Haplotyping of Rice Genotypes Using Simple Sequence Repeat Markers Associated with Salt Tolerance

Salt stress is a major problem in most of the rice growing areas in the world. A major QTLSaltol associated with salt tolerance at the seedling stage has been mapped on chromosome 1 in rice.This study aimed to characterize the haplotype diversity at Saltol and additional QTLs associated withsalt tolerance. Salt tolerance at the seedling stage was assessed in 54 rice genotypes in the scale of 1to 9 score at EC = 10 dSm^-1 under controlled environmental conditions. Seven new breeding linesincluding three KMR3/O. rufipogon introgression lines showed similar salt tolerant ability as FL478 andcan be good sources of new genes/alleles for salt tolerance. Simple sequence repeat （SSR） markerRM289 showed only two alleles and RM8094 showed seven alleles. Polymorphic information contentvalue varied from 0.55 for RM289 to 0.99 for RM8094 and RM493. Based on 14 SSR markers, the 54lines were clearly separated into two major clusters. Fourteen haplotypes were identified based onSaltol linked markers with FL478 as the reference. Alleles of RM8094 and RM3412 can discriminatebetween the salt tolerant and susceptible genotypes clearly and hence can be useful in marker-assistedselection at the seedling stage. Other markers RM10720 on chromosome 1 and RM149 and RM264 onchromosome 8 can also distinguish tolerant and susceptible lines but with lesser stringency.

Identifying normal embryos from reciprocal translocation carriers by whole chromosome haplotyping

Reciprocal translocation is a chromosomal structural abnormal- ity that arises when two non-homologous chromosomes rearrange and attach with each other, an incidence that occurs in about 1/500 to 1/625 newborns （Mackie and Scriven, 2002）. This event typically does not lead to any significant loss of genetic material, thus recip- rocal translocation carriers do not exhibit any severe abnormal phenotypes （Scriven et al., 1998; Zhang et al., 2016）.

Genetic diversity and population genetic structure of Paeonia suffruticosa by chloroplast DNA simple sequence repeats(cpSSRs)

Paeonia suffruticosa Andr.is an endemic shrub flower in China with 2n=10.This study used 228 cultivars from four populations,i.e.,Jiangnan,Japan,Northwest,and Zhongyuan,as materials to explore the genetic diversity levels among different populations of tree peony varieties.The results showed that 34 bands were amplified using five pairs of cp SSR primers,with an average of 6.8 bands per primer pair.The average number of different alleles(N_(a)),effective alleles(N_(e)),Shannon's information index(I),diversity(H),and polymorphic information content(PIC)were 3.600,2.053,0.708,0.433,and 0.388,respectively.The PIC value was between 0.250 and 0.500,indicating a moderate level of polymorphism for the five cp SSR primer pairs.The genetic diversity levels of peony cultivars varied among different populations,with the Northwest population showing relatively lower levels(I=0.590,H=0.289,and PIC=0.263).A total of 52 haplotypes were identified in the four examined populations,and the number of haplotypes per population ranged from 11 to 22.Forty-four private haplotypes were detected across populations,and the Northwest population exhibiting the highest count of private haplotypes with 17.The mean number of effective number of haplotypes(N_(eh)),haplotypic richness(R_h),and diversity(H)were 8.351,6.824,and 0.893,respectively.Analysis of molecular variance indicated that genetic variation within tree peony germplasm was greater than that between germplasm resources,and the main variation was found within individuals of peony germplasm.Cluster analysis,principal coordinate analysis,and genetic structure analysis classified tree peonies from different origins into two groups,indicating a certain degree of genetic differentiation among these four tree peony cultivation groups.This study provides a theoretical basis for the exploration,utilization,and conservation of peony germplasm resources,as well as for research on the breeding of excellent varieties.

The Haplotyping Problem：An Overview of Computational Models and Solutions

The investigation of genetic differences among humans has given evidence thatmutations in DNA sequences are responsible for some genetic diseases. The most common mutation isthe one that involves only a single nucleotide of the DNA sequence, which is called a singlenucleotide polymorphism (SNP). As a consequence, computing a complete map of all SNPs occurring inthe human populations is one of the primary goals of recent studies in human genomics. Theconstruction of such a map requires to determine the DNA sequences that from all chromosomes. Indiploid organisms like humans, each chromosome consists of two sequences called haplotypes.Distinguishing the information contained in both haplotypes when analyzing chromosome sequencesposes several new computational issues which collectively form a new emerging topic of ComputationalBiology known as Haplotyping. This paper is a comprehensive study of some new combinatorialapproaches proposed in this research area and it mainly focuses on the formulations and algorithmicsolutions of some basic biological problems. Three statistical approaches are briefly discussed atthe end of the paper.

Genetic dissection and validation of a major QTL for grain weight on chromosome 3B in bread wheat(Triticum aestivum L.)

Grain weight is one of the key components of wheat(Triticum aestivum L.)yield.Genetic manipulation of grain weight is an efficient approach for improving yield potential in breeding programs.A recombinant inbred line(RIL)population derived from a cross between W7268 and Chuanyu 12(CY12)was employed to detect quantitative trait loci(QTLs)for thousand-grain weight(TGW),grain length(GL),grain width(GW),and the ratio of grain length to width(GLW)in six environments.Seven major QTLs,QGl.cib-2D,QGw.cib-2D,QGw.cib-3B,QGw.cib-4B.1,QGlw.cib-2D.1,QTgw.cib-2D.1 and QTgw.cib-3B.1,were consistently identified in at least four environments and the best linear unbiased estimation(BLUE)datasets,and they explained 2.61 to 34.85%of the phenotypic variance.Significant interactions were detected between the two major TGW QTLs and three major GW loci.In addition,QTgw.cib-3B.1 and QGw.cib-3B were co-located,and the improved TGW at this locus was contributed by GW.Unlike other loci,QTgw.cib-3B.1/QGw.cib-3B had no effect on grain number per spike(GNS).They were further validated in advanced lines using Kompetitive Allele Specific PCR(KASP)markers,and a comparison analysis indicated that QTgw.cib-3B.1/QGw.cib-3B is likely a novel locus.Six haplotypes were identified in the region of this QTL and their distribution frequencies varied between the landraces and cultivars.According to gene annotation,spatial expression patterns,ortholog analysis and sequence variation,the candidate gene of QTgw.cib-3B.1/QGw.cib-3B was predicted.Collectively,the major QTLs and KASP markers reported here provide valuable information for elucidating the genetic architecture of grain weight and for molecular marker-assisted breeding in grain yield improvement.

Genome-wide association study of grain micronutrient concentrations in bread wheat

Bread wheat(Triticum aestivum)is a staple food crop worldwide.The genetic dissection of important nutrient traits is essential for the biofortification of wheat to meet the nutritional needs of the world's growing population.Here,45,298 single-nucleotide polymorphisms(SNPs)from 55K chip arrays were used to genotype a panel of 768 wheat cultivars,and a total of 154 quantitative trait loci(QTLs)were detected for eight traits under three environments by genome-wide association study(GWAS).Three QTLs(qMn-3B.1,qFe-3B.4,and qSe-3B.1/qFe-3B.6)detected repeatedly under different environments or traits were subjected to subsequent analyses based on linkage disequilibrium decay and the P-values of significant SNPs.Significant SNPs in the three QTL regions formed six haplotypes for qMn-3B.1,three haplotypes for qFe-3B.4,and three haplotypes for qSe-3B.1/qFe-3B.6.Phenotypic analysis revealed significant differences among haplotypes.These results indicated that the concentrations of several nutrient elements have been modified during the domestication of landraces to modern wheat.Based on the QTL regions,we identified 15 high-confidence genes,eight of which were stably expressed in different tissues and/or developmental stages.TraesCS3B02G046100 in qMn-3B.1 and TraesCS3B02G199500 in qSe-3B.1/qFe-3B.6 were both inferred to interact with metal ions according to the Gene Ontology(GO)analysis.TraesCS3B02G199000,which belongs to qSe-3B.1/qFe-3B.6,was determined to be a member of the WRKY gene family.Overall,this study provides several reliable QTLs that may significantly affect the concentrations of nutrient elements in wheat grain,and this information will facilitate the breeding of wheat cultivars with improved grain properties.

Insights into genetic diversity and phenotypic variations in domestic geese through comprehensive population and pan-genome analysis

Background Domestic goose breeds are descended from either the Swan goose(Anser cygnoides)or the Greylag goose(Anser anser),exhibiting variations in body size,reproductive performance,egg production,feather color,and other phenotypic traits.Constructing a pan-genome facilitates a thorough identification of genetic variations,thereby deepening our comprehension of the molecular mechanisms underlying genetic diversity and phenotypic variability.Results To comprehensively facilitate population genomic and pan-genomic analyses in geese,we embarked on the task of 659 geese whole genome resequencing data and compiling a database of 155 RNA-seq samples.By constructing the pan-genome for geese,we generated non-reference contigs totaling 612 Mb,unveiling a collection of 2,813 novel genes and pinpointing 15,567 core genes,1,324 softcore genes,2,734 shell genes,and 878 cloud genes in goose genomes.Furthermore,we detected an 81.97 Mb genomic region showing signs of genome selection,encompassing the TGFBR2 gene correlated with variations in body weight among geese.Genome-wide association studies utilizing single nucleotide polymorphisms(SNPs)and presence-absence variation revealed significant genomic associations with various goose meat quality,reproductive,and body composition traits.For instance,a gene encoding the SVEP1 protein was linked to carcass oblique length,and a distinct gene-CDS haplotype of the SVEP1 gene exhibited an association with carcass oblique length.Notably,the pan-genome analysis revealed enrichment of variable genes in the“hair follicle maturation”Gene Ontology term,potentially linked to the selection of feather-related traits in geese.A gene presence-absence variation analysis suggested a reduced frequency of genes associated with“regulation of heart contraction”in domesticated geese compared to their wild counterparts.Our study provided novel insights into gene expression features and functions by integrating gene expression patterns across multiple organs and tissues in geese and analyzing population variation.Conclusion This accomplishment originates from the discernment of a multitude of selection signals and candidate genes associated with a wide array of traits,thereby markedly enhancing our understanding of the processes underlying domestication and breeding in geese.Moreover,assembling the pan-genome for geese has yielded a comprehensive apprehension of the goose genome,establishing it as an indispensable asset poised to offer innovative viewpoints and make substantial contributions to future geese breeding initiatives.

Exploring the genetic basis of pre-harvest sprouting in rice through a genome-wide association study-based haplotype analysis

Pre-harvest sprouting(PHS)poses a significant global challenge to cereal production,impacting both yield and quality.In this study,we employed genome-wide association studies(GWAS)on diverse rice accessions to identify novel PHS-associated haplotypes.An assessment of 127 cultivated accessions for panicle germination(PHS)and detached grain germination(germination rate of detached grains at the 14th day(D14))revealed considerable phenotypic variation among rice ecotypes.GWAS analysis identified 91 significant signals at–log10(P-value)>5,including 15SNPs for PHS and 76 SNPs for D14.A subsequent linkage disequilibrium(LD)block-based GWAS analysis detected 227 significant SNPs for both traits,consisting of 18 nonsynonymous substitutions located on the coding regions of nine genes.Further haplotype analysis identified 32 haplotypes,with 10 specific to cultivated accessions,19 specific to the wild type,and three shared between them.A phenotypic assessment of major haplotypes revealed significant differences between resistant(Hap1 and Hap2)and susceptible haplotypes(Hap5,Hap27,and Hap28),distinguished by a G/A SNP within a novel gene,Os04g0545200.The identified haplotypes offer promising prospects for haplotypebased breeding aimed at enhancing PHS resistance in rice.

Analysis of Phenotypes Associated with Deficiency of PAX6 Haplotypes in Chinese Aniridia Families

Objective To examine the clinical phenotype and genetic deficiencies present in Chinese aniridia families with PAX6 haplotype deficiency.Methods A comprehensive questionnaire and ophthalmological assessments were administered to both affected patients and unaffected relatives.The clinical feature analysis included the evaluation of visual acuity,intraocular pressure,slit-lamp anterior segment examination,fundus photography,and spectral domain optical coherence tomography.To identify the mutation responsible for aniridia,targeted next-generation sequencing was used as a beneficial technique.Results A total of 4 mutations were identified,consisting of two novel frameshift mutations(c.314delA,p.K105Sfs*33 and c.838_845dup AACACACC,p.S283Tfs*85),along with two recurring nonsense mutations(c.307C>T,p.R103X and c.619A>T,p.K207*).Complete iris absence,macular foveal hypoplasia,and nystagmus were consistent in these PAX6 haplotype-deficient Chinese aniridia families,while corneal lesions,cataracts,and glaucoma exhibited heterogeneity both among the families and within the same family.Conclusion In our study,two novel PAX6 mutations associated with aniridia were identified in Chinese families,which expanded the phenotypic and genotypic spectrum of PAX6 mutations.We also analyzed the clinical characteristics of PAX6 haplotype deficiency in Chinese aniridia families.

Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper(Plectropomus leopardus)

The leopard coral grouper(Plectropomus leopardus)is a species of significant economic importance.Although artificial cultivation of P.leopardus has thrived in recent decades,the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data.In this study,we identified over 8.73 million single nucleotide polymorphisms(SNPs)through whole-genome resequencing of 326 individuals spanning six distinct groups.Furthermore,we categorized 226 individuals with high-coverage sequencing depth(≥14×)into eight clusters based on their genetic profiles and phylogenetic relationships.Notably,four of these clusters exhibited pronounced genetic differentiation compared with the other populations.To identify potentially advantageous loci for P.leopardus,we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity(θπ)and fixation index(FST)in these four clusters.Using these high-coverage resequencing data,we successfully constructed the first haplotype reference panel specific to P.leopardus.This achievement holds promise for enabling high-quality,cost-effectiveimputationmethods.Additionally,we combined low-coverage sequencing data with imputation techniques for a genome-wide association study,aiming to identify candidate SNP loci and genes associated with growth traits.A significant concentration of these genes was observed on chromosome 17,which is primarily involved in skeletal muscle and embryonic development and cell proliferation.Notably,our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs,showing potential for genetic selective breeding efforts.These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P.leopardus.

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.

Multi-genome evolutionary study of the ABC1 gene family and identification of the pleiotropic effects of OsABC1-13 in rice development

In four rice genomes,85 ABC1-family genes were identified by comparative genomics,evolution,genetics,and physiology.One,OsABC1-13,was shown by knockdown and knockout experiments to affect plant height,grain size,and photosynthetic capability.

A novel Effective Panicle Number per Plant 4 haplotype enhances grain yield by coordinating panicle number and grain number in rice

Increasing effective panicle number per plant(EPN)is one approach to increase yield potential in rice.However,molecular mechanisms underlying EPN remain unclear.In this study,we integrated mapbased cloning and genome-wide association analysis to identify the EPN4 gene,which is allelic to NARROW LEAF1(NAL1).Overexpression lines containing the Teqing allele(TQ)of EPN4 had significantly increased EPN.NIL-EPN4^(TQ) in japonica(geng)cultivar Lemont(LT)exhibited significantly improved EPN but decreased grain number and flag leaf size relative to LT.Haplotype analysis indicated that accessions with EPN4-1 had medium EPN,medium grain number,and medium grain weight,but had the highest grain yield among seven haplotypes,indicating that EPN4-1 is an elite haplotype of EPN4 for positive coordination of the three components of grain yield.Furthermore,accessions carrying the combination of EPN4-1 and haplotype GNP1-6 of GNP1 for grain number per panicle showed higher grain yield than those with other allele combinations.Therefore,pyramiding of EPN4-1 and GNP1-6 could be a preferred approach to obtain high yield potential in breeding.

Genetic diversity of the S-type small subunit ribosomal RNA gene of Plasmodium knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia

Objective:To determine the genetic diversity of Plasmodium(P.)knowlesi isolates from Sabah,Malaysian Borneo and Peninsular Malaysia,targeting the S-type SSU rRNA gene and including aspects of natural selection and haplotype.Methods:Thirty-nine blood samples infected with P.knowlesi were collected in Sabah,Malaysian Borneo and Peninsular Malaysia.The S-type SSU rRNA gene was amplified using polymerase chain reaction,cloned into a vector,and sequenced.The natural selection and haplotype of the S-type SSU rRNA gene sequences were determined using DnaSP v6 and illustrated using NETWORK v10.This study's 39 S-type SSU rRNA sequences and eight sequences from the Genbank database were subjected to phylogenetic analysis using MEGA 11.Results:Overall,the phylogenetic analysis showed no evidence of a geographical cluster of P.knowlesi isolates from different areas in Malaysia based on the S-type SSU rRNA gene sequences.The S-type SSU rRNA gene sequences were relatively conserved and with a purifying effect.Haplotype sharing of the S-type SSU rRNA gene was observed between the P.knowlesi isolates in Sabah,Malaysian Borneo,but not between Sabah,Malaysian Borneo and Peninsular Malaysia.Conclusions:This study suggests that the S-type SSU rRNA gene of P.knowlesi isolates in Sabah,Malaysian Borneo,and Peninsular Malaysia has fewer polymorphic sites,representing the conservation of the gene.These features make the S-type SSU rRNA gene suitable for comparative studies,such as determining the evolutionary relationships and common ancestry among P.knowlesi species.

Genome-wide association mapping and genomic prediction of stalk rot in two mid-altitude tropical maize populations

Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We performed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpe?o and non-Tuxpe?o heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating genotype-by-environment(G×E)interaction increased genomic prediction accuracy.

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.

GSW3.1,a novel gene controlling grain size and weight in rice

Grain size and weight are closely related traits determining yield in rice(Oryza sativa L.).Since indica and japonica rice varieties differ significantly in multiple traits,a high-generation recombinant inbred line(RIL)population derived from the crossing LH9(indica)and RPY(japonica)was used to map grainrelated traits in six environments.Pyramiding of the quantitative trait loci(QTL)for thousand-grain weight showed that combinations of multiple QTL significantly increased the phenotypic effect.A novel gene named GSW3.1 controlling grain size and weight was discovered using the major QTL for the colocalization of grain width and thousand-grain weight on chromosome 3.Gene editing revealed that GSW3.1(LOC_Os03g16850)was pleiotropic,positively regulating grain size and weight while affecting several other agronomic traits.Haplotype analysis indicated that some traits,including grain width and weight,were highly correlated with indica-japonica differentiation.

Multi‑omics integration identifies regulatory factors underlying bovine subclinical mastitis

Background Mastitis caused by multiple factors remains one of the most common and costly disease of the dairy industry.Multi-omics approaches enable the comprehensive investigation of the complex interactions between mul-tiple layers of information to provide a more holistic view of disease pathogenesis.Therefore,this study investigated the genomic and epigenomic signatures and the possible regulatory mechanisms underlying subclinical mastitis by integrating RNA sequencing data(mRNA and lncRNA),small RNA sequencing data(miRNA)and DNA methylation sequencing data of milk somatic cells from 10 healthy cows and 20 cows with naturally occurring subclinical mastitis caused by Staphylococcus aureus or Staphylococcus chromogenes.Results Functional investigation of the data sets through gene set analysis uncovered 3458 biological process GO terms and 170 KEGG pathways with altered activities during subclinical mastitis,provided further insights into subclin-ical mastitis and revealed the involvement of multi-omics signatures in the altered immune responses and impaired mammary gland productivity during subclinical mastitis.The abundant genomic and epigenomic signatures with sig-nificant alterations related to subclinical mastitis were observed,including 30,846,2552,1276 and 57 differential methylation haplotype blocks(dMHBs),differentially expressed genes(DEGs),lncRNAs(DELs)and miRNAs(DEMs),respectively.Next,5 factors presenting the principal variation of differential multi-omics signatures were identified.The important roles of Factor 1(DEG,DEM and DEL)and Factor 2(dMHB and DEM),in the regulation of immune defense and impaired mammary gland functions during subclinical mastitis were revealed.Each of the omics within Factors 1 and 2 explained about 20%of the source of variation in subclinical mastitis.Also,networks of impor-tant functional gene sets with the involvement of multi-omics signatures were demonstrated,which contributed to a comprehensive view of the possible regulatory mechanisms underlying subclinical mastitis.Furthermore,multi-omics integration enabled the association of the epigenomic regulatory factors(dMHBs,DELs and DEMs)of altered genes in important pathways,such as‘Staphylococcus aureus infection pathway’and‘natural killer cell mediated cyto-toxicity pathway’,etc.,which provides further insights into mastitis regulatory mechanisms.Moreover,few multi-omics signatures(14 dMHBs,25 DEGs,18 DELs and 5 DEMs)were identified as candidate discriminant signatures with capac-ity of distinguishing subclinical mastitis cows from healthy cows.Conclusion The integration of genomic and epigenomic data by multi-omics approaches in this study provided a better understanding of the molecular mechanisms underlying subclinical mastitis and identified multi-omics candidate discriminant signatures for subclinical mastitis,which may ultimately lead to the development of more effective mastitis control and management strategies.

Influence of Hemoglobin S Haplotypes on the Responses to Hydroxyurea Treatment in Children with Sickle Cell Disease in Abidjan, Côte d’Ivoire

Background: In Côte d’Ivoire so far, the circulating haplotypes have been inferred on the phenotypic profiling of SCD patients. The impact of the circulating haplotypes on the use of Hydroxyurea has not been assessed yet. Therefore the objective of this study is to identify in Abidjan the HbS haplotypes that modulate HU treatment responses. Methods: In a cross-sectional descriptive and analytical study, children aged 5 to 15 years with SCD, and carrying the hemoglobin phenotypes SSFA2 and SFA2, were recruited into a HU treatment cohort. Various parameters on the haplotypes and the outcomes of the treatment were analyzed. Results: Thirty nine children with SCD were included. The phenotypic profile of the cohort was 86.6% of SSFA2 and 15.4% of SFA2. Three haplotypes were found, the Benin haplotype, the Senegal haplotype, and an atypical one. The participants belonged to three genotypes, Benin/atypical (64.1%), Benin/Senegal (33.3%) and Senegal/Senegal (2.6%). Overall, HU treatment was successful in all haplotypes with 12 out of 39 patients failing treatment after 12 months in the Benin haplotype group. The association between HU treatment success and the Benin haplotype was found in terms of the decrease in the number of white blood cells and the students missing class. Conclusion: The study revealed that inferring haplotype based on the phenotypic profile could be inaccurate. The proportion of atypical haplotype that were not previously described in Côte d’Ivoire was high. All the haplotypes seemed to be associated with HU treatment success but some patients with Benin haplotype did not respond well.

Genetic Structure of the Oriental River Prawn (Macrobrachium nipponense) from the Yangtze and Lancang Rivers, Inferred from COI Gene Sequence

This study analyzed nueleotide sequences from the mitochondrial eytochrome oxidase submit （COI） gene region （450 bp） to investigate the genetic structure of the oriental river prawn （ Macrobrachium nipponense ） among nine populations from the Yangtze and Lancang Rivers. A total of 79 individuals were collected for this work. Eighty-nine nucleotides were found to be variable, resulting in 46 haplotypes. Among the nine populations, the population from Kunming shows the greatest level of variability （h = 1.000, π = 0.028）, whereas the population from Cbongqing exhibits the lowest level of variability （h = 0.700,π = 0.008）. Analysis of molecular variance suggested that of the total genetic diversity, 9.66% was attributable to inter-population diversity and the remainder （90.34%） to differences within populations. A molecular phylogenetic tree constructed using the Neighbor-joining （N J） method showed that the 46 haplotypes were assigned to two clades associated with geographic regions. These results provide basic information for the conservation and sustainable exploitation of this species.