Development of a core set of KASP markers for assaying genetic diversity in Brassica rapa subsp. chinensis Makino

Single‐nucleotide polymorphisms (SNPs) are rapid, economical and reliable genotyping tools. Non‐heading Chinese cabbage (Brassica rapa L. subsp. chinensis Makino) is now an economically important vegetable crop worldwide. In this study, 1,167 SNPs were evaluated for 7polymorphism among 70 representative non‐heading Chinese cabbage inbred lines using a Kompetitive Allele Specific PCR (KASP) genotyping assay. On the basis of identified polymorphisms and the results of a principal component analysis, we selected 50 core SNPs that were balanced sufficiently to provide adequate information for genetic identification. The core SNPs were used for construction of a neighbour‐joining dendrogram that separated the 70 inbred lines into four main groups and several subgroups corresponding to Caixin, Heiyebaicai, Huangxinwu, Naibaicai, Taitsai, Pak‐choi, and Wutatsai. This categorization was superior to that achieved using a dataset of 479 polymorphic SNPs. To confirm the utility of the core SNP markers in genetic identification, we tested their stability and resolution using 162 commercial hybrid cultivars. The SNPs, which represent a cost‐effective, accurate marker set for germplasm analysis and cultivar identification, are suitable for molecular marker‐assisted breeding in non‐heading Chinese cabbage.     

Morphological differences among Raphanus raphanistrum populations and their relationship to related crops

Wild radish (Raphanus raphanistrum) has developed introgressed populations after hybridization with its cultivated counterpart (R. sativus) in California. Hybridization with various Brassica and Sinapis species is also possible. To determine if hybridization is responsible of the genetic diversity of European populations, six wild radish populations with distinct morphological traits were sampled from geographically distant regions in Europe. Plants were cultivated in an oilseed rape field and in insect‐proof cages. Silique and flower morphology, growth, and reproductive traits were measured. The wild radish populations could be discriminated by the morphological traits, but not related to geographic regions. In particular, populations of one region showed wide variability in terms of silique shape and growth behaviour, and small‐sized flowers. Although the origin of morphological diversity in wild radish is unclear, i.e. native or due to gene flow from the cultivated radish or other Brassicaceae, significant morphological divergence was found that could have relevant effects on plant ecology and adaptation.     

红富士苹果芽变系DNA甲基化研究

以35份富士苹果(Malus×domestica Borkh.‘Fuji’)芽变材料为试材,利用甲基化敏感扩增多态性(Methylation Sensitive Amplified Polymorphism,MSAP)分析和UPGMA聚类方法,对其基因组甲基化修饰水平、变异模式以及表观遗传变异关系进行研究。结果表明:(1)不同富士系得到不同的MSAP扩增,总DNA甲基化水平27.90%～36.16%,平均32.87%,双链全甲基化为主要甲基化方式;(2)富士芽变材料绝大多数位点保持了原有甲基化模式;(3)绝大多数芽变(68.57%)检测到全部的甲基化变异模式(12种),去甲基化频率极显著高于甲基化频率(P <0.01),且CG去甲基化极显著高于CHG;(4)36份种质遗传相似系数平均值0.89(0.79～0.92),在聚类图上,富士原种分布在芽变系集中区外,新近发生的芽变系更倾向于聚在一起,着色系片红型和条红型芽变呈分散排布状态。总的来看,富士芽变的甲基化变异模式丰富,超甲基化和去甲基化相伴发生,但以去甲基化为主;‘富士’着色芽变与其最原始品种富士,以及芽变之间发生了较大表观遗传变异;片红和条红型芽变聚类未表现明显偏好性。本研究将为进一步开展富士着色系芽变机理研究提供指导,可以CG去甲基化为切入点展开深入研究。     

Development of a kompetitive allele‐specific PCR marker for selection of the mutated Wx‐D1d allele in wheat breeding

Waxy (Wx) protein is a key enzyme for synthesis of amylose in endosperm. Amylose content in wheat grain influences the quality of end‐use products. Seven alleles have been described at the Wx‐D1 locus, but only two of them (Wx‐D1b, Wx‐D1e) were genotyped with codominant markers. The waxy wheat line K107Wx1 developed by treating ‘Kanto 107’ seeds with ethyl methanesulphonate carries the Wx‐D1d allele. However, no molecular basis supports this nomenclature. In the present study, DNA sequence analysis confirmed that a single nucleotide polymorphism in the sixth exon of Wx‐D1 changed tryptophan at position 301 into a termination codon. Based on this sequence variation, a PCR‐based KASP marker was developed to detect this point mutation using 68 BC₈F₁ plants and 297 BC₈F₂ lines derived from the cross ‘Ningmai 14’*9/K107Wx1. Combined with codominant markers for the Wx‐A1 and Wx‐B1 alleles, waxy and non‐waxy near‐isogenic lines were distinguished. The KASP marker was efficient in identifying the mutant allele and can be used to transfer waxiness to elite lines.     

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.     

Silicon-mediated genotoxic alterations in Brassica juncea under arsenic stress: A comparative study of biochemical and molecular markers

Arsenic (As), one of the most harmful toxicant at the global level, severely affects plant metabolism when taken up. Interestingly, the presence of silicon (Si) as a fertilizer in As-contaminated soil is an effective strategy to decrease As accumulation in plants. Brassica juncea (var. Varuna) were grown hydroponically to investigate the role of Si at biochemical and molecular levels under arsenite (As³⁺) stress. Seedlings of B. juncea were exposed to As³⁺, Si, and a combination of both elements. Our data demonstrated that seedlings exposed to As³⁺ showed an inhibition in shoot length, chlorophyll, carotenoid, and protein, while co-application of Si improved these growth parameters. Silicon supplementation reduced As accumulation in shoot. Increase/decrease was observed in stress-related parameters (cysteine and proline), antioxidant enzymes (superoxide dismutase, ascorbate peroxidase, and catalase), and oxidative stress markers (malondialdehyde and H₂O₂), which were improved upon co-application of Si as compared to As³⁺ alone treatment. Random amplified polymorphic DNA (RAPD) is a suitable biomarker assay for plants for assessing the genotoxicity. Seven RAPD primers produced a total of 39 and 48 bands in the leaves of the untreated and treated seedlings, respectively. The RAPD band-profiles and genomic template stability were consistent with other growth and physiological parameters. In conclusion, the genotoxic alterations along with the biochemical parameters indicate that the exposure to Si mitigates As³⁺-induced oxidative stress by improving the stress-related parameters and antioxidant system in B. juncea.     

应用SRAP标记对六个鸡腿菇菌株的多态性分析

研究了6个鸡腿菇菌株的序列相关扩增多态性(SRAP)。结果表明,不同菌株间存在着丰富的遗传多样性,SRAP扩增指纹能有效分辨不同菌株的基因型。聚类分析表明,供试菌株在0.877的相似水平上可分为三大类:第一大类包括CC170、CC180和CC33;第二大类包括鸡腿菇和CC168;第三大类仅CC224。为鸡腿菇菌株鉴定和遗传研究提供了新的DNA分子标记技术手段。     

山楂海棠RAPD亲缘关系研究

应用RAPD分子标记技术,对山楂海棠的分类地位进行了探讨。根据RAPD分子标记聚类分析,将14份苹果材料分为5类,8份山楂材料分为4类,山楂海棠的亲缘关系位于山楂和苹果之间,但与苹果较近,认为山楂海棠可能是苹果和山楂的属间杂交种。     

柏氏鲤与荷包红鲤抗寒品系杂交子二代的RAPD分析

采用随机扩增多态性DNA（RAPD）分子标记技术，对荷包红鲤抗寒品系与柏氏鲤进行杂交所获得的F2代个体进行亲子鉴定分析。从180个随机引物中筛选出5个多态性较丰富的引物，并对其产生的多态性DNA片段进行统计分析，结果显示：双亲的RAPD谱带全部在F2代中表现出来，而子代中产生的所有谱带在双亲中的表现率在AB02、AB05、AC20、AI10、AI13几个引物中分别为87．0％、100．0％、92．1％、82．8％、92．6％。这也表明BAPD技术在对鲤的亲子鉴定中具有很强的可行性。     

云南屏边大围山微型鸡遗传多样性*

 云南屏边大围山微型鸡是我国具有独特遗传特性的、属于亚热带热带型早熟地方家禽品种。研究采用了33个家鸡特异性的微卫星标记对该鸡种自然群体中30个个体进行了多态性电泳检测,目的在于阐明其群体遗传变异和遗传结构状况。研究结果显示：33个微卫星座位共检测到65个等位基因,每个座位的等位基因数在1～3个之间,这些等位基因的频率大小在0.0333～1.000之间,平均每个座位的等位基因数为1.9697个,有效等位基因数在100～263个之间, 平均有效等位基因数为1.6846。群体平均杂合度（H）和群体平均多态信息含量（PIC）为0.1737和0.3279。结果表明,大围山微型鸡群体平均杂合度和群体平均多态信息含量较低,纯合度较高,未受到其它外来血液的混杂,是一个封闭的原始群体,具有较高的遗传一致性