Soybean mosaic virus(SMV)is a worldwide disease significantly decreasing soybean yield and seed quality.In this study,a genome-wide association study(GWAS)for SMV-SC3 resistance was conducted by using a deep re-sequen...Soybean mosaic virus(SMV)is a worldwide disease significantly decreasing soybean yield and seed quality.In this study,a genome-wide association study(GWAS)for SMV-SC3 resistance was conducted by using a deep re-sequencing dataset of 547 soybean accessions.A total of 11,405 SNPs and 1566 InDels were significantly associated with disease index(DI)at seedling stage and eight yield-and seed quality-related traits to SC3 resistance under eight environments.Among these genetic loci,952 SNPs and 118 InDels were firstly identified to control SC3 resistance,and 52.42% and 42.37% of them were pleiotropic loci across multiple environments.Notably,the 8.47-8.89 Mb genomic region on chromosome 18 was firstly discovvered to associate with DI at seedling stage and four related traits at adult stage across multiple environments.Furthermore,the causal gene Gm18GRSC3 was identified and validated in this stable and pleiotropic locus for resistance to SC3 via positive and negative transgenic strategies.Overexpression of Gm18GRSC3 significantly decreased the accumulation of SC3 in transgenic soybean hairy roots,while silencing of Gm18GRSC3 significantly increased SC3 accumulation in soybean leaves.A functional marker,FM18GSC3,was developed based on the allelic variation of Gm18GRSC3,and the detection efficiency reached to 76% in another 100 soybean accessions.These findings provide valuable genetic loci and a functional gene for the improvement of SMV resistance in soybean.展开更多
Efficient and accurate identification of candidate causal genes within quantitative trait loci(QTL)is a significant challenge in genetic research.Conventional linkage analysis methods often require substantial time an...Efficient and accurate identification of candidate causal genes within quantitative trait loci(QTL)is a significant challenge in genetic research.Conventional linkage analysis methods often require substantial time and resources to identify causal genes.This paper proposes a QTG-LGBM method for prioritizing causal genes in maize based on the Light GBM algorithm.QTG-LGBM dynamically adjusts gene weights and sample proportions during training to mitigate the effects of class imbalance.The method prevents overfitting in datasets with small samples by introducing a regularization term.Experimental results on maize traits,including plant height(PH),flowering time(FT),and tassel branch number(TBN),demonstrated that QTG-LGBM outperforms the commonly used methods QTG-Finder,GBDT,XGBoost,Bernoulli NB,SVM,CNN,and ensemble learning.We validated the generalization of QTG-LGBM using Arabidopsis,rice,Setaria,and sorghum.We also applied QTG-LGBM using reported QTL that affect traits of maize PH,FT and TBN,and FT in Arabidopsis,rice,and sorghum,as well as known causal genes within the QTL.When examining the top 20%of ranked genes,QTG-LGBM demonstrated a significantly higher recall rate of causal genes compared to random selection methods.We identified key gene features affecting phenotypes through feature importance analysis.QTG-LGBM is available at http://www.deepcba.com/QTG-LGBM.展开更多
Root system architecture plays an essential role in water and nutrient acquisition in plants,and it is significantly involved in plant adaptations to various environmental stresses.In this study,a panel of 242 cotton ...Root system architecture plays an essential role in water and nutrient acquisition in plants,and it is significantly involved in plant adaptations to various environmental stresses.In this study,a panel of 242 cotton accessions was collected to investigate six root morphological traits at the seedling stage,including main root length(MRL),root fresh weight(RFW),total root length(TRL),root surface area(RSA),root volume(RV),and root average diameter(AvgD).The correlation analysis of the six root morphological traits revealed strong positive correlations of TRL with RSA,as well as RV with RSA and AvgD,whereas a significant negative correlation was found between TRL and AvgD.Subsequently,a genome-wide association study(GWAS)was performed using the root phenotypic and genotypic data reported previously for the 242 accessions using 56,010 single nucleotide polymorphisms(SNPs)from the CottonSNP80K array.A total of 41 quantitative trait loci(QTLs)were identified,including nine for MRL,six for RFW,nine for TRL,12 for RSA,12 for RV and two for AvgD.Among them,eight QTLs were repeatedly detected in two or more traits.Integrating these results with a transcriptome analysis,we identified 17 candidate genes with high transcript values of transcripts per million(TPM)≥30 in the roots.Furthermore,we functionally verified the candidate gene GH_D05G2106,which encodes a WPP domain protein 2in root development.A virus-induced gene silencing(VIGS)assay showed that knocking down GH_D05G2106significantly inhibited root development in cotton,indicating its positive role in root system architecture formation.Collectively,these results provide a theoretical basis and candidate genes for future studies on cotton root developmental biology and root-related cotton breeding.展开更多
Cotton fiber quality is a persistent concern that determines planting benefits and the quality of finished textile products.However,the limitations of measurement instruments have hindered the accurate evaluation of s...Cotton fiber quality is a persistent concern that determines planting benefits and the quality of finished textile products.However,the limitations of measurement instruments have hindered the accurate evaluation of some important fiber characteristics such as fiber maturity,fineness,and neps,which in turn has impeded the genetic improvement and industrial utilization of cotton fiber.Here,12 single fiber quality traits were measured using Advanced Fiber Information System(AFIS)equipment among 383 accessions of upland cotton(Gossypium hirsutum L.).In addition,eight conventional fiber quality traits were assessed by the High Volume Instrument(HVI)System.Genome-wide association study(GWAS),linkage disequilibrium(LD)block genotyping and functional identification were conducted sequentially to uncover the associated elite loci and candidate genes of fiber quality traits.As a result,the previously reported pleiotropic locus FL_D11 regulating fiber length-related traits was identified in this study.More importantly,three novel pleiotropic loci(FM_A03,FF_A05,and FN_A07)regulating fiber maturity,fineness and neps,respectively,were detected based on AFIS traits.Numerous highly promising candidate genes were screened out by integrating RNA-seq and qRT-PCR analyses,including the reported GhKRP6 for fiber length,the newly identified GhMAP8 for maturity and GhDFR for fineness.The origin and evolutionary analysis of pleiotropic loci indicated that the selection pressure on FL_D11,FM_A03 and FF_A05 increased as the breeding period approached the present and the origins of FM_A03 and FF_A05 were traced back to cotton landraces.These findings reveal the genetic basis underlying fiber quality and provide insight into the genetic improvement and textile utilization of fiber in G.hirsutum.展开更多
The AGCU X Plus STR system is a newly developed multiplex PCR kit that detects 32 X-chromosomal STR loci simultaneously.These are DXS6807,DXS9895,linkage group 1(DXS10148,DXS10135,DXS8378),DXS9902,DXS6795,DXS6810,DXS1...The AGCU X Plus STR system is a newly developed multiplex PCR kit that detects 32 X-chromosomal STR loci simultaneously.These are DXS6807,DXS9895,linkage group 1(DXS10148,DXS10135,DXS8378),DXS9902,DXS6795,DXS6810,DXS10159,DXS10162,DXS10164,DXS7132,linkage group 2(DXS10079,DXS10074,DXS10075),DXS981,DXS6800,DXS6803,DXS6809,DXS6789,DXS7424,DXS101,DXS7133,GATA172D05,GATA165B12,linkage group 3(DXS10103,HPRTB,DXS10101),GATA31E08 and linkage group 4(DXS8377,DXS10134,DXS7423).A major advantage of this kit is that it takes into account linkage between loci,in addition to detecting more X-STR loci.In order to evaluate the forensic application of 32 X-STR fl uorescence amplifi cation system,PCR settings,sensitivity,species specifi city,stability,DNA mixtures,concordance,stutter,sizing precision,and population genetics investigation were evaluated according to the Scientific Working Group on DNA Analysis Methods(SWGDAM)developmental validation guidelines.The study showed that the genotyping results of each locus were signifi cantly accurate when the DNA template was at least 62.5 pg.Complete profi les were obtained for the 1∶1 and 1∶3 combinations.A total of 209 unrelated individuals from Southern Chinese Han community,consisting of 84 females and 125 males,were selected for population studies,and 285 allele profi les were detected from 32 X-STR loci.The polymorphism information content(PIC)ranged from 0.2721 in DXS6800,to 0.9105 in DXS10135,with an average of 0.6798.DXS10135(PIC=0.9105)was the most polymorphic locus,with discrimination power(DP)of 0.9164 and 0.9871 for the male and female.The cumulative PD_(F),PD_(M),MEC_(trio) and MEC_(duo) valu es were all greater than 0.999999999.There were 78 different DXS10103-HPRTB-DXS10101 haplotypes among the 125 males,and the haplotype diversity was 0.9810.There was no signifi cant difference in the cumulative PD_(F),PD_(M),MEC_(trio) and MEC_(duo) values whether considering linkage or not.In summary,the new X-STR multiplex typing system is effective and reliable,which can be useful in human genetic analysis and kinship testing as a potent complement to autosomal STR typing.展开更多
A genetic linkage map with 89 SSR marker loci was constructed based on a maize (Zea mays L.) population consisting of 184 F-2 individuals from the cross, Huangzao 4 X Ye 107. The 184 F-3 families were evaluated in the...A genetic linkage map with 89 SSR marker loci was constructed based on a maize (Zea mays L.) population consisting of 184 F-2 individuals from the cross, Huangzao 4 X Ye 107. The 184 F-3 families were evaluated in the field under well-watered and drought-stressed regimes in Shanxi Province of China. The objectives of the study were to identify genetic segments responsible for the expression of anthesis-silking interval (ASI), ear setting and grain yield, and to examine if the quantitative trait loci (QTLs) for ASI or yield components can be used in marker-assisted selection (MAS) to improve grain yield under drought conditions. Results showed that under well-watered and drought-stressed regimes, three and two QTLs involved in the expression of ASI were detected on chromosomes 1, 2 and 3, and 2 and 5, respectively. Under well-watered regime, two QTLs for ear setting were detected on chromosomes 3 and 6, explaining about 19.9% of the phenotypic variance, and displayed additive and partial dominant effects, respectively. Under drought-stressed condition, four QTLs for ear setting were detected on chromosomes 3, 7 and 10, which were responsible for interpreting 60.4% of the phenotypic variance, and showed dominant or partial dominant effects. Under well-watered condition, four QTLs controlling grain yield were identified on chromosomes 3, 6 and 7, while five QTLs were identified under drought stress on chromosomes 1, 2, 4 and 8. The gene action was of additive or partial dominant effects, and each QTL could explain 7.3% to 22.0% of the phenotypic variance, respectively. Under drought conditions, ASI and ear setting percentage were highly correlated with grain yield, which can be used as secondary traits for grain yield selection. Based on linked markers detected and gene action analyzed, an MAS strategy for yield improvement under drought condition could be established, which consists of QTLs contributing to decreased ASI and to increased ear setting and grain yield, respectively.展开更多
Quantitative trait loci （QTL） were detected for 8 internal organ traits, 3 carcass length traits, and teat number trait in 214 pigs in a resource population that included 180 F2 individuals. A total of 39 microsatel...Quantitative trait loci （QTL） were detected for 8 internal organ traits, 3 carcass length traits, and teat number trait in 214 pigs in a resource population that included 180 F2 individuals. A total of 39 microsatellite markers were examined on SSC4, SSC6, SSC7, SSC8, and SSC13. The genetic traits included heart weight （HW）, lung weight （LW）, liver and gallbladder weight （LGW）, spleen weight （SPW）, stomach weight （STW）, small intestine weight （S1W）, large intestine weight （LIW）, kidney weight （KW）, carcass length to the first cervical vertebra （CL1）, carcass length to the first thoracic vertebra （CL2）, rib numbers （RNS）, and teat numbers （TNS）. Results indicated that, 3 highly significant QTL （P≤0.01 at chromosome-wise level） for HW （at 30 cM on SSC6）, RNS （at 115 cM on SSC7）, TNS （at 110 cM on SSC7）, and 6 significant QTL （P≤0.05 at chromosome-wise level） for LW （at 119 cM on SSC13）, LGW （at 94 cM on SSC6）, SPW （at 106 cM on SSC8）, SIW （0 cM on SSC4）, LIW （170 cM on SSC 4）, and TNS （at 95 cM on SSC6） were detected. The phenotypic variances for which these QTL were accounted ranged from 0.04 % to 14.06 %. Most of these QTL had not been previously reported.展开更多
This paper studies the offspring＇s genotype frequency of the selfing population on multiple alleles with limited loci.A recursive algorithm is given for it.It is discovered that the genotype frequency of homozygous g...This paper studies the offspring＇s genotype frequency of the selfing population on multiple alleles with limited loci.A recursive algorithm is given for it.It is discovered that the genotype frequency of homozygous gene of limited loci increases by generations.Relative increment reduces by generations and the genotype frequency tends to a definite value finally.The genotype frequency of limited loci with hybrid gene tends to 0 finally.But it is possibility that the genotype frequency increases in previous generations then reduces later.It is found that the number of the hybrid gene are more,the speeds tending to 0 are quicker.展开更多
The Chinese Bamboo Partridge(Bambusicola thoracica) is a gamebird endemic to China.Ten polymorphic microsatellite(simple sequence repeat) markers were obtained through cross-species amplification for this partridge fr...The Chinese Bamboo Partridge(Bambusicola thoracica) is a gamebird endemic to China.Ten polymorphic microsatellite(simple sequence repeat) markers were obtained through cross-species amplification for this partridge from its relative species Gallus gallus.The number of alleles per locus varied from 4 to 13.The observed heterozygosity ranged from 0.1220 to 1.0000 and the expected heterozygosity from 0.1183 to 0.8898.Four microsatellite loci showed significant differences from the Hardy-Weinberg equilibrium.These polymorphic loci provide a valuable tool for the investigation of the phylogeography and conservation genetics of this partridge.展开更多
To identify genetic factors underlying phosphorus (P) uptake and use efficiency under low_P stress in rice (Oryza sativa L.), 84 selected genotypes (recombinant inbred lines) and their parents (which differed in toler...To identify genetic factors underlying phosphorus (P) uptake and use efficiency under low_P stress in rice (Oryza sativa L.), 84 selected genotypes (recombinant inbred lines) and their parents (which differed in tolerance for low_P stress) “IR20” and IR55178_3B_9_3, were cultured in liquid medium supplemented with adequate and low P levels in a greenhouse. Plants were sampled after 6 weeks in culture for measurements of plant dry weight, P concentration, P uptake and P use efficiency under both P sufficient and stress conditions. A total of 179 molecular markers, including 26 RFLPs and 153 AFLPs, mapped on all 12 chromosomes of rice based on the 84 selected genotypes were used to detect the quantitative trait loci (QTLs) underlying tolerance for low_P stress. Three QTLs were detected on chromosomes 6, 7 and 12, respectively, for relative plant dry weight (RPDW) and relative P uptake (RPUP). One of the QTLs flanked by RG9 and RG241 on chromosome 12 had a major effect which explained about 50% of the variations in the two parameters across the population. The results coincided with the QTLs for low_P stress based on relative tillering ability from the same population from a cross between Nipponbare and Kasalath under soil condition. The identical major QTL for P uptake and plant growth under low_P stress in both liquid medium and soil strongly suggests that the ability of P uptake mainly controls rice tolerance for low_P stress.展开更多
1000-Grain weight and spikelet number per panicle are two important components for rice grain yield. In our previous study, eight quantitative trait loci （QTLs） conferring spikelet number per panicle and 1000-grain ...1000-Grain weight and spikelet number per panicle are two important components for rice grain yield. In our previous study, eight quantitative trait loci （QTLs） conferring spikelet number per panicle and 1000-grain weight were mapped through sequencing-based genotyping of 150 rice recombinant inbred lines （RILs）. In this study, we validated the effects of four QTLs from Nipponbare using chromosome segment substitution lines （CSSLs）, and pyramided eight grain yield related QTLs. The new lines containing the eight QTLs with positive effects showed increased panicle and spikelet size as compared with the parent variety 93-11. We further proposed a novel pyramid breeding scheme based on marker-assistant and phenotype selection （MAPS）. This scheme allowed pyramiding of as many as 24 QTLs at a single hybridization without massive cross work. This study provided insights into the molecular basis of rice grain yield for direct wealth for high-yielding rice breeding.展开更多
In this study,28,691 genome sequences and16,566 expressed sequence tags(ESTs) of Eucalyptus were derived from the Gen Bank database.A total of 2292 SSR loci were sought out from 1785 effective sequences.Through analys...In this study,28,691 genome sequences and16,566 expressed sequence tags(ESTs) of Eucalyptus were derived from the Gen Bank database.A total of 2292 SSR loci were sought out from 1785 effective sequences.Through analyses of SSR loci information,the SSR motif length was negatively correlated with the abundance of the SSRs.In the EST sequences of Eucalyptus,triplet repeat motifs were the most abundant,and dinucleotide repeats motifs had the highest frequencies.Subsequently,395 pairs of primers were designed based on the SSR loci.Using optimized SSR-PCR conditions,340 pairs of primers were successfully screened,with a success rate of 86.1%.By construction of a maximum likelihood phylogenetic tree of six eucalypt species,represented by five species of the genus Eucalyptus and one of the genus Corymbia,the genetic relationships of Eucalyptus urophylla and E.camaldulensis suggested by this tree was found to differ from that suggested by traditional morphological taxonomy.The results provide insights for evaluating geneticdiversity of Eucalyptus and analysis of Eucalyptus phylogenetics using SSR markers.展开更多
Objective To elucidate the important functions of microRNAs （miRNAs） in regulating synaptic assembly and function, we performed a computational analysis for the genetic loci required for the synaptic structure and f...Objective To elucidate the important functions of microRNAs （miRNAs） in regulating synaptic assembly and function, we performed a computational analysis for the genetic loci required for the synaptic structure and function and their corresponding miRNAs in C. elegans. Methods Total 198 genetic loci required for the synaptic structure and function were selected. Sequence alignment was combined with E value evaluation to investigate and identify the possible corresponding miRNAs. Results Total 163 genes among the 198 genetic loci selected have their possibly corresponding regulatory miRNA （s）, which covered most of the important genetic loci required for the synaptic structure and function. Moreover, only 22 genes among the analyzed 38 genetic loci encoding synaptic proteins have more possibility to under the control of non-coding RNA genes. In addition, the distribution of miRNAs along the 3＇ untranslated region （UTR） of these 22 genes exhibits different patterns. Condusion Here we provide the computational screen and analysis results for the genetic loci required for synaptic structure and function and their possible corresponding miRNAs. These data will be useful for the further attempt to systematically determine the roles of miRNAs in synaptic assembly and function regulation in worms.展开更多
Photoperiod sensitivity in maize plays an essential role in utilizing tropic and sub-tropic germplasm to temperate areas. This study aims to identify and map the QTLs responsible for the characteristics measuring phot...Photoperiod sensitivity in maize plays an essential role in utilizing tropic and sub-tropic germplasm to temperate areas. This study aims to identify and map the QTLs responsible for the characteristics measuring photoperiod sensitivity, days from planting to silking （SD）, photoperiod response coefficient of silking （PRC）, and anthesis-silking interval （ASI）. Using the population derived from Zheng 58, photoperiod-insensitive parent, and Ya 8701, photoperiod-sensitive parent, a linkage map was constructed with 93 single sequence repeat （SSR） markers. Phenotyping of 296 F2-3 families of the population in replicated-field test was conducted in both long-day （Beijing, China） and short-day （Sichuan, China） conditions. Ten QTLs were identified to be associated with the SD and ASI on chromosomes 3, 4, 6, 8, and 10 in the longday conditions, and 11 QTLs were detected to be related to the SD and ASI on chromosomes 2, 3, 4, 5, 6, 8, and 10 in the short-day conditions, respectively. A QTL associated with the PRC as a major effect in the long-day conditions located in the same position as the QTL related to the SD and ASI in the map, and was on chromosome 10 linked with marker bnlg1655. Using these QTLs in the marker-assisted selection, the photoperiod sensibility could be reduced by selection of the alleles responsible for the SD, PRC, and ASI in breeding programs.展开更多
Synthetic hexaploid wheat(SHW),possesses numerous genes for drought that can help breeding for drought-tolerant wheat varieties.We evaluated 10 root traits at seedling stage in 111 F9 recombinant inbred lines derived ...Synthetic hexaploid wheat(SHW),possesses numerous genes for drought that can help breeding for drought-tolerant wheat varieties.We evaluated 10 root traits at seedling stage in 111 F9 recombinant inbred lines derived from a F2 population of a SHW line(SHW-L1)and a common wheat line,under normal(NC)and polyethylene glycol-simulated drought stress conditions(DC).We mapped quantitative trait loci(QTLs)for root traits using an enriched high-density genetic map containing 120370 single nucleotide polymorphisms(SNPs),733 diversity arrays technology markers(DArT)and 119 simple sequence repeats(SSRs).With four replicates per treatment,we identified 19 QTLs for root traits under NC and DC,and 12 of them could be consistently detected with three or four replicates.Two novel QTLs for root fresh weight and root diameter under NC explained 9 and 15.7%of the phenotypic variation respectively,and six novel QTLs for root fresh weight,the ratio of root water loss,total root surface area,number of root tips,and number of root forks under DC explained 8.5–14%of the phenotypic variation.Here seven of eight novel QTLs could be consistently detected with more than three replicates.Results provide essential information for fine-mapping QTLs related to drought tolerance that will facilitate breeding drought-tolerant wheat cultivars.展开更多
The present study was carried out to illustrate high-efficient detection of quantitative trait loci （QTLs） with selected introgression lines （ILs） and the existence of ＇hidden genes＇ conferring drought tolerance...The present study was carried out to illustrate high-efficient detection of quantitative trait loci （QTLs） with selected introgression lines （ILs） and the existence of ＇hidden genes＇ conferring drought tolerance （DT）. 52 selected DT ILs, derived from BC2Fz population developed by crossing and backcrossing the susceptible recurrent parent （RP） IR64 with the susceptible donor Khazar were planted under irrigation and drought condition. Four important agronomic traits, e.g., grain yield （GY）, heading date （HD）, panicle numbers per plant （PN）, and plant height （PH） were evaluated and 83 SSR polymorphic molecular markers were used for genotypic analysis. Chi-square test based on genetic hitch-hiking and one-way analysis of variances （ANOVA） were used to detect drought-related loci. Nine and 36 loci were detected by chi-square test and one-way ANOVA, respectively. Five common loci were observed by comparing the results of the two methods, among which two QTLs linked with RM7, and RM241 were detected under irrigation condition, both of the favorable alleles were from RP and explained 13% phenotypic variation （PV） for GY and 28% PV for PH, respectively. The other three QTLs linked with RM 163, RM 18, and RM270 were detected under drought condition, the favorable alleles were all from the donor and explained 10, 24, and 19% PV for HD, PH, and PH, respectively. Five common loci were observed by comparing the results of chi-square test and one-way ANOVA including two QTLs （one for GY and one for PH） under irrigation condition and three QTLs （one for HD and two for PH） under drought condition. By combining phenotypic and genotypic analysis, drought escape could be inferred as the main mechanism for drought tolerance in the present study. The results in present study suggested that the selected ILs population analyzed by chi-square test and one-way ANOVA was quite effective for DT QTL detection with low inputs and could also produce useful materials for breeding with wide genetic diversity for drought tolerance.展开更多
Associations between ＂lipid-related＂ candidate genes,blood lipid concentrations and coronary artery disease（CHD） risk are not clear.We aimed to investigate the effect of three newly identified lipids loci from gen...Associations between ＂lipid-related＂ candidate genes,blood lipid concentrations and coronary artery disease（CHD） risk are not clear.We aimed to investigate the effect of three newly identified lipids loci from genome-wide association studies on CHD and blood lipid levels in Chinese Han population.The genotypes of SNPs at three newly identified lipid loci and blood lipids concentrations were examined in 1360 CHD patients and 1360 age-and sex-frequency matched controls from an unrelated Chinese Han population.Allele T of rs16996148 occurred less frequently in CHD patients with the odds ratio（OR） being 0.64（95% CI 0.50 to 0.81）,after adjusting for conventional risk factors and was associated with a 33% decreased CHD risk（P0.01） comparing with the major allele G.Individuals with GT genotype had the lowest CHD risk.No associations were found between the polymorphisms of other two loci with CHD risk and all three SNPs had no effect on lipid profile in this population.SNP rs16996148 on chromosome 19p13 is significantly associated with lower risk for CHD in Chinese Han population.However,it remains unresolved why these lipid-related loci had significantly less effects than the correspondingly expected effects on blood lipids levels in this population.展开更多
Rice straw is always regarded as a by-product of rice production,but it could be a significant energy source for ruminant animals.Knowledge of the genetic variation and genetic architecture of cell wall traits will fa...Rice straw is always regarded as a by-product of rice production,but it could be a significant energy source for ruminant animals.Knowledge of the genetic variation and genetic architecture of cell wall traits will facilitate rice breeders by improving relevant traits through selective breeding and genetic engineering.The common wild rice,Oryza rufipogon Griff.,which is considered to be the progenitor of Oryza sativa,has been widely utilized for the identification of genes of agronomic importance for rice genetic improvement.In the present study,the mapping of quantitative trait loci (QTLs) for acid detergent fiber (ADF),neutral detergent fiber (NDF),acid detergent lignin (ADL),and ADL/NDF ratio was carried out in two environments using a backcrossed inbred line (BIL) population derived from a cross between the recurrent parent Xieqingzao B (XB) and an accession of Dongxiang wild rice (DWR).The results indicated that all four traits tested were continuously distributed among the BILs,but many BILs showed transgressive segregation.A total of 16 QTLs were identified for the four traits,but no QTLs were in common in two environments,suggesting that environment has dramatic effects on fiber and lignin syntheses.Compared to the QTL positions for grain yield-related traits,there were no unfavorable correlations between grain yield components and cell wall traits in this population.The QTLs identified in this study are useful for the development of dual-purpose rice varieties that are high in grain yield and are also high in straw quality.展开更多
基金supported by the Project of Hebei Province Science and Technology Support Program(17927670H)the Science and Technology Innovation Team of Soybean Modern Seed Industry in Hebei(21326313D)。
文摘Soybean mosaic virus(SMV)is a worldwide disease significantly decreasing soybean yield and seed quality.In this study,a genome-wide association study(GWAS)for SMV-SC3 resistance was conducted by using a deep re-sequencing dataset of 547 soybean accessions.A total of 11,405 SNPs and 1566 InDels were significantly associated with disease index(DI)at seedling stage and eight yield-and seed quality-related traits to SC3 resistance under eight environments.Among these genetic loci,952 SNPs and 118 InDels were firstly identified to control SC3 resistance,and 52.42% and 42.37% of them were pleiotropic loci across multiple environments.Notably,the 8.47-8.89 Mb genomic region on chromosome 18 was firstly discovvered to associate with DI at seedling stage and four related traits at adult stage across multiple environments.Furthermore,the causal gene Gm18GRSC3 was identified and validated in this stable and pleiotropic locus for resistance to SC3 via positive and negative transgenic strategies.Overexpression of Gm18GRSC3 significantly decreased the accumulation of SC3 in transgenic soybean hairy roots,while silencing of Gm18GRSC3 significantly increased SC3 accumulation in soybean leaves.A functional marker,FM18GSC3,was developed based on the allelic variation of Gm18GRSC3,and the detection efficiency reached to 76% in another 100 soybean accessions.These findings provide valuable genetic loci and a functional gene for the improvement of SMV resistance in soybean.
基金supported by the Biological Breeding-Major Projects(2023ZD04067)Hubei Provincial Natural Science Foundation of China(2023AFB832)+1 种基金Guizhou Provincial Basic Research Program(Natural Science)(MS[2025]096)Major Project of Hubei Hongshan Laboratory(2022HSZD031)。
文摘Efficient and accurate identification of candidate causal genes within quantitative trait loci(QTL)is a significant challenge in genetic research.Conventional linkage analysis methods often require substantial time and resources to identify causal genes.This paper proposes a QTG-LGBM method for prioritizing causal genes in maize based on the Light GBM algorithm.QTG-LGBM dynamically adjusts gene weights and sample proportions during training to mitigate the effects of class imbalance.The method prevents overfitting in datasets with small samples by introducing a regularization term.Experimental results on maize traits,including plant height(PH),flowering time(FT),and tassel branch number(TBN),demonstrated that QTG-LGBM outperforms the commonly used methods QTG-Finder,GBDT,XGBoost,Bernoulli NB,SVM,CNN,and ensemble learning.We validated the generalization of QTG-LGBM using Arabidopsis,rice,Setaria,and sorghum.We also applied QTG-LGBM using reported QTL that affect traits of maize PH,FT and TBN,and FT in Arabidopsis,rice,and sorghum,as well as known causal genes within the QTL.When examining the top 20%of ranked genes,QTG-LGBM demonstrated a significantly higher recall rate of causal genes compared to random selection methods.We identified key gene features affecting phenotypes through feature importance analysis.QTG-LGBM is available at http://www.deepcba.com/QTG-LGBM.
基金supported by the Jiangsu Natural Science Foundation,China(BK20231468)the Fundamental Research Funds for the Central Universities,China(ZJ24195012)+3 种基金the National Natural Science Foundation in China(31871668)the Jiangsu Key R&D Program,China(BE2022384)the Xinjiang Uygur Autonomous Region Science and Technology Support Program,China(2021E02003)the Jiangsu Collaborative Innovation Center for Modern Crop Production Project,China(No.10)。
文摘Root system architecture plays an essential role in water and nutrient acquisition in plants,and it is significantly involved in plant adaptations to various environmental stresses.In this study,a panel of 242 cotton accessions was collected to investigate six root morphological traits at the seedling stage,including main root length(MRL),root fresh weight(RFW),total root length(TRL),root surface area(RSA),root volume(RV),and root average diameter(AvgD).The correlation analysis of the six root morphological traits revealed strong positive correlations of TRL with RSA,as well as RV with RSA and AvgD,whereas a significant negative correlation was found between TRL and AvgD.Subsequently,a genome-wide association study(GWAS)was performed using the root phenotypic and genotypic data reported previously for the 242 accessions using 56,010 single nucleotide polymorphisms(SNPs)from the CottonSNP80K array.A total of 41 quantitative trait loci(QTLs)were identified,including nine for MRL,six for RFW,nine for TRL,12 for RSA,12 for RV and two for AvgD.Among them,eight QTLs were repeatedly detected in two or more traits.Integrating these results with a transcriptome analysis,we identified 17 candidate genes with high transcript values of transcripts per million(TPM)≥30 in the roots.Furthermore,we functionally verified the candidate gene GH_D05G2106,which encodes a WPP domain protein 2in root development.A virus-induced gene silencing(VIGS)assay showed that knocking down GH_D05G2106significantly inhibited root development in cotton,indicating its positive role in root system architecture formation.Collectively,these results provide a theoretical basis and candidate genes for future studies on cotton root developmental biology and root-related cotton breeding.
基金supported by the National Key Research and Development Program of China(2022YFD1200300)the Central Plain Scholar Program,China(234000510004)the National Supercomputing Center in Zhengzhou,China。
文摘Cotton fiber quality is a persistent concern that determines planting benefits and the quality of finished textile products.However,the limitations of measurement instruments have hindered the accurate evaluation of some important fiber characteristics such as fiber maturity,fineness,and neps,which in turn has impeded the genetic improvement and industrial utilization of cotton fiber.Here,12 single fiber quality traits were measured using Advanced Fiber Information System(AFIS)equipment among 383 accessions of upland cotton(Gossypium hirsutum L.).In addition,eight conventional fiber quality traits were assessed by the High Volume Instrument(HVI)System.Genome-wide association study(GWAS),linkage disequilibrium(LD)block genotyping and functional identification were conducted sequentially to uncover the associated elite loci and candidate genes of fiber quality traits.As a result,the previously reported pleiotropic locus FL_D11 regulating fiber length-related traits was identified in this study.More importantly,three novel pleiotropic loci(FM_A03,FF_A05,and FN_A07)regulating fiber maturity,fineness and neps,respectively,were detected based on AFIS traits.Numerous highly promising candidate genes were screened out by integrating RNA-seq and qRT-PCR analyses,including the reported GhKRP6 for fiber length,the newly identified GhMAP8 for maturity and GhDFR for fineness.The origin and evolutionary analysis of pleiotropic loci indicated that the selection pressure on FL_D11,FM_A03 and FF_A05 increased as the breeding period approached the present and the origins of FM_A03 and FF_A05 were traced back to cotton landraces.These findings reveal the genetic basis underlying fiber quality and provide insight into the genetic improvement and textile utilization of fiber in G.hirsutum.
文摘The AGCU X Plus STR system is a newly developed multiplex PCR kit that detects 32 X-chromosomal STR loci simultaneously.These are DXS6807,DXS9895,linkage group 1(DXS10148,DXS10135,DXS8378),DXS9902,DXS6795,DXS6810,DXS10159,DXS10162,DXS10164,DXS7132,linkage group 2(DXS10079,DXS10074,DXS10075),DXS981,DXS6800,DXS6803,DXS6809,DXS6789,DXS7424,DXS101,DXS7133,GATA172D05,GATA165B12,linkage group 3(DXS10103,HPRTB,DXS10101),GATA31E08 and linkage group 4(DXS8377,DXS10134,DXS7423).A major advantage of this kit is that it takes into account linkage between loci,in addition to detecting more X-STR loci.In order to evaluate the forensic application of 32 X-STR fl uorescence amplifi cation system,PCR settings,sensitivity,species specifi city,stability,DNA mixtures,concordance,stutter,sizing precision,and population genetics investigation were evaluated according to the Scientific Working Group on DNA Analysis Methods(SWGDAM)developmental validation guidelines.The study showed that the genotyping results of each locus were signifi cantly accurate when the DNA template was at least 62.5 pg.Complete profi les were obtained for the 1∶1 and 1∶3 combinations.A total of 209 unrelated individuals from Southern Chinese Han community,consisting of 84 females and 125 males,were selected for population studies,and 285 allele profi les were detected from 32 X-STR loci.The polymorphism information content(PIC)ranged from 0.2721 in DXS6800,to 0.9105 in DXS10135,with an average of 0.6798.DXS10135(PIC=0.9105)was the most polymorphic locus,with discrimination power(DP)of 0.9164 and 0.9871 for the male and female.The cumulative PD_(F),PD_(M),MEC_(trio) and MEC_(duo) valu es were all greater than 0.999999999.There were 78 different DXS10103-HPRTB-DXS10101 haplotypes among the 125 males,and the haplotype diversity was 0.9810.There was no signifi cant difference in the cumulative PD_(F),PD_(M),MEC_(trio) and MEC_(duo) values whether considering linkage or not.In summary,the new X-STR multiplex typing system is effective and reliable,which can be useful in human genetic analysis and kinship testing as a potent complement to autosomal STR typing.
文摘A genetic linkage map with 89 SSR marker loci was constructed based on a maize (Zea mays L.) population consisting of 184 F-2 individuals from the cross, Huangzao 4 X Ye 107. The 184 F-3 families were evaluated in the field under well-watered and drought-stressed regimes in Shanxi Province of China. The objectives of the study were to identify genetic segments responsible for the expression of anthesis-silking interval (ASI), ear setting and grain yield, and to examine if the quantitative trait loci (QTLs) for ASI or yield components can be used in marker-assisted selection (MAS) to improve grain yield under drought conditions. Results showed that under well-watered and drought-stressed regimes, three and two QTLs involved in the expression of ASI were detected on chromosomes 1, 2 and 3, and 2 and 5, respectively. Under well-watered regime, two QTLs for ear setting were detected on chromosomes 3 and 6, explaining about 19.9% of the phenotypic variance, and displayed additive and partial dominant effects, respectively. Under drought-stressed condition, four QTLs for ear setting were detected on chromosomes 3, 7 and 10, which were responsible for interpreting 60.4% of the phenotypic variance, and showed dominant or partial dominant effects. Under well-watered condition, four QTLs controlling grain yield were identified on chromosomes 3, 6 and 7, while five QTLs were identified under drought stress on chromosomes 1, 2, 4 and 8. The gene action was of additive or partial dominant effects, and each QTL could explain 7.3% to 22.0% of the phenotypic variance, respectively. Under drought conditions, ASI and ear setting percentage were highly correlated with grain yield, which can be used as secondary traits for grain yield selection. Based on linked markers detected and gene action analyzed, an MAS strategy for yield improvement under drought condition could be established, which consists of QTLs contributing to decreased ASI and to increased ear setting and grain yield, respectively.
基金This work was supported by the State Key Basic Research and Development Plan of China (No. 2006CB102102)the National Natural Science Foundation of China (No. 30500358).
文摘Quantitative trait loci （QTL） were detected for 8 internal organ traits, 3 carcass length traits, and teat number trait in 214 pigs in a resource population that included 180 F2 individuals. A total of 39 microsatellite markers were examined on SSC4, SSC6, SSC7, SSC8, and SSC13. The genetic traits included heart weight （HW）, lung weight （LW）, liver and gallbladder weight （LGW）, spleen weight （SPW）, stomach weight （STW）, small intestine weight （S1W）, large intestine weight （LIW）, kidney weight （KW）, carcass length to the first cervical vertebra （CL1）, carcass length to the first thoracic vertebra （CL2）, rib numbers （RNS）, and teat numbers （TNS）. Results indicated that, 3 highly significant QTL （P≤0.01 at chromosome-wise level） for HW （at 30 cM on SSC6）, RNS （at 115 cM on SSC7）, TNS （at 110 cM on SSC7）, and 6 significant QTL （P≤0.05 at chromosome-wise level） for LW （at 119 cM on SSC13）, LGW （at 94 cM on SSC6）, SPW （at 106 cM on SSC8）, SIW （0 cM on SSC4）, LIW （170 cM on SSC 4）, and TNS （at 95 cM on SSC6） were detected. The phenotypic variances for which these QTL were accounted ranged from 0.04 % to 14.06 %. Most of these QTL had not been previously reported.
基金Supported by Research Project from Education Department of Guangxi(200807MS065)Mathematical Modeling in Population Genetics from Talents Scheme of Universities in Guangxi~~
文摘This paper studies the offspring＇s genotype frequency of the selfing population on multiple alleles with limited loci.A recursive algorithm is given for it.It is discovered that the genotype frequency of homozygous gene of limited loci increases by generations.Relative increment reduces by generations and the genotype frequency tends to a definite value finally.The genotype frequency of limited loci with hybrid gene tends to 0 finally.But it is possibility that the genotype frequency increases in previous generations then reduces later.It is found that the number of the hybrid gene are more,the speeds tending to 0 are quicker.
基金supported by the National Natural Science Foundation of China (Grant No. 30760036,30960051)Young Scientists (Jinggang Star) Training Scheme of Jiangxi ProvinceNatural Science Foundation of Jiangxi Province (2009GZN0075)
文摘The Chinese Bamboo Partridge(Bambusicola thoracica) is a gamebird endemic to China.Ten polymorphic microsatellite(simple sequence repeat) markers were obtained through cross-species amplification for this partridge from its relative species Gallus gallus.The number of alleles per locus varied from 4 to 13.The observed heterozygosity ranged from 0.1220 to 1.0000 and the expected heterozygosity from 0.1183 to 0.8898.Four microsatellite loci showed significant differences from the Hardy-Weinberg equilibrium.These polymorphic loci provide a valuable tool for the investigation of the phylogeography and conservation genetics of this partridge.
文摘To identify genetic factors underlying phosphorus (P) uptake and use efficiency under low_P stress in rice (Oryza sativa L.), 84 selected genotypes (recombinant inbred lines) and their parents (which differed in tolerance for low_P stress) “IR20” and IR55178_3B_9_3, were cultured in liquid medium supplemented with adequate and low P levels in a greenhouse. Plants were sampled after 6 weeks in culture for measurements of plant dry weight, P concentration, P uptake and P use efficiency under both P sufficient and stress conditions. A total of 179 molecular markers, including 26 RFLPs and 153 AFLPs, mapped on all 12 chromosomes of rice based on the 84 selected genotypes were used to detect the quantitative trait loci (QTLs) underlying tolerance for low_P stress. Three QTLs were detected on chromosomes 6, 7 and 12, respectively, for relative plant dry weight (RPDW) and relative P uptake (RPUP). One of the QTLs flanked by RG9 and RG241 on chromosome 12 had a major effect which explained about 50% of the variations in the two parameters across the population. The results coincided with the QTLs for low_P stress based on relative tillering ability from the same population from a cross between Nipponbare and Kasalath under soil condition. The identical major QTL for P uptake and plant growth under low_P stress in both liquid medium and soil strongly suggests that the ability of P uptake mainly controls rice tolerance for low_P stress.
基金supported by the Ministry of Science and Technology(Grant No. 2011 CB 100205)the Ministry of Agriculture of China (Grant Nos.2011ZX08001-004 and 2011ZX08009-002)the National Natural Science Foundation of China(Grant No. 31121063)
文摘1000-Grain weight and spikelet number per panicle are two important components for rice grain yield. In our previous study, eight quantitative trait loci （QTLs） conferring spikelet number per panicle and 1000-grain weight were mapped through sequencing-based genotyping of 150 rice recombinant inbred lines （RILs）. In this study, we validated the effects of four QTLs from Nipponbare using chromosome segment substitution lines （CSSLs）, and pyramided eight grain yield related QTLs. The new lines containing the eight QTLs with positive effects showed increased panicle and spikelet size as compared with the parent variety 93-11. We further proposed a novel pyramid breeding scheme based on marker-assistant and phenotype selection （MAPS）. This scheme allowed pyramiding of as many as 24 QTLs at a single hybridization without massive cross work. This study provided insights into the molecular basis of rice grain yield for direct wealth for high-yielding rice breeding.
基金funded by the Special Fund for Forestry Scientific Research in the Public Interest(201504204)
文摘In this study,28,691 genome sequences and16,566 expressed sequence tags(ESTs) of Eucalyptus were derived from the Gen Bank database.A total of 2292 SSR loci were sought out from 1785 effective sequences.Through analyses of SSR loci information,the SSR motif length was negatively correlated with the abundance of the SSRs.In the EST sequences of Eucalyptus,triplet repeat motifs were the most abundant,and dinucleotide repeats motifs had the highest frequencies.Subsequently,395 pairs of primers were designed based on the SSR loci.Using optimized SSR-PCR conditions,340 pairs of primers were successfully screened,with a success rate of 86.1%.By construction of a maximum likelihood phylogenetic tree of six eucalypt species,represented by five species of the genus Eucalyptus and one of the genus Corymbia,the genetic relationships of Eucalyptus urophylla and E.camaldulensis suggested by this tree was found to differ from that suggested by traditional morphological taxonomy.The results provide insights for evaluating geneticdiversity of Eucalyptus and analysis of Eucalyptus phylogenetics using SSR markers.
文摘Objective To elucidate the important functions of microRNAs （miRNAs） in regulating synaptic assembly and function, we performed a computational analysis for the genetic loci required for the synaptic structure and function and their corresponding miRNAs in C. elegans. Methods Total 198 genetic loci required for the synaptic structure and function were selected. Sequence alignment was combined with E value evaluation to investigate and identify the possible corresponding miRNAs. Results Total 163 genes among the 198 genetic loci selected have their possibly corresponding regulatory miRNA （s）, which covered most of the important genetic loci required for the synaptic structure and function. Moreover, only 22 genes among the analyzed 38 genetic loci encoding synaptic proteins have more possibility to under the control of non-coding RNA genes. In addition, the distribution of miRNAs along the 3＇ untranslated region （UTR） of these 22 genes exhibits different patterns. Condusion Here we provide the computational screen and analysis results for the genetic loci required for synaptic structure and function and their possible corresponding miRNAs. These data will be useful for the further attempt to systematically determine the roles of miRNAs in synaptic assembly and function regulation in worms.
基金supported forthis work by the program for Changjiang Scholars andInnovative Research Team in University of China(IRT0453)support was provided by the National Natural Science Foundation of China(30571173)
文摘Photoperiod sensitivity in maize plays an essential role in utilizing tropic and sub-tropic germplasm to temperate areas. This study aims to identify and map the QTLs responsible for the characteristics measuring photoperiod sensitivity, days from planting to silking （SD）, photoperiod response coefficient of silking （PRC）, and anthesis-silking interval （ASI）. Using the population derived from Zheng 58, photoperiod-insensitive parent, and Ya 8701, photoperiod-sensitive parent, a linkage map was constructed with 93 single sequence repeat （SSR） markers. Phenotyping of 296 F2-3 families of the population in replicated-field test was conducted in both long-day （Beijing, China） and short-day （Sichuan, China） conditions. Ten QTLs were identified to be associated with the SD and ASI on chromosomes 3, 4, 6, 8, and 10 in the longday conditions, and 11 QTLs were detected to be related to the SD and ASI on chromosomes 2, 3, 4, 5, 6, 8, and 10 in the short-day conditions, respectively. A QTL associated with the PRC as a major effect in the long-day conditions located in the same position as the QTL related to the SD and ASI in the map, and was on chromosome 10 linked with marker bnlg1655. Using these QTLs in the marker-assisted selection, the photoperiod sensibility could be reduced by selection of the alleles responsible for the SD, PRC, and ASI in breeding programs.
基金supported by the National Natural Science Foundation of China(31771794,91731305 and 31560388)the outstanding Youth Foundation of the Department of Science and Technology of Sichuan Province,China(2016JQ0040)+1 种基金the Key Technology Research and Development Program of the Department of Science and Technology of Sichuan Province,China(2016NZ0057)the International Science&Technology Cooperation Program of the Bureau of Science and Technology of Chengdu,China(2015DFA306002015-GH03-00008-HZ)。
文摘Synthetic hexaploid wheat(SHW),possesses numerous genes for drought that can help breeding for drought-tolerant wheat varieties.We evaluated 10 root traits at seedling stage in 111 F9 recombinant inbred lines derived from a F2 population of a SHW line(SHW-L1)and a common wheat line,under normal(NC)and polyethylene glycol-simulated drought stress conditions(DC).We mapped quantitative trait loci(QTLs)for root traits using an enriched high-density genetic map containing 120370 single nucleotide polymorphisms(SNPs),733 diversity arrays technology markers(DArT)and 119 simple sequence repeats(SSRs).With four replicates per treatment,we identified 19 QTLs for root traits under NC and DC,and 12 of them could be consistently detected with three or four replicates.Two novel QTLs for root fresh weight and root diameter under NC explained 9 and 15.7%of the phenotypic variation respectively,and six novel QTLs for root fresh weight,the ratio of root water loss,total root surface area,number of root tips,and number of root forks under DC explained 8.5–14%of the phenotypic variation.Here seven of eight novel QTLs could be consistently detected with more than three replicates.Results provide essential information for fine-mapping QTLs related to drought tolerance that will facilitate breeding drought-tolerant wheat cultivars.
基金funded by the National Basic Research Program of China (973 Program, 2004CB117204)the Program for Introduction of International Advanced Ag-ricultural Sciences & Technologies from the Ministry of Agriculture of China [948 Progam, 2006-G1(A)]the Project of Rockefeller Foundation, USA (RF2000)
文摘The present study was carried out to illustrate high-efficient detection of quantitative trait loci （QTLs） with selected introgression lines （ILs） and the existence of ＇hidden genes＇ conferring drought tolerance （DT）. 52 selected DT ILs, derived from BC2Fz population developed by crossing and backcrossing the susceptible recurrent parent （RP） IR64 with the susceptible donor Khazar were planted under irrigation and drought condition. Four important agronomic traits, e.g., grain yield （GY）, heading date （HD）, panicle numbers per plant （PN）, and plant height （PH） were evaluated and 83 SSR polymorphic molecular markers were used for genotypic analysis. Chi-square test based on genetic hitch-hiking and one-way analysis of variances （ANOVA） were used to detect drought-related loci. Nine and 36 loci were detected by chi-square test and one-way ANOVA, respectively. Five common loci were observed by comparing the results of the two methods, among which two QTLs linked with RM7, and RM241 were detected under irrigation condition, both of the favorable alleles were from RP and explained 13% phenotypic variation （PV） for GY and 28% PV for PH, respectively. The other three QTLs linked with RM 163, RM 18, and RM270 were detected under drought condition, the favorable alleles were all from the donor and explained 10, 24, and 19% PV for HD, PH, and PH, respectively. Five common loci were observed by comparing the results of chi-square test and one-way ANOVA including two QTLs （one for GY and one for PH） under irrigation condition and three QTLs （one for HD and two for PH） under drought condition. By combining phenotypic and genotypic analysis, drought escape could be inferred as the main mechanism for drought tolerance in the present study. The results in present study suggested that the selected ILs population analyzed by chi-square test and one-way ANOVA was quite effective for DT QTL detection with low inputs and could also produce useful materials for breeding with wide genetic diversity for drought tolerance.
基金supported by grants from the National Natural Sciences Foundation of China (No. 30525031 and No.30430590)
文摘Associations between ＂lipid-related＂ candidate genes,blood lipid concentrations and coronary artery disease（CHD） risk are not clear.We aimed to investigate the effect of three newly identified lipids loci from genome-wide association studies on CHD and blood lipid levels in Chinese Han population.The genotypes of SNPs at three newly identified lipid loci and blood lipids concentrations were examined in 1360 CHD patients and 1360 age-and sex-frequency matched controls from an unrelated Chinese Han population.Allele T of rs16996148 occurred less frequently in CHD patients with the odds ratio（OR） being 0.64（95% CI 0.50 to 0.81）,after adjusting for conventional risk factors and was associated with a 33% decreased CHD risk（P0.01） comparing with the major allele G.Individuals with GT genotype had the lowest CHD risk.No associations were found between the polymorphisms of other two loci with CHD risk and all three SNPs had no effect on lipid profile in this population.SNP rs16996148 on chromosome 19p13 is significantly associated with lower risk for CHD in Chinese Han population.However,it remains unresolved why these lipid-related loci had significantly less effects than the correspondingly expected effects on blood lipids levels in this population.
基金Project supported by the National Basic Research Program (973) of China (No. 2002CCC00800)the Jiangxi Provincial Inviting Tender Project for Principal Research Topic (No. 20068)the Ministry of Agriculture of China (Nos. 200803034 and 201103007)
文摘Rice straw is always regarded as a by-product of rice production,but it could be a significant energy source for ruminant animals.Knowledge of the genetic variation and genetic architecture of cell wall traits will facilitate rice breeders by improving relevant traits through selective breeding and genetic engineering.The common wild rice,Oryza rufipogon Griff.,which is considered to be the progenitor of Oryza sativa,has been widely utilized for the identification of genes of agronomic importance for rice genetic improvement.In the present study,the mapping of quantitative trait loci (QTLs) for acid detergent fiber (ADF),neutral detergent fiber (NDF),acid detergent lignin (ADL),and ADL/NDF ratio was carried out in two environments using a backcrossed inbred line (BIL) population derived from a cross between the recurrent parent Xieqingzao B (XB) and an accession of Dongxiang wild rice (DWR).The results indicated that all four traits tested were continuously distributed among the BILs,but many BILs showed transgressive segregation.A total of 16 QTLs were identified for the four traits,but no QTLs were in common in two environments,suggesting that environment has dramatic effects on fiber and lignin syntheses.Compared to the QTL positions for grain yield-related traits,there were no unfavorable correlations between grain yield components and cell wall traits in this population.The QTLs identified in this study are useful for the development of dual-purpose rice varieties that are high in grain yield and are also high in straw quality.
