Single step genomic evaluation for female fertility in Nordic Red dairy cattle

Joint Nordic (Denmark, Finland, Sweden) genetic evaluation of female fertility is currently based on the multiple trait multilactation animal model (BLUP). Here, single step genomic model (ssGBLUP) was applied for the Nordic Red dairy cattle fertility evaluation. The 11 traits comprised of nonreturn rate and days from first to last insemination in heifers and first three parities, and days from calving to first insemination in the first three parities. Traits had low heritabilities (0.015–0.04), but moderately high genetic correlations between the parities (0.60–0.88). Phenotypic data included 4,226,715 animals with records and pedigree 5,445,392 animals. Unknown parents were assigned into 332 phantom parent groups (PPG). In mixed model equations animals were associated with PPG effects through the pedigree or both the pedigree and genomic information. Genotype information of 46,914 SNPs was available for 33,969 animals in the pedigree. When PPG used pedigree information only, BLUP converged after 2,420 iterations whereas the ssGBLUP evaluation needed over ten thousand iterations. When the PPG effects were solved accounting both the pedigree and the genomic information, the ssGBLUP model converged after 2,406 iterations. Also, with the latter model breeding values by ssGBLUP and BLUP became more consistent and genetic trends followed each other well. Models were validated using forward prediction of the young bulls. Reliabilities and variance inflation of predicted genomic breeding values (values for parent averages in brackets) for the 11 traits ranged 0.22–0.31 (0.10–0.27) and 0.81–0.95 (0.83–1.06), respectively. The ssGBLUP model gave always higher validation reliabilities than BLUP, but largest increases were for the cow fertility traits.     

广谱植物内生真菌枫香拟茎点霉生态功能的研究进展

旨在证明枫香拟茎点霉(Phomopsis liquidambari)有潜力成为广谱内生菌的模式菌株之一,有利于促进内生真菌与宿主植物之间的研究更加系统化、完整化。本研究综述了一株广谱植物内生真菌P.liquidambari在改善土壤化学特性,修复受污染的土壤,优化农业生态,提高农作物产量方面的作用。并从真菌定殖情况、植物生理响应和土壤环境优化三个方面,将该菌株与当前研究较多的印度梨形孢(Piriformospora indica)进行比较,并展望了P.liquidambari的研究前景。     

番茄萼片形态性状遗传分析

【目的】探索番茄萼片形态性状的遗传规律,为番茄新品种选育过程中萼片形态性状选择提供依据。【方法】以萼片包被(TI1101-1,P_1)和萼片上卷番茄(J53,P_2)材料为亲本,构建4个世代P_1、P_2、F_1和F_2遗传群体,用游标卡尺对4个世代番茄萼片形态及其形态性状(萼片长度、宽度、厚度、面积、上翘度、卷曲度)进行测量和统计,从而对番茄萼片形态性状的遗传规律、中亲优势、遗传模型进行分析。【结果】番茄F_1代正反交萼片形态一致,均为基平,说明萼片形态的遗传属于细胞核遗传。在F_2代分离群体中,萼片形态包被、基平、上翘、上卷的分离比为1∶34.4∶9∶1.6,即不符合孟德尔遗传规律,属于数量性状。萼片长度、宽度、厚度、面积、上翘度、卷曲度的中亲优势率分别为3.55%,-6.77%,-9.90%,0.51%,-32.42%,-62.02%。同时,运用植物数量性状主基因+多基因遗传分析法对6个萼片形态性状测量值的分析得出:萼片长符合2对等加性主基因+加性-显性多基因遗传模型(MX2-EAED-AD),萼片厚度、面积、卷曲度符合2对加性-主基因+加性-显性多基因遗传模型(MX2-ADI-AD),萼片宽度、上翘度符合2对加性-显性-上位性主基因+加性-显性-上位性多基因遗传模型(MX2-ADI-ADI)。萼片长度、宽度、厚度、面积、上翘度、卷曲度的主基因遗传率为42.59%～77.15%,多基因遗传率为0%～39.89%。【结论】该组合6个番茄萼片形态性状均受2对主基因控制,且主基因遗传率大于多基因遗传率,以主基因遗传为主。     

18份杨树资源的遗传多样性分析

【目的】正确评价杨树资源的遗传多样性，为其新品种选育和资源利用提供理论依据。【方法】以来自黑杨派和白杨派的18个杨树无性系为试验材料，利用聚丙烯酰胺凝胶电泳从84对SSR引物中初步筛选出多态性较好的12对，再利用12对SSR荧光引物构建18个杨树无性系的指纹图谱并进行遗传多样性分析，同时依据遗传相似系数构建聚类图并进行亲缘关系分析。【结果】筛选出的12对引物共检测到91个多态性位点，每对引物检测到的多态性位点为4~12个，平均为7.6个，观测杂合度平均为0.482 8，Shannon信息指数平均为1.801 5，Nei’s基因多样性指数平均为0.794 8；通过引物PMGC-2385和PMGC-2500构建了18个无性系的指纹图谱，该指纹图谱可将全部无性系区分开。UPGMA聚类分析表明，18个无性系的遗传相似系数在0.549~0.978，平均遗传相似系数为0.764，黑杨派与白杨派无性系遗传相似系数变幅分别在0.681~0.978和0.549~0.912，均具有较高的遗传变异性；18个无性系被分为黑杨与白杨2大类及6个亚群，与传统形态分类学结果基本一致。【结论】18份杨树资源的遗传多样性较为丰富，SSR分子标记技术结合STR分型检测技术在杨树资源的鉴定与分类中具有一定的可靠性。     

湖南省饭豆地方种质资源遗传多样性的RAPD和ISSR分析

为揭示湖南省饭豆地方品种的遗传多样性,促进种质资源的有效保护和利用。本研究利用RAPD和ISSR标记分析了源于湖南省各地36份古老饭豆地方品种的遗传多样性,并采用UPGMA方法进行了遗传聚类分析。结果表明：12个RAPD引物和4个ISSR引物在供试材料中共扩增产生81条带型清晰的条带,平均每个引物扩增产生5.06个条带;其中59个为多态性条带,占总扩增条带的72.84%,具有多态性引物的PIC值在0.397~0.968之间;通过UPGMA法进行聚类分析表明供试材料的遗传相似系数在0.605~0.877之间,供试材料被分为4大类,且聚类结果表现明显的地域特征。本研究结果可为本省饭豆种质资源保护和育种研究提供理论依据。     

利用InDel分子标记分析海南山栏稻品种籼粳特性

为明确海南山栏稻品种的籼粳分化特性与遗传变异规律,利用34个籼粳特异InDel分子标记和24个SSR分子标记对22个海南山栏稻品种的籼粳特性与遗传变异进行分析。InDel分子标记鉴定结果表明,供试品种粳型基因频率变幅在0.68~0.83,以粳型品种为主,占到总品种的63.6%,未发现籼型或偏籼型品种。海拔梯度分析表明,海南山栏稻中粳型品种分布范围更为广泛,具有更强的环境适应能力。遗传变异分析表明,在供试群体中共检测到191个等位基因,其中稀有等位基因(基因频率≤0.05)数为86个,占到总等位基因数的45.03%。在供试的3个地理来源中,琼中县的遗传多样性最为丰富。     

Genetic divergence in two tropical maize composites after four cycles of reciprocal recurrent selection

Two tropical maize composites were subjected to four cycles of reciprocal recurrent selection to develop divergent inbred lines with good combining ability. This study was conducted to examine the extent of genetic diversity, changes in allele composition and genetic structure, of 100 randomly selected S₁ lines each from the original (C₀) and advanced (C₄) selection cycles of TZL COMP3 and TZL COMP4, genotyped using single nucleotide polymorphism (SNP) markers. Results revealed that the proportion of alleles at both low and high frequencies decreased from C₀ to C₄, whereas those at intermediate frequencies increased at C₄ in the two composites. More unique and other alleles were lost at C₄ in TZL COMP3 relative to those in TZL COMP4. The changes in different measures of genetic diversity were either small or negligible with selection in the two composites. The proportion of markers departing from Hardy–Weinberg equilibrium (HWE) decreased with selection, whereas the total number of pairs of markers in linkage disequilibrium increased with selection in the two composites. Examination of changes in population structures using a model‐based approach as well as cluster and multivariate analyses found a high degree of concordance in stratifying the 400 S₁ lines into four non‐overlapping groups corresponding to the two selection cycles each within the reciprocal composites. The observed molecular‐based divergence between cycles within the same composite and the clear differentiation between the complementary composites highlight the importance of reciprocal recurrent selection for preserving genetic diversity for long‐term selection. This increases the potential of the advanced selection cycles to sustain genetic gain in productivity of hybrids adapted to the savannas in West and Central Africa.     

甜菜DAMD-PCR体系的建立及优化

为了建立甜菜DAMD扩增体系,以期利用DAMD引物应用于甜菜品种指纹图谱的构建及分子标记辅助育种。本实验利用单因素变量的方法对甜菜DAMD体系进行优化。同时选用12个甜菜品种,利用优化的体系对25条DAMD引物进行扩增。获得甜菜的最适DAMD体系:总体积为20μL,包含模板DNA 10~80 ng、0.75 U的DNA聚合酶、0.2μL的d NTPs(2.5 mmol/L each)以及2.0μL的引物(10μmol/L)。同时25条引物均扩增出了清晰条带,除了个别引物多态性较差外,其余引物多态性都非常的丰富,其中引物62H(-)就可以把实验中用到的12个甜菜品种全部区分开。由此可见,DAMD引物的扩增效率很高,并且扩增结果稳定,条带清晰,非常适合甜菜品种指纹图谱的构建及遗传多样性分析。     

喀斯特山区2个鲫鱼群体基于转铁蛋白的遗传多样性研究

为了解喀斯特山区2个不同鲫鱼群体在蛋白质水平的遗传多样性及其遗传差异,运用聚丙烯酰胺凝胶电泳方法对喀斯特山区2个群体鲫鱼的血清转铁蛋白电泳表型及多样性进行研究。结果表明:群体克隆多样性指数表现为草海鲫鱼(0.32)﹥红鲫(0.25,对照)﹥普安鲫鱼(0.13);3个鲫鱼群体的13个克隆由9个不同的等位基因产生,等位基因的频率分别为Tf~a0.144 9、Tf~b0.202 9、Tf~c0.036 2、Tf~d0.058 0、Tf~e0.007 2、Tf~f0.239 1、Tf~g0.014 5、Tf~h0.275 4、Tf~i0.029 0;普安鲫鱼与草海鲫鱼和红鲫无共享的基因型;普安鲫鱼与草海鲫鱼之间的遗传相似性指数较高(0.714 3),遗传距离较小(0.285 7)。总体来看,草海鲫鱼的克隆多样性水平较高,其转铁蛋白多样性程度较普安鲫鱼丰富;2个群体之间存在较近的亲缘关系,未达到遗传距离种的分化标准。     

基于全基因序列的中国北方3省(区)马铃薯Y病毒遗传多样性分析

本研究以马铃薯Y病毒(PVY)全基因组为基础,分析吉林、黑龙江和内蒙古3省(区)PVY群体遗传多样性和群体分化,并评估突变、重组、选择等遗传力所起的作用。根据已报道的PVY全基因序列保守区设计4对引物,采用片段重叠法对来自内蒙古和吉林的24个PVY分离物全基因序列进行测定,并联合NCBI中已登录的9个黑龙江分离物全基因组序列进行遗传多样性参数评估、群体分化检验和分子变异等分析。结果显示,我国北方3省(区)PVY群体遗传多样性高,其中内蒙古和黑龙江PVY群体遗传多样性高于吉林群体,并且3个群体之间呈现一定程度的遗传分化。分子变异分析发现在PVY基因组中存在1 786个变异位点,表明我国北方3省(区)PVY群体变异程度较高,并且这种高变异度有85.54%来自各个马铃薯种植区内PVY个体的遗传变异。重组分析和系统发育分析发现,我国北方3省(区)PVY群体中重组株系占比高达90.3%,并具有明显的株系多样性,表明PVY重组株系已成为我国北方3省(区)马铃薯种植区的流行株系。选择压力分析显示,使用FEL和IFEL法分别检测出501个和315个净化压力选择位点,这表明3省(区)PVY群体受净化选择压力为主。以上结果表明,中国北方3省(区)PVY群体遗传多样性高,突变、重组和自然选择都对遗传多样性和群体分化存在一定影响。