芝麻EST-SSR标记的开发和初步研究

为了加速分子标记在芝麻研究中的应用,利用网上现有的芝麻EST(expressed sequence tags)数据信息,开展了芝麻EST-SSR功能性标记的开发和利用研究。 在所有的3 328条芝麻EST序列中共确认得到1 785条非冗余EST序列。其中,在含有微卫星重复的148条序列中共检测有155个EST-SSR。非冗余EST序列总长为774.266 kb,平均每4.99 kb含有一个EST-SSR。EST-SSR的分布频率和特征分析表明,以AG/TC为重复基元(motif)的SSR出现最多,占总SSR的37.42%。利用这些序列,设计开发了50对EST-SSR引物,并分别选用36个芝麻、2个棉花、2个大豆和2个油葵进行多态性和通用性研究。其中44对引物在供试芝麻材料中扩增出条带,共产生108个位点,平均每对引物产生2.45个位点,多态信息含量(polymorphism information content, PIC)平均值为0.390。根据遗传相似性系数进行聚类,有26个芝麻材料聚类在两个大的亚类(III和IV)中,聚类结果表明芝麻的基因型与地理来源之间没有必然的联系。此外,分别有2对、3对和4对引物可以在棉花、大豆和油葵中进行通用性扩增。本研究证实这种全新开发的芝麻EST-SSR标记在芝麻遗传多样性分析、遗传图谱构建以及比较基因组等研究方面有广阔的利用前景。     

应用SRAP标记分析黑芝麻核心种质遗传多样性

利用SRAP分子标记技术对中国芝麻资源核心收集品中的黑芝麻种质进行遗传多样性分析。结果表明,13对引物组合对100份黑芝麻核心种质共扩增出稳定清晰的条带182条,其中多态性条带126条,占69.2%,每对引物组合的条带数和多态性带数分别为14.0个和9.7个;供试材料间成对遗传相似系数介于0.469~0.986,平均为0.726,通过UPGMA法,在遗传相似系数为0.68处可将供试材料聚为5个类群,表明黑芝麻核心种质具有较丰富的遗传多样性,聚类结果与地理分布没有明显的关系;遗传多样性指数是南方黑芝麻核心种质(0.3557)＞中部种质(0.3415)＞北方种质(0.2986)。本研究结果较全面反映了中国保存的黑芝麻种质资源遗传多样性特点,为我国黑芝麻资源进一步考察收集和引进,以及优异黑芝麻基因资源挖掘和育种利用提供了理论依据。     

利用荧光SSR分析中国糜子遗传多样性

分析糜子种质资源的遗传多样性,有助于了解糜子起源与进化,可为糜子优异种质发掘及资源高效利用提供理论基础。本研究利用15个糜子特异性荧光SSR标记检测来源于中国11个省(区)的132份糜子种质资源,检测到107个等位变异,每个位点等位变异数为2~14个,平均7个;基因多样性指数为0.0936~0.8676,平均0.5298;多态性信息含量为0.0893~0.8538,平均0.4864。采用遗传距离的聚类将试验材料分为4类,类群I来自东北春糜子区,类群II来自黄土高原春、夏糜子区,类群III来自于北方春糜子区,类群IV来自北方春糜子区和黄土高原春、夏糜子区。分析模型的遗传结构表明,中国糜子资源来自4个(东北地区、黄土高原、北方地区和西北地区)基因库,与基于遗传距离的聚类结果基本一致,均与材料的地理起源相关。糜子遗传变异丰富,主要存在于糜子材料间。该结果从分子水平上准确揭示了中国糜子的遗传多样性。     

山西芝麻种质资源遗传多样性分析

为了解山西芝麻种质资源遗传多样性,本研究对189份山西芝麻种质资源的10个质量性状和8个数量性状进行遗传多样性分析和聚类分析。结果表明：189份山西芝麻种质资源的表型性状存在较大的遗传差异,质量性状以主茎茸毛量的遗传多样性指数最高,为1.15,以蒴果棱数的变异系数最高,为63.88%;数量性状以节间长度的遗传多样性指数最高,为2.09,以单株产量的变异系数最高,为47.66%;通过聚类分析,将189份山西芝麻种质资源分为4个类群,类群Ⅰ可作为选育八棱、高秆品种的亲本材料,类群Ⅱ为矮秆、短节间特异材料,类群Ⅲ为高产选育目标材料,综合性状较好,可直接作为优异亲本加以利用,类群Ⅳ包含一批单花、高产特异材料。     

基于表型性状构建中国花生地方品种骨干种质

中国花生地方品种遗传多样性丰富,是花生新品种选育的重要亲本来源。本研究以种质库保存的2741份地方种质为材料,基于种植区划和植物学类型分组,平方根法确定取样量,组内按13个表型数据进行UPGMA聚类分析,类内随机取样,构建骨干种质。利用t检验、F测验、卡方测验、极差、表型保留比例、表型相关性等对骨干种质代表性进行检验和评价;并利用主成分分析和直方图对骨干种质进行确认。结果表明,构建了包含259份种质的中国花生地方品种骨干种质,占全部种质的9.4%,包括多粒型14份、珍珠豆型85份、龙生型42份、普通型103份、中间型15份。在P <0.05概率条件下,骨干种质13个性状的均值、方差、变异系数、香农指数与全部种质无显著差异,且保留了全部种质的分布范围、表型保留比例和表型相关性;二者的植物学类型组成和生态分布是一致的,具有相似的遗传结构和分布频率。建立的骨干种质很好地代表了全部种质的遗传变异和群体结构,可为花生种质创新和优异等位基因发掘奠定良好的基础。     

广西野生桃金娘亲缘关系的SRAP分析

为弄清广西桃金娘资源的亲缘关系并发掘其优异种性,进行驯化或为将来选育种提供优异亲本材料。本研究采用SRAP技术对8份野生桃金娘种质进行亲缘关系分析,从99对SRAP引物中筛选出18对多态性好、分辨率高的引物。结果显示,18对引物共获得142条带,其中多态性位点107个,多态条带比率为75.35%,表明不同桃金娘种质基因型间存在着较丰富的遗传多样性;8份桃金娘种质的相似系数在0.6800~0.7950之间。在相似系数0.7203处可将8份种质分为3大类群:类群1包括岑溪、昭平、容县;类群2包括北海、龙州小连城、桂林;类群3包括龙州大青山和龙州彬桥。试验材料中亲缘关系最近的是龙州大青山与龙州彬桥,亲缘关系最远的是桂林与岑溪。研究表明,SRAP分子标记可有效地应用于桃金娘种质亲缘关系研究,结果可为桃金娘种质的资源保存鉴定、亲本选配和遗传改良提供理论依据。     

芝麻种质资源SSR标记遗传多样性与群体结构

利用42对具明显多态性的SSR引物, 分析国内外545份芝麻品种的遗传多样性和群体结构。结果检测到106个等位变异位点, 引物多态位点范围为3~9个, 平均为3.8个/引物, Y1994引物的等位位点最多, 为9个。引物Shannon信息指数(I)范围为1.4834~0.1233, 平均值为0.6450; 多态信息指数(PIC)范围为0.7481~0.0516, 平均值为0.4092, 平均杂合度(He)为0.1162。UPGMA聚类、二元主成分及群体结构分析结果基本一致; 供试545份芝麻资源可被分为3个UPGMA组群, 在群体结构上分为3个亚群; 芝麻资源整体遗传分化较小, 亲缘关系较近。中国7个生态群种质相似系数范围为0.9811~0.5462, 东北西北等区域资源与黄淮、江汉、华中华南等区的亲缘关系较远; 国外7个生态群相似系数为0.9726~0.7442, 非洲区与日本区种质亲缘关系较近, 与中国资源亲缘关系较远。中国种质资源遗传基础较为狭窄, 遗传多样性与地理分布不完全相关, 而国外资源遗传多样性丰富。在今后芝麻育种工作中, 应加强国外资源的引进与利用, 并注重国内不同类群资源利用, 拓宽我国芝麻品种遗传基础。     

一个芝麻应用核心种质的DNA分子身份证构建

构建并研究应用核心种质是深入挖掘芝麻优异基因和提高育种效率的有效途径。经过对核心种质农艺、形态等性状4年4点的观察统计, 构建了包括大粒、高木酚素、高油等23种应用型在内的131份芝麻应用核心种质。为了准确鉴别这批应用核心种质并对芝麻DNA分子身份证的构建方法进行探索, 本研究利用SSR变性聚丙烯酰胺凝胶电泳技术, 从基于芝麻全基因组开发的32对SSR引物中, 筛选出7对核心引物, 进而采用SSR荧光标记毛细管电泳技术, 共检测出53个多态性位点, 最多一个引物检测到12个多态性位点。将毛细管电泳得到的分子量数据以数字+英文字母方式编码, 用ID Analysis 4.0软件根据最少引物区分最多种质的原则选核心引物中的6对(ZMM1494、ZMM1648、ZMM3037、ZMM2818、ZMM1851、ZMM1935)组合, 构建出如“4A32645(AC017)”这种简单、易使用的字符串DNA分子身份证, 并确定了不同应用型的组内引物组合。还对131份应用核心种质构建了条形码和二维码DNA分子身份证, 可迅速被电子设备识别, 拓宽了DNA分子身份证的使用范围, 并为以后芝麻种质标准化和品种DNA分子身份证库的构建奠定了重要的技术基础。     

Study of genetic diversity in Indian and exotic sesame (Sesamum indicum L.) germplasm using random amplified polymorphic DNA (RAPD) markers

Fifty-eight accessions of sesame (Sesamum indicum L.), an important oil seed crop of the tropics and subtropics were analysed using random amplified polymorphic DNA (RAPD) technique. The material analysed comprised 36 collections from 18 different states of India and four adjoining countries of the Indian subcontinent, and 22 exotic accessions from 21 sesame growing countries around the world. The results from PCR amplifications with the selected 24 random 10-mer primers were statistically analysed. The value of Jaccard’s similarity coefficients ranged from 0.19 to 0.89. The results indicated the presence of high level of genetic diversity. However, the extent of genetic diversity was greater in the collections from Indian subcontinent as compared to the exotics. Among the Indian accessions, the collections from Rajasthan and North-eastern states were highly diverse. The phenetic analysis grouped 48 out of 58 accessions in six clusters and the remaining highly diverse accessions were placed outside these close-knit clusters. The Bootstrap estimates obtained by Wagner parsimony analysis were significant for seven out of 49 nodes in the majority-rule consensus tree (<95% occurrence). The results of both the analyses were, however, broadly comparable when the constitution of the individual clusters were considered. The principal components analysis indicated that the first two components accounted for only 21% of the total variations and in order to explain <75% of variations 18 components were required. The high level of genetic diversity prevalent among the Indian collections is probably indicative of the nativity of this crop species. Similarly, the relatively lower level of polymorphism in exotic germplasm could be ascribed to the comparatively recent introductions of limited germplasm of this crop into some of the non-traditional sesame growing countries. This revised version was published online in August 2006 with corrections to the Cover Date.     

Association mapping of leaf traits in spinach (Spinacia oleracea L.)

Spinach (Spinacia oleracea L.) is an important leafy vegetable crop grown worldwide. Leaf traits, surface texture (smooth, savoy or semi‐savoy), petiole colour (different shades of green vs. purple) and edge shape (serrate vs. entire), are important commercial traits of spinach. Association mapping for the three traits was conducted on 323 USDA spinach germplasm accessions, originally collected from 33 countries and representing the entire USDA spinach germplasm collection. The majority of accessions were from Europe (36.3%), Asia (25.3%) and North America (15.8%). The majority of the spinach accessions (82.0%) were smooth (unwrinkled types), whereas the savoy and semi‐savoy types (wrinkled types) accounted for 18.0%. The collection contained 74.9% green petiole types, while the purple petioles consisted of 25.1%. The collection consisted of 27.2% serrated leaf types and 72.8% entire leaf edge types. Genotyping‐by‐sequencing (GBS) was used for single nucleotide polymorphism (SNP) discovery, and SNPs were used as genotypic data to conduct genetic diversity and association mapping of the three leaf traits. Five genetic subpopulations and principal components (PCs) were postulated by structure 2 and JMP Genomics 7 for this association panel. Five, seven and 14 SNPs were identified to be associated with surface texture, edge shape and petiole colour, respectively. This study provides us an approach to identify SNP markers through association analysis in spinach and thus leads to select these three leaf traits through marker‐assisted selection in spinach breeding programme.     

64份苦荞种质资源农艺性状遗传多样性分析与综合评价

采用Shannon-Wienerˊs多样性指数、主成分分析、综合得分F值及聚类分析等方法对干旱地区64份苦荞种质资源的主要农艺性状进行了遗传多样性分析和综合评价。结果表明,单株粒重的遗传多样性指数最高,为13.630,主茎粗的变异系数最高,为30.6%;主成分分析将苦荞种质的11个农艺性状降维为累计贡献率达87.580%的6个主成分;综合得分F值与生育期、株高、主茎节数、千粒重和单株粒重等具有极显著的相关性,可作为苦荞种质资源综合评价的主要指标;根据综合得分F值和聚类分析结果筛选出7份具有不同育种目标选择潜力的优良材料。     

Field variation in a tetraploid progeny derived by selfing a Solanum commersonii (+) S. tuberosum somatic hybrid: A multivariate analysis

A phenotypic diversity index (PDI) was calculated using 10 agronomiccharacteristics recorded in 90 accessions of 2-row spring barleys and 29accessions of 6-row spring barleys grown in the Nordic Region. The PDIranged from 0.0308 to 0.6245 in 2-row barley accessions and from0.0314 to 0.7016 in 6-row barley accessions. The average PDIs were0.2178 and 0.2438 in 2-row and 6-row barley germplasm, which confirmsthat some older cultivars were parents of newer cultivars. The lowest PDIwas between accessions with the same name, which suggest that irrespectiveof their market source, they were the same cultivars. The largest PDI rangesin 2-row barley cultivars within the same country or release decade werecorrelated to the number of accessions in the respective cluster, whichsuggests that phenotypic diversity in this germplasm depends on the numberof cultivars included in the cluster. However, this association was not alwaysobserved in 6-row barley cultivars. The most distinct 2-row cultivars wereArla and Akka from Sweden, whereas Sigur and Tampa from Iceland werethe most distinct 6-row cultivars as determined by both PDI and averagelinkage cluster analysis. This analysis also confirm that the 2-row barleyaccessions Jenny, Triumph, and Vega, which were obtained from twodistinct market sources, and the 6-row barley accessions under the nameAgneta (but from three market sources) were the same. The analysis ofvariance of the PDI indicates that 6-row germplasm may be clusteredaccording to their geographical origin or decade of release, but this was notobserved in 2-row barley germplasm. This research demonstrates theadvantage of PDI to assess variation among breeding pools.     

核桃壳厚度表型变异及其与重要农艺性状间相关分析

为探讨壳厚度在群体水平上的表型变异,将其应用于核桃育种,以66 个核桃品种为试材,对包括壳厚度在内的9 个性状进行相关回归分析,采用聚类分析及主成分分析的方法分析群体结构效应对壳厚度表型变异的影响。核桃壳厚度在群体水平上变异范围为0.60~1.50,变异系数最大,为0.21;壳厚度与出仁率在P=0.01 水平上显著负相关,相关系数为-0.61,与其他性状不相关;聚类分析和主成分分析显示4 个亚群(pop-population)可以解释该群体(Q,population)的群体结构;前3 个主成分可以解释总表型变异的77%。研究结果可以为薄壳核桃新品种选育提供理论参考。     

Genetic and QTL analysis of pericarp thickness and ear architecture traits of Korean waxy corn germplasm

Pericarp thickness and ear traits are important selection criteria for breeding fresh market waxy corn. This research was conducted to better understand genetic control of these traits in popular South Korean germplasm now grown in Illinois. Pericarp thickness on five kernel regions, and ten inflorescence architecture traits were measured on ears from 264 F_2:3 families from a cross between Korean inbreds BH20 and BH30. All five pericarp thickness traits showed high heritabilities and were highly correlated. Multivariate principal components analysis (PCA) revealed that just one principal component (PC) explained most of the total phenotypic variation. A number of univariate quantitative trait loci (QTL) were detected and most were associated with more than one kernel pericarp region. Four out of seven PC-QTL were located in chromosome positions where three or more pericarp thickness univariate QTL were detected. Conversely, three PC-QTL were found in regions with just a single or two univariate QTL, indicating that these QTL regions may be more important for overall pericarp thickness than suggested by univariate analysis. The PCA, QTL, and PC-QTL results indicate that pericarp thickness on different kernel regions may be controlled by common genes with pleiotropic effects. Additive effects of QTL for thinner pericarp thickness came from both BH20 and BH30. For ear architecture traits, heritability varied from 0.38 to 0.72, and several traits were correlated. The PCA reduced these traits into three independent PCs, and all substantial component traits for these PCs were also significantly correlated. A number of univariate QTL were clustered closely, and some PC-QTL were detected in these regions. Some PC-QTL were found in chromosome regions where univariate QTL were not detected, again suggesting that these regions may have larger overall effects on ear architecture than suggested by univariate analyses. Collectively, these QTL may be useful for marker assisted introgression into germplasm more adapted to the U.S.     

Genetic diversity of a global collection of maize genetic resources in relation to their subspecies assignments,geographic origin,and drought tolerance

The genetic diversity among an international collection of 40 maize accessions has been evaluated using DNA ISSR fingerprinting. Among the 180 ISSR markers scored by 15 primers, 161 markers (89.59%) were polymorphic and 19 were unique in 16 accessions. A cluster tree based on the average distance coefficients and the Dice similarity indices divided the accessions into three major groups, each including clusters of accessions assigned to their subspecies. However, a low level of genetic differentiation among the accessions was demonstrated by the STRUCTURE analysis of ISSR data in agreement with the low gene flow (Nm) value among the accessions. A scatter diagram of the principal component analysis (PCA) based on ISSR data analysis revealed that the accessions were differentiated into three groups comparable to those produced by the cluster analysis, in which some accessions of the same subspecies showed a close similarity to each other. A scatter diagram of the principal coordinate analysis (PCoA) based on the drought tolerance indices (DTIs) showed that nine genetically similar accessions share drought tolerance characteristics; these include four of subsp. indurata, three of subsp. everata, and two of subsp. indentata. An abundance of unique ISSR alleles found in the 16 accessions, including the nine drought-tolerant accessions, represents rich untapped genetic resources and these accessions may be exploited in the future breeding of maize commercial lines.     

柚类种质资源表型多样性分析及综合评价

为了建立合理的柚类分类系统并为柚类育种提供参考,本研究以82份柚类种质资源为试材,采用变异系数、Shannon-Weaver多样性指数、方差、相关性、主成分、聚类、回归分析等对其26个表型性状进行多样性分析、差异分析及综合评价。结果表明:这82个品种的26个性状的变异系数为0.26%。其中翼叶面积和果心面积变异较大,其他性状遗传特性较稳定;单果重、果横径、果形指数、果皮厚、囊瓣数、种子数、果心长和宽、叶片长和宽、叶片面积、花瓣宽、花柄长等性状等级分布均匀,翼叶面积、花瓣数、雄蕊长分级较少且分布不均;来源于中国大陆以外品种的果皮厚、叶柄长、翼叶长,明显优于长江流域和珠江流域来源的材料,但雌蕊长则相反;选育品种的叶片长、宽和面积显著大于遗传材料和地方品种;82个品种可聚为大翼叶大果型、大翼叶小果型,小翼叶大果型,小翼叶小果型4个类群;前7个主成分累计贡献率75.57%,包含了柚类表型性状的大部分信息;26个性状F平均值0.45,其中早暹柚得分最高为0.69,红肉琯溪蜜柚最低为0.24;囊瓣数、种子数等12个性状与F值极显著相关;回归方程筛选出单果重、囊瓣数等19个性状。本研究说明柚类种质资源具有较高的表型多样性,筛选出的19个性状可作为柚类综合评价指标,为柚类育种提供科学依据。     

芝麻耐旱性的鉴定方法及关联分析

为了解芝麻的耐旱性及获得与芝麻耐旱性相关的分子标记,在发芽期,采用不同浓度PEG 6000处理不同来源不同种皮颜色的10份芝麻品种,测定其形态特征和生理特征及各指标的差异显著性。结果表明,模拟芝麻干旱处理的最佳PEG 6000浓度为15%;综合各项指标的主成分分析、最优回归方程分析及相关性分析表明,相对成苗率可以作为芝麻发芽期耐旱性鉴定的关键指标;利用上述方法对216份核心种质资源群体进行耐旱性鉴定,相对成苗率耐旱系数值位于12.15%~93.52%,平均为60.74%,变异系数为25.22,变异丰富且呈正态分布;资源群体的耐旱性指标值与608个多态性标记位点的关联分析,获得与芝麻发芽期耐旱性有显著关联的标记30个(P<0.05),解释率在1.99%~4.96%之间,平均2.84%。试验表明,相对成苗率是最适且最方便的耐旱性鉴定指标,适用于芝麻资源的耐旱性鉴定。