High-throughput phenotyping: Breaking through the bottleneck in future crop breeding

With the rapid development of genetic analysis techniques and crop population size,phenotyping has become the bottleneck restricting crop breeding.Breaking through this bottleneck will require phenomics,defined as the accurate,high-throughput acquisition and analysis of multi-dimensional phenotypes during crop growth at organism-wide levels,ranging from cells to organs,individual plants,plots,and fields.Here we offer an overview of crop phenomics research from technological and platform viewpoints at various scales,including microscopic,ground-based,and aerial phenotyping and phenotypic data analysis.We describe recent applications of high-throughput phenotyping platforms for abiotic/biotic stress and yield assessment.Finally,we discuss current challenges and offer perspectives on future phenomics research.

Construction and Exploration of Ideological and Political Education in Crop Breeding Course

In order to start a new situation for the development of higher education in China,and to achieve the goal of educating people through the whole process and all-round education in colleges and universities,this paper takes Crop Breeding Course as an example,from the characteristics of the curriculum,the history of crop breeding and the ideological and political elements of professional courses,explored the curriculum construction in the aspects of excavation,and summarized the effects of the ideological and political construction of Crop Breeding Course.

Investigation on Breeding Direction of Grain Crops——Taking Henan Province as an example

[Objective] This paper aimed to investigate the breeding direction of grain crops in Henan Province. [Method] Superior varieties are the basis of grain yield-increase, and a proper breeding direction is essential for breeding of superior varieties. According to the actual situation and production requirements in Henan Province, by using statistical data of grain production, this paper analyzed the current situation and influencing factors of grain production in Henan Province, and summarized the breeding direction of current grain production. [Result] The increase of grain output in Henan Province mainly relies on the increase of grain yield per unit area and is achieved based on the increase of wheat and corn yield. There are several main factors affecting grain production in Henan Province, including the frequent meteorological disasters, low resistance to natural disasters, excessive chemical fertilizer inputs, decreased material conversion efficiency, aggravated pollution of the agricultural surface source, imbalanced quality and the distribution of cultivated land, emphasizing yield traits but neglecting related traits during crop breeding pro- cess, unitary dominant varieties resulting from narrow germplasm resources, and reduced grain-planting population with the migration of rural labor force. On this basis, the grain breeding direction is proposed with high yield, high efficiency, adaptability, stress resistance, specificity and safety, to enhance the grain crop breeding level, breed superior varieties, and realize the intensive use of cultivated land, intensive saving of materials, intensive substitution of labor force, intensive protection of environment and intensive efficiency of technologies by adjusting the breeding direction, thus promoting the sustained and stable development of grain production. [Conclusion] This paper provides basis for the breeding of superior varieties of grain crops and improvement of grain output in Henan Province.

Crop Breeding Chips and Genotyping Platforms： Progress, Challenges, and Perspectives

There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing （GBS） platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop mo- lecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype- phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of （a） rapid development in gene discovery of important traits, （b） deepened understanding of quantitative traits through new analytical models and population designs, （c） integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and （d） improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.

Using Interactome Big Data to Crack Genetic Mysteries and Enhance Future Crop Breeding

The functional genes underlying phenotypic variation and their interactions represent“genetic mysteries”.Understanding and utilizing these genetic mysteries are key solutions for mitigating the current threats to agriculture posed by population growth and individual food preferences.Due to advances in highthroughput multi-omics technologies,we are stepping into an Interactome Big Data era that is certain to revolutionize genetic research.In this article,we provide a brief overview of current strategies to explore genetic mysteries.We then introduce the methods for constructing and analyzing the Interactome Big Data and summarize currently available interactome resources.Next,we discuss how Interactome Big Data can be used as a versatile tool to dissect genetic mysteries.We propose an integrated strategy that could revolutionize genetic research by combining Interactome Big Data with machine learning,which involves mining information hidden in Big Data to identify the genetic models or networks that control various traits,and also provide a detailed procedure for systematic dissection of genetic mysteries,Finally,we discuss three promising future breeding strategies utilizing the Interactome Big Data to improve crop yields and quality.

The CRISPR/Cas revolution continues: From efficient gene editing for crop breeding to plant synthetic biology

Since the discovery that nucleases of the bacterial CRISPR(clustered regularly interspaced palindromic repeat)-associated(Cas) system can be used as easily programmable tools for genome engineering,their application massively transformed different areas of plant biology. In this review, we assess the current state of their use for crop breeding to incorporate attractive new agronomical traits into specific cultivars of various crop plants. This can be achieved by the use of Cas9/12 nucleases for double-strand break induction,resulting in mutations by non-homologous recombinatr e-tion. Strategies for performing such experiments à from Rthe design of guide RNA to the use of different transformation technologies à are evaluated. Furtherweive-more, we sum up recent developments regarding the use of nuclease-deficient Cas9/12 proteins, as DNAbinding moieties for targeting different kinds of enzyme activities to specific sites within the genome. Progress in base deamination, transcriptional induction and transcriptional repression, as well as in imaging in plants, is also discussed. As different Cas9/12 enzymes are at hand, the simultaneous application of various enzyme activities, to multiple genomic sites, is now in reach to redirect plant metabolism in a multifunctional manner and pave the way for a new level of plant synthetic biology.

New and Emerging Genomics-based Approaches in Crop Breeding

Rapid progress in genome sequencing has enabled develop- ments of new powerful approaches for fast-forward genetic study. Sequencing-based genotyping and genome-wide associ- ation mapping advanced crop functional genomic study. Genome sequence information can be applied in various ways for crop improvement. One of the goals of this special issue is to review the progresses of developments of functional genomics in three crops of rice, soybean and cotton as well as a vegetable crop of tomato. Rice （Oryza sativa L.） is the staple food for more than half of the world population. Soybean and cotton are the most important economic crops. Solanum represents one of the most diverse plant genera and used widely around the world. In this issue, six papers report development of genomics approaches on crop genetic studies. Below we highlight some of the advances noted in this special issue.

Comparison of Statistical Models for Regional Crop Trial Analysis

Based on the review and comparison of main statistical analysis models for estimating variety-environment cell means in regional crop trials, a new statistical model, LR-PCA composite model was proposed, and the predictive precision of these models were compared by cross validation of an example data. Results showed that the order of model precision was LR-PCA model > AMMI model > PCA model > Treatment Means (TM) model > Linear Regression (LR) model > Additive Main Effects ANOVA model. The precision gain factor of LR-PCA model was 1.55, increasing by 8.4% compared with AMMI.

A Preliminary Study on Systems Engineering-Based Method for the Evaluation of Allelopathic Potential in Crops and Its Application

The objective of this study was to develop a method to assess and analyze the total allelopathic potential of crop germplasm and to test this method on four winter wheat accessions commonly planted in the Loess Plateau. A systems engineering model was developed and used to evaluate the total allelopathic potential of crop cultivars. In addition, a method for quantifying the total allelopathic potential in crop accessions was presented. Total allelopathic potential of four winter wheat accessions from the Loess Plateau was estimated and compared using a systems theory approach. The model assessed allelopathic potential in different parts of the plants from the time wheat turned green in spring until maturity. Results from these models indicated that the four wheat accessions had very weak allelopathic potential. Allelopathic potential declined in the order Xiaoyan 22 〉 Ningdong 1 〉 Fengchan 3 〉 Bima 1. This system engineering evaluation method allows for the assessment of allelopathic potential among crop varieties. It will help plant breeders to select and develop allelopathic crop accessions that combine weed suppression properties with agronomic traits related to yield and quality.

Modern phenomics to empower holistic crop science, agronomy, and breeding research

Crop phenomics enables the collection of diverse plant traits for a large number of samples along different time scales,representing a greater data collection throughput compared with traditional measurements.Most modern crop phenomics use different sensors to collect reflective,emitted,and fluorescence signals,etc.,from plant organs at different spatial and temporal resolutions.Such multi-modal,high-dimensional data not only accelerates basic research on crop physiology,genetics,and whole plant systems modeling,but also supports the optimization of field agronomic practices,internal environments of plant factories,and ultimately crop breeding.Major challenges and opportunities facing the current crop phenomics research community include developing community consensus or standards for data collection,management,sharing,and processing,developing capabilities to measure physiological parameters,and enabling farmers and breeders to effectively use phenomics in the field to directly support agricultural production.

Engineering the future cereal crops with big biological data:toward intelligence-driven breeding by design

How to feed 10 billion human populations is one of the challenges that need to be addressed in the following decades,especially under an unpredicted climate change.Crop breeding,initiating from the phenotype-based selection by local farmers and developing into current biotechnology-based breeding,has played a critical role in securing the global food supply.However,regarding the changing environment and ever-increasing human population,can we breed outstanding crop varieties fast enough to achieve high productivity,good quality,and widespread adaptability?This review outlines the recent achievements in understanding cereal crop breeding,including the current knowledge about crop agronomic traits,newly developed techniques,crop big biological data research,and the possibility of integrating them for intelligence-driven breeding by design,which ushers in a new era of crop breeding practice and shapes the novel architecture of future crops.This review focuses on the major cereal crops,including rice,maize,and wheat,to explain how intelligence-driven breeding by design is becoming a reality.

Creating a novel herbicide-tolerance OsALS allele using CRISPR/Cas9-mediated gene editing

Weeds and weedy rice plague commercial rice fields in many countries. Developingherbicide-tolerance rice is the most efficient strategy to control weed proliferation. CRISPR/Cas9-mediated gene editing, which generates small InDels and nucleotide substitutions atand around target sites using error-prone non-homologous end joining DNA repairing, hasbeen widely adopted for generation of novel crop germplasm with a wide range of geneticvariation in important agronomic traits. We created a novel herbicide-tolerance allele inrice by targeting the acetolactate synthase (OsALS) gene using CRISPR/Cas9-mediated geneediting. The novel allele (G628W) arose from a G-to-T transversion at position 1882 of OsALSand conferred a high level of herbicide tolerance. Transgene-free progeny carryinghomozygous G628W allele were identified and showed agronomic performance similar tothat of wild-type plants, suggesting that the G628W allele is a valuable resource fordeveloping elite rice varieties with strong herbicide tolerance. To promote use of the G628Wallele and to accelerate introgression and/or pyramiding of the G628W allele with other elitealleles, we developed a DNA marker for the G628W allele that accurately and robustlydistinguished homozygous from heterozygous segregants. Our result further demonstratesthe feasibility of CRISPR/Cas9-mediated gene editing in creating novel genetic variation forcrop breeding.

RAPD Assessment of Genetic Diversity of Yunjie(Eruca sativa Mill.)in China

Genetic diversity of Yunjie(.Eruca sativa Mill.)in China was assessed by analyses of RAPD(randomly amplified polymorphic DNA)markers. Twenty native cultivars representing Yunjie-growing eco-types in China were selected as material in this study. Twelve out of the 64 tested random decamer primers were able to identify 131 stable RAPD bands from these Yunjie cultivars. Of them 105 bands, or 80.15% of the total, were polymorphic. Most Yunjie cultivars from the same ecotype had their characteristic DNA bands. Cluster analysis by unweighted pair group method of arithmetic means(UPGMA)suggested that the 20 Yunjie genotypes could be divided into four groups. The genetic distances among the 20 cultivars varied from 0.117 8 between Shuozhou and Shenchi to 0. 499 4 between Hetian and Xiliang. Hetian alone could be a new type of Yunjie identified in China because it had the greatest genetic distance from all the other tested cultivars. These results indicate that Chinese Yunjie have abundant genetic diversity. Classification of Chinese Yunjie based on the RAPD information was in good agreement with the relationships between these Yunjie cultivars in their geographic origins and their plant morphology.

Nuclear Fusion during Early Stage of Microspore Embryogenesis Indicates Chromosome Doubling in Wheat (Triticum aestivum)

Studies of barley and maize indicate that chromosome doubling occurs via nuclear fusion during an early stage of microspore embryogenesis, but the time and mechanism by which chromosome doubling occurs in bread wheat (Triticum aestivum) remains undetermined. The purpose of this study was to determine the relative time during induction culture when chromosome doubling may occur in wheat, and to identify early indicators for doubled haploid microspores. Microspore nuclei were stained with 4’,6-diamidino-2-phenylindole (DAPI) and observed under a fluorescent microscope on the day of isolation, three days after isolation, and six days after isolation. The change in the percentage of microspores containing a single small nucleus, two small nuclei, a single enlarged nucleus, and three or more nuclei was then tracked throughout the six-day period. Ploidy levels were estimated by determining the cross-sectional area and number of nucleoli in microspores containing small and large nuclei then comparing the results of each respective cell-type. The percentage of microspores containing enlarged nuclei increased throughout the six-day test period, and the percentage of binucleated microspores containing small nuclei decreased. Comparison of the changes in average percentage of microspores containing a single small nucleus, binucleated microspores, microspores containing a single large nucleus, and multinucleate microspores on days 0, 3, and 6 indicates that nuclei classified as “small” are likely haploids and nuclei classified as “large” are doubled haploids. The percentage of microspores with enlarged nucleus (nuclei) during the first six days of induction culture could be used as an early indicator for the frequency of chromosome doubling in wheat microspore culture.

Development and Application of Prime Editing in Plants

Clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)-mediated genome editing has greatly accelerated progress in plant genetic research and agricultural breeding by enabling targeted genomic modifications.Moreover,the prime editing system,derived from the CRISPR/Cas system,has opened the door for even more precise genome editing.Prime editing has the capability to facilitate all 12 types of base-to-base conversions,as well as desired insertions or deletions of fragments,without inducing double-strand breaks and requiring donor DNA templet.In a short time,prime editing has been rapidly verified as functional in various plants,and can be used in plant genome functional analysis as well as precision breeding of crops.In this review,we summarize the emergence and development of prime editing,highlight recent advances in improving its efficiency in plants,introduce the current applications of prime editing in plants,and look forward to future prospects for utilizing prime editing in genetic improvement and precision molecular breeding.

Research Progress and Application of Plant Branching

Plant branching development plays an important role in plant morphogenesis(aboveground plant type),the number and angle of branches are important agronomic characters that determine crop plant type.Effective branches determine the number of panicles or pods of crops and then control the yield of crops.With the rapid development of plant genomics and molecular genetics,great progress has been made in the study of branching development.In recent years,a series of important branching-related genes have been validated from Arabidopsis thaliana,rice,pea,tomato and maize mutants.It is reviewed that plant branching development is controlled by genetic elements and plant hormones,such as auxin,cytokinin and lactones(or lactone derivatives),as well as by environment and genetic elements.Meanwhile,shoot architecture in crop breeding was discussed in order to provide theoretical basis for the study of crop branching regulation.

Rice E3 ubiquitin ligases: From key modulators of host immunity to potential breeding applications

To combat pathogen attacks, plants have developed a highly advanced immune system, which requires tight regulation to initiate robust defense responses while simultaneously preventing autoimmunity. The ubiquitin-proteasome system (UPS), which is responsible for degrading excess or misfolded proteins, has vital roles in ensuring strong and effective immune responses. E3 ligases, as key UPS components, play extensively documented roles in rice immunity by modulating the ubiquitination and degradation of downstream substrates involved in various immune signaling pathways. Here, we summarize the crucial roles of rice E3 ligases in both pathogen/microbe/damage-associated molecular pattern-triggered immunity and effector-triggered immunity, highlight the molecular mechanisms by which E3 ligases function in rice immune signaling, and emphasize the functions of E3 ligases as targets of pathogen effectors for pathogenesis. We also discuss potential strategies for application of immunity-associated E3 ligases in breeding of disease-resistant rice varieties without growth penalty. This review provides a comprehensive and updated understanding of the sophisticated and interconnected regulatory functions of E3 ligases in rice immunity and in balancing immunity with growth and development.

The essential roles of sugar metabolism for pollen development and male fertility in plants

Sugar metabolism plays an essential role in plant male reproduction. Defects in sugar metabolism during anther and pollen development often result in genic male sterility(GMS). In this review, we summarize the recent progresses of the sugar metabolism-related GMS genes and their roles during plant anther and pollen development, including callose wall and primexine formation, intine development, pollen maturation and starch accumulation, anther dehiscence, and pollen germination and tube growth. We predict 112 putative sugar metabolic GMS genes in maize based on bioinformatics and RNA-seq analyses, and most of them have peak expression patterns during middle or late anther developmental stages.Finally, we outline the potential applications of sugar metabolic GMS genes in crop hybrid breeding and seed production. This review will deepen our understanding on sugar metabolic pathways in controlling pollen development and male fertility in plants.

Development and application of plant transformation techniques

Genetic transformation is a powerful biotechnology for introducing novel genes into economically important plants from distantly-related plants or even unrelated species such as microbes and animals.This feat is impossible to be achieved by conventional breeding techniques.Development of transgenic plants has been a controversial subject since 1971 when the first genetically modified organism（GMO）was developed（James and Krattiger1996）.

Breeding New Crops

Chinese scientists have developed new crop species that contribute to people’s quality of life and food