Estimating Key Phenological Dates of Multiple Rice Accessions Using Unmanned Aerial Vehicle-Based Plant Height Dynamics for Breeding

Efficient and high-quality estimation of key phenological dates in rice is of great significance in breeding work. Plant height(PH) dynamics are valuable for estimating phenological dates. However, research on estimating the key phenological dates of multiple rice accessions based on PH dynamics has been limited. In 2022, field traits were collected using unmanned aerial vehicle(UAV)-based images across 435 plots, including 364 rice varieties. PH, dates of initial heading(IH) and full heading(FH), and panicle initiation(PI), and growth period after transplanting(GPAT) were collected during the rice growth stage. PHs were extracted using a digital surface model(DSM) and fitted using Fourier and logistic models. Machine learning algorithms, including multiple linear regression, random forest(RF), support vector regression, least absolute shrinkage and selection operator, and elastic net regression, were employed to estimate phenological dates. Results indicated that the optimal percentile of the DSM for extracting rice PH was the 95th(R^(2) = 0.934, RMSE = 0.056 m). The Fourier model provided a better fit for PH dynamics compared with the logistic models. Additionally, curve features(CF) and GPAT were significantly associated with PI, IH, and FH. The combination of CF and GPAT outperformed the use of CF alone, with RF demonstrating the best performance among the algorithms. Specifically, the combination of CF extracted from the logistic models, GPAT, and RF yielded the best performance for estimating PI(R^(2) = 0.834, RMSE = 4.344 d), IH(R^(2) = 0.877, RMSE = 2.721 d), and FH(R^(2) = 0.883, RMSE = 2.694 d). Overall, UAV-based rice PH dynamics combined with machine learning effectively estimated the key phenological dates of multiple rice accessions, providing a novel approach for investigating key phenological dates in breeding work.

Dry Breeding and Dry Planting Techniques for Indica Hybrid Rice in Karst Mountain Areas of Gejiu City

Based on the arable land situation in Gejiu City,upland dry planting of indica hybrid rice is being expanded in Karst mountain areas with a rainfall of over 1400 mm and an altitude of 1100-1600 m to develop grain production.This paper gives a specific description of hybrid rice upland dry seedling technology,upland transplanting technology,fertilization technology,field management,weed prevention and control technology,and disease and pest control.

Artificial selection of the Green Revolution gene Semidwarf 1 is implicated in upland rice breeding

Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution. The Green Revolution gene Semidwarf 1(SD1), which modulates gibberellic acid(GA) biosynthesis, plays a principal role in determining rice plant height. Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production. The plant height mediated by SD1 also favors grain yield under certain conditions. However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production. In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions. In response to dryland environments, rice requires a reduction in plant height to cope with water deficits. Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation. Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem. Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields. In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height. During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height. Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production. All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides further insights concerning greater plant height in upland rice breeding.

Key Techniques of an Ecological Pattern“Planting Rice in One Season and Breeding Red Swamp Crawfish in Three Seasons” for Green Production in Lixiahe Region of Jiangsu Province

Three big field projects, independent irrigation and drainage facilities, and a blocking net, which are auxiliary projects of a green planting and breeding pattern composed of rice and red swamp crawfish （Procambarus clarkii）, spatial and temporal coupling technology of ＂planting rice in one season and breeding red swamp crawfish in three seasons＂, green fertilization technology, green prevention and control technology, control technology of water level, and throwing technology of bait in Lixiahe region of Jiangsu Province were introduced successively, which can provide technical support for the development of ecological planting and breeding patterns and realization of green production in paddy fields.

Breeding against mycorrhizal symbiosis:Modern cotton (Gossypium hirsutum L.) varieties perform more poorly than older varieties except at very high phosphorus supply levels

Cotton (Gossypium hirsutum L.) is an importantfiber cash crop,but its root traits related to phosphorus (P) acquisition,including mycorrhizal root traits,are poorly understood.Eight cotton varieties bred in northwestern China that were released between 1950 and 2013 were grown in pots with or without one arbuscular mycorrhizal fungal (AMF) species(Funneliformis mosseae) at three P supply levels (0,50 and 300 mg P as KH_(2)PO_(4)kg^(-1)).Eleven root traits were measured and calculated after 7 wk of growth.The more recent accessions had smaller root diameters,acquired less P and produced less biomass,indicating an (inadvertent) varietal selection for thinner roots that provided less cortical space for AMF,which then increased the need for a high P fertilizer level.At the two lower P levels,the mycorrhizal plants acquired more P and produced more biomass than non-mycorrhizal plants (3.2 vs.0.9 mg P per plant;1.8 vs.0.9 g biomass per plant at P_(0);14.5 vs.1.7 mg P per plant;and 4.7 vs.1.6 g biomass per plant at P_(50)).At the highest P level,the mycorrhizal plants acquired more P than non-mycorrhizal plants (18.8 vs.13.4 mg per P plant),but there was no difference in biomass (6.2 vs.6.3 g per plant).At the intermediate P level,root diameter was significantly positively correlated with shoot biomass,P concentration and the P content of mycorrhizal plants.The results of our study support the importance of the outsourcing model of P acquisition in the root economics space framework.Inadvertent varietal selection in the last decades,resulting in thinner roots and a lower benefit from AMF,has led to a lower productivity of cotton varieties at moderate P supply (i.e.,when mycorrhizal,the average biomass of older varieties 5.0 g per plant vs.biomass of newer varieties 4.4 g per plant),indicating the need to rethink cotton breeding efforts in order to achieve high yields without very high P input.One feasible way to solve the problem of inadvertent varietal selection for cotton is to be aware of the trade-offs between the root do-it-yourself strategy and the outsourcing towards AMF strategy,and to consider both morphological and mycorrhizal root traits when breeding cotton varieties.

A Preliminary Study on Breeding of Ideal Plant in Millet

To further increase millet yield, the ideal plant in millet has become the goal of high yield breeding for millet. Taking crossbreeding or dynamic breeding technique as dominant and technologies such as modern selection or system selection as subsidiary, progenies with ideal plant are selected by using new germplasms such as Lilvgu and Lizigu with the significant difference in plant type to other cultivars as parents. The ge- netic characteristics of new germplasms in breeding are also emphatically analyzed to summarize the breeding experience of ideal plant, which has been proved that the combination of ideal plant and heterosis utilization is one of the important ways to raise millet yield breakthrough.

Genomic dissection of widely planted soybean cultivars leads to a new breeding strategy of crops in the post-genomic era

Soybeans specially the widely planted cultivars have been dramatically improved in agronomic performance and is well adapted to local planting environments after long-time domestication and breeding.Uncovering the unique genomic features of popular cultivars will help to understand how soybean genomes have been modified through breeding.We re-sequenced 134 soybean cultivars that were released and most widely planted over the last century in China.Phylogenetic analyses established that these cultivars comprise two geographically distinct sub-populations:Northeast China (NE) versus the HuangHuai-Hai River Valley and South China (HS).A total of 309 selective regions were identified as being impacted by geographical origins.The HS sub-population exhibited higher genetic diversity and linkage disequilibrium decayed more rapidly compared to the NE sub-population.To study the association between phenotypic differences and geographical origins,we recorded the vegetative period under different growing conditions for two years,and found that clustering based on the phenotypic data was closely correlated with cultivar geographical origin.By iteratively calculating accumulated genetic diversity,we established a platform panel of cultivars and have proposed a novel breeding strategy named "Potalaization"for selecting and utilizing the platform cultivars that represent the most genetically diversity and the highest available agronomic performance as the "plateau"for accumulating elite loci and traits,breeding novel widely adapted cultivars,and upgrading breeding technology.In addition to providing new genomic information for the soybean research community,the "Potalaization"strategy that we devised will also be practical for integrating the conventional and molecular breeding programs of crops in the post-genomic era.

Germplasm and molecular breeding in horticultural crops

Horticulture is an important part of agricultural planting and production, which is of great significance for enriching human nutrition and beautifying and transforming the human living environment. At present, the area of horticultural crops in China is about 40 million ha, accounting for about onefourth of the national crop planting area, while the production of primary agricultural products is 1 billion tons, and the output value accounts for more than half of the total output value of the planting industry.

Pre-Breeding Genetic Diversity Assessment of Tomato(Solanum lycopersicum L.)Cultivars Based on Molecular,Morphological and Physicochemical Parameters

Appropriate knowledge of the parental cultivars is a pre-requisite for a successful breeding program.This study characterized fruit yield,quality attributes,and molecular variations of ten tomato cultivars during three consecutive generations under greenhouse conditions.Peto 86,Castle Rock,and Red Star cultivars showed the highest fruit yield(kg/plant),total phenolic compounds(TPC),and sap acidity.Principal component analysis categorized the evaluated fruit yield into three groups based on their quality attributes.A robust positive correlation appeared among traits inside each group.A positive correlation was likewise noticed between the first and the second groups.However,a negative correlation was detected between the first,the second and the third group.Molecular profiling,using seven inter-simple sequence repeat(ISSR)primers,produced 60 loci,including 49 polymorphic loci.The molecular analysis also pinpointed the highest genetic similarity(0.92)between P73 and Moneymaker,while the lowest genetic similarity(0.46)was observed between Castle Rock and Moneymaker.The cultivars P73 and Moneymaker showed the lowest genetic distance(2.24),while the highest genetic distance(5.92)was observed between Super Marmand and Peto86,on the one hand,and between Castle Rock and Moneymaker,on the other hand.The chemical analysis of fruit sap indicated the highest levels of TPC,total flavonoids,anthocyanin,ascorbic acid and total soluble solids in Peto 86 and Castle Rock cultivars.Phylogeny analysis of tomato cultivars based on morphological and molecular attributes indicated four distinct clades.Peto 86,Castle Rock,and Red star cultivars can be recommended for the tomato hybridization breeding programs in the future,with other tomato cultivars as potentially high-yielding parents.

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.

Participatory Plant Breeding and Selection Impact on Adoption of Improved Sweetpotato Varieties in Uganda

This study analyzed the impact of participatory plant breeding （PPB） and participatory variety selection （PVS） on the adoption of improved sweetpotato varieties （ISPV） in central Uganda. The study quantitatively assessed how the two approaches influence farmers＇ uptake of the improved sweetpotato varieties and also determined other factors influencing this adoption. This was done by estimating a robust standard errors logit model. Both PPB and PVS positively and significantly influenced the likelihood of adoption of improved sweetpotato varieties at 5% and 10% levels, respectively. Other variables that positively influenced the adoption are extension services, training in sweetpotato production, farming experience, and off-farm income of the household. Farmers who participated in the plant breeding and variety selection processes were 37 and 6.7 times more likely to adopt the improved sweetpotato varieties than those who had not, respectively. Farmers who were trained specifically in sweetpotato production were 8.8 times more likely to adopt the improved varieties than those who had not received this type of training.

Preliminary Study of Mutation Breeding Combining Heavy Ion Beam Irradiation and Plant Tissue Culture in Taraxacum kok-saghyz

Rubber dandelion(Taraxacum Kok-saghyz,TKS)is a valuable alternative source of natural rubber,thus it is very important and urgent to breed new varieties to increase the biomass or natural rubber content in its roots.

Computational tools for plant genomics and breeding

Plant genomics and crop breeding are at the intersection of biotechnology and information technology.Driven by a combination of highthroughput sequencing,molecular biology and data science,great advances have been made in omics technologies at every step along the central dogma,especially in genome assembling,genome annotation,epigenomic profiling,and transcriptome profiling.These advances further revolutionized three directions of development.One is genetic dissection of complex traits in crops,along with genomic prediction and selection.The second is comparative genomics and evolution,which open up new opportunities to depict the evolutionary constraints of biological sequences for deleterious variant discovery.The third direction is the development of deep learning approaches for the rational design of biological sequences,especially proteins,for synthetic biology.All three directions of development serve as the foundation for a new era of crop breeding where agronomic traits are enhanced by genome design.

Improving the phenotypic expression of rice genotypes:Rethinking “intensification” for production systems and selection practices for rice breeding

Intensification in rice crop production is generally understood as requiring increased use of material inputs: water, inorganic fertilizers, and agrochemicals. However, this is not the only kind of intensification available. More productive crop phenotypes, with traits such as more resistance to biotic and abiotic stresses and shorter crop cycles, are possible through modifications in the management of rice plants, soil, water, and nutrients, reducing rather than increasing material inputs. Greater factor productivity can be achieved through the application of new knowledge and more skill, and(initially) more labor, as seen from the System of Rice Intensification(SRI), whose practices are used in various combinations by as many as 10 million farmers on about 4 million hectares in over 50 countries. The highest yields achieved with these management methods have come from hybrids and improved rice varieties, confirming the importance of making genetic improvements. However,unimproved varieties are also responsive to these changes, which induce better growth and functioning of rice root systems and more abundance, diversity, and activity of beneficial soil organisms. Some of these organisms as symbiotic endophytes can affect and enhance the expression of rice plants' genetic potential as well as their phenotypic resilience to multiple stresses, including those of climate change. SRI experience and data suggest that decades of plant breeding have been selecting for the best crop genetic endowments under suboptimal growing conditions, with crowding of plants that impedes their photosynthesis and growth, flooding of rice paddies that causes roots to degenerate and forgoes benefits derived from aerobic soil organisms, and overuse of agrochemicals that adversely affect these organisms as well as soil and human health. This review paper reports evidence from research in India and Indonesia that changes in crop and water management can improve the expression of rice plants' genetic potential, thereby creating more productive and robustphenotypes from given rice genotypes. Data indicate that increased plant density does not necessarily enhance crop yield potential, as classical breeding methods suggest. Developing cultivars that can achieve their higher productivity under a wide range of plant densities—breeding for density-neutral cultivars using alternative selection strategies—will enable more effective exploitation of available crop growth resources. Density-neutral cultivars that achieve high productivity under ample environmental growth resources can also achieve optimal productivity under limited resources, where lower densities can avert crop failure due to overcrowding. This will become more important to the extent that climatic and other factors become more adverse to crop production. Focusing more on which management practices can evoke the most productive and robust phenotypes from given genotypes is important for rice breeding and improvement programs since it is phenotypes that feed our human populations.

The apple REFPOP—a reference population for genomics-assisted breeding in apple

Breeding of apple is a long-term and costly process due to the time and space requirements for screening selection candidates.Genomics-assisted breeding utilizes genomic and phenotypic information to increase the selection efficiency in breeding programs,and measurements of phenotypes in different environments can facilitate the application of the approach under various climatic conditions.Here we present an apple reference population:the apple REFPOP,a large collection formed of 534 genotypes planted in six European countries,as a unique tool to accelerate apple breeding.The population consisted of 269 accessions and 265 progeny from 27 parental combinations,representing the diversity in cultivated apple and current European breeding material,respectively.A high-density genome-wide dataset of 303,239 SNPs was produced as a combined output of two SNP arrays of different densities using marker imputation with an imputation accuracy of 0.95.Based on the genotypic data,linkage disequilibrium was low and population structure was weak.Two well-studied phenological traits of horticultural importance were measured.We found marker–trait associations in several previously identified genomic regions and maximum predictive abilities of 0.57 and 0.75 for floral emergence and harvest date,respectively.With decreasing SNP density,the detection of significant marker–trait associations varied depending on trait architecture.Regardless of the trait,10,000 SNPs sufficed to maximize genomic prediction ability.We confirm the suitability of the apple REFPOP design for genomics-assisted breeding,especially for breeding programs using related germplasm,and emphasize the advantages of a coordinated and multinational effort for customizing apple breeding methods in the genomics era.

Mapping and validation of the epistatic D and P genes controlling anthocyanin biosynthesis in the peel of eggplant (Solanum melongena L.) fruit

Fruit color is an important trait inf luencing the commercial value of eggplant fruits.Three dominant genes(D,P and Y)cooperatively control the anthocyanin coloration in eggplant fruits,but none has been mapped.In this study,two white-fruit accessions(19141 and 19147)and their F2 progeny,with 9:7 segregation ratio of anthocyanin pigmented versus non-pigmented fruits,were used for mapping the D and P genes.A high-density genetic map was constructed with 5270 SNPs spanning 1997.98 cM.Three QTLs were identified,including two genes on chromosome 8 and one on chromosome 10.Gene expression analyses suggested that the SmANS on chromosome 8 and SmMYB1 on chromosome 10 were the putative candidate genes for P and D,respectively.We further identified(1)a SNP leading to a premature stop codon within the conserved PLN03176 domain of SmANS in 19141,(2)a G base InDel in the promoter region leading to an additional cis-regulatory element and(3)a 6-bp InDel within the R2-MYB DNA binding domain of SmMYB1,in 19147.Subsequently,these three variations were validated by PARMS technology as related to phenotypes in the F2 population.Moreover,silencing of SmANS or SmMYB1 in the purple red fruits of F1(E3316)led to inhibition of anthocyanin biosynthesis in the peels.Conversely,overexpression of SmANS or SmMYB1 restored anthocyanin biosynthesis in the calli of 19141 and 19147 respectively.Our findings demonstrated the epistatic interactions underlying the white color of eggplant fruits,which can be potentially applied to breeding of eggplant fruit peel color.

Breeding polyploid Populus:progress and perspective

Populus is a genus of 25−30 species of deciduous flowering plants in the family Salicaceae,which are primarily planted in short-rotation planations for producing timber,pulpwood,wooden products as well as bioenergy feedstock;they are also widely planted in agricultural fields and along roadsides as shelter forest belts for windbreak,decoration,and reduction of pollutants and noise.Moreover,their fast-growth and good adaptation to marginal lands enable them to provide some critical ecosystem services at various phytoremediation sites for land restoration and reclaimation.Thanks to their important roles,breeding for fast growing poplar trees has been one of the most important objectives for nearly a century.One of the most demonstrated,documented achievements in this aspect is polyploid breeding,especially triploid breeding.This paper critically reviews the various techniques used in inducing triploid plants,including natural 2n formation,artificial induction of 2n male and female gemmates through chemical or physical treatments,trait characterization of the triploid and tetraploid breeding populations,unveiling the molecular mechanisms underpinning the significantly improved traits,and identification and selection of the best triploid progenies.This review also recapitulated the challenges and strategies facing the future of triploid breeding in Populus,including amelioration of 2n gamete induction techniques and efficiency,selection of the best parents and identification of the best progrenies,utilization of the huge amount of genomic,transcriptomic,proteomic,metabolomic,and other omics data for selecting parents for improving target traits.