林木遗传图谱构建的研究进展

高密度分子遗传连锁图谱对分析植物遗传变异、标记目标性状、数量性状定位和分子辅助选择改良性状均具重要价值.由于林木具有世代长、高度杂合、遗传负荷大等遗传特性,使其遗传图谱研究不同于其他物种,其遗传连锁图谱的构建相对复杂.目前,一些林木的遗传连锁图谱已经产生.简要综述了林木遗传图谱研究现状和策略,并对构建高质量林木遗传图谱作了展望.     

作物数量性状(QTL)基因研究进展

从作物数量性状基因座QTL(quantitative trait locus)作图群体类型及特点,QTL定位的原理和方法,作物QTL研究现状,以及QTL精细定位、克隆、利用等方面进行了综述。对作物QTL分子标记辅助选择育种进行了探讨,并对目前QTL定位中存在的问题和今后QTL的研究方向提出了一些思考。     

利用显性分子标记和F_1群体进行林木遗传连锁图谱的构建

构建遗传图谱是当前生物学研究领域中的一个热点,进行图谱构建,林木与作物既有共性,又有各自的特点。因为进行图谱构建一是要有合适的分离群体,二是要有能揭示亲本多态性的遗传标记。两者可利用的遗传标记是一样的,但在进行作图群体构建时却存在一定差异,林木的遗传组成高度杂合,大多数林木为长期异交的树种,一般都有自交不亲合和近交衰退现象,象作物那样利用近交系或其它的高世代群体进行遗传图谱构建是不太可能的。由于研究方法的不同,以前的林木育种工作者很少留意建立和保存谱系清楚的Ｆ_２和ＢＣ_１群体,由于林木生命周期很长,建立这样一些高世代的群体也需要很长的时间,而且除了杨树、柳树等一些可在温室内水培杂交的物种,大多数林木的控制授粉杂交操作也是很困难的。因此研究过程中,等待材料的问题成为目前林木遗传图谱构建的主要限制因子之一。如何利用现成的材料和低世代群体,对林木遗传图谱构建工作的广泛开展具有重要意义。下面就这一问题作一些理论上的探讨和分析。     

数量性状基因座位及其在家禽中的定位

近年来随着现代分子生物学的发展 ,一些高效的分子遗传标记将各种畜禽的遗传图谱研究推向深入。为高密度、覆盖面广的连锁图谱的构建及QTL的定位奠定了基础。有关QTL的基本理论、QTL定位的步骤、QTL的检测方法以及家禽中定位的QTL已经展开了深入的研究 ,但目前QTL定位中存在诸多问题的问题     

大豆遗传图谱的构建和若干农艺性状的QTL定位分析

大豆许多重要农艺性状都是由微效多基因控制的数量性状,对这些数量性状进行QTL定位是大豆数量性状遗传研究领域的一个重要内容.本研究利用栽培大豆科新3号为父本、中黄20为母本杂交得到含192个单株的F2分离群体,构建了含122 个SSR标记、覆盖1719.6cM、由33个连锁群组成的连锁遗传图谱.利用复合区间作图法,对该群体的株高、主茎节数、单株粒重和蛋白质含量等农艺性状的调查数据进行QTL分析,共找到两个株高QTL,贡献率分别为9.15%和6.08%;两个主茎节数QTL,贡献率分别为10. 1%和8.6%;一个蛋白质含量QTL,贡献率为9.8%;一个单株粒重QTL,贡献率为11.4% .通过遗传作图共找到与所定位的4个农艺性状QTL连锁的6个SSR标记,这些标记可以应用于大豆种质资源的分子标记辅助选择,从而为大豆分子标记辅助育种提供理论依据.     

林木分子遗传图谱的构建

介绍了林木分遗传图谱构建中所使用的分离群体和分子标记,着重综述了国内外林木遗传图谱研究的现状,对已建立图谱的树种的作图情况作了较尽的总结。     

豌豆遗传图谱构建及QTL定位研究进展

豌豆的许多性状是多基因控制的数量性状,QTL定位就是以分子标记技术为工具、以遗传连锁图谱为基础、利用分子标记与QTL之间的连锁关系确定控制数量性状的基因在基因组中的位置.本文对QTL定位原理、方法进行了简单介绍;对豌豆遗传图谱构建及主要性状,如产量、品质、抗病性等QTL定位、遗传效应分析等方面的研究进行综述;对目前基于QTL豌豆分子标记育种存在的问题、应用前景进行了探讨.     

基于SRAP分子标记的冰草遗传连锁图谱构建

构建高密度遗传连锁图谱是冰草抗性、品质、产量等重要性状QTL精细定位及标记辅助育种研究的基础。该试验以四倍体杂交冰草F2群体的202个分离单株及其亲本为材料,利用SRAP分子标记技术和Join Map 4.0作图软件对冰草的遗传连锁图谱进行了构建。结果表明:(1)共筛选出22对多态性好、标记位点清晰稳定的SRAP适宜引物,对冰草杂种F2分离单株的基因组DNA进行PCR扩增,共获得510个SRAP多态性标记位点,其比率占88.2%。(2)偏分离分析表明,偏分离标记比率仅为14.12%,符合遗传作图的要求。(3)成功构建了冰草的SRAP分子标记遗传连锁图谱,该图谱有14个连锁群、510个标记,连锁群间长度范围86.4～179.0cM,覆盖基因组总长度1 912.9cM,标记间平均间距3.75cM,为高密度遗传图谱。     

基于F2群体的香菇遗传图谱构建及其在QTL定位中的应用

以171个F2双核体菌株为作图群体,通过相互配对的2个单核体的基因型推断双核体基因型,构建了第一张基于双核体群体的香菇遗传图谱。该图谱包含分布于15个连锁群的459个标记,覆盖长度为989.7cM,平均标记间隔为2.2cM。此外,以此双核体群体作为表型分离群体,定位了6个与香菇双核体菌丝生长速度相关的QTLs,位于5个连锁群上。采用全同胞单核体随机交配策略,易于构建相对大的双核体群体,用于连锁图构建和QTL定位。研究表明,在食用菌连锁图谱构建及QTL定位研究中,利用F2群体,可能为提高遗传作图效率,解决作图群体与表型分离群体间不一致问题提供新的途径。     

QTL定位的研究方法

QTL 定位就是采用类似单基因定位的方法将QTL定位在遗传图谱上 ,确定 QTL与遗传标记间的距离 (以重组率表示 ) [1]。根据标记数目的不同 ,可分为单标记、双标记和多标记几种方法。根据统计分析方法的不同 ,可分为方差与均值分析法、回归及相关分析法、矩估计及最大似然法等。根据标记区间数可分为零区间作图、单区间作图和多区间作图。此外 ,还有将不同方法结合起来的综合分析方法 ,如 QTL复合区间作图 (CIM)、多区间作图 (MIM)、多 QTL作图、多性状作图 (MTM)等等。建立在标记与数量性状之间相互关联基础上的关联分析方法主要有…     

A dense linkage map of hybrid cottonwood (Populus fremontii x P. angustifolia) contributes to long-term ecological research and comparison mapping in a model forest tree

Cottonwoods are foundation riparian species, and hybridization among species is known to produce ecological effects at levels higher than the population, including effects on dependent species, communities and ecosystems. Because these patterns result from increased genetic variation in key cottonwood traits, novel applications of genetic tools (for example, QTL mapping) could be used to place broad-scale ecological research into a genomic perspective. In addition, linkage maps have been produced for numerous species within the genus, and, coupled with the recent publication of the Populus genome sequence, these maps present a unique opportunity for genome comparisons in a model system. Here, we conducted linkage analyses in order to (1) create a platform for QTL and candidate gene studies of ecologically important traits, (2) create a framework for chromosomal-scale perspectives of introgression in a natural population, and (3) enhance genome-wide comparisons using two previously unmapped species. We produced 246 backcross mapping (BC(1)) progeny by crossing a naturally occurring F(1) hybrid (Populus fremontii x P. angustifolia) to a pure P. angustifolia from the same population. Linkage analysis resulted in a dense linkage map of 541 AFLP and 111 SSR markers distributed across 19 linkage groups. These results compared favorably with other Populus linkage studies, and addition of SSR loci from the poplar genome project provided coarse alignment with the genome sequence. Preliminary applications of the data suggest that our map represents a useful framework for applying genomic research to ecological questions in a well-studied system, and has enhanced genome-wide comparisons in a model tree.     

林木数量性状基因定位中的若干问题

随着ＤＮＡ分子标记技术的迅速发展,ＱＴＬ定位已成为当前生物学研究领域的前沿。迄今已对许多种动、植物定位了许多重要性状的ＱＴＬ。这些研究促进了遗传学的发展,并将作为育种的新策略应用。与作物相比,林木ＱＴＬ定位有其特性。本文详细讨论了林木的生物学特性对ＱＴＬ定位的影响、ＱＴＬ定位的系谱设计和统计分析方法。     

水产养殖动物遗传连锁图谱及QTL定位研究进展

自1997年美国农业部启动5种水产养殖动物基因组计划以来,在不到10年的时间里,世界各国都相继开展了本国主要水产养殖动物基因组研究。截至2005年底,有近17种海淡水养殖动物公布了遗传连锁图谱：属于高密度连锁图谱的有虹鳟和大西洋鲑（标记数超过1000）;属于中密度遗传连锁图谱的有罗非鱼、沟鲶、黑虎虾、日本牙鲆和欧洲海鲈（标记数为400-1000）;属于低密度遗传连锁图谱的有泰国的胡鲶,中国的栉孔扇贝、鲤鱼,日本的黄尾鲕,美国的牡蛎等近10种养殖种类（标记数少于400）。水产养殖动物遗传连锁图谱的构建和发展,促进了一些与经济性状（如生长、抗逆、发育等）相关的数量性状位点（QTL）的定位研究。然而,QTL定位研究目前只在具有中高密度遗传连锁图谱的鲑科鱼类（虹鳟、大西洋鲑和北极嘉鱼）、罗非鱼、沟鲶和日本牙鲆等种类中开展,而且定位研究仍处在初级水平。遗传连锁图谱的高分辨率和QTL在图谱上的精确定位,是今后能否实现对主要水产养殖动物的经济性状进行遗传操作的技术保证,同时也是实现分子标记或基因辅助育种在水产养殖动物中成功运用的制胜法宝。     

3Increasing the source/sink ratio in Vitis vinifera (cv Sangiovese) induces extensive transcriptome reprogramming and modifies berry ripening

Background

The genomic architecture of bud phenology and height growth remains poorly known in most forest trees. In non model species, QTL studies have shown limited application because most often QTL data could not be validated from one experiment to another. The aim of our study was to overcome this limitation by basing QTL detection on the construction of genetic maps highly-enriched in gene markers, and by assessing QTLs across pedigrees, years, and environments.

Results

Four saturated individual linkage maps representing two unrelated mapping populations of 260 and 500 clonally replicated progeny were assembled from 471 to 570 markers, including from 283 to 451 gene SNPs obtained using a multiplexed genotyping assay. Thence, a composite linkage map was assembled with 836 gene markers. For individual linkage maps, a total of 33 distinct quantitative trait loci (QTLs) were observed for bud flush, 52 for bud set, and 52 for height growth. For the composite map, the corresponding numbers of QTL clusters were 11, 13, and 10. About 20% of QTLs were replicated between the two mapping populations and nearly 50% revealed spatial and/or temporal stability. Three to four occurrences of overlapping QTLs between characters were noted, indicating regions with potential pleiotropic effects. Moreover, some of the genes involved in the QTLs were also underlined by recent genome scans or expression profile studies. Overall, the proportion of phenotypic variance explained by each QTL ranged from 3.0 to 16.4% for bud flush, from 2.7 to 22.2% for bud set, and from 2.5 to 10.5% for height growth. Up to 70% of the total character variance could be accounted for by QTLs for bud flush or bud set, and up to 59% for height growth.

Conclusions

This study provides a basic understanding of the genomic architecture related to bud flush, bud set, and height growth in a conifer species, and a useful indicator to compare with Angiosperms. It will serve as a basic reference to functional and association genetic studies of adaptation and growth in Picea taxa. The putative QTNs identified will be tested for associations in natural populations, with potential applications in molecular breeding and gene conservation programs. QTLs mapping consistently across years and environments could also be the most important targets for breeding, because they represent genomic regions that may be least affected by G × E interactions.     

High-density genotyping: an overkill for QTL mapping? Lessons learned from a case study in maize and simulations

High-density genotyping is extensively exploited in genome-wide association mapping studies and genomic selection in maize. By contrast, linkage mapping studies were until now mostly based on low-density genetic maps and theoretical results suggested this to be sufficient. This raises the question, if an increase in marker density would be an overkill for linkage mapping in biparental populations, or if important QTL mapping parameters would benefit from it. In this study, we addressed this question using experimental data and a simulation based on linkage maps with marker densities of 1, 2, and 5 cM. QTL mapping was performed for six diverse traits in a biparental population with 204 doubled haploid maize lines and in a simulation study with varying QTL effects and closely linked QTL for different population sizes. Our results showed that high-density maps neither improved the QTL detection power nor the predictive power for the proportion of explained genotypic variance. By contrast, the precision of QTL localization, the precision of effect estimates of detected QTL, especially for small and medium sized QTL, as well as the power to resolve closely linked QTL profited from an increase in marker density from 5 to 1 cM. In conclusion, the higher costs for high-density genotyping are compensated for by more precise estimates of parameters relevant for knowledge-based breeding, thus making an increase in marker density for linkage mapping attractive.     

林木遗传连锁图谱构建研究进展与发展方向

本文就目前国内外林木连锁遗传图谱领域的研究进展进行了综述,指出了该领域研究中存在的主要问题,即一方面是作图个体的数量有限,另一方面是采用的标记以随机标记为主,导致了建成的图谱以及利用图谱获得的数量性状基因位点（QTLs）信息具有杂交组合特异性,造成了QTLs的可信度和在林木遗传改良以及标记辅助选择中的实用性降低等现象。针对存在的问题,讨论了根据林木生物学特点选择合适遗传标记的意义,指出进行林木比较作图研究的重要性和必要性。文中接着较为详尽地介绍了国外重要林木表达序列标签（EST）测序项目的研究进展,论述了功能已知和种间高度保守的表达序列标签多态性（ESTP）标记的由来,阐述了获得ESTP标记的主要方法,并指出应当利用ESTP标记进行林木遗传图谱构建、QTL定位和比较作图的研究。文中最后讨论了未来林木遗传图谱构建和QTL定位研究的发展方向,并探讨了我国在该领域取得重大进展的突破口,指出我国应首先进行杨树尤其是中国乡土杨树树种该方面的研究。 Abstract:The research progress in genetic linkage map construction of forest tree species both at home and abroad were reviewed in the paper.Two main problems involved in the field were discussed.One was the limitation of the number of individuals of mapping populations and the other was the random markers mostly employed by the majority of studies.These problems have resulted in crossing combination specificity in the constructed maps and the QTLs located on the basis of the maps.As a result,the QTLs discovered up to now have low credibility and poor practicability in marker-assisted selection.Therefore considering the biological characteristics of forest tree species,the selection of the most suitable genetic markers is crucial to obtain a high quality genetic linkage map,and it is both important and necessary to carry out comparative genetic mapping.Progress in the ongoing expressed sequence tag (EST) sequencing projects were summarized and EST polymorphism (ESTP),the most informative and highly conservative marker with known function,as well as the main ESTP detection techniques were elaborated.It was pointed out that ESTP markers should be integrated into the present studies of genetic linkage map construction,QTL mapping and genome comparative mapping.Finally the future prospects in the fields of genetic linkage map and QTL mapping were discussed.In China,Such studies around Populus,especially in the local Populus species should make a breakthrough in the related fields.     

Association mapping in forest trees and fruit crops

Association mapping (AM), also known as linkage disequilibrium (LD) mapping, is a viable approach to overcome limitations of pedigree-based quantitative trait loci (QTL) mapping. In AM, genotypic and phenotypic correlations are investigated in unrelated individuals. Unlike QTL mapping, AM takes advantage of both LD and historical recombination present within the gene pool of an organism, thus utilizing a broader reference population. In plants, AM has been used in model species with available genomic resources. Pursuing AM in tree species requires both genotyping and phenotyping of large populations with unique architectures. Recently, genome sequences and genomic resources for forest and fruit crops have become available. Due to abundance of single nucleotide polymorphisms (SNPs) within a genome, along with availability of high-throughput resequencing methods, SNPs can be effectively used for genotyping trees. In addition to DNA polymorphisms, copy number variations (CNVs) in the form of deletions, duplications, and insertions also play major roles in control of expression of phenotypic traits. Thus, CNVs could provide yet another valuable resource, beyond those of microsatellite and SNP variations, for pursuing genomic studies. As genome-wide SNP data are generated from high-throughput sequencing efforts, these could be readily reanalysed to identify CNVs, and subsequently used for AM studies. However, forest and fruit crops possess unique architectural and biological features that ought to be taken into consideration when collecting genotyping and phenotyping data, as these will also dictate which AM strategies should be pursued. These unique features as well as their impact on undertaking AM studies are outlined and discussed.     

Genetic linkage mapping in fungi: current state, applications, and future trends

Genetic mapping is a basic tool for eukaryotic genomic research. Linkage maps provide insights into genome organization and can be used for genetic studies of traits of interest. A genetic linkage map is a suitable support for the anchoring of whole genome sequences. It allows the localization of genes of interest or quantitative trait loci (QTL) and map-based cloning. While genetic mapping has been extensively used in plant or animal models, this discipline is more recent in fungi. The present article reviews the current status of genetic linkage map research in fungal species. The process of linkage mapping is detailed, from the development of mapping populations to the construction of the final linkage map, and illustrated based on practical examples. The range of specific applications in fungi is browsed, such as the mapping of virulence genes in pathogenic species or the mapping of agronomically relevant QTL in cultivated edible mushrooms. Future prospects are finally discussed in the context of the most recent advances in molecular techniques and the release of numerous fungal genome sequences.     

Editor's choice: High-Resolution Linkage and Quantitative Trait Locus Mapping Aided by Genome Survey Sequencing: Building Up An Integrative Genomic Framework for a Bivalve Mollusc

Genetic linkage maps are indispensable tools in genetic and genomic studies. Recent development of genotyping-by-sequencing (GBS) methods holds great promise for constructing high-resolution linkage maps in organisms lacking extensive genomic resources. In the present study, linkage mapping was conducted for a bivalve mollusc (Chlamys farreri) using a newly developed GBS method—2b-restriction site-associated DNA (2b-RAD). Genome survey sequencing was performed to generate a preliminary reference genome that was utilized to facilitate linkage and quantitative trait locus (QTL) mapping in C. farreri. A high-resolution linkage map was constructed with a marker density (3806) that has, to our knowledge, never been achieved in any other molluscs. The linkage map covered nearly the whole genome (99.5%) with a resolution of 0.41 cM. QTL mapping and association analysis congruously revealed two growth-related QTLs and one potential sex-determination region. An important candidate QTL gene named PROP1, which functions in the regulation of growth hormone production in vertebrates, was identified from the growth-related QTL region detected on the linkage group LG3. We demonstrate that this linkage map can serve as an important platform for improving genome assembly and unifying multiple genomic resources. Our study, therefore, exemplifies how to build up an integrative genomic framework in a non-model organism.     

Regulation of Arabidopsis defense responses against Spodoptera littoralis by CPK-mediated calcium signaling

Background

Genetic markers and linkage mapping are basic prerequisites for marker-assisted selection and map-based cloning. In the case of the key grassland species Lolium spp., numerous mapping populations have been developed and characterised for various traits. Although some genetic linkage maps of these populations have been aligned with each other using publicly available DNA markers, the number of common markers among genetic maps is still low, limiting the ability to compare candidate gene and QTL locations across germplasm.

Results

A set of 204 expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers has been assigned to map positions using eight different ryegrass mapping populations. Marker properties of a subset of 64 EST-SSRs were assessed in six to eight individuals of each mapping population and revealed 83% of the markers to be polymorphic in at least one population and an average number of alleles of 4.88. EST-SSR markers polymorphic in multiple populations served as anchor markers and allowed the construction of the first comprehensive consensus map for ryegrass. The integrated map was complemented with 97 SSRs from previously published linkage maps and finally contained 284 EST-derived and genomic SSR markers. The total map length was 742 centiMorgan (cM), ranging for individual chromosomes from 70 cM of linkage group (LG) 6 to 171 cM of LG 2.

Conclusions

The consensus linkage map for ryegrass based on eight mapping populations and constructed using a large set of publicly available Lolium EST-SSRs mapped for the first time together with previously mapped SSR markers will allow for consolidating existing mapping and QTL information in ryegrass. Map and markers presented here will prove to be an asset in the development for both molecular breeding of ryegrass as well as comparative genetics and genomics within grass species.