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.

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.

Non-Targeted Metabolomics Reveals the Metabolic Alterations in Response to Artificial Selective Breeding in the Fast-Growing Strains of Pacific Oyster

Pacific oyster(Crassostrea gigas)is one of the most important mollusks cultured all around the world.Selective breeding programs of Pacific oysters in China is initiated since 2006 and developed the genetically improved strain with fast-growing trait.However,little is known about the metabolic signatures of the fast-growing trait.In the present study,the non-targeted metabolomics was performed to analyze the metabolic signatures of adductor muscle tissue in one-year old Pacific oysters from fast-growing strain and the wild population.A total of 7767 and 10174 valid peaks were extracted and quantified in ESI^(+)and ESI^(−)modes,resulting in 399 and 381 annotated metabolites,respectively.PCA and OPLS-DA revealed that considerable separation among samples from fastgrowing strain and wild population,suggesting the differences in metabolic signatures.Meanwhile,81 significantly different metabolites(SDMs)were identified in the comparisons between fast-growing strain and wild population,based on the strict thresholds.It was found that there were highly correlation and conserved coordination among these SDMs.KEGG enrichment analysis indicated that the SDMs were tightly related to pantothenate and CoA biosynthesis,steroid hormone biosynthesis,riboflavin metabolism,and arginine and proline metabolism.Of them,the CoA biosynthesis and metabolism,affected by pantetheine and pantothenic acid,might be important for the growth of Pacific oysters under artificial selective breeding.The study provides the comprehensive views of metabolic signatures in response to artificially selective breeding,and is helpful to better understand the molecular mechanism of fastgrowing traits in Pacific oysters.

Genomic signatures of selection,local adaptation and production type characterisation of East Adriatic sheep breeds

Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations.Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production(carcass,wool and milk yield).Therefore,eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation(EAS),are generally considered as multipurpose breeds(milk,meat and wool),not specialised for a particular type of production,but known for their robustness and resistance to certain environmental conditions.Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures,decipher their biological and productive functionality,and provide a"genomic"characterization of EAS adaptation and determine its production type.Results We identified positive selection signatures in EAS using several methods based on reduced local variation,linkage disequilibrium and site frequency spectrum(eROHi,iHS,nSL and CLR).Our analyses identified numerous genomic regions and genes(e.g.,desmosomal cadherin and desmoglein gene families)associated with environmental adaptation and economically important traits.Most candidate genes were related to meat/production and health/immune response traits,while some of the candidate genes discovered were important for domestication and evolutionary processes(e.g.,HOXa gene family and FSIP2).These results were also confirmed by GO and QTL enrichment analysis.Conclusions Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type,ultimately providing a new opportunity for future breeding programmes.At the same time,the numerous genes identified will improve our understanding of ruminant(sheep)robustness and resistance in the harsh and specific Mediterranean environment.

A review of the pangenome:how it affects our understanding of genomic variation,selection and breeding in domestic animals?

As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of origin and migration,suggesting a possible omission of some population-specific sequences in the current reference genome.Conversely,the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals(core genome)and is also able to display sequence information unique to each individual(variable genome).The progress of pangenome research in humans,plants and domestic animals has proved that the missing genetic components and the identification of large structural variants(SVs)can be explored through pangenomic studies.Many individual specific sequences have been shown to be related to biological adaptability,phenotype and important economic traits.The maturity of technologies and methods such as third-generation sequencing,Tel-omere-to-telomere genomes,graphic genomes,and reference-free assembly will further promote the development of pangenome.In the future,pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals,providing better insights into animal domestication,evolution and breeding.In this review,we mainly discuss how pangenome analysis reveals genetic variations in domestic animals(sheep,cattle,pigs,chickens)and their impacts on phenotypes and how this can contribute to the understanding of species diversity.Additionally,we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.

Genomewide selection for fruit quality traits in apple: breeding insights gained from prediction and postdiction

Many fruit quality traits in apple(Malus domestica Borkh.)are controlled by multiple small-effect quantitative trait loci(QTLs).Genomewide selection(genomic selection)might be an effective breeding approach for highly quantitative traits in woody perennial crops with long generation times like apple.The goal of this study was to determine if genomewide prediction is an effective breeding approach for fruit quality traits in an apple scion breeding program.Representative apple scion breeding germplasm(nindividuals=955),high-quality single nucleotide polymorphism(SNP)data(nSNPs=977),and breeding program fruit quality trait data at harvest were analyzed.Breeding parents‘Honeycrisp’and‘Minneiska’were highly represented.Moderate to high predictive abilities were observed for most fruit quality traits at harvest.For example,when 25%random subsets of the germplasm set were used as training sets,mean predictive abilities ranged from 0.35 to 0.54 across traits.Trait,training and test sets,family size for within family prediction,and number of SNPs per chromosome affected model predictive ability.Inclusion of large-effect QTLs as fixed effects resulted in higher predictive abilities for some traits(e.g.percent red overcolor).Postdiction(i.e.retrospective)analyses demonstrated the impact of culling threshold on selection decisions.The results of this study demonstrate that genomewide selection is a useful breeding approach for certain fruit quality traits in apple.

Breeding Habitat Selection of Reeves’s Pheasant (Syrmaticus reevesii) in Dongzhai National Nature Reserve, Henan Province, China

Reeves＇s Pheasant （Syrmaticus reevesii） is a threatened pheasant species endemic to China. The habitat use of territorial male birds was surveyed by the help of live decoys in a core area of Dongzhai NationaI Nature Reserve. The breeding habitat selection of this pheasant was examined at two scales （115 m and 250 m scale, i.e. 4.15 hm^2 and 19.63 hm^2, respectively）, including the characteristics at distance scale. Investigation was based on line transect, RS and GIS in Dongzhai National Natural Reserve from 2001 to 2003. Moreover, a range of habitat variables were compared between used and control points at each scale, and stepwise logistic regression was applied to select the key scale and the key habitat factors in relation to breeding habitat selection of this bird. Our results stated that the territorial males at Baiyun occurred mostly in mixed forests, followed by fir forests, pine forests, shrubs, and broadleaf forests. The area of conifer forests was the key factor influencing habitat selection of this bird in breeding period at the scales of 115 m and 250 m, and the proximity of farmland was important for habitat selection in breeding seasons. Furthermore, Reeves＇s Pheasants attached great importance to the scale of 115 m. When considering a range of habitat variables at all scales within a multivariate regression, the leading factors having effect on habitat selection in the breeding period were areas of conifer forests at 115 m scale and the distance to farmland. In addition, these above results suggested that strengthening the management of suitable habitat, and optimizing the habitat configuration are important in promoting conservation of this bird. However, it also highlighted the importance of initiating future researches on the conifer forests and their impact on the population of Reeves＇s Pheasants, which would be beneficial to promote the habitat conservation of this pheasant more effectively.

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.

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.

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.

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.

Selection and application of four QTLs for grain protein content in modern wheat cultivars

The grain protein content(GPC)is the key parameter for wheat grain nutritional quality.This study conducted a resampling GWAS analysis using 406 wheat accessions across eight environments,and identified four previously reported GPC QTLs.An analysis of 87 landraces and 259 modern cultivars revealed the loss of superior GPC haplotypes,especially in Chinese cultivars.These haplotypes were preferentially adopted in different agroecological zones and had broad effects on wheat yield and agronomic traits.Most GPC QTLs did not significantly reduce yield,suggesting that high GPC can be achieved without a yield penalty.The results of this study provide a reference for future GPC breeding in wheat using the four identified QTLs.

Epistasis-aware genome-wide association studies provide insights into the efficient breeding of high-yield and high-quality rice

Marker-assisted selection(MAS)and genomic selection(GS)breeding have greatly improved the efficiency of rice breeding.Due to the influences of epistasis and gene pleiotropy,ensuring the actual breeding effect of MAS and GS is still a difficult challenge to overcome.In this study,113 indica rice varieties(V)and their 565 testcross hybrids(TC)were used as the materials to investigate the genetic basis of 12 quality traits and nine agronomic traits.The original traits and general combining ability of the parents,as well as the original traits and midparent heterosis of TC,were subjected to genome-wide association analysis.In total,381 primary significantly associated loci(SAL)and 1,759 secondary SALs that had epistatic interactions with these primary SALs were detected.Among these loci,322 candidate genes located within or nearby the SALs were screened,204 of which were cloned genes.A total of 39 MAS molecular modules that are beneficial for trait improvement were identified by pyramiding the superior haplotypes of candidate genes and desirable epistatic alleles of the secondary SALs.All the SALs were used to construct genetic networks,in which 91 pleiotropic loci were investigated.Additionally,we estimated the accuracy of genomic prediction in the parent V and TC by incorporating either no SALs,primary SALs,secondary SALs or epistatic effect SALs as covariates.Although the prediction accuracies of the four models were generally not significantly different in the TC dataset,the incorporation of primary SALs,secondary SALs,and epistatic effect SALs significantly improved the prediction accuracies of 5(26%),3(16%),and 11(58%)traits in the V dataset,respectively.These results suggested that SALs and epistatic effect SALs identified based on an additive genotype can provide considerable predictive power for the parental lines.They also provide insights into the genetic basis of complex traits and valuable information for molecular breeding in rice.

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.

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.

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.

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.

A Portfolio Selection Method Based on Pattern Matching with Dual Information of Direction and Distance

Pattern matching method is one of the classic classifications of existing online portfolio selection strategies. This article aims to study the key aspects of this method—measurement of similarity and selection of similarity sets, and proposes a Portfolio Selection Method based on Pattern Matching with Dual Information of Direction and Distance (PMDI). By studying different combination methods of indicators such as Euclidean distance, Chebyshev distance, and correlation coefficient, important information such as direction and distance in stock historical price information is extracted, thereby filtering out the similarity set required for pattern matching based investment portfolio selection algorithms. A large number of experiments conducted on two datasets of real stock markets have shown that PMDI outperforms other algorithms in balancing income and risk. Therefore, it is suitable for the financial environment in the real world.

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.