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.

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.

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.

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.

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.

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 and Application Techniques of a New Rice Variety Liliang-you 3822 with High Yield and Disease Resistance

Liliangyou 3822 is a novel indica hybrid rice variety that exhibits disease resistance,high yield,lodging resistance,and late maturity.It employs a self-selected two-line sterile line,Li 38S,and a self-selected restorer line,R22.This variety was subjected to a regional test of indica late-maturing groups in the middle and lower reaches of the Yangtze River in 2020.The results demonstrated that the average yield of the variety was 9.95 t/hm 2,which was 10.67%higher than that of the control Fengliangyou 4,indicating a highly significant yield increase.In the continuous test in 2021,the average yield was 9.74 t/hm 2,representing a 6.52%increase over the control,which also exhibited a significant increase.Finally,the average yield of the two years regional test was 9.84 t/hm 2,which was 8.58%higher than that of the control.In the 2021 production test,the average yield of the variety was 9.32 t/hm 2,which was 12.19%higher than that of the control,indicating a remarkably significant yield increase.In 2022,the variety was validated by the National Crop Variety Approval Committee(GSD 20220143).

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.

The complete reference genome for grapevine (Vitis vinifera L.) genetics and breeding

Grapevine is one of the most economically important crops worldwide.However,the previous versions of the grapevine reference genome tipically consist of thousands of fragments with missing centromeres and telomeres,limiting the accessibility of the repetitive sequences,the centromeric and telomeric regions,and the study of inheritance of important agronomic traits in these regions.Here,we assembled a telomere-to-telomere(T2T)gap-free reference genome for the cultivar PN40024 using PacBio HiFi long reads.The T2T reference genome(PN_T2T)is 69 Mb longer with 9018 more genes identified than the 12X.v0 version.We annotated 67%repetitive sequences,19 centromeres and 36 telomeres,and incorporated gene annotations of previous versions into the PN_T2T assembly.We detected a total of 377 gene clusters,which showed associations with complex traits,such as aroma and disease resistance.Even though PN40024 derives from nine generations of selfing,we still found nine genomic hotspots of heterozygous sites associated with biological processes,such as the oxidation–reduction process and protein phosphorylation.The fully annotated complete reference genome therefore constitutes an important resource for grapevine genetic studies and breeding programs.

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.

Development of a target capture sequencing SNP genotyping platform for genetic analysis and genomic breeding in rapeseed

Rapeseed(Brassica napus)is an oil crop grown worldwide,making it a key plant species in molecular breeding research.However,the complexity of its polyploid genome increases sequencing costs and reduces sequencing accuracy.Target capture coupled with high-throughput sequencing is an efficient approach for detecting genetic variation at genomic regions or loci of interest.In this study,588 resequenced accessions of rapeseed were used to develop a target capture sequencing SNP genotyping platform named BnaPan50T.The platform comprised 54,765,with 54,058 resequenced markers from the pan-genome,and 855 variant trait-associated markers for 12 agronomic traits.The capture quality of BnaPan50T was demonstrated well in 12 typical accessions.Compared with a conventional genotyping array,BnaPan50T has a high SNP density and a high proportion of SNPs in unique physical positions and in annotated functional genes,promising wide application.Target capture sequencing and wholegenome resequencing in 90 doubled-haploid lines yielded 60%specificity,78%uniformity within tenfold coverage range,and 93%genotyping accuracy for the platform.BnaPan50T was used to construct a genetic map for quantitative trait loci(QTL)mapping,identify 21 unique QTL,and predict several candidate genes for yield-related traits in multiple environments.A set of 132 core SNP loci was selected from BnaPan50T to construct DNA fingerprints and germplasm identification resources.This study provides genomics resources to support target capture sequencing,genetic analysis and genomic breeding of rapeseed.

Rape Breeding and Its Intellectual Property Protection in China

Rape is the third largest oil crop in the world and the first one in China.The national average rapeseed yield is only 2077.5 kg/hm^(2),and the rapeseed oil yield is 894 kg/hm^(2).This paper introduced the main types,germplasm resources,breeding bases and breeding progress of Chinese rape,and studied its high-quality varieties,breeding patents and new varieties of agricultural plants.We analyzed the main problems such as serious loss of germplasm resources in Brassica campestris L.and Brassica juncea(L.)Czern.et Coss and weak"agricultural chip"in rape field,and put forward strategies such as strengthening the protection of rape germplasm resources,encouraging the development of"agricultural chip"in rape industry clusters with national advantages and characteristics,and strengthening the protection of agricultural intellectual property rights.

Rice3K56 is a high-quality SNP array for genome-based genetic studies and breeding in rice(Oryza sativa L.)

Single nucleotide polymorphism(SNP)genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants.In this study,a highquality and custom-designed Rice3K56 SNP array was developed with the resequencing data of 3024 rice accessions worldwide,which was then tested extensively in 192 representative rice samples.Printed on the Gene Titan chips of Affymetrix Axiom each containing 56,606 SNP markers,the Rice3K56 array has a high genotyping reliability(99.6%),high and uniform genome coverage(an average of 6.7-kb between adjacent SNPs),abundant polymorphic information and easy automation,compared with previously developed rice SNP arrays.When applied in rice varietal differentiation,population diversity analysis,gene mapping of 13 complex traits by a genome-wide association study analysis(GWAS),and genome selection experiments in a recombinant inbred line and a multi-parent advanced generation inter-cross populations,these properties of the Rice3K56 array were well demonstrated for its power and great potential to be a highly efficient tool for rice genetic research and genomic breeding.

Breeding design in wheat by combining the QTL information in a GWAS panel with a general genetic map and computer simulation

A large amount of genome-wide association study(GWAS)panels together with quantitative-trait locus(QTL)information associated with breeding-targeted traits have been described in wheat(Triticum aestivum L.).However,the application of mapping results from a GWAS panel to conventional wheat breeding remains a challenge.In this study,we first report a general genetic map which was constructed from 44 published linkage maps.It permits the estimation of genetic distances between any two genetic loci with physical map positions,thereby unifying the linkage relationships between QTL,genes,and genomic markers from multiple genetic populations.Second,we describe QTL mapping in a wheat GWAS panel of 688 accessions,identifying 77 QTL associated with 12 yield and grain-quality traits.Because these QTL have known physical map positions,they could be mapped onto the general map.Finally,we present a design approach to wheat breeding by using known QTL information and computer simulation.Potential crosses between parents in the GWAS panel may be evaluated by the relative frequency of the target genotype,trait correlations in simulated progeny populations,and genetic gain of selected progenies.It is possible to simultaneously improve yield and grain quality by suitable parental selection,progeny population size,and progeny selection scheme.Applying the design approach will allow identifying the most promising crosses and selection schemes in advance of the field experiment,increasing predictability and efficiency in wheat breeding.

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.

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.

Abiotic stress tolerance:Genetics,genomics,and breeding

1.Tenth anniversary of The Crop Journal The Crop Journal will be 10 years old in October 2023.The journal is sponsored by the Crop Science Society of China,the Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,and China Science Publishing&Media Group Ltd.(Science Press).It is published by Science Press and Ke Ai (founded by China Science Publishing&Media Ltd.and Elsevier).

Socio-Economic and Technical Characteristics of Beef Cattle Breeding in Ndé Division, West Region of Cameroon

Insight is here provided into the socio-economic and technical characteristics of cattle production in the Ndé Division (West Cameroon region). Using a semi-structured questionnaire, information on the activity was assessed following onsite visits and interviewing breeders. Through a random sampling scheme, 110 breeders in the four subdivisions of the Ndé Division were shadowed. The majority (98.18%) of breeders were men aged 20 to 40 and married (91.82%). They belong to the Mbororo ethnic group, having cumulated more than 10 years in the activity. Most respondents (50.91%) did not attend school and earn their living mainly from livestock (78.18%). Cattle were raised for sale and to feed the breeder’s family (77.27%). The main mode of acquisition of animals was through inheritance (81.82%). The cattle breeds were mostly made up of white Fulani (70%), living in private farms using a combination of stake and barbed wires (67.27%) as fences. The combination of natural fodder and cooking salt was used by most breeders (59.09%) as a daily ration. Reproduction was by natural mating (97.07%). Parasites (internal and external) and foot-and-mouth disease were the main diseases reported by the majority of farmers. Self-treatment (50%) was the main prophylactic measure taken by farmers in case of disease symptoms. Cattle herders faced several challenges, such as insufficient pasture (67.27%), agro-pastoral conflicts (76.36%) and diseases (90.91%). Cattle breeding was rather a widespread activity with no particular restriction.

Genomic basis of selective breeding from the closest wild relative of large-fruited tomato

The long and intricate domestication history of the tomato(Solanum lycopersicum)includes selection sweeps that have not been fully explored,and these sweeps show significant evolutionary trajectories of domestication traits.Using three distinct selection strategies,we represented comprehensive selected sweeps from 53 Solanum pimpinellifolium(PIM)and 166 S.lycopersicum(BIG)accessions,which are defined as pseudo-domestication in this study.We identified 390 potential selection sweeps,some of which had a significant impact on fruit-related traits and were crucial to the pseudo-domestication process.During tomato pseudo-domestication,we discovered a minor–effect allele of the SlLEA gene related to fruit weight(FW),as well as the major haplotypes of fw2.2/cell number regulator(CNR),fw3.2/SlKLUH,and fw11.3/cell size regulator(CSR)in cultivars.Furthermore,18 loci were found to be significantly associated with FW and six fruit-related agronomic traits in genome-wide association studies.By examining population differentiation,we identified the causative variation underlying the divergence of fruit flavonoids across the large-fruited tomatoes and validated BRI1-EMS-SUPPRESSOR 1.2(SlBES1.2),a gene that may affect flavonoid content by modulating the MYB12 expression profile.Our results provide new research routes for the genetic basis of fruit traits and excellent genomic resources for tomato genomics-assisted breeding.

Combined genome-wide association studies and expression quantitative trait locus analysis uncovers a genetic regulatory network of floral organ number in a tree peony (Paeonia suffruticosa Andrews) breeding population

Great progress has been made in our understanding of floral organ identity determination and its regulatory network in many species;however,the quantitative genetic basis of floral organ number variation is far less well understood for species-specific traits from the perspective of population variation.Here,using a tree peony(Paeonia suffruticosa Andrews,Paeoniaceae)cultivar population as a model,the phenotypic polymorphism and genetic variation based on genome-wide association studies(GWAS)and expression quantitative trait locus(eQTL)analysis were analyzed.Based on 24 phenotypic traits of 271 representative cultivars,the transcript profiles of 119 cultivars were obtained,which indicated abundant genetic variation in tree peony.In total,86 GWAS-related cis-eQTLs and 3188 trans-eQTL gene pairs were found to be associated with the numbers of petals,stamens,and carpels.In addition,19 floral organ number-related hub genes with 121 cis-eQTLs were obtained by weighted gene co-expression network analysis,among which five hub genes belonging to the ABCE genes of the MADS-box family and their spatial–temporal co-expression and regulatory network were constructed.These results not only help our understanding of the genetic basis of floral organ number variation during domestication,but also pave the way to studying the quantitative genetics and evolution of flower organ number and their regulatory network within populations.