扁蓿豆叶绿体基因组密码子偏好性分析

为阐明扁蓿豆（Medicago ruthenica）叶绿体基因组密码子使用模式，以其50条蛋白编码序列（CDS）为对象，利用软件CodonW 1.4.2、Excel以及在线程序对其ENC，RSCU，GC含量、中性绘图、PR2-plot、最优密码子等进行分析得到以下结果：基因组平均GC含量为40.58%，其中GC1>GC2>GC3；ENC的取值介于35.77～56.62之间，表明密码子使用偏好性较弱；基因组中共有30个密码子RSCU>1，其中29个以A/U结尾；ENC-plot绘图分析结果中多数基因分布于标准曲线下方，22个基因ENC比值在—0.05～0.05之间，密码子偏好性主要受选择影响；PR2-plot分析表明碱基T的使用频率大于A，G大于C，说明密码子偏好性还受其他因素影响；该基因组中共有UUU，UUA，ACU等11个最优密码子并均以A/U结尾。以上研究结果可为扁蓿豆叶绿体基因组优良基因利用提供理论与基础。     

基于甘蔗热带种(LA-purple)全基因组序列的SSR开发及特征分析

现代甘蔗栽培品种(2n=100~130)是由甘蔗热带种(2n=80)与割手密(2n=40~128)种间杂交而来,形成异源多倍体、非整倍体作物,使得甘蔗栽培品种中80%~90%的染色体来源于热带种。开发热带种基因组SSR分子标记,有助于甘蔗遗传多样性分析、分子标记辅助选择、遗传图谱的构建等。本研究基于热带种LA-purple的全基因组测序数据的255 398个预测基因序列(累计总长为1 029 222 285 bp),利用Perl程序与生物信息学软件结合,发掘SSR位点,获得了153 150个SSR位点,平均每1.67个基因有1个SSR位点,其中二、三核苷酸重复基序分别为39 556个和50 072个,占总SSR位点数的58.5%。在二核苷酸重复基序中,TA/AT所占比例最高,占41.4%,CG/GC所占比例最低,占4.6%;在三核苷酸碱基重复基序中,TGT/ACA所占比例最高,为15.6%。在TA/AT重复类型中选取100个基序重复次数在60~90之间的SSR位点,进行引物设计与合成,在12个甘蔗属材料中进行PCR扩增分析,从中筛选出52对具有多态性SSR引物,其中有27对引物在研究的2个甘蔗栽培品种间表现为多态。这些基因组SSR标记的开发,不仅可以用于甘蔗栽培品种DNA指纹图谱分析,而且为甘蔗属不同种的遗传图谱构建、遗传多样性分析和重要性状的遗传机制解析奠定基础,为甘蔗分子育种研究提供重要支撑。     

Detection and characterization of a rhabdovirus causing mortality in black bullhead catfish,Ameiurus melas

This study fully describes a severe disease outbreak occurred in 2016 in black bullhead catfish farmed in Italy. Affected fish showed nervous clinical signs as well as emaciations and haemorrhagic petechiae on the skin at the fin bases, abdomen and gills. Viral isolation in cell culture allowed the subsequent identification of a rhabdovirus, tentatively named ictalurid rhabdovirus (IcRV), through electron microscopy, immunofluorescence and whole genome sequencing (WGS). The newly isolated virus, together with 14 additional viral strains stored in our repository and detected during similar mortality episodes in the period 1993–2016, was phylogenetically analysed on the basis of the nucleoprotein and the glycoprotein nucleotide and amino acid sequences. The genetic distances among Italian IcRV strains were also estimated. Our results show that all the IcRV strains belong to the genus Sprivivirus and are closely related to the tench rhabdovirus (TenRV). Italian catfish production is constantly decreasing, mainly due to viral infections, which include the newly characterized IcRV. Data presented in this work will assist to investigate the molecular epidemiology and the diffusive dynamics of this virus and to develop adequate surveillance activities.     

Two-year surveillance of tilapia lake virus (TiLV) reveals its wide circulation in tilapia farms and hatcheries from multiple districts of Bangladesh

Tilapia lake virus (TiLV) is an emerging pathogen in aquaculture, reportedly affecting farmed tilapia in 16 countries across multiple continents. Following an early warning in 2017 that TiLV might be widespread, we executed a surveillance programme on tilapia grow-out farms and hatcheries from 10 districts of Bangladesh in 2017 and 2019. Among farms experiencing unusual mortality, eight out of 11 farms tested positive for TiLV in 2017, and two out of seven tested positive in 2019. Investigation of asymptomatic broodstock collected from 16 tilapia hatcheries revealed that six hatcheries tested positive for TiLV. Representative samples subjected to histopathology confirmed pathognomonic lesions of syncytial hepatitis. We recovered three complete genomes of TiLV from infected fish, one from 2017 and two from 2019. Phylogenetic analyses based on both the concatenated coding sequences of 10 segments and only segment 1 consistently revealed that Bangladeshi TiLV isolates formed a unique cluster within Thai clade, suggesting a close genetic relation. In summary, this study revealed the circulation of TiLV in 10 farms and six hatcheries located in eight districts of Bangladesh. We recommend continuing TiLV-targeted surveillance efforts to identify contaminated sources to minimize the countrywide spread and severity of TiLV infection.     

Genome‐wide association analysis of salmon lice (Lepeophtheirus salmonis) resistance in a North American Atlantic salmon population

Our objective was to detect single nucleotide polymorphisms (SNPs) associated with resistance to the salmon louse in the Saint John River aquacultural population of North American Atlantic salmon using estimated breeding values (EBVs) and 6K genotypes from the parent‐generation and lice count phenotypes from the challenged, but ungenotyped, offspring‐generation. In 2011 and 2012, we challenged recent smolts with approximately 100 copepodids each. Fish were euthanized once the lice reached the chalimus stages and lice count, sex, tank and salt water weight were recorded. We used a multiple trait model to estimate breeding values for the parent‐generation using their own fresh water weights and the salt water weights and lice counts of the offspring‐generation. Salmon lice count heritability for untransformed and transformed data was 0.17 and 0.29 respectively. Two different genome‐wide association study methods were compared: (i) forward multiple linear regression and (ii) a mixed linear model using principal components to correct for population stratification as implemented in the egscore function of GenABEL. The two methods detected different SNPs located on different chromosomes. The multiple regression method incorporated 70 SNPs found on chromosomes 2, 7, 9, 12, 14, 15, 21, 22, 1p/23, 24. Many SNPs entered into the forward multiple regression are likely to be false positives from not correcting for the observed population stratification and cryptic relatedness. In contrast, the mixed linear model identified only two SNPs, one on chromosome 1p/23 (6.9%) and one on chromosome 1q (6.1%) consistent with louse‐resistance being a quantitative trait.     

玉米矮花叶病毒分离物基因组克隆及多样性分析

玉米是重要的粮食和经济作物,在国民经济中占有重要地位。玉米矮花叶病毒(Sugercan mosaic virus,SCMV)广泛分布在世界各玉米主产区,严重威胁玉米的安全生产。系统研究SCMV的发生危害、遗传结构与进化机制,对病毒病的防治具有重要意义。从山西省4个玉米主产区采集122个玉米叶片样品(2015年62份,2016年60份)。经RT-PCR检测证实36个样品(2015年20个样品,2016年16个样品)为SCMV阳性,且广泛分布于山西省玉米各个产区。从这些阳性样品中分离、测序、克隆得到了一个新的SCMV分离物,该分离物(包括5'-UTR和3'-UTR端)基因组全长9 539 bp,编码3 063个氨基酸。该分离物与26个SCMV分离物(NCBI)进行一致率、系统发育分析表明SCMV存在较大遗传变异,27个分离物被划分为3个与地理位置无明显相关性的不同进化群体。选择压力分析表明,负向选择可能是SCMV遗传变异的原因之一。对变异位点统计分析发现,该结果将为评估SCMV在中国的流行病学特征奠定基础,有助于SCMV的长期可持续防控策略的制定。     

Molecular breeding technologies and strategies for rust resistance in wheat (Triticum aestivum) for sustained food security

Wheat is an important cereal food crop providing key nutrients to humankind. Rusts are the most destructive pathogens of cereal crops, with the exception of rice, across the world and resistant cultivars have been widely employed to reduce the yield losses caused by them. The modern intensive monoculture of cultivars and changing climatic conditions has created congenial conditions for the emergence of new virulent races such as Ug99, which is a great concern for world food security. Conventional breeding efforts have not been effective in quickly developing new varieties with durable and broad‐spectrum resistance against the rapidly evolving rust pathogen races. However, in the last two decades, biotechnological methods such as marker‐assisted selection (MAS) and transgenic technology have provided novel strategies for enhancing resistance levels and durability in crop plants in a short span of time. Nevertheless, broad application of transgenics in agriculture is hindered by biosafety apprehensions. In recent years, improved versions of biotechnological breeding methods such as genomic selection, genome editing technologies, cisgenesis and intragenesis, RNA‐dependent DNA methylation (RdDM), agroinfiltration and reverse breeding are gaining popularity. These technologies provide a tremendous capability to manipulate crop plants more precisely than before and accelerate crop improvement efforts for sustained food production as well as overcoming safety concerns associated with food crops.     

Genome-wide detection of selective signatures in a Jinhua pig population

The aim of this study was to detect evidence for signatures of recent selection in the Jinhua pig genome. These results can be useful to better understand the regions under selection in Jinhua pigs and might shed some lights on groups of genes that control production traits. In the present study, we performed extended haplotype homozygosity(EHH) tests to identify significant core regions in 202 Jinhua pigs. A total of 26 161 core regions spanning 636.42 Mb were identified, which occupied approximately 28% of the genome across all autosomes, and 1 158 significant(P0.01) core haplotypes were selected. Genes in these regions were related to several economically important traits, including meat quality, reproduction, immune responses and exterior traits. A panel of genes including ssc-mir-365-2, KDM8, RABEP2, GSG1L, RHEB, RPH3AL and a signal pathway of PI3K-Akt were detected with the most extreme P-values. The findings in our study could draw a comparatively genome-wide map of selection signature in the pig genome, and also help to detect functional candidate genes under positive selection for further genetic and breeding research in Jinhua and other pigs.