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.     

入侵性食叶害虫椰子织蛾的单倍型多样性分析

【目的】分析危害棕榈科Palmae植物的一种重要入侵食叶害虫椰子织蛾Opisina arenosella单倍型在原产地和入侵地的分布特点,揭示椰子织蛾入侵我国的虫源信息。【方法】利用线粒体COI基因分析16个地理种群共计172个样本,比较椰子织蛾印度种群和入侵地(中国、马来西亚和泰国)种群的遗传关系。【结果】片段长度为625 bp的172条序列共鉴定出12个单倍型,包含15个变异位点,构成2个明显的单倍型分支,其中一个分支由11个单倍型(IN1～IN11)组成,均来自印度种群,单倍型IN1是6个印度种群的共享单倍型,IN2～IN11为独享单倍型;另一个分支为单倍型HAP,由来自中国、马来西亚和泰国的种群共享;HAP与11个来自印度的单倍型IN1～IN11均存在4个变异位点。【结论】入侵地区的椰子织蛾种群来自同一基因型或者具有相同的入侵源;椰子织蛾种群入侵后受环境选择压力,在新栖息地产生新的突变或杂交。     

基于叶绿体DNA分析的楸子种质遗传多样性研究

利用4对叶绿体DNA引物扩增49份楸子[Malus prunifolia（Willd.）Borkh.]种质资源的4个叶绿体DNA基因间区trnH-psbA、trnS-trnG spacer + intron、trnT-5′trnL和5′trnL-trnF序列，基于4个叶绿体DNA基因间区的序列变异，从母系遗传的角度评价楸子的遗传多样性水平。结果显示：4个叶绿体DNA基因间区序列经测序、拼接、比对和合并之后的片段长度为3 790 bp，共有173个多态性变异位点，其中包含2个单一突变位点、20个简约信息位点和151个插入/缺失位点。在49份楸子种质中，trnH-psbA、trnS-trnG spacer + intron、trnT-5′trnL和5′trnL-trnF区域的变异位点的数量分别为26个、25个、120个和2个，单倍型数量分别为9个、7个、8个和3个，合并之后的叶绿体DNA片段的单倍型有14个。核苷酸多样性和单倍型多样性最高的区域均为trnH-psbA（Hd = 0.775，Pi = 0.02143），最低的为5′trnL-trnF（Hd = 0.481，Pi = 0.00072）。49份楸子种质4个叶绿体DNA区域合并后的遗传多样性较高（Hd = 0.854，Pi = 0.00949）。Tajima’s D检验中，4个叶绿体DNA区域在P > 0.10水平上均不显著，楸子的4个叶绿体DNA区域在进化上遵循中性进化模型。楸子的遗传变异主要存在于群体内部，不同居群间基因交流频繁，多数居群间遗传分化较少，与地理距离不完全相关。     

Current situation and characterization of Pseudomonas syringae pv. actinidiae on kiwifruit in Galicia (northwest Spain)

Bacterial canker of kiwifruit, caused by Pseudomonas syringae pv. actinidiae (Psa), is a disease that is spreading rapidly in several kiwifruit‐producing countries, causing significant economic losses. In 2011, it was detected for the first time in Spain, in the south of Galicia (northwest Spain). Kiwifruit orchards were therefore inspected and sampled in 2011 and 2012 to determine the pathogen distribution, and the isolates obtained were characterized by morphology, fatty acids profile, biochemical tests and molecular techniques. Isolates were obtained from Actinidia deliciosa ‘Hayward’ (from leaves, canes, flower buds, fruits and roots), from A. deliciosa ‘Summer’, from Actinidia chinensis ‘Jin Tao’ (from canes and leaves) and from A. chinensis pollinator ‘Belén’ (from canes). Results of the analysis of the cfl gene (phytotoxin production‐related), the tox–argK gene cluster and phylogenetic analysis of the cts gene demonstrated that all Psa isolates from northwest Spain correspond to the Psa3 population, which includes strains of haplotype 2. This is the first record of Psa3 and haplotype 2 in Spain.     

Phylogenetic relationships and population structure of Ralstonia solanacearum isolated from diverse origins in Taiwan

Bacterial wilt caused by Ralstonia solanacearum is a destructive disease for many crops. The aim of this study was to investigate the phylogenetic relationships and genetic structure of an R. solanacearum population from diverse origins in Taiwan. All 58 tested isolates belonged to phylotype I, except the two biovar 2 isolates from potato. These belonged to phylotype IIB sequevar 1 and were identical to known potato brown rot strains, which were probably introduced. Phylotype I isolates were grouped into 10 sequevars. Sequevar 15 was predominant (34 out of 56 isolates). Its distribution covered the whole island and it was largely associated with solanaceous crops such as tomato, and with tomato field soil. A total of 14 haplotypes were identified based on a partial endoglucanase gene sequence. Parsimony network analysis revealed that haplotype A was the oldest haplotype in the local population. It encompassed all but one of the sequevar 15 isolates. Large variation in virulence on tomato was observed among the 58 isolates, and seven pathotypes were identified. Significant genetic differentiation was detected among pathotypes. Moreover, genetic differentiation was detected between biovar 3 and biovar 4 subgroups and between the strains associated with solanaceous and non‐solanaceous species, but none was detected between strains from different geographic origins. The results suggest that the phylotype I population in Taiwan is homogeneous, while mutation and local adaptation to specific ecological niches keep shaping the population.     

Genetic basis and origin of resistance to acetolactate synthase inhibitors in Amaranthus palmeri from Spain and Italy

BACKGROUND

Amaranthus palmeri is an aggressive annual weed native to the United States, which has become invasive in some European countries. Populations resistant to acetolactate synthase (ALS) inhibitors have been recorded in Spain and Italy, but the evolutionary origin of the resistance traits remains unknown. Bioassays were conducted to identify cross-resistance to ALS inhibitors and a haplotype-based genetic approach was used to elucidate the origin and distribution of resistance in both countries.

RESULTS

Amaranthus palmeri populations were resistant to thifensulfuron-methyl and imazamox, and the 574-Leu mutant ALS allele was found to be the main cause of resistance among them. In two Spanish populations, 376-Glu and 197-Thr mutant ALS alleles were also found. The haplotype analyses revealed the presence of two and four distinct 574-Leu mutant haplotypes in the Italian and Spanish populations, respectively. None was common to both countries, but some mutant haplotypes were shared between geographically close populations or between populations more than 100 km apart. Wide genetic diversity was found in two very close Spanish populations.

CONCLUSION

ALS-resistant A. palmeri populations were introduced to Italy and Spain from outside Europe. Populations from both countries have different evolutionary histories and originate from independent introduction events. ALS resistance then spread over short and long distances by seed dispersal. The higher number and genetic diversity among mutant haplotypes from the Spanish populations indicated recurrent invasions. The implementation of control tactics to limit seed dispersal and the establishment of A. palmeri is recommended in both countries. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.     

A genetic tool for evaluating male‐mediated stock introgression in Atlantic salmon

1. The Atlantic salmon shows strong population structure with reduced gene flow, owing to homing behaviour. Supportive breeding with allochtonous parr or fish‐farm escapees could affect native population genetic structure by the introgression of foreign genes. Mature male parr are potentially powerful vehicles for promoting introgression: they can fertilize eggs in competition with anadromous males. As a consequence, foreign males contribute more to introgression than foreign females. This effect must be taken into account for the correct development of conservation programmes. Foreign males constitute an inadvertent way to disrupt the genetic structure, as the allochtonous parr or fish‐farm escapees can survive in the river during the parr stage.
2. A short polymorphic fragment of the sex‐determining gene (sdY) was used as a marker to assess introgression via males into south European salmon populations. In order to find haplotype variants for the intronic sequence of sdY, samples were investigated from 16 different rivers across the distribution range of the salmon, together with historical samples (1950–1960) from three Spanish rivers.
3. Two novel haplotypes, in addition to the three already described in Atlantic salmon, were found for this locus. Most samples, including historical ones, displayed the common haplotype (D) previously found in salmon all over Europe; however, north European haplotype variants were also detected in salmon inhabiting the southern European rivers that were systematically supplemented with foreign stocks between 1981 and 1994.
4. Analysis of haplotype variation in the sdY intron constitutes a powerful and inexpensive tool, not only to specifically assess male‐mediated introgression into natural populations of Atlantic salmon, but also for monitoring salmon escapees.

     

猪抗酶基因1(AZ1)5’调控区单核甘酸多态性与屠宰性状的相关性分析

通过PCR-RFLP方法检测了长白与蓝塘猪F2代群体抗酶基因1(AZ1)5’调控区-792～-433单核苷酸多态性,共获得3个SNP:-731C＞T,-584A＞C和-476G＞A.-713位点处T为优势等位基因,频率为0.777,优势基因型TT频率为0.598;-584位点处A为优势等位基因,频率为0.769,优势基...     

中国黄牛Y-STRs遗传多样性与起源研究

[目的]研究中国黄牛Y染色体STRs的遗传多样性及父系起源。[方法]利用非变性聚丙烯酰胺凝胶电泳,选择2个牛Y-STRs位点INRA189和BM861,分析16个中国地方黄牛品种284头公牛与4头缅甸黄牛公牛的Y染色体遗传多样性。[结果]在中国16个黄牛品种中,2个Y-STR位点可以区分中国黄牛中的普通牛和瘤牛类型,表明中国黄牛有普通牛和瘤牛两种父系起源。4头缅甸黄牛均为瘤牛类型。在中国16个黄牛品种中,普通牛和瘤牛分布频率分别为57.0%和43.0%,其中普通牛频率在北方黄牛中占优势(98.3%),瘤牛频率在南方黄牛中占优势(76.1%),中原黄牛中普通牛频率较高为63.8%,瘤牛频率为36.2%。[结论]中国黄牛存在普通牛和瘤牛两种父系起源;普通牛频率自北向南逐渐减少,瘤牛频率自北向南逐渐增加,中原地区为普通牛和瘤牛的交汇处。