Current Situations of Competitive Scientific Research Projects for Agri-scientific Research Institutions: A Case Study of Tropical Crops Genetic Resources Institute of Chinese Academy of Tropical Agricultural Sciences

This paper collected and arranged competitive scientific research projects undertaken by Tropical Crops Genetic Resources Institute of Chinese Academy of Tropical Agricultural Sciences in 2003-2014. Through statistical analysis on quantity of projects,funded amount,age of person responsible,professional title of person responsible,academic degree of person responsible,research object,it discussed relevant characteristics and rules. Finally,it came up with pertinent measures and recommendations,in the hope of providing services for decision-making and scientific and technological management.

Construction and Establishment of Sci-tech Platform for Agricultural Scientific Research Institutions: A Case Study of Tropical Crops Genetic Resources Institute of Chinese Academy of Tropical Agricultural Sciences

Taking Tropical Crops Genetic Resources Institute( TCGRI) of Chinese Academy of Tropical Agricultural Sciences( CATAS) as an example,this paper discussed current situation of construction of sci-tech platform,analyzed existing problems,and finally came up with pertinent recommendations.

Phylogenetic diversity of eastern Asia-eastern North America disjunct plants is mainly associated with divergence time

The underlying causes of biodiversity disparities among geographic regions have long been a fundamental theme in ecology and evolution.However,the patterns of phylogenetic diversity(PD) and phylogenetic beta diversity(PBD) of congeners that are disjunctly distributed between eastern Asia-eastern North America(EA-ENA disjuncts) and their associated factors remain unknown.Here we investigated the standardized effect size of PD(SES-PD),PBD,and potentially associated factors in 11natural mixed forest sites(five in EA and six in ENA) where abundant EA-ENA disjuncts occur.We found that the disjuncts in ENA possessed higher SES-PD than those in EA at the continental scale(1.96vs-1.12),even though the number of disjunct species in ENA is much lower than in EA(128 vs 263).SESPD of the EA-ENA disjuncts tended to decrease with increasing latitude in 11 sites.The latitudinal diversity gradient of SES-PD was stronger in EA sites than in ENA sites.Based on the unweighted unique fraction metric(UniFrac) distance and the phylogenetic community dissimilarity,PBD showed that the two northern sites in EA were more similar to the six-site ENA group than to the remaining southern EA sites.Based on the standardized effect size of mean pairwise distances(SES-MPD),nine of eleven studied sites showed a neutral community structure(-1.96 ≤SES-MPD ≤1.96).Both Pearson’s r and structural equation modeling suggested that SES-PD of the EA-ENA disjuncts was mostly associated with mean divergence time.Moreover,SES-PD of the EA-ENA disjuncts was positively correlated with temperaturerelated climatic factors,although negatively correlated with mean diversification rate and community structure.By applying approaches from phylogenetics and community ecology,our work sheds light on historical patterns of the EA-ENA disjunction and paves the way for further research.

Genetic Analysis of the First Female Flower Node and the First Male Flower Node in Bitter Gourd

Exploring genetic mechanism of the first female flower node and the first male flower node in bitter gourd has practical significance for formulating breeding strategy. In this article, a cross was made between CN19-1 and Thai4-6, and the F2segregation population was also constructed through F1selfing. The genetic characteristics of the first female flower node and the first male flower node were analyzed by adopting the major gene plus polygene mixed genetic model. The data analysis results showed that the first female flower node and the first male flower node were continuous distribution in the F2segregation population. E-2 model was the most suitable model for the genetic analysis of the first female flower node and the first male flower node. The additive effect values of the 2 pairs of major genes controlling the first female flower node were 2.722 and 1.862 8 respectively, the dominant effect values were-2.721 6 and-0.171 8, respectively. The additive effect value of polygene was-0.839 2, and the dominant effect value of polygene was 2.225 4. The heritability of major genes and polygene were 83.73% and 1.54%, respectively. The additive effect values of the 2 pairs of major genes controlling the first male flower node were 17.746 9 and 3.972, respectively, the dominant effect values were 5.191 6 and-3.972, respectively. The additive effect value of polygene was-20.530 5, and the dominant effect value was-4.141 4. The heritability of major genes and polygene was 92.34% and 4.7%, respectively. This study could provide a theoretical basis for bitter gourd breeding.

The haplotype-resolved T2T genome of teinturier cultivar Yan73 reveals the genetic basis of anthocyanin biosynthesis in grapes

Teinturier grapes are characterized by the typical accumulation of anthocyanins in grape skin,flesh,and vegetative tissues,endowing them with high utility value in red wine blending and nutrient-enriched foods developing.However,due to the lack of genome information,the mechanism involved in regulating teinturier grape coloring has not yet been elucidated and their genetic utilization research is still insufficient.Here,the cultivar‘Yan73’was used for assembling the telomere-to-telomere(T2T)genome of teinturier grapes by combining the High Fidelity(HiFi),Hi-C and ultralong Oxford Nanopore Technologies(ONT)reads.Two haplotype genomes were assembled,at the sizes of 501.68 Mb and 493.38 Mb,respectively.In the haplotype 1 genome,the transposable elements(TEs)contained 32.77%of long terminal repeats(LTRs),while in the haplotype 2 genome,31.53%of LTRs were detected in TEs.Furthermore,obvious inversions were identified in chromosome 18 between the two haplotypes.Transcriptome profiling suggested that the gene expression patterns in‘Cabernet Sauvignon’and‘Yan73’were diverse depending on tissues,developmental stages,and varieties.The transcription program of genes in the anthocyanins biosynthesis pathway between the two cultivars exhibited high similarity in different tissues and developmental stages,whereas the expression levels of numerous genes showed significant differences.Compared with other genes,the expression levels of VvMYBA1 and VvUFGT4 in all samples,VvCHS2 except in young shoots and VvPAL9 except in the E-L23 stage of‘Yan73’were higher than those of‘Cabernet Sauvignon’.Further sequence alignments revealed potential variant gene loci and structure variations of anthocyanins biosynthesis related genes and a 816 bp sequence insertion was found in the promoter of VvMYBA1 of‘Yan73’haplotype 2 genome.The‘Yan73’T2T genome assembly and comparative analysis provided valuable foundations for further revealing the coloring mechanism of teinturier grapes and the genetic improvement of grape coloring traits.

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.

Identific tion of quantitative trait loci and associated candidate genes for pregnancy success in Angus–Brahman crossbred heifers

Background In beef cattle, more than 50% of the energy input to produce a unit of beef is consumed by the female that produced the calf. Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef production.Results Genome-wide association studies(GWAS) were performed using a single-step genomic best linear unbiased prediction approach on pregnancy outcome traits from a population of Angus–Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another farm. Heifers were genotyped with the Bovine GGP F250 array that contains 221,077 SNPs. In the discovery population, heifers were bred in winter breeding seasons involving a single round of timed artificial insemination(AI) followed by natural mating for 3 months. Two phenotypes were analyzed: pregnancy outcome to first-service AI(PAI;n = 1,481) and pregnancy status at the end of the breeding season(PEBS;n = 1,725). The heritability was estimated as 0.149 and 0.122 for PAI and PEBS, respectively. In the PAI model, one quantitative trait locus(QTL), located between 52.3 and 52.5 Mb on BTA7, explained about 3% of the genetic variation, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5% and 1% of the genetic variation were found on BTA12 and 25. In the PEBS model, a large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTLs located on BTA5, 9, 10, 11, 19, and 20. The validation population for pregnancy status at the end of the breeding season were Angus–Brahman crossbred heifers bred by natural mating. In concordance with the discovery population, the large QTL on BTA7 and QTLs on BTA10 and 12 were identified.Conclusions In summary, QTLs and candidate SNPs identified were associated with pregnancy outcomes in beef heifers, including a large QTL associated with a group of protocadherin genes. Confirmation of these associations with larger populations could lead to the development of genomic predictions of reproductive function in beef cattle. Moreover, additional research is warranted to study the function of candidate genes associated with QTLs.

Fine mapping and cloning of the sterility gene Bra2Ms in nonheading Chinese cabbage(Brassica rapa ssp.chinensis)

The application of a male-sterile line is an ideal approach for hybrid seed production in non-heading Chinese cabbage(Brassica rapa ssp.chinensis).However,the molecular mechanisms underlying male sterility in B.rapa are still largely unclear.We previously obtained the natural male sterile line WS24-3 of non-heading Chinese cabbage and located the male sterile locus,Bra2Ms,on the A2 chromosome.Cytological observations revealed that the male sterility of WS24-3 resulted from disruption of the meiosis process during pollen formation.Fine mapping of Bra2Ms delimited the locus within a physical distance of about 129 kb on the A2 chromosome of B.rapa.The Bra039753 gene encodes a plant homeodomain(PHD)-finger protein and is considered a potential candidate gene for Bra2Ms.Bra039753 was significantly downregulated in sterile line WS24-3 compared to the fertile line at the meiotic anther stage.Sequence analysis of Bra039753 identified a 369 bp fragment insertion in the first exon in male sterile plants,which led to an amino acid insertion in the Bra039753 protein.In addition,the 369 bp fragment insertion was found to cosegregate with the male sterility trait.This study identified a novel locus related to male sterility in non-heading Chinese cabbage,and the molecular marker obtained in this study will be beneficial for the marker-assisted selection of excellent sterile lines in non-heading Chinese cabbage and other Brassica crops.

Understanding the educational inequalities in suicide attempts and their mediators:a Mendelian randomisation study

Background Educational inequalities in suicide have become increasingly prominent over the past decade.Elucidating modifiable risk factors that serve as intermediaries in the impact of low educational attainment on suicide has the potential to reduce health disparities.Aims To examine the risk factors that mediate the relationship between educational attainment and suicide attempts and quantify their contributions to the mediation effect.Methods We conducted a two-sample Mendelian randomisation(MR)analysis to estimate the causal effect of educational attainment on suicide attempts,utilising genome-wide association study summary statistics from the Integrative Psychiatric Research(iPSYCH;6024 cases and 44240 controls)and FinnGen(8978 cases and 368299 controls).We systematically evaluated 42 putative mediators within the causal pathway connecting reduced educational attainment to suicide attempts and employed two-step and multivariable MR to quantify the proportion of the mediated effect.Results In the combined analysis of iPSYCH and FinnGen,each standard deviation(SD)decrease in genetically predicted educational attainment(equating to 3.4 years of education)was associated with a 105%higher risk of suicide attempts(odds ratio(OR):2.05;95%confidence interval(Cl):1.81 to 2.31).0f the 42 risk factors analysed,the two-step MR identified five factors that mediated the association between educational attainment and suicide attempts.The respective proportions of mediation were 47%(95%Cl:29%to 66%)for smoking behaviour,36%(95%Cl:0%to 84%)for chronic pain,49%(95%Cl:36%to 61%)for depression,35%(95%Cl:12%to 59%)for anxiety and 26%(95%Cl:18%to 34%)for insomnia.Multivariable MR implicated these five mediators collectively,accounting for 68%(95%Cl:40%to 96%)of the total effect.Conclusions This study identified smoking,chronic pain and mental disorders as primary intervention targets for attenuating suicide risk attributable to lower educational levels in the European population.

The pathogenic mechanism of syndactyly type V identified in aHoxd13Q50R knock-in mice

Syndactyly type V (SDTY5) is an autosomal dominant extremity malformation characterized by fusion of the fourth and fifthmetacarpals. In the previous publication, we first identified a heterozygous missense mutation Q50R in homeobox domain (HD) ofHOXD13 in a large Chinese family with SDTY5. In order to substantiate the pathogenicity of the variant and elucidate the underlyingpathogenic mechanism causing limb malformation, transcription-activator-like effector nucleases (TALEN) was employed togenerate a Hoxd13Q50R mutant mouse. The mutant mice exhibited obvious limb malformations including slight brachydactyly andpartial syndactyly between digits 2-4 in the heterozygotes, and severe syndactyly, brachydactyly and polydactyly in homozygotes.Focusing on BMP2 and SHH/GREM1/AER-FGF epithelial mesenchymal (e-m) feedback, a crucial signal pathway for limbdevelopment, we found the ectopically expressed Shh, Grem1 and Fgf8 and down-regulated Bmp2 in the embryonic limb bud atE10.5 to E12.5. A transcriptome sequencing analysis was conducted on limb buds (LBs) at E11.5, revealing 31 genes that exhibitednotable disparities in mRNA level between the Hoxd13Q50R homozygotes and the wild-type. These genes are known to be involvedin various processes such as limb development, cell proliferation, migration, and apoptosis. Our findings indicate that the ectopicexpression of Shh and Fgf8, in conjunction with the down-regulation of Bmp2, results in a failure of patterning along both theanterior-posterior and proximal-distal axes, as well as a decrease in interdigital programmed cell death (PCD). This cascadeultimately leads to the development of syndactyly and brachydactyly in heterozygous mice, and severe limb malformations inhomozygous mice. These findings suggest that abnormal expression of SHH, FGF8, and BMP2 induced by HOXD13Q50R may beresponsible for the manifestation of human SDTY5.

Molecular analyses display the increasing diversity of Podostemaceae in China

Podostemaceae(riverweed family),one of the largest aquatic plant families in the world,comprises about 350 species in 51 genera placed in three subfamilies,Podostemoideae,Weddellinoideae,and Tristichoideae(Koi et al.,2022).Most Podostemaceae genera(~38)are monotypic or oligotypic,with a high level of endemism(Koi et al.,2018,2022).Members of Podostemaceae adhere to rocks in fast-flowing rivers,streams,or waterfalls in the subtropics and tropics(Koi et al.,2018).As an adaptation to fastrunning currents,the morphological structure of river-weeds tends to be extremely reduced,including a loss or reduction of primary shoots or roots(Koi and Kato,2007).The vegetative mass of these plants resembles lichens or bryophytes,and are thus known commonly as“dream bryophytes”(Philbrick and Retana,1998).Podostemaceae plants flower when the water level drops during the dry season.In recent years,anthropogenic factors and climate change have severely affected river weed habitats,decreasing populations of these plants.

Mobilizing and integrating big data in studies of spatial and phylogenetic patterns of biodiversity

The current global challenges that threaten biodiversity are immense and rapidly growing.These biodiversity challenges demand approaches that meld bioinformatics,large-scale phylogeny reconstruction,use of digitized specimen data,and complex post-tree analyses(e.g.niche modeling,niche diversification,and other ecological analyses).Recent developments in phylogenetics coupled with emerging cyberinfrastructure and new data sources provide unparalleled opportunities for mobilizing and integrating massive amounts of biological data,driving the discovery of complex patterns and new hypotheses for further study.These developments are not trivial in that biodiversity data on the global scale now being collected and analyzed are inherently complex.The ongoing integration and maturation of biodiversity tools discussed here is transforming biodiversity science,enabling what we broadly term"next-generation"investigations in systematics,ecology,and evolution(i.e.,"biodiversity science").New training that integrates domain knowledge in biodiversity and data science skills is also needed to accelerate research in these areas.Integrative biodiversity science is crucial to the future of global biodiversity.We cannot simply react to continued threats to biodiversity,but via the use of an integrative,multifaceted,big data approach,researchers can now make biodiversity projections to provide crucial data not only for scientists,but also for the public,land managers,policy makers,urban planners,and agriculture.

Immunogenetic phenotypes in inflammatory bowel disease

当前接受的 etiopathogenic 假设建议长期的肠的发炎和煽动性的肠疾病(IBD ) 的相关全身的表明特征由于对居民钠的过分好攻击或病理学的有免疫力的回答细菌的成分。预先安排的因素是粘膜免疫者回答或障碍功能的基因 dysregulation，与环境刺激触发的发作。这些因素和他们的相互作用可以也是疾病显型和疾病前进的重要决定因素。免疫的出现基因显型把支持借给不同免疫者处理的危险性基因调整的建议假设，由钠抗原开车，表示了接着在 IBD 影响临床的显型的同样特定的有免疫力的显型病人。

Construction of a Genetic Linkage Map of Mango Based on SRAP, AFLP and ISSR Markers

A hybrid Ft population was obtained by crossing between mango cultivars ＇ Jinhuang＇ and ＇ Guifei＇. Among the hybrid population, 98 F1 plants were selected as the mapping population. The molecular genetic map of mango was constructed by linkage analysis by SRAP, AFLP and ISSR markers using Joinmap4. 0 software. The genetic linkage map consisted of 33 linkage groups, with a total genetic distance of 1 561.1 cM. Moreover, the genetic linkage map involved 245 polymorphic markers, including 149 SRAP markers, 90 AFLP markers and 6 ISSR markers, with an average genetic distance of 6.37 cM. This study laid a founda- tion for further investigation of the important agronomic traits of mango.

Colorectal cancer: The epigenetic role of microbiome

Colorectal cancer(CRC)is the third most common cancer in men(746000 cases per year)and the second most common cancer in women globally(614000 cases per year).The incidence rate of CRC in developed countries(737000 cases per year)is higher than that in less developed countries(624000 cases per year).CRC can arise from genetic causes such as chromosomal instability and microsatellite instability.Several etiologic factors underlie CRC including age,diet,and lifestyle.Gut microbiota represent a proven cause of the disease,where they play pivotal roles in modulating and reshaping the host epigenome.Several active microbial metabolites have been found to drive carcinogenesis,invasion,and metastasis via modifying both the methylation landscape along with histone structure in intestinal cells.Gut microbiota,in response to diet,can exert both beneficial and harmful functions in humans,according to the intestinal balance of number and types of these bacteria.Although the intestinal microbial community is diverse among individuals,these microbes cumulatively produce 100-fold more proteins than the human genome itself,which calls for further studies to elaborate on the complicated interaction between these microorganisms and intestinal cells.Therefore,understanding the exact role that gut microbiota play in inducing CRC will help attain reliable strategies to precisely diagnose and treat this fatal disease.

Genetic behavior of Triticum aestivum–Dasypyrum villosum translocation chromosomes T6V#4S·6DL and T6V#2S·6AL carrying powdery mildew resistance

T6V#2S·6AL and T6V#4S·6DL translocation chromosomes developed from the cross of wheat and different Dasypyrum villosum accessions have good powdery mildew （PM） resistance, but their pairing and pyramiding behavior remains unclear. Results in this study indicated that the pairing frequency rate of the two differently originated 6VS chromosomes in their F1 hybrid was 18.9% according to genomic in situ hybridization （GISH）; the PM resistance plants in the F2 generation from the cross between T6V#4S·6DL translocation line Pm97033 and its PM susceptible wheat variety Wan7107 was fewer than expected. However, the ratio of the resistant vs. the susceptible plants of 15：1 in the F2 generation derived from the cross between the two translocation lines of T6V#2S·6AL and T6V#4S·6DL fitted well. Plants segregation ratio （homozygous：heterozygous：lacking） revealed by molecular marker for T6V#4S·6DL or T6V#2S·6AL in their F2 populations fitted the expected values of 1：2：1 well, inferring that the pairing of the two alien chromosome arms facilitates the transmission of T6V#4S·6DL from the F1 to the F2 generation. A quadrivalent was also observed in 21% of pollen mother cells （PMCs） of homozygote plants containing the two pairs of translocated chromosomes. The chromosome pairing between 6V#2S and 6V#4S indicates that it will be possible to obtain recombinants and clarify if the PM resistance determinant on one alien chromosome arm is different from that on the other.

Fusarium Wilt Resistance Identification and Genetic Analysis of Momordica charantia L. Germplasm

Fusarium wilt seriously affects the yield and quality of Momordica charantia L.Breeding resistant varieties is the most economical and effective measure to control Fusarium wilt in M.charantia L.This study had comprehensively conducted pathogen identification of Fusarium wilt,resistance evaluation of M.charantia L.germplasm to Fusarium wilt,and genetic analysis of Fusarium wilt resistance in M.charantia L.,so as to provide reference for breeding resistant varieties and accelerating the breeding process.

A Review of Microsatellite Markers and their Application on Genetic Diversity Studies in Parrots

The ability of a population to adapt to a changing environment depends on its genetic variation. Thus, the study of genetic diversity within and among species or populations is especially important on conservation biology scopes. One way to assess the genetic diversity is through the use of microsatellite molecular markers. Microsatellites have been widely used to answer population genetics issues as gene flow, parentage, and population structure, mostly resulting in data on the distribution of genetic variability within and among natural populations, which are essential for ex situ and in situ conservation procedures. As the Psittacidae family comprehends one of the birds group with the largest number of endangered species, studies that aim to investigate the genetic diversity of these animals may support their conservation. This article is a review of genetic data on parrots, through the use of microsatellite markers, that have been published since 2004.

Whole-genome sequencing provides insights into the genetic diversity and domestication of bitter gourd(Momordica spp.)

Bitter gourd(Momordica charantia)is a popular cultivated vegetable in Asian and African countries.To reveal the characteristics of the genomic structure,evolutionary trajectory,and genetic basis underlying the domestication of bitter gourd,we performed whole-genome sequencing of the cultivar Dali-11 and the wild small-fruited line TR and resequencing of 187 bitter gourd germplasms from 16 countries.The major gene clusters(Bi clusters)for the biosynthesis of cucurbitane triterpenoids,which confer a bitter taste,are highly conserved in cucumber,melon,and watermelon.Comparative analysis among cucurbit genomes revealed that the Bi cluster involved in cucurbitane triterpenoid biosynthesis is absent in bitter gourd.Phylogenetic analysis revealed that the TR group,including 21 bitter gourd germplasms,may belong to a new species or subspecies independent from M.charantia.Furthermore,we found that the remaining 166 M.charantia germplasms are geographically differentiated,and we identified 710,412,and 290 candidate domestication genes in the South Asia,Southeast Asia,and China populations,respectively.This study provides new insights into bitter gourd genetic diversity and domestication and will facilitate the future genomics-enabled improvement of bitter gourd.

Genetic Diversity Analysis of Cherry Tomato Core Collection Based on Genotypic Values

Taking 65 cherry tomato core germplasms as experimental materials,the genetic diversity of seven agronomic traits were analyzed.The correlation between any two of the seven agronomic traits and the genetic relationships of these germplasms were analyzed based on genotypic values.The genetic diversity indices of the seven agronomic traits were 4.15,4.13,4.16,4.13,4.13,4.13 and 4.01,respectively,showing that the cherry tomato core collection had abundant genetic diversity.The correlation analysis between traits based on genotype effect values showed that leaf length was significantly correlated with leaf width with the correlation coefficient of 0.56.The fruit width was significantly correlated with fruit length with the correlation coefficient of 0.52.The flesh thickness was significantly correlated with fruit length and fruit width with the correlation coefficients of 0.49 and 0.39,respectively.The single fruit weight was significantly correlated with fruit length,fruit width and flesh thickness with the correlation coefficients of 0.44,0.61 and 0.62,respectively.When the genetic distances between core germplasms of cherry tomato were calculated based on the phenotypic values,65 core germplasms of cherry tomato were divided into three groups with the rescaled distance of 10.When the genetic distances between core germplasms of cherry tomato were calculated based on the genotypic values,the 65 core germplasms of cherry tomato were divided into four groups with the rescaled distance of 10.Comparing the 2 clustering results,it could find that genotypic value-based clustering analysis could better clarify the genetic relationship between core germplasms.This study could provide a theoretical basis for the effective utilization of cherry tomato core germplasms.