水产动物遗传连锁图谱的研究现状及应用展望

综述了近年来遗传连锁图谱在水产生物中的研究现状,包括作图群体、作图方法等,并对连锁图谱的应用前景作了展望,指出其在分子标记辅助育种、基因定位与克隆及比较基因组学等方面的应用潜力。 Abstract:Constructing genetic linkage map is an essential tool to acknowledge genome in aquaculture species.This paper has reviewed the current status of genetic linkage map research,including mapping population,mapping method and molecular markers used to construct linkage map.Linkage map has great potential in marker assisted selection (MAS),gene locating and cloning,and comparative genome mapping.Genetic linkage map with high density and wide coverage of genome will allow cloning the genes which contribute to economically important traits.The ultimate aim of the constructing linkage map is the development of fast-growing,disease-resistant strains of the major aquaculture species.     

绵羊基因组研究进展

过去几年中,家畜基因组计划取得了巨大进展。已经构建了猪、鸡、牛、绵羊、马、鹿的遗传图谱,其遗传标记间距在5～20cM。这些图谱对于家畜中与重要经济性状相关的基因或遗传标记的鉴定非常重要。该文从绵羊的基因图谱、比较图谱、重要经济性状基因及QTL定位方面对绵羊基因组的研究进展作了简要阐述。 Abstract:During the last few years,advances in livestock genome projects have been remarkable.Species-specific genetic maps exist for pig,chicken,cattle,sheep,horse,and deer with marker intervals of 5 to 20 cM.These maps have been essential for the identification of genes and genetic markers associated with importantly economic traits in livestock.In this paper,advances of gene map,comparative map,the genes for importantly economic traits and quantitative trait loci (QTL) mapping were briefly introduced in sheep.     

Quantitative Trait Loci Mapping of Leaf Morphological Traits and Chlorophyll Content in Cultivated Tetraploid Cotton

Genetic mapping provides a powerful tool for quantitative trait loci （QTL） analysis at the molecular level. A simple sequence repeat （SSR） genetic map containing 590 markers and a BCI population from two cultivated tetraploid cotton （Gossypium hirsutum L.） cultivars, namely TM-1 and Hai 7124 （G. barbadense L.）, were used to map and analyze QTL using the composite interval mapping （CIM） method. Thirty one QTLs, 10 for lobe length, 13 for lobe width, six for lobe angle, and two for leaf chlorophyll content, were detected on 15 chromosomes or linkage groups at logarithm of odds （LOD）≥2.0, of which 15 were found for leaf morphology at LOD≥3.0. The genetic effects of the QTL were estimated. These results are fundamental for marker-assisted selection （MAS） of these traits in tetraploid cotton breeding.     

Fine mapping quantitative trait loci affecting milk production traits on bovine chromosome 6 in a Chinese Holstein population

To fine map the previously detected quantitative trait loci （QTLs） affecting milk production traits on bovine chromosome 6 （BTA6）, 15 microsatellite markers situated within an interval of 14.3 cM spanning from BMS690 to BM4528 were selected and 918 daughters of 8 sires were genotyped. Two mapping approaches, haplotype sharing based LD mapping and single marker regression mapping, were used to analyze the data. Both approaches revealed a quantitative trait locus （QTL） with significant effects on milk yield, fat yield and protein yield located in the segment flanked by markers BMS483 and MNB209, which spans a genetic distance of 0.6 cM and a physical distance of 1.5 Mb. In addition, the single marker regression mapping also revealed a QTL affecting fat percentage and protein percentage at marker DIK2291. Our fine mapping work will facilitate the cloning of candidate genes underlying the QTLs for milk production traits.     

Mapping QTLs with epistatic effects and QTL×environment interactions for plant height using a doubled haploid population in cultivated wheat

Quantitative trait loci (QTLs) for plant height in wheat (Triticum aestivum L.) were studied using a set of 168 doubled haploid (DH) lines, which were derived from the cross Huapei 3/Yumai 57. A genetic linkage map was constructed using 283 SSR and 22 EST-SSR markers. The DH population and the parents were evaluated for wheat plant height in 2005 and 2006 in Tai’an and 2006 in Suzhou. QTL analyses were performed using the software of QTLNetwork version 2.0 based on the mixed linear model. Four additive QTLs and five pairs of epistatic effects were detected, which were distributed on chromosomes 3A, 4B, 4D, 5A, 6A, 7B, and 7D. Among them, three additive QTLs and three pairs of epistatic QTLs showed QTL×environment interactions (QEs). Two major QTLs, Qph4B and Qph4D, which accounted for 14.51% and 20.22% of the phenotypic variation, were located similar to the reported locations of the dwarfing genes Rht1 and Rht2, respectively. The Qph3A-2 with additive effect was not reported in previous linkage mapping studies. The total QTL effects detected for the plant height explained 85.04% of the phenotypic variation, with additive effects 46.07%, epistatic effects 19.89%, and QEs 19.09%. The results showed that both additive effects and epistatic effects were important genetic bases of wheat plant height, which were subjected to environmental modifications, and caused dramatic changes in phenotypic effects. The information obtained in this study will be useful for manipulating the QTLs for wheat plant height by molecular marker-assisted selection (MAS).     

Genetic Mapping of Laminaria japonica and L. Iongissima Using Amplified Fragment Length Polymorphism Markers in a ＂Two-Way Pseudo- Testcross＂ Strategy

With a ＂two-way pseudo-testcross＂ mapping strategy, we applied the amplified fragment length polymorphism （AFLP） markers to construct two moderate density genetic linkage maps for Laminaria. The linkage maps were generated from the 60 progenies of the F1 cross family （Laminaria iongissima Aresch. × L. Japonica Miyabe） with twenty pairs of primer combinations. Of the 333 polymorphic loci scored in 60 progenies, 173 segregated in a 1：1 ratio, corresponding to DNA polymorphisms heterozygous in a single parent, and the other 58 loci existing in both parents followed a 3：1 Mendelian segregation ratio. Among the loci with 1：1 segregating ratios, 79 loci were ordered in 14 linkage groups （648.6 cM） of the paternal map, and 72 loci were ordered in 14 linkage groups （601.9 cM） of the maternal map. The average density of loci was approximately 1 per 8 cM. To Investigate the homologies between two parental maps, we used 58 loci segregated 3：1 for further analysis, and deduced one homologous linkage group. The linkage data developed in these maps will be useful for detecting loci-controlling commercially important traits for Laminaria.     

小麦基因组研究进展

本文从小麦遗传图谱、物理图谱、比较基因组、基因组测序和EST 5个方面,介绍国内外小麦基因组的研究进展。我们利用W7984×Opata重组近交系的RFLP作图群体,对33个与小麦水分利用效率有关的性状进行了QTL遗传图谱比较分析,结果显明：在第一部分同源群染色体（1A,1B）上的着丝粒周围,分布有控制光合作用和根系特性的基因簇。在第二部分同源染色体上,有控制单株水分利用效率、根冠形态和生长发育的基因簇存在。在第六部分同源染色体上,6A和6B上都分别有由控制根系多个QTL组成的基因簇,6D染色体着丝粒周围有一个大的基因簇,由7个控制叶片和单株水分利用效率的QTL组成,说明第六部分同源染色体在小麦水分利用效率遗传方面起重要作用。 Abstract:Research development of genetic mapping,physics mapping,genome sequencing and expressed sequence tags in wheat have been reviewed in this paper.RFLP genetic linkage map of wheat recombinant inbred lines derived from W7984×Opata,was used to study QTL of 33 traits associated with water use efficiency.Compared with QTL map of 7 group homeologues chromosomes,the results were showed as follows:nearby the centromeric region of 1A and 1B chromosome,the gene cluster of controlling photosynthetic and root traits were located.The gene clusters of controlling water use efficiency per plant,root and plant height and growth rate were located on the 2 group chromosomes.The gene clusters of controlling root traits were located on the 6A an 6B chromosome,there was a big gene cluster mad up by 7 QTLs controlling water use efficiency of wheat leaf and per plant nearby the centromeric region of 6D chromosome.It showed that 6th homeologous chromosomes play an important role in controlling water use efficiency in wheat.     

QTL Scanning for Rice Yield Using a Whole Genome SNP Array

High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line （RIL） population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length ofl.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.     

Linkage Map Construction and Quantitative Trait Loci Analysis for Bolting Based on a Double Haploid Population of Brassica rapa

Early bolting of Chinese cabbage （Brassica rapa L.） during spring cultivation often has detrimental effects on the yield and quality of the harvested products. Breeding late bolting varieties is a major objective of Chinese cabbage breeding programs. In order to analyze the genetic basis of bolting traits, a genetic map of B. rapa was constructed based on amplified fragment-length poiymorphism （AFLP）, sequence-related amplified poiymorphism （SRAP）, simple sequence repeat （SSR）, random amplification of polymorphic DNA （RAPD）, and isozyme markers. Marker analysis was carried out on 81 double haploid （DH） lines obtained by microspore culture from F1 progeny of two homozygous parents： B. rapa L. ssp. pekinensis （BY） （an extra-early bolting Chinese cabbage line） and B. rapa L. ssp. rapifera （MM） （an extra-late bolting European turnip line）. A total of 326 markers including 130 AFLPs, 123 SRAPs, 16 SSRs, 43 RAPDs and 14 isozymes were used to construct a linkage map with 10 linkage groups covering 882 cM with an average distance of 2.71 cM between loci. The bolting trait of each DH line was evaluated by the bolting index under controlled conditions. Quantitative trait loci （QTL） analysis was conducted using multiple QTL model mapping with MapQTL5.0 software. Eight QTLs controlling bolting resistance were identified. These QTLs, accounting for 14.1% to 25.2% of the phenotypic variation with positive additive effects, were distributed into three linkage groups. These results provide useful information for molecular marker-assisted selection of late bolting traits in Chinese cabbage breeding programs.     

Progress in the Study of Molecular Genetic Improvements of Poplar in China

The poplar is one of the most economically important and intensively studied tree species owing to its wide application in the timber industry and as a model material for the study of woody plants. The natural resource of poplars in China is replete. Over the past 10 years, the application of molecular biological techniques to genetic improvements in poplar species has been widely studied in China. Recent advances in molecular genetic improvements of poplar, including cDNA library construction, gene cloning and identification, genetic engineering, gene expression, genetic linkage map construction, mapping of quantitative trait loci （QTL） and molecular-assisted selection, are reviewed in the present paper. In addition, the application of modern biotechnology to molecular improvements in the genetic traits of the poplar and some unsolved problems are discussed.     

林木遗传图谱研究现状及发展趋势

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。高质量林木遗传图谱,可进行林木近缘树种比较图谱研究,了解林木的基因组结构和进化历程,进行有效QTL定位研究及开展林木复杂性状的标记辅助选择。目前林木作图存在着群体较小,构建的图谱和定位的QTL存在连锁平衡,以及作图策略未充分考虑林木的遗传学特性等问题。扩大作图群体、选择高度保守的标记系统以及研究适合林木作图的理论和方法将有助于林木基因组研究向纵深发展 。     

Identification of quantitative trait loci for wood quality and growth across eight full-sib coastal Douglas-fir families

Typical linkage and quantitative trait locus (QTL) analyses in forest trees have been conducted in single pedigrees with sex-averaged linkage maps. The results of a QTL analysis for wood quality and growth traits of coastal Douglas-fir using eight full-sib families, each consisting of 40 progeny, replicated on four sites are presented. The resulting map of segregating genetic markers consisted of 120 amplified fragment length polymorphism (AFLP) loci distributed across 19 linkage groups. The wood quality traits represent the widest suite of traits yet examined for QTL analysis in a tree species in a single study. Wood fiber traits showed the lowest number of QTLs (3) with relatively small effect (ca. 4%); wood density traits also showed just three QTLs but with slightly larger effect; wood chemistry traits showed more QTLs (7), while ring density traits showed many QTLs with large numbers of QTLs (78) and interesting patterns of temporal variation. Growth traits gave just five QTLs but of major effect (10–16%). Trees, with their long generation times, provide a rich resource for studies of temporal variation of QTL expression.     

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。     

林木基因组学研究进展

林木基因组学研究进展迅速。结构基因组学方面,已构建了近40个主要造林树种的遗传连锁图谱,在不同树种中定位了30余个重要的数量性状位点,在部分树种中开展了基因组比较和综合图谱构建研究,杨树的全基因组测序已经完成,桉树的全基因组测序正在进行。功能基因组学方面,已分析了主要造林树种多种组织的转录组EST序列,对林木次生生长与木材形成、开花和抗寒性的形成等过程开展了功能基因组学研究。另外,探讨了林木基因组学研究的发展趋势,以期为我国林木基因组学研究提供有益的参考。     

QTL Mapping of Growth-Related Traits in a Full-Sib Family of Rubber Tree (Hevea brasiliensis) Evaluated in a Sub-Tropical Climate

The rubber tree (Hevea spp.), cultivated in equatorial and tropical countries, is the primary plant used in natural rubber production. Due to genetic and physiological constraints, inbred lines of this species are not available. Therefore, alternative approaches are required for the characterization of this species, such as the genetic mapping of full-sib crosses derived from outbred parents. In the present study, an integrated genetic map was obtained for a full-sib cross family with simple sequence repeats (SSRs) and expressed sequence tag (EST-SSR) markers, which can display different segregation patterns. To study the genetic architecture of the traits related to growth in two different conditions (winter and summer), quantitative trait loci (QTL) mapping was also performed using the integrated map. Traits evaluated were height and girth growth, and the statistical model was based in an extension of composite interval mapping. The obtained molecular genetic map has 284 markers distributed among 23 linkage groups with a total length of 2688.8 cM. A total of 18 QTLs for growth traits during the summer and winter seasons were detected. A comparison between the different seasons was also conducted. For height, QTLs detected during the summer season were different from the ones detected during winter season. This type of difference was also observed for girth. Integrated maps are important for genetics studies in outbred species because they represent more accurately the polymorphisms observed in the genitors. QTL mapping revealed several interesting findings, such as a dominance effect and unique segregation patterns that each QTL could exhibit, which were independent of the flanking markers. The QTLs identified in this study, especially those related to phenotypic variation associated with winter could help studies of marker-assisted selection that are particularly important when the objective of a breeding program is to obtain phenotypes that are adapted to sub-optimal regions.     

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.     

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.     

Model selection for quantitative trait loci mapping in a full-sib family

Statistical methods for mapping quantitative trait loci (QTLs) in full-sib forest trees, in which the number of alleles and linkage phase can vary from locus to locus, are still not well established. Previous studies assumed that the QTL segregation pattern was fixed throughout the genome in a full-sib family, despite the fact that this pattern can vary among regions of the genome. In this paper, we propose a method for selecting the appropriate model for QTL mapping based on the segregation of different types of markers and QTLs in a full-sib family. The QTL segregation patterns were classified into three types: test cross (1:1 segregation), F₂ cross (1:2:1 segregation) and full cross (1:1:1:1 segregation). Akaike’s information criterion (AIC), the Bayesian information criterion (BIC) and the Laplace-empirical criterion (LEC) were used to select the most likely QTL segregation pattern. Simulations were used to evaluate the power of these criteria and the precision of parameter estimates. A Windows-based software was developed to run the selected QTL mapping method. A real example is presented to illustrate QTL mapping in forest trees based on an integrated linkage map with various segregation markers. The implications of this method for accurate QTL mapping in outbred species are discussed.     

An AFLP and RFLP linkage map and quantitative trait locus (QTL) analysis of growth traits in Salix

A genetic linkage map of Salix (2n = 38), composed of 325 AFLP and 38 RFLP markers has been constructed. The map was based on a population ( n = 87) derived from a cross between the male hybrid clone "Bj?rn" ( Salix viminalis x Salix schwerinii) and the female clone "78183" ( S. viminalis). Three hundred fifty seven AFLPs corresponding to DNA polymorphisms heterozygous in one parent and null in the other were scored. A total of 87 RFLP probes, most (83) derived from the Populus genome, yielded 39 and 11 polymorphic loci segregating in a 1:1 and 1:2:1 ratio respectively. Two maps, one for each parent, were constructed according to the "two-way pseudo-testcross" mapping strategy. The S. viminalis x S. schwerinii map (2,404 cM) included 217 markers and formed 26 major linkage groups while S. viminalis (1,844 cM) consisted of 146 markers placed on 18 major groups. In addition, eight and 14 additional minor linkage groups composed of less than four markers (doubles and triplets) were obtained in the S. viminalis x S. schwerinii and the S. viminalis maps, respectively. Both maps provided 70-80% genome coverage with an average density of markers of 14 cM. To investigate possible homologies between the parental maps, 20 AFLPs and 11 RFLPs segregating in 3:1 or 1:2:1 ratios were included in the linkage analysis. Eight linkage groups homologous between the two maps were detected. The present genetic map was used to identify quantitative trait loci (QTLs) affecting growth-related traits. Eleven QTLs were identified; seven QTLs for height growth, one QTL for stem diameter, one QTL for the height: diameter ratio, one QTL for the number of vegetative buds during flowering time and one QTL for the number of shoots. The estimated magnitude of the QTL effect ranged from 14 to 22% of the total phenotypic variance. One QTL associated with height growth and one affecting the height: diameter ratio were overlapping in the same marker interval with the QTL affecting stem diameter. QTL stability over years was estimated for traits measured in multiple years. Generally, QTLs were only significant in a single year although two QTLs for height growth were close to reaching the significance level in 2 consecutive years.     

Exploring the genetic characteristics of 93-11 and Nipponbare recombination inbred lines based on the GoldenGate SNP assay

Understanding genetic characteristics in rice populations will facilitate exploring evolutionary mechanisms and gene cloning. Numerous molecular markers have been utilized in linkage map construction and quantitative trait locus (QTL) mappings. However, segregation-distorted markers were rarely considered, which prevented understanding genetic characteristics in many populations. In this study, we designed a 384-marker GoldenGate SNP array to genotype 283 recombination inbred lines (RILs) derived from 93-11 and Nipponbare Oryza sativa crosses. Using 294 markers that were highly polymorphic between parents, a linkage map with a total genetic distance of 1,583.2 cM was constructed, including 231 segregation-distorted markers. This linkage map was consistent with maps generated by other methods in previous studies. In total, 85 significant quantitative trait loci (QTLs) with phenotypic variation explained (PVE) values≥5% were identified. Among them, 34 QTLs were overlapped with reported genes/QTLs relevant to corresponding traits, and 17 QTLs were overlapped with reported sterility-related genes/QTLs. Our study provides evidence that segregation-distorted markers can be used in linkage map construction and QTL mapping. Moreover, genetic information resulting from this study will help us to understand recombination events and segregation distortion. Furthermore, this study will facilitate gene cloning and understanding mechanism of inter-subspecies hybrid sterility and correlations with important agronomic traits in rice.