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 （Mack...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）.展开更多
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 charact...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.展开更多
Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challengin...Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challenging due to its large genome size and high proportion of repetitive sequences.Allele-specific expression(ASE)plays a key role in regulating plant development and evolution,yet research on ASE in coconut is limited(Shao et al.,2019;Li et al.,2021;Zhang et al.,2021;Hu et al.,2022).Among phenotypic traits,fruit color is especially important as an indicator of maturity,guiding harvest timing and post-harvest processes(Kapoor et al.,2022).While prior studies have explored various coconut traits such as salt tolerance,fiber content,and plant height(Wang et al.,2021;Yang et al.,2021),investigations into ASE and fruit color remain scarce.展开更多
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 nucleot...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.展开更多
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 le...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.展开更多
Spike length(SL)is an important factor affecting yield in wheat(Triticum aestivum L.).Here,a recombinant inbred line(RIL)population derived from a cross between Shannong 4155(SN4155)and Shimai 12(SM12)was used to map ...Spike length(SL)is an important factor affecting yield in wheat(Triticum aestivum L.).Here,a recombinant inbred line(RIL)population derived from a cross between Shannong 4155(SN4155)and Shimai 12(SM12)was used to map quantitative trait loci(QTL)controlling SL.A QTL,q SL2B,on chromosome 2B was identified in all experiments and explained 9.92%–12.71%of the phenotypic variation.Through transcriptome and gene expression analysis,we identified a gene encoding Elongation Factor 1-alpha(Tae EF1A)as the candidate gene for q SL2B.Genome editing of Tae EF1A demonstrated that Tae EF1A positively regulates SL,spikelet number per spike(SNS),and grain number per spike(GN).Transcriptome analysis showed that Tae EF1A may affect the protein translation process and photosynthesis to regulate spike development.We used haplotype analysis of wheat germplasm to identify seven types of genetic variations in Tae EF1A,with TypeⅠ,TypeⅡ,and TypeⅢbeing the major haplotypes.Screening of 428 cultivars and breeding lines identified 225 and 203 accessions as TypeⅠand TypeⅡhaplotypes,respectively,with TypeⅢnot detected.Comparison of SL,SNS,and GN between the TypeⅠand TypeⅡhaplotypes revealed that the TypeⅠallele can increase SL,SNS,and GN simultaneously,and is thus preferred for use in wheat molecular breeding efforts to increase SL,SNS,and GN.展开更多
Coat color polymorphism in domestic animals provides a robust framework for elucidating mechanisms of species adaptation,domestication,and genomic diversity.Leiqiong cattle,a representative indicine breed from souther...Coat color polymorphism in domestic animals provides a robust framework for elucidating mechanisms of species adaptation,domestication,and genomic diversity.Leiqiong cattle,a representative indicine breed from southern China,are predominantly yellow-coated,although a subset exhibits a solid black phenotype.To determine the genetic basis of this variation,a genome-wide association study(GWAS)was performed in 212 Leiqiong bulls.A pronounced association signal was detected on chromosome 6 within the fifth intron of the CORIN gene,providing the first evidence of the potential influence of CORIN on bovine coat color variation.Integration of these results with publicly available genomic datasets and haplotype analyses indicated that the yellow coat phenotype is derived from Indian indicine ancestry,whereas the black coat phenotype emerged through introgression from wild bovine lineages and artificial hybridization with Wagyu cattle.Comparative analysis of Indian indicine cattle with divergent coat colors revealed distinct LEF1 haplotypes within a shared CORIN background,suggesting an ancient and complex domestication history underlying coat color variation.These findings provide direct evidence that introgression has shaped phenotypic variation in East Asian cattle and offer novel insights into the genetic architecture of pigmentation,with implications for future breeding strategies.展开更多
Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into a...Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.展开更多
Sagittaria trifolia L.is a perennial aquatic herb that primarily reproduces clonally and through generative propagation.In recent years,S.trifolia has evolved a drastic resistance to acetohydroxy acid synthase(AHAS)-i...Sagittaria trifolia L.is a perennial aquatic herb that primarily reproduces clonally and through generative propagation.In recent years,S.trifolia has evolved a drastic resistance to acetohydroxy acid synthase(AHAS)-inhibiting herbicides in Northeast China.The phylogeographic patterns of S.trifolia with 31 purified resistance genotypes and five sensitive genotypes using chloroplast DNA(cpDNA)atpB-rbcL intergenic spacers were studied.Five haplotypes were characterized,and two of them were widely distributed in 36 genotypes.The dose response to bensulfuron-methyl showed that the GR50 ranged from 2.07 g a.i.·hm^(-2) to 220.15 g a.i.·hm^(-2).Sequencing of the AHAS gene indicated that 17 genotypes with the Pro197 mutation were distributed in haplotype 1,six genotypes with the Trp574 mutation were distributed in haplotype 3,and 13 genotypes with the wild AHAS gene were distributed in haplotypes 2,4 and 5.In the minimum-spanning network,the ancestral haplotypes 1 and 2 were widely distributed.Two primary clades were separated in the Bayes tree,and the result was consistent with the maximum likelihood tree.展开更多
Coconut(Cocos nucifera L.)is a key tropical economic tree valued for its fruit flavor,particularly 2-acetyl-1-pyrroline(2AP),a vital aroma metabolite.To enhance high-aromatic coconut breeding efforts,it is essential t...Coconut(Cocos nucifera L.)is a key tropical economic tree valued for its fruit flavor,particularly 2-acetyl-1-pyrroline(2AP),a vital aroma metabolite.To enhance high-aromatic coconut breeding efforts,it is essential to deeply understand the hereditary factors governing the production of 2AP.In this study,a genome-wide association analysis identifies 32 loci that exhibit significant associations with 2AP content based on single nucleotide polymorphism(SNP)variations from 168 aromatic coconut germplasm resources.Transcriptome analysis then pinpoints 22 candidate genes near significant loci involved in 2AP metabolism.Proteins encoded by these genes are involved in amino acid metabolism,glycolysis,and secondary metabolism.Among these,Asparagine synthetase coding gene ASN1,Gamma-glutamylcysteine synthetase coding gene GSH1,and UbiA prenyltransferase coding gene UBIA are enriched in the linkage region constructed by significant locus Chr04_61490504.In particular,the SNP mutation of CnASN1 leads to amino acid changes in the functional region of the coding protein,potentially resulting in differences in 2AP content among haplotype populations.Identifying variations in related candidate genes,particularly the gene CnASN1,provides molecular markers closely associated with 2AP synthesis for coconut breeding and offers further insights into the metabolic mechanisms of 2AP.展开更多
FLOWERING LOCUS T (FT),a key regulator of photoperiod pathway,plays a pivotal role in modulating flowering time and growth period-related traits in plants.In this study,we identified 10 FT family genes in soybean and ...FLOWERING LOCUS T (FT),a key regulator of photoperiod pathway,plays a pivotal role in modulating flowering time and growth period-related traits in plants.In this study,we identified 10 FT family genes in soybean and examined their functional divergences through sequence alignment analysis.Phylogenetic and amino acid sequence analysis revealed that the 92nd residue and the Segment B domain (sites 129,131,134,135) are the critical determinants of potential functional divergence and activity variation among Gm FT.Using the Soy Omics website,we detected natural variations in the genomic and promoter regions of Gm FTs,along with numerous haplotypes.By correlating these haplotypes with flowering time,we identified 7 potential KASP markers associated with soybean growth period:Gm FT1a-60297360,Gm FT1b-60311669,Gm FT2a-31695562,Gm FT2b-31739433,Gm FT3a-4106476,Gm FT5a-4078626,and Gm FT5b-37490962.All KASP markers exhibited high selection efficiency (97.56%–100.00%) and reliable genotyping accuracy when validated across 82 soybean varieties spanning multiple maturity groups (MGs).This study systematically elucidates the functional divergence of Gm FTs and develops efficient KASP markers,providing essential technological support for photoperiodadaptive breeding and germplasm innovation.展开更多
Elucidating crops'physiological and molecular mechanisms to adapt to low nitrogen environment and promoting nitrogen transfer from senescent leaves to new leaves is crucial in improving Brassica's nitrogen use...Elucidating crops'physiological and molecular mechanisms to adapt to low nitrogen environment and promoting nitrogen transfer from senescent leaves to new leaves is crucial in improving Brassica's nitrogen use efficiency(NUE).Glutamine synthetase gene(GS)plays a vital role in helping plants reassimilate ammonium released from protein degradation in leaves,and it was the focus of our research on this topic.In this study,we identified high(H141)and low(L65)NUE genotypes of Brassica juncea with different responses to low-nitrogen stress.We found that H141 has a lower nitrate content but higher ammonium and free amino acid contents as well as higher nitrate reductase and GS activities in the shoots.These physiological indicators are responsible for the high NUE of H141.Wholegenome resequencing data revealed that 5,880 genes associated with NUE are polymorphic between H141 and L65.These genes participate in various amino acid,carbohydrate,and energy metabolic pathways.Haplotype analysis revealed two haplotypes for BjuB05.GS1.4,Hap1 and Hap2,which have multiple single nucleotide polymorphisms or insertions/deletions in the regulatory regions of the 5′and 3′untranslated regions and introns.Furthermore,the shoot NUE of Hap1 is significantly lower than that of Hap2.These two haplotypes of BjuB05.GS1.4 lead to differences in the shoot NUEs of different genetic populations of mustard and are associated with the local soil nitrogen content,suggesting that they might help mustard to adapt to different geographic localities.In conclusion,the results of our study shed light on the physiological and molecular mechanisms underlying different mustard NUE genotypes and demonstrate the enormous potential of NUE breeding in B.juncea.展开更多
Understanding the genetic diversity–area relationship(GAR)is essential for comprehending how species adapt to environmental changes,as genetic diversity is an indicator of a species’adaptive potential.Variation in e...Understanding the genetic diversity–area relationship(GAR)is essential for comprehending how species adapt to environmental changes,as genetic diversity is an indicator of a species’adaptive potential.Variation in environmental adaptation capacity exists among species and animal taxa with different distribution areas,highlighting the importance of understanding the GAR.To obtain a more comprehensive understanding of the GAR in terrestrial vertebrates,we assessed both haplotype diversity–area and nucleotide diversity–area relationships using 25,453 cytochrome c oxidase subunit I(COI)sequences from 142 amphibian species,574 bird species,and 342 mammal species.We found that both measures of genetic diversity increased with species range size across major animal groups.Nevertheless,the GAR did not differ among animal groups,while haplotype diversity performed better than nucleotide diversity in profiling the GAR,as indicated by higher R2 values.The difference in the modeling fit may stem from the distinct biological and mathematical significance of nucleotide diversity and haplotype diversity.These results suggest that the GAR follows similar rules among different animal taxa.Furthermore,haplotype diversity may serve as a more reliable indicator for assessing the potential effects of area size changes on animal populations and provide better guidance for conserving genetic diversity.展开更多
Objective To investigate the relationship of four single nucleotide polymorphism （SNP） haplotypes in the angiotensinogen （AGT） gene to the primary hypertension with or without cerebral infarction in the Li nationa...Objective To investigate the relationship of four single nucleotide polymorphism （SNP） haplotypes in the angiotensinogen （AGT） gene to the primary hypertension with or without cerebral infarction in the Li nationality of Hainan, China. Methods Total 300 subjects were allocated into three different groups： Groupl, 100 patients who have primary hypertension; Group 2, 100 patients who have primary hypertension with cerebral infarction; and control group, 100 healthy individuals. The genotypes of all subjects were determined by PCR-sequencing to analyze the four poly- morphisms at position - 152 （G-A）, -20 （A-C）, - 18 （C-T）, and -6 （A-G） in the promoter region of AGT. Results The frequen- cies ofCT genotype of AGT-18 and T allele in Group 1 （P = 0.003, P = 0.004） and Group 2 （P = 0.002, P = 0.002） were both significantly higher than in healthy controls. The frequency of G allele of AGT-6 was significantly higher in Group 2 than in the control group （P = 0.016）, while there is no significant difference between Group 1 and the control. Haplotype analysis revealed that H6 haplotype frequency which included -20C and -6G was significantly increased in Group 2 （P = 0.003） compared with the control group, while H5 haplotype frequency which included -20C and -18T was signifi- cantly increased in Group 1 （P = 0.006） versus the control. Conclusion The -20 （A-C） and - 18 （C-T） of the AGT may play an important role in pathogenesis of primary hypertension; and -20 （A-C）, -18 （C-T）, and -6 （A-G） may be the genetic risk factors for the onset of primary hypertension with cerebral infarction in the Li nationality of Halnan, China.展开更多
The Hooded Crane (Grus monacha) is a waterbird wintering in the wetlands of the middle and lower reaches of the Yangtze River, China. The gradual habitat loss resulting from wetland degradation may have posed negative...The Hooded Crane (Grus monacha) is a waterbird wintering in the wetlands of the middle and lower reaches of the Yangtze River, China. The gradual habitat loss resulting from wetland degradation may have posed negative effects on the structure of our wintering populations. For its effective protection, it is important to conduct an intensive study on the genetic structure of this population. A total of 221 faecal samples, nine feather samples and four muscle samples of Hooded Cranes from four wintering populations, i.e., from Caizi Lake and Shengjin Lake in Anhui, Poyang Lake in Jiangxi and Chongming Dongtan in Shanghai, were collected for this study. Full-length 1103–1104 bp mtDNA D-loop sequences from 72 samples were amplified using PCR. Based on our amplified D-loop sequences and the sequences of two individual birds obtained from GenBank (AB017625 and AB023813), we analyzed the genetic structure of these four wintering Hooded Crane populations. Twenty six variable sites were found among 72 target sequences in the four wintering populations and 23 haplotypes were defined. Genetic diversity analyses showed that the haplotype diversity of Hooded Cranes was 0.823 ± 0.042 with a nucleotide diversity of 0.00157 ± 0.00021. The FST values of the four populations show that there is no significant genetic differentiation among the populations of Hooded Cranes wintering in the middle and lower reaches of the Yangtze River. Tajima’s D and Fu’s tests suggest that the Hooded Crane populations may have experienced population expansion in their evolutionary history.展开更多
[Objective] This study aimed to analyze the genetic structure of eight populations of Spartina alterniflora in China at the nuclear DNA level.[Method] The EH277045-derived sequences were amplified from 75 samples in 8...[Objective] This study aimed to analyze the genetic structure of eight populations of Spartina alterniflora in China at the nuclear DNA level.[Method] The EH277045-derived sequences were amplified from 75 samples in 8 populations and directly sequenced.Nucleotide diversity,haplotype diversity,the mean value of Nei＇s genetic distance,genetic differentiation index FST and other genetic parameters were calculated to estimate the genetic diversity and genetic differentiation of S.alterniflora populations in China.[Result] 75 samples were divided into 25 haplotypes by 28 polymorphic sites.Relatively high nucleotide diversity（π=0.011） and haplotype diversity（Hd=0.794） were detected.The mean value of Nei＇s genetic distance and genetic differentiation index FST among eight populations were 0.056 and 0.222,respectively,the Nei＇s genetic distance ranged from 0.000 to 0.189 and FST ranged from 0.000 to 0.444 between each pair of the eight populations.AMOVA result revealed that 79% and 21% of the total genetic variation was partitioned within and among S.alterniflora populations,respectively.[Conclusion] At the nuclear DNA level,there were a relatively high level of genetic diversity and a relatively low level of genetic differentiation among S.alterniflora populations in China,and the genetic diversity existed mainly within rather than among populations.展开更多
Polyploidy is common among agriculturally important crops. Popular genetic methods and their implementations cannot always be applied to polyploid genetic data. We give an overview about available tools and their limi...Polyploidy is common among agriculturally important crops. Popular genetic methods and their implementations cannot always be applied to polyploid genetic data. We give an overview about available tools and their limitations in terms of levels of ploidy, auto- and allo-ploidy. The main classes of tools are genotype calling, linkage mapping and haplotyping. The usability of the tools is discussed with a focus on their applicability to data sets produced by state of the art technologies. We show that many challenges remain until the toolset for polyploidy provides similar functionalities as those which are already available for diploids. Some tools have been developed over a decade ago and are now outdated. In addition, we discuss necessary steps to overcome this shortage in the future.展开更多
Preimplantation genetic testing refers to the procedure to determine the genetic status of embryos formed by in vitro fertilization(IVF) prior to initiating a pregnancy.Traditional genetic methods for preimplantation ...Preimplantation genetic testing refers to the procedure to determine the genetic status of embryos formed by in vitro fertilization(IVF) prior to initiating a pregnancy.Traditional genetic methods for preimplantation genetic diagnosis(PGD) examine distinct parts of an individua genome, require the development of a custom assay for every patient family, and are time consuming and inefficient. In the last decade technologies for wholegenome amplification(WGA) from single cells have led to innovative strategies for preimplantation testing.Applications of WGA technology can lead to a universa approach that uses single-nucleotide polymorphisms(SNPs) and mutations across the entire genome for the analysis. Single-cell WGA by multiple displacement amplification has enabled a linkage approach to PGD known as "preimplantation genetic haplotyping", as well as microarray-based techniques for preimplantation diagnosis. The use of microarrays in preimplantation diagnosis has provided genome-wide testing for gains or losses of single chromosomes(aneuploidies)or chromosomal segments. Properly designed randomized controlled trials are, however, needed to determine whether these new technologies improve IVF outcomes by increasing implantation rates and decreasing mis-carriage rates. In genotype analysis of single cells, allele dropout occurs frequently at heterozygous loci. Preimplantation testing of multiple cells biopsied from blastocysts, however, can reduce allele dropout rates and increase the accuracy of genotyping, but it allows less time for PGD. Future development of fast SNP microarrays will enable a universal preimplantation testing for aneuploidies, single-gene disorders and unbalanced translocations within the time frame of an IVF cycle.展开更多
In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values w...In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large numberof samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study withhigh efficiency. The platform has been well evaluated by several sets of real data.展开更多
基金supported by the National Natural Science Foundation of China (No. 31522034)Ministry of Science and Technology of China (2016YFC0900103)the National High Technology Research and Development Program Grant (2015AA020407)
文摘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）.
基金Financial support of Department of Biotechnology,Government of India[Grant Nos.BT/AB/FG-2(PH-II)2009 and BT/PR13357/AGR/02/695/2009]
文摘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.
基金supported by Central Public-interest Scientific Institution Basal Research Fund(CATAS-Nos.1630152023007,1630152023011,1630152023012,1630152023013)the National Natural Science Foundation of China(Grant No.32071805).
文摘Coconut(Cocos nucifera L.),a major oil and fruit crop of the Arecaceae family,is extensively cultivated across the Asia—Pacific region.Despite its agricultural importance,genome assembly in coconut remains challenging due to its large genome size and high proportion of repetitive sequences.Allele-specific expression(ASE)plays a key role in regulating plant development and evolution,yet research on ASE in coconut is limited(Shao et al.,2019;Li et al.,2021;Zhang et al.,2021;Hu et al.,2022).Among phenotypic traits,fruit color is especially important as an indicator of maturity,guiding harvest timing and post-harvest processes(Kapoor et al.,2022).While prior studies have explored various coconut traits such as salt tolerance,fiber content,and plant height(Wang et al.,2021;Yang et al.,2021),investigations into ASE and fruit color remain scarce.
文摘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.
基金supported by Innovation Scientists and Technicians Troop Construction Projects of Henan Province(Grant No.212101510003)the Central Plains Scholar Workstation Project(Grant No.224400510002)+1 种基金the Youth Science Foundation of Henan Province(Grant No.202300410136)the Experimental Development Foundation of Henan University of Science and Technology(Grant No.SY2324004)。
文摘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.
基金supported by the Key R&D Program of Shandong province(2022LZGC001,2024CXPT072)the National Natural Science Foundation of China(32201863)the Tai’shan Scholars Program。
文摘Spike length(SL)is an important factor affecting yield in wheat(Triticum aestivum L.).Here,a recombinant inbred line(RIL)population derived from a cross between Shannong 4155(SN4155)and Shimai 12(SM12)was used to map quantitative trait loci(QTL)controlling SL.A QTL,q SL2B,on chromosome 2B was identified in all experiments and explained 9.92%–12.71%of the phenotypic variation.Through transcriptome and gene expression analysis,we identified a gene encoding Elongation Factor 1-alpha(Tae EF1A)as the candidate gene for q SL2B.Genome editing of Tae EF1A demonstrated that Tae EF1A positively regulates SL,spikelet number per spike(SNS),and grain number per spike(GN).Transcriptome analysis showed that Tae EF1A may affect the protein translation process and photosynthesis to regulate spike development.We used haplotype analysis of wheat germplasm to identify seven types of genetic variations in Tae EF1A,with TypeⅠ,TypeⅡ,and TypeⅢbeing the major haplotypes.Screening of 428 cultivars and breeding lines identified 225 and 203 accessions as TypeⅠand TypeⅡhaplotypes,respectively,with TypeⅢnot detected.Comparison of SL,SNS,and GN between the TypeⅠand TypeⅡhaplotypes revealed that the TypeⅠallele can increase SL,SNS,and GN simultaneously,and is thus preferred for use in wheat molecular breeding efforts to increase SL,SNS,and GN.
基金supported by the National Key R&D Program of China(2022YFF1000100)Shaanxi Innovation Team Project(2022TD-10)+1 种基金Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project(2022GD-TSLD-46-0401)Postdoctoral Research Funding of Hainan Province。
文摘Coat color polymorphism in domestic animals provides a robust framework for elucidating mechanisms of species adaptation,domestication,and genomic diversity.Leiqiong cattle,a representative indicine breed from southern China,are predominantly yellow-coated,although a subset exhibits a solid black phenotype.To determine the genetic basis of this variation,a genome-wide association study(GWAS)was performed in 212 Leiqiong bulls.A pronounced association signal was detected on chromosome 6 within the fifth intron of the CORIN gene,providing the first evidence of the potential influence of CORIN on bovine coat color variation.Integration of these results with publicly available genomic datasets and haplotype analyses indicated that the yellow coat phenotype is derived from Indian indicine ancestry,whereas the black coat phenotype emerged through introgression from wild bovine lineages and artificial hybridization with Wagyu cattle.Comparative analysis of Indian indicine cattle with divergent coat colors revealed distinct LEF1 haplotypes within a shared CORIN background,suggesting an ancient and complex domestication history underlying coat color variation.These findings provide direct evidence that introgression has shaped phenotypic variation in East Asian cattle and offer novel insights into the genetic architecture of pigmentation,with implications for future breeding strategies.
基金supported by the Shenzhen Science and Technology Program,China(Grant No.KCXFZ20211020163808012)the Nanfan Special Project,Chinese Academy of Agricultural Sciences,China(Grant No.YBXM2426).
文摘Alkaline soil is characterized by high soluble salt content,elevated pH levels,and ionic imbalance,all of which collectively intensify the harmful effects of alkaline stress on plants.To gain molecular insights into alkaline tolerance(AT),we evaluated 13 AT-related traits in 508 diverse rice accessions from the 3K Rice Germplasm Project at the seedling stage.A total of 2929764,2059114,and 1365868 single nucleotide polymorphisms were used to identify alkaline-tolerance QTLs via genome-wide association studies(GWAS)in the entire population as well as in the xian and geng subpopulations,respectively.Candidate genes and their superior haplotypes were further identified through gene-based association,haplotype analysis,and gene function annotation.In total,99 QTLs were identified for AT by GWAS,and three genes(LOC_Os03g49050 for qSSD3.1,LOC_Os05g48760 for qSKC5,and LOC_Os12g01922 for qSNC12)were selected as the most promising candidate genes.Furthermore,we successfully mined superior alleles of key candidate genes from natural variants associated with AT-related traits.This study identified crucial candidate genes and their favorable alleles for AT traits,laying a foundation for further gene cloning and the development of AT rice varieties via marker-assisted selection.
基金Supported by the"Young Talents"Project of Northeast Agricultural University(22QC04)the Domestic Post Training Excellent Program of Northeast Agricultural University(23ZYZZ0706)。
文摘Sagittaria trifolia L.is a perennial aquatic herb that primarily reproduces clonally and through generative propagation.In recent years,S.trifolia has evolved a drastic resistance to acetohydroxy acid synthase(AHAS)-inhibiting herbicides in Northeast China.The phylogeographic patterns of S.trifolia with 31 purified resistance genotypes and five sensitive genotypes using chloroplast DNA(cpDNA)atpB-rbcL intergenic spacers were studied.Five haplotypes were characterized,and two of them were widely distributed in 36 genotypes.The dose response to bensulfuron-methyl showed that the GR50 ranged from 2.07 g a.i.·hm^(-2) to 220.15 g a.i.·hm^(-2).Sequencing of the AHAS gene indicated that 17 genotypes with the Pro197 mutation were distributed in haplotype 1,six genotypes with the Trp574 mutation were distributed in haplotype 3,and 13 genotypes with the wild AHAS gene were distributed in haplotypes 2,4 and 5.In the minimum-spanning network,the ancestral haplotypes 1 and 2 were widely distributed.Two primary clades were separated in the Bayes tree,and the result was consistent with the maximum likelihood tree.
基金supported by the Major Science and Technology Project of Hainan Province(ZDKJ2021012)National Natural Science Foundation of China(32071805)the National Key Research and Development Program of China(2023YFD2200700)。
文摘Coconut(Cocos nucifera L.)is a key tropical economic tree valued for its fruit flavor,particularly 2-acetyl-1-pyrroline(2AP),a vital aroma metabolite.To enhance high-aromatic coconut breeding efforts,it is essential to deeply understand the hereditary factors governing the production of 2AP.In this study,a genome-wide association analysis identifies 32 loci that exhibit significant associations with 2AP content based on single nucleotide polymorphism(SNP)variations from 168 aromatic coconut germplasm resources.Transcriptome analysis then pinpoints 22 candidate genes near significant loci involved in 2AP metabolism.Proteins encoded by these genes are involved in amino acid metabolism,glycolysis,and secondary metabolism.Among these,Asparagine synthetase coding gene ASN1,Gamma-glutamylcysteine synthetase coding gene GSH1,and UbiA prenyltransferase coding gene UBIA are enriched in the linkage region constructed by significant locus Chr04_61490504.In particular,the SNP mutation of CnASN1 leads to amino acid changes in the functional region of the coding protein,potentially resulting in differences in 2AP content among haplotype populations.Identifying variations in related candidate genes,particularly the gene CnASN1,provides molecular markers closely associated with 2AP synthesis for coconut breeding and offers further insights into the metabolic mechanisms of 2AP.
基金supported by the National Key R&D Program of China (2023YFD1201300)the Nanfan Special Project of Chinese Academy of Agricultural Sciences (YBXM2428)the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences。
文摘FLOWERING LOCUS T (FT),a key regulator of photoperiod pathway,plays a pivotal role in modulating flowering time and growth period-related traits in plants.In this study,we identified 10 FT family genes in soybean and examined their functional divergences through sequence alignment analysis.Phylogenetic and amino acid sequence analysis revealed that the 92nd residue and the Segment B domain (sites 129,131,134,135) are the critical determinants of potential functional divergence and activity variation among Gm FT.Using the Soy Omics website,we detected natural variations in the genomic and promoter regions of Gm FTs,along with numerous haplotypes.By correlating these haplotypes with flowering time,we identified 7 potential KASP markers associated with soybean growth period:Gm FT1a-60297360,Gm FT1b-60311669,Gm FT2a-31695562,Gm FT2b-31739433,Gm FT3a-4106476,Gm FT5a-4078626,and Gm FT5b-37490962.All KASP markers exhibited high selection efficiency (97.56%–100.00%) and reliable genotyping accuracy when validated across 82 soybean varieties spanning multiple maturity groups (MGs).This study systematically elucidates the functional divergence of Gm FTs and develops efficient KASP markers,providing essential technological support for photoperiodadaptive breeding and germplasm innovation.
基金supported by the National Natural Science Foundation of China(U21A20236,32072664)the Natural Science Foundation of Hunan Province,China(2022RC3053,2021JC0001,2021RC3086,2022NK2009)+1 种基金the China Agriculture Research System(CARS-01-30)the Innovation Foundation for Graduate of Hunan Agricultural University,China(2023XC116)。
文摘Elucidating crops'physiological and molecular mechanisms to adapt to low nitrogen environment and promoting nitrogen transfer from senescent leaves to new leaves is crucial in improving Brassica's nitrogen use efficiency(NUE).Glutamine synthetase gene(GS)plays a vital role in helping plants reassimilate ammonium released from protein degradation in leaves,and it was the focus of our research on this topic.In this study,we identified high(H141)and low(L65)NUE genotypes of Brassica juncea with different responses to low-nitrogen stress.We found that H141 has a lower nitrate content but higher ammonium and free amino acid contents as well as higher nitrate reductase and GS activities in the shoots.These physiological indicators are responsible for the high NUE of H141.Wholegenome resequencing data revealed that 5,880 genes associated with NUE are polymorphic between H141 and L65.These genes participate in various amino acid,carbohydrate,and energy metabolic pathways.Haplotype analysis revealed two haplotypes for BjuB05.GS1.4,Hap1 and Hap2,which have multiple single nucleotide polymorphisms or insertions/deletions in the regulatory regions of the 5′and 3′untranslated regions and introns.Furthermore,the shoot NUE of Hap1 is significantly lower than that of Hap2.These two haplotypes of BjuB05.GS1.4 lead to differences in the shoot NUEs of different genetic populations of mustard and are associated with the local soil nitrogen content,suggesting that they might help mustard to adapt to different geographic localities.In conclusion,the results of our study shed light on the physiological and molecular mechanisms underlying different mustard NUE genotypes and demonstrate the enormous potential of NUE breeding in B.juncea.
基金supported by the National Natural Science Foundation of China(32130013,32070434)the National Key Research and Development Program of China(2022YFC2601601)+1 种基金the Second Tibetan Plateau Scientific Expedition and Research(STEP)program(2019QZKK05010112,2019QZKK0304-02)Hainan Tropical Rainforest Conservation Research Project,ZDYF2023RDYL01(supported by the Hainan Institute of National Park,HINP,KY-24ZK02).
文摘Understanding the genetic diversity–area relationship(GAR)is essential for comprehending how species adapt to environmental changes,as genetic diversity is an indicator of a species’adaptive potential.Variation in environmental adaptation capacity exists among species and animal taxa with different distribution areas,highlighting the importance of understanding the GAR.To obtain a more comprehensive understanding of the GAR in terrestrial vertebrates,we assessed both haplotype diversity–area and nucleotide diversity–area relationships using 25,453 cytochrome c oxidase subunit I(COI)sequences from 142 amphibian species,574 bird species,and 342 mammal species.We found that both measures of genetic diversity increased with species range size across major animal groups.Nevertheless,the GAR did not differ among animal groups,while haplotype diversity performed better than nucleotide diversity in profiling the GAR,as indicated by higher R2 values.The difference in the modeling fit may stem from the distinct biological and mathematical significance of nucleotide diversity and haplotype diversity.These results suggest that the GAR follows similar rules among different animal taxa.Furthermore,haplotype diversity may serve as a more reliable indicator for assessing the potential effects of area size changes on animal populations and provide better guidance for conserving genetic diversity.
基金the Science Foundation of the Health Department of Hainan Province, China （No. 2005-65）.
文摘Objective To investigate the relationship of four single nucleotide polymorphism （SNP） haplotypes in the angiotensinogen （AGT） gene to the primary hypertension with or without cerebral infarction in the Li nationality of Hainan, China. Methods Total 300 subjects were allocated into three different groups： Groupl, 100 patients who have primary hypertension; Group 2, 100 patients who have primary hypertension with cerebral infarction; and control group, 100 healthy individuals. The genotypes of all subjects were determined by PCR-sequencing to analyze the four poly- morphisms at position - 152 （G-A）, -20 （A-C）, - 18 （C-T）, and -6 （A-G） in the promoter region of AGT. Results The frequen- cies ofCT genotype of AGT-18 and T allele in Group 1 （P = 0.003, P = 0.004） and Group 2 （P = 0.002, P = 0.002） were both significantly higher than in healthy controls. The frequency of G allele of AGT-6 was significantly higher in Group 2 than in the control group （P = 0.016）, while there is no significant difference between Group 1 and the control. Haplotype analysis revealed that H6 haplotype frequency which included -20C and -6G was significantly increased in Group 2 （P = 0.003） compared with the control group, while H5 haplotype frequency which included -20C and -18T was signifi- cantly increased in Group 1 （P = 0.006） versus the control. Conclusion The -20 （A-C） and - 18 （C-T） of the AGT may play an important role in pathogenesis of primary hypertension; and -20 （A-C）, -18 （C-T）, and -6 （A-G） may be the genetic risk factors for the onset of primary hypertension with cerebral infarction in the Li nationality of Halnan, China.
基金supported by the National Natural Science Foundation of China (Grant No 31172117)the Anhui Academic and Technical Leaders Fund
文摘The Hooded Crane (Grus monacha) is a waterbird wintering in the wetlands of the middle and lower reaches of the Yangtze River, China. The gradual habitat loss resulting from wetland degradation may have posed negative effects on the structure of our wintering populations. For its effective protection, it is important to conduct an intensive study on the genetic structure of this population. A total of 221 faecal samples, nine feather samples and four muscle samples of Hooded Cranes from four wintering populations, i.e., from Caizi Lake and Shengjin Lake in Anhui, Poyang Lake in Jiangxi and Chongming Dongtan in Shanghai, were collected for this study. Full-length 1103–1104 bp mtDNA D-loop sequences from 72 samples were amplified using PCR. Based on our amplified D-loop sequences and the sequences of two individual birds obtained from GenBank (AB017625 and AB023813), we analyzed the genetic structure of these four wintering Hooded Crane populations. Twenty six variable sites were found among 72 target sequences in the four wintering populations and 23 haplotypes were defined. Genetic diversity analyses showed that the haplotype diversity of Hooded Cranes was 0.823 ± 0.042 with a nucleotide diversity of 0.00157 ± 0.00021. The FST values of the four populations show that there is no significant genetic differentiation among the populations of Hooded Cranes wintering in the middle and lower reaches of the Yangtze River. Tajima’s D and Fu’s tests suggest that the Hooded Crane populations may have experienced population expansion in their evolutionary history.
基金Supported by National Natural Science Foundation of China(30900161)~~
文摘[Objective] This study aimed to analyze the genetic structure of eight populations of Spartina alterniflora in China at the nuclear DNA level.[Method] The EH277045-derived sequences were amplified from 75 samples in 8 populations and directly sequenced.Nucleotide diversity,haplotype diversity,the mean value of Nei＇s genetic distance,genetic differentiation index FST and other genetic parameters were calculated to estimate the genetic diversity and genetic differentiation of S.alterniflora populations in China.[Result] 75 samples were divided into 25 haplotypes by 28 polymorphic sites.Relatively high nucleotide diversity（π=0.011） and haplotype diversity（Hd=0.794） were detected.The mean value of Nei＇s genetic distance and genetic differentiation index FST among eight populations were 0.056 and 0.222,respectively,the Nei＇s genetic distance ranged from 0.000 to 0.189 and FST ranged from 0.000 to 0.444 between each pair of the eight populations.AMOVA result revealed that 79% and 21% of the total genetic variation was partitioned within and among S.alterniflora populations,respectively.[Conclusion] At the nuclear DNA level,there were a relatively high level of genetic diversity and a relatively low level of genetic differentiation among S.alterniflora populations in China,and the genetic diversity existed mainly within rather than among populations.
文摘Polyploidy is common among agriculturally important crops. Popular genetic methods and their implementations cannot always be applied to polyploid genetic data. We give an overview about available tools and their limitations in terms of levels of ploidy, auto- and allo-ploidy. The main classes of tools are genotype calling, linkage mapping and haplotyping. The usability of the tools is discussed with a focus on their applicability to data sets produced by state of the art technologies. We show that many challenges remain until the toolset for polyploidy provides similar functionalities as those which are already available for diploids. Some tools have been developed over a decade ago and are now outdated. In addition, we discuss necessary steps to overcome this shortage in the future.
基金Supported by Department of Pediatrics,Medical College of Wisconsin,Milwaukee,WI,United States
文摘Preimplantation genetic testing refers to the procedure to determine the genetic status of embryos formed by in vitro fertilization(IVF) prior to initiating a pregnancy.Traditional genetic methods for preimplantation genetic diagnosis(PGD) examine distinct parts of an individua genome, require the development of a custom assay for every patient family, and are time consuming and inefficient. In the last decade technologies for wholegenome amplification(WGA) from single cells have led to innovative strategies for preimplantation testing.Applications of WGA technology can lead to a universa approach that uses single-nucleotide polymorphisms(SNPs) and mutations across the entire genome for the analysis. Single-cell WGA by multiple displacement amplification has enabled a linkage approach to PGD known as "preimplantation genetic haplotyping", as well as microarray-based techniques for preimplantation diagnosis. The use of microarrays in preimplantation diagnosis has provided genome-wide testing for gains or losses of single chromosomes(aneuploidies)or chromosomal segments. Properly designed randomized controlled trials are, however, needed to determine whether these new technologies improve IVF outcomes by increasing implantation rates and decreasing mis-carriage rates. In genotype analysis of single cells, allele dropout occurs frequently at heterozygous loci. Preimplantation testing of multiple cells biopsied from blastocysts, however, can reduce allele dropout rates and increase the accuracy of genotyping, but it allows less time for PGD. Future development of fast SNP microarrays will enable a universal preimplantation testing for aneuploidies, single-gene disorders and unbalanced translocations within the time frame of an IVF cycle.
基金This work was supported by the Major State Basic Research Development program of Chinathe National High Technology Research and Development Program of China.
文摘In multiloci-based genetic association studies of complex diseases, a powerful and high efficient tool for analyses oflinkage disequilibrium (LD) between markers, haplotype distributions and many chi-square/p values with a large numberof samples has been sought for long. In order to achieve the goal of obtaining meaningful results directly from raw data,we developed a robust and user-friendly software platform with a series of tools for analysis in association study withhigh efficiency. The platform has been well evaluated by several sets of real data.
