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.

Corrigendum to“Migration pattern of a population of Barn Swallows(Hirundo rustica)breeding in East Asian tropical region”[Avian Res.15(2024)100192]

The authors regret that the caption of Fig.4 should be replaced as below.

Creating large EMS populations for functional genomics and breeding in wheat

Wheat germplasm is a fundamental resource for basic research,applied studies,and wheat breeding,which can be enriched normally by several paths,such as collecting natural lines,accumulating breeding lines,and introducing mutagenesis materials.Ethyl methane sulfonate(EMS)is an alkylating agent that can effectively introduce genetic variations in a wide variety of plant species.In this study,we created a million-scale EMS population(MEP)that started with the Chinese wheat cultivars‘Luyan 128’,‘Jimai 38’,‘Jimai 44’,and‘Shannong 30’.In the M1 generation,the MEP had numerous phenotypical variations,such as>3,000 chlorophyll-deficient mutants,2,519 compact spikes,and 1,692 male sterile spikes.There were also rare mutations,including 30 independent tillers each with double heads.Some M1 variations of chlorophyll-deficiency and compact spikes were inheritable,appearing in the M2 or M3 generations.To advance the entire MEP to higher generations,we adopted a single-seed descendent(SSD)approach.All other seed composites of M2 were used to screen other agronomically important traits,such as the tolerance to herbicide quizalofop-P-methyl.The MEP is available for collaborative projects,and provides a valuable toolbox for wheat genetics and breeding for sustainable agriculture.

Rice Heat Tolerance Breeding: A Comprehensive Review and Forward Gaze

The yield potential of rice is seriously affected by heat stress due to climate change. Since rice is a staple food globally, it is imperative to develop heat-resistant rice varieties. Thus, a thorough understanding of the complex molecular mechanisms underlying heat tolerance and the impact of high temperatures on various critical stages of the crop is needed. Adoption of both conventional and innovative breeding strategies offers a long-term advantage over other methods, such as agronomic practices, to counter heat stress. In this review, we summarize the effects of heat stress, regulatory pathways for heat tolerance, phenotyping strategies, and various breeding methods available for developing heat-tolerant rice. We offer perspectives and knowledge to guide future research endeavors aimed at enhancing the ability of rice to withstand heat stress and ultimately benefit humanity.

Drought-Tolerant Rice at Molecular Breeding Eras:An Emerging Reality

Rice(Oryza sativa L.)stands as the most significantly influential food crop in the developing world,with its total production and yield stability affected by environmental stress.Drought stress impacts about 45%of the world’s rice area,affecting plants at molecular,biochemical,physiological,and phenotypic levels.The conventional breeding method,predominantly employing single pedigree selection,has been widely utilized in breeding numerous drought-tolerant rice varieties since the Green Revolution.With rapid progress in plant molecular biology,hundreds of drought-tolerant QTLs/genes have been identified and tested in rice crops under both indoor and field conditions.Several genes have been introgressed into elite germplasm to develop commercially accepted drought-tolerant varieties,resulting in the development of several drought-tolerant rice varieties through marker-assisted selection and genetically engineered approaches.This review provides up-to-date information on proof-of-concept genes and breeding methods in the molecular breeding era,offering guidance for rice breeders to develop drought-tolerant rice varieties.

Topgrafting as a tool in operational Scots pine breeding

Effective breeding requires multiplying desired genotypes,keeping them at a convenient location to perform crosses more efficiently,and building orchards to generate material for reforestation.While some of these aims can be achieved by conventional grafting involving only rootstock and scion,topgrafting is known to deliver all in a shorter time span.In this study,Scots pine scions were grafted onto the upper and lower tree crowns in two clonal archives with the aim of inducing early female and male strobili produc-tion,respectively.Their survival rates and strobili production were analyzed with generalized linear mixed models.Sur-vival was low(14%)to moderate(41%),and mainly affected by the topgraft genotype,interstock genotype,crown posi-tion and weather conditions in connection with the grafting procedure.Survival was not affected by the cardinal position in the crown(south or north).Male flowering was ample three years after grafting and reached 56%in the first year among live scions,increasing to 62 and 59%in consecutive years.Female flowering was scarce and was 9%at first,later increasing to 26 and 20%of living scions but was strongly affected by the topgraft genotype.In one subset of scions,female flowering was observed 1 year after grafting.Overall,flowering success was mainly affected by the topgraft and interstock genotypes,and secondary growth of scions.This is one of few reports on topgrafting in functional Scots pine clonal archives.

Efficient Breeding of Early-Maturing Rice Cultivar by Editing Hd6 via CRISPR/Cas9

Rice heading date,or flowering time,is important for yield optimization and regional adaptation.While many genes controlling this trait in rice are known,breeders often need only slight adjustments.Our study used the CRISPR/Cas9 method to edit the Hd6 gene in the early-maturing,late-season japonica rice cultivar Nanjing 46(NJ46),creating three mutants with reduced flowering times of 9-12 d under natural conditions in Nanjing city,Jiangsu Province,China.These mutants showed higher Hd3a and RFT1 expression levels without compromising yield or eating and cooking quality,demonstrating that Hd6 gene editing is an effective precision breeding tool for shortening heading date without laborious traditional methods.

Breeding and Seed Reproduction Techniques of a New Tetraploid Common Buckwheat Variety‘Pintianqiao 3’

[Objectives]This study was conducted to actively carry out the breeding of new tetraploid common buckwheat varieties and its supporting breeding techniques.[Methods]Pintianqiao 3 is a new tetraploid common buckwheat variety developed by College of Agriculture of Shanxi Agricultural University and Agricultural Genetic Resources Center of Shanxi Agricultural University,using‘Pintianqiao 1’as the parent,through mutation treatment with 0.2%colchicine aqueous solution,grain selection,plant selection,isolation and identification,variety comparison,regional test and field investigation.The variety has chromosomes 2n=4X=32,and shows a spring sowing period of 101 d and a summer sowing period of 80 d,large flowers and seeds(with a 1000-grain weight of 41.4 g),and good resistance to lodging.[Results]From 2021 to 2022,Pintianqiao 3 participated in the independent joint regional test of common buckwheat varieties in Shanxi Province,and the average yield in 10 test positions was 1.8 kg,equivalent to 1800 kg/hm^(2),which was 8.4%higher than the control.It passed the field investigation conducted by Shanxi provincial expert group for identification of non-major crop varieties in Dongyang and Kelan experimental sites on September 2-3,2022.On January 4,2024,it passed the preliminary examination of Shanxi Provincial Crop Variety Approval Committee.The seed reproduction technique of Pintianqiao 3 including land selection,preparation before sowing,sowing,field management and timely harvesting has been developed.[Conclusions]This study provides technical support for the demonstration and popularization of this new variety.

Seed Storability in Rice: Physiological Foundations, Molecular Mechanisms, and Applications in Breeding

Long-term storage of crop seeds is critical for the conservation of germplasm resources, ensuring food supply, and supporting sustainable production. Rice, as a major food staple, has a substantial stock for consumption and production worldwide. However, its food value and seed viability tend to decline during storage. Understanding the physiological responses and molecular mechanisms of aging tolerance forms the basis for enhancing seed storability in rice. This review outlines the latest progress in influential factors, evaluation methods, and identification indices of seed storability. It also discusses the physiological consequences, molecular mechanisms, and strategies for breeding aging-tolerant rice in detail. Finally, it highlights challenges in seed storability research that require future attention. This review offers a theoretical foundation and research direction for uncovering the mechanisms behind seed storability and breeding aging-tolerant rice.

Long-term trends in the abundance and breeding performance in Adélie penguins:the Argentine Ecosystem Monitoring Program

In this work,we report long-term trends in the abundance and breeding performance of Adélie penguins(Pygoscelis adeliae)nesting in three Antarctic colonies(i.e.,at Martin Point,South Orkneys Islands;Stranger Point/Cabo Funes,South Shetland Islands;and Esperanza/Hope Bay in the Antarctic Peninsula)from 1995/96 to 2022/23.Using yearly count data of breeding groups selected,we observed a decline in the number of breeding pairs and chicks in crèche at all colonies studied.However,the magnitude of change was higher at Stranger Point than that in the remaining colonies.Moreover,the index of breeding success,which was calculated as the ratio of chicks in crèche to breeding pairs,exhibited no apparent trend throughout the study period.However,it displayed greater variability at Martin Point compared to the other two colonies under investigation.Although the number of chicks in crèche of Adélie penguins showed a declining pattern,the average breeding performance was similar to that reported in gentoo penguin colonies,specifically,those undergoing a population increase(even in sympatric colonies facing similar local conditions).Consequently,it is plausible to assume a reduction of the over-winter survival as a likely cause of the declining trend observed,at least in the Stranger Point and Esperanza colonies.However,we cannot rule out local effects during the breeding season affecting the Adélie population of Martin Point.

Advances in Understanding Cadmium Stress and Breeding of Cadmium-Tolerant Crops

Cadmium(Cd) pollution has emerged as a critical global environmental concern, due to its significant toxicity, environmental persistence, and the pervasiveness of contamination. Significantly, the bioaccumulation of Cd in agricultural crops constitutes a primary vector for its entry into the human diet. This issue warrants urgent attention from both the scientific community and policymakers to develop and implement effective mitigation strategies. This review delves into the physiological impacts of Cd stress on plants, including the suppression of photosynthetic activity, amplification of oxidative stress, and disruptions in mineral nutrient homeostasis. Additionally, the resistance mechanisms deployed by plants in response to Cd stress have been explored, and the prospective contributions of molecular breeding strategies in augmenting crop tolerance to Cd and minimizing its bioaccumulation have been assessed. By integrating and analyzing these findings, we seek to inform future research trajectories and proffer strategic approaches to enhance agricultural sustainability, safeguard human health, and protect environmental integrity.

Feeding Practices and Use of Lysine and Methionine in Pigrationing on Intensified Pig Breeding in the West Center and Hauts Bassins Regions of Burkina Faso

The aim of the study was to assess feeding practices and the use of lysine and methionine in pig rationing on intensified and semi-intensive pig breeding in the Koudougou and Bobo-Dioulasso areas. To this end, a cross-sectional survey was carried out on 87 breeding in these towns. A Discriminant Factorial Analysis (DFA) confirming a k-means classification of the data collected was used to retain 71 breeding divided into three breeding classes: Class A (32.4% of breeding), Class B (14.08%) and Class C (53.52%). The results show that the majority of pig breeders were men between the ages of 36 and 59. Average herd sizes were 35 ± 28;79 ± 42 and 89 ± 21 pigs for Classes A, B and C respectively. The main breeds of pig found on the breeding were crossbred, Large white, local, Landrace and Duroc. Class A (26.1%), B (30%) and C (15.8%) breeders were familiar with both lysine and methionine. Class A breeders distributed feed staggered (65.2%) and in rations (34.8%). Lysine (13%) and methionine (8.7%) were purchased at 5250 FCFA/kg. Those in class B distributed feed staggered (50%) and in the form of rations (50%), in which they incorporated lysine (30%) and methionine (30%) purchased at a cost of 2500 FCFA/kg and 3000 FCFA/kg respectively. Rationing and staggered feeding were practiced by 23.7% and 76.3% of Class C breeders respectively. Only lysine purchased at 3400 FCFA/kg was incorporated into rations by 10.5% of breeders. The high cost of lysine and methionine was incriminated by Class A (100%), B (33.3%) and C (50%) breeders. In conclusion, intensive pig breeding, the practice of rationing and the incorporation of the amino acids lysine and methionine are of ascending importance from classes C, A to B. The high cost of feedstuffs, particularly lysine and methionine, compromises their use in rations, which could have a negative impact on expected breeding performance. The screening and use of feeds rich in and/or enriched with these amino acids, through the development or adaptation of technologies, could improve the efficiency of rations and the productivity of intensive pig breeding in Burkina Faso.

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.

Genotypic effects on accelerated propagation of oil palm breeding materials selected(Elaeis guineensis jacq.)using somatic embryogenesis

Vegetable oil production from oil palm(Elaeis guineensis Jacq.)is an important industry due to the rising demand every year.The somatic embryogenesis culture can propagate oil palm duplicate as parent plant,which can be selected as breeding material to produce new planting germplasm with high production or disease resistance.This study aims to evaluate the genotypic effect of somatic embryogenesis,while immature leaflets were employed as explants.The culture used embryo induction medium based on Murashige and Skoog(MS)modifications that contained 5 mg/L Naphthalene Acetic acid(NAA)and 0.5 mg/L Benzyl Amino Purine(BAP).The genotypic effect was statistically significant in the percentage of callus induction,producing somatic embryos,and germination embryos.In this study,we successfully cloned thirteen oil palm genotypes(GE-02,GE-03,GE-06,GE-07,GE-09,GE-23,GE-24,GE-27,GE-28,GE-32,GE-33,GE-34,and GE-35),with the highest number of somatic embryos formed on GE-27 with a percentage of 70.1%.The cloning was successful in accelerating the propagation of oil palm for materials breeding programs to create new varieties with high production and disease resistance.It is necessary to observation the performance of these clones in the field in terms of mantle flower appearance.

Correlation of gut microorganisms and non-volatile flavor substances provides new insights for breeding Scylla paramamosain

The farming of Scylla paramamosain with specific flavors has a higher commercial value,and the flavors are related to the integrated farming environment and non-volatile flavor substances,while the survival environment is one of the important ways to source gut microorganisms in the organism.In this study,the levels of dominant taxa in the gut flora of S.paramamosain from Mong Cai,Vietnam(VN),Taishan City,Guangdong Province(TS)of China,and Ninghai County,Ningbo City(NB)Zhejiang Province of China converged with those of S.paramamosain from Sanmen County,Ningbo City(CK 1,CK 2,and CK 3)at 28 d of domestication.The top 15 genera with the highest abundance of VN,TS,and NB gut flora were the same as CK 1,CK 2,and CK 3,but with different percentages,and gradually converged to CK 1,CK 2,and CK 3,respectively,at 28 d of domestication.Correlation between intestinal flora and non-volatile flavor substances in the hepatopancreas at the percentage level of relative abundance of bacterial genera found that above 28 d of domestication,Muribaculaceae,Psychrilyobacter,Clostridia_vadinBB 60_group,Halarcobacter Carboxylicivirga,Sediminispirochaeta may be the most important genera affecting flavor amino acids of VN.Sediminispirochaeta,Carboxylicivirga,Halarcobacter,Photobacterium,ZOR 0006,Psychrilyobacter,and Pseudomonas may be the most important genera affecting flavor amino acids of NB.Sediminispirochaeta,Carboxylicivirga,Halarcobacter,Photobacterium,ZOR 0006,Vibrio,and Sphingomonas may be the most important genera affecting flavor amino acids of TS.These results show that the intestinal flora structure of crabs from different areas were domesticated in the same area for at least 28 d before they converged to that of the domesticated crab,and the most important genera affecting the flavor amino acids of TS,VN,and NB were also identified.The results of this study provide a reference and basis for the technique of directional cultivation of the flavor quality of the crab.

Changes in the adult sex ratio of six duck species breeding populations over two decades

Despite all efforts,long-term changes in the adult sex ratios of breeding duck populations are still unclear;this uncertainty is especially true for male-bias populations,which are often under the scrutiny of researchers lacking convenient results for the active protection of endangered species.Species with male-bias populations are usually strongly affected by a decline in population size that leads to a higher extinction risk.In this study,we examined our long-term data of the abundance of breeding populations in six duck species(Mallard Anas platyrhynchos,Gadwall Mareca strepera,Red-crested Pochard Netta rufina,Common Pochard Aythya ferina,Tufted Duck Aythya fuligula,and Common Goldeneye Bucephala clangula)from fishponds in South Bohemia,Czechia,between 2004 and 2022.This evidence was used to assess long-term changes in the adult sex ratio in these breeding populations and investigate the possible effects of the NAO index(North Atlantic Oscillation index)on them,indicating climate conditions in winter.We determined a long-term decrease of the proportion of females in the breeding season in two of the six examined species:Common Pochard and Red-crested Pochard,which is driven by the long-term increase in the number of males in contrast to the decreasing or stable number of females likely caused by different migration behaviours between females and males.In the case of Common Pochard,in breeding populations,we estimated 60-65%of males in the early 2000s rising to 75-80%in the early 2020s.However,we establish no significant effects linked to climate conditions of the previous winter in these species as a crucial cause of the changes of the proportion of females in the breeding population.

Identification of new cotton fiber-quality QTL by multiple genomic analyses and development of markers for genomic breeding

Cotton fiber is one of the main raw materials for the textile industry.In recent years,many cotton fiber quality QTL have been identified,but few were applied in breeding.In this study,a genome wide association study(GWAS)of fiber-quality traits in 265 upland cotton breeding intermediate lines(GhBreeding),combined with genome-wide selective sweep analysis(GSSA)and genomic selection(GS),revealed 25 QTL.Most of these QTL were ignored by only using GWAS.The CRISPR/Cas9 mutants of GhMYB_D13 had shorter fiber,which indicates the credibility of QTL to a certain extent.Then these QTL were verified in other cotton natural populations,5 stable QTL were found having broad potential for application in breeding.Additionally,among these 5 stable QTL,superior genotypes of 4 showed an enrichment in most improved new varieties widely cultivated currently.These findings provide insights for how to identify more QTL through combined multiple genomic analysis to apply in breeding.

A method for Improving the Efficiency of Pear Tree Crossbreeding

In view of the short blooming period of pear tree crossbreeding and the complexity of pollination process, a method that can improve the efficiency of crossbreeding of pear trees was provided. Meanwhile, this method can also be applied to the study of pollen xenia effect, pollination tree selection and pure pollen collection in pear tree cultivation.

3D genome organization and its study in livestock breeding

Eukaryotic genomes are hierarchically packaged into cell nucleus,affecting gene regulation.The genome is organized into multiscale structural units,including chromosome territories,compartments,topologically associating domains(TADs),and DNA loops.The identification of these hierarchical structures has benefited from the development of experimental approaches,such as 3C-based methods(Hi-C,ChIA-PET,etc.),imaging tools(2D-FISH,3D-FISH,Cryo-FISH,etc.)and ligation-free methods(GAM,SPRITE,etc.).In recent two decades,numerous studies have shown that the 3D organization of genome plays essential roles in multiple cellular processes via various mechanisms,such as regulating enhancer activity and promoter-enhancer interactions.However,there are relatively few studies about the 3D genome in livestock species.Therefore,studies for exploring the function of 3D genomes in livestock are urgently needed to provide a more comprehensive understanding of potential relationships between the genome and production traits.In this review,we summarize the recent advances of 3D genomics and its biological functions in human and mouse studies,drawing inspiration to explore the 3D genomics of livestock species.We then mainly focus on the biological functions of 3D genome organization in muscle development and its implications in animal breeding.

Breeding of a New Medium Indica Variety Liangyou 7968 with Good Quality and Disease Resistance

With global warming and frequent occurrence of severe weather,rice diseases are also on the rise.Therefore,the breeding of new rice varieties with disease resistance is still the breeding direction for rice breeding experts."Liangyou 7968"is a new hybrid rice combination with double resistance to bacterial blight and rice blast.This paper introduced the breeding process,characteristics,high-yielding cultivation techniques and high-yielding seed production technical regulations for Liangyou 7968.