灰楸不同流域种质变异与多样性研究

通过对灰楸4个流域的137份种质资源的1年生嫁接苗10个表型性状的变异与多样性分析,结果表明:10个表型性状在流域间、流域内均达极显著差异。流域间10个表型性状平均变异系数、遗传变异系数分别为15.81%、29.08%;遗传方差分量都约在70%及以上,说明10个表型性状的差异主要为遗传因素,从流域内变异看,叶部指标和皮孔数在泾河流域和汾河流域变异较大,生长指标和比叶重、含水量、在渭河流域和嘉陵江流域变异较大。总的Shannon-Weaver指数为6.995,趋势是嘉陵江流域>泾河流域>汾河流域>渭河流域。基于表型性状的聚类分析把4个流域的种质在遗传距离为3.65处分为3类。第1类包含来自渭河流域的28份种质和嘉陵江流域的46份种质,第2类是汾河流域的24份种质,第3类是来自泾河流域的39份种质,叶长、叶宽、叶柄长、叶面积、生长量5个表型性状变异随海拔的升高具有一定的连续性。     

基于种实性状的无患子天然群体表型多样性研究

无患子(Sapindus mukorossi Gaertn.)是我国长江以南地区传统的重要绿化树种,其果皮富含皂苷,种仁富含油脂,是国家林业局审定的新型木本油料树种之一。为揭示无患子群体间和群体内种实表型性状变异式样,采用单因素方差分析、巢式方差分析、相关分析和主成分分析等方法,对无患子13个天然群体的10个种实表型性状进行比较分析,研究其群体间和群体内种实表型多样性以及表型变异与地理生态因子间的相关性。结果表明:无患子种实表型性状变异系数平均为7.34%,在群体间和群体内均存在丰富的表型变异。表型性状分化系数平均为62.21%,群体间变异(39.93%)大于群体内(27.46%),是无患子种实表型性状变异的主要来源。多数性状在群体间差异显著,不同程度的表现出边缘群体易于分化的特点,但地理变化规律不连续,而在群体内不同性状的差异性亦不一致。种子形态受群体地理生态的影响较果实形态大,西北部群体种子趋于椭圆形,东部、南部则趋于圆球形;地理纬度、年平均气温与多数种实性状间呈显著相关,是无患子种实表型性状变异的主要地理生态影响因子。可见,无患子种实表型性状在群体间、群体内变异都较为丰富,这些变异是由遗传和环境因素共同作用的结果。群体间和群体内多层次的变异为无患子优良种质资源保育和利用提供了物质基础。     

无患子关联分析实生群体的表型性状

为寻找适于进行关联分析的无患子(Sapindus mukorossi Gaertn.)群体,寻找开发与主要经济性状紧密关联的分子标记,在无患子主要分布区选出一个由110棵实生单株组成的满足关联分析的群体。对群体内每单株的25个表型性状利用单因素方差分析、主成分分析和相关性分析等方法进行分析。结果表明:该群体25个表型性状中23个性状变异为显著(P0.05),其中7个表征经济的性状变异达到极显著(P0.01),25个性状的变异程度差异较大,变异系数范围为5.53%~65.67%;主成分分析表明种实性状、树体性状和果枝性状是主要的性状变异;表型变异在群体内分布均匀、无明显层次结构,但性状间存在不同层次的相关性。结果表明,该群体是进行无患子关联分析研究的理想群体,可以以该群体为基础选择不同利用目标的优良单株,可以该种群为基础材料开展无患子分子辅助育种工作。     

贵州省野生皂荚种实表型性状多样性分析

为深入了解贵州省野生皂荚(Gleditsia sinensis)荚果表型性状的遗传多样性及其变异类型,为皂荚的遗传改良、种质鉴定、亲本选择以及品种培育奠定理论基础。该研究以贵州省7个野生皂荚群体70个个体为研究对象,采用方差分析、主成分分析、相关性分析及多性状综合评价等方法对皂荚群体的10个种实表型性状进行系统分析和综合评价。结果显示：(1)所测皂荚的表型性状差异在群体内均达到极显著水平(P＜0.01);在群体间,除每荚粒数、种子宽、种子长宽积以及种子长宽比之外,其余表型性状的差异均达极显著水平(P＜0.01)。(2)7个居群野生皂荚各性状平均变异系数为21.16%,其中凯里市(P4)居群的变异系数最高(24.44%);居群间荚果的变异(29.22%)高于种子的变异(11.04%),且变异主要来自于群体内。(3)相关分析显示,皂荚种实各性状之间存在不同程度的关联性;主成分分析显示,前4个主成分(皂荚种子大小、单个荚果出籽数量、种子形态指数因子、与荚果长和种子厚相关的因子)的累积贡献率达69.783%,可基本反映皂荚表型性状的大部分信息;以10个种实性状对皂荚野生群体进行综合评价发现,来自于惠水县(P7)群体的皂荚种实性状综合评价最高。研究表明,贵州省野生皂荚在群体间及群体内具有丰富的表型变异,且群体内的变异大于群体间的变异,变异主要来自于群体内。     

秦岭秀雅杜鹃7个野生群体形态性状的变异分析

对秦岭山区的7个秀雅杜鹃野生群体的表型变异情况进行分析。结果表明:秀雅杜鹃表型性状在种群间和种群内都存在一定程度的变异,但变异不大。各性状总的平均变异系数在0(雄蕊数目)~0.28(花梗长)之间,种群间总的平均变异系数在0.08(周至)~0.14(南郑),花色性状种群间变异大,种群内变异较小。秀雅杜鹃表型性状与地理生态因子的相关分析表明,各个性状的变异和地理生态因子并无显著的相关性,说明表型受环境影响的程度相对较小。利用群体间欧氏距离进行的UPGMA聚类分析结果表明,秀雅杜鹃野生群体可以划分为3类。     

红松种子园种群表型多样性研究

为揭示红松（Pinus koraiensis Sieb.et Zucc.）不同种群的表型分化程度和变异规律,以吉林省露水河红松种子园6个种群红松为研究对象,采用巢式方差分析、多重比较、变异系数和聚类分析等方法对红松的叶片、球果和种子共15个表型性状进行了系统分析。结果表明：（1）红松15个表型性状在种群间和种群内均存在着极显著的差异,红松种群遗变异比较丰富,在松属植物中属于中等水平,其中纬度最低的露水河种群在其中10个表型性状均值上表现出最高值;（2）红松种群间的表型分化系数（Vst）均值为12.39%,种群内的变异（87.61%）大于种群间的变异（12.39%）,种群内的变异是主要变异来源;（3）各表型性状平均变异系数为13.28%,变幅为6.16%-31.48%,叶片、球果、种子的平均变异系数依次为：球果17.86% > 针叶11.19% > 种子9.87%,种子性状最小,成为最稳定的表型性状,带岭和丰林种群表型性状遗传多样性要高于其他种群;（4）利用欧氏平均距离对红松种群进行UPGMA聚类分析,红松种群的表型性状按照地理距离而聚类,可将红松种子园6个种群分为4类,其表型性状跟地形（东北山脉）有一定的契合。红松种群具有中等水平的表型遗传多样性,种群间和种群内均存在丰富的表型变异,研究结果为顺利开展红松种质资源收集、保存,以及良种选育等工作提供依据。     

灯盏花种质资源群体表型多样性研究

以采集自云南和贵州的21份灯盏花种质资源为材料,观测了它们的群体表型性状特征,并分析了这些表型性状的遗传多样性.结果表明:灯盏花种质资源的表型质量性状在居群内外均有丰富变异,不同质量性状的频率不同,并以多叶型的植株、绿色的茎、疏的茎毛、倒披针型的基生叶、全缘叶、锐尖的叶尖、花色淡紫和黄色的管状花冠口等为代表性表型性状.居群内各数量性状间以单株基生叶数和单株分枝数变异系数较高(均超过50%),而花序直径变异系数最低(18.14%);居群间各表型性状以株高和单序管状花数变异系数较高(52.98%和41.98%),而单株基生叶数和基生叶长变异系数较低(<20%).地理类群间表型分化系数为26.58%,地理类群内表型分化系数为73.42%.灯盏花性状表型多样性指数以株高最高(2.243),以单株分枝数和单株基生叶数较低(1.723和1.874),总体平均表型多样性指数为2.028;不同地理类群的表型多样性指数为1.589~1.890,并以楚雄地区最高,曲靖地区最低.研究发现,灯盏花种质资源具有丰富的质量和数量性状变异,多数性状的地理类群内变异大于地理类群间,且表型多样性指数相对较高,对其地理类群内变异的保护和利用对灯盏花育种具有重要的意义.     

灰木莲种源幼苗叶片性状表型多样性分析

以越南收集的12个灰木莲（Manglietia conifera Dandy）种源为材料,对叶片形态性状（叶长、叶宽、叶面积、叶周长、长宽比、叶柄）以及微形态特征（气孔器密度、气孔器长、气孔器宽、气孔器面积、长宽比）进行测定,采用方差分析、变异系数、相关分析和主成分分析等方法进行分析。结果表明：灰木莲不同种源间的叶表型性状存在显著差异;种源中,LC2的叶形态性状的平均变异系数最大（22.09%）,TQ2的变异系数最小（12.76%）;叶表型性状中,叶面积的变异系数最大（28.60%）,气孔器宽的变异系数最小（5.19%）;相关性分析结果表明叶表型性状间存在显著或极显著的相关关系,而地理因素中经度与叶周长显著相关,经纬度与叶长宽比呈显著相关,海拔与叶表型性状间的相关性不显著（P<0.05）;主成分分析表明前3个主成分的累计贡献率达到了89.29%,基本代表原始性状的全部信息。灰木莲12个种源经聚类分析在欧式距离5阈值处可分为4类。灰木莲种源间的叶表型性状存在着丰富的变异,纬度对灰木莲叶形态特征有明显影响,灰木莲种源间和性状间的变异程度存在着差异,本研究为灰木莲遗传改良提供理论依据。     

皂荚南方天然群体种实表型多样性

以系统揭示表型变异程度和变异规律为目的, 对皂荚(Gleditsia sinensis)南方分布区的10个天然群体的11个种实性状进行了比较分析。采用方差分析、多重比较、相关分析等多种分析方法, 对群体间和群体内的表型多样性以及与地理、环境因子的相关性进行了讨论。方差分析结果表明; 皂荚果实、种子等性状在群体间和群体内存在丰富的变异, 11个性状在群体间、群体内均达显著差异; 荚果性状在群体间和群体内的变异均大于种子性状, 11个性状的平均表型分化系数为20.42%, 群体内的变异(32.28%)大于群体间的变异(7.19%), 群体内的变异是皂荚的主要变异来源; 皂荚各性状平均变异系数为11.20%, 变异幅度为4.55%-18.38%。群体间荚果的变异(14.75%)高于群体间种子变异(6.95%), 表明种子变异稳定性高。荚果和种子各性状之间多呈极显著或显著正相关, 表现为荚果越大, 则种子越大, 种子的千粒重也越大; 荚果表现为同地理经度的南北变异, 种子则表现为同地理纬度的东西变异。研究结果为进一步开展皂荚遗传育种、保护生物学研究和皂荚种质资源利用奠定了基础。     

枫香树种群种子与果实表型性状变异分析

为了明确我国枫香树(Liquidambar formosana)种子与果实表型变异程度和变异规律, 采用方差分析、相关分析和回归分析等方法对36个天然种群枫香树的10个种子与果实的表型性状在种群间和种群内表型变异和地理变异模式进行探讨。研究结果表明, 枫香树平均表型分化系数为57.55%, 种群间的变异是其表型变异的主要来源; 种子和果实表型性状的变异丰富, 变异幅度为10.05%-24.31%, 平均变异系数为15.83%; 不同种群间变异差别明显, 安福种群平均变异系数最大(16.73%), 建阳种群平均变异系数最小(11.48%)。枫香树多数种子与果实表型性状在地理变化上是随机的, 地理相近种群在表型上没有显著相关性。地理气候因子中1月平均气温、海拔和纬度对种子与果实性状起主要的影响。种子与果实性状与海拔相关分析表明, 枫香树种子长宽比随海拔的升高而减小, 种子长宽比可以推测种群所在的海拔高度。探讨枫香树种群表型多样性, 可为野生优异种质的收集、多目标品种选育等工作提供依据。     

Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles

ABSTRACT: BACKGROUND: Many beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions. RESULTS: Each marker was mapped with high confidence (e < 1 x 10-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 plus or minus 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles. CONCLUSION: Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within crop species such as S. lycopersicum will help inform conservation and utilization of crop germplasm diversity, for example, facilitating the purging of undesirable linkage drag or the exploitation of novel, favorable alleles.     

Exploring the natural variation for seedling traits and their link with seed dimensions in tomato

The success of germination, growth and final yield of every crop depends to a large extent on the quality of the seeds used to grow the crop. Seed quality is defined as the viability and vigor attribute of a seed that enables the emergence and establishment of normal seedlings under a wide range of environments. We attempt to dissect the mechanisms involved in the acquisition of seed quality, through a combined approach of physiology and genetics. To achieve this goal we explored the genetic variation found in a RIL population of Solanum lycopersicum (cv. Moneymaker) x Solanum pimpinellifolium through extensive phenotyping of seed and seedling traits under both normal and nutrient stress conditions and root system architecture (RSA) traits under optimal conditions. We have identified 62 major QTLs on 21 different positions for seed, seedling and RSA traits in this population. We identified QTLs that were common across both conditions, as well as specific to stress conditions. Most of the QTLs identified for seedling traits co-located with seed size and seed weight QTLs and the positive alleles were mostly contributed by the S. lycopersicum parent. Co-location of QTLs for different traits might suggest that the same locus has pleiotropic effects on multiple traits due to a common mechanistic basis. We show that seed weight has a strong effect on seedling vigor and these results are of great importance for the isolation of the corresponding genes and elucidation of the underlying mechanisms.     

Development of a set of PCR-based anchor markers encompassing the tomato genome and evaluation of their usefulness for genetics and breeding experiments

Tomato and potato expressed sequence tag (EST) sequences contained in the solanaceae genomics network (SGN) database were screened for simple sequence repeat (SSR) motifs. A total of 609 SSRs were identified and assayed on Solanum lycopersicum LA925 (formerly Lycopersicon esculentum) and S. pennellii LA716 (formerly L. pennellii). The SSRs that did not amplify, gave multiple band products, or did not exhibit a polymorphism that could be readily detected on standard agarose gels in either of these species were eliminated. A set of 76 SSRs meeting these criteria was then placed on the S. lycopersicum (LA925) x S. pennellii (LA716) high-density map. A set of 76 selected cleaved amplified polymorphism (CAP) markers was also developed and mapped onto the same population. These 152 PCR-based anchor markers are uniformly distributed and encompass 95% of the genome with an average spacing of 10.0 cM. These PCR-based markers were further used to characterize S. pennellii introgression lines (Eshed and Zamir, Genetics 141:1147-1162, 1995) and should prove helpful in utilizing these stocks for high-resolution mapping experiments. The majority of these anchor markers also exhibit polymorphism between S. lycopersicum and two wild species commonly used as parents for mapping experiments, S. pimpinellifolium (formerly L. pimpinellifolium) and S. habrochaites (formerly L. hirsutum), indicating that they will be useful for mapping in other interspecific populations. Sixty of the mapped SSRs plus another 49 microsatellites were tested for polymorphism in seven tomato cultivars, four S. lycopersicum var. cerasiforme accessions and eight accessions of five different wild tomato species. Polymorphism information content values were highest among the wild accessions, with as many as 13 alleles detected per locus over all accessions. Most of the SSRs (90%) had accession-specific alleles, with the most unique alleles and heterozygotes usually found in accessions of self-incompatible species. The markers should be a useful resource for qualitative and quantitative trait mapping, marker-assisted selection, germplasm identification, and genetic diversity studies in tomato. The genetic map and marker information can be found on SGN (http://www.sgn.cornell.edu).     

Metabolic profiling of leaves and fruit of wild species tomato: a survey of the Solanum lycopersicum complex

The domestication of the tomato Solanum lycopersicum and associated selective pressures eventually led to the large-fruited varieties cultivated today. S. lycopersicum varieties are generally red-fruited, but display considerable variance in fruit colour intensity, shape, and quality. The increase in productivity on cultivation is, however, somewhat offset by the narrowing of the crops genetic base which leads to increased susceptibility to biotic and abiotic stresses. Since S. lycopersicum can easily be crossed with its wild species relatives, this exotic germplasm can provide a valuable source for the improvement of agriculturally important traits. A GC-MS based survey is presented here of the relative metabolic levels of leaves and fruit of S. lycopersicum and five wild species of tomato that can be crossed with it (S. pimpinellifolium, S. neorickii, S. chmielewskii, S. habrochaites, and S. pennellii). Changes in metabolite contents were identified in the wild species that are potentially important with respect to stress responses, as well as in metabolites of nutritional importance. The significance of these changes is discussed with respect to the use of the various wild species for metabolic engineering within wide breeding strategies.     

Morphological variation in tomato: a comprehensive study of quantitative trait loci controlling fruit shape and development

Variation in fruit morphology is a prevalent characteristic among cultivated tomato. The genetic and developmental mechanisms underlying similarities and differences in shape between the fruit of two elongated tomato varieties were investigated. Fruit from two F2 populations constructed from either Solanum lycopersicum cv. Howard German or cv. Banana Legs crossed with S. pimpinellifolium accession LA1589, and one BC1 population constructed with S. lycopersicum Howard German as the recurrent parent, were analysed for shape by using a new software program Tomato Analyzer. Quantitative trait loci (QTLs) controlling 15 individual shape attributes were mapped by both single and multitrait composite interval mapping in each population. In addition, principal components analysis and canonical discriminant analysis were conducted on these shape attributes to determine the greatest sources of variation among and between the populations. Individual principal components and canonical variates were subjected to QTL analysis to map regions of the genome influencing fruit shape in the cultivars. Common and unique regions, as well as previously known and novel QTLs, underlying fruit morphology in tomato were identified. Four major loci were found to control multiple fruit shape traits, principal components, and canonical variates in the populations. In addition, QTLs associated with the principal components better revealed regions of the genome that varied among populations than did the QTL associated with canonical variates. The QTL identified can be compared across additional populations of tomato and other fruit-bearing crop species.     

Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene

Phylogeographical studies are emerging as a powerful tool for understanding the population structure and evolution of wild relatives of crop species. Because of their value as genetic resources, there is great interest in exploring the distribution of variation in wild relatives of cultivated plants. In this study, we use sequence variation from the nuclear gene, fruit vacuolar invertase (Vac), to investigate the population history of Solanum pimpinellifolium. Solanum pimpinellifolium is a close relative of the cultivated tomato and has repeatedly served as a source of valuable traits for crop improvement. We sequenced the second intron of the Vac gene in 129 individuals, representing 16 populations from the northern half of Peru. Patterns of haplotype sharing among populations indicate that there is isolation by distance. However, there is no congruence between the geographical distribution of haplotypes and their genealogical relationships. Levels of outcrossing decrease towards the southernmost populations, as previously observed in an allozyme study. The geographical pattern of Vac variation supports a centre of origin in northern Peru for S. pimpinellifolium and a gradual colonization along the Pacific coast. This implies that inbreeding populations are derived from outcrossing ones and that variation present at the Vac locus predates the spread of S. pimpinellifolium. The expansion of cities and human agricultural activity in the habitat of S. pimpinellifolium currently pose a threat to the species.     

Metabolomics-assisted refinement of the pathways of steroidal glycoalkaloid biosynthesis in the tomato clade

Steroidal glycoalkaloids (SGAs) are nitrogen-con-taining secondary metabolites of the Solanum species, which are known to have large chemical and bioactive diversity in nature. While recent effort and ...     

Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species

Association mapping has been proposed as an efficient approach to assist in the identification of the molecular basis of agronomical traits in plants. For this purpose, we analyzed the phenotypic and genetic diversity of a large collection of tomato accessions including 44 heirloom and vintage cultivars (Solanum lycopersicum), 127 S. lycopersicum var. cerasiforme (cherry tomato) and 17 Solanum pimpinellifolium accessions. The accessions were genotyped using a SNPlex? assay of 192 SNPs, among which 121 were informative for subsequent analysis. Linkage disequilibrium (LD) of pairwise loci and population structure were analyzed, and the association analysis between SNP genotypes and ten fruit quality traits was performed using a mixed linear model. High level of LD was found in the collection at the whole genome level. It was lower when considering only the 127 S. lycopersicum var. cerasiforme accessions. Genetic structure analysis showed that the population was structured into two main groups, corresponding to cultivated and wild types and many intermediates. The number of associations detected per trait varied, according to the way the structure was taken into account, with 0–41 associations detected per trait in the whole collection and a maximum of four associations in the S. lycopersicum var. cerasiforme accessions. A total of 40 associations (30 %) were co-localized with previously identified quantitative trait loci. This study thus showed the potential and limits of using association mapping in tomato populations.     

Variation in Response of Wild Lycopersicon and Solanum spp. against Tomato Powdery Mildew (Oidium lycopersici)

A set of 154 accessions of nine wild Lycopersicon spp. and five accessions of three closely related Solanum spp. were tested for resistance to tomato powdery mildew ( Oidium lycopersici ). Screening revealed valuable sources of resistance, mainly among L. hirsutum, L. pennellii, L. cheesmanii, L. chilense, L. peruvianum and L. parviflorum. L. esculentum (all ssp.) and L. pimpinellifolium expressed high susceptibility to O. lycopersici inoculation. Results of variance and cluster analysis of responses to O. lycopersici coincide with recent taxonomic classification and genetic relationships within genus Lycopersicon .