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Huang S, Guo S, Dai L, Mi L, Li W, Xing J, Hu Z, Wu W, Duan Z, Li B, Sun T, Wang B, Zhang Y, Xiao T, Xue Y, Tang N, Li H, Zhang C, Song CP. Tubulin participates in establishing protoxylem vessel reinforcement patterns and hydraulic conductivity in maize. PLANT PHYSIOLOGY 2024; 196:931-947. [PMID: 38850036 DOI: 10.1093/plphys/kiae329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/09/2024]
Abstract
Water transportation to developing tissues relies on the structure and function of plant xylem cells. Plant microtubules govern the direction of cellulose microfibrils and guide secondary cell wall formation and morphogenesis. However, the relevance of microtubule-determined xylem wall thickening patterns in plant hydraulic conductivity remains unclear. In the present study, we identified a maize (Zea mays) semi-dominant mutant, designated drought-overly-sensitive1 (ZmDos1), the upper leaves of which wilted even when exposed to well-watered conditions during growth; the wilting phenotype was aggravated by increased temperatures and decreased humidity. Protoxylem vessels in the stem and leaves of the mutant showed altered thickening patterns of the secondary cell wall (from annular to spiral), decreased inner diameters, and limited water transport efficiency. The causal mutation for this phenotype was found to be a G-to-A mutation in the maize gene α-tubulin4, resulting in a single amino acid substitution at position 196 (E196K). Ectopic expression of the mutant α-tubulin4 in Arabidopsis (Arabidopsis thaliana) changed the orientation of microtubule arrays, suggesting a determinant role of this gene in microtubule assembly and secondary cell wall thickening. Our findings suggest that the spiral wall thickenings triggered by the α-tubulin mutation are stretched during organ elongation, causing a smaller inner diameter of the protoxylem vessels and affecting water transport in maize. This study underscores the importance of tubulin-mediated protoxylem wall thickening in regulating plant hydraulics, improves our understanding of the relationships between protoxylem structural features and functions, and offers candidate genes for the genetic enhancement of maize.
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Affiliation(s)
- Shiquan Huang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
- Sanya Institute of Henan University, Sanya 572025, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
- Sanya Institute of Henan University, Sanya 572025, China
| | - Liufeng Dai
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Lingyu Mi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Wenrao Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Jingjing Xing
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
- Sanya Institute of Henan University, Sanya 572025, China
| | - Wenqiang Wu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Zhikun Duan
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Baozhu Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Ting Sun
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Baojie Wang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yi Zhang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Tiqiao Xiao
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Yanling Xue
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, China
| | - Ning Tang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Han Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Changqing Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
| | - Chun-Peng Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng 475004, China
- Sanya Institute of Henan University, Sanya 572025, China
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Wu L, Liu Q, Gou W, Li J, Cao Q, He C. Deciphering the evolutionary development of the "Chinese lantern" within Solanaceae. PLANTA 2024; 260:98. [PMID: 39292428 DOI: 10.1007/s00425-024-04535-7] [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: 05/27/2024] [Accepted: 09/15/2024] [Indexed: 09/19/2024]
Abstract
MAIN CONCLUSION The key genetic variation underlying the evo-devo of ICS in Solanaceae may be further pinpointed using an integrated strategy of forward and reverse genetics studies under the framework of phylogeny. The calyx of Physalis remains persistent throughout fruit development. Post-flowering, the fruiting calyx is inflated rapidly to encapsulate the berry, giving rise to a "Chinese lantern" structure called inflated calyx syndrome (ICS). It is unclear how this novelty arises. Over the past 2 decades, the role of MADS-box genes in the evolutionary development (evo-devo) of ICS has mainly been investigated within Solanaceae. In this review, we analyze the main achievements, challenges, and new progress. ICS acts as a source for fruit development, provides a microenvironment to protect fruit development, and assists in long-distance fruit dispersal. ICS is a typical post-floral trait, and the onset of its development is triggered by specific developmental signals that coincide with fertilization. These signals can be replaced by exogenous gibberellin and cytokinin application. MPF2-like heterotopic expression and MBP21-like loss have been proposed to be two essential evolutionary events for ICS origin, and manipulating the related MADS-box genes has been shown to affect the ICS size, sepal organ identity, and/or male fertility, but not completely disrupt ICS. Therefore, the core genes or key links in the ICS biosynthesis pathways may have undergone secondary mutations during evolution, or they have not yet been pinpointed. Recently, we have made some encouraging progress in acquiring lantern mutants in Physalis floridana. In addition to technological innovation, we propose an integrated strategy to further analyze the evo-devo mechanisms of ICS in Solanaceae using forward and reverse genetics studies under the framework of phylogeny.
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Affiliation(s)
- Lanfeng Wu
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Qianqian Liu
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Wei Gou
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Jun Li
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Qianhui Cao
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China
| | - Chaoying He
- State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Yuquan Road 19, Beijing, 100049, China.
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Dong J, Li J, Zuo Y, Wang J, Chen Y, Tu W, Wang H, Li C, Shan Y, Wang Y, Song B, Cai X. Haplotype-resolved genome and mapping of freezing tolerance in the wild potato Solanum commersonii. HORTICULTURE RESEARCH 2024; 11:uhae181. [PMID: 39247882 PMCID: PMC11374536 DOI: 10.1093/hr/uhae181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 07/01/2024] [Indexed: 09/10/2024]
Abstract
Solanum commersonii (2n = 2x = 24, 1EBN, Endosperm Balance Number), native to the southern regions of Brazil, Uruguay, and northeastern Argentina, is the first wild potato germplasm collected by botanists and exhibits a remarkable array of traits related to disease resistance and stress tolerance. In this study, we present a high-quality haplotype-resolved genome of S. commersonii. The two identified haplotypes demonstrate chromosome sizes of 706.48 and 711.55 Mb, respectively, with corresponding chromosome anchoring rates of 94.2 and 96.9%. Additionally, the contig N50 lengths are documented at 50.87 and 45.16 Mb. The gene annotation outcomes indicate that the haplotypes encompasses a gene count of 39 799 and 40 078, respectively. The genome contiguity, completeness, and accuracy assessments collectively indicate that the current assembly has produced a high-quality genome of S. commersonii. Evolutionary analysis revealed significant positive selection acting on certain disease resistance genes, stress response genes, and environmentally adaptive genes during the evolutionary process of S. commersonii. These genes may be related to the formation of diverse and superior germplasm resources in the wild potato species S. commersonii. Furthermore, we utilized a hybrid population of S. commersonii and S. verrucosum to conduct the mapping of potato freezing tolerance genes. By combining BSA-seq analysis with traditional QTL mapping, we successfully mapped the potato freezing tolerance genes to a specific region on Chr07, spanning 1.25 Mb, with a phenotypic contribution rate of 18.81%. In short, current research provides a haplotype-resolved reference genome of the diploid wild potato species S. commersonii and establishes a foundation for further cloning and unraveling the mechanisms underlying cold tolerance in potatoes.
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Affiliation(s)
- Jianke Dong
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Jingwen Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Yingtao Zuo
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Jin Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Ye Chen
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Tu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
- College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang 438000, China
| | - Haibo Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
- College of Biological and Food Engineering, Hubei Minzu University, Enshi 445000, China
| | - Chenxi Li
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Yacheng Shan
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Ying Wang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Botao Song
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
| | - Xingkui Cai
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs; Huazhong Agricultural University, Wuhan 430070, China
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Zhang W, Zhang H, Zhu X, Li Y, Yuan G, Ma J. Genetic analysis and preliminary mapping by BSA-seq of the CmSR gene regulating the spotted rind trait in melon (Cucumis melo L.). Genet Mol Biol 2024; 47:e20240062. [PMID: 39162661 PMCID: PMC11334433 DOI: 10.1590/1678-4685-gmb-2024-0062] [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: 03/19/2024] [Accepted: 06/05/2024] [Indexed: 08/21/2024] Open
Abstract
Melon (Cucumis melo L.) is an economically important horticultural crop. Spotted rind at maturity is an important appearance quality trait in melons. However, the gene controlling this trait remains unknown. In this study, the inheritance pattern of this trait was explored, and the candidate gene underlying this trait was also successfully identified. Genetic analysis showed that a single dominant gene, Cucumis melo Spotted Rind (CmSR), regulates the spotted rind trait. A preliminary genetic mapping analysis was conducted based on a BSA-seq approach. The CmAPRR2 gene was identified to be linked with the spotted rind trait and was located on the short arm of chromosome 4. It harbored two single-nucleotide mutations (chr4: 687014 G/A and chr4: 687244 C/A) in the non-spotted line 'Yellow 2', which may result in the alternative splicing of the transcript and an amino acid change in the respective protein, from proline to glutamine, respectively. Moreover, marker SNP687014-G/A was developed and co-segregated with the spotted rind trait. Therefore, it is speculated that the CmAPRR2 gene may be involved in the regulation of the spotted rind trait in melon. This study provides a theoretical foundation for further research on the gene regulatory mechanism of the rind color in melon.
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Affiliation(s)
- Weiyan Zhang
- Nantong College of Science and Technology, Nantong, Jiangsu, P.R. China
| | - Huijun Zhang
- Huaibei Normal University, School of Life Science, Anhui Province Watermelon and Melon Biological Breeding Engineering Research Center, Huaibei, Anhui, P.R. China
| | - Xiuxiu Zhu
- Huaibei Normal University, School of Life Science, Anhui Province Watermelon and Melon Biological Breeding Engineering Research Center, Huaibei, Anhui, P.R. China
| | - Yahui Li
- Huaibei Normal University, School of Life Science, Anhui Province Watermelon and Melon Biological Breeding Engineering Research Center, Huaibei, Anhui, P.R. China
| | - Guoliang Yuan
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing, P.R. China
- Beijing Academy of Agriculture and Forestry Sciences, Beijing Vegetable Research Center (BVRC), Beijing, P.R. China
| | - Jian Ma
- Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing, P.R. China
- Beijing Academy of Agriculture and Forestry Sciences, Beijing Vegetable Research Center (BVRC), Beijing, P.R. China
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Guo S, Tian M, Du H, Liu S, Yu R, Shen H. Quantitative Trait Loci Mapping and Comparative Transcriptome Analysis of Fruit Weight (FW) in Watermelon ( Citrullus lanatus L.). Genes (Basel) 2024; 15:933. [PMID: 39062712 PMCID: PMC11276344 DOI: 10.3390/genes15070933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The watermelon (Citrullus lanatus L.) holds substantial economic value as a globally cultivated horticultural crop. However, the genetic architecture of watermelon fruit weight (FW) remains poorly understood. In this study, we used sh14-11 with small fruit and N14 with big fruit to construct 100 recombinant inbred lines (RILs). Based on whole-genome resequencing (WGR), 218,127 single nucleotide polymorphisms (SNPs) were detected to construct a high-quality genetic map. After quantitative trait loci (QTL) mapping, a candidate interval of 31-38 Mb on chromosome 2 was identified for FW. Simultaneously, the bulked segregant analysis (BSA) in the F2 population corroborated the identification of the same interval, encompassing the homologous gene linked to the known FW-related gene fas. Additionally, RNA-seq was carried out across 11 tissues from sh14-11 and N14, revealing expression profiles that identified 1695 new genes and corrected the annotation of 2941 genes. Subsequent differential expression analysis unveiled 8969 differentially expressed genes (DEGs), with 354 of these genes exhibiting significant differences across four key developmental stages. The integration of QTL mapping and differential expression analysis facilitated the identification of 14 FW-related genes, including annotated TGA and NAC transcription factors implicated in fruit development. This combined approach offers valuable insights into the genetic basis of FW, providing crucial resources for enhancing watermelon cultivation.
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Affiliation(s)
- Song Guo
- Horticulture College, China Agricultural University, Beijing 100193, China;
| | - Mei Tian
- Institute of Horticultural Research, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (M.T.); (H.D.); (S.L.)
| | - Huiying Du
- Institute of Horticultural Research, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (M.T.); (H.D.); (S.L.)
| | - Shengfeng Liu
- Institute of Horticultural Research, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (M.T.); (H.D.); (S.L.)
| | - Rong Yu
- Institute of Horticultural Research, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, China; (M.T.); (H.D.); (S.L.)
| | - Huolin Shen
- Horticulture College, China Agricultural University, Beijing 100193, China;
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Ontoy JC, Ham JH. Mapping and Omics Integration: Towards Precise Rice Disease Resistance Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:1205. [PMID: 38732420 PMCID: PMC11085595 DOI: 10.3390/plants13091205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024]
Abstract
Rice (Oryza sativa), as a staple crop feeding a significant portion of the global population, particularly in Asian countries, faces constant threats from various diseases jeopardizing global food security. A precise understanding of disease resistance mechanisms is crucial for developing resilient rice varieties. Traditional genetic mapping methods, such as QTL mapping, provide valuable insights into the genetic basis of diseases. However, the complex nature of rice diseases demands a holistic approach to gain an accurate knowledge of it. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, enable a comprehensive analysis of biological molecules, uncovering intricate molecular interactions within the rice plant. The integration of various mapping techniques using multi-omics data has revolutionized our understanding of rice disease resistance. By overlaying genetic maps with high-throughput omics datasets, researchers can pinpoint specific genes, proteins, or metabolites associated with disease resistance. This integration enhances the precision of disease-related biomarkers with a better understanding of their functional roles in disease resistance. The improvement of rice breeding for disease resistance through this integration represents a significant stride in agricultural science because a better understanding of the molecular intricacies and interactions underlying disease resistance architecture leads to a more precise and efficient development of resilient and productive rice varieties. In this review, we explore how the integration of mapping and omics data can result in a transformative impact on rice breeding for enhancing disease resistance.
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Affiliation(s)
- John Christian Ontoy
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA;
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA;
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
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Zhang L, Duan Y, Zhang Z, Zhang L, Chen S, Cai C, Duan S, Zhang K, Li G, Cheng F. OcBSA: An NGS-based bulk segregant analysis tool for outcross populations. MOLECULAR PLANT 2024; 17:648-657. [PMID: 38369755 DOI: 10.1016/j.molp.2024.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Constructing inbred lines for self-incompatible species and species with long generation times is challenging, making the use of F1 outcross/segregating populations the main strategy for genetic studies of such species. However, there is a lack of dedicated algorithms/tools for rapid quantitative trait locus (QTL) mapping using the F1 populations. To this end, we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations. OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 population. Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy. In addition, the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple, pear, peach, citrus, grape, tea, and rice. We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study. The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene, which regulates potato flower color. Taken together, these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing species. For ease of use, we have developed both Windows and Linux versions of OcBSA, which are freely available at: https://gitee.com/Bioinformaticslab/OcBSA.
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Affiliation(s)
- Lingkui Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanfeng Duan
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zewei Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lei Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shumin Chen
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengcheng Cai
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shaoguang Duan
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangcun Li
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Tuber and Root Crop of Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Wang X, Han L, Li J, Shang X, Liu Q, Li L, Zhang H. Next-generation bulked segregant analysis for Breeding 4.0. Cell Rep 2023; 42:113039. [PMID: 37651230 DOI: 10.1016/j.celrep.2023.113039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 07/11/2023] [Accepted: 08/10/2023] [Indexed: 09/02/2023] Open
Abstract
Functional cloning and manipulation of genes controlling various agronomic traits are important for boosting crop production. Although bulked segregant analysis (BSA) is an efficient method for functional cloning, its low throughput cannot satisfy the current need for crop breeding and food security. Here, we review the rationale and development of conventional BSA and discuss its strengths and drawbacks. We then propose next-generation BSA (NG-BSA) integrating multiple cutting-edge technologies, including high-throughput phenotyping, biological big data, and the use of machine learning. NG-BSA increases the resolution of genetic mapping and throughput for cloning quantitative trait genes (QTGs) and optimizes candidate gene selection while providing a means to elucidate the interaction network of QTGs. The ability of NG-BSA to efficiently batch-clone QTGs makes it an important tool for dissecting molecular mechanisms underlying various traits, as well as for the improvement of Breeding 4.0 strategy, especially in targeted improvement and population improvement of crops.
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Affiliation(s)
- Xi Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Juan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiaoyang Shang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Qian Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
| | - Hongwei Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Wu H, Ma W, Yan L, Liu F, Xu S, Ji P, Gao S, Zhang L, Liu G. Investigation of SNP markers for the melatonin production trait in the Hu sheep with bulked segregant analysis. BMC Genomics 2023; 24:502. [PMID: 37648999 PMCID: PMC10466869 DOI: 10.1186/s12864-023-09494-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/29/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND As an important reproductive hormone, melatonin plays an important role in regulating the reproductive activities of sheep and other mammals. Hu sheep is a breed favoring for meat, with prolific traits. In order to explore the relationship between melatonin and reproductive function of Hu sheep, 7,694,759 SNPs were screened out through the whole genome sequencing analysis from high and low melatonin production Hu sheep. RESULTS A total of 68,673 SNPs, involving in 1126 genes, were identified by ED association analysis. Correlation analysis of SNPs of AANAT/ASMT gene and MTNR1A/MTNR1B gene were carried out. The melatonin level of CG genotype 7,981,372 of AANAT, GA genotype 7,981,866 of ASMT and GG genotype 17,355,171 of MTNR1A were higher than the average melatonin level of 1.64 ng/mL. High melatonin Hu sheep appear to have better multiple reproductive performance. CONCLUSIONS By using different methods, three SNPs which are associated with high melatonin production trait have been identified in Hu sheep. These 3 SNPs are located in melatonin synthetase AANAT/ASMT and receptor MTNR1A, respectively. Considering the positive association between melatonin production and reproductive performance in ruminants, these three SNPs can be served as the potential molecular markers for breading Hu sheep with the desirable reproductive traits.
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Affiliation(s)
- Hao Wu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Wenkui Ma
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China
| | - Laiqing Yan
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China
| | - Fenze Liu
- Inner Mongolia Golden Grassland Ecological Technology Group Co., LTD., Bayannaoer, 015000, China
| | - Shang Xu
- Inner Mongolia Golden Grassland Ecological Technology Group Co., LTD., Bayannaoer, 015000, China
| | - Pengyun Ji
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China
| | - Shuai Gao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China
| | - Lu Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China
| | - Guoshi Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, No 2, Yuanmingyuan West Road, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
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10
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Duan H, Xue Z, Ju X, Yang L, Gao J, Sun L, Xu S, Li J, Xiong X, Sun Y, Wang Y, Zhang X, Ding D, Zhang X, Tang J. The genetic architecture of prolificacy in maize revealed by association mapping and bulk segregant analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:182. [PMID: 37555969 DOI: 10.1007/s00122-023-04434-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/26/2023] [Indexed: 08/10/2023]
Abstract
KEY MESSAGE Here, we revealed maize prolificacy highly correlated with domestication and identified a causal gene ZmEN1 located in one novel QTL qGEN261 that regulating maize prolificacy by using multiple-mapping methods. The development of maize prolificacy (EN) is crucial for enhancing yield and breeding specialty varieties. To achieve this goal, we employed a genome-wide association study (GWAS) to analyze the genetic architecture of EN in maize. Using 492 inbred lines with a wide range of EN variability, our results demonstrated significant differences in genetic, environmental, and interaction effects. The broad-sense heritability (H2) of EN was 0.60. Through GWAS, we identified 527 significant single nucleotide polymorphisms (SNPs), involved 290 quantitative trait loci (QTL) and 806 genes. Of these SNPs, 18 and 509 were classified as major effect loci and minor loci, respectively. In addition, we performed a bulk segregant analysis (BSA) in an F2 population constructed by a few-ears line Zheng58 and a multi-ears line 647. Our BSA results identified one significant QTL, qBEN1. Importantly, combining the GWAS and BSA, four co-located QTL, involving six genes, were identified. Three of them were expressed in vegetative meristem, shoot tip, internode and tip of ear primordium, with ZmEN1, encodes an unknown auxin-like protein, having the highest expression level in these tissues. It suggested that ZmEN1 plays a crucial role in promoting axillary bud and tillering to encourage the formation of prolificacy. Haplotype analysis of ZmEN1 revealed significant differences between different haplotypes, with inbred lines carrying hap6 having more EN. Overall, this is the first report about using GWAS and BSA to dissect the genetic architecture of EN in maize, which can be valuable for breeding specialty maize varieties and improving maize yield.
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Affiliation(s)
- Haiyang Duan
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Zhengjie Xue
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Xiaolong Ju
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Lu Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, People's Republic of China
| | - Jionghao Gao
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Li Sun
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Shuhao Xu
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Jianxin Li
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Xuehang Xiong
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Yan Sun
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Yan Wang
- Zhucheng Mingjue Tender Company Limited, Weifang, People's Republic of China
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, People's Republic of China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China.
- The Shennong Laboratory, Zhengzhou, People's Republic of China.
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11
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Cheng C, Nie H, Li H, Adjibolosoo D, Li B, Jiang K, Cui Y, Zhu M, Zhou B, Guo A, Hua J. Identification of fertility restoration candidate genes from a restorer line R186 for Gossypium harknessii cytoplasmic male sterile cotton. BMC PLANT BIOLOGY 2023; 23:175. [PMID: 37016285 PMCID: PMC10071737 DOI: 10.1186/s12870-023-04185-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The utilization of heterosis based on three-line system is an effective strategy in crop breeding. However, cloning and mechanism elucidation of restorer genes for cytoplasmic male sterility (CMS) in upland cotton have yet been realized. RESULTS This research is based on CMS line 2074A with the cytoplasm from Gossypium harknessii (D2-2) and restorer line R186. The offspring of 2074A × R186 were used to conduct genetic analysis. The fertility mechanism of 2074A can be speculated to be governed by multiple genes, since neither the single gene model nor the double genes model could be used. The bulked segregant analysis (BSA) for (2074A × R186) F2 determined the genetic interval of restorer genes on a region of 4.30 Mb on chromosome D05 that contains 77 annotated genes. Four genes were identified as candidates for fertility restoration using the RNA-seq data of 2074A, 2074B, and R186. There are a number of large effect variants in the four genes between 2074A and R186 that could cause amino acid changes. Evolutionary analysis and identity analysis revealed that GH_D05G3183, GH_D05G3384, and GH_D05G3490 have high identity with their homologs in D2-2, respectively. Tissue differential expression analysis revealed that the genes GH_D05G3183, GH_D05G3384, and GH_D05G3490 were highly expressed in the buds of the line R186. The predicted results demonstrated that GH_D05G3183, GH_D05G3384 and GH_D05G3490 might interact with GH_A02G1295 to regulate orf610a in mitochondria. CONCLUSION Our study uncovered candidate genes for fertility restoration in the restorer line R186 and predicted the possible mechanism for restoring the male fertility in 2074A. This research provided valuable insight into the nucleoplasmic interactions.
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Affiliation(s)
- Cheng Cheng
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Hushuai Nie
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Huijing Li
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Daniel Adjibolosoo
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Bin Li
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Kaiyun Jiang
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Yanan Cui
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Meng Zhu
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Baixue Zhou
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Anhui Guo
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China.
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12
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Wu H, Yi Q, Ma W, Yan L, Guan S, Wang L, Yang G, Tan X, Ji P, Liu G. Genome-wide analysis for the melatonin trait associated genes and SNPs in dairy goat ( Capra hircus) as the molecular breeding markers. Front Genet 2023; 14:1118367. [PMID: 37021000 PMCID: PMC10067595 DOI: 10.3389/fgene.2023.1118367] [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: 12/07/2022] [Accepted: 02/28/2023] [Indexed: 04/07/2023] Open
Abstract
Previous studies have reported that the endogenous melatonin level is positively associated with the quality and yield of milk of cows. In the current study, a total of 34,921 SNPs involving 1,177 genes were identified in dairy goats by using the whole genome resequencing bulked segregant analysis (BSA) analysis. These SNPs have been used to match the melatonin levels of the dairy goats. Among them, 3 SNPs has been identified to significantly correlate with melatonin levels. These 3 SNPs include CC genotype 147316, GG genotype 147379 and CC genotype 1389193 which all locate in the exon regions of ASMT and MT2 genes. Dairy goats with these SNPs have approximately 5-fold-higher melatonin levels in milk and serum than the average melatonin level detected in the current goat population. If the melatonin level impacts the milk production in goats as in cows, the results strongly suggest that these 3 SNPs can serve as the molecular markers to select the goats having the improved milk quality and yield. This is a goal of our future study.
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Affiliation(s)
- Hao Wu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Qi Yi
- Sanya Institute of China Agricultural University, Sanya, China
| | - Wenkui Ma
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Laiqing Yan
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengyu Guan
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Likai Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Guang Yang
- Sanya Institute of China Agricultural University, Sanya, China
| | - Xinxing Tan
- Inner Mongolia Grassland Hongbao Food Co., Ltd., Bayannaoer, China
| | - Pengyun Ji
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Guoshi Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agricultural, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Sanya, China
- *Correspondence: Guoshi Liu,
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Khan MHU, Wang S, Wang J, Ahmar S, Saeed S, Khan SU, Xu X, Chen H, Bhat JA, Feng X. Applications of Artificial Intelligence in Climate-Resilient Smart-Crop Breeding. Int J Mol Sci 2022; 23:11156. [PMID: 36232455 PMCID: PMC9570104 DOI: 10.3390/ijms231911156] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/18/2022] [Accepted: 09/19/2022] [Indexed: 11/21/2022] Open
Abstract
Recently, Artificial intelligence (AI) has emerged as a revolutionary field, providing a great opportunity in shaping modern crop breeding, and is extensively used indoors for plant science. Advances in crop phenomics, enviromics, together with the other "omics" approaches are paving ways for elucidating the detailed complex biological mechanisms that motivate crop functions in response to environmental trepidations. These "omics" approaches have provided plant researchers with precise tools to evaluate the important agronomic traits for larger-sized germplasm at a reduced time interval in the early growth stages. However, the big data and the complex relationships within impede the understanding of the complex mechanisms behind genes driving the agronomic-trait formations. AI brings huge computational power and many new tools and strategies for future breeding. The present review will encompass how applications of AI technology, utilized for current breeding practice, assist to solve the problem in high-throughput phenotyping and gene functional analysis, and how advances in AI technologies bring new opportunities for future breeding, to make envirotyping data widely utilized in breeding. Furthermore, in the current breeding methods, linking genotype to phenotype remains a massive challenge and impedes the optimal application of high-throughput field phenotyping, genomics, and enviromics. In this review, we elaborate on how AI will be the preferred tool to increase the accuracy in high-throughput crop phenotyping, genotyping, and envirotyping data; moreover, we explore the developing approaches and challenges for multiomics big computing data integration. Therefore, the integration of AI with "omics" tools can allow rapid gene identification and eventually accelerate crop-improvement programs.
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Affiliation(s)
- Muhammad Hafeez Ullah Khan
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- Zhejiang Lab, Hangzhou 310012, China
| | - Shoudong Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- Zhejiang Lab, Hangzhou 310012, China
| | - Jun Wang
- Zhejiang Lab, Hangzhou 310012, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Sumbul Saeed
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shahid Ullah Khan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | | | | | | | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- Zhejiang Lab, Hangzhou 310012, China
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