Assessing the conservation impact of Chinese indigenous chicken populations between ex-situ and in-situ using genome-wide SNPs

Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations. In this study, we conducted a comparative analysis of two indigenous Chinese chicken breeds, Gushi and Xichuan black-bone, using whole-genome SNPs to understand their genetic diversity, track changes over time and population structure. The breeds were divided into five conservation populations(GS1, 2010, ex-situ;GS2, 2019, ex-situ;GS3, 2019, in-situ;XB1, 2010, in-situ;and XB2, 2019, in-situ) based on conservation methods and generations. The genetic diversity indices of three conservation populations of Gushi chicken showed consistent trends, with the GS3 population under in-situ strategy having the highest diversity and GS2 under ex-situ strategy having the lowest. The degree of inbreeding of GS2 was higher than that of GS1 and GS3. Conserved populations of Xichuan black-bone chicken showed no obvious changes in genetic diversity between XB1 and XB2. In terms of population structure, the GS3 population were stratified relative to GS1 and GS2. According to the conservation priority, GS3 had the highest contribution to the total gene and allelic diversity in GS breed, whereas the contribution of XB1 and XB2 were similar. We also observed that the genetic diversity of GS2 was lower than GS3, which were from the same generation but under different conservation programs(in-situ and ex-situ). While XB1 and XB2 had similar levels of genetic diversity. Overall, our findings suggested that the conservation programs performed in ex-situ could slow down the occurrence of inbreeding events, but could not entirely prevent the loss of genetic diversity when the conserved population size was small, while in-situ conservation populations with large population size could maintain a relative high level of genetic diversity.

Identification of Fusarium wilt resistance gene SiRLK1 in Sesamum indicum L.

Sesame Fusarium wilt(SFW),caused by Fusarium oxysporum f.sp.sesami(Fos),is one of the most devastating diseases affecting sesame cultivation.Deciphering the genetic control of SFW resistance is pivotal for effective disease management in sesame.An inheritance study on a cross between the highly resistant variety Yuzhi 11 and the highly susceptible accession Sp1 using a Fos pathogenicity group 1 isolate indicated that resistance was conferred by a single dominant allele.The target locus was located in a 1.24 Mb interval on chromosome 3 using a combination of cross-population association mapping and bulked segregant analysis.Fine genetic mapping further narrowed the interval between 21,350 and 21,401 kb.The locus Sindi_0812400 was identified as the SFW resistance gene and officially designated SiRLK1.This gene encodes a specific malectin/receptor-like protein kinase with three putative tandem kinase domains and is considered a kinase fusion protein.Sequence analysis revealed that a high proportion(49.44%)of variants within the locus was located within the kinase domainⅢ,and several of which were evidently associated with the diversity in SFW response,indicating the critical role of kinase domainⅢin expression of disease resistance.These findings provide valuable information for further functional analysis of SFW resistance genes and marker-assisted resistance breeding in sesame.

ZmCYP90D1 regulates maize internode development by modulating brassinosteroid-mediated cell division and growth

Plant height(PH)is associated with lodging resistance and planting density,which is regulated by a complicated gene network.In this study,we identified a spontaneous dwarfing mutation in maize,m30,with decreased internode number and length but increased internode diameter.A candidate gene,ZmCYP90D1,which encodes a member of the cytochrome P450 family,was isolated by map-based cloning.ZmCYP90D1 was constitutively expressed and showed highest expression in basal internodes,and its protein was targeted to the nucleus.A G-to-A substitution was identified to be the causal mutation,which resulted in a truncated protein in m30.Loss of function of ZmCYP90D1 changed expression of hormoneresponsive genes,in particular brassinosteroid(BR)-responsive genes which is mainly involved in cell cycle regulation and cell wall extension and modification in plants.The concentration of typhasterol(TY),a downstream intermediate of ZmCYP90D1 in the BR pathway,was reduced.A haplotype conferring dwarfing without reducing yield was identified.ZmCYP90D1 was inferred to influence plant height and stalk diameter via hormone-mediated cell division and cell growth via the BR pathway.

Fine-mapping of a candidate gene for web blotch resistance in Arachis hypogaea L.

Peanut(Arachis hypogaea L.)is a globally important oil crop.Web blotch is one of the most important foliar diseases affecting peanut,which results in serious yield losses worldwide.Breeding web blotch-resistant peanut varieties is the most effective and economically viable method for minimizing yield losses due to web blotch.In the current study,a bulked segregant analysis with next-generation sequencing was used to analyze an F2:3 segregating population and identify candidate loci related to web blotch resistance.Based on the fine-mapping of the candidate genomic interval using kompetitive allele-specific PCR(KASP)markers,we identified a novel web blotch resistance-related locus spanning approximately 169 kb on chromosome 16.This region included four annotated genes,of which only Arahy.35VVQ3 had a non-synonymous single nucleotide polymorphism in the coding region between the two parents.Two markers(Chr.16.12872635 and Chr.16.12966357)linked to this gene were shown to be co-segregated with the resistance of peanut web blotch by 72 randomly selected recombinant inbred lines(RIL),which could be used in marker-assisted breeding of resistant peanut varieties.

Rapid identification of Psathyrostachys huashanica Keng chromosomes in wheat background based on ND-FISH and SNP array methods

Psathyrostachys huashanica Keng(2n=2x=14,NsNs)is regarded as a valuable wild relative species for common wheat cultivar improvement because of its abundant beneficial agronomic traits.However,although the development of many wheat–P.huashanica-derived lines provides a germplasm base for the transfer of excellent traits,the lag in the identification of P.huashanica chromosomes in the wheat background has limited the study of these lines.In this study,three novel nondenaturing fluorescence in situ hybridization(ND-FISH)-positive oligo probes were developed.Among them,HS-TZ3 and HS-TZ4 could specifically hybridize with P.huashanica chromosomes,mainly in the telomere area,and HS-CHTZ5 could hybridize with the chromosomal centromere area.We sequentially constructed a P.huashanica FISH karyotype and idiogram that helped identify the homologous groups of introduced P.huashanica chromosomes.In detail,1Ns and 2Ns had opposite signals on the short and long arms,3Ns,4Ns,and 7Ns had superposed two-color signals,5Ns and 6Ns had fluorescent signals only on their short arms,and 7Ns had signals on the intercalary of the long arm.In addition,we evaluated different ways to identify alien introgression lines by using low-density single nucleotide polymorphism(SNP)arrays and recommended the SNP homozygosity rate in each chromosome as a statistical pattern.The 15K SNP array is widely applicable for addition,substitution,and translocation lines,and the 40K SNP array is the most accurate for recognizing transposed intervals between wheat and alien chromosomes.Our research provided convenient methods to distinguish the homologous group of P.huashanica chromosomes in a common wheat background based on ND-FISH and SNP arrays,which is of great significance for efficiently identifying wheat–P.huashanica-derived lines and the further application of Ns chromosomes.

Are the two polymorphic sites of anti-Marek’s disease in White Leghorn chickens also suitable for Partridge Shank chickens?

Background:The selection of Marek’s disease(MD)-resistant breeds in Partridge Shank chicken,a popular local chicken breed in Henan Province of China,has practical value.We hypothesized that the two polymorphic sites(rs14527240 located in SMOC1 and GGaluGA156129 located in PTPN3)related to MD resistance in White Leghorn chickens are also applicable to Partridge Shank chickens.Methods:In this experiment,we screened 10 live hens and 2 live roosters with the double GG genotype by genotyping the two sites from 6500 Partridge Shank chickens.Nineteen one-day-old chicks with the double GG genotype were obtained by artificial insemination.Seventy-two one-day-old chickens(19 from the population expansion test and 53 randomly selected from chicken farms)were injected with 2000 plaque-forming units of the Md5 virus strain.After 100 days of infection,all chickens were examined by pathological anatomical examination,histological sectioning,genotyping,and a quantitative polymerase chain reaction of SMOC1 and PTPN3.Results:There was only one site(rs14527240 located in SMOC1)associated with MD in Partridge Shank chickens(p<0.05),but the GG genotype of SMOC1 in Partridge Shank chickens indicated susceptibility to MD.SMOC1 expression in MD-susceptible chickens was also significantly higher than that in MDresistant chickens(p<0.05).Conclusion:Therefore,the MD resistance sites selected from White Leghorn chickens were not completely suitable for Partridge Shank chickens,but they can be used as a reference.This study indicated that SMOC1 plays an important role in screening for MD resistance in poultry.

Integrated top-down and bottom-up proteomics mass spectrometry for the characterization of endogenous ribosomal protein heterogeneity

Ribosomes are abundant,large RNA-protein complexes that are the sites of all protein synthesis in cells.Defects in ribosomal proteins(RPs),including proteoforms arising from genetic variations,alternative splicing of RNA transcripts,post-translational modifications and alterations of protein expression level,have been linked to a diverse range of diseases,including cancer and aging.Comprehensive characterization of ribosomal proteoforms is challenging but important for the discovery of potential disease biomarkers or protein targets.In the present work,using E.coli 70S RPs as an example,we first developed a top-down proteomics approach on a Waters Synapt G2 Si mass spectrometry(MS)system,and then applied it to the HeLa 80S ribosome.The results were complemented by a bottom-up approach.In total,50 out of 55 RPs were identified using the top-down approach.Among these,more than 30 RPs were found to have their N-terminal methionine removed.Additional modifications such as methylation,acetylation,and hydroxylation were also observed,and the modification sites were identified by bottomup MS.In a HeLa 80S ribosomal sample,we identified 98 ribosomal proteoforms,among which multiple truncated 80S ribosomal proteoforms were observed,the type of information which is often overlooked by bottom-up experiments.Although their relevance to diseases is not yet known,the integration of topdown and bottom-up proteomics approaches paves the way for the discovery of proteoform-specific disease biomarkers or targets.

Development of Oligo-GISH kits for efficient detection of chromosomal variants in peanut

Oligo probe staining is a low-cost and efficient chromosome identification technique.In this study,oligo genomic in situ hybridization(Oligo-GISH)technology was established in peanut.Peanut A and B subgenome-specific interspersed repeat(IR)oligo probe sets were developed based on clustering and electronic localization of tandem repeat sequences in the reference genome of Tifrunner.The OligoGISH kit was then used to perform staining of 15 Arachis species.The A-subgenome probe set stained the chromosomes of A-and E-genome Arachis species,the B-subgenome probe set stained those of B-,F-,K-,and E-genome species,and neither set stained those of H-genome species.These results indicate the relationships among the genomes of these Arachis species.The Oligo-GISH kit was also used for batch staining of the chromosomes of 389 seedlings from the irradiated M1generation,allowing 67 translocation and deletion lines to be identified.Subsequent Oligo-FISH karyotyping,FISH using single-copy probe libraries,and trait investigation identified seven homozygous chromosomal variants from the M3generation and suggested that there may be genes on chromosome 4B controlling seed number per pod.These findings demonstrate that the IR probe sets and method developed in this study can facilitate research on distant hybridization and genetic improvement in peanut.

A peptide chain release factor 2a gene regulates maize kernel development by modulating mitochondrial function

Mitochondrial protein translation that is essential for aerobic energy production includes four essential steps of the mitochondrial ribosome cycle,namely,initiation,elongation,termination of the polypeptide,and ribosome recycling.Translation termination initiates when a stop codon enters the A site of the mitochondrial ribosome where it is recognized by a dedicated peptide release factor(RF).However,RFs and mechanisms involved in translation in plant mitochondria,especially in monocotyledons,remain largely unknown.Here,we identified a crumpled kernel(crk5 allele)mutant,with significantly decreased kernel size,100-kernel weight,and an embryo-lethal phenotype.The Crk5 allele was isolated using map-based cloning and found to encode a mitochondrial localization RF2a.As it is an ortholog of Arabidopsis mitochondrial RF2a,we named the gene ZmmtRF2a.ZmmtRF2a is missing the 5th–7th exons in the crk5 resulting in deletion of domains containing motifs GGQ and SPF that are essential for release activity of RF,mitochondrial ribosome binding,and stop codon recognition.Western blot and qRT-PCR analyses indicate that the crk5 mutation results in abnormal mitochondrion structure and function.Intriguingly,we observed a feedback loop in the crk5 with up-regulated transcript levels detected for several mitochondrial ribosome and mitochondrial-related components,in particular mitochondrial complexes CI,CIV,and a ribosome assembly related PPR.Together,our data support a crucial role for ZmmtRF2a in regulation of mitochondrial structure and function in maize.

Production profile and comparison analysis of main toxin components of Fusarium oxysporum f.sp.sesami isolates with different pathogenicity levels

Fusarium wilt is a common fungal disease in sesame caused by Fusarium oxysporum f.sp.sesami(FOS).To determine the toxin production profiles of the FOS isolates with different pathogenicity levels under various culture conditions,we assessed the content variation of fusaric acid(FA)and 9,10-dehydrofusaric acid(9,10-DFA)produced by the four representative FOS isolates.Results indicated that the concentration of FA reached to a maximum of 2848.66μg/mL in Czapek medium,while 9,10-DFA was mainly produced in Richard and Lowcarbon Richard medium.The concentration of 9,10-DFA on Richard culture medium varied from 0μg/mL to 716.89μg/mL.Of the five culture media used in this study,Czapek culture medium was the most conductive to produce FA.FA production was significantly affected by culture medium,culture time,and their interactions.Results suggest that there is no correlation between toxin production and pathogenicity level of FOS isolates.These findings provide key information for the mechanism analysis of FOS-sesame interaction and pathogen control.

A new phase of treasure hunting in plant genebanks

The United Nations has estimated that the world population will surpass 8 billion on Nov.15,2022,and will continue to rise to 11.2 billion by 2100.Considering that agricultural resources are limited,it will be a huge challenge to produce sufficient food to feed such a rapidly rising global population.Furthermore,the ongoing climate changes are adding more pressures on worldwide crop productions.To cope with these problems,it is both imperative and urgent to develop the crop cultivars with higher yield potential,improved nutritional quality,and better resilience to environmental stresses.

Quantitative disease resistance:Multifaceted players in plant defense

In contrast to large-effect qualitative disease resistance,quantitative disease resistance(QDR)exhibits partial and generally durable resistance and has been extensively utilized in crop breeding.The molecular mechanisms underlying QDR remain largely unknown but considerable progress has been made in this area in recent years.In this review,we summarize the genes that have been associated with plant QDR and their biological functions.Many QDR genes belong to the canonical resistance gene categories with predicted functions in pathogen perception,signal transduction,phytohormone homeostasis,metabolite transport and biosynthesis,and epigenetic regulation.However,other"atypical"QDR genes are predicted to be involved in processes that are not commonly associated with disease resistance,such as vesicle trafficking,molecular chaperones,and others.This diversity of function for QDR genes contrasts with qualitative resistance,which is often based on the actions of nucleotidebinding leucine-rich repeat(NLR)resistance proteins.An understanding of the diversity of QDR mechanisms and of which mechanisms are effective against which classes of pathogens will enable the more effective deployment of QDR to produce more durably resistant,resilient crops.

The chimeric gene atp6c confers cytoplasmic male sterility in maize by impairing the assembly of the mitochondrial ATP synthase complex

Cytoplasmic male sterility(CMS)is a powerful tool for the exploitation of hybrid heterosis and the study of signaling and interactions between the nucleus and the cytoplasm.C-type CMS(CMS-C)in maize has long been used in hybrid seed production,but the underlying sterility factor and its mechanism of action remain unclear.In this study,we demonstrate that the mitochondrial gene atp6c confers male sterility in CMS-C maize.The ATP6C protein shows stronger interactions with ATP8 and ATP9 than ATP6 during the assembly of F1F0-ATP synthase(F-type ATP synthase,ATPase),thereby reducing the quantity and activity of assem-bled F_(1)F_(o)-ATP synthase.By contrast,the quantity and activity of the F1'component are increased in CMS-C lines.Reduced F1F0-ATP synthase activity causes accumulation of excess protons in the inner membrane space of the mitochondria,triggering a burst of reactive oxygen species(ROS),premature programmed cell death of the tapetai cells,and pollen abortion.Collectively,our study identifies a chimeric mitochondrial gene(ATP6C)that causes CMS in maize and documents the contribution of ATP6C to F1F0-ATP synthase assembly,thereby providing novel insights into the molecular mechanisms of male sterility in plants.

An MCIA-like complex is required for mitochondrial complex Ⅰ assembly and seed development in maize

During adaptive radiation,mitochondria have co-evolved with their hosts,leading to gain or loss of subunits and assembly factors of respiratory complexes.Plant mitochondrial complex Ⅰ harbors40 nuclearand 9 mitochondrial-encoded subunits,and is formed by stepwise assembly during which different intermediates are integrated via various assembly factors.In mammals,the mitochondrial complex Ⅰ intermediate assembly(MCIA)complex is required for building the membrane arm module.However,plants have lost almost all of the MCIA complex components,giving rise to the hypothesis that plants follow an ancestral pathway to assemble the membrane arm subunits.Here,we characterize a maize crumpled seed mutant,crk1,and reveal by map-based cloning that CRK1 encodes an ortholog of human complex Ⅰ assembly factor 1,zNDUFAF1,the only evolutionarily conserved MCIA subunit in plants.zNDUFAF1 is localized in the mitochondria and accumulates in two intermediate complexes that contain complex Ⅰ membrane arm subunits.Disruption of zNDUFAF1 results in severe defects in complex Ⅰ assembly and activity,a cellular bioenergetic shift to aerobic glycolysis,and mitochondrial vacuolation.Moreover,we found that zNDUFAF1,the putative mitochondrial import inner membrane translocase ZmTIM17-1,and the isovaleryl-coenzyme A dehydrogenase ZmIVD1 interact each other,and could be co-precipitated from the mitochondria and co-migrate in the same assembly intermediates.Knockout of either ZmTIM17-1 or ZmIVD1 could lead to the significantly reduced complex Ⅰ stability and activity as well as defective seeds.These results suggest that zNDUFAF1,ZmTIM17-1 and ZmIVD1 probably form an MCIA-like complex that is essential for the biogenesis of mitochondrial complex Ⅰ and seed development in maize.Our findings also imply that plants and mammals recruit MCIA subunits independently for mitochondrial complex Ⅰ assembly,highlighting the importance of parallel evolution in mitochondria adaptation to their hosts.

An epic war between an oomycete pathogen and plants

Oomycetes,commonly known as water molds and phylogenetically belonging to stramenopiles,can infect a wide range of plants and animals,with some members eliciting the most destructive plant diseases and posing severe threats to globalfood security and natural ecosystems(Thines,2018).For example,Phytophthora infestans causes potato late blight and triggered the Irish Famine in the 1840s,and Phytophthora sojae damages soybean production worldwide.Breeding resistant cultivars is the most efficient measure for managing the diseases instigated by oomycetes,but the success of the endeavor requires a sound and deep understanding of the molecular basis underlying pathogen-host interactions.Recently,Sun et al.(2022)elucidated the mechanism underlying the recognition of XEG1,a key virulent effector of P.sojae,by host immune receptor through combining genetic,molecular,and structural approaches,which represents a significant step forward in deeply understanding the infection biology and host immune responses in oomycete diseases.

VAMP726 from maize and Arabidopsis confers pollen resistance to heat and UV radiation by influencing lignin content of sporopollenin

Sporopollenin in the pollen cell wall protects male gametophytes from stresses.Phenylpropanoid derivatives,including guaiacyl(G)lignin units,are known to be structural components of sporopollenin,but the exact composition of sporopollenin remains to be fully resolved.We analyzed the phenylpropanoid derivatives in sporopollenin from maize and Arabidopsis by thioacidolysis coupled with nuclear magnetic resonance(NMR)and gas chromatography–mass spectrometry(GC–MS).The NMR and GC–MS results confirmed the presence of p-hydroxyphenyl(H),G,and syringyl(S)lignin units in sporopollenin from maize and Arabidopsis.Strikingly,H units account for the majority of lignin monomers in sporopollenin from these species.We next performed a genome-wide association study to explore the genetic basis of maize sporopollenin composition and identified a vesicle-associated membrane protein(ZmVAMP726)that is strongly associated with lignin monomer composition of maize sporopollenin.Genetic manipulation of VAMP726 affected not only lignin monomer composition in sporopollenin but also pollen resistance to heat and UV radiation in maize and Arabidopsis,indicating that VAMP726 is functionally conserved in monocot and dicot plants.Our work provides new insight into the lignin monomers that serve as structural components of sporopollenin and characterizes VAMP726,which affects sporopollenin composition and stress resistance in pollen.

CRISPR/CasΦ2-mediated gene editing in wheat and rye

The recent advancements in developing the CRISPR/Cas9 system and various derivative tools(e.g.,base editors)have accelerated basic plant science research and crop improvement by creating multiple types of genetic variations(Li et al.,2023a).