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Voothuluru P, Wu Y, Sharp RE. Not so hidden anymore: Advances and challenges in understanding root growth under water deficits. THE PLANT CELL 2024; 36:1377-1409. [PMID: 38382086 PMCID: PMC11062450 DOI: 10.1093/plcell/koae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 02/23/2024]
Abstract
Limited water availability is a major environmental factor constraining plant development and crop yields. One of the prominent adaptations of plants to water deficits is the maintenance of root growth that enables sustained access to soil water. Despite early recognition of the adaptive significance of root growth maintenance under water deficits, progress in understanding has been hampered by the inherent complexity of root systems and their interactions with the soil environment. We highlight selected milestones in the understanding of root growth responses to water deficits, with emphasis on founding studies that have shaped current knowledge and set the stage for further investigation. We revisit the concept of integrated biophysical and metabolic regulation of plant growth and use this framework to review central growth-regulatory processes occurring within root growth zones under water stress at subcellular to organ scales. Key topics include the primary processes of modifications of cell wall-yielding properties and osmotic adjustment, as well as regulatory roles of abscisic acid and its interactions with other hormones. We include consideration of long-recognized responses for which detailed mechanistic understanding has been elusive until recently, for example hydrotropism, and identify gaps in knowledge, ongoing challenges, and opportunities for future research.
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Affiliation(s)
- Priya Voothuluru
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
| | - Yajun Wu
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA
| | - Robert E Sharp
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
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Bektas H, Hohn CE, Lukaszewski AJ, Waines JG. On the Possible Trade-Off between Shoot and Root Biomass in Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2513. [PMID: 37447071 DOI: 10.3390/plants12132513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/15/2023]
Abstract
Numerous studies have shown that under a limited water supply, a larger root biomass is associated with an increased above-ground biomass. Root biomass, while genetically controlled, is also greatly affected by the environment with varying plasticity levels. In this context, understanding the relationship between the biomass of shoots and roots appears prudent. In this study, we analyze this relationship in a large dataset collected from multiple experiments conducted up to different growth stages in bread wheat (Triticum aestivum L.) and its wild relatives. Four bread wheat mapping populations as well as wild and domesticated members of the Triticeae tribe were evaluated for the root and shoot biomass allocation patterns. In the analyzed dataset the root and shoot biomasses were directly related to each other, and to the heading date, and the correlation values increased in proportion to the length of an experiment. On average, 84.1% of the observed variation was explained by a positive correlation between shoot and root biomass. Scatter plots generated from 6353 data points from numerous experiments with different wheats suggest that at some point, further increases in root biomass negatively impact the shoot biomass. Based on these results, a preliminary study with different water availability scenarios and growth conditions was designed with two cultivars, Pavon 76 and Yecora Rojo. The duration of drought and water level significantly affected the root/shoot biomass allocation patterns. However, the responses of the two cultivars were quite different, suggesting that the point of diminishing returns in increasing root biomass may be different for different wheats, reinforcing the need to breed wheats for specific environmental challenges.
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Affiliation(s)
- Harun Bektas
- Department of Agricultural Biotechnology, Siirt University, Siirt 56100, Turkey
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Christopher E Hohn
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Adam J Lukaszewski
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - John Giles Waines
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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Zhang J, Debernardi JM, Burguener GF, Choulet F, Paux E, O'Connor L, Enk J, Dubcovsky J. A second-generation capture panel for cost-effective sequencing of genome regulatory regions in wheat and relatives. THE PLANT GENOME 2023; 16:e20296. [PMID: 36484157 DOI: 10.1002/tpg2.20296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/11/2022] [Indexed: 05/10/2023]
Abstract
As genome resources for wheat (Triticum L.) expand at a rapid pace, it is important to update targeted sequencing tools to incorporate improved sequence assemblies and regions of previously unknown significance. Here, we developed an updated regulatory region enrichment capture for wheat and other Triticeae species. The core target space includes sequences from 2-Kbp upstream of each gene predicted in the Chinese Spring wheat genome (IWGSC RefSeq Annotation v1.0) and regions of open chromatin identified with an assay for transposase-accessible chromatin using sequencing from wheat leaf and root samples. To improve specificity, we aggressively filtered candidate repetitive sequences using a combination of nucleotide basic local alignment search tool (BLASTN) searches to the Triticeae Repetitive Sequence Database (TREP), identification of regions with read over-coverage from previous target enrichment experiments, and k-mer frequency analyses. The final design comprises 216.5 Mbp of predicted hybridization space in hexaploid wheat and showed increased specificity and coverage of targeted sequences relative to previous protocols. Test captures on hexaploid and tetraploid wheat and other diploid cereals show that the assay has broad potential utility for cost-effective promoter and open chromatin resequencing and general-purpose genotyping of various Triticeae species.
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Affiliation(s)
- Junli Zhang
- Dep. of Plant Sciences, Univ. of California, Davis, CA, 95616, USA
| | | | | | | | | | | | - Jacob Enk
- Daicel Arbor Biosciences, Ann Arbor, MI, 48103, USA
| | - Jorge Dubcovsky
- Dep. of Plant Sciences, Univ. of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
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Zhang X, Wang H, Sun H, Li Y, Feng Y, Jiao C, Li M, Song X, Wang T, Wang Z, Yuan C, Sun L, Lu R, Zhang W, Xiao J, Wang X. A chromosome-scale genome assembly of Dasypyrum villosum provides insights into its application as a broad-spectrum disease resistance resource for wheat improvement. MOLECULAR PLANT 2023; 16:432-451. [PMID: 36587241 DOI: 10.1016/j.molp.2022.12.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/27/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Dasypyrum villosum is one of the most valuable gene resources in wheat improvement, especially for disease resistance. The mining of favorable genes from D. villosum is frustrated by the lack of a whole genome sequence. In this study, we generated a doubled-haploid line, 91C43DH, using microspore culture and obtained a 4.05-GB high-quality, chromosome-scale genome assembly for D. villosum. The assembly contains39 727 high-confidence genes, and 85.31% of the sequences are repetitive. Two reciprocal translocation events were detected, and 7VS-4VL is a unique translocation in D. villosum. The prolamin seed storage protein-coding genes were found to be duplicated; in particular, the genes encoding low-molecular-weight glutenin at the Glu-V3 locus were significantly expanded. RNA sequencing (RNA-seq) analysis indicated that, after Blumeria graminearum f.sp tritici (Bgt) inoculation, there were more upregulated genes involved in the pattern-triggered immunity and effector-triggered immunity defense pathways in D. villosum than in Triticum urartu. MNase hypersensitive sequencing (MH-seq) identified two Bgt-inducible MH sites (MHSs), one in the promoter and one in the 3' terminal region of the powdery mildew resistance (Pm) gene NLR1-V. Each site had two subpeaks and they were termed MHS1 (MHS1.1/1.2) and MHS2 (MHS2.1/2.2). Bgt-inducible MHS2.2 was uniquely present in D. villosum, and MHS1.1 was more inducible in D. villosum than in wheat, suggesting that MHSs may be critical for regulation of NLR1-V expression and plant defense. In summary, this study provides a valuable genome resource for functional genomics studies and wheat-D. villosum introgression breeding. The identified regulatory mechanisms may also be exploited to develop new strategies for enhancing Pm resistance by optimizing gene expression in wheat.
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Affiliation(s)
- Xu Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Haiyan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Haojie Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Yingbo Li
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yilong Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Chengzhi Jiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Mengli Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Xinying Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Tong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Zongkuan Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Chunxia Yuan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Li Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Ruiju Lu
- Biotech Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Wenli Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China
| | - Jin Xiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China.
| | - Xiue Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cytogenetics Institute, Nanjing Agricultural University/JCIC-MCP, Nanjing, Jiangsu 210095, China.
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Dosage differences in 12-OXOPHYTODIENOATE REDUCTASE genes modulate wheat root growth. Nat Commun 2023; 14:539. [PMID: 36725858 PMCID: PMC9892559 DOI: 10.1038/s41467-023-36248-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/20/2023] [Indexed: 02/03/2023] Open
Abstract
Wheat, an essential crop for global food security, is well adapted to a wide variety of soils. However, the gene networks shaping different root architectures remain poorly understood. We report here that dosage differences in a cluster of monocot-specific 12-OXOPHYTODIENOATE REDUCTASE genes from subfamily III (OPRIII) modulate key differences in wheat root architecture, which are associated with grain yield under water-limited conditions. Wheat plants with loss-of-function mutations in OPRIII show longer seminal roots, whereas increased OPRIII dosage or transgenic over-expression result in reduced seminal root growth, precocious development of lateral roots and increased jasmonic acid (JA and JA-Ile). Pharmacological inhibition of JA-biosynthesis abolishes root length differences, consistent with a JA-mediated mechanism. Transcriptome analyses of transgenic and wild-type lines show significant enriched JA-biosynthetic and reactive oxygen species (ROS) pathways, which parallel changes in ROS distribution. OPRIII genes provide a useful entry point to engineer root architecture in wheat and other cereals.
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Marker-assisted introgression of genes into rye translocation leads to the improvement in bread making quality of wheat (Triticum aestivum L.). Heredity (Edinb) 2022; 128:531-541. [PMID: 35568742 DOI: 10.1038/s41437-022-00538-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 04/19/2022] [Accepted: 04/19/2022] [Indexed: 11/08/2022] Open
Abstract
Introgression of genes from related species can be a powerful way to genetically improve crop yields, but selection for one trait can come at the cost to others. Wheat varieties with translocation of the short arm of chromosome 1 from the B genome of wheat (1BS) with the short arm of chromosome 1 from rye (1RS) are popular globally for their positive effect on yield and stress resistance. Unfortunately, this translocation (1BL.1RS) is also associated with poor bread making quality, mainly due to the presence of Sec-1 on its proximal end, encoding secalin proteins, and the absence of Glu-B3/Gli-B1-linked loci on its distal end, encoding low molecular weight glutenin subunits (LMW-GS). The present study aims to replace these two important loci on the 1RS arm with the wheat 1BS loci, in two popular Indian wheat varieties, PBW550 and DBW17, to improve their bread-making quality. Two donor lines in the cultivar Pavon background with absence of the Sec-1 locus and presence of the Glu-B3/Gli-B1 locus, respectively, were crossed and backcrossed with these two selected wheat varieties. In the advancing generations, marker assisted foreground selection was done for Sec-1- and Glu-B3/Gli-B1+ loci while recurrent parent recovery was done with the help of SSR markers. BC2F5 and BC2F6 near isosgenic lines (NILs) with absence of Sec-1 and presence of Glu-B3/Gli-B1 loci were evaluated for two years in replicated yield trials. As a result of this selection, thirty promising lines were generated that demonstrated improved bread making quality but also balanced with improved yield-related traits compared to the parental strains. The study demonstrates the benefits of using marker-assisted selection to replace a few loci with negative effects within larger alien translocations for crop improvement.
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Luo J, Liao R, Duan Y, Fu S, Tang Z. Variations of subtelomeric tandem repeats and rDNA on chromosome 1RS arms in the genus Secale and 1BL.1RS translocations. BMC PLANT BIOLOGY 2022; 22:212. [PMID: 35468732 PMCID: PMC9036760 DOI: 10.1186/s12870-022-03598-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The wheat-rye 1BL.1RS translocations have played an important role in common wheat breeding programs. Subtelomeric tandem repeats have been often used to investigate polymorphisms of 1RS arms, but further research about their organizations on the 1RS chromosome is needed. RESULTS 162 1RS arms from a wild rye species (Secale strictum) and six cultivated rye accessions (Secale cereale L.) (81 plants), 102 1BL.1RS and one 1AL.1RS translocations were investigated using oligo probes Oligo-TaiI, Oligo-pSc119.2-1, Oligo-pTa71A-2, Oligo-pSc200 and Oligo-pSc250, which were derived from tandem repeats TaiI, pSc119.2, pTa71, pSc200 and pSc250, respectively. The variations of 1RS arms were revealed by signal intensity of probes Oligo-pSc119.2-1, Oligo-pTa71A-2, Oligo-pSc200 and Oligo-pSc250. Proliferation of rDNA sequences on the 1RS chromosomes was observed. According to the presence of probe signals, 34, 127 and 144 of the 162 1RS arms contained TaiI, pSc200 and pSc250, respectively, and all of them contained pSc119.2 and pTa71. Most of the 1RS arms in rye contained three kinds of subtelomeric tandem repeats, the combination of pSc119.2, pSc200 and pSc250 was most common, and only eight of them contained TaiI, pSc119.2, pSc200 and pSc250. All of the 1RS arms in 1BL.1RS and 1AL.1RS translocations contained pSc119.2, pTa71, pSc200 and pSc250, but the presence of the TaiI family was not observed. CONCLUSION New organizations of subtelomeric tandem repeats on 1RS were found, and they reflected new genetic variations of 1RS arms. These 1RS arms might contain abundant allelic diversity for agricultural traits. The narrow genetic base of 1RS arms in 1BL.1RS and 1AL.1RS translocations currently used in agriculture is seriously restricting their use in wheat breeding programs. This research has found new 1RS sources for the future restructuring of 1BL.1RS translocations. The allelic variations of these 1RS arms should be studied more intensely as they may enrich the genetic diversity of 1BL.1RS translocations.
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Affiliation(s)
- Jie Luo
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Ruiying Liao
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yanling Duan
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Shulan Fu
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, Chengdu, 611130, Sichuan, China.
| | - Zongxiang Tang
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
- Provincial Key Laboratory for Plant Genetics and Breeding, Wenjiang, Chengdu, 611130, Sichuan, China.
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