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Genomics and Applied Biology (online), 2024, Vol. 15 ISSN 1925-1602 https://bioscipublisher.com/index.php/gab © 2024 BioSciPublisher, an online publishing platform of Sophia Publishing Group. All Rights Reserved. Sophia Publishing Group (SPG), founded in British Columbia of Canada, is a multilingual publisher Latest Content The Interplay between Bird Migration Behavior and Genetic Diversity JingLin Genomics and Applied Biology, 2024, Vol. 15, No. 1 A New Chapter in Sugarcane Genomics: Constructing the R570 Reference Genome and the Future of Agricultural Biotechnology May Wang, Jim Fang Genomics and Applied Biology, 2024, Vol. 15, No. 2 Genome-wide Association Studies of Disease Resistance Genes in Maize IvyChen Genomics and Applied Biology, 2024, Vol. 15, No. 3 Portable Nanopore Sequencing Technology: A Revolutionary Progress in Bioinformatics JimManson Genomics and Applied Biology, 2024, Vol. 15, No. 4 The Latest Progress of Cryo Electron Microscopy Technology in Protein Structure Analysis WeiWang Genomics and Applied Biology, 2024, Vol. 15, No. 5 The Application of Single-Cell Omics Technologies in Neuroscientific Research Jiayao Zhou Genomics and Applied Biology, 2024, Vol. 15, No. 6 Genetic Mechanism of Cassava Disease Resistance: From Traditional Breeding to CRISPR/Cas Application Wenzhong Huang, Zhongmei Hong Genomics and Applied Biology, 2024, Vol. 15, No. 7 Genomic Diversity and Evolutionary Mechanisms in the Oryza Genus: A Comparative Analysis Jianquan Li, Fu Jiong Genomics and Applied Biology, 2024, Vol. 15, No. 8
Genomics and Applied Biology 2024, Vol.15, No.1, 1-7 http://bioscipublisher.com/index.php/gab 1 Review and Progress Open Access The Interplay between Bird Migration Behavior and Genetic Diversity JingLin Biotechnology Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, China Corresponding email: 2644034884@qq.com Genomics and Applied Biology, 2024, Vol.15, No.1 doi: 10.5376/gab.2024.15.0001 Received: 29 Dec., 2023 Accepted: 30 Dec., 2023 Published: 01 Jan., 2024 Copyright © 2024 Lin, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Lin J., 2024, The interplay between bird migration behavior and genetic diversity, Genomics and Applied Biology, 15(1): 1-7 (doi: 10.5376/gab.2024.15.0001) Abstract Avian migration is a significant phenomenon in biodiversity, and genetic diversity during migration is crucial for the adaptability and survival of species. This review begins by introducing the diversity of avian migration behavior and the pivotal role of genetic diversity. It then delves into analyzing the impact of climate change on avian migration, particularly focusing on the influence of rising temperatures on migration patterns and habitats. The review explores the potential effects of these changes on the genetic diversity of birds. It also discusses genetic adaptation and changes, revealing the survival strategies adopted by birds in response to climate change. Furthermore, it examines the response of genetic diversity in avian migration, including its relationship with adaptability, gene flow, migration paths, and genomic stability. These analyses are crucial for better understanding the dynamic changes in genetic diversity during avian migration, leading to the development of more effective conservation policies and ecosystem management. Through in-depth exploration, we can better protect and preserve avian migration, ensuring its continued prosperity in the face of challenges posed by climate change. Keywords Bird migration; Genetic diversity; Climate change; Adaptability; Ecosystem management The relationship between bird migration behavior and genetic diversity constitutes a stunning biological landscape, revealing a magical and ancient tradition in nature. The miraculous behavior not only demonstrates the wisdom of bird survival, but also highlights the perfection of the natural ecosystem. However, as global climate change becomes increasingly frequent and significant, bird migration faces unprecedented challenges. In recent decades, temperatures have continued to rise and extreme weather events have occurred frequently, which have had a profound impact on the migration of birds. The rise in temperature not only changes the seasonal climate pattern, but also directly affects the breeding, migration time, location, and route selection of birds. These changes are directly related to the behavioral habits, habitat selection, and resource allocation of birds, affecting the genetic diversity and genetic structure of the entire bird population (Tamario et al., 2019). Genetic diversity plays a crucial role in bird migration. It is the foundation for bird populations to adapt to environmental changes and determines their ability to adapt to different environmental pressures (Berthold, 2002). However, climate change may have a negative impact on genetic diversity, making migratory populations more susceptible to genetic bottlenecks and drift, thereby reducing their adaptability and survival ability (Morganti, 2015). This study aims to comprehensively explore the impact of climate change on genetic diversity in bird migration. By conducting in-depth analysis of the relationship between gene diversity and adaptability, gene flow and migration pathways, as well as genome stability and environmental changes, this study will examine the biological responses of bird populations to high temperature and climate change. Exploring the relationship between bird migration and genetic diversity in depth will also provide a more comprehensive understanding and insight for the protection and sustainable management of global ecosystems. Exploring the impact of climate change on bird migration is an inevitable choice for in-depth thinking and research on this magnificent phenomenon in nature. Only through continuous deepening of understanding can people better protect and maintain this rich and diverse Earth ecosystem.
Genomics and Applied Biology 2024, Vol.15, No.1, 1-7 http://bioscipublisher.com/index.php/gab 2 1 Bird Migration and Genetic Diversity 1.1 Overview of bird migration The migration of birds is a miracle of life, performing magnificent rhythms in the changing seasons. They cross the sky, from south to north, from east to west, carrying the wonders of the ecosystem on their migration journey. The ancient migration tradition is not only an instinct of birds, but also a key factor in ecological balance. However, as the climate continues to change, this magnificent migration faces many challenges. Bird migration varies in scale and distance. Some birds only migrate for short distances within relatively localized areas, while others migrate for long distances across thousands of miles, continents, and even ocean currents. These movements are not accidental, they are closely related to seasonal climate change. Environmental factors such as temperature, light, and wind play important roles in bird migration. The changes in these factors will directly affect the feeding locations, breeding areas, and overall migration paths of birds. Migration is not only related to seasonal environmental changes, but also closely related to reproductive cycles, reproductive behavior, and foraging habits. During the migration process, birds require a large amount of energy to support long flights, and many birds need to search for food to maintain their physical strength during the migration. Therefore, the smooth progress of migration is crucial for the survival and reproduction of birds (Morganti, 2015). The migration of birds covers a wide range of species and regions, and the migration patterns and scales of each bird species vary (Table 1). For example, the Red billed Quelea exhibits billions of swarms on the African savannah, exhibiting astonishing large-scale swarm migration; The Arctic tern, on the other hand, has the longest migration route in the world, spanning tens of thousands of miles within a year, crossing the poles of the entire Earth. These migrations of different scales and distances not only vary in itinerary, but also directly affect the genetic diversity of bird populations. Table 1 Representative migratory bird information (Xu et al., 2021) The order, family, and genus of migratory birds Representative types Distribution location Migration distance Craniformes, crane family, white crane genus Grus leucogeranus Distributed mostly in Eurasia and Africa 8 000 kilometers Chariotiformes, gull family, tern genus Sterna paradisaea Distributed near the Arctic 70 00 kilometers Storyliformes, Egret family, Egret genus Egretta garzetta Distributed mostly in Africa, Madagascar, and Eurasia 900 kilometers Falcons, family Falconidae, genus Falcon Falco peregrinus Distributed mostly near the Arctic Circle 6 400 kilometers Passeriformes, family Orioles, genus Orioles Phylloscopus trochilus yakutensis Distributed mostly near Siberia 13 000 kilometers The different patterns and scales of bird migration have varying degrees of impact on genetic diversity. In small-scale migration, the genetic relationships of the population may be closer, and the flow of genetic information during the migration process is relatively limited. In contrast, birds that migrate over long distances globally may experience more extensive gene flow, and populations from different regions may exchange genetic information more frequently, thereby affecting the genetic diversity and structure of the population. Therefore, understanding and studying the impact of migration of different scales and distances on gene diversity is crucial for comprehensively grasping the genetic characteristics of bird ecosystems. 1.2 The concept of genetic diversity Genetic diversity refers to the degree of diversity in genotype and gene frequency within a specific species or population. It involves the differences in individual genes within a population, including genotype diversity, changes in gene frequency, and the magnitude of genetic variation. In the context of bird migration, genetic diversity focuses on the differences between individual genes within a population, which directly relates to the adaptability of the population to environmental changes.
Genomics and Applied Biology 2024, Vol.15, No.1, 1-7 http://bioscipublisher.com/index.php/gab 3 Genetic diversity plays a crucial role in bird populations. It is the cornerstone for a group to adapt to environmental changes and cope with stress. Rich genetic diversity means that there is more genotype and genetic information within the population, thereby increasing the likelihood of the population responding to changes in the external environment. This diversity helps to improve the survival ability of populations and reduce the risk of ecosystem and population collapse caused by environmental changes (De Meester et al., 2017). The genetic diversity of bird migration is not only reflected in the migration behavior itself, but also in the selection of migration paths, adaptability to different habitats, and rapid adaptation to new environments. During migration, genetic diversity of populations may be challenged due to changes in geography and environment. This change may trigger gene flow, variation, and selection, thereby having a profound impact on the adaptability and survival strategies of the population (Lü et al., 2021). Some birds may change their migration paths or residence locations due to climate change to adapt to new environmental conditions. The behavioral change may lead to changes in gene flow and genetic structure within the population, increasing the frequency of different genotypes and thus affecting the survival strategy of the population. The richness of genetic diversity can provide populations with greater genetic adaptability, making them more likely to survive in constantly changing environments. 1.3 The impact of migration types on gene diversity The migration types of birds have a significant impact on gene diversity. Different types of migration patterns, such as seasonal migration, partial migration, or periodic migration, can have varying impacts on genetic diversity and distribution within a population. Seasonal migration may trigger broader gene flow, as migratory birds navigate multiple geographic locations during the migration season, leading to gene exchange and mixing. This frequent gene flow may reduce genetic differences between migrating populations, increase gene exchange in the overall population, and thus maintain relatively high gene diversity. In contrast, birds that migrate partially or regularly may exhibit greater genetic differentiation. If some individuals or groups choose to stay in place while others choose to migrate, this may lead to gene segregation and differences. Over the long term, this may result in genetic diversity differences between different subspecies, populations, or individuals. The type of migration can also have an impact on genetic adaptability and population genetic structure. Migration strategies are related to environmental adaptability, therefore bird populations under different migration patterns may exhibit different adaptive genotypes to different environmental pressures (Hoffmann and Sgrò, 2011). Furthermore, migration strategies may affect the gene frequency and genetic structure within bird populations, resulting in varying degrees of gene differentiation and differences, which may affect the adaptability and survival ability of the population. 2 Genomic Stability and Environmental Changes 2.1 The challenge of environmental changes to genomic stability Genomic stability plays a crucial role in the relationship between bird migration and environmental changes, and this stability is the cornerstone of species genetic diversity and adaptability. The changes in the environment challenge the stability of the genome, and their impact involves multiple aspects such as genetic variation, genotype frequency changes, and gene flow. Environmental changes may trigger genetic variations in the genome. Climate anomalies, habitat destruction, or interference from human activities may induce mutations or rearrangements in the genome, which may lead to changes in the genetic structure of species. This variation may sometimes have a positive impact on the adaptability of bird populations, but it may also increase the risk of disease or reduce the adaptability of the population. Environmental stress may also lead to changes in specific genotypes or gene frequencies in the genome. Some specific genotypes may be more adaptable to changing environments, therefore, under environmental pressure, the frequency of these genotypes may increase. However, such changes may lead to a decrease in genetic diversity, increasing the risk of disease or other environmental pressures on the population (Tamario et al., 2019).
Genomics and Applied Biology 2024, Vol.15, No.1, 1-7 http://bioscipublisher.com/index.php/gab 4 Moreover, environmental changes may also affect gene flow in the genome. Bird migration is often influenced by seasonal and regional environments, but when these environments change, the migration path and location may change. It may lead to a decrease or increase in gene flow between migratory populations, thereby affecting the maintenance and development of gene diversity. 2.2 The relationship between genomic stability and avian adaptability Genomic stability plays an important role in the adaptability of bird populations. It affects genetic diversity, adaptive evolution, and the health status of populations, thereby affecting the survival and reproductive ability of birds in the face of environmental changes. Genomic stability affects the genetic diversity of bird populations. A genome stable population often has richer genetic diversity, which enables the population to better adapt to various environmental conditions. However, when genomic stability is affected, it may lead to a decrease in genetic diversity, thereby reducing the population's ability to adapt to environmental changes. Genomic stability is also closely related to the adaptive evolution of birds. When the environment changes, bird populations with stable genomes may be more likely to cope with such changes through natural selection and adaptive evolution. The stability helps to maintain some adaptive genotypes, allowing birds to maintain high adaptability in new environments. In addition, genomic stability is closely related to the population health and survival ability of birds. A population with a stable genome is more likely to avoid the spread of genetic diseases and maintain the health and survival of the population (Pulido and Berthold, 2010). 2.3 The relationship between genetic stability of bird populations and climate change There is a close relationship between the genetic stability of bird populations and climate change. With global temperature changes and frequent extreme weather events, the genetic stability of bird populations is facing unprecedented challenges. Climate change may limit gene flow, lead to a decrease in gene diversity and an increase in genetic drift, thereby affecting population stability and adaptability. Climate change may hinder gene flow in bird populations. Migratory birds often choose migration paths and locations based on seasonal and environmental changes to adapt to different seasons and resource changes. However, climate change may alter migration pathways or locations, limiting gene flow between different populations and affecting the genetic stability of some populations (Pauls et al., 2012). Climate change may also lead to a decrease in genetic diversity in bird populations. Changes in ecosystems may affect the habitat and resource allocation of birds, resulting in changes in certain genotypes or gene frequencies. The change may lead to a decrease in genetic diversity, thereby reducing the population's ability to adapt to new environments. In addition, climate change may lead to increased genetic drift in bird populations. When the environment undergoes drastic changes, the population may face adaptive pressure, which may lead to drastic changes in the frequency of certain genotypes in the genome, resulting in genetic drift. 3 Genetic Diversity Response in Bird Migration 3.1 Genetic diversity and adaptability Genetic diversity provides a genetic basis for bird migration, endowing them with the ability to adapt to different environments and cope with various pressures. This diversity is crucial for the health and reproduction of populations, especially when facing various challenges during migration. Genetic diversity provides bird populations with stronger adaptability, enabling them to better cope with different environmental pressures. Under different climate and habitat conditions, different genotypes may exhibit higher survival and reproductive abilities. This adaptability enables birds to adapt to new environmental conditions more quickly during migration. Genetic diversity can also improve the survival rate and reproductive success rate of populations. Individuals with more genetic variations are usually more resilient and able to resist environmental changes and disease stress. During migration, this resilience helps bird populations overcome various challenges and maintain their healthy state (Coppack and Both, 2002).
Genomics and Applied Biology 2024, Vol.15, No.1, 1-7 http://bioscipublisher.com/index.php/gab 5 For example, during bird migration, individuals with more genetic variations may be more likely to adapt to different migration paths or new habitats. These mutated genotypes may enable birds to better utilize resources in different geographical environments, thereby improving their chances of survival and reproduction. In addition, genetic diversity in combating pathogens or other environmental pressures is also crucial. Birds with more resistance genotypes may be better able to avoid disease transmission or adapt to survival challenges under different environmental conditions during migration. 3.2 Gene flow and migration pathways The understanding of bird migration pathways and the impact of gene flow on population genetic diversity provide important clues for humans to understand the genetic structure and population dynamics of bird populations. These knowledge not only help explain the genetic changes during migration, but also provide important scientific basis for the protection and management of bird populations. Gene flow describes the mutual exchange of genotypes between different geographical regions. The migration path of birds typically spans multiple geographical regions, including different environments and habitat conditions. This migration pattern leads to gene exchange between different populations, forming a complex and diverse gene flow network. This flow not only shapes and influences genetic diversity within populations, but also establishes genetic connections between populations on a global scale. The choice of migration path has an impact on the distribution of different genotypes in the population. Some birds may choose relatively stable migration paths, following similar migration routes and habitats. But other birds may flexibly adjust their migration paths to cope with different environmental conditions and resource changes. This path selection may lead to genotype differences between populations on different paths, forming a genotype composition specific to migration paths (Knudsen, 2011). For example, some migratory bird populations may choose to stop or forage during their migration, and meet or mix with other populations during this period. This mutual communication may lead to mixing between different genotypes and have an impact on the genetic structure and diversity of the population. In addition, in some cases, geographical barriers along migration paths may lead to relative isolation of certain genotypes in specific regions, which may result in populations in these regions having specific genetic characteristics (Charmantier and Gienapp, 2013). 3.3 The relationship between genomic stability and environmental changes There is a close relationship between genomic stability in bird migration and environmental changes. Genomic stability refers to the degree to which the genome maintains and maintains itself in both time and space, as well as its ability to respond to external environmental pressures. During migration, bird populations may be influenced by various environmental factors, such as temperature, climate change, availability of food resources, and changes in habitat conditions. The changes in these environmental factors may have an impact on genome stability, thereby affecting the adaptability and survival ability of bird populations. The maintenance of genomic stability is crucial for the adaptability and survival of birds during migration (Dawson et al., 2011). Some genotypes may be more adaptable, able to better adapt to environmental changes and maintain their stability. This genomic stability may affect the adaptability and survival rate of bird populations, and is crucial for ecosystem function and ecological balance during migration (Berthold, 2002). 4Prospect The relationship between bird migration and genetic diversity is a fascinating and challenging field. In this field, it can be seen how bird populations rely on their genetic diversity to adapt to constantly changing environments. Migration is a crucial part of bird life cycle, involving complex processes from seasonal climate change to adaptation to different habitats. The migration path selection and gene flow of birds play an important role in shaping the genetic structure and diversity of populations. In this field, future research will aim to gain a deeper understanding of the impact of different migration patterns on genotype distribution, as well as the role of genomic stability in environmental changes.
Genomics and Applied Biology 2024, Vol.15, No.1, 1-7 http://bioscipublisher.com/index.php/gab 6 Genetic diversity has been proven to be crucial for the adaptability of bird populations. Individuals with more genetic variations are often better able to adapt to different environmental pressures during migration. This diversity provides key mechanisms for resisting diseases and adapting to new environments, increasing opportunities for the survival and reproduction of bird populations. Future research will delve deeper into how these genotypes affect the selection of migration pathways and their resource utilization capabilities in different geographical environments. On the other hand, environmental changes pose a challenge to genome stability, which is crucial for the survival ability of bird populations. With global climate change, birds may face changes in their migration paths, which may limit gene flow and affect the maintenance of gene diversity. Therefore, an understanding of genomic stability under environmental changes will provide us with more information about the survival ability and adaptability of populations. Technological innovation will be an important driving force for future bird conservation. The development of genomics and remote sensing technology will provide humans with more refined genetic information and habitat monitoring data, which will provide more support for the study of bird migration and genetic diversity. Interdisciplinary cooperation will also be the key to future research, integrating knowledge from ecology, genetics, and environmental science can provide humans with a more comprehensive understanding, assist in bird conservation, and promote sustainable development of ecosystems. Overall, the interaction between bird migration and genetic diversity will continue to lead the forefront of research in biology and environmental science. Future research will delve deeper into these relationships, providing richer and more comprehensive insights into bird conservation, ecosystem robustness, and human sustainable use of the environment. The continuous exploration in this field is expected to provide more solutions for humans, thereby better understanding how bird migration shapes the genetic structure of populations, and how genetic diversity affects the survival and reproductive ability of birds under different environmental conditions. These research findings will have important inspiration and guidance for the maintenance of biodiversity, ecosystem balance, and sustainable environmental management. References Berthold P., 2002, Bird migration: the present view of evolution, control, and further development as global warming progresses, Dongwu Xuebao (Current Zoology), 48(3): 291-301. Charmantier A., and Gienapp P., 2013, Climate change and timing of avian breeding and migration: evolutionary versus plastic changes, Evol. Appl., 7(1): 15-28. https://doi.org/10.1111/eva.12126 Coppack T., and Both C., 2002, Predicting life-cycle adaptation of migratory birds to global climate change, Ardea, 55(1-2): 369-378. Dawson T.P., Jackson S.T., House J.I., Prentice I.C., and Mace G.M., 2011, Beyond predictions: biodiversity conservation in a changing climate, Science, 332(6025): 53-58. https://doi.org/10.1126/science.1200303 De Meester L., Stoks R., and Brans K.I., 2017, Genetic adaptation as a biological buffer against climate change: Potential and limitations, Integr. Zool., 13(4): 372-391. https://doi.org/10.1111/1749-4877.12298 Hoffmann A.A., and Sgrò C.M., 2011, Climate change and evolutionary adaptation, Nature, 470: 479-485. https://doi.org/10.1038/nature09670 Knudsen E., Lindén A., Both C., Jonzén N., Pulido F., Saino N., Sutherland W.J., Bach L.A., Coppack T., Ergon T., Gienapp P., Gill J.A., Gordo O., Hedenström A., Lehikoinen E., Marra P.P., Møller A.P., Nilsson A.L.K., Péron G., Ranta E., Rubolini D., Sparks T.H., Spina F., Studds C.E., Sæther S.A., Tryjanowski P., Stenseth N.C., 2011, Challenging claims in the study of migratory birds and climate change, Biological Reviews, 86(4): 928-946. https://doi.org/10.1111/j.1469-185X.2011.00179.x Lü X.Y., Li B.Q., Cui J., Zhang Q.Y., Chen Q., and Wang Y.Y., 2021, Genetic diversity analysis of anatidae based on mitochondrial genome, Jiyin Zuxue yu Yingyong Shengwuxue (Genomics and Applied Biology), 40(Z1): 2008-2019. Morganti M., 2015, Birds facing climate change: a qualitative model for the adaptive potential of migratory behaviour, Rivista Italiana Di Ornitologia, 85(1): 3-13. https://doi.org/10.4081/rio.2015.197 Pauls S.U., Nowak C., Bálint M., Pfenninger M., 2012, The impact of global climate change on genetic diversity within populations and species, Molecular Ecology, 22(4): 925-946. https://doi.org/10.1111/mec.12152
Genomics and Applied Biology 2024, Vol.15, No.1, 1-7 http://bioscipublisher.com/index.php/gab 7 Pulido F., and Berthold P., 2010, Current selection for lower migratory activity will drive the evolution of residency in a migratory bird population, PNAS, 107(16): 7341-7346. https://doi.org/10.1073/pnas.0910361107 Tamario C., Sunde J., Petersson E., Tibblin P., and Forsman A., 2019, Ecological and evolutionary consequences of environmental change and management actions for migrating fish, Front. Ecol. Evol., 7(271): 1-24. https://doi.org/10.3389/fevo.2019.00271 Xu J., Xu H., Zhang M., Cao J., Liu C., and Zhou H., 2021, A review of bird migration research, Shijie Shengtaixue (International Journal of Ecology), 10(2): 274-280. https://doi.org/10.12677/IJE.2021.102032
Genomics and Applied Biology 2024, Vol.15, No.1, 8-11 http://bioscipublisher.com/index.php/gab 8 Scientific Review Open Access A New Chapter in Sugarcane Genomics: Constructing the R570 Reference Genome and the Future of Agricultural Biotechnology MayWang , JimFang Hainan Institute of Tropical Agricultural Resources, Sanya, 572024, China Corresponding email: whmj919@gmail.com Genomics and Applied Biology, 2024, Vol.15, No.1 doi: 10.5376/gab.2024.15.0002 Received: 20 Nov., 2023 Accepted: 22 Dec., 2023 Published: 5 Jan., 2024 Copyright © 2024 Wang and Fang, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Wang M., and Fang J., 2024, A new chapter in sugarcane genomics: constructing the R570 reference genome and the future of agricultural biotechnology, Genomics and Applied Biology, 15(1): 8-11 (doi: 10.5376/gab.2024.15.0002) A paper titled "The Complex Polyploid Genome Architecture of Sugarcane" by A.L. Healey, O. Garsmeur, J.T. Lovell, et al., from institutions including the Hudson Alpha Institute for Biotechnology, CIRAD, and the University of Queensland, was published in the journal Nature on March 27, 2024. This research successfully constructed a polyploid reference genome for the sugarcane (Saccharum spp.) variety R570. As the highest-yielding crop worldwide, sugarcane is a crucial source of sugar and biomass production. Despite certain successes in adapting to new environments and pathogens through traditional breeding methods, the increase in sugarcane's sugar yield has plateaued in recent years. By generating a polyploid reference genome for the R570 variety, this study fills a gap in the lack of high-quality reference genomes for modern sugarcane varieties, marking an important step forward for biotechnological advancements in sugarcane. 1 Experimental Data Analysis The study employed a range of cutting-edge genomics technologies, including high-throughput Illumina sequencing, high-accuracy PacBio HiFi sequencing, and precise chromosome flow sorting, to successfully construct a high-continuity reference genome for the sugarcane variety R570. The genome size is estimated at 10Gb, reflecting the characteristic traits of a modern hybrid variety created through the breeding of two primary parent species of sugarcane: Saccharum officinarum and Saccharum spontaneum. Furthermore, the genome annotation work identified 194,593 genes, significantly enriching our understanding of the complex polyploid genome structure of sugarcane and providing valuable resources for exploring the genetic diversity and functional genomics of sugarcane. The size of this genome and the number of genes reflect the genetic complexity and richness of sugarcane as a significant agricultural and bioenergy plant, laying a solid foundation for further molecular breeding, genetic improvement, and disease prevention research. Figure 1 illustrates the pedigree and genome structure of the hybrid sugarcane R570. From Figure 1a, it is seen that R570 is a sugarcane variety approximately 4 meters in height. Figure 1b details the breeding pedigree of R570, where pie charts show the genome contributions from wild sugarcane (red) and sweet sugarcane (blue) to R570. The asterisks "*" represent the diploid chromosome transmission in the first two generations, and the "+" indicates the first generation of hybrids. Although the exact pedigrees of ‘R331’ and ‘Co213’ are unknown, they are estimated to be BC2F2 and BC2:BC1 F1, respectively. Figure 1c shows R570 chromosomes prepared after in situ hybridization with wild sugarcane-specific probes, with the red parts marking the chromosomes from wild sugarcane. Figure 1d is the karyotype of R570, with colors corresponding to those in figure 1b. This information helps researchers understand the complex polyploid genome structure of R570 hybrid sugarcane. Figure 2 presents the genome assembly information for the sugarcane variety R570. Figure 2a is a schematic of the main assembly of the R570 genome, showing that each homologous chromosome has about 12 chromosome copies, but almost identical haplotypes are folded in the genome assembly due to backcrossing and 2n+n chromosome transmission (indicated by different colored shadows). Figure 2b shows the one-to-one orthologous
Genomics and Applied Biology 2024, Vol.15, No.1, 8-11 http://bioscipublisher.com/index.php/gab 9 genes between R570's main chromosomes and chromosomes 1 to 10 of sorghum (Sorghum bicolor v.3.1.1), colored according to ancestral contributions in R570. Figure 2c is a homology map between R570 and related genomes generated by GENESPACE, from bottom to top: sorghum, wild sugarcane genotype AP85-441, R570's main genome, and the assembly of R570's haplotype genome. This chart aids researchers in understanding the complex homology between R570 and other species' genomes. Figure 1 The pedigree and genome organization of R570 hybrid sugarcane Figure 2 The genome assembly of sugarcane cultivar R570 Figure 3 focuses on the Bru1 gene locus in the sugarcane variety R570, which is associated with resistance to brown rust disease. Figure 3a shows leaves from two selfed progenies of R570: the upper leaf carries the Bru1 locus and exhibits resistance to brown rust disease; the lower leaf lacks the Bru1 locus, showing susceptibility to the disease. Figure 3b displays the filled haplotype assembly, identifying the TKP gene as the candidate causative gene for persistent resistance to brown rust disease. In the diagram, blue pentagons represent organized gene models, and gray pentagons represent large transposable elements. Candidate genes TKP7 and TKP8 for Bru1 are shown in red and marked on the 3D chromosome. This indicates that through detailed gene localization and functional annotation, researchers can identify key genes related to sugarcane's disease resistance traits, which is significant for breeding. 2 Analysis of Research Findings This study successfully constructed an 870 million base pair polyploid reference genome for the sugarcane variety R570, revealing the complex genome structure resulting from the hybridization of Saccharum officinarum and Saccharum spontaneum. Identifying 194,593 genes, the study provides a critical foundation for research into sugarcane's genetic diversity and molecular breeding. Through detailed analysis of the R570 genome, the study not only revealed the genetic contributions of parent species to modern varieties, especially in disease resistance and sugar accumulation but also identified candidate genes for the brown rust resistance gene Bru1, offering molecular tools for improving sugarcane's disease resistance in the future. Additionally, the study delved into the structural variations in the sugarcane genome, the diversity of orthologous genes, and the evolution of specific functional genes, uncovering the relationship between sugar accumulation and certain gene families. This research not only deepens our understanding of the complexity of the sugarcane genome but also provides valuable genetic resources for sugarcane breeding, disease management, and biotechnological improvements, marking a new phase in sugarcane genome research.
Genomics and Applied Biology 2024, Vol.15, No.1, 8-11 http://bioscipublisher.com/index.php/gab 10 Figure 3Bru1candidate gene locus 3 Evaluation of the Research This research represents a milestone achievement in the field of sugarcane genomics, constructing a complex polyploid reference genome for the sugarcane variety R570 through highly innovative methods. The findings not only deepen the scientific community's understanding of sugarcane's genetic complexity but also significantly advance the application of genomics in sugarcane research, particularly in improving disease resistance and productivity. By thoroughly analyzing key resistance genes like Bru1, this study provides molecular targets for sugarcane disease-resistant breeding and also offers potential resistance mechanisms for other crops. Moreover, the success of this study demonstrates the power of interdisciplinary collaboration, integrating techniques and knowledge from bioinformatics, molecular biology, genetics, and other fields, reflecting the composite and interconnected nature of modern scientific research. The publication of this study not only provides valuable resources for sugarcane breeding and improvement but also offers clues to solving challenges faced by global agricultural production, showcasing the key role of genomic research in modern agricultural science. 4 Conclusions The successful construction of the polyploid reference genome for sugarcane R570 marks a milestone in sugarcane genome research, advancing the study of this important economic crop to a new level. Through the use of the latest sequencing technologies and bioinformatics analysis, this work provides an unprecedented detailed view of sugarcane's genetic diversity and complex genome structure, as well as identifying genes controlling key agronomic traits such as sugar accumulation and disease resistance, providing important molecular markers and candidate genes for future molecular breeding and genetic improvement. Moreover, the outcomes of this research pave the way for advances in sugarcane biotechnology, offering scientific evidence and technical tools for developing new disease-resistant varieties and increasing sugarcane sugar yield. Against the backdrop of global
Genomics and Applied Biology 2024, Vol.15, No.1, 8-11 http://bioscipublisher.com/index.php/gab 11 climate change and the challenges of sustainable agricultural production, this study not only has profound significance for the sugarcane industry but also provides valuable experience and insights for the genome research and improvement of other crops. By deeply exploring the genetic potential of sugarcane, this research provides a solid foundation for improving the productivity and adaptability of sugarcane, as well as further utilizing this crop as a source of biomass energy. 5 Access the Full Text Healey, A.L., Garsmeur, O., Lovell, J.T. et al. The complex polyploid genome architecture of sugarcane. Nature (2024). https://doi.org/10.1038/s41586-024-07231-4. Acknowledgement The authors sincerely thank Nature magazine for providing the research paper by Healey, A.L., Garsmeur, O., Lovell, J.T., et al. on the complex polyploid genome architecture of sugarcane in an open access (OA) manner, allowing for the timely sharing of this important finding with academic colleagues. This act not only exemplifies the spirit of scientific sharing but also deepens our understanding and knowledge of the field.
Genomics and Applied Biology 2024, Vol.15, No.1, 12-21 http://bioscipublisher.com/index.php/gab 12 Review and Progress Open Access Genome-wide Association Studies of Disease Resistance Genes in Maize IvyChen Cuixi Biotechnology Research Institute is now the Agricultural Research Center, Zhuji, 311800, China Corresponding email: Ivychen@hotmail.com Genomics and Applied Biology, 2024, Vol.15, No.1 doi: 10.5376/gab.2024.15.0003 Received: 22 Nov., 2023 Accepted: 25 Dec., 2023 Published: 7 Jan., 2024 Copyright © 2024 Chen, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Chen I., 2024, Genome-wide association studies of disease resistance genes in maize, Genomics and Applied Biology, 15(1): 12-21 (doi: 10.5376/gab.2024.15.0003) Abstract Corn occupies a core position in global food production, but its yield and quality are seriously threatened by a variety of diseases. Genome-wide association studies (GWAS), as a powerful genetic analysis tool, provides a new way to reveal the genetic basis of disease resistance traits in maize. This study reviews the application of GWAS in corn disease resistance research, from theoretical basis to practical cases, and discusses in detail the key disease resistance genes identified through GWAS and their potential applications in breeding. We review the principles of GWAS methods and the progress made in corn disease resistance research, including the successful identification of key genes or gene regions related to southern corn rust, corn leaf spot, and corn cob rot. Furthermore, challenges and future directions in translating these findings into practical breeding strategies are discussed. This study aims to provide scientific basis and new ideas for improving corn disease resistance and further promote the cultivation of highly disease-resistant corn varieties to meet global food security challenges. Keywords Maize (Zeamays); Genome-wide association studies (GWAS); Disease resistance; Breeding; Genetic studies Corn (Zea mays) is not only the second largest food crop in the world, but its role in global food security and sustainable agricultural development has become increasingly prominent. As an important source of food, feed and industrial raw materials, corn is critical to meeting the needs of the world's growing population. However, disease problems encountered during corn production, such as corn leaf spot, corn rust, and corn mosaic virus, have greatly limited the increase in yield and the assurance of quality. These diseases not only cause yield losses, but may also reduce the nutritional value and processing quality of corn, bringing a huge economic burden to agricultural production. Against this background, it is particularly important to research and develop corn varieties with high disease resistance. Although traditional breeding methods have made some progress in improving disease resistance, progress is slow and inefficient due to the complex genetic basis of disease resistance traits. In recent years, the development of genome -wide association studies (GWAS) technology has provided new ideas and methods for the study of corn disease resistance. By analyzing the association between genetic variation and trait expression, GWAS can quickly identify genes or genetic markers related to corn disease resistance across the entire genome. The application of this method not only deepens our understanding of the genetic mechanism of disease resistance in maize, but also provides effective molecular tools for breeding (Ren et al., 2022). This study illustrates the application of GWAS in the study of corn disease resistance and its impact on breeding practice. First, the article briefly introduces the background of corn disease resistance research and emphasizes the important role of GWAS in revealing the genetic basis of complex traits. Next, several key genes for corn disease resistance successfully identified through GWAS methods were discussed in detail, as well as the functions and mechanisms of these genes. These successful cases not only demonstrate the potential of GWAS in identifying corn disease resistance genes, but also provide valuable information for understanding disease resistance mechanisms. In addition, this study also explores ways to translate GWAS findings into practical breeding strategies, including the application of molecular marker-assisted selection (MAS) and gene editing technologies. The combined use of these methods has greatly accelerated the development of highly disease-resistant corn varieties.
Genomics and Applied Biology 2024, Vol.15, No.1, 12-21 http://bioscipublisher.com/index.php/gab 13 This study also discusses the current challenges of GWAS in improving corn disease resistance, such as functional verification of candidate genes, the impact of environment and genotype interactions, and the challenges of big data analysis. At the same time, future research directions are looked forward to, including using multi-omics data to improve the accuracy of GWAS, and accelerating the development of disease-resistant corn varieties by integrating genetic resources and new breeding technologies. This study aims to review the application of GWAS in corn disease resistance research and discuss the entire process from theoretical basis to practical application. The article first reviews the background of corn disease resistance research and the basic principles of genome-wide association studies, then details the successful cases of identifying corn disease resistance genes through GWAS, and discusses how these findings can be translated into practical breeding strategies. Finally, the challenges and future development directions of GWAS in improving corn disease resistance were discussed, aiming to provide scientific basis and new ideas for corn disease resistance breeding. Through this structural arrangement, this study hopes to provide a comprehensive perspective for corn disease resistance research and breeding practice. 1 Theoretical Basis of GWAS in Research on Corn Disease Resistance 1.1 Principles and methods of GWAS Genome-wide association studies (GWAS) is a powerful genetic research method that uses statistical methods to find associations between genetic variations and phenotypic traits. The core principle of this method is based on the theory of population genetics, that is, in natural populations, there may be a correlation between specific genetic variations (such as single nucleotide polymorphisms, SNPs) and variations in certain phenotypic traits. By analyzing genetic variation and phenotypic data from a large number of samples, GWAS can identify genes or gene regions related to target traits across the entire genome. The key technical steps of GWAS mainly include sample collection and genotype determination, accurate measurement of phenotypic data, statistical analysis, and verification of associated signals. First, researchers need to collect a sufficient number of samples and conduct genotype determination on the samples through high-throughput sequencing technology or gene chip technology to obtain a large amount of genetic marker information. Subsequently, precise measurement of phenotypic traits in each sample is critical to increase the accuracy of GWAS in discovering true association signals. After the data is prepared, the association between genetic markers and phenotypes is analyzed through statistical analysis methods (such as linear mixed models) to identify genetic variants associated with the target traits. Finally, the association signals discovered by GWAS are verified through further genetic and functional studies to ensure their true role in the target traits (Zhang, 2017). In plant disease resistance research, GWAS are widely used to identify genes or gene regions that control disease resistance traits. Since plant disease resistance traits are often complex traits controlled by multiple genes, traditional genetic analysis methods have limitations in the study of these traits. GWAS can systematically explore genetic variations related to disease resistance across the entire genome without knowing the gene function in advance, providing an effective method for revealing the genetic basis of plant disease resistance. GWAS can not only discover known disease resistance genes, but also reveal new and unexpected disease resistance-related genes or gene regions, which greatly promotes the understanding of plant disease resistance mechanisms and the development of disease-resistant breeding materials. 1.2 Genetic background of corn disease resistance genes Genome-wide association studies (GWAS) is a powerful genetic research tool that identifies effects by analyzing genome-wide associations between genetic markers (such as single nucleotide polymorphisms, SNPs) and specific traits. Genes or gene regions for these traits. This method is particularly suitable for studying the genetic basis of complex traits, such as disease resistance in corn, which is a typical quantitative trait that is jointly affected by multiple genes and environmental factors.
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