Genetic structure of the oriental white stork (Ciconia boyciana): implications for a breeding colony in a non‐breeding area

The oriental white stork (Ciconia boyciana) is a threatened species, and their numbers are still in decline due to habitat loss and poaching. China is a breeding and main wintering area for this animal and in recent years some individuals have been found breeding in wintering areas and at some stopover sites. These new breeding colonies are an exciting sign, however, little is understood of the genetic structure of this species. Based on the analysis of a 463‐bp mitochondrial DNA (mtDNA) control region, we investigated the genetic structure and genetic diversity of 66 wild oriental white storks from a Chinese population. We analyzed the sequences of 66 storks obtained in this study and the data of 17 storks from a Japanese population. Thirty‐seven different haplotypes were detected among the 83 samples. An analysis of molecular variance showed a significant population subdivision between the two populations (F_ST= 0.316, P < 0.05). However, the phylogenetic analysis revealed that the samples from the different populations did not form separate clusters and that there were genetic exchanges between the two populations. Compared with the Japanese population, the Chinese population had a relatively higher genetic diversity with a haplotype diversity (hπ SD) of 0.953 ± 0.013 and a nucleotide diversity (π± SD) of 0.013 ± 0.007. The high haplotype diversity and low nucleotide diversity indicate that this population might be in a rapidly increasing period from a small effective population. A neighbor‐joining tree analysis indicated that genetic exchange had occurred between the newly arisen southern breeding colony and the northern breeding colony wintering in the middle and lower Yangtze River floodplain. These results have important implications for the conservation of the oriental white stork population in China.     

Allele‐specific polymerase chain reaction typing and sequencing of mitochondrial D‐loop region in broiler chickens in Japan

This study aimed to comprehend a feature of single nucleotide polymorphism (SNP) in mitochondrial DNA (mtDNA) mainly of general broiler chickens in Japan. We typed two SNP sites (199C/T and 792A/G) of the D‐loop region in mtDNA by allele‐specific PCR (AS‐PCR) in 359 broiler (182 chunky and 177 cobb) and 506 layer (233 White Leghorn, 140 Barred Plymouth Rock and 133 Rhode Island Red) chickens. The SNP of 199C or 792A by AS‐PCR was observed in the chunky and cobb chickens, and not in the layers. The haplotype 199T/792G was observed in a part of cobb and all layers. By the result of AS‐PCR haplotyping and the broiler brands, the D‐loop region was sequenced in 44 broiler chickens (20 chunky and 24 cobb) and compared with the layers’ sequence data. Among the broiler and layer chickens, 21 SNP sites (including one insertion) and 11 sequence haplotypes were observed. Haplotype variation or correspondence was observed in and between the broiler brands. This study provides important information to establish a chicken meat traceability system by SNP haplotyping of mtDNA in Japan.     

黑龙江腐烂茎线虫群体的分离和鉴定

 本研究对分离自黑龙江省马铃薯中的1个线虫群体Hp1进行形态观察与测量,采用线虫通用引物对其rDNA-ITS进行扩增与序列分析,利用PAUP软件以ML法构建系统发育树,并测定其致病性。结果显示,该线虫群体有6条侧线,头部略缢缩,口针明显,中食道球呈长纺锤形,食道峡部窄而细长;雌虫阴门稍突起,后阴子宫囊较长;雄虫交合刺略向腹面弯曲,引带短,具交合伞。其形态测量值与腐烂茎线虫(Ditylenchus destructor)基本一致。rDNA-ITS PCR扩增片段916 bp,经BLAST比对,该ITS序列与腐烂茎线虫序列相似度最高。系统发育树显示,该群体没有与腐烂茎线虫A、B基因型群体聚在一起,而是与C、D型群体聚为1个分支,且与C型亲缘关系更近。据此,将群体Hp1鉴定为腐烂茎线虫C基因型,这是首次在黑龙江省发现腐烂线虫为害马铃薯。     

连锁不平衡的研究与应用

早在20世纪初期，Jinnings就提出了连锁不平衡(Linkage disequilibrium，LD)的概念。近年来随着单核苷酸多态性(Single nucleotide polymorphisms，SNPs)及其单倍型(Haplotypes)研究的兴起，LD也日益成为人们研究的热点。本文借助SNPs和单倍型两种方法来论述LD的研究，并简要介绍了LD研究与关联分析的关系。     

The Northern Ireland Phytophthora infestans population 1998–2002 characterized by genotypic and phenotypic markers

A total of 204 isolates of Phytophthora infestans from Northern Ireland, almost all from commercial potato crops, were collected over 5 years (1998–2002). Phenotypic diversity was assessed using mating type and metalaxyl resistance; genotypic diversity was assessed using two allozyme loci (glucose-6-phosphate isomerase, Gpi, and peptidase, Pep ), mitochondrial DNA haplotype and the multilocus RFLP probe RG57. All isolates were A1 mating type and Gpi 100/100 . The majority were Pep 100/100 , but four Pep 83/100 and six Pep 96/100 isolates were identified. Three mtDNA haplotypes were detected; haplotype IIa was the most common, but each year up to 2001 its frequency declined, with a concomitant increase in Ia isolates. Three isolates had the rare haplotype IIb, but this was only detected in 1998. Metalaxyl resistance and mtDNA haplotype were markedly associated: most haplotype Ia isolates were metalaxyl-resistant, whereas haplotype IIa was more commonly associated with metalaxyl sensitivity. Analysis of a subsample of 91 isolates revealed nine RG57 genotypes, three associated exclusively with haplotype IIa and six exclusively with haplotype Ia. The most common RG57 genotype (51% of isolates) comprised both metalaxyl-resistant and -sensitive haplotype IIa isolates. However, of haplotype Ia isolates, all metalaxyl-resistant phenotypes belonged to one of four RG57 types, one of which was the second most frequent overall (29% of isolates), while all metalaxyl-sensitive isolates belonged to one of two other types. The P. infestans population in Northern Ireland appears to consist of a limited number of clones related to, but differentiated from, the populations in mainland Britain and elsewhere in Europe.     

Pinpointing the candidate region for muscular dystrophy in chickens with an abnormal muscle gene

Muscular dystrophies, a group of inherited diseases with the progressive weakness and degeneration of skeletal muscle, contain genetically variable diseases. Though chicken muscular dystrophy with abnormal muscle (AM) has long been known, the gene responsible has not yet been identified. In this study, a resource family for AM was established with 487 F2 individuals and 22 gene markers, including microsatellite and insertion–deletion markers, were developed. The haplotypes were analyzed with these markers for the candidate region of GGA2q described in a previous study. The candidate region was successfully narrowed down to approximately 1Mbp. The region included seven functional genes predicted as the most likely AM candidates.     

Phenotypic and genetic variation in Finnish potato-late blight populations, 1997–2000

This study was conducted on potato late blight samples collected for monitoring early attacks in Finland from 1997 to 2000. Most of the 1726 Phytophthora infestans isolates were collected soon after the onset of the epidemics. Most of the isolates were tested for mating type as well as metalaxyl and propamocarb hydrochloride (HCl) sensitivity, while virulence on potato R-gene differentials and mitochondrial DNA (mtDNA) haplotype were determined for a subset of the isolates. In half of the fields from which more than one isolate was tested, both mating types were detected, indicating strong potential for sexual reproduction. The mating types coexisted more often in organic fields or gardens than in conventional fields. The proportion of A1 mating type decreased from approximately 80% (1997 and 1998) to 22% by the year 2000. Simultaneously, the proportion of isolates resistant to metalaxyl decreased from approximately 40% to 16%. Resistance to metalaxyl was confined to the IIa mtDNA haplotype and clearly associated with the A1 mating type, as resistance was 10 times more common among A1 isolates than among A2 isolates. Resistance to metalaxyl therefore probably derives from common descent from an isolate with the IIa haplotype. Most of the regional variation in metalaxyl sensitivity was also linked to mating type, as both metalaxyl resistance and the A1 mating type were most common in the north and south-west of Finland. In contrast to metalaxyl, only three propamocarb-HCl-insensitive isolates were found, but propamocarb-HCl sensitivity decreased significantly during the study.     

利用线粒体D-loop区分析家鸭品种遗传多态性与系统进化

通过线粒体DNA控制区的结构和多态性来研究我国家鸭的遗传多态性与系统进化。利用DNA测序技术测定了我国9个家鸭品种106个个体线粒体DNA控制区多变序列。序列分析结果显示:A、C、T、G碱基的平均含量分别为25.6%、33.3%、15.2%和25.9%。检测到34个变异位点,约占分析位点总数的5.1%,有转换、颠换、插入/缺失4种类型的变异。确定了31种单倍型,其中单倍型A7为家鸭的主体单倍型,品种之间有9种共享单倍型。9个家鸭品种单倍型多样度(Hd)平均为0.798,核苷酸多样度(Pi)平均为0.28%,单倍型多样度在荆江麻鸭中最高,其次是攸县麻鸭和恩施麻鸭,在文登黑鸭中最低。9个品种家鸭之间双参数距离范围为0.001 3~0.004 4。31个家鸭单倍型序列的系统发生分析表明,9个家鸭品种只有1个母系起源,没有发现东亚斑嘴鸭对9个家鸭品种起源有贡献的证据。     

甘肃省部分地区马铃薯晚疫病菌交配型及线粒体DNA单倍型分析

由致病疫霉Phytophthora infestans(Mont.) de Bary侵染引起的马铃薯晚疫病是一种世界范围内的毁灭性病害。为了明确甘肃省马铃薯晚疫病菌的遗传结构,对2018年甘肃省定西市、张掖市和陇南市采集的130株晚疫病菌进行了交配型和线粒体DNA (mtDNA)单倍型测定。结果表明：从130株晚疫病菌中检测到A1和A2两种交配型,A1交配型为14株(10.77%),A2交配型为116株(89.23%);检测到Ⅰa、Ⅱa和Ⅱb 3种线粒体DNA单倍型,发生频率分别为88.46%、3.85%和7.69%。Ⅰa单倍型菌株的交配型为A1和A2,Ⅱa单倍型菌株交配型为A1和A2,Ⅱb单倍型菌株交配型为A1。该结果表明甘肃省部分地区马铃薯晚疫病菌以A2交配型,Ⅰa mtDNA单倍型为主。甘肃省各采集地晚疫病菌群体结构或与当地种薯繁育、调运有关。