普通玉米和特用玉米的SSR标记聚类

利用SSR标记研究了64份玉米自交系（包括普通玉米和特用玉米自交系）的亲缘关系。用30对扩增带型稳定的SSR引物,从供试材料中检测出116个等位基因变异,每对引物检测出等位基因2~10个,平均3.87个。SSR引物的PIC介于0.306~0.893之间,平均多态性信息量为0.717。按UPGMA方法对供试自交系进行聚类,以遗传距离0.586为基准,可将材料划分为11类。64份自交系的SSR标记聚类分析表明,普通玉米与特用玉米糯玉米、甜玉米、爆裂玉米等并不能严格地各自划为一类,只有亲缘关系较近的特用玉米自交系聚在一起,有些特用玉米与普通玉米聚在一起,部分特用玉米具有丰富的普通玉米种质资源遗传背景。特用玉米自交系间的遗传距离与普通玉米自交系间的遗传距离差异达到0.01的极显著水平。此外,不同类型特用玉米间、特用玉米与普通玉米间的遗传差异较大,特用玉米在进化和选育过程中积累并保存了丰富的遗传变异。     

Into the vault of the Vavilov wheats: old diversity for new alleles

Intensive selection in wheat (Triticum aestivum L.) breeding programs over the past 100 years has led to a genetic bottleneck in modern bread wheat. Novel allelic variation is needed to break the yield plateau, particularly in the face of climate change and rapidly evolving pests and pathogens. Landraces preserved in seed banks likely harbour valuable sources of untapped genetic diversity because they were cultivated for thousands of years under diverse eco-geographical conditions prior to modern breeding. We performed the first genetic characterisation of bread wheat accessions sourced from the N. I. Vavilov Institute of Plant Genetic Resources (VIR) in St Petersburg, Russia. A panel comprising 295 accessions, including landraces, breeding lines and cultivars was subject to single seed descent (SSD) and genotyped using the genotyping-by-sequencing Diversity Arrays Technology platform (DArT-seq); returning a total of 34,311 polymorphic markers (14,228 mapped and 20,083 unmapped). Cluster analysis identified two distinct groups; one comprising mostly breeding lines and cultivars, and the other comprising landraces. Diversity was benchmarked in comparison to a set of standards, which revealed a high degree of genetic similarity among breeding material from Australia and the International Maize and Wheat Improvement Center (CIMMYT). Further, 11,025 markers (1888 mapped and 9137 unmapped) were polymorphic in the diversity panel only, thus representing allelic diversity potentially not present in Australian or CIMMYT germplasm. Open-access to DArT-seq markers and seed for SSD lines will empower researchers, pre-breeders and breeders to rediscover genetic diversity in the VIR collection and accelerate utilisation of novel alleles to improve wheat.     

玉米自交系48-2和R08辐照后代M_3株系遗传变异的SSR分析

为研究玉米自交系辐射诱变后代的性状遗传变异规律,促进突变体的高效选择和利用,本研究用3种剂量梯度的60Coγ射线对玉米自交系48-2和R08的种子进行辐射诱变处理,用32个多态性SSR分子标记对48-2和R08及其辐射诱变后代M3株系等103份材料进行了遗传变异分析。结果表明：48-2和R08 M3株系位点多态信息量（...     

Cryptic genetic bottlenecks during restoration of an endangered tropical conifer

Forest restoration programmes aim to use material for re-planting that is genetically diverse and not inbred. However, restricted seed sampling, high variance in reproductive output, and the production of inbred seeds that survive in the nursery but not in the wild can lead to forest restoration stock being genetically compromised. The aim of this study was to evaluate whether the reproductive biology of the New Caledonian endemic conifer Araucaria nemorosa makes it susceptible to these genetic problems and to assess whether there is evidence for genetic bottlenecks and elevated inbreeding in nursery stock compared to seedlings and adults from wild source populations. Reproductive output was low with high variance among trees (only 14% of adult trees surveyed produced mature cones, >50% of examined cones had <10 viable seeds). Evidence for an extreme genetic bottleneck was detected in a nursery population established from cones collected from adult trees. A second nursery population established with seed collected from the forest floor showed no evidence of a genetic bottleneck, but was inbred compared to its wild source population. In light of these results, we do not recommend collecting cones directly from A. nemorosa as an efficient means of establishing genetically diverse stock for restoration programmes. Collecting seed from the forest floor is likely to be more effective, but the planting stock may contain a high proportion of inbred individuals. Collecting established wild seedlings already subjected to natural selection is suggested as an alternative method of maximising the diversity captured, whilst minimising sampling effort and proportion of inbred individuals.     

大刍草(Zea mexicana schard)×自交系K169选系的核型和SSR分析

本研究以玉米自交系K169及其与大刍草(Zea mexicana schard)远缘杂交而成的5个选系为研究材料,对它们进行核型和SSR分析,以期从细胞学和分子水平的角度为玉米远缘杂交育种提供理论依据。结果表明,5个远缘选系和轮回亲本K169体细胞染色体数目均为2n=20,但在核型结构上却存在较大差异,其中自交系K169和远缘选系1191在第6染色体的短臂上有随体,1183和1189在第8染色体的短臂上有随体,1193和1195未发现带随体的染色体;选系1183、1193和1195的染色体长度比(最长/最短)与K169之间存在较大差异;选系1183和1195的核型类型与K169不一致。96对SSR引物在5个选系和轮回亲本K169中共检测出27个多态性位点,位点多态信息量(PIC)的平均值为0.724;基因型多样性(H′)的平均值为1.400,它们之间的遗传相似系数平均值为0.5791。综合分析表明,这些选系与其轮回亲本K169之间存在真实的遗传差异,是一批新的玉米种质资源。     

利用SSR对60个玉米自交系进行杂种优势群划分初探

用SSR对60个玉米自交系的DNA进行分子标记和杂种优势群划分研究。利用14对SSR引物在供试材料中检测出57个等位基因变异,每对引物检测等位基因2～7个,平均为4．07个,多态信息量变化范围为0．389～0．832,平均为0．692。自交系间遗传相似系数变幅为0．058～0．756,UPGMA聚类分析表明,供试自交系可分为五个类群。利用这14对具有较高多态性信息量的引物,可以对供试材料进行初步鉴定。     

Genetic diversity of cowpea [<Emphasis Type="Italic">Vigna unguiculata</Emphasis> (L.) Walp.] in four West African and USA breeding programs as determined by AFLP analysis

Cowpea is an important grain legume and hay crop of many tropical and subtropical regions, especially in the dry savanna region of West Africa. The cowpea gene pool may be narrow because of a genetic bottleneck during domestication. Genetic variation within specific breeding programs may be further restricted due to breeding methods, ‘founder effects’ and limited exchange of germplasm between breeding programs. Genetic relationships among 60 advanced breeding lines from six breeding programs in West Africa and USA, and 27 landrace accessions from Africa, Asia, and South America were examined using amplified fragment length polymorphism (AFLP) markers with six near infrared fluorescence labeled EcoRI + 3/1bases/MseI + 3/1bases primer sets. A total of 382 bands were scored among the accessions with 207 polymorphic bands (54.2%). Despite a diverse origin, the 87 cowpea accessions shared a minimum 86% genetic similarity. Principal coordinates analysis showed clustering of breeding lines by program origin, indicating lack of genetic diversity compared to potential diversity. Accessions from Asia and the Americas overlapped and were distinct from West African breeding lines, indicating that germplasm from Asia and the Americas have common origins outside West Africa. US and Asian breeding programs could increase genetic variability in their programs substantially by incorporating germplasm from West Africa, while national programs in West Africa should consider introgression of Asian germplasm and germplasm from other parts of Africa into their programs to ensure long-term gains from selection.     

Analysis of genetic diversity in a sweet potato (Ipomoea batatas L.) germplasm collection from Tanzania as revealed by AFLP

Sweet potato (Ipomoea batatas L.) is the fifth most important crop in the developing countries after rice, wheat, maize and cassava. The amplified fragment length polymorphism (AFLP) method was used to study the genetic diversity and relationships of sweet potato accessions in the germplasm collection of Sokoine University of Agriculture, Morogoro and Sugarcane Research Institute, Kibaha, Tanzania. AFLP analysis of 97 sweet potato accessions using ten primer combinations gave a total of 202 clear polymorphic bands. Each one of the 97 sweet potato accessions could be distinguished based on these primer combinations. Estimates of genetic similarities were obtained by the Dice coefficient, and a final dendrogram was constructed with the un-weight pair-group method using arithmetic average. AFLP-based genetic similarity varied from 0.388 to 0.941, with a mean of 0.709. Cluster analysis using genetic similarity divided the accessions into two main groups suggesting that there are genetic relationships among the accessions. Principal Coordinate analysis confirmed the pattern of the cluster analysis. Analysis of molecular variance revealed greater variation within regions (96.19%) than among regions (3.81%). The results from the AFLP analysis revealed a relatively low genetic diversity among the germplasm accessions and the genetic distances between regions were low. A maximally diverse subset of 13 accessions capturing 97% of the molecular markers diversity was identified. We were able to detect duplicates accessions in the germplasm collection using the highly polymorphic markers obtained by AFLP, which were found to be an efficient tool to characterize the genetic diversity and relationships of sweet potato accessions in the germplasm collection in Tanzania.     

不同水分环境下玉米叶形相关性状与SSR标记的关联分析

玉米的叶形结构与其抗旱性紧密相关,挖掘不同水分环境下调控玉米叶形相关性状的显著关联分子标记位点,可为揭示玉米叶形结构的分子遗传机理、克隆相关调控基因并进行抗旱理想株型育种提供参考。本研究在不同水分环境下分析187份玉米自交系叶长、叶宽、叶夹角、叶向值、叶面积、叶形系数及叶片卷曲度等7个叶形相关性状的变化,采用SSR标记对这些材料进行全基因组扫描并分析其遗传多样性,采用一般线性模型(GLM)寻找不同水分环境下与玉米7个叶形相关性状关联的分子标记。结果表明:1)干旱环境下187份玉米自交系的叶长、叶宽、叶夹角、叶面积均显著降低,而叶向值、叶形系数及叶片卷曲度均明显升高,且干旱环境下这7个叶形相关性状的变异比率为30.53%～198.31%。2)145对SSR标记共检测出652个等位变异,变异范围在2～13个;多态性信息量(PIC)变异范围为0.201～0.966,平均0.478。采用UPGMA聚类及群体遗传结构分析均将供试材料分为旅大红骨(LRC)、唐四平头(TSPT)、兰卡斯特(Lan)、P及瑞德(Reid)等5大类群。3)采用GLM模型,在不同水分环境下共检测到15个SSR标记与玉米的7个叶形相关性状在P0.01水平下关联,各标记对表型的解释率为2.25%～27.30%,72.97%的标记可在干旱环境下被检测到;其中umc1124、umc2363、umc2214、umc1742、phi331888、umc1378、bnlg1863、umc2134和umc1345标记同时与不同水分环境下的多个叶形相关性状连锁,表现出明显的"一因多效"现象。这些研究结果将为玉米叶形结构的遗传改良及抗旱理想株型分子标记辅助选择育种提供参考。     

Genetic differentiation among selected tepary bean collections revealed by morphological traits and simple sequence repeat markers

Understanding the genetic relationship of crop ideotypes is essential for genetic analysis and breeding. The objective of this study was to determine genetic differentiation present among 20 selected tepary bean (Phaseolus acutifolius A. Gray) genotypes using morphological traits and simple sequence repeat (SSR) markers in order to identify genetically unique parental lines to develop breeding populations. Phenotypic diversity was estimated using Shannon-Weaver diversity index (H’), principal component analysis (PCA) and cluster analysis (CA). Genotypic diversity was estimated using Jaccard's genetic distances and CA. Shannon-Weaver diversity index values for the studied morphological traits ranged from 0.89 to 0.99, with a mean of 0.95 revealing high phenotypic differences among test genotypes. PCA identified four useful principal components (PC's) which contributed to 73% of the total phenotypic variation of collections. PC1 accounted for 28% of the total variation correlated to dry shoot mass and number of pods per plant. PC2 correlated with number of seeds per pod, grain yield and harvest index and contributed to 21% of total variation. The mean observed (H_o) and expected (H_e) heterozygosity values were 0.45 and 0.51, respectively revealing moderate genetic differentiation among genotypes. The mean polymorphic information content was 0.52, suggesting efficient discriminatory power of the SSR loci useful in future tepary bean genetic diversity analysis. The current study revealed moderate genetic differentiation among the studied tepary bean genotypes. Morphological traits and SSR markers well-correlated in allocating the tepary bean genotypes. The following genotypes were genetically distinct: G40201, G40237, G40068, G40033 and G40063 which are recommended for further crosses, selection and population development.     

Low genetic diversity in wild emmer (T. turgidum L. subsp. dicoccoides (Körn. ex Asch. et Graebn.) Thell.) from South-eastern Turkey revealed by Restriction Fragment Length Polymorphism

The present work was carried out to study genetic diversity among 17 populations of wild emmer wheat sampled from South-eastern Turkey, considered to be an important region for domestication of wheat. Eleven RFLP clones and 4 restriction enzymes combinations were used to probe the genomic DNA. A total of 151 polymorphic loci were obtained from the enzyme-probe combinations. The Genetic Distance (GD) values were from 0.019 (Gaziantep-3 and Sanliurfa-4) to 0.200 (Gaziantep-1 and K. Maras). Cluster analysis results showed that populations formed 2 clades within the dendrogram. Population Gaziantep-1 was unique and genetically most diverse from the remaining 16 populations. The results of average genetic distance (GD) among populations suggested that narrow genetic variability exist among 17 populations in the present study.     

Genetic diversity in oil and vegetable mustard (<Emphasis Type="Italic">Brassica</Emphasis><Emphasis Type="Italic">juncea</Emphasis>) landraces revealed by SRAP markers

Mustard (Brassica juncea) is an important crop in both ancient and modern world. It has a broad resource of genetic diversity that is used primarily as oilseed but as vegetables, condiment and medicines also. Its superior tolerance to adverse environments, e.g., drought, high temperature and low fertility suggests its better adaptability in future possible harsh environments. Chinese vegetable mustard displays a wide spectrum of morphotypes. A collection of 95 accessions of B. juncea representing oil and vegetable mustards from China, France, India, Pakistan, and Japan were assessed to determine diversity at the molecular level using sequence-related amplified polymorphism (SRAP). Eight SRAP primer combinations identified a total of 326 scorable fragments of which 161 were polymorphic (49.39%). The percentage of polymorphism for each primer combination varied from 21.88 to 66.67%. Both Shannon-Weaver and Simpson genetic diversity index indicated that the level of genetic diversity within vegetable mustard is much higher than within oil mustard, and also winter oil mustards are genetically more diverse than spring oil mustards. Based on the Cluster and Principal Coordinates analysis, which were conducted on the similarity matrix of SRAP marker data, vegetable, spring oil and winter oil mustard were clearly divided into three distinct groups and among these three groups, spring and winter oil mustard are geneticlly closer than vegetable mustard. This suggests that bilateral gene exchange between oil and vegetable gene pools in the breeding program will effectively elevate the genetic potential in developing higher yields, more disease resistance, better quality and better adapted lines.     

Genetic diversity of Pakistan wheat germplasm as revealed by RAPD markers

Wheat breeding in Pakistan started in 1930s before partition in the United India and so far has released more than 68 cultivars, but no systematic analyses of the genetic diversity of Pakistan wheat have been made. Twenty Pakistan wheat cultivars released from 1933 to 2002 were examined for genetic diversity and relationships using random amplified polymorphic DNA (RAPD) markers. Forty-two RAPD primers were applied and 184 polymorphic bands were generated for each cultivar. Most of the cultivars were genetically interrelated, although six of them displayed some genetic distinctness. The RAPD variation observed among these cultivars was low. Only 40.7% of the total scorable bands were polymorphic, and 26.1% of the polymorphic bands were observed most frequently (f = 0.95) among the 20 cultivars. The proportions of polymorphic bands for each cultivar ranged from 0.67 in ‘Yecora’ to 0.84 in ‘C-250’ with an average of 0.76. About 1.4% of the RAPD variation might have been fixed over the 69 years of wheat breeding, but such fixation was not statistically significant. These results are significant for future improvement and conservation of Pakistan wheat.     

Comparison of nitrogen accumulation and nitrogen utilization efficiency between elite inbred lines and the landraces of maize

Abstract

Inadequate supply of nitrogen (N) fertilizers results in lower N use efficiency (NUE) and higher N losses which cause environmental deterioration, such as nitrate pollution of groundwater and emission of nitrous greenhouse gases. One way to increase NUE is to use N-efficient cultivars, which grow better under reduced N supplies. Both elite inbred lines and landraces are the basis for hybrid breeding in maize. While inbred lines are mostly selected from high N input conditions, landraces are historically distributed in poor soils with low N availability. Therefore, some potential NUE-related traits conserved in the landraces may have been lost during modern breeding processes. In the present study, the N accumulation and utilization efficiency of 15 elite inbred lines and four landraces of maize were compared at low (LN) and high N (HN) input conditions. In general, the grain yields of the inbred lines and the landraces were similar at both N rates. However, nitrogen accumulation ability in landraces was much higher than that of the inbred lines. The high N accumulation of landraces was closely related to their higher biomass, indicating that growth potential is the main driving force for N accumulation. Nevertheless, N utilization efficiency (grain produced per unit N absorbed) of the landraces was significantly lower than that in inbred lines. Correspondingly, assimilation allocation for grain formation, as indicated by the harvest index, was much lower in landraces than in inbred lines. The higher growth potential, and hence, the ability of N accumulation in landraces may be a valuable trait in breeding programs aiming to further improve N use efficiency.     

卫星搭载后玉米诱变系的SRAP分析

为探索空间诱变对玉米种子后代的影响,本研究用16对SRAP引物对玉米自交系＂968＂及其诱变系进行PCR检测,共检测到154个等位基因变异,每对引物检测出5～18个等位基因,平均为9.6个;94份材料间的遗传相似系数表明诱变系与对照间的遗传相似系数变化幅度为0.481～1.000,平均为0.903,其中诱变系37号与对...     

Genetic relationship among selected heat and drought tolerant bread wheat genotypes using SSR markers,agronomic traits and grain protein content

ABSTRACT

Assessing the genetic variation and relationships present in crop germplasm is a pre-requisite for parental selection and breeding. The objective of this study was to determine the genetic relationships present among selected heat and drought tolerant wheat genotypes using simple sequence repeat (SSR) markers, agronomic traits and grain quality parameters to select desirable parents for breeding. Twenty-four agronomically selected wheat genotypes sourced from the International Maize and Wheat Improvement Centre (CIMMYT)’s heat and drought tolerance nursery and four local check varieties were genotyped using 12 selected polymorphic SSR markers. The test genotypes were phenotyped using yield and yield-component traits, and grain protein content (GPC) under non-stressed (NS) and drought-stressed (DS) conditions. Expected heterozygosity mean value of 0.58 indicated moderate genetic diversity for breeding. The studied wheat genotypes were delineated into six genetic groups using cluster analysis. Significant genotypic differences were observed for agronomic traits and GPC under NS and DS conditions. Genetically unrelated breeding parents including LM02, LM13, LM23, LM41, LM44, LM71, LM73 and LM75 were selected for population development and breeding for enhanced grain yield and protein content under heat and drought-stressed environments.     

转Bt基因玉米自交系及其杂交种的抗螟性鉴定

采用基因枪法将Bt基因(GFM CrylA)导入东北春玉米自交系铁7922的幼胚中,获得转基因植株。经过连续3年的田间接卵、室内饲喂玉米螟鉴定,获得稳定抗虫转基因系。以此为亲本与常规自交系配制了四密25Bt、通单24Bt、吉单209Bt3个杂交种。转基因自交系和杂交种的抗螟性鉴定结果表明：转基因系间抗虫性差异极显著,同一转基因系单株间和配制的3个杂交种间抗虫性也存在差异;与对照相比,转基因系配制的杂交种抗虫性明显提高,差异显著。农艺性状鉴定结果显示,转基因系配制的杂交种与对照在株高、穗长、穗行数、行粒数、百粒重上无显著差异。本研究认为,GFM CrylA(Bt)基因可用于玉米的抗螟性改良,也为转Bt基因玉米自交系能够直接用于育种提供了依据。     

Assessment of genetic diversity among African cassava Manihot esculenta Grantz accessions resistant to the cassava mosaic virus disease using SSR markers

A study was conducted to determine the extent of genetic diversity among African cassava (Manihot esculenta Crantz) accessions resistant to the cassava mosaic virus disease (CMD), using simple sequence repeat (SSR) markers. The accessions included a breeding stock (clone 58308), five improved lines, 62 CMD resistant and 10 CMD susceptible landraces. Genetic diversity was assessed among accessions in five cluster groups derived from UPGMA analysis on data from 18 SSR primer pairs. Average gene diversity, He, was high in all cluster groups, with an average heterozygosity of 0.591 ± 0.061. The estimator of inbreeding Fis revealed a low level of inbreeding within groups and averaged −0.262 ± 0.142. Gene diversity among all accessions was 51.4% and gene diversity within cluster groups was 46.6%, while 4.8% was due to diversity between the different cluster groups. The amount of genetic differentiation measured by Gst and Fst were 9.6% and 12.1% respectively, indicating a weak genetic structure.     

Genetic diversity of <Emphasis Type="Italic">Guizotia abyssinica</Emphasis> (L. f.) Cass. (Asteraceae) from Ethiopia as revealed by random amplified polymorphic DNA (RAPD)

Genetic diversity of 70 populations of niger (Guizotia abyssinica) representing all its growing regions in Ethiopia was investigated using random amplified polymorphic DNA (RAPD) to reveal the extent of its populations genetic diversity. Ninety-seven percent of the loci studied was revealed to be polymorphic for the whole data set. The within population diversity estimated by Shannon diversity index and Nei gene diversity estimates was revealed to be 0.395 and 0.158, respectively. The extent of genetic variation of populations from major niger producing regions was significantly lower than that of populations from other regions; however, it is distributed regardless of altitude of growth. Genetic differentiation between populations was estimated with Shannon index as G^′ _ST (0.432), Nei’s G _ST (0.242) and AMOVA based F _ST (0.350) and appears to be equivalent to the average values calculated from various RAPD based studies on outcrossing species. Higher proportion of the variation detected by AMOVA resided within populations (64.58%) relative to the amount of variation among populations (35.42%). UPGMA cluster analysis showed that most of the populations were clustered according to their region of origin. However, some populations were genetically distant from the majority and seem to have unique genetic properties. It is concluded that the crop has a wide genetic basis that may be used for the improvement of the species through conventional breeding and/or marker assisted selection. Collection of germplasm from areas not yet covered and/or underrepresented is the opportunity to broaden the genetic basis of genebank collection.     

Microsatellites and RAPD Markers to Study Genetic Relationships Among Cowpea Breeding Lines and Local Varieties in Senegal

Genetic diversity in local cowpea varieties and breeding lines from Senegal were studied using random amplified polymorphic DNA (RAPD) and microsatellite (SSR) techniques. Among the 61 RAPD primers used, twelve show polymorphism. Fifteen of the 30 microsatellite primer pairs were polymorphic, detecting one to nine alleles per locus. The RAPD and SSR data were analyzed both separately and in combination to assess relationships among genetic lines. Although RAPD provided information on levels of genetic diversity, microsatellite markers are most effective in determining the relationship among cowpea accessions and varieties. The SSR results support the genetic diversification of cowpea in Senegal and underscore their potential in elucidating patterns of germplasm diversity of cowpea in Senegal. An erratum to this article is available at .