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Hu X, Yasir M, Zhuo Y, Cai Y, Ren X, Rong J. Genomic insights into glume pubescence in durum wheat: GWAS and haplotype analysis implicates TdELD1-1A as a candidate gene. Gene 2024; 909:148309. [PMID: 38417687 DOI: 10.1016/j.gene.2024.148309] [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: 09/21/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
Glume pubescence is an important morphological trait for the characterization of wheat cultivars. It shows tolerance to biotic and abiotic stresses to some extent. Hg1 (formerly named Hg) locus on chromosome 1AS controls glume pubescence in wheat. Its genetic analysis, fine-mapping and candidate gene analysis have been widely studied recently, however, the cloning of Hg1 has not yet been reported. Here, we conducted a GWAS between a dense panel of 171,103 SNPs and glume pubescence (Gp) in a durum wheat population of 145 lines, and further analyzed the candidate genes of Hg1 combined with the gene expression, functional annotation, and haplotype analysis. As a results, TRITD0Uv1G104670 (TdELD1-1A), encoding glycosyltransferase-like ELD1/KOBITO 1, was detected as the most promising candidate gene of Hg1 for glume pubescence in durum wheat. Our findings not only contribute to a deeper understanding of its cloning and functional validation but also underscore the significance of accurate genome sequences and annotations. Additionally, our study highlights the relevance of unanchored sequences in chrUn and the application of bioinformatics analysis for gene discovery in durum wheat.
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Affiliation(s)
- Xin Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Muhammad Yasir
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Yujie Zhuo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Yijing Cai
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
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Wu H, Liu X, Zong Y, Yang L, Wang J, Tong C, Li H. Leaf morphology related genes revealed by integrating Pan-transcriptome, GWAS and eQTL analyses in a Liriodendron population. PHYSIOLOGIA PLANTARUM 2024; 176:e14392. [PMID: 38887911 DOI: 10.1111/ppl.14392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/15/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024]
Abstract
Leaf plays an indispensable role in plant development and growth. Although many known genes related to leaf morphology development have been identified, elucidating the complex genetic basis of leaf morphological traits remains a challenge. Liriodendron plants are common ornamental trees due to their unique leaf shapes, while the molecular mechanism underlying Liriodendron leaf morphogenesis has remained unknown. Herein, we firstly constructed a population-level pan-transcriptome of Liriodendron from 81 accessions to explore the expression presence or absence variations (ePAVs), global expression differences at the population level, as well as differentially expressed genes (DEGs) between the Liriodendron chinense and Liriodendron tulipifera accessions. Subsequently, we integrated a genome-wide association study (GWAS), expression quantitative trait loci (eQTL), and transcriptome-wide association study (TWAS) to identify candidate genes related to leaf morphology. Through GWAS analysis, we identified 18 and 17 significant allelic loci in the leaf size and leaf shape modules, respectively. In addition, we discerned 16 candidate genes in relation to leaf morphological traits via TWAS. Further, integrating the co-localization results of GWAS and eQTL, we determined two regulatory hotspot regions, hot88 and hot758, related to leaf size and leaf shape, respectively. Finally, co-expression analysis, eQTL, and linkage mapping together demonstrated that Lchi_4g10795 regulate their own expression levels through cis-eQTL to affect the expression of downstream genes and cooperatively participate in the development of Liriodendron leaf morphology. These findings will improve our understanding of the molecular regulatory mechanism of Liriodendron leaf morphogenesis and will also accelerate molecular breeding of Liriodendron.
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Affiliation(s)
- Hainan Wu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Xiao Liu
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yaxian Zong
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Lichun Yang
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Jing Wang
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Chunfa Tong
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Huogen Li
- State Key Laboratory of Tree Genetics and Breeding, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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3
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Feng J, Wang Y, Ge W, Zhang K, Cui J. Regulatory mechanism of the miR172e-LbrAP2 module during the vegetative growth phase transition in Lilium. PLANTA 2023; 259:26. [PMID: 38110586 DOI: 10.1007/s00425-023-04308-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 12/01/2023] [Indexed: 12/20/2023]
Abstract
MAIN CONCLUSION It was proved for the first time that the miR172e-LbrAP2 module regulated the vegetative growth phase transition in Lilium, which provided a new approach to shorten the juvenile stage of Lilium, improved the reproduction rate, and reduced the propagation cost of Lilium commercial bulbs. Lilium is an ornamental bulb plant that takes at least 3 years to cultivate into commercial seed bulbs under natural conditions. The aim of this study was to shorten the Lilium expansion cycle. In this study, the growth cycle of lily tubers induced by low temperature of 15 °C was significantly shorter than that of tubers grown at a conventional temperature. Quantitative real-time PCR analysis showed that the expression patterns of miR172e and LbrAP2 were negatively correlated. GUS histochemical staining confirmed that miR172e and LbrAP2 in tobacco leaves interacted with each other after co-transformation. The shear sites of miR172e and its target gene, LbrAP2, upon binding, were identified by RLM 5' RACE analysis. In addition, miR172e and LbrAP2 showed opposite expression patterns after the transformation of Arabidopsis. miR172e overexpression accelerated the transition from juvenile to adult plants, whereas LbrAP2 overexpression inhibited this process, thus indicating that miR172e negatively regulated the target gene LbrAP2. Upregulation of the transcription factor LbrAP2 delayed the phase transition of plants, whereas miR172 inhibited the transcriptional translation of LbrAP2, thereby accelerating the phase transition. Low-temperature treatment of Lilium bulbs can shorten Lilium development, which provides a new approach to accelerating Lilium commercial bulb breeding and reducing breeding costs.
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Affiliation(s)
- Junting Feng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Yiqing Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Wei Ge
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China
| | - Kezhong Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.
- Laboratory of Urban and Rural Ecological Environment, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.
| | - Jinteng Cui
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.
- Laboratory of Urban and Rural Ecological Environment, Beijing University of Agriculture, Beijing, 102206, People's Republic of China.
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Peng L, Li Y, Tan W, Wu S, Hao Q, Tong N, Wang Z, Liu Z, Shu Q. Combined genome-wide association studies and expression quantitative trait locus analysis uncovers a genetic regulatory network of floral organ number in a tree peony ( Paeonia suffruticosa Andrews) breeding population. HORTICULTURE RESEARCH 2023; 10:uhad110. [PMID: 37577399 PMCID: PMC10419549 DOI: 10.1093/hr/uhad110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/16/2023] [Indexed: 08/15/2023]
Abstract
Great progress has been made in our understanding of floral organ identity determination and its regulatory network in many species; however, the quantitative genetic basis of floral organ number variation is far less well understood for species-specific traits from the perspective of population variation. Here, using a tree peony (Paeonia suffruticosa Andrews, Paeoniaceae) cultivar population as a model, the phenotypic polymorphism and genetic variation based on genome-wide association studies (GWAS) and expression quantitative trait locus (eQTL) analysis were analyzed. Based on 24 phenotypic traits of 271 representative cultivars, the transcript profiles of 119 cultivars were obtained, which indicated abundant genetic variation in tree peony. In total, 86 GWAS-related cis-eQTLs and 3188 trans-eQTL gene pairs were found to be associated with the numbers of petals, stamens, and carpels. In addition, 19 floral organ number-related hub genes with 121 cis-eQTLs were obtained by weighted gene co-expression network analysis, among which five hub genes belonging to the ABCE genes of the MADS-box family and their spatial-temporal co-expression and regulatory network were constructed. These results not only help our understanding of the genetic basis of floral organ number variation during domestication, but also pave the way to studying the quantitative genetics and evolution of flower organ number and their regulatory network within populations.
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Affiliation(s)
- Liping Peng
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Yang Li
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Wanqing Tan
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shangwei Wu
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qing Hao
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China
| | - Ningning Tong
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Zhanying Wang
- Peony Research Institute, Luoyang Academy of Agricultural and Forestry Sciences, Luoyang 471000, China
| | - Zheng’an Liu
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingyan Shu
- Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
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5
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Jin Y, Li D, Liu M, Cui Z, Sun D, Li C, Zhang A, Cao H, Ruan Y. Genome-Wide Association Study Identified Novel SNPs Associated with Chlorophyll Content in Maize. Genes (Basel) 2023; 14:genes14051010. [PMID: 37239370 DOI: 10.3390/genes14051010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Chlorophyll is an essential component that captures light energy to drive photosynthesis. Chlorophyll content can affect photosynthetic activity and thus yield. Therefore, mining candidate genes of chlorophyll content will help increase maize production. Here, we performed a genome-wide association study (GWAS) on chlorophyll content and its dynamic changes in 378 maize inbred lines with extensive natural variation. Our phenotypic assessment showed that chlorophyll content and its dynamic changes were natural variations with a moderate genetic level of 0.66/0.67. A total of 19 single-nucleotide polymorphisms (SNPs) were found associated with 76 candidate genes, of which one SNP, 2376873-7-G, co-localized in chlorophyll content and area under the chlorophyll content curve (AUCCC). Zm00001d026568 and Zm00001d026569 were highly associated with SNP 2376873-7-G and encoded pentatricopeptide repeat-containing protein and chloroplastic palmitoyl-acyl carrier protein thioesterase, respectively. As expected, higher expression levels of these two genes are associated with higher chlorophyll contents. These results provide a certain experimental basis for discovering the candidate genes of chlorophyll content and finally provide new insights for cultivating high-yield and excellent maize suitable for planting environment.
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Affiliation(s)
- Yueting Jin
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Dan Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Meiling Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhenhai Cui
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Daqiu Sun
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Cong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Ao Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Huiying Cao
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
- Liaoning Province Research Center of Plant Genetic Engineering Technology, Shenyang Key Laboratory of Maize Genomic Selection Breeding, Shenyang 110866, China
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6
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Lorenzo CD, Debray K, Herwegh D, Develtere W, Impens L, Schaumont D, Vandeputte W, Aesaert S, Coussens G, De Boe Y, Demuynck K, Van Hautegem T, Pauwels L, Jacobs TB, Ruttink T, Nelissen H, Inzé D. BREEDIT: a multiplex genome editing strategy to improve complex quantitative traits in maize. THE PLANT CELL 2023; 35:218-238. [PMID: 36066192 PMCID: PMC9806654 DOI: 10.1093/plcell/koac243] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/30/2022] [Indexed: 05/04/2023]
Abstract
Ensuring food security for an ever-growing global population while adapting to climate change is the main challenge for agriculture in the 21st century. Although new technologies are being applied to tackle this problem, we are approaching a plateau in crop improvement using conventional breeding. Recent advances in CRISPR/Cas9-mediated gene engineering have paved the way to accelerate plant breeding to meet this increasing demand. However, many traits are governed by multiple small-effect genes operating in complex interactive networks. Here, we present the gene discovery pipeline BREEDIT, which combines multiplex genome editing of whole gene families with crossing schemes to improve complex traits such as yield and drought tolerance. We induced gene knockouts in 48 growth-related genes into maize (Zea mays) using CRISPR/Cas9 and generated a collection of over 1,000 gene-edited plants. The edited populations displayed (on average) 5%-10% increases in leaf length and up to 20% increases in leaf width compared with the controls. For each gene family, edits in subsets of genes could be associated with enhanced traits, allowing us to reduce the gene space to be considered for trait improvement. BREEDIT could be rapidly applied to generate a diverse collection of mutants to identify promising gene modifications for later use in breeding programs.
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Affiliation(s)
| | | | - Denia Herwegh
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Ward Develtere
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Lennert Impens
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Dries Schaumont
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), B-9820 Merelbeke, Belgium
| | - Wout Vandeputte
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Stijn Aesaert
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Griet Coussens
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Yara De Boe
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Kirin Demuynck
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Tom Van Hautegem
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Laurens Pauwels
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Thomas B Jacobs
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
| | - Tom Ruttink
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), B-9820 Merelbeke, Belgium
| | - Hilde Nelissen
- Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium
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7
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Transcriptional signatures of wheat inflorescence development. Sci Rep 2022; 12:17224. [PMID: 36241895 PMCID: PMC9568521 DOI: 10.1038/s41598-022-21571-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/28/2022] [Indexed: 01/06/2023] Open
Abstract
In order to maintain global food security, it will be necessary to increase yields of the cereal crops that provide most of the calories and protein for the world's population, which includes common wheat (Triticum aestivum L.). An important wheat yield component is the number of grain-holding spikelets which form on the spike during inflorescence development. Characterizing the gene regulatory networks controlling the timing and rate of inflorescence development will facilitate the selection of natural and induced gene variants that contribute to increased spikelet number and yield. In the current study, co-expression and gene regulatory networks were assembled from a temporal wheat spike transcriptome dataset, revealing the dynamic expression profiles associated with the progression from vegetative meristem to terminal spikelet formation. Consensus co-expression networks revealed enrichment of several transcription factor families at specific developmental stages including the sequential activation of different classes of MIKC-MADS box genes. This gene regulatory network highlighted interactions among a small number of regulatory hub genes active during terminal spikelet formation. Finally, the CLAVATA and WUSCHEL gene families were investigated, revealing potential roles for TtCLE13, TtWOX2, and TtWOX7 in wheat meristem development. The hypotheses generated from these datasets and networks further our understanding of wheat inflorescence development.
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8
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The Italian Research on the Molecular Characterization of Maize Kernel Development. Int J Mol Sci 2022; 23:ijms231911383. [PMID: 36232684 PMCID: PMC9570349 DOI: 10.3390/ijms231911383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/17/2022] Open
Abstract
The study of the genetic control of maize seed development and seed-related pathways has been one of the most important themes approached by the Italian scientific community. Maize has always attracted the interest of the Italian community of agricultural genetics since its beginning, as some of its founders based their research projects on and developed their “schools” by adopting maize as a reference species. Some of them spent periods in the United States, where maize was already becoming a model system, to receive their training. In this manuscript we illustrate the research work carried out in Italy by different groups that studied maize kernels and underline their contributions in elucidating fundamental aspects of caryopsis development through the characterization of maize mutants. Since the 1980s, most of the research projects aimed at the comprehension of the genetic control of seed development and the regulation of storage products’ biosyntheses and accumulation, and have been based on forward genetics approaches. We also document that for some decades, Italian groups, mainly based in Northern Italy, have contributed to improve the knowledge of maize genomics, and were both fundamental for further international studies focused on the correct differentiation and patterning of maize kernel compartments and strongly contributed to recent advances in maize research.
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Li C, Jia Y, Zhou R, Liu L, Cao M, Zhou Y, Wang Z, Di H. GWAS and RNA-seq analysis uncover candidate genes associated with alkaline stress tolerance in maize ( Zea mays L.) seedlings. FRONTIERS IN PLANT SCIENCE 2022; 13:963874. [PMID: 35923879 PMCID: PMC9340071 DOI: 10.3389/fpls.2022.963874] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/24/2022] [Indexed: 06/15/2023]
Abstract
Soil salt-alkalization is a common yet critical environmental stress factor for plant growth and development. Discovering and exploiting genes associated with alkaline tolerance in maize (Zea mays L.) is helpful for improving alkaline resistance. Here, an association panel consisting of 200 maize lines was used to identify the genetic loci responsible for alkaline tolerance-related traits in maize seedlings. A total of nine single-nucleotide polymorphisms (SNPs) and their associated candidate genes were found to be significantly associated with alkaline tolerance using a genome-wide association study (GWAS). An additional 200 genes were identified when the screen was extended to include a linkage disequilibrium (LD) decay distance of r2 ≥ 0.2 from the SNPs. RNA-sequencing (RNA-seq) analysis was then conducted to confirm the linkage between the candidate genes and alkali tolerance. From these data, a total of five differentially expressed genes (DEGs; |log2FC| ≥ 0.585, p < 0.05) were verified as the hub genes involved in alkaline tolerance. Subsequently, two candidate genes, Zm00001d038250 and Zm00001d001960, were verified to affect the alkaline tolerance of maize seedlings by qRT-PCR analysis. These genes were putatively involved protein binding and "flavonoid biosynthesis process," respectively, based on Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses. Gene promoter region contains elements related to stress and metabolism. The results of this study will help further elucidate the mechanisms of alkaline tolerance in maize, which will provide the groundwork for future breeding projects.
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Hu X, Zuo J. Population Genomics and Haplotype Analysis in Bread Wheat Identify a Gene Regulating Glume Pubescence. FRONTIERS IN PLANT SCIENCE 2022; 13:897772. [PMID: 35909788 PMCID: PMC9328021 DOI: 10.3389/fpls.2022.897772] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Glume hairiness or pubescence is an important morphological trait with high heritability to distinguish/characterize wheat and is related to the resistance to biotic and abiotic stresses. Hg1 (formerly named Hg) on chromosome arm 1AS controlled glume hairiness in wheat. Its genetic analysis and mapping have been widely studied, yet more useful and accurate information for fine mapping of Hg1 and identification of its candidate gene is lacking. The cloning of this gene has not yet been reported for the large complex wheat genome. Here, we performed a GWAS between SNP markers and glume pubescence (Gp) in a wheat population with 352 lines and further demonstrated the gene expression and haplotype analysis approach for isolating the Hg1 gene. One gene, TraesCSU02G143200 (TaELD1-1A), encoding glycosyltransferase-like ELD1/KOBITO 1, was identified as the most promising candidate gene of Hg1. The gene annotation, expression pattern, function SNP variation, haplotype analysis, and co-expression analysis in floral organ (spike) development indicated that it is likely to be involved in the regulation of glume pubescence. Our study demonstrates the importance of high-quality reference genomes and annotation information, as well as bioinformatics analysis, for gene cloning in wheat.
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Affiliation(s)
- Xin Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Jianfang Zuo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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11
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Rahmani RS, Decap D, Fostier J, Marchal K. BLSSpeller to discover novel regulatory motifs in maize. DNA Res 2022; 29:6651838. [PMID: 35904558 PMCID: PMC9358016 DOI: 10.1093/dnares/dsac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Abstract
With the decreasing cost of sequencing and availability of larger numbers of sequenced genomes, comparative genomics is becoming increasingly attractive to complement experimental techniques for the task of transcription factor (TF) binding site identification. In this study, we redesigned BLSSpeller, a motif discovery algorithm, to cope with larger sequence datasets. BLSSpeller was used to identify novel motifs in Zea mays in a comparative genomics setting with 16 monocot lineages. We discovered 61 motifs of which 20 matched previously described motif models in Arabidopsis. In addition, novel, yet uncharacterized motifs were detected, several of which are supported by available sequence-based and/or functional data. Instances of the predicted motifs were enriched around transcription start sites and contained signatures of selection. Moreover, the enrichment of the predicted motif instances in open chromatin and TF binding sites indicates their functionality, supported by the fact that genes carrying instances of these motifs were often found to be co-expressed and/or enriched in similar GO functions. Overall, our study unveiled several novel candidate motifs that might help our understanding of the genotype to phenotype association in crops.
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Affiliation(s)
- Razgar Seyed Rahmani
- Department of Plant Biotechnology and Bioinformatics, Ghent University , Gent, Belgium
- Department of Information Technology, IDLab, Ghent University—imec , Gent, Belgium
| | - Dries Decap
- Department of Information Technology, IDLab, Ghent University—imec , Gent, Belgium
| | - Jan Fostier
- Department of Information Technology, IDLab, Ghent University—imec , Gent, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University , Gent, Belgium
- Department of Information Technology, IDLab, Ghent University—imec , Gent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria , Pretoria, South Africa
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Burnett AC, Kromdijk J. Can we improve the chilling tolerance of maize photosynthesis through breeding? JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3138-3156. [PMID: 35143635 PMCID: PMC9126739 DOI: 10.1093/jxb/erac045] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/02/2022] [Indexed: 05/11/2023]
Abstract
Chilling tolerance is necessary for crops to thrive in temperate regions where cold snaps and lower baseline temperatures place limits on life processes; this is particularly true for crops of tropical origin such as maize. Photosynthesis is often adversely affected by chilling stress, yet the maintenance of photosynthesis is essential for healthy growth and development, and most crucially for yield. In this review, we describe the physiological basis for enhancing chilling tolerance of photosynthesis in maize by examining nine key responses to chilling stress. We synthesize current knowledge of genetic variation for photosynthetic chilling tolerance in maize with respect to each of these traits and summarize the extent to which genetic mapping and candidate genes have been used to understand the genomic regions underpinning chilling tolerance. Finally, we provide perspectives on the future of breeding for photosynthetic chilling tolerance in maize. We advocate for holistic and high-throughput approaches to screen for chilling tolerance of photosynthesis in research and breeding programmes in order to develop resilient crops for the future.
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Affiliation(s)
- Angela C Burnett
- Department of Plant Sciences, University of CambridgeCambridge, UK
- Correspondence:
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Santos C, Martins DC, González-Bernal MJ, Rubiales D, Vaz Patto MC. Integrating Phenotypic and Gene Expression Linkage Mapping to Dissect Rust Resistance in Chickling Pea. FRONTIERS IN PLANT SCIENCE 2022; 13:837613. [PMID: 35463408 PMCID: PMC9021875 DOI: 10.3389/fpls.2022.837613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Rusts are among the most important foliar biotrophic fungal diseases in legumes. Lathyrus cicera crop can be severely damaged by Uromyces pisi, to which partial resistance has been identified. Nevertheless, the underlying genetic basis and molecular mechanisms of this resistance are poorly understood in L. cicera. To prioritise the causative variants controlling partial resistance to rust in L. cicera, a recombinant inbred line (RIL) population, segregating for response to this pathogen, was used to combine the detection of related phenotypic- and expression-quantitative trait loci (pQTLs and eQTLs, respectively). RILs' U. pisi disease severity (DS) was recorded in three independent screenings at seedling (growth chamber) and in one season of exploratory screening at adult plant stage (semi-controlled field conditions). A continuous DS range was observed in both conditions and used for pQTL mapping. Different pQTLs were identified under the growth chamber and semi-controlled field conditions, indicating a distinct genetic basis depending on the plant developmental stage and/or the environment. Additionally, the expression of nine genes related to U. pisi resistance in L. cicera was quantified for each RIL individual and used for eQTL mapping. One cis-eQTL and one trans-eQTL were identified controlling the expression variation of one gene related to rust resistance - a member of glycosyl hydrolase family 17. Integrating phenotyping, gene expression and linkage mapping allowed prioritising four candidate genes relevant for disease-resistance precision breeding involved in adaptation to biotic stress, cellular, and organelle homeostasis, and proteins directly involved in plant defence.
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Affiliation(s)
- Carmen Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Davide Coelho Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | | | - Diego Rubiales
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Zhang X, Zhu Y, Kremling KAG, Romay MC, Bukowski R, Sun Q, Gao S, Buckler ES, Lu F. Genome-wide analysis of deletions in maize population reveals abundant genetic diversity and functional impact. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:273-290. [PMID: 34661697 DOI: 10.1007/s00122-021-03965-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Two read depth methods were jointly used in next-generation sequencing data to identify deletions in maize population. GWAS by deletions were analyzed for gene expression pattern and classical traits, respectively. Many studies have confirmed that structural variation (SV) is pervasive throughout the maize genome. Deletion is one type of SV that may impact gene expression and cause phenotypic changes in quantitative traits. In this study, two read count approaches were used to analyze the deletions in the whole-genome sequencing data of 270 maize inbred lines. A total of 19,754 deletion windows overlapped 12,751 genes, which were unevenly distributed across the genome. The deletions explained population structure well and correlated with genomic features. The deletion proportion of genes was determined to be negatively correlated with its expression. The detection of gene expression quantitative trait loci (eQTL) indicated that local eQTL were fewer but had larger effects than distant ones. The common associated genes were related to basic metabolic processes, whereas unique associated genes with eQTL played a role in the stress or stimulus responses in multiple tissues. Compared with the eQTL detected by SNPs derived from the same sequencing data, 89.4% of the associated genes could be detected by both markers. The effect of top eQTL detected by SNPs was usually larger than that detected by deletions for the same gene. A genome-wide association study (GWAS) on flowering time and plant height illustrated that only a few loci could be consistently captured by SNPs, suggesting that combining deletion and SNP for GWAS was an excellent strategy to dissect trait architecture. Our findings will provide insights into characteristic and biological function of genome-wide deletions in maize.
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Affiliation(s)
- Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China.
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA.
| | - Yonghui Zhu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, China
| | - Karl A G Kremling
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
| | - M Cinta Romay
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
| | - Robert Bukowski
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Qi Sun
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Shibin Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, Sichuan, China
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA
- USDA-ARS, R. W. Holley Center, Cornell University, Ithaca, NY, USA
| | - Fei Lu
- Institute for Genomic Diversity, Cornell University, 175 Biotechnology Building, Ithaca, NY, USA.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Phitaktansakul R, Kim KW, Aung KM, Maung TZ, Min MH, Somsri A, Lee W, Lee SB, Nam J, Kim SH, Lee J, Kwon SW, Nawade B, Chu SH, Park SW, Kang KK, Cho YH, Lee YS, Chung IM, Park YJ. Multi-omics analysis reveals the genetic basis of rice fragrance mediated by betaine aldehyde dehydrogenase 2. J Adv Res 2021; 42:303-314. [PMID: 36513420 PMCID: PMC9788947 DOI: 10.1016/j.jare.2021.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/15/2021] [Accepted: 12/11/2021] [Indexed: 02/08/2023] Open
Abstract
INTRODUCTION Fragrance is an important economic and quality trait in rice. The trait is controlled by the recessive gene betaine aldehyde dehydrogenase 2 (BADH2) via the production of 2-acetyl-1-pyrroline (2AP). OBJECTIVES Variation in BADH2 was evaluated at the population, genetic, transcriptional, and metabolic levels to obtain insights into fragrance regulation in rice. METHODS Whole-genome resequencing of the Korean World Rice Collection of 475 rice accessions, including 421 breeding lines and 54 wild accessions, was performed. Transcriptome analyses of a subset of 279 accessions, proteome analyses of 64 accessions, and volatile profiling of 421 breeding lines were also performed. RESULTS We identified over 3.1 million high-quality single nucleotide polymorphisms (SNPs) in Korean rice collection. Most SNPs were present in intergenic regions (79%), and 190,148 SNPs (6%) were located in the coding sequence, of which 53% were nonsynonymous. In total, 38 haplotypes were identified in the BADH2 coding region, including four novel haplotypes (one in cultivated and three in wild accessions). Tajima's D values suggested that BADH2 was under balancing selection in japonica rice. Furthermore, we identified 316 expression quantitative trait loci (eQTL), including 185 cis-eQTLs and 131 trans-eQTLs, involved in BADH2 regulation. A protein quantitative trait loci (pQTL) analysis revealed the presence of trans-pQTLs; 13 pQTLs were mapped 1 Mbp from the BADH2 region. Based on variable importance in projection (VIP) scores, 15 volatile compounds, including 2AP, discriminated haplotypes and were potential biomarkers for rice fragrance. CONCLUSION We generated a catalog of haplotypes based on a resequencing analysis of a large number of rice accessions. eQTLs and pQTLs associated with BADH2 gene expression and protein accumulation are likely involved in the regulation of 2AP variation in fragrant rice. These data improve our understanding of fragrance and provide valuable information for rice breeding.
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Affiliation(s)
- Rungnapa Phitaktansakul
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Kyu-Won Kim
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic of Korea
| | - Kyaw Myo Aung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Thant Zin Maung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Myeong-Hyeon Min
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Aueangporn Somsri
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Wondo Lee
- Seedpia, 85 Maesil-ro, Kwonsun-ku, Suwon 16395, Republic of Korea
| | - Sang-Beom Lee
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Jungrye Nam
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic of Korea
| | - Seung-Hyun Kim
- Department of Applied Bioscience, Konkuk University, Seoul 05029, Republic of Korea
| | - Joohyun Lee
- Department of Applied Bioscience, Konkuk University, Seoul 05029, Republic of Korea
| | - Soon-Wook Kwon
- Department of Plant Bioscience, Pusan National University, Pusan 46241, Republic of Korea
| | - Bhagwat Nawade
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea
| | - Sang-Ho Chu
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic of Korea
| | - Sang-Won Park
- Chemical Safety Division, National Institute of Agriculture Science (NIAS), Wanju 55365, Republic of Korea
| | - Kwon Kyoo Kang
- Department of Horticultural Life Science, Hankyong National University, Anseong 17579, Republic of Korea
| | - Yoo-Hyun Cho
- Seedpia, 85 Maesil-ro, Kwonsun-ku, Suwon 16395, Republic of Korea
| | - Young-Sang Lee
- Department of Medical Biotechnology, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Ill-Min Chung
- Department of Applied Bioscience, Konkuk University, Seoul 05029, Republic of Korea,Corresponding authors at: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Korea (Yong-Jin Park); Department of Applied Bioscience, Konkuk University, Seoul 05029, Korea (Ill-Min Chung).
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Republic of Korea,Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan 32439, Republic of Korea,Corresponding authors at: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan 32439, Korea (Yong-Jin Park); Department of Applied Bioscience, Konkuk University, Seoul 05029, Korea (Ill-Min Chung).
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