Rice3K56 is a high-quality SNP array for genome-based genetic studies and breeding in rice(Oryza sativa L.)

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.

Rapid identification of Psathyrostachys huashanica Keng chromosomes in wheat background based on ND-FISH and SNP array methods

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.

染色体核型分析与SNP array技术联合在超声异常胎儿产前诊断中的应用

目的:研究核型分析与SNP array技术在超声软指标异常时,对于胎儿产前诊断的诊断效力和实践价值。方法:研究对象为本院2020年10月至2022年1月产前超声筛查提示存在胎儿发育异常进行产前诊断的孕妇,研究方法即染色体核型分析及SNP array检测主要通过羊水抽取并分析孕妇羊水细胞相关成分的方式进行。在产前超声筛查预先显示异常的情况下,进一步比较染色体核型分析的结果与SNP array技术检出的染色体畸变之间的异同情况。结果:一共59名孕妇参与了本次研究,其中SNP array检测显示染色体异常的孕妇有9例(15.25%),核型分析结果为染色体异常的孕妇11例(18.64%),两者存在的检测结果差异具有统计学意义(P<0.01)。另有SNP array检测结果及核型分析结果均异常的孕妇1例(1.69%),核型分析结果正常但SNP array检测显示染色体异常的孕妇共10例(16.95%),核型分析显示染色体异常但SNP array检测结果正常8例(13.56%)。将UA1组与UA≥2组的检验结果进行比较,发现SNP array的染色体异常检出率明显更高,且在统计学角度存在显著差异(P<0.01)。结论:染色体核型分析与SNP array技术联合检测可提高胎儿染色体畸变检出率;建议产前超声筛查结果中异常数目不小于2项的孕妇后续增加上述两种检测,进一步确认是否存在染色体畸变的风险,最大程度地减少缺陷胎儿降生的可能。

Development of a 50K SNP Array for Japanese Flounder and Its Application in Genomic Selection for Disease Resistance

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.

Improvement of three popular Indian groundnut varieties for foliar disease resistance and high oleic acid using SSR markers and SNP array in marker-assisted backcrossing

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.

Re-evaluating data quality of dog mitochondrial,Y chromosomal,and autosomal SNPs genotyped by SNP array

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.

Comparison of sequencing-based and array-based genotyping platforms for genomic prediction of maize hybrid performance

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.

QTL Scanning for Rice Yield Using a Whole Genome SNP Array

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.

核型分析联合其他遗传学检测技术在高龄孕妇产前诊断中的应用

目的探讨核型分析联合单核苷酸多态性微阵列技术(single nucleotide polymorphism array,SNP array)或荧光原位杂交技术(fluorescence in situ hybridization,FISH)或细菌人工染色体微珠标记技术(BACs on Beads,BoBs)在高龄孕妇产前诊断中的应用价值。方法回顾性研究因高龄行产前诊断的930例孕妇,全部行核型分析,联合BoBs检测420例,联合SNP array检测343例,联合FISH检测167例,分析其染色体结果及妊娠结局。结果930例胎儿中,核型异常192例(20.7%),三体综合征中以21-三体居多,性染色体异常中以克氏征居多。在核型联合其他检测中,联合SNP array检测可显著提高胎儿染色体异常检出率,差异有统计学意义(χ^(2)=6.191,P=0.013)。对于染色体嵌合体的诊断,核型联合FISH检测可更精准地确定嵌合类型及比例。孤立性高龄胎儿染色体异常风险相对较低,高龄合并无创高危胎儿染色体异常率最高,在高龄合并超声软指标中,随超声软指标数目增多,染色体异常率随之升高(P=0.001)。高龄孕妇年龄与核型异常、非整倍体尤其21三体的发生率呈正相关(P<0.05)。结论孤立性高龄孕妇胎儿染色体异常风险相对较低,高龄合并无创高危胎儿染色体异常的风险高,随超声软指标数目增多、孕妇年龄增长胎儿染色体异常的风险增加,核型联合FISH检测可更精准地确定嵌合类型及比例,核型分析联合其他检测尤其与SNP array技术可显著提高染色体异常检出率,有利于遗传咨询及再生育指导,是高龄孕妇首选的产前诊断方案。

QTL mapping of seedling biomass and root traits under different nitrogen conditions in bread wheat(Triticum aestivum L.)

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.

Development and Validation of a High-Density SNP Genotyping Array for African Oil Palm

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.

CAS Array:design and assessment of a genotyping array for Chinese biobanking

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.

Identification of the resistance gene to powdery mildew in Chinese wheat landrace Baiyouyantiao

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.

两种不同遗传学分析方法用于诊断自然流产组织的比较

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。

5例16p13.11微重复胎儿的产前诊断及遗传学分析

目的针对5例16p13.11区出现拷贝数变异(copy number variants,CNVs)的胎儿进行产前诊断及遗传学分析。方法对2019年9月至2022年12月在福建医科大学附属福州市第一医院5例因不同产前诊断指征的胎儿羊水进行常规染色体G显带和单核苷酸多态性微阵列(single nucleotide polymorphism array,SNP array)检测,对诊断为16p13.11微重复的胎儿遗传学进行回顾性分析。结果5例胎儿染色体核型分析结果未见异常;SNP array结果显示在16p13.11区域存在着846.1~1600 kb的微重复,共涉及到NDE1、ABCC6、MYH11等6个OMIM基因;其中2例未进行遗传溯源,另3例遗传自父源或母源的16p13.11微重复片段的胎儿足月分娩,随访未见异常。结论16p13.11片段微重复胎儿产前诊断存在表型不完全外显,且缺乏特异性的表型。

Added value of molecular karyotype in childhood acute lymphoblastic leukemia

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.

6例复发性17p12微缺失/微重复胎儿产前诊断

目的分析6例复发性17p12区域的微缺失/重复胎儿的临床资料,探讨其致病性、宫内临床表型的相关性及包含基因等,为判断预后提供遗传学依据。方法采用常规G显带和单核苷酸多态性微阵列(single nucleotide polymorphism,SNP array)对2017年1月至2021年12月福建医科大学附属福州市第一医院6例不同产前诊断指征的胎儿羊水进行检测并对其结果进行描述性分析。结果5例孕中期胎儿涉及心脏、大脑、肾脏等系统的超声异常;G显带分析结果显示,6例胎儿染色体核型分析均未见异常;SNP array检测结果显示,6例胎儿在17p12区域存在1.3~1.4 Mb拷贝数变异,涉及PMP22、COX10、HS3ST3B1和TEKT3等4个OMIM基因,17p12区域和PMP22基因具有单倍剂量效应;4例胎儿存在CNV微缺失,2例胎儿存在CNV微重复;其中2例胎儿的变异遗传自无临床表型父亲,1例胎儿是新发变异,其他3例胎儿未进行变异溯源。经遗传咨询后,3例孕妇及家属选择继续妊娠,出生时胎儿情况正常,出生后半年随访婴儿发育良好;1例胎儿早产,出生18个月随访存在三尖瓣轻度反流;2例孕妇及家属选择终止妊娠。结论复发性17p12区域的微缺失/重复胎儿产前缺乏特异性表型,PMP22可能为该区域关键致病基因。

产前诊断胎儿7q11.23重复综合征一例

目的报告一例7q11.23重复综合征胎儿,探讨多种产前诊断技术的联合应用价值,为患者提供可靠的遗传咨询。方法采集1例孕中期胎儿的羊水行染色体核型分析,并提取羊水DNA,进行BoBs检测和单核苷酸多态性微阵列芯片(single nucleotide polymorphism array,SNP array)检测。结果胎儿羊水细胞染色体核型未见异常;BoBs检测结果提示胎儿7q11.23区域可见重复;SNP array检测结果显示胎儿7q11.23区段存在1.4Mb片段的重复,提示arr[hg19]7q11.23(72,701,098-74,162,823)×3。结论染色体核型分析联合BoBs检测,并用SNP array验证,明确诊断一例7q11.23重复综合征胎儿,在产前诊断中具有较好的应用价值。

单核苷酸多态性微阵列技术在胎儿颈部淋巴水囊瘤产前诊断中的应用研究

目的 探讨单核苷酸多态性微阵列技术(single nucleotide polymorphism array, SNP array)在胎儿颈部淋巴水囊瘤(cervical cystic hygroma, CCH)产前诊断中的应用价值。方法 收集2019年1月至2021年5月在广西壮族自治区妇幼保健院经超声诊断为CCH的170例胎儿,应用SNP array检测染色体拷贝数变异(copy number variation, CNV),采用G显带进行染色体核型分析。结果 综合染色体核型分析和SNP array检测结果,在170例CCH胎儿中,71例检测到染色体异常(41.8%):特纳综合征最多(15.98%,27/170)、其次为21-三体综合征(10%,18/170)、18-三体综合征(7.1%,12/170)、13-三体综合征(0.6%,1/170)、47,XXX综合征(0.6%,1/170)和15-三体的嵌合(0.6%,1/170)。SNP array在12例胎儿中检出CNV(7.1%,12/170),其中10例致病性CNV,2例临床意义不明CNV。在细胞培养失败和染色体核型分析结果正常的CCH胎儿中,SNP array分别检出2例和8例染色体异常。结论 胎儿CCH与染色体异常相关,以染色体非整倍体为主,但也存在CNV、易位等染色体异常。因此,针对B超诊断为CCH的胎儿,同时进行染色体核型分析和SNP array检测,可以为胎儿CCH的遗传咨询和预后评估提供更为精准的信息和依据。

Cytogenetic identification and molecular marker development for the novel stripe rust-resistant wheat- Thinopyrum intermedium translocation line WTT11

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.