13%) of repetitive sequences and 31,000 protein-coding genes, of which 30,721 (99.1%) were functionally annotated. Phylogenetic analysis indicates that S. japonica separated from Arabidopsis thaliana and Glycine max ∼107.53 and 61.24 million years ago, respectively. We detected evidence of species-specific and common-legume whole-genome duplication events in S. japonica. We further found that multiple TF families (e.g. BBX and PAL) have expanded in S. japonica, which might have led to its enhanced tolerance to abiotic stress. In addition, S. japonica harbours more genes involved in the lignin and cellulose biosynthesis pathways than the other two species. Finally, population genomic analyses revealed no obvious differentiation among geographical groups and the effective population size continuously declined since 2 Ma. Our genomic data provide a powerful comparative framework to study the adaptation, evolution and active ingredients biosynthesis in S. japonica. More importantly, our high-quality S. japonica genome is important for elucidating the biosynthesis of its main bioactive components, and improving its production and/or processing.
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Affiliation(s)
- Weixiao Lei
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Zefu Wang
- Key Laboratory of Bio-resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610000, China
| | - Man Cao
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Hui Zhu
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Min Wang
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Yi Zou
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Yunchun Han
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Dandan Wang
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Bingbing Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan 030006, China
- To whom correspondence should be addressed. Tel. 13880788291. (D.R.); Tel. 13880788291. (B.L.)
| | - Dafu Ru
- State Key Laboratory of Grassland Agro-Ecosystems, and College of Ecology, Lanzhou University, Lanzhou 730000, China
- To whom correspondence should be addressed. Tel. 13880788291. (D.R.); Tel. 13880788291. (B.L.)
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31
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Abstract
H+-ATPases, including the phosphorylated intermediate-type (P-type) and vacuolar-type (V-type) H+-ATPases, are important ATP-driven proton pumps that generate membrane potential and provide proton motive force for secondary active transport. P- and V-type H+-ATPases have distinct structures and subcellular localizations and play various roles in growth and stress responses. A P-type H+-ATPase is mainly regulated at the posttranslational level by phosphorylation and dephosphorylation of residues in its autoinhibitory C terminus. The expression and activity of both P- and V-type H+-ATPases are highly regulated by hormones and environmental cues. In this review, we summarize the recent advances in understanding of the evolution, regulation, and physiological roles of P- and V-type H+-ATPases, which coordinate and are involved in plant growth and stress adaptation. Understanding the different roles and the regulatory mechanisms of P- and V-type H+-ATPases provides a new perspective for improving plant growth and stress tolerance by modulating the activity of H+-ATPases, which will mitigate the increasing environmental stress conditions associated with ongoing global climate change.
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Affiliation(s)
- Ying Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Houqing Zeng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Feiyun Xu
- Center for Plant Water-Use and Nutrition Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China;
| | - Feng Yan
- Institute of Agronomy and Plant Breeding, Justus Liebig University of Giessen, Giessen, Germany
| | - Weifeng Xu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, College of Agriculture, Yangzhou University, Yangzhou, China
- Center for Plant Water-Use and Nutrition Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China;
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32
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Wu P, Zhang L, Zhang K, Yin Y, Liu A, Zhu Y, Fu Y, Sun F, Zhao S, Feng K, Xu X, Chen X, Cheng F, Li L. The adaptive evolution of Euryale ferox to the aquatic environment through paleo-hexaploidization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:627-645. [PMID: 35218099 PMCID: PMC9314984 DOI: 10.1111/tpj.15717] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/24/2022] [Accepted: 02/20/2022] [Indexed: 05/25/2023]
Abstract
Occupation of living space is one of the main driving forces of adaptive evolution, especially for aquatic plants whose leaves float on the water surface and thus have limited living space. Euryale ferox, from the angiosperm basal family Nymphaeaceae, develops large, rapidly expanding leaves to compete for space on the water surface. Microscopic observation found that the cell proliferation of leaves is almost completed underwater, while the cell expansion occurs rapidly after they grow above water. To explore the mechanism underlying the specific development of leaves, we performed sequences assembly and analyzed the genome and transcriptome dynamics of E. ferox. Through reconstruction of the three sub-genomes generated from the paleo-hexaploidization event in E. ferox, we revealed that one sub-genome was phylogenetically closer to Victoria cruziana, which also exhibits gigantic floating leaves. Further analysis revealed that while all three sub-genomes promoted the evolution of the specific leaf development in E. ferox, the genes from the sub-genome closer to V. cruziana contributed more to this adaptive evolution. Moreover, we found that genes involved in cell proliferation and expansion, photosynthesis, and energy transportation were over-retained and showed strong expression association with the leaf development stages, such as the expression divergence of SWEET orthologs as energy uploaders and unloaders in the sink and source leaf organs of E. ferox. These findings provide novel insights into the genome evolution through polyploidization, as well as the adaptive evolution regarding the leaf development accomplished through biased gene retention and expression sub-functionalization of multi-copy genes in E. ferox.
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Affiliation(s)
- Peng Wu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijing100081China
| | - Lingkui Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijing100081China
| | - Kang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijing100081China
| | - Yulai Yin
- Suzhou Academy of Agricultural ScienceSuzhou215000China
| | - Ailian Liu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Yue Zhu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Yu Fu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Fangfang Sun
- Suzhou Academy of Agricultural ScienceSuzhou215000China
| | - Shuping Zhao
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Kai Feng
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Xuewen Xu
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Xuehao Chen
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino‐Dutch Joint Laboratory of Horticultural GenomicsBeijing100081China
| | - Liangjun Li
- School of Horticulture and Plant ProtectionYangzhou UniversityYangzhou225000China
- Joint International Research Laboratory of Agriculture and Agri‐Product Safety of Ministry of Education of ChinaYangzhou UniversityYangzhou225000China
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Wang Q, Guo Y, Huang T, Zhang X, Zhang P, Xie H, Liu J, Li L, Kong Z, Qin P. Transcriptome and Metabolome Analyses Revealed the Response Mechanism of Quinoa Seedlings to Different Phosphorus Stresses. Int J Mol Sci 2022; 23:ijms23094704. [PMID: 35563095 PMCID: PMC9105174 DOI: 10.3390/ijms23094704] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/21/2022] [Accepted: 04/22/2022] [Indexed: 11/23/2022] Open
Abstract
Quinoa (Chenopodium quinoa Willd.) is a dicotyledonous annual herb of Family Amaranthaceae and Subfamily Chenopodiaceae. It has high nutritional and economic value. Phosphorus (P) is an essential plant macronutrient, a component of many biomolecules, and vital to growth, development, and metabolism. We analyzed the transcriptomes and metabolomes of Dianli–1299 and Dianli–71 quinoa seedlings, compared their phenotypes, and elucidated the mechanisms of their responses to the phosphorus treatments. Phenotypes significantly varied with phosphorus level. The plants responded to changes in available phosphorus by modulating metabolites and genes implicated in glycerophospholipid, glycerolipid and glycolysis, and glyconeogenesis metabolism. We detected 1057 metabolites, of which 149 were differentially expressed (DEMs) and common to the control (CK) vs. the low-phosphorus (LP) treatment samples, while two DEMs were common to CK vs. the high-phosphorus (HP) treatment samples. The Kyoto Encyclopedia of genes and genomes (KEGG) annotated 29,232 genes, of which 231 were differentially expressed (DEGs) and common to CK vs. LP, while one was common to CK vs. HP. A total of 15 DEMs and 11 DEGs might account for the observed differences in the responses of the quinoa seedlings to the various phosphorus levels. The foregoing results may provide a theoretical basis for improving the phosphorus utilization efficiency in quinoa.
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Affiliation(s)
- Qianchao Wang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.G.); (T.H.); (X.Z.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Yirui Guo
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.G.); (T.H.); (X.Z.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Tingzhi Huang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.G.); (T.H.); (X.Z.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Xuesong Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.G.); (T.H.); (X.Z.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Ping Zhang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.G.); (T.H.); (X.Z.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Heng Xie
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.G.); (T.H.); (X.Z.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Junna Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.G.); (T.H.); (X.Z.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Li Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.G.); (T.H.); (X.Z.); (P.Z.); (H.X.); (J.L.); (L.L.)
| | - Zhiyou Kong
- College of Natural Resources and Environment, Baoshan University, Baoshan 678000, China
- Correspondence: (Z.K.); (P.Q.); Tel.: +86-130-9967-6866 (Z.K.); +86-135-0880-6942 (P.Q.)
| | - Peng Qin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China; (Q.W.); (Y.G.); (T.H.); (X.Z.); (P.Z.); (H.X.); (J.L.); (L.L.)
- Correspondence: (Z.K.); (P.Q.); Tel.: +86-130-9967-6866 (Z.K.); +86-135-0880-6942 (P.Q.)
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Osorio CE, Till BJ. A Bitter-Sweet Story: Unraveling the Genes Involved in Quinolizidine Alkaloid Synthesis in Lupinus albus. FRONTIERS IN PLANT SCIENCE 2022; 12:795091. [PMID: 35154186 PMCID: PMC8826574 DOI: 10.3389/fpls.2021.795091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/30/2021] [Indexed: 05/05/2023]
Abstract
Alkaloids are part of a structurally diverse group of over 21,000 cyclic nitrogen-containing secondary metabolites that are found in over 20% of plant species. Lupinus albus are naturally containing quinolizidine alkaloid (QA) legumes, with wild accessions containing up to 11% of QA in seeds. Notwithstanding their clear advantages as a natural protecting system, lupin-breeding programs have selected against QA content without proper understanding of quinolizidine alkaloid biosynthetic pathway. This review summarizes the current status in this field, with focus on the utilization of natural mutations such as the one contained in pauper locus, and more recently the development of molecular markers, which along with the advent of sequencing technology, have facilitated the identification of candidate genes located in the pauper region. New insights for future research are provided, including the utilization of differentially expressed genes located on the pauper locus, as candidates for genome editing. Identification of the main genes involved in the biosynthesis of QA will enable precision breeding of low-alkaloid, high nutrition white lupin. This is important as plant based high quality protein for food and feed is an essential for sustainable agricultural productivity.
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Affiliation(s)
- Claudia E. Osorio
- Instituto de Investigaciones Agropecuarias, INIA Carillanca, Temuco, Chile
| | - Bradley J. Till
- Veterinary Genetics Laboratory, University of California, Davis, Davis, CA, United States
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Xiong C, Li X, Wang X, Wang J, Lambers H, Vance CP, Shen J, Cheng L. Flavonoids are involved in phosphorus-deficiency-induced cluster-root formation in white lupin. ANNALS OF BOTANY 2022; 129:101-112. [PMID: 34668958 PMCID: PMC8829899 DOI: 10.1093/aob/mcab131] [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: 08/19/2021] [Accepted: 10/16/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Initiation of cluster roots in white lupin (Lupinus albus) under phosphorus (P) deficiency requires auxin signalling, whereas flavonoids inhibit auxin transport. However, little information is available about the interactions between P deficiency and flavonoids in terms of cluster-root formation in white lupin. METHODS Hydroponic and aeroponic systems were used to investigate the role of flavonoids in cluster-root formation, with or without 75 μm P supply. KEY RESULTS Phosphorus-deficiency-induced flavonoid accumulation in cluster roots depended on developmental stage, based on in situ determination of fluorescence of flavonoids and flavonoid concentration. LaCHS8, which codes for a chalcone synthase isoform, was highly expressed in cluster roots, and silencing LaCHS8 reduced flavonoid production and rootlet density. Exogenous flavonoids suppressed cluster-root formation. Tissue-specific distribution of flavonoids in roots was altered by P deficiency, suggesting that P deficiency induced flavonoid accumulation, thus fine-tuning the effect of flavonoids on cluster-root formation. Furthermore, naringenin inhibited expression of an auxin-responsive DR5:GUS marker, suggesting an interaction of flavonoids and auxin in regulating cluster-root formation. CONCLUSIONS Phosphorus deficiency triggered cluster-root formation through the regulation of flavonoid distribution, which fine-tuned an auxin response in the early stages of cluster-root development. These findings provide valuable insights into the mechanisms of cluster-root formation under P deficiency.
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Affiliation(s)
- Chuanyong Xiong
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Xiaoqing Li
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Xin Wang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Jingxin Wang
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
| | - Hans Lambers
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
- School of Biological Sciences and UWA Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Carroll P Vance
- Department of Agronomy and Plant Genetics, University of Minnesota and United States Department of Agriculture Agricultural Research Service, St. Paul, MN, USA
| | - Jianbo Shen
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
- For correspondence. E-mail ;
| | - Lingyun Cheng
- Department of Plant Nutrition, College of Resources and Environmental Sciences, Academy of National Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China
- For correspondence. E-mail ;
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Ying X, Fu J, Zeng M, Liu W, Zhang T, Shen P, Zhang X. BiOCl-Fe 2O 3@TiO 2 Mesoporous Composite for Photoelectrochemical Synthesis of Ammonia. ACTA CHIMICA SINICA 2022. [DOI: 10.6023/a21120562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Hufnagel B, Soriano A, Taylor J, Divol F, Kroc M, Sanders H, Yeheyis L, Nelson M, Péret B. Pangenome of white lupin provides insights into the diversity of the species. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2532-2543. [PMID: 34346542 PMCID: PMC8633493 DOI: 10.1111/pbi.13678] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/07/2021] [Accepted: 07/22/2021] [Indexed: 05/21/2023]
Abstract
White lupin is an old crop with renewed interest due to its seed high protein content and high nutritional value. Despite a long domestication history in the Mediterranean basin, modern breeding efforts have been fairly scarce. Recent sequencing of its genome has provided tools for further description of genetic resources but detailed characterization of genomic diversity is still missing. Here, we report the genome sequencing of 39 accessions that were used to establish a white lupin pangenome. We defined 32 068 core genes that are present in all individuals and 14 822 that are absent in some and may represent a gene pool for breeding for improved productivity, grain quality, and stress adaptation. We used this new pangenome resource to identify candidate genes for alkaloid synthesis, a key grain quality trait. The white lupin pangenome provides a novel genetic resource to better understand how domestication has shaped the genomic variability within this crop. Thus, this pangenome resource is an important step towards the effective and efficient genetic improvement of white lupin to help meet the rapidly growing demand for plant protein sources for human and animal consumption.
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Affiliation(s)
- Bárbara Hufnagel
- BPMPUniv MontpellierCNRSINRAEInstitut AgroMontpellierFrance
- Present address:
CIRADUMR AGAP InstitutSEAPAG TeamPetit‐BourgGuadeloupeF‐97170French West Indies
| | | | | | - Fanchon Divol
- BPMPUniv MontpellierCNRSINRAEInstitut AgroMontpellierFrance
| | - Magdalena Kroc
- Institute of Plant Genetics Polish Academy of SciencesPoznanPoland
| | | | | | | | - Benjamin Péret
- BPMPUniv MontpellierCNRSINRAEInstitut AgroMontpellierFrance
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Ulloa M, Nunes-Nesi A, da Fonseca-Pereira P, Poblete-Grant P, Reyes-Díaz M, Cartes P. The effect of silicon supply on photosynthesis and carbohydrate metabolism in two wheat (Triticum aestivum L.) cultivars contrasting in response to phosphorus nutrition. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 169:236-248. [PMID: 34808466 DOI: 10.1016/j.plaphy.2021.11.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Phosphorus (P) deficiency affects agricultural systems by limiting crop quality and yield. Studies have suggested that silicon (Si) improves P uptake in plants grown under P deficiency. However, the effects of Si on photosynthesis and carbohydrate metabolism under P stress remain unclear. We performed a hydroponic study using two wheat cultivars with contrasting sensitivity to P deficiency (Púrpura, sensitive; Fritz, semi-tolerant) that were exposed to P (0, 0.01, or 0.1 mM) and Si (0 or 2 mM), and we evaluated the photosynthetic performance and metabolic alterations. In plants from the sensitive cultivar undergoing P deficiency, Si application increased sucrose levels, starch breakdown and length of shoots, and also improved plant dry weight. In Fritz (the semi-tolerant cultivar), Si exposure reduced P concentration, and increased shoot length and P use efficiency (PUE) under P shortage. Interestingly, Si application altered cell wall composition, which was associated with higher mesophyll conductance and net CO2 assimilation in Fritz plants grown under P stress. Together, our results indicate that under P deficiency, Si nutrition positively affects photosynthesis and carbohydrate levels in a genotype-dependent manner. Furthermore, these results suggest that Si plays an important role in maintaining high photosynthetic rates in wheat plants undergoing P deficiency.
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Affiliation(s)
- Marlys Ulloa
- Doctoral Program in Science of Natural Resources, Universidad de La Frontera, Avenida Francisco Salazar 01145, P.O. Box 54-D, Temuco, 4780000, Chile; Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Avenida Francisco Salazar 01145, PO Box 54-D, Temuco, 4780000, Chile
| | - Adriano Nunes-Nesi
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | | | - Patricia Poblete-Grant
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Avenida Francisco Salazar 01145, PO Box 54-D, Temuco, 4780000, Chile
| | - Marjorie Reyes-Díaz
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Avenida Francisco Salazar 01145, PO Box 54-D, Temuco, 4780000, Chile; Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, PO Box 54-D, Temuco, 4780000, Chile
| | - Paula Cartes
- Center of Plant, Soil Interaction and Natural Resources Biotechnology, Scientific and Biotechnological Bioresource Nucleus (BIOREN-UFRO), Universidad de La Frontera, Avenida Francisco Salazar 01145, PO Box 54-D, Temuco, 4780000, Chile; Departamento de Ciencias Químicas y Recursos Naturales, Facultad de Ingeniería y Ciencias, Universidad de La Frontera, Avenida Francisco Salazar 01145, PO Box 54-D, Temuco, 4780000, Chile.
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Liu C, Liu WS, van der Ent A, Morel JL, Zheng HX, Wang GB, Tang YT, Qiu RL. Simultaneous hyperaccumulation of rare earth elements, manganese and aluminum in Phytolacca americana in response to soil properties. CHEMOSPHERE 2021; 282:131096. [PMID: 34470158 DOI: 10.1016/j.chemosphere.2021.131096] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 05/15/2021] [Accepted: 05/29/2021] [Indexed: 06/13/2023]
Abstract
The plant Phytolacca americana L. simultaneously hyperaccumulates manganese (Mn) and rare earth elements (REEs), but the underlying mechanisms are largely unknown. In this study, P. americana and the corresponding rhizosphere soil samples were collected from an ion-adsorption REE mine area in China, and the elemental composition and soil properties were analyzed in order to explore the relationship between metal accumulation and soil properties. The results show that P. americana accumulates high concentrations of REEs (up to 1040 mg kg-1), Mn (up to 10400 mg kg-1) and aluminum (Al) (up to 5960 mg kg-1) in leaves. The REE concentrations in leaves were positively correlated with those of Al, Fe and Zn, while light REE concentrations were negatively correlated with P concentrations (p < 0.05). The soil properties explained 81.7%, 72.9% and 67.1% of REEs, Mn and Al accumulated in P. americana, respectively. The variation of REE accumulation in P. americana was primarily explained by plant available P (24.4%), pH (12.9%), TOC (9.4%) and total P (7.7%). The accumulation of Mn was primarily explained by plant available REEs (42.9%) and available Al (13.1%) while Al in P. americana was primarily explained by soil pH (14.4%). This study suggests the potential by regulation of soil properties in improving the efficiency of phytoextraction for REEs by hyperaccumulators.
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Affiliation(s)
- Chong Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Wen-Shen Liu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510006, China
| | - Antony van der Ent
- Centre for Mined Land Rehabilitation, Sustainable Minerals Institute, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Jean Louis Morel
- Université de Lorraine, INRA, Laboratoire Sols et Environnement, Nancy, 54000, France
| | - Hong-Xiang Zheng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Guo-Bao Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Ye-Tao Tang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Rong-Liang Qiu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Provincial Engineering Research Center for Heavy Metal Contaminated Soil Remediation, Sun Yat-sen University, Guangzhou, 510006, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, China.
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Aslam MM, Waseem M, Zhang Q, Ke W, Zhang J, Xu W. Identification of ABC transporter G subfamily in white lupin and functional characterization of L.albABGC29 in phosphorus use. BMC Genomics 2021; 22:723. [PMID: 34615466 PMCID: PMC8495970 DOI: 10.1186/s12864-021-08015-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND White lupin (Lupinus albus) is a leguminous crop with elite adaptive ability in phosphorus-deficient soil and used as a model plant for studying phosphorus (P) use. However, the genetic basis of its adaptation to low P (LP) remains unclear. ATPase binding cassette (ABC) transports G subfamily play a crucial role in the transportation of biological molecules across the membrane. To date, identification of this subfamily has been analyzed in some plants, but no systematic analysis of these transporters in phosphorus acquisition is available for white lupin. RESULTS This study identified 66 ABCG gene family members in the white lupin genome using comprehensive approaches. Phylogenetic analysis of white lupin ABCG transporters revealed six subclades based on their counterparts in Arabidopsis, displaying distinct gene structure and motif distribution in each cluster. Influences of the whole genome duplication on the evolution of L.albABCGs were investigated in detail. Segmental duplications appear to be the major driving force for the expansion of ABCGs in white lupin. Analysis of the Ka/Ks ratios indicated that the paralogs of the L.albABCG subfamily members principally underwent purifying selection. However, it was found that L.albABCG29 was a result of both tandem and segmental duplications. Overexpression of L.albABCG29 in white lupin hairy root enhanced P accumulation in cluster root under LP and improved plant growth. Histochemical GUS staining indicated that L.albABCG29 expression increased under LP in white lupin roots. Further, overexpression of L.albABCG29 in rice significantly improved P use under combined soil drying and LP by improving root growth associated with increased rhizosheath formation. CONCLUSION Through systematic and comprehensive genome-wide bioinformatics analysis, including conserved domain, gene structures, chromosomal distribution, phylogenetic relationships, and gene duplication analysis, the L.albABCG subfamily was identified in white lupin, and L.albABCG29 characterized in detail. In summary, our results provide deep insight into the characterization of the L.albABCG subfamily and the role of L.albABCG29 in improving P use.
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Affiliation(s)
- Mehtab Muhammad Aslam
- College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Water and Nutrient in Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muhammad Waseem
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Qian Zhang
- Joint International Research Laboratory of Water and Nutrient in Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wang Ke
- Joint International Research Laboratory of Water and Nutrient in Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianhua Zhang
- College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Department of Biology, Hong Kong Baptist University, Stake Key Laboratory of Agrobiotechnology and Chinese University of Hong Kong, Kowloon Tong, Hong Kong
| | - Weifeng Xu
- Joint International Research Laboratory of Water and Nutrient in Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Wang K, Xu F, Yuan W, Zhang D, Liu J, Sun L, Cui L, Zhang J, Xu W. Rice G protein γ subunit qPE9-1 modulates root elongation for phosphorus uptake by involving 14-3-3 protein OsGF14b and plasma membrane H + -ATPase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1603-1615. [PMID: 34216063 DOI: 10.1111/tpj.15402] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 06/07/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Heterotrimeric G protein is involved in plant growth and development, while the role of rice (Oryza sativa) G protein γ subunit qPE9-1 in response to low-phosphorus (LP) conditions remains unclear. The gene expression of qPE9-1 was significantly induced in rice roots under LP conditions. Rice varieties carrying the qPE9-1 allele showed a stronger primary root response to LP than the varieties carrying the qpe9-1 allele (mutant of the qPE9-1 allele). Transgenic rice plants with the qPE9-1 allele had longer primary roots and higher P concentrations than those with the qpe9-1 allele under LP conditions. The plasma membrane (PM) H+ -ATPase was important for the qPE9-1-mediated response to LP. Furthermore, OsGF14b, a 14-3-3 protein that acts as a key component in activating PM H+ -ATPase for root elongation, is also involved in the qPE9-1 mediation. Moreover, the overexpression of OsGF14b in WYJ8 (carrying the qpe9-1 allele) partially increased primary root length under LP conditions. Experiments using R18 peptide (a 14-3-3 protein inhibitor) showed that qPE9-1 is important for primary root elongation and H+ efflux under LP conditions by involving the 14-3-3 protein. In addition, rhizosheath weight, total P content, and the rhizosheath soil Olsen-P concentration of qPE9-1 lines were higher than those of qpe9-1 lines under soil drying and LP conditions. These results suggest that the G protein γ subunit qPE9-1 in rice plants modulates root elongation for phosphorus uptake by involving the 14-3-3 protein OsGF14b and PM H+ -ATPase, which is required for rice P use.
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Affiliation(s)
- Ke Wang
- Joint International Research Laboratory of Water and Nutrient in Crops and College of Life Sciences, Center for Plant Water-Use and Nutrition Regulation and College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Feiyun Xu
- Joint International Research Laboratory of Water and Nutrient in Crops and College of Life Sciences, Center for Plant Water-Use and Nutrition Regulation and College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Yuan
- Joint International Research Laboratory of Water and Nutrient in Crops and College of Life Sciences, Center for Plant Water-Use and Nutrition Regulation and College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Dongping Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Jianping Liu
- Joint International Research Laboratory of Water and Nutrient in Crops and College of Life Sciences, Center for Plant Water-Use and Nutrition Regulation and College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Leyun Sun
- Joint International Research Laboratory of Water and Nutrient in Crops and College of Life Sciences, Center for Plant Water-Use and Nutrition Regulation and College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liyou Cui
- Joint International Research Laboratory of Water and Nutrient in Crops and College of Life Sciences, Center for Plant Water-Use and Nutrition Regulation and College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Weifeng Xu
- Joint International Research Laboratory of Water and Nutrient in Crops and College of Life Sciences, Center for Plant Water-Use and Nutrition Regulation and College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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Kroc M, Tomaszewska M, Czepiel K, Bitocchi E, Oppermann M, Neumann K, Guasch L, Bellucci E, Alseekh S, Graner A, Fernie AR, Papa R, Susek K. Towards Development, Maintenance, and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Lupins. Curr Protoc 2021; 1:e191. [PMID: 34242495 DOI: 10.1002/cpz1.191] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Well-characterized genetic resources are fundamental to maintain and provide the various genotypes for pre-breeding programs for the production of new cultivars (e.g., wild relatives, unimproved material, landraces). The aim of the current article is to provide protocols for the characterization of the genetic resources of two lupin crop species: the European Lupinus albus and the American Lupinus mutabilis. Intelligent nested collections of lupins derived from homozygous lines (single-seed descent) are being developed, established, and exploited using cutting-edge approaches for genotyping, phenotyping, data management, and data analysis within the INCREASE project (EU Horizon 2020). This will allow us to predict the phenotypic performance of genotyped lines, and will further boost research and development in lupins. Lupins stand out due to their high-quality seed protein (∼40% of seed dry weight) and other primary components in the seeds, which include fatty acids, dietary fiber, and minerals. The potential of lupins as a crop is highlighted by the multiple benefits of plant-based food in terms of food security, nutrition, human health, and sustainable production. The use of lupins in foods, along with other well-studied and widely used food legumes, will also provide a greatly diversified plant-based food palette to meet the Global Goals for Sustainable Development to improve people's lives by 2030. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Lupin seed phenotypic descriptors Basic Protocol 2: Lupin seed imaging Basic Protocol 3: Standardized phenotypic characterization of lupin genetic resources grown towards primary seed increase (development of single-seed descent genetic resources).
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Affiliation(s)
- Magdalena Kroc
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Magdalena Tomaszewska
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna Czepiel
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Elena Bitocchi
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Seeland, Germany
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Seeland, Germany
| | - Luis Guasch
- Spanish Plant Genetic Resources National Center, Alcalá de Henares, Spain
| | - Elisa Bellucci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Seeland, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Karolina Susek
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
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Thudi M, Chen Y, Pang J, Kalavikatte D, Bajaj P, Roorkiwal M, Chitikineni A, Ryan MH, Lambers H, Siddique KHM, Varshney RK. Novel Genes and Genetic Loci Associated With Root Morphological Traits, Phosphorus-Acquisition Efficiency and Phosphorus-Use Efficiency in Chickpea. FRONTIERS IN PLANT SCIENCE 2021; 12:636973. [PMID: 34122467 PMCID: PMC8192852 DOI: 10.3389/fpls.2021.636973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/04/2021] [Indexed: 06/05/2023]
Abstract
Chickpea-the second most important grain legume worldwide-is cultivated mainly on marginal soils. Phosphorus (P) deficiency often restricts chickpea yields. Understanding the genetics of traits encoding P-acquisition efficiency and P-use efficiency will help develop strategies to reduce P-fertilizer application. A genome-wide association mapping approach was used to determine loci and genes associated with root architecture, root traits associated with P-acquisition efficiency and P-use efficiency, and any associated proxy traits. Using three statistical models-a generalized linear model (GLM), a mixed linear model (MLM), and a fixed and random model circulating probability unification (FarmCPU) -10, 51, and 40 marker-trait associations (MTAs), respectively were identified. A single nucleotide polymorphism (SNP) locus (Ca1_12310101) on Ca1 associated with three traits, i.e., physiological P-use efficiency, shoot dry weight, and shoot P content was identified. Genes related to shoot P concentration (NAD kinase 2, dynamin-related protein 1C), physiological P-use efficiency (fasciclin-like arabinogalactan protein), specific root length (4-coumarate-CoA ligase 1) and manganese concentration in mature leaves (ABC1 family protein) were identified. The MTAs and novel genes identified in this study can be used to improve P-use efficiency in chickpea.
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Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Yinglong Chen
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Jiayin Pang
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Danamma Kalavikatte
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Megan H Ryan
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Hans Lambers
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
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Liu J, Liao W, Nie B, Zhang J, Xu W. OsUEV1B, an Ubc enzyme variant protein, is required for phosphate homeostasis in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:706-719. [PMID: 33570751 DOI: 10.1111/tpj.15193] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Phosphorus is a crucial macronutrient for plant growth and development. The mechanisms for maintaining inorganic phosphate (Pi) homeostasis in rice are not well understood. The ubiquitin-conjugating enzyme variant protein OsUEV1B was previously found to interact with OsUbc13 and mediate lysine63-linked polyubiquitination. In the present study, we found OsUEV1B was specifically inhibited by Pi deficiency, and was localized in the nucleus and cytoplasm. Both osuev1b mutant and OsUEV1B-RNA interference (RNAi) lines displayed serious symptoms of toxicity due to Pi overaccumulation. Some Pi starvation inducible and phosphate transporter genes were upregulated in osuev1b mutant and OsUEV1B-RNAi plants in association with enhanced Pi acquisition, and representative Pi starvation responses, including stimulation of acid phosphatase activity and root hair growth, were also activated in the presence of sufficient Pi. A yeast two-hybrid screen revealed an interaction between OsUEV1B and OsVDAC1, which was confirmed by bimolecular fluorescence complementation and firefly split-luciferase complementation assays. OsVDAC1 encoded a voltage-dependent anion channel protein localized in the mitochondria, and OsUbc13 was shown to interact with OsVDAC1 via yeast two-hybrid and bimolecular fluorescence complementation assays. Under sufficient Pi conditions, similar to osuev1b, a mutation in OsVDAC1 resulted in significantly greater Pi concentrations in the roots and second leaves, improved acid phosphatase activity, and enhanced expression of the Pi starvation inducible and phosphate transporter genes compared with wild-type DongJin, whereas overexpression of OsVDAC1 had the opposite effects. OsUEV1B or OsVDAC1 knockout reduced the mitochondrial membrane potential and adenosine triphosphate levels. Moreover, overexpression of OsVDAC1 in osuev1b partially restored its high Pi concentration to a level between those of osuev1b and DongJin. Our results indicate that OsUEV1B is required for rice phosphate homeostasis.
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Affiliation(s)
- Jianping Liu
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wencheng Liao
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bo Nie
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianhua Zhang
- College of Agriculture, Yangzhou University, Yangzhou, China
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Weifeng Xu
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, China
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Quantitative Control of Early Flowering in White Lupin ( Lupinus albus L.). Int J Mol Sci 2021; 22:ijms22083856. [PMID: 33917799 PMCID: PMC8068107 DOI: 10.3390/ijms22083856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/25/2021] [Accepted: 04/03/2021] [Indexed: 12/03/2022] Open
Abstract
White lupin (Lupinus albus L.) is a pulse annual plant cultivated from the tropics to temperate regions for its high-protein grain as well as a cover crop or green manure. Wild populations are typically late flowering and have high vernalization requirements. Nevertheless, some early flowering and thermoneutral accessions were found in the Mediterranean basin. Recently, quantitative trait loci (QTLs) explaining flowering time variance were identified in bi-parental population mapping, however, phenotypic and genotypic diversity in the world collection has not been addressed yet. In this study, a diverse set of white lupin accessions (n = 160) was phenotyped for time to flowering in a controlled environment and genotyped with PCR-based markers (n = 50) tagging major QTLs and selected homologs of photoperiod and vernalization pathway genes. This survey highlighted quantitative control of flowering time in white lupin, providing statistically significant associations for all major QTLs and numerous regulatory genes, including white lupin homologs of CONSTANS, FLOWERING LOCUS T, FY, MOTHER OF FT AND TFL1, PHYTOCHROME INTERACTING FACTOR 4, SKI-INTERACTING PROTEIN 1, and VERNALIZATION INDEPENDENCE 3. This revealed the complexity of flowering control in white lupin, dispersed among numerous loci localized on several chromosomes, provided economic justification for future genome-wide association studies or genomic selection rather than relying on simple marker-assisted selection.
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Meng X, Chen WW, Wang YY, Huang ZR, Ye X, Chen LS, Yang LT. Effects of phosphorus deficiency on the absorption of mineral nutrients, photosynthetic system performance and antioxidant metabolism in Citrus grandis. PLoS One 2021; 16:e0246944. [PMID: 33596244 PMCID: PMC7888624 DOI: 10.1371/journal.pone.0246944] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/28/2021] [Indexed: 11/19/2022] Open
Abstract
Phosphorus (P) is an essential macronutrient for plant growth, development and production. However, little is known about the effects of P deficiency on nutrient absorption, photosynthetic apparatus performance and antioxidant metabolism in citrus. Seedlings of 'sour pummelo' (Citrus grandis) were irrigated with a nutrient solution containing 0.2 mM (Control) or 0 mM (P deficiency) KH2PO4 until saturated every other day for 16 weeks. P deficiency significantly decreased the dry weight (DW) of leaves and stems, and increased the root/shoot ratio in C. grandis but did not affect the DW of roots. The decreased DW of leaves and stems might be induced by the decreased chlorophyll (Chl) contents and CO2 assimilation in P deficient seedlings. P deficiency heterogeneously affected the nutrient contents of leaves, stems and roots. The analysis of Chl a fluorescence transients showed that P deficiency impaired electron transport from the donor side of photosystem II (PSII) to the end acceptor side of PSI, which showed a greater impact on the performance of the donor side of PSII than that of the acceptor side of PSII and photosystem I (PSI). P deficiency increased the contents of ascorbate (ASC), H2O2 and malondialdehyde (MDA) as well as the activities of superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR) and glutathione reductase (GR) in leaves. In contrast, P deficiency increased the ASC content, reduced the glutathione (GSH) content and the activities of SOD, CAT, APX and monodehydroascorbate reductase (MDHAR), but did not increase H2O2 production, anthocyanins and MDA content in roots. Taking these results together, we conclude that P deficiency affects nutrient absorption and lowers photosynthetic performance, leading to ROS production, which might be a crucial cause of the inhibited growth of C. grandis.
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Affiliation(s)
- Xin Meng
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei-Wei Chen
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan-Yu Wang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeng-Rong Huang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xin Ye
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li-Song Chen
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lin-Tong Yang
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, China
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The Puzzling Fate of a Lupin Chromosome Revealed by Reciprocal Oligo-FISH and BAC-FISH Mapping. Genes (Basel) 2020; 11:genes11121489. [PMID: 33322080 PMCID: PMC7764521 DOI: 10.3390/genes11121489] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 11/22/2022] Open
Abstract
Old World lupins constitute an interesting model for evolutionary research due to diversity in genome size and chromosome number, indicating evolutionary genome reorganization. It has been hypothesized that the polyploidization event which occurred in the common ancestor of the Fabaceae family was followed by a lineage-specific whole genome triplication (WGT) in the lupin clade, driving chromosome rearrangements. In this study, chromosome-specific markers were used as probes for heterologous fluorescence in situ hybridization (FISH) to identify and characterize structural chromosome changes among the smooth-seeded (Lupinus angustifolius L., Lupinus cryptanthus Shuttlew., Lupinus micranthus Guss.) and rough-seeded (Lupinus cosentinii Guss. and Lupinus pilosus Murr.) lupin species. Comparative cytogenetic mapping was done using FISH with oligonucleotide probes and previously published chromosome-specific bacterial artificial chromosome (BAC) clones. Oligonucleotide probes were designed to cover both arms of chromosome Lang06 of the L. angustifolius reference genome separately. The chromosome was chosen for the in-depth study due to observed structural variability among wild lupin species revealed by BAC-FISH and supplemented by in silico mapping of recently released lupin genome assemblies. The results highlighted changes in synteny within the Lang06 region between the lupin species, including putative translocations, inversions, and/or non-allelic homologous recombination, which would have accompanied the evolution and speciation.
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