Single nucleotide polymorphism(SNP)genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants.In this study,a highquality and custom-d...Single nucleotide polymorphism(SNP)genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants.In this study,a highquality and custom-designed Rice3K56 SNP array was developed with the resequencing data of 3024 rice accessions worldwide,which was then tested extensively in 192 representative rice samples.Printed on the Gene Titan chips of Affymetrix Axiom each containing 56,606 SNP markers,the Rice3K56 array has a high genotyping reliability(99.6%),high and uniform genome coverage(an average of 6.7-kb between adjacent SNPs),abundant polymorphic information and easy automation,compared with previously developed rice SNP arrays.When applied in rice varietal differentiation,population diversity analysis,gene mapping of 13 complex traits by a genome-wide association study analysis(GWAS),and genome selection experiments in a recombinant inbred line and a multi-parent advanced generation inter-cross populations,these properties of the Rice3K56 array were well demonstrated for its power and great potential to be a highly efficient tool for rice genetic research and genomic breeding.展开更多
Psathyrostachys huashanica Keng(2n=2x=14,NsNs)is regarded as a valuable wild relative species for common wheat cultivar improvement because of its abundant beneficial agronomic traits.However,although the development ...Psathyrostachys huashanica Keng(2n=2x=14,NsNs)is regarded as a valuable wild relative species for common wheat cultivar improvement because of its abundant beneficial agronomic traits.However,although the development of many wheat–P.huashanica-derived lines provides a germplasm base for the transfer of excellent traits,the lag in the identification of P.huashanica chromosomes in the wheat background has limited the study of these lines.In this study,three novel nondenaturing fluorescence in situ hybridization(ND-FISH)-positive oligo probes were developed.Among them,HS-TZ3 and HS-TZ4 could specifically hybridize with P.huashanica chromosomes,mainly in the telomere area,and HS-CHTZ5 could hybridize with the chromosomal centromere area.We sequentially constructed a P.huashanica FISH karyotype and idiogram that helped identify the homologous groups of introduced P.huashanica chromosomes.In detail,1Ns and 2Ns had opposite signals on the short and long arms,3Ns,4Ns,and 7Ns had superposed two-color signals,5Ns and 6Ns had fluorescent signals only on their short arms,and 7Ns had signals on the intercalary of the long arm.In addition,we evaluated different ways to identify alien introgression lines by using low-density single nucleotide polymorphism(SNP)arrays and recommended the SNP homozygosity rate in each chromosome as a statistical pattern.The 15K SNP array is widely applicable for addition,substitution,and translocation lines,and the 40K SNP array is the most accurate for recognizing transposed intervals between wheat and alien chromosomes.Our research provided convenient methods to distinguish the homologous group of P.huashanica chromosomes in a common wheat background based on ND-FISH and SNP arrays,which is of great significance for efficiently identifying wheat–P.huashanica-derived lines and the further application of Ns chromosomes.展开更多
Single nucleotide polymorphism(SNP)armays are a powerful genotyping tool used in genetic research and genomic breeding programs.Japanese flounder(Paralichthys olivaceus)is an economically-important aquaculture flatfis...Single nucleotide polymorphism(SNP)armays are a powerful genotyping tool used in genetic research and genomic breeding programs.Japanese flounder(Paralichthys olivaceus)is an economically-important aquaculture flatfish in many countries.However,the lack of high-efficient genotyping tools has impeded the genomic breeding programs for Japanese flounder.We developed a 50K Japanese flounder SNP array,"Yuxin No.1,"and report its utility in genomic selection(GS)for disease resistance to bacterial pathogens.We screened more than 42,.2 million SNPs from the whole-genome resequencing data of 1099 individuals and selected 48697 SNPs that were evenly distributed across the genome to anchor the array with Affymetrix Axiom genotyping technology.Evaluation of the array performance with 168 fishs howed that 74.7%of the loci were successfully genotyped with high call rates(>98%)and that the poly-morphic SNPs had good cluster separations.More than 85%of the SNPs were concordant with SNPs obtained from the whole-genome resequencing data.To validate"Yuxin No.1"for GS,the arrayed geno-typing data of 27 individuals from a candidate population and 931 individuals from a reference popula-tion were used to calculate the genomic estimated breeding values(GEBVs)for disease resistance toEdwardsiella tarda.There was a 21.2%relative increase in the accuracy of GEBV using the weighted geno-mic best linear unpiased prediction(wGBLUJP),compared to traditional pedigree-based best linear unbi-ased prediction(ABLUP),suggesting good performance of the'Yuxin No.1"SNP array for GS.In summary,we developed the"Yuxin No.1"50K SNP array,which provides a useful platform for high-quality geno-typing that may be beneficial to the genomic selective breeding of Japanese flounder.展开更多
Foliar fungal diseases(rust and late leaf spot)incur large yield losses,in addition to the deterioration of fodder quality in groundnut worldwide.High oleic acid has emerged as a key market trait in groundnut,as it in...Foliar fungal diseases(rust and late leaf spot)incur large yield losses,in addition to the deterioration of fodder quality in groundnut worldwide.High oleic acid has emerged as a key market trait in groundnut,as it increases the shelf life of the produce/products in addition to providing health benefits to consumers.Marker-assisted backcrossing(MABC)is the most successful approach to introgressing or pyramiding one or more traits using traitlinked markers.We used MABC to improve three popular Indian cultivars(GJG 9,GG 20,and GJGHPS 1)for foliar disease resistance(FDR)and high oleic acid content.A total of 22 BC3F4 and 30 BC2F4 introgression lines(ILs)for FDR and 46 BC3F4 and 41 BC2F4 ILs for high oleic acid were developed.Recurrent parent genome analysis using the 58 K Axiom_Arachis array identified several lines showing upto 94%of genome recovery among second and third backcross progenies.Phenotyping of these ILs revealed FDR scores comparable to the resistant parent,GPBD 4,and ILs with high(~80%)oleic acid in addition to high genome recovery.These ILs provide further opportunities for pyramiding FDR and high oleic acid in all three genetic backgrounds as well as for conducting multi-location yield trials for further evaluation and release for cultivation in target regions of India.展开更多
Quality deficiencies in single nucleotide polymorphism (SNP) analyses have important implications. We used missingness rates to investigate the quality of a recently published dataset containing 424 mitochonddal, 21...Quality deficiencies in single nucleotide polymorphism (SNP) analyses have important implications. We used missingness rates to investigate the quality of a recently published dataset containing 424 mitochonddal, 211 Y chromosomal, and 160 432 autosomal SNPs generated by a semicustom Illumina SNP array from 5 392 dogs and 14 grey wolves. Overall, the individual missingness rate for mitochondrial SNPs was -43.8%, with 980 (18.1%)individuals completely missing mitochondrial SNP genotyping (missingness rate=l). In males, the genotype missingness rate was -28.8% for Y chromosomal SNPs, with 374 males recording rates above 0.96. These 374 males also exhibited completely failed mitochondrial SNPs genotyping, indicative of a batch effect. Individual missingness rates for autosomal markers were greater than zero, but less than 0.5. Neither mitochondrial nor Y chromosomal SNPs achieved complete genotyping (locus missingness rate=0), whereas 5.9% of autosomal SNPs had a locus missingness rate=l. The high missingness rates and possible batch effect show that caution and rigorous measures are vital when genotyping and analyzing SNP array data for domestic animals. Further improvements of these arrays will be helpful to future studies.展开更多
High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide eval...High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line (RIL) population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length ofl.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.展开更多
Genomic selection(GS)is a powerful tool for improving genetic gain in maize breeding.However,its routine application in large-scale breeding pipelines is limited by the high cost of genotyping platforms.Although seque...Genomic selection(GS)is a powerful tool for improving genetic gain in maize breeding.However,its routine application in large-scale breeding pipelines is limited by the high cost of genotyping platforms.Although sequencing-based and array-based genotyping platforms have been used for GS,few studies have compared prediction performance among platforms.In this study,we evaluated the predictabilities of four agronomic traits in 305 maize hybrids derived from 149 parental lines subjected to genotyping by sequencing(GBS),a 40K SNP array,and target sequence capture(TSC)using eight GS models.The GBS marker dataset yielded the highest predictabilities for all traits,followed by TSC and SNP array datasets.We investigated the effect of marker density and statistical models on predictability among genotyping platforms and found that 1K SNPs were sufficient to achieve comparable predictabilities to 10K and all SNPs,and BayesB,GBLUP,and RKHS performed well,while XGBoost performed poorly in most cases.We also selected significant SNP subsets using genome-wide association study(GWAS)analyses in three panels to predict hybrid performance.GWAS facilitated selecting effective SNP subsets for GS and thus reduced genotyping cost,but depended heavily on the GWAS panel.We conclude that there is still room for optimization of the existing SNP array,and using genotyping by target sequencing(GBTS)techniques to integrate a few functional markers identified by GWAS into the 1K SNP array holds great promise of being an effective strategy for developing desirable GS breeding arrays.展开更多
Plant nitrogen assimilation and use efficiency in the seedling's root system are beneficial for adult plants in field condition for yield enhancement.Identification of the genetic basis between root traits and N u...Plant nitrogen assimilation and use efficiency in the seedling's root system are beneficial for adult plants in field condition for yield enhancement.Identification of the genetic basis between root traits and N uptake plays a crucial role in wheat breeding.In the present study,198 doubled haploid lines from the cross of Yangmai 16/Zhongmai 895 were used to identify quantitative trait loci(QTLs)underpinning four seedling biomass traits and five root system architecture(RSA)related traits.The plants were grown under hydroponic conditions with control,low and high N treatments(Ca(NO_(3))_(2)·4H_(2)O at 0,0.05 and 2.0 mmol L^(-1),respectively).Significant variations among the treatments and genotypes,and positive correlations between seedling biomass and RSA traits(r=0.20 to 0.98)were observed.Inclusive composite interval mapping based on a high-density map from the Wheat 660 K single nucleotide polymorphisms(SNP)array identified 51 QTLs from the three N treatments.Twelve new QTLs detected on chromosomes 1 AL(1)in the control,1 DS(2)in high N treatment,4 BL(5)in low and high N treatments,and 7 DS(3)and 7 DL(1)in low N treatments,are first reported in influencing the root and biomass related traits for N uptake.The most stable QTLs(RRS.caas-4 DS)on chromosome 4 DS,which were related to ratio of root to shoot dry weight trait,was in close proximity of the Rht-D1 gene,and it showed high phenotypic effects,explaining 13.1%of the phenotypic variance.Twenty-eight QTLs were clustered in 12 genetic regions.SNP markers tightly linked to two important QTLs clusters C10 and C11 on chromosomes 6 BL and 7 BL were converted to kompetitive allele-specific PCR(KASP)assays that underpin important traits in root development,including root dry weight,root surface area and shoot dry weight.These QTLs,clusters and KASP assays can greatly improve the efficiency of selection for root traits in wheat breeding programmes.展开更多
High-density single nucleotide polymorphism (SNP) genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP d...High-density single nucleotide polymorphism (SNP) genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP discovery was performed using deep resequencing of eight libraries derived from 132 Elaeis guineen- sis and Elaeis oleifera palms belonging to 59 origins, resulting in the discovery of 〉3 million putative SNPs. After SNP filtering, the Illumina OP200K custom array was built with 170 860 successful probes. Phenetic clustering analysis revealed that the array could distinguish between palms of different origins in a way consistent with pedigree records. Genome-wide linkage disequilibrium declined more slowly for the commercial populations (ranging from 120 kb at r2 = 0.43 to 146 kb at r2 = 0.50) when compared with the semi-wild populations (19.5 kb at r2 = 0.22). Genetic fixation mapping comparing the semi-wild and commercial population identified 321 selective sweeps. A genome-wide association study (GWAS) detected a significant peak on chromosome 2 associated with the polygenic component of the shell thick- ness trait (based on the trait shell-to-fruit; S/F %) in tenera palms. Testing of a genomic selection model on the same trait resulted in good prediction accuracy (r = 0.65) with 42% of the S/F % variation explained. The first high-density SNP genotyping array for oil palm has been developed and shown to be robust for use in genetic studies and with potential for developing early trait prediction to shorten the oil palm breeding cycle.展开更多
Background:Chronic diseases are becoming a critical challenge to the aging Chinese population.Biobanks with extensive genomic and environmental data offer opportunities to elucidate the complex gene-environment intera...Background:Chronic diseases are becoming a critical challenge to the aging Chinese population.Biobanks with extensive genomic and environmental data offer opportunities to elucidate the complex gene-environment interactions underlying their aetiology.Genome-wide genotyping array remains an efficient approach for large-scale genomic data collection.However,most commercial arrays have reduced performance for biobanking in the Chinese population.Materials and methods:Deep whole-genome sequencing data from 2641 Chinese individuals were used as a reference to develop the CAS array,a custom-designed genotyping array for precision medicine.Evaluation of the array was performed by comparing data from 384 individuals assayed both by the array and whole-genome sequencing.Validation of its mitochondrial copy number estimating capacity was conducted by examining its association with established covariates among 10162 Chinese elderly.Results:The CAS Array adopts the proven Axiom technology and is restricted to 652429 single-nucleotide polymorphism(SNP)markers.Its call rate of 99.79% and concordance rate of 99.89% are both higher than for commercial arrays.Its imputation-based genome coverage reached 98.3% for common SNPs and 63.0% for low-frequency SNPs,both comparable to commercial arrays with larger SNP capacity.After validating its mitochondrial copy number estimates,we developed a publicly available software tool to facilitate the array utility.Conclusion:Based on recent advances in genomic science,we designed and implemented a high-throughput and low-cost genotyping array.It is more cost-effective than commercial arrays for large-scale Chinese biobanking.展开更多
Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most damaging diseases to wheat in the world. The cultivation of resistant varieties of wheat is essential for controlling the powdery ...Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most damaging diseases to wheat in the world. The cultivation of resistant varieties of wheat is essential for controlling the powdery mildew epidemic. Wheat landraces are important resources of resistance to many diseases. Mapping powdery mildew resistance genes from wheat landraces will promote the development of new varieties with disease resistance. The Chinese wheat landrace Baiyouyantiao possesses characteristic of disease resistance to powdery mildew. To identify the resistance gene in this landrace, Baiyouyantiao was crossed with the susceptible cultivar Jingshuang 16 and seedlings of parents and F1, BC1, F2, and F~:3 were tested with Bgt isolate E09. The genetic results showed that the resistance of Baiyouyantiao to E09 was controlled by a single recessive gene, tentatively designated PmBYYT. An Illumina wheat 90K single-nucleotide polymorphism (SNP) array was applied to screen polymorphisms between F2-resistant and F2-susceptible DNA bulks for identifying the chromosomal location of PmBYYT. A high percentage of polymorphic SNPs between the resistant and susceptible DNA bulks was found on chro- mosome 7B, indicating that PmBYYT may be located on this chromosome. A genetic linkage map of PmBYYTconsisting of two simple sequence repeat markers and eight SNP markers was developed. The two flanking markers were SNP markers W7BL-8 and W7BL-15, with genetic distances of 3 and 2.9 cM, respectively. The results of this study demonstrated the rapid characterization of a wheat disease resistance gene and SNP marker development using the 90K SNP assay. The flanking markers of gene PmBYYTwill benefit marker-assisted selection (MAS) and map-based cloning in breeding wheat cultivars with powdery mildew resistance.展开更多
目的研究探讨不同遗传学分析方法对诊断自然流产组织产生原因的应用效果。方法选择广西壮族自治区妇幼保健院2014年9月至2014年11月收治的自然流产患者42例为研究对象。所有研究对象均采用染色体核型分析和SNP Array检测分析方法,比较...目的研究探讨不同遗传学分析方法对诊断自然流产组织产生原因的应用效果。方法选择广西壮族自治区妇幼保健院2014年9月至2014年11月收治的自然流产患者42例为研究对象。所有研究对象均采用染色体核型分析和SNP Array检测分析方法,比较分析结果。结果两种不同遗传分析方法能够诊断出自然流产41例,使用染色体核型分析成功37例,绒毛细胞培养染色体核型分析成功34例,染色体核型分析准确成功率为88%,绒毛细胞培养染色体核型分析成功诊断率为80.9%;两种遗传分析方法同时应用于自然流产原因诊断中,诊断准确率提高到97.6%。结论 SNP Array检测方法分析具有可行性。两种遗传学检测方法比较,染色体核型分析诊断概率比较高。在临床诊断的过程中,两种遗传检测方法结合使用,大大提高了自然流产原因的诊断准确率。展开更多
Background:Thanks to an improved therapeutic regimen in childhood B-cell precursor acute lymphoblastic leukemia(BCP-ALL),5 year-overall survival now exceeds 90%.Unfortunately,the 25%of children who relapse have an ini...Background:Thanks to an improved therapeutic regimen in childhood B-cell precursor acute lymphoblastic leukemia(BCP-ALL),5 year-overall survival now exceeds 90%.Unfortunately,the 25%of children who relapse have an initial poor prognosis,potentially driven by pre-existing or emerging molecular anomalies.The latter are initially and essentially identified by cytogenetics.However,some subtle alterations are not visible through karyotyping.Methods:Single nucleotide polymorphisms(SNP)array is an alternative way of chromosomal analysis allowing for a more in-depth evaluation of chromosomal modifications such as the assessment of copy number alterations(CNA)and loss of heterozygosity(LOH).This method was applied here in retrospective diagnosis/relapse paired samples from seven children with BCP-ALL and in a prospective cohort of 38 newly diagnosed childhood cases.Results:In the matched study,compared to the initial karyotype,SNP array analysis reclassified two patients as poor prognosis cases.Modulation during relapse was seen for 4 CNA and 0.9 LOH.In the prospective study,SNP reclassified the 10 patients with intermediate karyotype as 7 good prognosis and 3 poor prognosis.Ultimately,in all the children tested,SNP array allowed to identify additional anomalies compared to conventional karyotype,refine its prognostic value and identify some druggable anomalies that could be used for precision medicine.Overall,the anomalies detected could be segregated in four groups respectively involved in B-cell development,cell proliferation,transcription and molecular pathways.Conclusion:SNP therefore appears to be a method of choice in the integrated diagnosis of BCP ALL,especially for patients initially classified as intermediate prognosis.This complementary method of both cytogenetics and high throughput sequencing allows to obtain further classified information and can be useful in case of failure of these techniques.展开更多
Stripe rust,caused by Puccinia striformis f.sp.tritici(Pst),is one of the most destructive diseases of wheat(Triticum aestivum L)worldwide.Xiaoyan 78829,a partial amphidiploid developed by crossing common wheat with T...Stripe rust,caused by Puccinia striformis f.sp.tritici(Pst),is one of the most destructive diseases of wheat(Triticum aestivum L)worldwide.Xiaoyan 78829,a partial amphidiploid developed by crossing common wheat with Thinopyrum intermedium,is immune to wheat stripe rust.To transfer the resis-tance gene of this excellent germplasm resource to wheat,the tr anslocation line WTT11 was produced by pollen irradiation and assessed for immunity to stripe rust races CYR32,CYR33 and CYR34.A novel stripe rust-resistance locus derived from Th.intermedium was confirmed by linkage and diagnostic marker analyses.Molecular cytogenetic analyses revealed that WTT11 carries a TTh 2DL translocation.The breakpoint of 1B was located at 95.5 MB,and the alien segments were found to be homoeologous to wheat-group chromosomes 6 and 7 according to a wheat660K single-nucleotide polymorphism(SNP)array analysis.Ten previously developed PCR-based markers were confirmed to rapidly trace the alien segments of WTT11,and 20 kompetitive allele-specific PCR(KASP)markers were developed to enable genotyping of Th.intermedium and common wheat.Evaluation of agronomic traits in two consecutive crop seasons uncovered some favorable agronomic traits in WTT11,such as lower plant height and longer main panicles,that may be applicable to wheat improvement.As a novel genetic resource,the new resistance locus may be useful for wheat disease-resistance breeding.展开更多
基金supported by the National Natural Science Foundation of China(31971927 and U21A20214)the Science and Technology Major Project of Anhui Province(2021d06050002)+4 种基金the Improved Varieties Joint Research(Rice)Project of Anhui Province(the 14th five-year plan)the National Key Research and Development Program of China(2020YFE0202300)the CAAS Innovative Team Awardthe Hainan Provincial Joint Project of Sanya Yazhou Bay Science and Technology City(B21HJ0215,B21HJ0223,and B21HJ0508)Nanfan Special Project,CAAS(YBXM04)。
文摘Single nucleotide polymorphism(SNP)genotyping arrays provide an optimal high-throughput platform for genetic research and molecular breeding programs in both animals and plants.In this study,a highquality and custom-designed Rice3K56 SNP array was developed with the resequencing data of 3024 rice accessions worldwide,which was then tested extensively in 192 representative rice samples.Printed on the Gene Titan chips of Affymetrix Axiom each containing 56,606 SNP markers,the Rice3K56 array has a high genotyping reliability(99.6%),high and uniform genome coverage(an average of 6.7-kb between adjacent SNPs),abundant polymorphic information and easy automation,compared with previously developed rice SNP arrays.When applied in rice varietal differentiation,population diversity analysis,gene mapping of 13 complex traits by a genome-wide association study analysis(GWAS),and genome selection experiments in a recombinant inbred line and a multi-parent advanced generation inter-cross populations,these properties of the Rice3K56 array were well demonstrated for its power and great potential to be a highly efficient tool for rice genetic research and genomic breeding.
基金the National Natural Science Foundation of China(31501301)the National Key Research and Development Program of China(2018YFD0100904)+1 种基金the Natural Science Foundation of Henan Province,China(162300410077)the International Cooperation Project of Henan Province,China(172102410052)。
文摘Psathyrostachys huashanica Keng(2n=2x=14,NsNs)is regarded as a valuable wild relative species for common wheat cultivar improvement because of its abundant beneficial agronomic traits.However,although the development of many wheat–P.huashanica-derived lines provides a germplasm base for the transfer of excellent traits,the lag in the identification of P.huashanica chromosomes in the wheat background has limited the study of these lines.In this study,three novel nondenaturing fluorescence in situ hybridization(ND-FISH)-positive oligo probes were developed.Among them,HS-TZ3 and HS-TZ4 could specifically hybridize with P.huashanica chromosomes,mainly in the telomere area,and HS-CHTZ5 could hybridize with the chromosomal centromere area.We sequentially constructed a P.huashanica FISH karyotype and idiogram that helped identify the homologous groups of introduced P.huashanica chromosomes.In detail,1Ns and 2Ns had opposite signals on the short and long arms,3Ns,4Ns,and 7Ns had superposed two-color signals,5Ns and 6Ns had fluorescent signals only on their short arms,and 7Ns had signals on the intercalary of the long arm.In addition,we evaluated different ways to identify alien introgression lines by using low-density single nucleotide polymorphism(SNP)arrays and recommended the SNP homozygosity rate in each chromosome as a statistical pattern.The 15K SNP array is widely applicable for addition,substitution,and translocation lines,and the 40K SNP array is the most accurate for recognizing transposed intervals between wheat and alien chromosomes.Our research provided convenient methods to distinguish the homologous group of P.huashanica chromosomes in a common wheat background based on ND-FISH and SNP arrays,which is of great significance for efficiently identifying wheat–P.huashanica-derived lines and the further application of Ns chromosomes.
文摘Single nucleotide polymorphism(SNP)armays are a powerful genotyping tool used in genetic research and genomic breeding programs.Japanese flounder(Paralichthys olivaceus)is an economically-important aquaculture flatfish in many countries.However,the lack of high-efficient genotyping tools has impeded the genomic breeding programs for Japanese flounder.We developed a 50K Japanese flounder SNP array,"Yuxin No.1,"and report its utility in genomic selection(GS)for disease resistance to bacterial pathogens.We screened more than 42,.2 million SNPs from the whole-genome resequencing data of 1099 individuals and selected 48697 SNPs that were evenly distributed across the genome to anchor the array with Affymetrix Axiom genotyping technology.Evaluation of the array performance with 168 fishs howed that 74.7%of the loci were successfully genotyped with high call rates(>98%)and that the poly-morphic SNPs had good cluster separations.More than 85%of the SNPs were concordant with SNPs obtained from the whole-genome resequencing data.To validate"Yuxin No.1"for GS,the arrayed geno-typing data of 27 individuals from a candidate population and 931 individuals from a reference popula-tion were used to calculate the genomic estimated breeding values(GEBVs)for disease resistance toEdwardsiella tarda.There was a 21.2%relative increase in the accuracy of GEBV using the weighted geno-mic best linear unpiased prediction(wGBLUJP),compared to traditional pedigree-based best linear unbi-ased prediction(ABLUP),suggesting good performance of the'Yuxin No.1"SNP array for GS.In summary,we developed the"Yuxin No.1"50K SNP array,which provides a useful platform for high-quality geno-typing that may be beneficial to the genomic selective breeding of Japanese flounder.
基金sponsored by Department of Agriculture and Co-operation and Farmer Welfare(DAC&FW),Ministry of Agriculture,Government of India and Mars Wrigley,USAthe award of Junior/Senior Research Fellowship from Department of Biotechnology,Government of Indiapart of the CGIAR Research Program on Grain Legumes and Dryland Cereals(GLDC)
文摘Foliar fungal diseases(rust and late leaf spot)incur large yield losses,in addition to the deterioration of fodder quality in groundnut worldwide.High oleic acid has emerged as a key market trait in groundnut,as it increases the shelf life of the produce/products in addition to providing health benefits to consumers.Marker-assisted backcrossing(MABC)is the most successful approach to introgressing or pyramiding one or more traits using traitlinked markers.We used MABC to improve three popular Indian cultivars(GJG 9,GG 20,and GJGHPS 1)for foliar disease resistance(FDR)and high oleic acid content.A total of 22 BC3F4 and 30 BC2F4 introgression lines(ILs)for FDR and 46 BC3F4 and 41 BC2F4 ILs for high oleic acid were developed.Recurrent parent genome analysis using the 58 K Axiom_Arachis array identified several lines showing upto 94%of genome recovery among second and third backcross progenies.Phenotyping of these ILs revealed FDR scores comparable to the resistant parent,GPBD 4,and ILs with high(~80%)oleic acid in addition to high genome recovery.These ILs provide further opportunities for pyramiding FDR and high oleic acid in all three genetic backgrounds as well as for conducting multi-location yield trials for further evaluation and release for cultivation in target regions of India.
基金supported by grants from the NSFC(91531303)the 973 programs(2013CB8352002013CB835202)
文摘Quality deficiencies in single nucleotide polymorphism (SNP) analyses have important implications. We used missingness rates to investigate the quality of a recently published dataset containing 424 mitochonddal, 211 Y chromosomal, and 160 432 autosomal SNPs generated by a semicustom Illumina SNP array from 5 392 dogs and 14 grey wolves. Overall, the individual missingness rate for mitochondrial SNPs was -43.8%, with 980 (18.1%)individuals completely missing mitochondrial SNP genotyping (missingness rate=l). In males, the genotype missingness rate was -28.8% for Y chromosomal SNPs, with 374 males recording rates above 0.96. These 374 males also exhibited completely failed mitochondrial SNPs genotyping, indicative of a batch effect. Individual missingness rates for autosomal markers were greater than zero, but less than 0.5. Neither mitochondrial nor Y chromosomal SNPs achieved complete genotyping (locus missingness rate=0), whereas 5.9% of autosomal SNPs had a locus missingness rate=l. The high missingness rates and possible batch effect show that caution and rigorous measures are vital when genotyping and analyzing SNP array data for domestic animals. Further improvements of these arrays will be helpful to future studies.
基金supported by the grants from the National High-tech R&D Program(863 Program) on functional genomics of stress resistance and nutrient utility in rice(No.2012AA10A303)the National Basic Research Program(No.2007CB109001)+1 种基金Agriculture Public Welfare Scientific Research Project(No.201303008)the National Special Program for Research of Transgenic Plants of China(No.2011ZX08009-001)
文摘High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line (RIL) population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length ofl.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.
基金supported by grants from the National Natural Science Foundation of China(32061143030,32170636,32100448)the Key Research and Development Program of Jiangsu Province(BE2022343)+6 种基金the Seed Industry Revitalization Project of Jiangsu Province(JBGS[2021]009)Project of Hainan Yazhou Bay Seed Lab(B21HJ0223)the State Key Laboratory of North China Crop Improvement and Regulation(NCCIR2021KF-5,NCCIR2021ZZ-4)Jiangsu Province Agricultural Science and Technology Independent Innovation(CX(21)1003)the Independent Scientific Research Project of the Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding(PLR202102)the Open Funds of the Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding(PL202005)Yangzhou University High-end Talent Support Program,and the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD).
文摘Genomic selection(GS)is a powerful tool for improving genetic gain in maize breeding.However,its routine application in large-scale breeding pipelines is limited by the high cost of genotyping platforms.Although sequencing-based and array-based genotyping platforms have been used for GS,few studies have compared prediction performance among platforms.In this study,we evaluated the predictabilities of four agronomic traits in 305 maize hybrids derived from 149 parental lines subjected to genotyping by sequencing(GBS),a 40K SNP array,and target sequence capture(TSC)using eight GS models.The GBS marker dataset yielded the highest predictabilities for all traits,followed by TSC and SNP array datasets.We investigated the effect of marker density and statistical models on predictability among genotyping platforms and found that 1K SNPs were sufficient to achieve comparable predictabilities to 10K and all SNPs,and BayesB,GBLUP,and RKHS performed well,while XGBoost performed poorly in most cases.We also selected significant SNP subsets using genome-wide association study(GWAS)analyses in three panels to predict hybrid performance.GWAS facilitated selecting effective SNP subsets for GS and thus reduced genotyping cost,but depended heavily on the GWAS panel.We conclude that there is still room for optimization of the existing SNP array,and using genotyping by target sequencing(GBTS)techniques to integrate a few functional markers identified by GWAS into the 1K SNP array holds great promise of being an effective strategy for developing desirable GS breeding arrays.
基金the National Key R&D Program of China(2016YFD0101804-6)the National Natural Science Foundation of China(31671691)the International Science&Technology Cooperation Program of China(2016YFE0108600)。
文摘Plant nitrogen assimilation and use efficiency in the seedling's root system are beneficial for adult plants in field condition for yield enhancement.Identification of the genetic basis between root traits and N uptake plays a crucial role in wheat breeding.In the present study,198 doubled haploid lines from the cross of Yangmai 16/Zhongmai 895 were used to identify quantitative trait loci(QTLs)underpinning four seedling biomass traits and five root system architecture(RSA)related traits.The plants were grown under hydroponic conditions with control,low and high N treatments(Ca(NO_(3))_(2)·4H_(2)O at 0,0.05 and 2.0 mmol L^(-1),respectively).Significant variations among the treatments and genotypes,and positive correlations between seedling biomass and RSA traits(r=0.20 to 0.98)were observed.Inclusive composite interval mapping based on a high-density map from the Wheat 660 K single nucleotide polymorphisms(SNP)array identified 51 QTLs from the three N treatments.Twelve new QTLs detected on chromosomes 1 AL(1)in the control,1 DS(2)in high N treatment,4 BL(5)in low and high N treatments,and 7 DS(3)and 7 DL(1)in low N treatments,are first reported in influencing the root and biomass related traits for N uptake.The most stable QTLs(RRS.caas-4 DS)on chromosome 4 DS,which were related to ratio of root to shoot dry weight trait,was in close proximity of the Rht-D1 gene,and it showed high phenotypic effects,explaining 13.1%of the phenotypic variance.Twenty-eight QTLs were clustered in 12 genetic regions.SNP markers tightly linked to two important QTLs clusters C10 and C11 on chromosomes 6 BL and 7 BL were converted to kompetitive allele-specific PCR(KASP)assays that underpin important traits in root development,including root dry weight,root surface area and shoot dry weight.These QTLs,clusters and KASP assays can greatly improve the efficiency of selection for root traits in wheat breeding programmes.
文摘High-density single nucleotide polymorphism (SNP) genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP discovery was performed using deep resequencing of eight libraries derived from 132 Elaeis guineen- sis and Elaeis oleifera palms belonging to 59 origins, resulting in the discovery of 〉3 million putative SNPs. After SNP filtering, the Illumina OP200K custom array was built with 170 860 successful probes. Phenetic clustering analysis revealed that the array could distinguish between palms of different origins in a way consistent with pedigree records. Genome-wide linkage disequilibrium declined more slowly for the commercial populations (ranging from 120 kb at r2 = 0.43 to 146 kb at r2 = 0.50) when compared with the semi-wild populations (19.5 kb at r2 = 0.22). Genetic fixation mapping comparing the semi-wild and commercial population identified 321 selective sweeps. A genome-wide association study (GWAS) detected a significant peak on chromosome 2 associated with the polygenic component of the shell thick- ness trait (based on the trait shell-to-fruit; S/F %) in tenera palms. Testing of a genomic selection model on the same trait resulted in good prediction accuracy (r = 0.65) with 42% of the S/F % variation explained. The first high-density SNP genotyping array for oil palm has been developed and shown to be robust for use in genetic studies and with potential for developing early trait prediction to shorten the oil palm breeding cycle.
基金supported by the National Key R&D Program of China(Grant No.2018YFC2001003)the Strategic Priority Research Program of the Chinese Academy of Sciences(category B,Grant No.XDB38020100).
文摘Background:Chronic diseases are becoming a critical challenge to the aging Chinese population.Biobanks with extensive genomic and environmental data offer opportunities to elucidate the complex gene-environment interactions underlying their aetiology.Genome-wide genotyping array remains an efficient approach for large-scale genomic data collection.However,most commercial arrays have reduced performance for biobanking in the Chinese population.Materials and methods:Deep whole-genome sequencing data from 2641 Chinese individuals were used as a reference to develop the CAS array,a custom-designed genotyping array for precision medicine.Evaluation of the array was performed by comparing data from 384 individuals assayed both by the array and whole-genome sequencing.Validation of its mitochondrial copy number estimating capacity was conducted by examining its association with established covariates among 10162 Chinese elderly.Results:The CAS Array adopts the proven Axiom technology and is restricted to 652429 single-nucleotide polymorphism(SNP)markers.Its call rate of 99.79% and concordance rate of 99.89% are both higher than for commercial arrays.Its imputation-based genome coverage reached 98.3% for common SNPs and 63.0% for low-frequency SNPs,both comparable to commercial arrays with larger SNP capacity.After validating its mitochondrial copy number estimates,we developed a publicly available software tool to facilitate the array utility.Conclusion:Based on recent advances in genomic science,we designed and implemented a high-throughput and low-cost genotyping array.It is more cost-effective than commercial arrays for large-scale Chinese biobanking.
基金funded by the National Key Research and Development Program of China (2017YFD0201701)the Special Fund for Agro-scientific Research in the Public Interest,China (201303016)the Science and Technology Project for Xingjiang Uygur Autonomous Region,China (2013911092)
文摘Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most damaging diseases to wheat in the world. The cultivation of resistant varieties of wheat is essential for controlling the powdery mildew epidemic. Wheat landraces are important resources of resistance to many diseases. Mapping powdery mildew resistance genes from wheat landraces will promote the development of new varieties with disease resistance. The Chinese wheat landrace Baiyouyantiao possesses characteristic of disease resistance to powdery mildew. To identify the resistance gene in this landrace, Baiyouyantiao was crossed with the susceptible cultivar Jingshuang 16 and seedlings of parents and F1, BC1, F2, and F~:3 were tested with Bgt isolate E09. The genetic results showed that the resistance of Baiyouyantiao to E09 was controlled by a single recessive gene, tentatively designated PmBYYT. An Illumina wheat 90K single-nucleotide polymorphism (SNP) array was applied to screen polymorphisms between F2-resistant and F2-susceptible DNA bulks for identifying the chromosomal location of PmBYYT. A high percentage of polymorphic SNPs between the resistant and susceptible DNA bulks was found on chro- mosome 7B, indicating that PmBYYT may be located on this chromosome. A genetic linkage map of PmBYYTconsisting of two simple sequence repeat markers and eight SNP markers was developed. The two flanking markers were SNP markers W7BL-8 and W7BL-15, with genetic distances of 3 and 2.9 cM, respectively. The results of this study demonstrated the rapid characterization of a wheat disease resistance gene and SNP marker development using the 90K SNP assay. The flanking markers of gene PmBYYTwill benefit marker-assisted selection (MAS) and map-based cloning in breeding wheat cultivars with powdery mildew resistance.
文摘目的研究探讨不同遗传学分析方法对诊断自然流产组织产生原因的应用效果。方法选择广西壮族自治区妇幼保健院2014年9月至2014年11月收治的自然流产患者42例为研究对象。所有研究对象均采用染色体核型分析和SNP Array检测分析方法,比较分析结果。结果两种不同遗传分析方法能够诊断出自然流产41例,使用染色体核型分析成功37例,绒毛细胞培养染色体核型分析成功34例,染色体核型分析准确成功率为88%,绒毛细胞培养染色体核型分析成功诊断率为80.9%;两种遗传分析方法同时应用于自然流产原因诊断中,诊断准确率提高到97.6%。结论 SNP Array检测方法分析具有可行性。两种遗传学检测方法比较,染色体核型分析诊断概率比较高。在临床诊断的过程中,两种遗传检测方法结合使用,大大提高了自然流产原因的诊断准确率。
基金Nantes University Hospital MEFRALL project,Grant/Award Number:RC_0144。
文摘Background:Thanks to an improved therapeutic regimen in childhood B-cell precursor acute lymphoblastic leukemia(BCP-ALL),5 year-overall survival now exceeds 90%.Unfortunately,the 25%of children who relapse have an initial poor prognosis,potentially driven by pre-existing or emerging molecular anomalies.The latter are initially and essentially identified by cytogenetics.However,some subtle alterations are not visible through karyotyping.Methods:Single nucleotide polymorphisms(SNP)array is an alternative way of chromosomal analysis allowing for a more in-depth evaluation of chromosomal modifications such as the assessment of copy number alterations(CNA)and loss of heterozygosity(LOH).This method was applied here in retrospective diagnosis/relapse paired samples from seven children with BCP-ALL and in a prospective cohort of 38 newly diagnosed childhood cases.Results:In the matched study,compared to the initial karyotype,SNP array analysis reclassified two patients as poor prognosis cases.Modulation during relapse was seen for 4 CNA and 0.9 LOH.In the prospective study,SNP reclassified the 10 patients with intermediate karyotype as 7 good prognosis and 3 poor prognosis.Ultimately,in all the children tested,SNP array allowed to identify additional anomalies compared to conventional karyotype,refine its prognostic value and identify some druggable anomalies that could be used for precision medicine.Overall,the anomalies detected could be segregated in four groups respectively involved in B-cell development,cell proliferation,transcription and molecular pathways.Conclusion:SNP therefore appears to be a method of choice in the integrated diagnosis of BCP ALL,especially for patients initially classified as intermediate prognosis.This complementary method of both cytogenetics and high throughput sequencing allows to obtain further classified information and can be useful in case of failure of these techniques.
基金the National Key Research and Development Pro-gram of China(2016YFD0102000)the National Natural Sci-ence Foundation of China(no.31971875).
文摘Stripe rust,caused by Puccinia striformis f.sp.tritici(Pst),is one of the most destructive diseases of wheat(Triticum aestivum L)worldwide.Xiaoyan 78829,a partial amphidiploid developed by crossing common wheat with Thinopyrum intermedium,is immune to wheat stripe rust.To transfer the resis-tance gene of this excellent germplasm resource to wheat,the tr anslocation line WTT11 was produced by pollen irradiation and assessed for immunity to stripe rust races CYR32,CYR33 and CYR34.A novel stripe rust-resistance locus derived from Th.intermedium was confirmed by linkage and diagnostic marker analyses.Molecular cytogenetic analyses revealed that WTT11 carries a TTh 2DL translocation.The breakpoint of 1B was located at 95.5 MB,and the alien segments were found to be homoeologous to wheat-group chromosomes 6 and 7 according to a wheat660K single-nucleotide polymorphism(SNP)array analysis.Ten previously developed PCR-based markers were confirmed to rapidly trace the alien segments of WTT11,and 20 kompetitive allele-specific PCR(KASP)markers were developed to enable genotyping of Th.intermedium and common wheat.Evaluation of agronomic traits in two consecutive crop seasons uncovered some favorable agronomic traits in WTT11,such as lower plant height and longer main panicles,that may be applicable to wheat improvement.As a novel genetic resource,the new resistance locus may be useful for wheat disease-resistance breeding.