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Wang Z, Lei Y, Liao B. Omics-driven advances in the understanding of regulatory landscape of peanut seed development. FRONTIERS IN PLANT SCIENCE 2024; 15:1393438. [PMID: 38766472 PMCID: PMC11099219 DOI: 10.3389/fpls.2024.1393438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/18/2024] [Indexed: 05/22/2024]
Abstract
Peanuts (Arachis hypogaea) are an essential oilseed crop known for their unique developmental process, characterized by aerial flowering followed by subterranean fruit development. This crop is polyploid, consisting of A and B subgenomes, which complicates its genetic analysis. The advent and progression of omics technologies-encompassing genomics, transcriptomics, proteomics, epigenomics, and metabolomics-have significantly advanced our understanding of peanut biology, particularly in the context of seed development and the regulation of seed-associated traits. Following the completion of the peanut reference genome, research has utilized omics data to elucidate the quantitative trait loci (QTL) associated with seed weight, oil content, protein content, fatty acid composition, sucrose content, and seed coat color as well as the regulatory mechanisms governing seed development. This review aims to summarize the advancements in peanut seed development regulation and trait analysis based on reference genome-guided omics studies. It provides an overview of the significant progress made in understanding the molecular basis of peanut seed development, offering insights into the complex genetic and epigenetic mechanisms that influence key agronomic traits. These studies highlight the significance of omics data in profoundly elucidating the regulatory mechanisms of peanut seed development. Furthermore, they lay a foundational basis for future research on trait-related functional genes, highlighting the pivotal role of comprehensive genomic analysis in advancing our understanding of plant biology.
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Affiliation(s)
- Zhihui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
- National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), Huazhong Agricultural University, Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
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Du H, Li C. Study on the mechanism of peanut resistance to Fusarium oxysporum infection induced by Bacillus thuringiensis TG5. Front Microbiol 2024; 14:1251660. [PMID: 38725557 PMCID: PMC11080293 DOI: 10.3389/fmicb.2023.1251660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/15/2023] [Indexed: 05/12/2024] Open
Abstract
Peanut root rot, commonly referred to as rat tail or root rot, is caused by a range of Fusarium species. A strain of bacteria (named TG5) was isolated from crop rhizosphere soil in Mount Taishan, Shandong Province, China, through whole genome sequencing that TG5 was identified as Bacillus thuringiensis, which can specifically produce chloramphenicol, bacitracin, clarithromycin, lichen VK21A1 and bacitracin, with good biological control potential. Based on liquid chromatography tandem mass spectrometry metabonomics analysis and transcriptome conjoint analysis, the mechanism of TG5 and carbendazim inducing peanut plants to resist F. oxysporum stress was studied. In general, for peanut root rot caused by F. oxysporum, B. thuringiensis TG5 has greater advantages than carbendazim and is environmentally friendly. These findings provide new insights for peanut crop genetics and breeding, and for microbial pesticides to replace traditional highly toxic and highly polluting chemical pesticides. Based on the current background of agricultural green cycle and sustainable development, it has significant practical significance and broad application prospects.
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Affiliation(s)
- Hongbo Du
- Forestry College, Shandong Agricultural University, Tai'an, Shandong, China
| | - Chuanrong Li
- Forestry College, Shandong Agricultural University, Tai'an, Shandong, China
- Taishan Forest Ecosystem Research Station/Key Laboratory of National Forestry and Grassland Administration for Silviculture of the Lower Yellow River, Tai'an, Shandong, China
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Wang Z, Zhang Y, Huai D, Chen Y, Wang X, Kang Y, Yan L, Jiang H, Liu K, Lei Y, Liao B. Detection of two homologous major QTLs and development of diagnostic molecular markers for sucrose content in peanut. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:61. [PMID: 38411751 DOI: 10.1007/s00122-024-04549-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 01/10/2024] [Indexed: 02/28/2024]
Abstract
KEY MESSAGE We identified two stable and homologous major QTLs for sucrose content in peanut, and developed breeder-friendly molecular markers for marker-assisted selection breeding. Sucrose content is a crucial quality trait for edible peanuts, and increasing sucrose content is a key breeding objective. However, the genetic basis of sucrose content in peanut remains unclear, and major quantitative trait loci (QTLs) for sucrose content have yet to be identified. In this study, a high-density genetic map was constructed based on whole-genome re-sequencing data from a peanut RIL population. This map consisted of 2,042 bins and 24,142 SNP markers, making it one of the most comprehensive maps to date in terms of marker density. Two major QTLs (qSCA06.2 and qSCB06.2) were identified, explaining 31.41% and 24.13% of the phenotypic variance, respectively. Notably, these two QTLs were located in homologous genomic regions between the A and B subgenomes. The elite allele of qSCA06.2 was exclusive to Valencia-type, while the elite allele of qSCB06.2 existed in other peanut types. Importantly, the distribution of alleles from two homologous QTLs in the RIL population and diverse germplasm accessions consistently demonstrated that only the combination of elite allelic genotypes from both QTLs/genes resulted in a significantly dominant phenotype, accompanied by a substantial increase in sucrose content. The newly developed diagnostic markers for these QTLs were confirmed to be reliable and could facilitate future breeding efforts to enhance sucrose content using marker-assisted selection techniques. Overall, this study highlights the co-regulation of sucrose content by two major homologous QTLs/genes and provides valuable insights into the genetic basis of sucrose in peanuts.
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Affiliation(s)
- Zhihui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
- National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yue Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China.
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences (CAAS), Wuhan, 430062, China.
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Yu B, Liu N, Huang L, Luo H, Zhou X, Lei Y, Yan L, Wang X, Chen W, Kang Y, Ding Y, Jin G, Pandey MK, Janila P, Kishan Sudini H, Varshney RK, Jiang H, Liu S, Liao B. Identification and application of a candidate gene AhAftr1 for aflatoxin production resistance in peanut seed (Arachis hypogaea L.). J Adv Res 2023:S2090-1232(23)00263-1. [PMID: 37739123 DOI: 10.1016/j.jare.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
INTRODUCTION Peanut is susceptible to infection of Aspergillus fungi and conducive to aflatoxin contamination, hence developing aflatoxin-resistant variety is highly meaningful. Identifying functional genes or loci conferring aflatoxin resistance and molecular diagnostic marker are crucial for peanut breeding. OBJECTIVES This work aims to (1) identify candidate gene for aflatoxin production resistance, (2) reveal the related resistance mechanism, and (3) develop diagnostic marker for resistance breeding program. METHODS Resistance to aflatoxin production in a recombined inbred line (RIL) population derived from a high-yielding variety Xuhua13 crossed with an aflatoxin-resistant genotype Zhonghua 6 was evaluated under artificial inoculation for three consecutive years. Both genetic linkage analysis and QTL-seq were conducted for QTL mapping. The candidate gene was further fine-mapped using a secondary segregation mapping population and validated by transgenic experiments. RNA-Seq analysis among resistant and susceptible RILs was used to reveal the resistance pathway for the candidate genes. RESULTS The major effect QTL qAFTRA07.1 for aflatoxin production resistance was mapped to a 1.98 Mbp interval. A gene, AhAftr1 (Arachis hypogaea Aflatoxin resistance 1), was detected structure variation (SV) in leucine rich repeat (LRR) domain of its production, and involved in disease resistance response through the effector-triggered immunity (ETI) pathway. Transgenic plants with overexpression of AhAftr1(ZH6) exhibited 57.3% aflatoxin reduction compared to that of AhAftr1(XH13). A molecular diagnostic marker AFTR.Del.A07 was developed based on the SV. Thirty-six lines, with aflatoxin content decrease by over 77.67% compared to the susceptible control Zhonghua12 (ZH12), were identified from a panel of peanut germplasm accessions and breeding lines through using AFTR.Del.A07. CONCLUSION Our findings would provide insights of aflatoxin production resistance mechanisms and laid meaningful foundation for further breeding programs.
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Affiliation(s)
- Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yingbin Ding
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Gaorui Jin
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Aird Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Aird Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Hari Kishan Sudini
- International Crops Research Institute for the Semi-Aird Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Rajeev K Varshney
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Australia
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China.
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Xu Y, Ding H, Zhang G, Li Z, Guo Q, Feng H, Qin F, Dai L, Zhang Z. Green manure increases peanut production by shaping the rhizosphere bacterial community and regulating soil metabolites under continuous peanut production systems. BMC PLANT BIOLOGY 2023; 23:69. [PMID: 36726076 PMCID: PMC9890850 DOI: 10.1186/s12870-023-04079-0] [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: 11/25/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Green manure (GM) is a crop commonly grown during fallow periods, which has been applied in agriculture as a strategy to regulate nutrient cycling, improve organic matter, and enhance soil microbial biodiversity, but to date, few studies have examined the effects of GM treatments on rhizosphere soil bacterial community and soil metabolites from continuous cropping peanut field. RESULTS In this study, we found that the abundances of several functionally significant bacterial groups containing Actinobacteria, Acidobacteria, and genus Sphingomonas, which are associated with nitrogen cycling, were dramatically increased in GM-applied soils. Consistent with the bacterial community results, metabolomics analysis revealed a strong perturbation of nitrogen- or carbon-related metabolisms in GM-applied soils. The substantially up-regulated beneficial metabolites including sucrose, adenine, lysophosphatidylcholine (LPC), malic acid, and betaines in GM-applied soils may contribute to overcome continuous cropping obstacle. In contrast to peanut continuous cropping, planting winter wheat and oilseed rape in winter fallow period under continuous spring peanut production systems evidently improved the soil quality, concomitantly with raised peanut pod yield by 32.93% and 25.20%, in the 2020 season, respectively. CONCLUSIONS GMs application is an effective strategy to overcome continuous cropping obstacle under continuous peanut production systems by improving nutrient cycling, soil metabolites, and rhizobacterial properties.
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Affiliation(s)
- Yang Xu
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Hong Ding
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Guanchu Zhang
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Zelun Li
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Qing Guo
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Hao Feng
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Feifei Qin
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Liangxiang Dai
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China.
| | - Zhimeng Zhang
- Shandong Peanut Research Institute, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China.
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Ali A, Altaf MT, Nadeem MA, Karaköy T, Shah AN, Azeem H, Baloch FS, Baran N, Hussain T, Duangpan S, Aasim M, Boo KH, Abdelsalam NR, Hasan ME, Chung YS. Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes. FRONTIERS IN PLANT SCIENCE 2022; 13:952759. [PMID: 36247536 PMCID: PMC9554552 DOI: 10.3389/fpls.2022.952759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
The world is facing rapid climate change and a fast-growing global population. It is believed that the world population will be 9.7 billion in 2050. However, recent agriculture production is not enough to feed the current population of 7.9 billion people, which is causing a huge hunger problem. Therefore, feeding the 9.7 billion population in 2050 will be a huge target. Climate change is becoming a huge threat to global agricultural production, and it is expected to become the worst threat to it in the upcoming years. Keeping this in view, it is very important to breed climate-resilient plants. Legumes are considered an important pillar of the agriculture production system and a great source of high-quality protein, minerals, and vitamins. During the last two decades, advancements in OMICs technology revolutionized plant breeding and emerged as a crop-saving tool in wake of the climate change. Various OMICs approaches like Next-Generation sequencing (NGS), Transcriptomics, Proteomics, and Metabolomics have been used in legumes under abiotic stresses. The scientific community successfully utilized these platforms and investigated the Quantitative Trait Loci (QTL), linked markers through genome-wide association studies, and developed KASP markers that can be helpful for the marker-assisted breeding of legumes. Gene-editing techniques have been successfully proven for soybean, cowpea, chickpea, and model legumes such as Medicago truncatula and Lotus japonicus. A number of efforts have been made to perform gene editing in legumes. Moreover, the scientific community did a great job of identifying various genes involved in the metabolic pathways and utilizing the resulted information in the development of climate-resilient legume cultivars at a rapid pace. Keeping in view, this review highlights the contribution of OMICs approaches to abiotic stresses in legumes. We envisage that the presented information will be helpful for the scientific community to develop climate-resilient legume cultivars.
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Affiliation(s)
- Amjad Ali
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Hajra Azeem
- Department of Plant Pathology, Faculty of Agricultural Sciences & Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Nurettin Baran
- Bitkisel Uretim ve Teknolojileri Bolumu, Uygulamali Bilimler Faku Itesi, Mus Alparslan Universitesi, Mus, Turkey
| | - Tajamul Hussain
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Saowapa Duangpan
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Kyung-Hwan Boo
- Subtropical/Tropical Organism Gene Bank, Department of Biotechnology, College of Applied Life Science, Jeju National University, Jeju, South Korea
| | - Nader R. Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Mohamed E. Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, South Korea
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High-Density Linkage Mapping and Identification of Quantitative Trait Loci Associated with Powdery Mildew Resistance in Flowering Dogwood (Cornus florida). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Flowering dogwood (Cornus florida L.) is a popular, spring-blooming ornamental tree native to the eastern United States. The species is in general very susceptible to powdery mildew caused by Erysiphe pulchra, which disfigures leaves, decreases growth, and negatively affects flowering. Breeding for resistance has been recognized as an ideal strategy for controlling the disease in C. florida, but efforts have been hindered by the rarity of PM resistance in available germplasm and knowledge of its genetic control. In this study, we mapped quantitative trait loci (QTL) associated with PM resistance/tolerance in two full sibling populations segregating for PM response: Rutgers H4AR15P25 (P25) × Rutgers H4AR15R28 (P28) (n = 195) and Rutgers H4AR15R25 × Rutgers H4AR15P35 (P35) (n = 83). High-density genetic linkage maps were constructed for the mapping populations using double digest restriction-site associated DNA sequencing-derived single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). The P25 × P28 map consisted of 2265 markers, spanning 1520 cM and 11 linkage groups (LGs) with an average marker spacing of 0.69 cM. The P25 × P35 map was constructed with 1788 markers, spanning 1256 cM and 11 LGs, with an average marker spacing of 0.72 cM. The maps had 604 markers in common and exhibited excellent collinearity. Through multiple QTL model mapping, one major QTL (LOD = 11.36 and R2 = 58.9%) was identified in P25 × P35. Furthermore, a minor QTL (LOD = 3.30 and R2 = 7.8%) was detected in P25 × P28. Due to their proximity onLG3, these QTL may be designating the same locus or tightly linked loci. The negative additive effects of both QTL signify that the PM susceptible male parents were contributing susceptibility alleles to the progeny. This is the first report of QTL associated with PM response on LG3 in C. florida and lays the groundwork for the development of marker-assisted selection for PM resistance in C. florida breeding programs.
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Nayak SN, Aravind B, Malavalli SS, Sukanth BS, Poornima R, Bharati P, Hefferon K, Kole C, Puppala N. Omics Technologies to Enhance Plant Based Functional Foods: An Overview. Front Genet 2021; 12:742095. [PMID: 34858472 PMCID: PMC8631721 DOI: 10.3389/fgene.2021.742095] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 10/13/2021] [Indexed: 11/25/2022] Open
Abstract
Functional foods are natural products of plants that have health benefits beyond necessary nutrition. Functional foods are abundant in fruits, vegetables, spices, beverages and some are found in cereals, millets, pulses and oilseeds. Efforts to identify functional foods in our diet and their beneficial aspects are limited to few crops. Advances in sequencing and availability of different omics technologies have given opportunity to utilize these tools to enhance the functional components of the foods, thus ensuring the nutritional security. Integrated omics approaches including genomics, transcriptomics, proteomics, metabolomics coupled with artificial intelligence and machine learning approaches can be used to improve the crops. This review provides insights into omics studies that are carried out to find the active components and crop improvement by enhancing the functional compounds in different plants including cereals, millets, pulses, oilseeds, fruits, vegetables, spices, beverages and medicinal plants. There is a need to characterize functional foods that are being used in traditional medicines, as well as utilization of this knowledge to improve the staple foods in order to tackle malnutrition and hunger more effectively.
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Affiliation(s)
- Spurthi N. Nayak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B. Aravind
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Sachin S. Malavalli
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B. S. Sukanth
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - R. Poornima
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Pushpa Bharati
- Department of Food Science and Nutrition, University of Agricultural Sciences, Dharwad, India
| | - Kathleen Hefferon
- Department of Microbiology, Cornell University, Ithaca, NY, United States
| | - Chittaranjan Kole
- President, International Phytomedomics and Nutriomics Consortium (ipnc.info), Daejeon, South Korea
| | - Naveen Puppala
- New Mexico State University-Agricultural Science Center at Clovis, New Mexico, NM, United States
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Jadhav MP, Gangurde SS, Hake AA, Yadawad A, Mahadevaiah SS, Pattanashetti SK, Gowda MVC, Shirasawa K, Varshney RK, Pandey MK, Bhat RS. Genotyping-by-Sequencing Based Genetic Mapping Identified Major and Consistent Genomic Regions for Productivity and Quality Traits in Peanut. FRONTIERS IN PLANT SCIENCE 2021; 12:668020. [PMID: 34630444 PMCID: PMC8495222 DOI: 10.3389/fpls.2021.668020] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 08/25/2021] [Indexed: 06/13/2023]
Abstract
With an objective of identifying the genomic regions for productivity and quality traits in peanut, a recombinant inbred line (RIL) population developed from an elite variety, TMV 2 and its ethyl methane sulfonate (EMS)-derived mutant was phenotyped over six seasons and genotyped with genotyping-by-sequencing (GBS), Arachis hypogaea transposable element (AhTE) and simple sequence repeats (SSR) markers. The genetic map with 700 markers spanning 2,438.1 cM was employed for quantitative trait loci (QTL) analysis which identified a total of 47 main-effect QTLs for the productivity and oil quality traits with the phenotypic variance explained (PVE) of 10-52% over the seasons. A common QTL region (46.7-50.1 cM) on Ah02 was identified for the multiple traits, such as a number of pods per plant (NPPP), pod weight per plant (PWPP), shelling percentage (SP), and test weight (TW). Similarly, a QTL (7.1-18.0 cM) on Ah16 was identified for both SP and protein content (PC). Epistatic QTL (epiQTL) analysis revealed intra- and inter-chromosomal interactions for the main-effect QTLs and other genomic regions governing these productivity traits. The markers identified by a single marker analysis (SMA) mapped to the QTL regions for most of the traits. Among the five potential candidate genes identified for PC, SP and oil quality, two genes (Arahy.7A57YA and Arahy.CH9B83) were affected by AhMITE1 transposition, and three genes (Arahy.J5SZ1I, Arahy.MZJT69, and Arahy.X7PJ8H) involved functional single nucleotide polymorphisms (SNPs). With major and consistent effects, the genomic regions, candidate genes, and the associated markers identified in this study would provide an opportunity for gene cloning and genomics-assisted breeding for increasing the productivity and enhancing the quality of peanut.
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Affiliation(s)
- Mangesh P. Jadhav
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sunil S. Gangurde
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Anil A. Hake
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Arati Yadawad
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | | | | | - M. V. Channabyre Gowda
- Department of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, India
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ramesh S. Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
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