Integrating artificial intelligence and high-throughput phenotyping for crop improvement

Crop improvement is crucial for addressing the global challenges of food security and sustainable agriculture.Recent advancements in high-throughput phenotyping(HTP)technologies and artificial intelligence(AI)have revolutionized the field,enabling rapid and accurate assessment of crop traits on a large scale.The integration of AI and machine learning algorithms with HTP data has unlocked new opportunities for crop improvement.AI algorithms can analyze and interpret large datasets,and extract meaningful patterns and correlations between phenotypic traits and genetic factors.These technologies have the potential to revolutionize plant breeding programs by providing breeders with efficient and accurate tools for trait selection,thereby reducing the time and cost required for variety development.However,further research and collaboration are needed to overcome the existing challenges and fully unlock the power of HTP and AI in crop improvement.By leveraging AI algorithms,researchers can efficiently analyze phenotypic data,uncover complex patterns,and establish predictive models that enable precise trait selection and crop breeding.The aim of this review is to explore the transformative potential of integrating HTP and AI in crop improvement.This review will encompass an in-depth analysis of recent advances and applications,highlighting the numerous benefits and challenges associated with HTP and AI.

Wild Barley,Hordeum spontaneum,a Genetic Resource for Crop Improvement in Cold and Arid Regions

Food security in cold and arid regions in the world is threatened by stressful and unpredictable environments.The sus-tainable and economically viable solution for increasing stability of food productivity in cold and arid regions is genetic improvement of crops towards high resistance to abiotic stresses,mainly cold and drought resistance.It is often empha-sized that crop genetic improvement lies in exploiting the gene pools of the wild relatives of the crop plant.Wild barley,H.spontaneum,the progenitor of cultivated barley,is a selfing annual grass of predominantly Mediterranean and Irano-Turanian distribution that penetrates into desert environments where it maintains stable populations.Wild barley is also found in cold regions,such as in Tibet.The adaptation of wild barley to the arid region in Israel and Jordan,and the cold region in Tibet has accumulated rich genetic diversities for drought,salt,and cold resistances in wild barley,which is the genetic resource for barley and other crop improvement in arid and cold regions.These genetic diversities are revealed by allozymes,DNA-based molecular markers,and morphological and physiological traits of wild barley plants.Quantita-tive trait loci(QTLs) related to drought resistance were identified in wild barley via the QTL mapping approach.Drought resistance genes such as dehydrins,hsdr4,and eibi1 were identified in wild barley based on the candidate gene approach,gene differential expression approach,and molecular genetic approach,respectively.Genetics and genomics of wild bar-ley cold resistance have not been exploited yet,remaining a huge treasure for future crop improvement of cold resistance.Advanced backcross QTL analysis,the introgression libraries based on wild barley as donors,a QTL approach based on wide crosses using wild barley,and positional cloning of natural QTLs will play prevailing roles to help us understand the molecular control of cold and drought tolerance.Integration of QTL information into a breeding pipeline aimed at im-proving tolerance to cold and drought will be achieved within a multidisciplinary context.

Cultivating potential:Harnessing plant stem cells for agricultural crop improvement

Meristems are stem cell-containing structures that produce all plant organs and are therefore important targets for crop improvement.Developmental regulators control the balance and rate of cell divisions within the meristem.Altering these regulators impacts meristem architecture and,as a consequence,plant form.In this review,we discuss genes involved in regulating the shoot apical meristem,inflorescence meristem,axillary meristem,root apical meristem,and vascular cambium in plants.We highlight several examples showing how crop breeders have manipulated developmental regulators to modify meristem growth and alter crop traits such as inflorescence size and branching patterns.Plant transformation techniques are another innovation related to plant meristem research because they make crop genome engineering possible.We discuss recent advances on plant transformation made possible by studying genes controlling meristem development.Finally,we conclude with discussions about how meristem research can contribute to crop improvement in the coming decades.

Integrating machine learning and genome editing for crop improvement

Genome editing is a promising technique that has been broadly utilized for basic gene function studies and trait improvements.Simultaneously,the exponential growth of computational power and big data now promote the application of machine learning for biological research.In this regard,machine learning shows great potential in the refinement of genome editing systems and crop improvement.Here,we review the advances of machine learning to genome editing optimization,with emphasis placed on editing efficiency and specificity enhancement.Additionally,we demonstrate how machine learning bridges genome editing and crop breeding,by accurate key site detection and guide RNA design.Finally,we discuss the current challenges and prospects of these two techniques in crop improvement.By integrating advanced genome editing techniques with machine learning,progress in crop breeding will be further accelerated in the future.

Genome editing for plant research and crop improvement

The advent of clustered regularly interspaced short palindromic repeat(CRISPR) has had a profound impact on plant biology, and crop improvement. In this review, we summarize the state-of-the-art development of CRISPR technologies and their applications in plants, from the initial introduction of random small indel(insertion or deletion) mutations at target genomic loci to precision editing such as base editing, prime editing and gene targeting. We describe advances in the use of class 2, types II, V, and VI systems for gene disruption as well as for precise sequence alterations, gene transcription, and epigenome control.

CRISPR/Cas: a Nobel Prize award-winning precise genome editing technology for gene therapy and crop improvement

Since it was first recognized in bacteria and archaea as a mechanism for innate viral immunity in the early 2010 s,clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)has rapidly been developed into a robust,multifunctional genome editing tool with many uses.Following the discovery of the initial CRISPR/Cas-based system,the technology has been advanced to facilitate a multitude of different functions.These include development as a base editor,prime editor,epigenetic editor,and CRISPR interference(CRISPRi)and CRISPR activator(CRISPRa)gene regulators.It can also be used for chromatin and RNA targeting and imaging.Its applications have proved revolutionary across numerous biological fields,especially in biomedical and agricultural improvement.As a diagnostic tool,CRISPR has been developed to aid the detection and screening of both human and plant diseases,and has even been applied during the current coronavirus disease 2019(COVID-19)pandemic.CRISPR/Cas is also being trialed as a new form of gene therapy for treating various human diseases,including cancers,and has aided drug development.In terms of agricultural breeding,precise targeting of biological pathways via CRISPR/Cas has been key to regulating molecular biosynthesis and allowing modification of proteins,starch,oil,and other functional components for crop improvement.Adding to this,CRISPR/Cas has been shown capable of significantly enhancing both plant tolerance to environmental stresses and overall crop yield via the targeting of various agronomically important gene regulators.Looking to the future,increasing the efficiency and precision of CRISPR/Cas delivery systems and limiting off-target activity are two major challenges for wider application of the technology.This review provides an in-depth overview of current CRISPR development,including the advantages and disadvantages of the technology,recent applications,and future considerations.

A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement

Gene regulation is central to all aspects of organism growth,and understanding it using large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in crops.However,the connection between massive functional datasets and trait-associated gene discovery for crop improvement is still lacking.In this study,we constructed a wheat integrative gene regulatory network(wGRN)by combining an updated genome annotation and diverse complementary functional datasets,including gene expression,sequence motif,transcription factor(TF)binding,chromatin accessibility,and evolutionarily conserved regulation.wGRN contains 7.2 million genome-wide interactions covering 5947 TFs and 127439 target genes,which were further verified using known regulatory relationships,condition-specific expression,gene functional information,and experiments.We used wGRN to assign genome-wide genes to 3891 specific biological pathways and accurately prioritize candidate genes associated with complex phenotypic traits in genome-wide association studies.In addition,wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution networks.We further unveiled novel regulators that enhance the power of spike phenotypic trait prediction using machine learning and contribute to the spike phenotypic differences among modern wheat accessions.Finally,we developed an interactive webserver,wGRN(http://wheat.cau.edu.cn/wGRN),for the community to explore gene regulation and discover trait-associated genes.Collectively,this community resource establishes the foundation for using large-scale functional datasets to guide trait-associated gene discovery for crop improvement.

Plant synthetic epigenomic engineering for crop improvement

Efforts have been directed to redesign crops with increased yield,stress adaptability,and nutritional value through synthetic biology—the application of engineering principles to biology.A recent expansion in our understanding of how epigenetic mechanisms regulate plant development and stress responses has unveiled a new set of resources that can be harnessed to develop improved crops,thus heralding the promise of“synthetic epigenetics.”In this review,we summarize the latest advances in epigenetic regulation and highlight how innovative sequencing techniques,epigenetic editing,and deep learning-driven predictive tools can rapidly extend these insights.We also proposed the future directions of synthetic epigenetics for the development of engineered smart crops that can actively monitor and respond to internal and external cues throughout their life cycles.

CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement

The central dogma(CD)of molecular biology is the transfer of genetic information from DNA to RNA to protein.Major CD processes governing genetic flow include the cell cycle,DNA replication,chromosome packaging,epigenetic changes,transcription,posttranscriptional alterations,translation,and posttranslational modifications.The CD processes are tightly regulated in plants to maintain genetic integrity throughout the life cycle and to pass genetic materials to next generation.Engineering of various CD processes involved in gene regulation will accelerate crop improvement to feed the growing world population.CRISPR technology enables programmable editing of CD processes to alter DNA,RNA,or protein,which would have been impossible in the past.Here,an overview of recent advancements in CRISPR tool development and CRISPR-based CD modulations that expedite basic and applied plant research is provided.Furthermore,CRISPR applications in major thriving areas of research,such as gene discovery(allele mining and cryptic gene activation),introgression(de novo domestication and haploid induction),and application of desired traits beneficial to farmers or consumers(biotic/abiotic stress-resilient crops,plant cell factories,and delayed senescence),are described.Finally,the global regulatory policies,challenges,and prospects for CRISPR-mediated crop improvement are discussed.

High-Throughput Phenotyping:A Platform to Accelerate Crop Improvement

Development of high-throughput phenotyping technologies has progressed considerably in the last 10 years.These technologies provide precise measurements of desired traits among thousands of field-grown plants under diversified environments;this is a critical step towards selection of better performing lines as to yield,disease resistance,and stress tolerance to accelerate crop improvement programs.High-throughput phenotyping techniques and platforms help unrave-ling the genetic basis of complex traits associated with plant growth and development and targeted traits.This review focuses on the advancements in technologies involved in high-throughput,field-based,aerial,and unmanned platforms.Development of user-friendly data management tools and softwares to better understand phenotyping will increase the use of field-based high-throughput techniques,which have potential to revolutionize breeding strategies and meet the future needs of stakeholders.

Advancing organelle genome transformation and editing for crop improvement

Plant cells contain three organelles that harbor DNA:the nucleus,plastids,and mitochondria.Plastid transformation has emerged as an attractive platformfor the generation of transgenic plants,also referred to as transplastomic plants.Plastid genomes have been genetically engineered to improve crop yield,nutritional quality,and resistance to abiotic and biotic stresses,as well as for recombinant protein production.Despite many promising proof-of-concept applications,transplastomic plants have not been commercialized to date.Sequence-specific nuclease technologies are widely used to precisely modify nuclear genomes,but these tools have not been applied to edit organelle genomes because the efficient homologous recombination system in plastids facilitates plastid genome editing.Unlike plastid transformation,successful genetic transformation of higher plant mitochondrial genome transformation was tested in several research group,but not successful to date.However,stepwise progress has been made in modifying mitochondrial genes and their transcripts,thus enabling the study of their functions.Here,we provide an overview of advances in organelle transformation and genome editing for crop improvement,and we discuss the bottlenecks and future development of these technologies.

A Germplasm Resource Repository:The Book Review of Illustrated Flora of Food Crops and Their Wild Related Plants in China

Illustrated Flora of Food Crops and Their Wild Related Plants in China systematically examines the botanical and morphological characteristics of China's major food crops,such as rice,wheat,corn,sweet potato,potato,mung bean,and buckwheat.Featuring more than 5000 color photos and 200 line drawings,it offers a comparative study that highlights the kinship and internal connections between cultivated and wild species.The book is an invaluable resource for breeders,offering a comprehensive morphological and genetic database that aids in the development of high-yielding,high-quality,and disease-resistant crop varieties.

Improvement of light uniformity by lighting arrangement for standardized crop production

In a commercialized, fully artificial plant factory, artificial luminaire is arranged in a unified way using a general illumination theory, an actual measurement, or an empirical methodology. However, with these methods, lightings are implemented without considering specific optical characteristics of lighting or material characteristics of each component that constructs a cultivation system, resulting in an amount of light that becomes irregular. The amount of lighting is closely related with the growth and quality of crops, and the deviation between points where cultivated crops are located causes quality difference in the produced crops, thus impairing the economic feasibility of a plant factory. In this regard, a simulation to figure out an optimum lighting layout was performed. Arrangements based on the spectrum distribution of light source and reflector materials were implemented to ascertain the distance between lighting and height of lighting and gather information in the pre-treatment process to improve the uniformity of light in the plant cultivation system. Improvement of around 15% in light uniformity is achieved compared with the existing system after the simulation is carried out. This result would reduce the deviation in crop growth to make uniform quality crop production possible.

Camelina sativa,a short gestation oilseed crop with biofuel potential:Opportunities for Indian scenario

Camelina is an oilseed crop which is being commercially produced globally as feedstock for biodiesel.Being a non-edible oil bearing low input crop owing to its low fertilizer and water requirement,fits well for biofuel production.In India,targets for biofuel blending has been set by New Biofuel Policy-2018 and to meet these targets efforts are being made to harness the potential of available feedstock in the country.Among these feedstock,contribution of short gestation oilseed bearing crop has been very important.Camelina has been introduced in India during 2009–10 as experimental crop by DIBER,DRDO.Since then various efforts have made to standardize the production technology of this crop under various agro-climatic regions of the country,crop improvement,oil quality analysis and development of high energy by-products.Camelina has various advantages to offer for Indian biofuel sector.This paper reviews the potential of this crop for Indian Biofuel scenario.

Strategies for Improving Enterprise Standardization Management of Tropical Crop Machinery

There are two categories of tropical crop machinery. One comprises operation machinery that is used for planting, managing and harvesting tropical crops, while the other comprises process machinery for processing tropical crops. Tropical crop machinery is distinguished from other agricultural machinery by the special crops that such machinery cultivates and processes.……

Domestication of Marama Bean in Arid Namibia: Challenges and Opportunities in a Climate Changing Agroecology

Tylosema esculentum (Burch.) A. Schreib. (Marama bean), referred to as marama in sections of this article, is an obligate outcrossing native plant with a yield potential of 2 ton/hectare which grows naturally in the deep sandy soils of the Kalahari Desert. It has adapted to the low precipitation levels in that agro-ecosystem. Marama serves as a staple food for the San and Bantus in that area. In Namibia, in the past you could find wild stands of marama in the Khomas region, Omaheke region, and the Otjozondjupa region without must struggle. It is renowned for its brown seeds, which are rich in high-quality oils and proteins. The tuberous root contains a significant amount of starch. The objective of domesticating orphaned marama is to provide farmers in this climate change-prone region with a viable alternative for food and nutrition security. This program, initiated in 2008 with an open-minded mindset, required swift implementation using harsh and occasionally unconventional methods. To introduce indigenous tools for resource-poor farmers, the domestication program prioritized the utilization of farmer-participatory methodologies. It was crucial to integrate old and new approaches to ensure learning from past and present experiences, leading to innovative solutions. There is little research and development of native crops in Africa because most of the currently cultivates crops were brought for use from abroad. Only a few numbers of indeginous African crops can be named. The arid Kalahari region, susceptible to climate change, necessitates the revival of indigenous crops like marama, which are resilient and well-adapted to the region’s conditions and have thrived for centuries. In many discussions regarding the health and nutrition of Africa, the recommendation to consume traditional foods to avoid exposure to modern foods, which may not be genetically compatible, is frequently emphasized. Regardless of their validity, these opinions must be acknowledged, and steps need to be taken to ensure a positive legacy for future generations. However, this chapter will address the limitations and challenges that exist in this regard. This article will summarize the progress made in the domestication program of the marama bean in Namibia thus far. Furthermore, this article will highlight the challenges that have been faced during the domestication journey for marama bean and other orphaned crops. The domestication program commenced with a broad germplasm collection, characterization, and preselection for breeding. Crop selection in this program was influenced by climate change-related concerns of shorter and uncertain rain seasons, and recurrent droughts. Selection included but was not limited to identifying marama genotypes with superior characteristics, early germination and many seeds per pod were among some of the identified and selected characteristics. The Namibia University of Science and Technology (NUST) has compiled a list of potential marama bean varieties and is currently testing marama seeds in anticipation of their introduction as a new crop alternative with good adaptation to the effects of climate change, since conventional crops like maize underperform due to persistent droughts. Marama bean, if properly developed, holds significant potential to address issues of hunger and malnutrition in arid regions of Southern Africa and other similar territories. The findings presented here are the result of ongoing field research and experiments conducted at multiple sites using superior marama bean varieties.

Graft-induced Inheritable Variation in Mungbean and Its Application in Mungbean Breeding

Graft can induce inheritable variations in the progenies of the scion plants. Seedling of mungbean ( Vigna radiata (L.) Wilczek) was grafted onto the stem of sweet potato ( Ipomoea batatas (L.) Lam.). The growth of the scion was maintained until the scion produced selfed seeds. We sowed the seeds for several generations under normal conditions. Distinct genetic variations appeared in the progenies. Similar variations did not appear in the generations of the scion sowed normally without graft. The variations seemed to be induced by the graft and they inherited steadily. For understanding the possible mechanism of the phenomenon (graft_induced inheritable variation), we analyzed the cytoplasmic and genomic DNA of the variations. The results showed that there was no restriction fragment length polymorphism (RFLP) in the cytoplasmic DNA between the original scion and the variation. However, significant difference between the scion and variation was recognized by random amplified polymorphic DNA (RAPD) analysis. In addition, there was no evidence that indicated the gene transformation from stock to scion. Our results suggest that the non_specific grafting has a pragmatic potential for plant breeding and crop improvement and, the genetic variation seems not to be caused simply by DNA transformation but most likely the stress induced mutation.

Genome Mapping to Enhance Efficient Marker-Assisted Selection and Breeding of the Oil Palm (<i>Elaeis guineensis</i>Jacq.)

The oil palm (Elaeis guineensis Jacq.) is one of the major cultivated crops among the economically important palm species. It is cultivated mainly for its edible oil. For a perennial crop like oil palm, the use of Marker Assisted Selection (MAS) techniques helps to reduce the breeding cycle and improve the economic products. Genetic and physical maps are important for sequencing experiments since they show the exact positions of genes and other distinctive features in the chromosomal DNA. This review focuses on the role of genome mapping in oil palm breeding. It assesses the role of genome mapping in oil palm breeding and discusses the major factors affecting such mapping. Generating a high-density map governed by several factors, for instance, marker type, marker density, number of mapped population, and software used are the major issues treated. The general conclusion is that genome mapping is pivotal in the construction of a genetic linkage map. It helps to detect QTL and identify genes that control quantitative traits in oil palm. In perspective, the use of high-density molecular markers with a large number of markers, a large number mapping population, and up-to-date software is necessary for oil palm genome mapping.

Here comes the sun:How optimization of photosynthetic light reactions can boost crop yields

Photosynthesis started to evolve some 3.5 billion years ago CO;is the substrate for photosynthesis and in the past 200-250 years,atmospheric levels have approximately doubled due to human industrial activities.However,this time span is not sufficient for adaptation mechanisms of photosynthesis to be evolutionarily manifested.Steep increases in human population,shortage of arable land and food,and climate change call for actions,now.Thanks to substantial research efforts and advances in the last century,basic knowledge of photosynthetic and primary metabolic processes can now be translated into strategies to optimize photosynthesis to its full potential in order to improve crop yields and food supply for the future.Many different approaches have been proposed in recent years,some of which have already proven successful in different crop species.Here,we summarize recent advances on modifications of the complex network of photosynthetic light reactions.These are the starting point of all biomass production and supply the energy equivalents necessary for downstream processes as well as the oxygen we breathe.