Effect of marker‐data editing on the accuracy of genomic prediction

Genomic selection is a method to predict breeding values using genome‐wide single‐nucleotide polymorphism (SNP) markers. High‐quality marker data are necessary for genomic selection. The aim of this study was to investigate the effect of marker‐editing criteria on the accuracy of genomic predictions in the Nordic Holstein and Jersey populations. Data included 4429 Holstein and 1071 Jersey bulls. In total, 48 222 SNP for Holstein and 44 305 SNP for Jersey were polymorphic. The SNP data were edited based on (i) minor allele frequencies (MAF) with thresholds of no limit, 0.001, 0.01, 0.02, 0.05 and 0.10, (ii) deviations from Hardy–Weinberg proportions (HWP) with thresholds of no limit, chi‐squared p‐values of 0.001, 0.02, 0.05 and 0.10, and (iii) GenCall (GC) scores with thresholds of 0.15, 0.55, 0.60, 0.65 and 0.70. The marker data sets edited with different criteria were used for genomic prediction of protein yield, fertility and mastitis using a Bayesian variable selection and a GBLUP model. De‐regressed EBV were used as response variables. The result showed little difference between prediction accuracies based on marker data sets edited with MAF and deviation from HWP. However, accuracy decreased with more stringent thresholds of GC score. According to the results of this study, it would be appropriate to edit data with restriction of MAF being between 0.01 and 0.02, a p‐value of deviation from HWP being 0.05, and keeping all individual SNP genotypes having a GC score over 0.15.     

甘蓝型油菜粒色遗传的复等位模型假说

通过分析GH06×94005和GH06×A800两组合各世代粒色分离情况,提出复等位遗传模型假说。据此模型,较好地解释了两组合各世代粒色显隐性遗传关系。有关复等位遗传模型假说的应用范围也做了初步讨论。     

Effect of the Y chromosome on testis weight in mice

We investigated the effect of the Y chromosome on testis weight in (B6.Cg-A^y × Y-consomic mouse strain) F₁ male mice. We obtained the following results: (1) Mice with the Mus musculus domesticus-type Y chromosome had significantly heavier testis than those with the M. m. musculus-type Y chromosome. (2) Variations in Usp9y and the number of CAG repeats in Sry were significantly associated with testes weight. The A^y allele was correlated with a reduced testis weight, and the extent of this reduction was significantly associated with a CAG repeat number polymorphism in Sry. These results suggest that Y chromosome genes not only influence testis weight but also modify the effect of the A^y allele in mediating this phenomenon.     

A rapid real-time PCR assay for detecting columnar growth in apples (Malus × domestica)

Columnar growth in apples can have considerable positive consequences for orchard maintenance, but the lack of columnar cultivars producing fruits with desired market quality prevents their broader utilization in orchards. New crossings focused on their breeding are therefore conducted throughout the world every year. Unfortunately, the reliable discrimination between columnar growth and normal phenotype is difficult until seedlings are 2–3 years of age. However, molecular marker–assisted selection (MAS) can be used in seedlings several weeks old providing immense help in breeding programmes focused on columnar apple production. Here, we describe a rapid and reliable method for the detection of both wild-type (WT) and columnar (Co) alleles originating from ‘McIntosh Wijcik’ in a single reaction using a real-time PCR allelic discrimination approach. Our assay was tested in 130 genotypes (80 normal and 50 columnar habit) from various crossings and their parents, and in all cases, genotype corresponded to phenotype. The assay is thus suitable for laboratories interested in high-throughput MAS for columnar tree habit breeding.     

基于简化基因组测序的越橘杂交后代鉴定

[目的]针对遗传群体测序数据开发一种杂交后代鉴定方法,以获得继承双亲基因的真杂种后代,为果树杂交育种、遗传分析及遗传图谱构建奠定基础.[方法]本研究以越橘正反交群体共计318个F1子代和2个亲本为试材,利用SLAF技术进行简化基因组测序并比对越橘参考基因组获得群体SNP数据,通过稀有等位变异分析和基于PCA、K-mea...     

氟烷基因在皮特兰猪群体中的分子标记辅助选择研究

【目的】探索氟烷基因(RYR1)在皮特兰猪群体中的辅助选择育种方法,以提高猪群的猪肉质量。【方法】利用PCR-RFLP的方法检测509头皮特兰猪中RYR1基因的等位基因频率,利用回归模型分析基因型与选育性状之间的相关性,采用Bootstrap方法分析等位基因频率与选育性状的相关性。【结果】在皮特兰猪群体中RYR1基因优势等位基因(N)频率占81.73%。NN基因型个体在日增质量方面表现明显优势,在背膘EBV、父系指数及母系指数中Nn基因型个体表现较好,nn基因型个体在肢蹄方面表现好于其他2种基因型。n等位基因频率达19%时,选育性状表现平衡;大于19%时,则瘦肉率较高,背膘较薄,体型较好;小于19%时,则生长速度较快。【结论】若皮特兰猪选育方向更注重瘦肉率、背膘厚、体型外貌等,可不优化RYR1基因;若是更注重生长速度、饲养抗应激、屠宰后肉质等方面的性状改良,则建议全面纯化皮特兰猪群体至RYR1基因优势等位基因纯合。     

甜樱桃DFR基因内含子2和内含子3的多态性

【目的】研究70个甜樱桃品种DFR基因多态性与果皮颜色的相关性。【方法】通过DNA序列分析,以不同果皮颜色的10个甜樱桃品种（Prunus avium L.）为材料,检测DFR基因的多态性。根据多态性出现的位点设计特异引物,通过PCR扩增检测70个甜樱桃品种DFR基因的多态性。【结果】获得甜樱桃DFR基因约1 kb的片段,测序结果用BLAST分析发现,其核苷酸序列与樱桃李（Prunus cerasifera）的核苷酸相似性为80 %,预测的氨基酸序列与已知的甜樱桃（P. avium）DFR氨基酸序列相似性达99 %。该片段由3个外显子和3个内含子组成,2个多态性位点分别在内含子2和内含子3上。在黄色、黄底红晕和红色果皮3个组的70个甜樱桃品种中发现3个单倍型,共5种单倍型组合。通过SAS 9.0软件分析发现,所检测到的DFR基因的等位基因频率在黄底红晕果皮品种组和红色品种果皮组中的分布无显著差异。【结论】本研究在甜樱桃DFR基因座上得到2个差异位点,分别在内含子2和内含子3内,其优势基因频率依次为：0.864和0.679;但未发现DFR基因内含子2和内含子3的多态性与果皮颜色之间存在直接关系。     

Allelic Variation in Loci for Adaptive Response and Its Effect on Agronomical Traits in Chinese Wheat (Triticum aestivum L.)

Heading date was an important trait that decided the adaptation of wheat to environments. It was modified by genes involved in vernalization response, photoperiod response and development rate. In this study, four loci Xgwm261, Xgwm219, Xbarc23 and Ppd-D1 which were previously reported related to heading time were analyzed based on three groups of wheat including landraces (L), varieties bred before 1983 (B82) and after 1983 (A83) collected from Chinese wheat growing areas. Generally, heading date of landrace was longer than that of varieties. Significant differences in the heading time existed within the groups, which implied that diversification selection was much helpful for adaptation in each wheat zone. Photoperiod insensitive allele Ppd-D1a was the first choice for both landrace and modern varieties, which promoted the heading date about four days earlier than that of sensitive allele Ppd-D1b. The three SSR loci had different characters in the three groups. Predominant allele combination for each zone was predicted for wheat group L and A83, which made great contribution to advantageous traits. Xgwm219 was found to be significantly associated with heading date in Yellow and Huai River Winter Wheat Zone (Zone II) and spike length in Middle and lower Yangtze Valley Winter Wheat Zone (Zone III), which implied functional diversification for adaption. Variation for earliness genes provided here will be helpful for whet breeding in future climatic change.     

陆地棉吐絮率的限制性两阶段多位点全基因组关联分析及候选基因预测

[目的]吐絮率是反映陆地棉(Gossypium hirsutum L.)早熟性状的重要指标之一,利用全基因组关联分析(genome-wide association study,GWAS)解析吐絮率的QTL(quantitative trait locus)及其遗传效应,为陆地棉早熟性状的分子育种提供理论基础.[方法]...