Response of Resistant and Susceptible Bell Pepper (Capsicum annuum) to a Southern California Meloidogyne incognita Population from a Commercial Bell Pepper Field

To determine the presence and level of root-knot nematode (Meloidogyne spp.) infestation in Southern California bell pepper (Capsicum annuum) fields, soil and root samples were collected in April and May 2012 and analyzed for the presence of root-knot nematodes. The earlier samples were virtually free of root-knot nematodes, but the later samples all contained, sometimes very high numbers, of root-knot nematodes. Nematodes were all identified as M. incognita. A nematode population from one of these fields was multiplied in a greenhouse and used as inoculum for two repeated pot experiments with three susceptible and two resistant bell pepper varieties. Fruit yields of the resistant peppers were not affected by the nematodes, whereas yields of two of the three susceptible pepper cultivars decreased as a result of nematode inoculation. Nematode-induced root galling and nematode multiplication was low but different between the two resistant cultivars. Root galling and nematode reproduction was much higher on the three susceptible cultivars. One of these susceptible cultivars exhibited tolerance, as yields were not affected by the nematodes, but nematode multiplication was high. It is concluded that M. incognita is common in Southern California bell pepper production, and that resistant cultivars may provide a useful tool in a nonchemical management strategy.     

Characterization of the Genetic Diversity and Population Structure for the Yellow Cattle in Taiwan Based on Microsatellite Markers

In recent years, the population size of Taiwan yellow cattle has drastically declined, even become endangered. A preservation project, Taiwan Yellow Cattle Genetic Preservation Project (TYCGPP), was carried out at the Livestock Research Institute (LRI) Hengchun branch (1988–present). An analysis of intra- and inter- population variability was performed to be the first step to preserve this precious genetic resource. In this work, a total number of 140 individuals selected from the five Taiwan yellow cattle populations were analyzed using 12 microsatellite markers (loci). These markers determined the level of genetic variation within and among populations as well as the phylogenetic structure. The total number of alleles detected (122, 10.28 per locus) and the expected heterozygosity (0.712) indicated that these five populations had a high level of genetic variability. Bayesian cluster analysis showed that the most likely number of groups was 2 (K = 2). Genetic differentiation among clusters was moderate (F _ST = 0.095). The result of AMOVA showed that yellow cattle in Taiwan had maintained a high level of within-population genetic differentiation (91%), the remainder being accounted for by differentiation among subpopulations (4%), and by differentiation among regions (5%). The results of STRUCTURE and principal component analysis (PCA) revealed two divergent clusters. The individual unrooted phylogenetic tree showed that some Kinmen yellow cattle in the Hengchun facility (KMHC individuals) were overlapped with Taiwan yellow cattle (TW) and Taiwan yellow cattle Hengchun (HC) populations. Also, they were overlapped with Kinmen × Taiwan (KT) and Kinmen yellow cattle (KM) populations. It is possible that KMHC kept similar phenotypic characteristics and analogous genotypes between TW and KM. A significant inbreeding coefficient (F _IS = 0.185; P < 0.01) was detected, suggesting a medium level of inbreeding for yellow cattle in Taiwan. The hypothesis that yellow cattle in Taiwan were derived from two different clusters was also supported by the phylogenetic tree constructed by the UPGMA, indicating that the yellow cattle in Taiwan and in Kinmen should be treated as two different management units. This result will be applied to maintain a good level of genetic variability and rusticity (stress-resistance) and to avoid further inbreeding for yellow cattle population in Taiwan.     

等位基因多态性群体遗传结构的多元非线性分析方法

长期以来,对于多维基因多态性数据的多元统计分析,如计算遗传距离时昕用的聚类分析、分析群体遗传结构时所用的主成分分析、因子分析和典型相关分析等,一直应用为无约束条件数据而设计的经典多元线性分析方法,并没有注意基因多态性数据的“闭合效应”所带来的问题。从分析基因多态性数据的分布和结构特征入手,文中指出了基因多态性分布具有“闭合数据”的特点,分析了由于“闭合效应”的影响,经典多元线性方法用于群体遗传结构分析昕面临的困难。根据成分数据统计分析的理论和方法,提出了基因多态性群体遗传结构的多元非线性分析基本方法。并以主成分分析为例,通过实例比较和分析了经典线性主成分分析和“对数比”非线性主成分分析的结果,证明“对数比”非线性主成分分析方法是研究基因多态性群体遗传结构的良好方法,具有特异、灵敏等优点,其结果符合群体遗传学规律。     

北沙柳群体遗传多样性和遗传结构分析

以内蒙古北沙柳(Salix psammophila)国家种质资源库内9个群体(P1~P9)288个无性系为实验材料,利用TP-M13-SSR技术,选取22对具有多态性EST-SSR北沙柳引物,采用毛细管电泳对PCR产物进行检测,分析北沙柳遗传多样性、分化程度和群体遗传结构,为北沙柳种质资源库遗传管理、无性系鉴定、品种选育、遗传改良和构建指纹图谱提供理论依据。结果显示:(1)22对EST-SSR引物共检测到222个等位基因,各位点平均等位基因数(A)为10,四倍体基因型丰富度(G)和特异基因型(G1)总和分别为1 460和802个,平均特异基因型比率(P1)和种质鉴别率(P2)分别为45.86%和13.21%。(2)9个群体平均等位基因数(A)为7.475,基因型丰富度(G)为15.586,观察杂合度(Ho)和期望杂合度(He)分别为0.577和0.638。以期望杂合度He为标准,北沙柳群体遗传多样性水平最低的是P1和P9。(3)北沙柳群体遗传分化系数仅为0.02,AMOVA分子变异分析显示,北沙柳群体大部分遗传变异来自群体内(97%),群体间变异仅为3%。(4)三维主成分、聚类和Structure群体遗传结构分析显示,9个群体被划分为2个组,Mantel检验表明北沙柳遗传距离与地理距离极显著相关(r=0.684 P0.001)。研究表明,北沙柳种质资源具有丰富的遗传多样性,这是其具有耐旱、耐寒、耐高温、耐沙埋和抗风蚀等适应性较强的分子基础;北沙柳的遗传变异集中在群体内;分布区群体呈现由中心向边缘群体扩张分化的趋势。     

云杉矮槲寄生遗传多样性及其群体遗传结构分析

该研究采用CTAB法提取云杉矮槲寄生(Arceuthobium sichuanense)的基因组DNA,利用ITS1片段的序列信息对中国9个不同地理群体的62份云杉矮槲寄生样本的遗传多样性及群体遗传结构进行分析。结果表明:(1)62条ITS1序列共定义16个单倍型(H1~H16),表现出较低的遗传多样性水平(h=0.678 5,π=0.005 9),而群体间的遗传多样性水平则表现出较大差异(h=0~1.000 0,π=0~0.009 4);AMOVA分析显示云杉矮槲寄生群体内的遗传变异占到51.37%,群体间为48.63%。(2)Network单倍型网络分析表明,单倍型H1和H12较为古老,且所有群体对2种单倍型无共享现象;单倍型H1是广布单倍型,存在于青海和甘肃的6个群体中,单倍型H12仅在四川的2个群体中有分布。(3)基于最大似然法(ML)构建的群体聚类和中介邻接法构建的单倍型网络图均显示,四川的3个群体为独立类群,区别于青海、甘肃群体,且甘肃和青海的群体之间没有明显分化。该研究首次报道了云杉矮槲寄生遗传多样性和遗传结构,为进一步研究其进化及后续的病害防控提供了一定的参考。     

基于分型测序技术的粒用高粱遗传多样性和群体结构分析

了解粒用高粱的遗传多样性和群体结构,能有效提高粒用高粱新品种的选育效率。本研究利用基因分型测序技术(GBS,genotyping by sequencing)对120份粒用高粱材料开展了全基因组基因分型,共获得了3456个多态性的SNP标记,其多态性信息含量指数(PIC,polymorphism information content)介于0.013～0.574之间,平均值为0.381。根据SNP标记在120份高粱材料中的基因分型数据,计算了材料间的遗传距离,其变异范围为0.084～0.613,平均遗传距离为0.365。群体进化树分析和主成分分析都将120份高粱材料划分为3个类群,类群1主要由包括美国材料MN-3609在内的亲缘关系较远的高粱材料组成,类群2主要由中国北方的高粱材料组成,类群3主要由中国南方的高粱材料组成。群体结构分析表明,当K=3时,ΔK取得最大值,说明120份高粱材料可以划分为3个类群,其划分结果与群体进化树分析和主成分分析基本一致。本研究从基因型多样性水平上阐释了粒用高粱的遗传背景和群体结构,为中国粒用高粱新品种的选育提供了理论依据。     

羚牛的遗传多样性及其种群遗传结构分析

羚牛是亚洲大陆一种特有的大型珍稀动物,目前正面临着栖息地丧失、片段化和人类活动的严重威胁。为了有效地保护这种濒危动物,全面了解羚牛的种群结构、进化历史和整个分布区内遗传多样性的分布是至关重要的。本研究以mtDNA D-loop330bp基因片段为分子标记,比较分析了来自陕西秦岭、甘肃南部、四川岷山、邛崃山和云南贡山的40个样品的序列差异,根据分布特点将所采集到的羚牛分为3个地理单元,即秦岭、四川和云南。结果表明,在3个地理单元中存在4种单倍型,且地理单元间不存在共享单倍型,相互单倍型之间的平均序列差异为1.66％。进一步分析表明,3个地理单元间的基因流较低,存在着显的遗传分化 ,说明羚牛具有明显的系统地理分布格局。同时提出应将分布于秦岭山区、唐家河青川地区、天全以及云南贡山地区作为独立的管理单元分别加以保护。     

内蒙古西伯利亚杏群体遗传多样性和遗传结构分析

利用27对SSR分子标记对内蒙古地区13个西伯利亚杏群体的遗传多样性和遗传结构进行分析,评价其遗传多样性水平和分化程度,为内蒙古西伯利亚杏资源的合理保护与利用提供理论依据。结果显示:(1)27对SSR引物共检测到512个等位基因(Na),各位点平均等位基因数(Na)和多态性信息含量(PIC)分别为19和0.84;物种水平上Shannons信息指数(I)和期望杂合度(He)分别为2.25和0.73。(2)群体水平上的等位基因(Na)、有效等位基因(Ne)、Shannons信息指数(I)、期望杂合度(He)和观察杂合度(Ho)分别为6.95、4.48、1.60、0.76和0.56;其中科左后旗群体遗传多样性最丰富,克什克腾旗群体遗传多样性最低。(3)基于F统计量分析的遗传分化系数(Fst)为0.12,基因流(Nm)为1.86;分子方差分析显示内蒙古西伯利亚杏群体大部分遗传变异来自群体内(92%),群体间的遗传变异仅占8%。(4)内蒙古西伯利亚杏群体遗传距离为0.04~0.67,遗传相似度为0.33~0.83;遗传相似度的聚类分析、遗传距离的主坐标分析和遗传结构分析(Structure)均将供试13个群体划分为4组。Mantel检测显示,内蒙古西伯利亚杏群体遗传距离与地理距离呈显著相关关系(r=0.453,P0.01)。研究表明,内蒙古西伯利亚杏资源具有丰富的遗传多样性,这一特性与其群体的大小、悠久的演化历史以及自身生物学特性相关;内蒙古西伯利亚杏群体间存在中等程度的遗传分化,这可能源于自然地理隔离以及近期人类活动引起的生境片段化。     

马铃薯实生群体遗传多样性的SSR分析

以云南马铃薯品种‘剑川红’植株1个浆果中的天然实生种子产生的70个单株以及B20[CIP010(♀)×CIP004(♂)]杂交组合后代100个实生苗单株为材料,采用12对SSR引物对自交种和杂交实生群体的遗传差异性进行分析,旨在从后代群体中找到与母本(亲本)在分子水平上表现一致的植株,为种质资源的长期保存提供依据。结果表明:(1)‘剑川红’自交群体的多态性比率为81.6%,比杂交组合B20实生群体的多态性比率72.8%略高,说明2个群体的多态性比率均较高。(2)聚类分析结果显示,自交后代和杂交后代群体的遗传相似系数均较高,变化范围均在0.74~0.96之间,说明2个群体均发生了不同程度的遗传分离,但分离的程度较小,绝大多数条带表现一致。(3)在所有供试材料中,同一浆果中均未发现与‘剑川红’母株在分子水平上表现完全一致的单株。研究认为,在分子水平上寻找完全不分离的实生群体难度非常大,需进一步评价与母株(亲本)在分子水平上相似株系的田间表现,从而确定是否可以通过相近或极相近株系来恢复种源。     

Genetic Diversity and Population Structure of the Brachiaria brizantha Germplasm

Brachiaria brizantha (Hochst. ex A. Rich.) Stapf. (syn. Urochloa brizantha (Hochst. ex A. Rich.) R.D. Webster) is a species used primarily as forage in tropical America and Southeast Asia. B. brizantha has been extensively researched since the 1980s with the initiation of the Tropical Forages Breeding Program conducted by the Brazilian Agricultural Research Corporation (Empresa Brasileira de Pesquisa Agropecuária; EMBRAPA), holding one of the largest germplasm collections in the world. This work has identified 15 new microsatellite markers for this species, which have been used in addition to five previously reported markers, to estimate the genetic similarities among 172 accessions and six cultivars of this species. Similarity index values ranged from 0.40 to 1.00. Two duplications were found in the germplasm. A Bayesian analysis performed using the STRUCTURE 2.3.3 program revealed the presence of three clusters with different allelic pools. This analysis is valuable for the performance of crosses to explore heterosis; however, the mode of reproduction of the accessions and ploidy barriers must be observed for effective exploration. A grouping analysis using the neighbor-joining method was consistent with the STRUCTURE analysis, and a combination approach suggested that this germplasm collection does not exhibit considerable genetic variability despite the presence of three distinct allelic pools. The lack of correlation between the genetic and geographic distances is also discussed.     

Genetic Diversity and Population Structure of Theileria annulata in Oman

Background

Theileriosis, caused by a number of species within the genus Theileria, is a common disease of livestock in Oman. It is a major constraint to the development of the livestock industry due to a high rate of morbidity and mortality in both cattle and sheep. Since little is currently known about the genetic diversity of the parasites causing theileriosis in Oman, the present study was designed to address this issue with specific regard to T. annulata in cattle.

Methods

Blood samples were collected from cattle from four geographically distinct regions in Oman for genetic analysis of the Theileria annulata population. Ten genetic markers (micro- and mini-satellites) representing all four chromosomes of T. annulata were applied to these samples using a combination of PCR amplification and fragment analysis. The resultant genetic data was analysed to provide a first insight into the structure of the T. annulata population in Oman.

Results

We applied ten micro- and mini-satellite markers to a total of 310 samples obtained from different regions (174 [56%] from Dhofar, 68 [22%] from Dhira, 44 [14.5%] from Batinah and 24 [8%] from Sharqia). A high degree of allelic diversity was observed among the four parasite populations. Expected heterozygosity for each site ranged from 0.816 to 0.854. A high multiplicity of infection was observed in individual hosts, with an average of 3.3 to 3.4 alleles per locus, in samples derived from Batinah, Dhofar and Sharqia regions. In samples from Dhira region, an average of 2.9 alleles per locus was observed. Mild but statistically significant linkage disequilibrium between pairs of markers was observed in populations from three of the four regions. In contrast, when the analysis was performed at farm level, no significant linkage disequilibrium was observed. Finally, no significant genetic differentiation was seen between the four populations, with most pair-wise F_ST values being less than 0.03. Slightly higher F_ST values (G_ST’ = 0.075, θ = 0.07) were detected when the data for T. annulata parasites in Oman was compared with that previously generated for Turkey and Tunisia.

Conclusion

Genetic analyses of T. annulata samples representing four geographical regions in Oman revealed a high level of genetic diversity in the parasite population. There was little evidence of genetic differentiation between parasites from different regions, and a high level of genetic diversity was maintained within each sub-population. These findings are consistent with a high parasite transmission rate and frequent movement of animals between different regions in Oman.     

Genetic Diversity and Population Structure of Dioscorea tokoro Makino, a Dioecious Climber

Abstract Dioscorea tokoro Makino is a herbaceous climber species widespread in East Asia. Genetic structure of a natural population of D. tokoro was examined employing starch gel electrophoresis of allozymes. Genotypes of seven loci were studied for 1,128 individuals. Twenty-six populations located mainly in the Kinki district of Japan were subgrouped into four large clusters by the geographical distribution of alleles. The D. tokoro population was revealed to contain greater total genetic diversity ( H_T =0.282) and higher intrapopulational genetic diversity ( H_S =0.258) than other outcrossing species for which data are available. On the other hand, interpopulational differentiation ( G_ST =0.096) was smaller than in other outcrossers. For the heterozygosity deficiency observed ( F_IT =0.125), population subdivision ( F_ST =0.096) and inbreeding within the population ( F_IS =0.067) were revealed to contribute to the same extent. From these F -statistics, the migration rate among subpopulations and the rate of between-relative matings were estimated. Overall results on the genetic structure of the D. tokoro population indicated a high gene flow among its subpopulations, and this may be the consequence of its life form as a climber and its habitat in a disturbed environment. During the study, the geographical cline of Pgi allele frequencies was observed. This finding was supposed to be the result of the selection imposed on Pgi by the temperature differences between localities.     

Effects of Low Oxygen on Photosynthesis, Translocation and Growth in Green Pepper (Capsicum annuum)

Green pepper (Capsicum annuum cv. Bell Boy) plants were exposedin chambers to low (2%) oxygen and controlled carbon dioxideconcentrations. Vegetative and fruiting plants showed short-termincreases in net photosynthesis in low oxygen or elevated carbondioxide (up to 900 µl CO₂ l^–1). Photosynthesis ofyoung vegetative plants increased in low oxygen in the short-termbut there was no long-term benefit. Low oxygen enhancement ofphotosynthesis declined with time and after 10 d, leaf areaand root dry weight were less than in plants grown in normalair. Labelled assimilates were translocated from leaves to otherregions at similar rates in low oxygen and normal air. Low oxygenreduced respiratory losses from leaves and reduced the proportionof soluble carbohydrate converted to polysaccharide in all plantparts. Thus, low-oxygen environments decrease the utilisationof assimilates which then may lead to inhibition of photosynthesis. Capsicum annuum, photosynthesis, photorespiration, translocation, utilization of assimilates     

Genetic Diversity and Population Genetic Structure Analysis of Echinococcus granulosus sensu stricto Complex Based on Mitochondrial DNA Signature

The genetic diversity and population genetics of the Echinococcus granulosus sensu stricto complex were investigated based on sequencing of mitochondrial DNA (mtDNA). Total 81 isolates of hydatid cyst collected from ungulate animals from different geographical areas of North India were identified by sequencing of cytochrome c oxidase subunit1 (coxi) gene. Three genotypes belonging to E. granulosus sensu stricto complex were identified (G1, G2 and G3 genotypes). Further the nucleotide sequences (retrieved from GenBank) for the coxi gene from seven populations of E. granulosus sensu stricto complex covering 6 continents, were compared with sequences of isolates analysed in this study. Molecular diversity indices represent overall high mitochondrial DNA diversity for these populations, but low nucleotide diversity between haplotypes. The neutrality tests were used to analyze signatures of historical demographic events. The Tajima’s D test and Fu’s FS test showed negative value, indicating deviations from neutrality and both suggested recent population expansion for the populations. Pairwise fixation index was significant for pairwise comparison of different populations (except between South America and East Asia, Middle East and Europe, South America and Europe, Africa and Australia), indicating genetic differentiation among populations. Based on the findings of the present study and those from earlier studies, we hypothesize that demographic expansion occurred in E. granulosus after the introduction of founder haplotype particular by anthropogenic movements.     

Genetic Diversity and Population Structure of Sitodiplosis mosellana in Northern China

The wheat midge, Sitodiplosis mosellana, is an important pest in Northern China. We tested the hypothesis that the population structure of this species arises during a range expansion over the past 30 years. This study used microsatellite and mitochondrial loci to conduct population genetic analysis of S. mosellana across its distribution range in China. We found strong genetic structure among the 16 studied populations, including two genetically distinct groups (the eastern and western groups), broadly consistent with the geography and habitat fragmentation. These results underline the importance of natural barriers in impeding dispersal and gene flow of S. mosellana populations. Low to moderate genetic diversity among the populations and moderate genetic differentiation (F _ST = 0.117) between the two groups were also found. The populations in the western group had lower genetic diversity, higher genetic differentiation and lower gene flow (F _ST = 0.116, Nm = 1.89) than those in the eastern group (F _ST = 0.049, Nm = 4.91). Genetic distance between populations was positively and significantly correlated with geographic distance (r = 0.56, P<0.001). The population history of this species provided no evidence for population expansion or bottlenecks in any of these populations. Our data suggest that the distribution of genetic diversity, genetic differentiation and population structure of S. mosellana have resulted from a historical event, reflecting its adaptation to diverse habitats and forming two different gene pools. These results may be the outcome of a combination of restricted gene flow due to geographical and environmental factors, population history, random processes of genetic drift and individual dispersal patterns. Given the current risk status of this species in China, this study can offer useful information for forecasting outbreaks and designing effective pest management programs.     

茄子种质遗传多样性及群体结构的SRAP分析

采用SRAP标记法对183份茄子(Solanum melongena)种质资源的遗传关系和群体结构进行分析。结果表明, 33对多态性SRAP引物组合共扩增出215条清晰稳定的多态性条带, 平均每对引物组合产生7条多态性条带。183份茄子种质的遗传相似系数介于0.276-0.813之间, 平均值为0.623, 表明茄子种质资源间遗传背景存在一定的差异。在遗传距离为0.345 6处可将183份茄子种质分为4组。通过群体结构分析可将种质划分为4个群体, 不同群体间的界限十分明显, 且群体间的基因渗透较高。     

Abnormal Stomatal Behaviour and Leaf Anatomy in Capsicum annuum, scabrous diminutive, a Wilty Mutant of Pepper

An attempt is made to explain the tendency to excessive wiltingin scabrous diminutive, a pepper mutant. For this, mutant andnormal plants were compared with respect to leaf anatomy, transpirationof whole plants and detached drying leaves, density and openingof stomata, staining of potassium in epidermal cells and rootpressure. A much greater proportion of intracellular space was found inthe mutant leaf which contains fewer and smaller mesophyll cellsthan the normal plant. The anticlinal walls of the epidermisof the mutant leaf were almost straight whereas those of thenormal were wavy. Transpiration per unit leaf area of wholeplants, percentage of stomata open both day and night, and waterloss from detached drying leaves were all higher in the mutant.Potassium staining in guard cells was similar in both planttypes, slightly less in darkness and marginally higher in light.The subsidiary cells of normal leaves did not stain at all,but those of the mutant leaves stained heavily in both lightand darkness. Root pressure was lower in the mutant. Possible explanations for the tendency of the pepper mutantto wilt are discussed.     

Genetic Diversity and Population Structure of Miscanthus sinensis Germplasm in China

Miscanthus is a perennial rhizomatous C4 grass native to East Asia. Endowed with great biomass yield, high ligno-cellulose composition, efficient use of radiation, nutrient and water, as well as tolerance to stress, Miscanthus has great potential as an excellent bioenergy crop. Despite of the high potential for biomass production of the allotriploid hybrid M. ×giganteus, derived from M. sacchariflorus and M. sinensis, other options need to be explored to improve the narrow genetic base of M. ×giganteus, and also to exploit other Miscanthus species, including M. sinensis (2n = 2x = 38), as bioenergy crops. In the present study, a large number of 459 M. sinensis accessions, collected from the wide geographical distribution regions in China, were genotyped using 23 SSR markers transferable from Brachypodium distachyon. Genetic diversity and population structure were assessed. High genetic diversity and differentiation of the germplasm were observed, with 115 alleles in total, a polymorphic rate of 0.77, Nei’s genetic diversity index (He) of 0.32 and polymorphism information content (PIC) of 0.26. Clustering of germplasm accessions was primarily in agreement with the natural geographic distribution. AMOVA and genetic distance analyses confirmed the genetic differentiation in the M. sinensis germplasm and it was grouped into five clusters or subpopulations. Significant genetic variation among subpopulations indicated obvious genetic differentiation in the collections, but within-subpopulation variation (83%) was substantially greater than the between-subpopulation variation (17%). Considerable phenotypic variation was observed for multiple traits among 300 M. sinensis accessions. Nine SSR markers were found to be associated with heading date and biomass yield. The diverse Chinese M. sinensis germplasm and newly identified SSR markers were proved to be valuable for breeding Miscanthus varieties with desired bioenergy traits.