Assessing the conservation impact of Chinese indigenous chicken populations between ex-situ and in-situ using genome-wide SNPs

Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations. In this study, we conducted a comparative analysis of two indigenous Chinese chicken breeds, Gushi and Xichuan black-bone, using whole-genome SNPs to understand their genetic diversity, track changes over time and population structure. The breeds were divided into five conservation populations(GS1, 2010, ex-situ;GS2, 2019, ex-situ;GS3, 2019, in-situ;XB1, 2010, in-situ;and XB2, 2019, in-situ) based on conservation methods and generations. The genetic diversity indices of three conservation populations of Gushi chicken showed consistent trends, with the GS3 population under in-situ strategy having the highest diversity and GS2 under ex-situ strategy having the lowest. The degree of inbreeding of GS2 was higher than that of GS1 and GS3. Conserved populations of Xichuan black-bone chicken showed no obvious changes in genetic diversity between XB1 and XB2. In terms of population structure, the GS3 population were stratified relative to GS1 and GS2. According to the conservation priority, GS3 had the highest contribution to the total gene and allelic diversity in GS breed, whereas the contribution of XB1 and XB2 were similar. We also observed that the genetic diversity of GS2 was lower than GS3, which were from the same generation but under different conservation programs(in-situ and ex-situ). While XB1 and XB2 had similar levels of genetic diversity. Overall, our findings suggested that the conservation programs performed in ex-situ could slow down the occurrence of inbreeding events, but could not entirely prevent the loss of genetic diversity when the conserved population size was small, while in-situ conservation populations with large population size could maintain a relative high level of genetic diversity.

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.

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.

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.

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.

Genetic parameter estimation and genome-wide association study(GWAS) of red blood cell count at three stages in a Duroc×Erhualian pig population

Red blood cells play an essential role in the immune system.Moreover,red blood cell count(RBC) is an important clinical indicator of various diseases,including anemia,type 2 diabetes and the metabolic syndrome.Thus,it is necessary to reveal the genetic mechanism of RBC for animal disease resistance breeding.However,quite a few studies had focused on porcine RBC,especially at different stages.Thus,studies on porcine RBC at different stages are needed for disease resistant breeding.In this study,the porcine RBC of 20-,33-,and 80-day old were measured,and genetic parameter estimation and genome-wide association study(GWAS) were both performed.As a result,the heritability was about 0.6 at the early stages,much higher than that at 80 days.Nine novel genome wide significant single nucleotide polymorphisms(SNPs),located at Sus scrofa chromosome(SSC)3,4,8,9,10 and 15,respectively,were identified.Further,TGFβ2,TMCC2 and PPP1 R15 B genes were identified as important candidate genes of porcine red blood cell count.So different SNPs and candidate genes were found significantly associated with porcine RBC at different stages,suggesting that different genes might play key roles on porcine RBC at different stages.Overall,new evidences were offered in this study for the genetic bases of animal RBC,and that the SNPs and candidate genes would be useful for disease resistant breeding of pig.

Genome-wide pedigree analysis of elite rice Shuhui 527 reveals key regions for breeding

Hybrid rice significantly contributes to the food supply worldwide. Backbone parents play important roles in elite hybrid rice breeding systems. In this study, we performed pedigree-based analysis of the elite backbone parent rice variety, namely, Shuhui 527(SH527, Oryza sativa), to exploit key genome regions during breeding. Twenty-four cultivars(including SH527, its six progenitors and 17 derived cultivars) were collected and analyzed with high-density single nucleotide polymorphism(SNP) array. Scanning all these cultivars with genome-wide SNP data indicated the unique contributions of progenitors to the SH527 genome and identified the key genomic regions of SH527 conserved within all its derivatives. These findings were further supported by known rice yield-related genes or unknown QTLs identified by genome-wide association study. This study reveals several key regions for SH527 and provides insights into hybrid rice breeding.

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.

A Scalable Method for Cross-Platform Merging of SNP Array Datasets

Single nucleotide polymorphism (SNP) array is a recently developed biotechnology that is extensively used in the study of cancer genomes. The various available platforms make cross-study validations/comparisons difficult. Meanwhile, sample sizes of the studies are fast increasing, which poses a heavy computational burden to even the fastest PC.Here, we describe a novel method that can generate a platform-independent dataset given SNP arrays from multiple platforms. It extracts the common probesets from individual platforms, and performs cross-platform normalizations and summari-zations based on these probesets. Since different platforms may have different numbers of probes per probeset (PPP), the above steps produce preprocessed signals with different noise levels for the platforms. To handle this problem, we adopt a platform-dependent smoothing strategy, and produce a preprocessed dataset that demonstrates uniform noise levels for individual samples.To increase the scalability of the method to a large number of samples, we devised an algorithm that split the samples into multiple tasks, and probesets into multiple segments before submitting to a parallel computing facility. This scheme results in a drastically reduced computation time and increased ability to process ultra-large sample sizes and arrays.

基于SNP数据检测染色体拷贝数结果可信度分析

利用SNP数据检测肿瘤细胞染色体拷贝数变异是癌症相关研究的一个热点,目前已有多种方法可以通过分析SNP array数据检测染色体拷贝数。然而在某些情况下,这些检测方法检测结果与真实拷贝数具有一定错误率。目前并没有方法研究预测结果发生错误的规律。本文分别分析了GPHMM,ASCAT两种检测方法结果信息熵与检测正确率的关系,发现检测正确率与信息熵存在很强的相关性。通过对比不同肿瘤细胞比例下信息熵与正确率关系,本文发现随着肿瘤细胞比例的增大,检测结果信息熵平均值增大,方差减小;同时平均检测正确率也越来越大,方差显著减小。这些结果显示信息熵的大小可以反映出检测结果正确率的高低。最后,本文以高肿瘤细胞比例下拷贝数检测结果为例,研究了在变异类型单一,信息熵小的情况下,染色体倍性检测的正确率。结果表明信息熵可以作为衡量检测结果可信度的指标:即信息熵越高,检测结果越可信。

Comparison between SSR and SNP systems of genetic diversity analysis in Brassica napus L.

Simple sequence repeat(SSR) capillary electrophoresis and single nucleotide polymorphism(SNP) array are widely used tools for investigating genetic diversity. However, efficiency between SSR and SNP on rapeseed genetic diversity has not been systematically assessed yet. In this study, both SSR and SNP were used on 446 worldwide B. napus germplasm lines. Data shows that 65 pairs of primers(70 SSRs) and 250 SNPs were necessary to identify the similar accessions. Furthermore, no significant differences were found between 2 systems on basic statistics, population structures, principal components and kinship parameters. In general, either SSR or SNP is efficient for genetic diversity estimation. However, our data revealed the fact that SNP array system shows slightly more accuracy than SSR system on ecotype groups division.

Identification of Risk Pathways and Functional Modules for Coronary Artery Disease Based on Genome-wide SNP Data

Coronary artery disease(CAD) is a complex human disease, involving multiple genes and their nonlinear interactions, which often act in a modular fashion. Genome-wide single nucleotide polymorphism(SNP) profiling provides an effective technique to unravel these underlying genetic interplays or their functional involvements for CAD. This study aimed to identify the susceptible pathways and modules for CAD based on SNP omics. First, the Wellcome Trust Case Control Consortium(WTCCC) SNP datasets of CAD and control samples were used to assess the jointeffect of multiple genetic variants at the pathway level, using logistic kernel machine regression model. Then, an expanded genetic network was constructed by integrating statistical gene–gene interactions involved in these susceptible pathways with their protein–protein interaction(PPI)knowledge. Finally, risk functional modules were identified by decomposition of the network. Of 276 KEGG pathways analyzed, 6 pathways were found to have a significant effect on CAD. Other than glycerolipid metabolism, glycosaminoglycan biosynthesis, and cardiac muscle contraction pathways, three pathways related to other diseases were also revealed, including Alzheimer's disease, non-alcoholic fatty liver disease, and Huntington's disease. A genetic epistatic network of 95 genes was further constructed using the abovementioned integrative approach. Of 10 functional modules derived from the network, 6 have been annotated to phospholipase C activity and cell adhesion molecule binding, which also have known functional involvement in Alzheimer's disease.These findings indicate an overlap of the underlying molecular mechanisms between CAD and Alzheimer's disease, thus providing new insights into the molecular basis for CAD and its molecular relationships with other diseases.

部分型母源性16单亲二体型与均称型胎儿生长受限

【目的】应用人类全基因组单核苷酸多态性芯片(SNP array)探讨特发性均称型胎儿生长受限(Symmetric FGR)的病因。【方法】对血清学筛查唐氏综合征高风险且系列超声检查发现20周前已出现胎儿生长受限征象的36例孕妇行羊水胎儿细胞G显带染色体核型分析,其中核型正常的34例孕妇,应用人类全基因组SNP array对羊水中的胎儿细胞及父母双方的外周血细胞进行遗传学分析。【结果】发现2例部分型母源性16单亲二体型(mUPD 16),1例位点为16p12.2-p13.3,长度约为21.0 Mbp和16q24.1-24.3,长度约为4.1 Mbp;另1例位点为16q21-q24.3,长度约为24.1 Mbp。【结论】部分型母源性16单亲二体型可能与均称型胎儿生长受限的发生有关,影响胎儿生长发育的基因有可能定位于16q24。

癌症相关遗传变异的新进展及其在诊断研发中的意义

＂了解更多癌症相关的遗传变异可能有助于癌症的预防和早期诊断,以及为癌症个体化诊断和治疗方案开辟新途径。＂

Genetic characterization and linkage disequilibrium mapping of resistance to gray leaf spot in maize(Zea mays L.)

Gray leaf spot(GLS),caused by Cercospora zeae-maydis,is an important foliar disease of maize(Zea mays L.)worldwide,resistance to which is controlled by multiple quantitative trait loci(QTL).To gain insights into the genetic architecture underlying the resistance to this disease,an association mapping population consisting of 161 inbred lines was evaluated for resistance to GLS in a plant pathology nursery at Shenyang in 2010 and 2011.Subsequently,a genome-wide association study,using 41,101 single-nucleotide polymorphisms(SNPs),identified 51 SNPs significantly(P<0.001)associated with GLS resistance,which could be converted into 31 QTL.In addition,three candidate genes related to plant defense were identified,including nucleotidebinding-site/leucine-rich repeat,receptor-like kinase genes similar to those involved in basal defense.Two genic SNPs,PZE-103142893 and PZE-109119001,associated with GLS resistance in chromosome bins 3.07 and 9.07,can be used for marker-assisted selection(MAS)of GLS resistance.These results provide an important resource for developing molecular markers closely linked with the target trait,enhancing breeding efficiency.

基于多元方差分析的成对肿瘤SNP array数据分段算法

单核苷酸多态性微阵列(SNP array)技术是近年来获得快速发展的一种高通量生物芯片技术,可以有效地对肿瘤细胞中的染色体变异进行检测.本文针对癌症药物治疗前后肿瘤的染色体变异的成对SNP array数据,提出了一种基于多元方差分析二维统计量的全新染色体异常区域分段算法.对模拟SNP array数据的测试表明,该算法可以精确地将成对肿瘤数据异常区域进行分段,其结果明显好于现有的循环二元分割(CBS)算法.同时,ROC性能曲线分析显示本文算法具有较好的抗噪性能.对赫赛汀治疗前后的成对乳腺癌SNP array数据的分析结果显示,该算法可准确地检测出重要致癌基因ERBB2在治疗前后的拷贝数变化.上述结果表明这种基于多元方差分析的算法是一种有效的SNP array数据分析工具.

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.

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 F_1,BC_1,F_2,and F_(2:3) 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 Pm BYYT.An Illumina wheat 90K single-nucleotide polymorphism(SNP)array was applied to screen polymorphisms between F_2-resistant and F_2-susceptible DNA bulks for identifying the chromosomal location of Pm BYYT.A high percentage of polymorphic SNPs between the resistant and susceptible DNA bulks was found on chromosome 7B,indicating that Pm BYYT may be located on this chromosome.A genetic linkage map of Pm BYYT consisting 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 c M,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 Pm BYYT will benefit marker-assisted selection(MAS)and map-based cloning in breeding wheat cultivars with powdery mildew resistance.

Co-location of QTL for Sclerotinia stem rot resistance and flowering time in Brassica napus

Sclerotinia stem rot(SSR) caused by Sclerotinia sclerotiorum(Lib.) de Bary is one of the most devastating diseases of Brassica napus worldwide. Both SSR resistance and flowering time(FT) adaptation are major breeding goals in B. napus. However, early maturing rapeseed varieties, which are important for rice-rapeseed rotation in China, are often highly susceptible to SSR. Here, we found that SSR resistance was significantly negatively correlated with FT in a natural population containing 521 rapeseed inbred lines and a double haploid(DH) population with 150 individual lines, both of which had great variation in FT. Four chromosomal regions on A2, A6, C2, and C8 affecting both SSR resistance and FT were identified using quantitative trait loci(QTL) mapping after constructing a high-density genetic map based on single nucleotide polymorphism markers in the DH population.Furthermore, we aligned QTL for the two traits identified in the present and previous studies to the B. napus reference genome, and identified four colocalized QTL hotspots of SSR resistance and FT on A2(0–7.7 Mb), A3(0.8–7.5 Mb), C2(0–15.2 Mb), and C6(20.2–36.6 Mb). Our results revealed a genetic link between SSR resistance and FT in B.napus, which should facilitate the development of effective strategies in both early maturing and SSR resistance breeding and in map-based cloning of SSR resistance QTL.