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.     

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.     

Functional polymorphism among members of abscisic acid receptor family(ZmPYL) in maize

Pyrabactin resistance 1-like proteins(PYLs) are direct receptors of abscisic acid(ABA). For the redundant and polymorphic functions, some members of the PYL family interact with components of other signaling pathways. Here, 253 positive colonies from a maize cDNA library were screened as interacting proteins with the members of ZmPYL family. After sequencing and function annotation, 17 of 28 interaction combinations were verified by yeast two-hybrid(Y2 H). The germination potential, taproot length and proline content of a quartet mutant of Arabidopsis PYL genes were significantly deceased comparing to the wild type(WT) under alkaline stress(pH 8.5) and 100 μmol L–1 methyl jasmonate(MeJA) induction. The malondialdehyde(MDA) content was significantly increased. After germinating in darkness, the characteristics of dark morphogenesis of the quartet mutant seedlings were more obvious than those of the WT. The differential expression of the related genes of photomorphogenesis in the mutant was much more than that in the WT. Three light and two JA responsive cis-affecting elements were identified during the promoter sequences of the AtPYL1 and AtPYL2 genes. These results suggested that functional polymorphism has evolved among the members of ZmPYL family. In response to developmental and environmental stimuli, they not only function as direct ABA receptors but also interact with components of other signaling pathways mediated JA, brassinosteroid(BR), auxin, etc., and even directly regulate downstream stress-related proteins. These signaling pathways can interact at various crosstalk points and different levels of gene expression within a sophisticated network.     

高含固率木质纤维素厌氧发酵物总DNA的4种提取方法比较

不同的样本特性和提取方法对获得微生物总DNA的质量有重要影响。文章基于高含固率木质纤维素厌氧发酵物腐殖酸、酚类物质含量高、质地均一性差、微生物浓度低的特点,研究了4种方法提取不同高含固率粪秸厌氧发酵物中微生物总DNA的效果。结果表明,常规的十二烷基磺酸钠法(sodium dodecyl sulfate,SDS)、十二烷基磺酸钠和溴化十六烷基三甲铵结合法(sodium dodecyl sulfate and cetyltrimethyl ammonium bromide,SDS-CTAB)和商业的粪便试剂盒法提取的DNA质量均较差,SDS法和试剂盒法未能获得聚合酶链式反应(polymerase chain reaction,PCR)扩增目的条带,SDS-CTAB法得到的条带较模糊;改进SDS-CTAB法获得的DNA杂质少、纯度高,具有较好的稳定性,A260/A280和A260/A230值分别为1.74~1.86和1.65~1.86,每克样品的DNA浓度在50 ng·μL^-1以上,电泳条带单一齐整、清晰明亮,PCR扩增的目的条带清晰度高,适宜后续分子生物学技术的分析。林格氏液洗脱、聚乙烯吡咯烷酮-40(Polyvinyl Pyrrolidone-40,PVP-40)洗涤液除杂以及裂解液和多种酶联合破壁是改进SDS-CTAB法获得该类专一性样本高质量微生物总DNA的关键步骤。     

淮南猪酸肉基因的多态性分析

为了研究淮南猪的种质特性,为淮南猪保种、可持续利用及种质创新提供依据,试验采用PCR-RFLP法,对96头淮南猪的RN基因进行了检测。结果表明,RN基因在淮南猪群体中存在隐性纯合子rn^+/rn^+和杂合子RN^-/rn^+,未发现显性纯合子RN^-/RN^-。其中,基因型rn^+/rn^+和RN^-/rn^+的频率分别为0.739 6和0.260 4;等位基因rn^+和RN^-的频率分别为0.869 8和0.130 2。卡方检验表明,rn^+和RN^-基因频率处于Hardy-Weinberg平衡状态,表明群体中RN基因没有受到选择的压力。     

绵羊Izumo1基因多态性及其与产羔数关联分析

为研究Izumo1基因多态性及与产羔数关系,本研究利用PCR和直接测序法对小尾寒羊和苏尼特羊的Izumo1基因DNA序列进行扩增、测序和BLAST分析,并和本课题组前期绵羊重测序数据进行比对,筛选出Izumo1基因SNP位点。同时,采用Sequenom MassARRAY~?技术进行基因分型,并对其SNP位点的基因型和等位基因频率在各群体中的分布进行研究。结果表明:小尾寒羊Izumo1基因DNA全长序列3 385 bp,苏尼特羊Izumo1基因DNA全长序列3 382 bp;筛选出8个Izumo1基因SNP位点,经过初步筛选,将在小尾寒羊、苏尼特羊、滩羊、萨福克羊、杜泊羊、草原藏羊这6个绵羊品种中位点分布没有差异的SNP位点排除,最终筛选获得的g.54412135AG和g.54412107CA 2个位点。Izumo1基因g.54412135AG位点在多羔和单羔绵羊品种中存在GG、GA和AA 3种基因型,G基因为优势等位基因;g.54412107CA在多羔品种中存在CC和CA 2种基因型,而在单羔品种中存在CC、CA和AA 3种基因型,C基因为优势等位基因,其基因型频率和基因频率在单、多羔绵羊群体间的分布差异均极显著(P0.01);群体遗传学分析得出g.54412135AG多态位点在6个品种中的多态信息含量(PIC)都属于低度多态(PIC0.25);g.54412107CA多态位点在杜泊羊中属于中度多态(0.25PIC0.5),在其他5个品种中都属于低度多态(PIC0.25),然而,关联分析发现Izumo1基因g.54412135AG和g.54412107CA位点的不同基因型与小尾寒羊不同胎次产羔数之间不存在显著关联(P0.05)。     

Relationship between three novel SNPs of BRCA1 and canine mammary tumors

The BRCA1 gene plays an important role in the development of human breast cancer, and recent research indicated that genetic variations of BRCA1 are also related to canine mammary tumors (CMTs). Here, using rapid amplification of cDNA ends (RACE), we cloned the 5′- and 3′-UTRs of BRCA1. By direct sequencing of the flanking sequences of the 5′- and 3′-UTRs of BRCA1, three previously unreported single-nucleotide polymorphisms (SNPs) were identified, two (−1228T >C, −1173C >T) in the putative promoter regions and one non-synonymous SNP (63449G >A) in exon 23. Compared with 16 normal samples, the sequences from 34 CMTs suggested that SNP (−1173C >T) was associated with the development of CMTs (odds ratio (OR)=2.57, 95% confidence interval (CI): 1.07–6.15).     

2019—2020年苏浙皖三省小麦叶锈菌群体的致病类型鉴定及毒性结构分析

为持续控制小麦叶锈病及促进小麦的抗叶锈病育种工作,2019—2020年自江苏、浙江和安徽3个省采集自然感叶锈病的小麦病叶,经分离获得小麦叶锈菌单孢分离物,利用43个小麦叶锈病鉴别寄主材料对其致病类型进行鉴定,并对其毒性结构进行分析。结果显示,从170份小麦叶锈菌单孢分离物中共鉴定出67个致病类型,主要致病类型为THS、SHJ、PHS和SHS,出现频率分别为8.8%、7.6%、5.9%和5.9%。江苏、浙江和安徽3个省的单孢分离物对携带抗叶锈基因Lr10、Lr12、Lr22a、Lr22b、Lr29、Lr33、Lr35和Lr36的鉴别寄主材料的苗期毒性频率均超过90.0%,而对携带抗叶锈基因Lr9、Lr24、Lr25、Lr28、Lr38、Lr40、Lr41、Lr42、Lr43和Lr13+3ka的鉴别寄主材料的苗期毒性频率均小于10.0%。卡方检验及Fisher精确检验显示,3个省小麦叶锈菌群体对抗叶锈基因Lr1、Lr2a、Lr3、Lr14b、Lr18、Lr21、Lr26、Lr27+31、Lr32和Lr37的毒力存在显著分化。浙江省小麦叶锈菌群体具有较少的毒性因子（4.73）和毒性值（600...