1
|
Ma S, Guo Y, Zhang T, Liu D, Wang L, Hu R, Zhou D, Zhou Y, Chen Q, Yu L. Comprehensive Identification and Expression Analysis of the Multidrug and Toxic Compound Extrusion (MATE) Gene Family in Brachypodium distachyon. PLANTS (BASEL, SWITZERLAND) 2024; 13:2586. [PMID: 39339561 PMCID: PMC11434668 DOI: 10.3390/plants13182586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 09/10/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024]
Abstract
The Multidrug and Toxic Compound Extrusion (MATE) proteins serve as pivotal transporters responsible for the extrusion of metabolites, thereby playing a significant role in both plant development and the detoxification of toxins. The MATE gene family within the Brachypodium distachyon, which is an important model organism of the Poaceae family, remains largely unexplored. Here, a comprehensive identification and analysis of MATE genes that complement B. distachyon were conducted. The BdMATE genes were systematically categorized into five distinct groups, predicated on an assessment of their phylogenetic affinities and protein structure. Furthermore, our investigation revealed that dispersed duplication has significantly contributed to the expansion of the BdMATE genes, with tandem and segmental duplications showing important roles, suggesting that the MATE genes in Poaceae species have embarked on divergent evolutionary trajectories. Examination of ω values demonstrated that BdMATE genes underwent purifying selection throughout the evolutionary process. Furthermore, collinearity analysis has confirmed a high conservation of MATE genes between B. distachyon and rice. The cis-regulatory elements analysis within BdMATEs promoters, coupled with expression patterns, suggests that BdMATEs play important roles during plant development and in response to phytohormones. Collectively, the findings presented establish a foundational basis for the subsequent detailed characterization of the MATE gene family members in B. distachyon.
Collapse
Affiliation(s)
- Sirui Ma
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yixian Guo
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Tianyi Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Di Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Linna Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ruiwen Hu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Demian Zhou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ying Zhou
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Qinfang Chen
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Lujun Yu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Stress Biology, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| |
Collapse
|
2
|
Li J, He C, Liu S, Guo Y, Zhang Y, Zhang L, Zhou X, Xu D, Luo X, Liu H, Yang X, Wang Y, Shi J, Yang B, Wang J, Wang P, Deng X, Sun C. Research progress and application strategies of sugar transport mechanisms in rice. FRONTIERS IN PLANT SCIENCE 2024; 15:1454615. [PMID: 39233915 PMCID: PMC11371564 DOI: 10.3389/fpls.2024.1454615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024]
Abstract
In plants, carbohydrates are central products of photosynthesis. Rice is a staple that contributes to the daily calorie intake for over half of the world's population. Hence, the primary objective of rice cultivation is to maximize carbohydrate production. The "source-sink" theory is proposed as a valuable principle for guiding crop breeding. However, the "flow" research lag, especially in sugar transport, has hindered high-yield rice breeding progress. This review concentrates on the genetic and molecular foundations of sugar transport and its regulation, enhancing the fundamental understanding of sugar transport processes in plants. We illustrate that the apoplastic pathway is predominant over the symplastic pathway during phloem loading in rice. Sugar transport proteins, such as SUTs and SWEETs, are essential carriers for sugar transportation in the apoplastic pathway. Additionally, we have summarized a regulatory pathway for sugar transport genes in rice, highlighting the roles of transcription factors (OsDOF11, OsNF-YB1, OsNF-YC12, OsbZIP72, Nhd1), OsRRM (RNA Recognition Motif containing protein), and GFD1 (Grain Filling Duration 1). Recognizing that the research shortfall in this area stems from a lack of advanced research methods, we discuss cutting-edge analytical techniques such as Mass Spectrometry Imaging and single-cell RNA sequencing, which could provide profound insights into the dynamics of sugar distribution and the associated regulatory mechanisms. In summary, this comprehensive review serves as a valuable guide, directing researchers toward a deep understanding and future study of the intricate mechanisms governing sugar transport.
Collapse
Affiliation(s)
- Jun Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Changcai He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shihang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuting Guo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuxiu Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lanjing Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xu Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Dongyu Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xu Luo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hongying Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaorong Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Wang
- College of Agricultural Science, Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Liangshan, China
| | - Jun Shi
- Mianyang Academy of Agricultural Sciences, Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang, China
| | - Bin Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pingrong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaojian Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Changhui Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Rice Research Institute, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
3
|
Zeng R, Chen T, Li X, Cao J, Li J, Xu X, Zhang L, Chen Y. Integrated physiological, transcriptomic and metabolomic analyses reveal the mechanism of peanut kernel weight reduction under waterlogging stress. PLANT, CELL & ENVIRONMENT 2024; 47:3198-3214. [PMID: 38722055 DOI: 10.1111/pce.14936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 07/12/2024]
Abstract
Waterlogging stress (WS) hinders kernel development and directly reduces peanut yield; however, the mechanism of kernel filling in response to WS remains unknown. The waterlogging-sensitive variety Huayu 39 was subjected to WS for 3 days at 7 days after the gynophores touched the ground (DAG). We found that WS affected kernel filling at 14, 21, and 28 DAG. WS decreased the average filling rate and kernel dry weight, while transcriptome sequencing and widely targeted metabolomic analysis revealed that WS inhibited the gene expression in starch and sucrose metabolism, which reduced sucrose input and transformation ability. Additionally, genes related to ethylene and melatonin synthesis and the accumulation of tryptophan and methionine were upregulated in response to WS. WS upregulated the expression of the gene encoding tryptophan decarboxylase (AhTDC), and overexpression of AhTDC in Arabidopsis significantly reduced the seed length, width, and weight. Therefore, WS reduced the kernel-filling rate, leading to a reduction in the 100-kernel weight. This survey informs the development of measures that alleviate the negative impact of WS on peanut yield and quality and provides a basis for exploring high-yield and high-quality cultivation, molecular-assisted breeding, and waterlogging prevention in peanut farming.
Collapse
Affiliation(s)
- Ruier Zeng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou, China
| | - Tingting Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou, China
| | - Xi Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou, China
| | - Jing Cao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou, China
| | - Jie Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou, China
| | - Xueyu Xu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou, China
| | - Lei Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou, China
| | - Yong Chen
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, College of Agronomy, South China Agricultural University, Guangzhou, China
| |
Collapse
|
4
|
Li J, Li J, Cheng X, Yang Z, Pang Y, Wang C, Wu J, Ji W, Chen X, Zhao J. The addition of Psathyrostachys Huashanica Keng 6Ns large segment chromosomes has positive impact on stripe rust resistance and plant spikelet number of common wheat. BMC PLANT BIOLOGY 2024; 24:685. [PMID: 39026182 PMCID: PMC11256485 DOI: 10.1186/s12870-024-05395-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 07/09/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Developing novel germplasm by using wheat wild related species is an effective way to rebuild the wheat resource bank. The Psathyrostachys huashanica Keng (P. huashanica, 2n = 2x = 14, NsNs) is regarded as a superior species to improve wheat breeding because of its multi-resistance, early maturation and numerous tiller traits. Introducing genetic components of P. huashanica into the common wheat background is the most important step in achieving the effective use. Therefore, the cytogenetic characterization and influence of the introgressed P. huashanica large segment chromosomes in the wheat background is necessary to be explored. RESULTS In this study, we characterized a novel derived line, named D88-2a, a progeny of the former characterized wheat-P. huashanica partial amphiploid line H8911 (2n = 7x = 49, AABBDDNs). Cytological identification showed that the chromosomal composition of D88-2a was 2n = 44 = 22II, indicating the addition of exogenous chromosomes. Genomic in situ hybridization demonstrated that the supernumerary chromosomes were a pair of homologues from the P. huashanica and could be stably inherited in the common wheat background. Molecular markers and 15 K SNP array indicated that the additional chromosomes were derived from the sixth homoeologous group (i.e., 6Ns) of P. huashanica. Based on the distribution of the heterozygous single-nucleotide polymorphism sites and fluorescence in situ hybridization karyotype of each chromosome, this pair of additional chromosomes was confirmed as P. huashanica 6Ns large segment chromosomes, which contained the entire short arm and the proximal centromere portion of the long arm. In terms of the agronomic traits, the addition line D88-2a exhibited enhanced stripe rust resistance, improved spike characteristics and increased protein content than its wheat parent line 7182. CONCLUSIONS The new wheat germplasm D88-2a is a novel cytogenetically stable wheat-P. huashanica 6Ns large segment addition line, and the introgressed large segment alien chromosome has positive impact on plant spikelet number and stripe rust resistance. Thus, this germplasm can be used for genetic improvement of cultivated wheat and the study of functional alien chromosome segment.
Collapse
Affiliation(s)
- Jiaojiao Li
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Jiachuang Li
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Xueni Cheng
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zujun Yang
- School of Life Sciences and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610000, China
| | - Yuhui Pang
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Chunping Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Jun Wu
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wanquan Ji
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xinhong Chen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Jixin Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| |
Collapse
|
5
|
Zuo Y, Liu H, Li B, Zhao H, Li X, Chen J, Wang L, Zheng Q, He Y, Zhang J, Wang M, Liang C, Wang L. The Idesia polycarpa genome provides insights into its evolution and oil biosynthesis. Cell Rep 2024; 43:113909. [PMID: 38451814 DOI: 10.1016/j.celrep.2024.113909] [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: 06/29/2023] [Revised: 01/26/2024] [Accepted: 02/20/2024] [Indexed: 03/09/2024] Open
Abstract
The deciduous tree Idesia polycarpa can provide premium edible oil with high polyunsaturated fatty acid contents. Here, we generate its high-quality reference genome, which is ∼1.21 Gb, comprising 21 pseudochromosomes and 42,086 protein-coding genes. Phylogenetic and genomic synteny analyses show that it diverged with Populus trichocarpa about 16.28 million years ago. Notably, most fatty acid biosynthesis genes are not only increased in number in its genome but are also highly expressed in the fruits. Moreover, we identify, through genome-wide association analysis and RNA sequencing, the I. polycarpa SUGAR TRANSPORTER 5 (IpSTP5) gene as a positive regulator of high oil accumulation in the fruits. Silencing of IpSTP5 by virus-induced gene silencing causes a significant reduction of oil content in the fruits, suggesting it has the potential to be used as a molecular marker to breed the high-oil-content cultivars. Our results collectively lay the foundation for breeding the elite cultivars of I. polycarpa.
Collapse
Affiliation(s)
- Yi Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Hongbing Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Bin Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Hang Zhao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiuli Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Jiating Chen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lu Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China
| | - Qingbo Zheng
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; China National Botanical Garden, Beijing 100093, China
| | - Yuqing He
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; Academician Workstation of Agricultural High-Tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying 257300, China
| | - Jiashuo Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Minxian Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Science, Beijing 100093, China; Academician Workstation of Agricultural High-Tech Industrial Area of the Yellow River Delta, National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land, Dongying 257300, China; China National Botanical Garden, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
6
|
Joshi P, Soni P, Sharma V, Manohar SS, Kumar S, Sharma S, Pasupuleti J, Vadez V, Varshney RK, Pandey MK, Puppala N. Genome-Wide Mapping of Quantitative Trait Loci for Yield-Attributing Traits of Peanut. Genes (Basel) 2024; 15:140. [PMID: 38397130 PMCID: PMC10888419 DOI: 10.3390/genes15020140] [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: 11/14/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024] Open
Abstract
Peanuts (Arachis hypogaea L.) are important high-protein and oil-containing legume crops adapted to arid to semi-arid regions. The yield and quality of peanuts are complex quantitative traits that show high environmental influence. In this study, a recombinant inbred line population (RIL) (Valencia-C × JUG-03) was developed and phenotyped for nine traits under two environments. A genetic map was constructed using 1323 SNP markers spanning a map distance of 2003.13 cM. Quantitative trait loci (QTL) analysis using this genetic map and phenotyping data identified seventeen QTLs for nine traits. Intriguingly, a total of four QTLs, two each for 100-seed weight (HSW) and shelling percentage (SP), showed major and consistent effects, explaining 10.98% to 14.65% phenotypic variation. The major QTLs for HSW and SP harbored genes associated with seed and pod development such as the seed maturation protein-encoding gene, serine-threonine phosphatase gene, TIR-NBS-LRR gene, protein kinase superfamily gene, bHLH transcription factor-encoding gene, isopentyl transferase gene, ethylene-responsive transcription factor-encoding gene and cytochrome P450 superfamily gene. Additionally, the identification of 76 major epistatic QTLs, with PVE ranging from 11.63% to 72.61%, highlighted their significant role in determining the yield- and quality-related traits. The significant G × E interaction revealed the existence of the major role of the environment in determining the phenotype of yield-attributing traits. Notably, the seed maturation protein-coding gene in the vicinity of major QTLs for HSW can be further investigated to develop a diagnostic marker for HSW in peanut breeding. This study provides understanding of the genetic factor governing peanut traits and valuable insights for future breeding efforts aimed at improving yield and quality.
Collapse
Affiliation(s)
- Pushpesh Joshi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India;
| | - Pooja Soni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India;
| | - Surendra S. Manohar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
| | - Sampath Kumar
- Agricultural Research Station, Andhra Pradesh Agricultural University, Anantapur 515591, India;
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India;
| | - Janila Pasupuleti
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
| | - Vincent Vadez
- Institut de Recherche pour le Development (IRD), Université de Montpellier, Unité Mixte de Recherche Diversité et Adaptation des Espèces (UMR DIADE), 34394 Montpellier, France;
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (P.J.); (V.S.); (S.S.M.); (J.P.); (R.K.V.)
| | - Naveen Puppala
- Agricultural Science Center at Clovis, New Mexico State University, Clovis, NM 88101, USA
| |
Collapse
|
7
|
Qin H, Yin W, Luo C, Liu L. The Identification, Characterization, and Functional Analysis of the Sugar Transporter Gene Family of the Rice False Smut Pathogen, Villosiclava virens. Int J Mol Sci 2024; 25:600. [PMID: 38203770 PMCID: PMC10779207 DOI: 10.3390/ijms25010600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/21/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
False smut, caused by Villosiclava virens, is becoming increasingly serious in modern rice production systems, leading to yield losses and quality declines. Successful infection requires efficient acquisition of sucrose, abundant in rice panicles, as well as other sugars. Sugar transporters (STPs) may play an important role in this process. STPs belong to a major facilitator superfamily, which consists of large multigenic families necessary to partition sugars between fungal pathogens and their hosts. This study identified and characterized the STP family of V. viren, and further analyzed their gene functions to uncover their roles in interactions with rice. Through genome-wide and systematic bioinformatics analyses, 35 STPs were identified from V.virens and named from VvSTP1 to VvSTP35. Transmembrane domains, gene structures, and conserved motifs of VvSTPs have been identified and characterized through the bioinformatic analysis. In addition, a phylogenetic analysis revealed relationship between VvSTPs and STPs from the other three reference fungi. According to a qRT-PCR and RNA-sequencing analysis, VvSTP expression responded differently to different sole carbon sources and H2O2 treatments, and changed during the pathogenic process, suggesting that these proteins are involved in interactions with rice and potentially functional in pathogenesis. In total, 12 representative VvSTPs were knocked out through genetic recombination in order to analyze their roles in pathogenicity of V. virens. The knock-out mutants of VvSTPs showed little difference in mycelia growth and conidiation, indicating a single gene in this family cannot influence vegetative growth of V. virens. It is clear, however, that these mutants result in a change in infection efficiency in a different way, indicating that VvSTPs play an important role in the pathogenicity of virens. This study is expected to contribute to a better understanding of how host-derived sugars contribute to V. virens pathogenicity.
Collapse
Affiliation(s)
- Huimin Qin
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China;
| | - Weixiao Yin
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Chaoxi Luo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Lianmeng Liu
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China;
| |
Collapse
|
8
|
Miao P, Meng X, Li Z, Sun S, Chen CY, Yang X. Mapping Quantitative Trait Loci (QTLs) for Hundred-Pod and Hundred-Seed Weight under Seven Environments in a Recombinant Inbred Line Population of Cultivated Peanut ( Arachis hypogaea L.). Genes (Basel) 2023; 14:1792. [PMID: 37761932 PMCID: PMC10531390 DOI: 10.3390/genes14091792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
The cultivated peanut (Arachis hypogaea L.) is a significant oil and cash crop globally. Hundred-pod and -seed weight are important components for peanut yield. To unravel the genetic basis of hundred-pod weight (HPW) and hundred-seed weight (HSW), in the current study, a recombinant inbred line (RIL) population with 188 individuals was developed from a cross between JH5 (JH5, large pod and seed weight) and M130 (small pod and seed weight), and was utilized to identify QTLs for HPW and HSW. An integrated genetic linkage map was constructed by using SSR, AhTE, SRAP, TRAP and SNP markers. This map consisted of 3130 genetic markers, which were assigned to 20 chromosomes, and covered 1998.95 cM with an average distance 0.64 cM. On this basis, 31 QTLs for HPW and HSW were located on seven chromosomes, with each QTL accounting for 3.7-10.8% of phenotypic variance explained (PVE). Among these, seven QTLs were detected under multiple environments, and two major QTLs were found on B04 and B08. Notably, a QTL hotspot on chromosome A08 contained seven QTLs over a 2.74 cM genetic interval with an 0.36 Mb physical map, including 18 candidate genes. Of these, Arahy.D52S1Z, Arahy.IBM9RL, Arahy.W18Y25, Arahy.CPLC2W and Arahy.14EF4H might play a role in modulating peanut pod and seed weight. These findings could facilitate further research into the genetic mechanisms influencing pod and seed weight in cultivated peanut.
Collapse
Affiliation(s)
- Penghui Miao
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Xinhao Meng
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Zeren Li
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Sainan Sun
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| | - Charles Y. Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL 36849, USA
| | - Xinlei Yang
- State Key Laboratory of North China for Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of Education Ministry, Key Laboratory of Crop Germplasm Resources of Hebei Province, Hebei Agricultural University, Baoding 071001, China
| |
Collapse
|
9
|
Sun Y, Yuan X, Chen K, Wang H, Luo Y, Guo C, Wang Z, Shu C, Yang Y, Weng Y, Zhou X, Yang Z, Chen Z, Ma J, Sun Y. Improving the yield and nitrogen use efficiency of hybrid rice through rational use of controlled-release nitrogen fertilizer and urea topdressing. FRONTIERS IN PLANT SCIENCE 2023; 14:1240238. [PMID: 37692439 PMCID: PMC10484103 DOI: 10.3389/fpls.2023.1240238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023]
Abstract
Introduction Controlled-release fertilizers effectively improve crop yield and nitrogen use efficiency (NUE). However, their use increases the cost of crop production. Optimal management modes involving urea replacement with controlled-release N fertilizers to increase rice yield through enhanced NUE are not widely explored. Methods Field experiments were conducted from 2017 to 2018 to determine the effects of different controlled-release N fertilizers combined with urea [urea-N (180 kg ha-1, N1)]. We used controlled-release N (150 kg ha-1, N2) as the base, and four controlled-release N and urea-N ratio treatments [(80%:0% (N3), 60%:20% (N4), 40%:40% (N5), or 20%:60% (N6) as the base with 20% urea-N as topdressing at the panicle initiation stage under 150 kg ha-1] to study their impact on the grain yield and NUE of machine-transplanted rice. Results and discussion Grain yield and NUE were positively correlated with increases in photosynthetic production, flag leaf net photosynthetic rate (Pn), root activity, N transport, and grain-filling characteristics. The photosynthetic potential and population growth rate from the jointing to the full-heading stage, highly effective leaf area index (LAI) rate and Pn at the full-heading stage, root activity at 15 d after the full-heading stage, and N transport in the leaves from the full-heading to mature stage were significantly increased by the N4 treatment, thereby increasing both grain yield and NUE. Furthermore, compared with the other N treatments, the N4 treatment promoted the mean filling rate of inferior grains, which is closely related to increased filled grains per spikelet and filled grains rate. These effects ultimately improved the grain yield (5.03-25.75%), N agronomic efficiency (NAE, 3.96-17.58%), and N partial factor productivity (NPP, 3.98-27.13%) under the N4 treatment. Thus, the N4 treatment with controlled-release N (60%) and urea-N (20%) as a base and urea-N (20%) as topdressing at the panicle-initiation stage proved effective in improving the grain yield and NUE of machine-transplanted hybrid indica rice. These findings offer a theoretical and practical basis for enhancing rice grain yield, NUE, and saving the cost of fertilizer.
Collapse
Affiliation(s)
- Yuanyuan Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Institute of Plateau Meteorology, China Meteorological Administration, Chengdu, Sichuan, China
| | - Xiaojuan Yuan
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Kairui Chen
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Haiyue Wang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yongheng Luo
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Changchun Guo
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zhonglin Wang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Chuanhai Shu
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yonggang Yang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yanfang Weng
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaobo Zhou
- Sichuan Agricultural Machinery Research Academy, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Zhiyuan Yang
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Zongkui Chen
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Jun Ma
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Yongjian Sun
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
10
|
Zhao H, Fu Y, Zhang G, Luo Y, Yang W, Liang X, Yin L, Zheng Z, Wang Y, Li Z, Zhu H, Huang J, Tan Q, Bu S, Liu G, Wang S, Liu Z. GS6.1 controls kernel size and plant architecture in rice. PLANTA 2023; 258:42. [PMID: 37432475 DOI: 10.1007/s00425-023-04201-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
MAIN CONCLUSION A novel QTL GS6.1 increases yield per plant by controlling kernel size, plant architecture, and kernel filling in rice. Kernel size and plant architecture are critical agronomic traits that greatly influence kernel yield in rice. Using the single-segment substitution lines (SSSLs) with an indica cultivar Huajingxian74 as a recipient parent and American Jasmine as a donor parent, we identified a novel quantitative trait locus (QTL), named GS6.1. Near isogenic line-GS6.1 (NIL-GS6.1) produces long and narrow kernels by regulating cell length and width in the spikelet hulls, thus increasing the 1000-kernel weight. Compared with the control, the plant height, panicles per plant, panicle length, kernels per plant, secondary branches per panicle, and yield per plant of NIL-GS6.1 are increased. In addition, GS6.1 regulates the kernel filling rate. GS6.1 controls kernel size by modulating the transcription levels of part of EXPANSINs, kernel filling-related genes, and kernel size-related genes. These results indicate that GS6.1 might be beneficial for improving kernel yield and plant architecture in rice breeding by molecular design.
Collapse
Affiliation(s)
- Hongyuan Zhao
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Yu Fu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Guiquan Zhang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Yingqin Luo
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Weifeng Yang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Xiaoya Liang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Lin Yin
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Zhenwu Zheng
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Yijun Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Zhan Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Haitao Zhu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Jinyan Huang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Quanya Tan
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Suhong Bu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Guifu Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China
| | - Shaokui Wang
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China.
| | - Zupei Liu
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510630, Guangdong, China.
| |
Collapse
|
11
|
Ma B, Zhang L, He Z. Understanding the regulation of cereal grain filling: The way forward. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:526-547. [PMID: 36648157 DOI: 10.1111/jipb.13456] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
During grain filling, starch and other nutrients accumulate in the endosperm; this directly determines grain yield and grain quality in crops such as rice (Oryza sativa), maize (Zea mays), and wheat (Triticum aestivum). Grain filling is a complex trait affected by both intrinsic and environmental factors, making it difficult to explore the underlying genetics, molecular regulation, and the application of these genes for breeding. With the development of powerful genetic and molecular techniques, much has been learned about the genes and molecular networks related to grain filling over the past decades. In this review, we highlight the key factors affecting grain filling, including both biological and abiotic factors. We then summarize the key genes controlling grain filling and their roles in this event, including regulators of sugar translocation and starch biosynthesis, phytohormone-related regulators, and other factors. Finally, we discuss how the current knowledge of valuable grain filling genes could be integrated with strategies for breeding cereal varieties with improved grain yield and quality.
Collapse
Affiliation(s)
- Bin Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lin Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Zuhua He
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| |
Collapse
|