大花君子兰叶绿体基因组及其特征

采用Illumina MiSeq测序平台对大花君子兰（Clivia miniata）叶片总DNA进行测序，通过组装获得了其叶绿体基因组（cpDNA）全长序列（158 114 bp）。对其cpDNA注释得到135个基因，包含87个蛋白编码基因、40个tRNA基因和8个rRNA基因。采用生物信息学方法对获得的cpDNA进行简单序列重复（SSR）分析和密码子偏好性分析。结果显示：①大花君子兰cpDNA中共有61个SSR位点，其中单核苷酸、二核苷酸、三核苷酸、四核苷酸、五核苷酸和六核苷酸重复数分别为38、9、2、8、3和1个，多数SSR分布在基因间隔区；②大花君子兰cpDNA密码子偏爱以A或U（T）结尾，亮氨酸使用频率最高，半胱氨酸使用频率最低。基于24种植物的cpDNA全长和23种植物的叶绿体ycf2基因序列进行系统发育分析，结果显示大花君子兰与石蒜科植物在同一分支，显示最近的亲缘关系，支持大花君子兰属于石蒜科。基于叶绿体ycf2的系统发育分析结果与基于cpDNA全长的系统发育分析研究结果大部分相同，支持ycf2基因可以代替cpDNA全长用于植物系统发育分析。     

哺乳动物附植前胚胎的基因表达调控

哺乳动物胚胎附植前期包括:合子的形成,胚胎基因组的激活和细胞分化的开始。在这个时期,发育由母源物质控制转为合子基因控制,在此过程,同时形成染色质介导的转录抑制时期,要解除抑制必须经过胚胎基因组的激活。通过对体内、外附植前胚胎的mRNA的表达特点以及它们与成功发育联系的研究,可以筛选出最佳的体外培养条件,设计最佳的核移植方案。     

不同光湿环境对葡萄花芽分化和叶绿体类囊体膜磷酸酯酶活性的影响

以欧亚种葡萄美人指(Vitisviniferacv.ManicureFinger)为试材,正常光湿为对照,采用正常光偏高湿、偏弱光正常湿度、偏弱光高湿、偏弱光临界高湿、临界弱光偏高湿和临界弱光临界高湿6种处理。试验表明:单一偏弱光处理,葡萄叶片叶绿素含量上升,其余处理叶绿素含量下降;6种处理叶绿体类囊体膜磷酸酯酶活性都低于对照,叶绿体类囊体膜磷酸酯酶活性与光照和湿度有关;正常光偏高湿和偏弱光正常湿度部分芽能分化花原基,但在偏弱光高湿或偏弱光临界高湿花芽分化质量严重下降,临界弱光偏高湿和临界弱光临界高湿几乎未发现花原基;单一的弱光因子比单一的高湿因子对叶绿体类囊体膜磷酸酯酶活性和花芽形态分化影响更大,但弱光与高湿同时存在比单一弱光或高湿因子作用于葡萄时,叶绿体类囊体膜磷酸酯酶活性下降更为显著,花芽更难以形成。     

猪繁殖与呼吸综合征病毒缺失变异株的基因组特征

对猪繁殖与呼吸综合征病毒(PRRSV)分离株HB2(sh)／2002的全基因组序列进行了测定与分析。该毒株基因组全长为15373nt(不包括PolyA尾)，与国内外美洲型PRRSV分离株全序列相似性介于88．7％～95．1％之间。序列分析表明，该毒株是1个天然存在缺失的变异毒株，其ORFla的Nsp2存在编码12个氨基酸的连续36个核苷酸的缺失，ORF、3存在编码1个氨基酸的3个核苷酸的缺失。这是国内外首次发现PRRSV存在缺失变异现象，研究结果补充和丰富了PRRSV毒株的基因组信息数据，为深入研究该毒株的遗传与变异及其与生物学特性的关系奠定了基础。     

Genetic risk factors for osteochondrosis in various horse breeds

Osteochondrosis (OC) is an injury to cartilage canals with a following necrosis in the growth cartilage, from there it can develop to osteochondrosis dissecans (OCD). Due to its high impact in the equine industry, new insights into predisposing factors and potential high‐risk genetic variants are warranted. This article reviews advancements in quantitative and molecular genetics in refining estimation of genetic parameters and identifying predisposing genetic loci. Heritabilities were highest for hock OC with estimates at 0.29–0.46 in Hanoverian warmblood and Norwegian trotters, whereas in Thoroughbreds only very low genetic variation seemed to be present in hock OC lesions. Whole genome scans using the Illumina Equine SNP50 or SNP70 Beadchip were performed in Thoroughbred, Standardbred, French and Norwegian trotter, Hanoverian and Dutch warmblood. Validation studies in Spanish Purebred and Hanoverian warmblood horses corroborated OC risk loci on ECA 3, 14, 27 and 29. Particularly, a strong association with hock‐OCD was found for a single nucleotide polymorphism (SNP) on horse chromosome (ECA) 3 upstream to the LCORL gene. Gene expression and microRNA analyses may be helpful to understand pathophysiological processes in equine OC and to connect OCD‐associated genomic regions with potential candidate genes. Furthermore progress in elucidating the underlying genetic variants and pathophysiological changes in OC may be expected from whole genome DNA and RNA next‐generation sequencing studies.     

羊草叶绿体非编码区多态性标记筛选及群体遗传多样性

为筛选多态性丰富的羊草叶绿体非编码区片段,本研究以9个不同地理位置的羊草居群为材料,通过对12个叶绿体非编码区DNA片段测序及其序列间变异分析试图从中找出有遗传差异的叶绿体DNA(cpDNA)片段,并利用有多态性的cpDNA片段进行遗传多样性分析。结果表明,序列ndhF-rpl32、trnL-trnF、trnC-ycf6、aptI-aptH具有比较丰富的变异,可作为下一步研究野生羊草群体遗传学和谱系地理学较为理想的分子标记。在37个羊草个体4条非编码区片段的合并序列中,共检测到15种单倍型,单倍型多态性(Hd)为0.928,核苷酸多态性(Pi)为0.00101;遗传分化指数(Fst)为0.58884,基因流(Nm)为0.17,基因流较小;中性检验Tajima’s D(-1.08542)和Fu’s Fs(-5.301)均为负值,且差异不显著(P>0.10),推测羊草遵循中性进化理论,可能经历过种群扩张;AMOVA结果显示,65%的分子变异出现在居群间,35%出现在居群内;Mantel检验得到,遗传距离与地理距离具有显著相关性(r=0.449,P<0.05);居群分化值Nst 0.386(0.1865)大于Gst 0.234(0.1506),差异显著(P<0.05),表明羊草居群存在分子谱系地理结构。通过系统发育树分析得到,羊草15个单倍型分为两大分支,H2和H10聚为一支,它们与别的居群个体亲缘关系较远,其余单倍型聚为另一支;单倍型网络图显示,H2和H12、H10和H12亲缘关系较远,与系统发育树分析结果基本一致。本研究为羊草的种质资源保护、谱系地理学研究等工作奠定了基础。     

The complete mitochondrial genome and molecular phylogeny of Lueyang black-bone chicken

ABSTRACT

1. The objectives of the current study were to investigate the mitochondrial genome and molecular phylogeny of Lueyang black-bone chicken, and provide molecule base to preserve and explore the specific chicken strain.

2. Based on sequencing and clustering, the complete mitochondrial DNA map and sequences of Lueyang black-bone chicken were revealed, and two phylogenetic trees of Lueyang black-bone chickens based on D-loop sequences and the mitochondrial genome were constructed.

3. The results showed that the complete mitochondrial genome of Lueyang black-bone chickens is 16,784bp in size, consisting of 22 transfer RNA genes, two ribosomal RNA genes, 13 protein-coding genes, and one non-coding control region. The base composition of the complete mtDNA sequence is 30.28% for A, 23.78% for T, 32.42% for C, 13.52% for G. Additionally, 10 haplotypes of D-loop sequences in 32 Lueyang black-bone chickens were detected, which were distributed into 4 clades (A, B, C and E).

4. It was concluded that genetic diversity is wide in Lueyang black-bone chickens, and this strain has multiple maternal origins from different regions in China and neighbouring regions.     

Improvements of TKC Technology Accelerate Isolation of Transgene-Free CRISPR/Cas9-Edited Rice Plants

Elimination of the CRISPR/Cas9 constructs in edited plants is a prerequisite for assessing genetic stability, conducting phenotypic characterization, and applying for commercialization of the plants. However, removal of the CRISPR/Cas9 transgenes by genetic segregation and by backcross is laborious and time consuming. We previously reported the development of the transgene killer CRISPR (TKC) technology that uses a pair of suicide genes to trigger self-elimination of the transgenes without compromising gene editing efficiency. The TKC technology enables isolation of transgene-free CRISPR-edited plants within a single generation, greatly accelerating crop improvements. Here, we presented two new TKC vectors that show great efficiency in both editing the target gene and in undergoing self-elimination of the transgenes. The new vectors replaced the CaMV35S promoter used in our previous TKC vector with two rice promoters to drive one of the suicide genes, providing advantages over our previous TKC vector under certain conditions. The vectors reported here offered more options and flexibility to conduct gene editing experiments in rice.