遗传基因组学(Genetical genomics)的研究进展

遗传基因组学(geneticalgenomics)是将微阵列技术和数量性状座位(QTL)分析结合起来,全基因组水平上定位基因表达的QTL(eQTL).它为研究复杂性状的分子机理和调控网络提供全新的手段.遗传基因组这个概念和研究策略在2001年由Janson和Nap首先提出,到目前为止,遗传基因组学已应用于酵母、老鼠、人以及玉米等植物.研究结果表明:基因表达水平的差异是可遗传的复杂性状;eQTL可以分为顺式作用eQTL和反式作用eQTL,顺式作用eQTL就是某个基因的eQTL定位到该基因所在的基因组区域,表明可能是该基因本身的差别引起mRNA水平的差别,反式作用就是eQTL定位到其他基因组区域,表明其他基因的差别控制该基因mRNA水平的差异.将eQTL结果、基因功能注解以及多种统计分析方法相结合,不仅能更准确地鉴别控制复杂性状及其相关基因表达的候选基因,而且能构建相应的基因调控网络.     

白菜型油菜黄子资源的初步遗传研究

对随机选取的国内外22份黄子白菜型油菜和22份褐子白菜型油菜进行了种皮色泽的显隐性关系鉴定、黄子性状的等位性测验以及遗传多样性分析。结果表明,黄子白菜型油菜与褐子白菜型油菜配组的杂交组合中,部分组合的F1种皮色泽呈现父本的种皮色泽,表现出花粉直感现象;自然界中存在多种白菜型油菜黄子类型,鉴定出的3种黄子白菜型油菜与褐色白菜型油菜的F2种皮色泽均为褐色,表明黄子性状对于褐子性状为隐性;分子标记方差分析结果显示,白菜型油菜的生长习性所解释的遗传变异大于种皮颜色所解释的遗传变异,表明国外不同生长习性的黄子白菜型油菜资源可用于国内黄子白菜型油菜遗传基础的拓宽。     

Genetic analysis of interspecific incompatibility in Brassica rapa

In interspecific pollination of Brassica rapa stigmas with Brassica oleracea pollen grains, pollen tubes cannot penetrate stigma tissues. This trait, called interspecific incompatibility, is similar to self-incompatibility in pollen tube behaviors of rejected pollen grains. Since some B. rapa lines have no interspecific incompatibility, genetic analysis of interspecific incompatibility was performed using two F₂ populations. Analysis with an F₂ population between an interspecific-incompatible line and a self-compatible cultivar ‘Yellow sarson’ having non-functional alleles of S-locus genes and MLPK, the stigmas of which are compatible with B. oleracea pollen grains, revealed no involvement of the S locus and MLPK in the difference of their interspecific incompatibility phenotypes. In QTL analysis of the strength of interspecific incompatibility, three peaks of LOD scores were found, but their LOD scores were as high as the threshold value, and the variance explained by each QTL was small. QTL analysis using another F₂ population derived from selected parents having the highest and lowest levels of interspecific incompatibility revealed five QTLs with high LOD scores, which did not correspond to those found in the former population. The QTL having the highest LOD score was found in linkage group A02. The effect of this QTL on interspecific incompatibility was confirmed by analyzing backcrossed progeny. Based on synteny of this QTL region with Arabidopsis thaliana chromosome 5, a possible candidate gene, which might be involved in interspecific incompatibility, is discussed.     

Genetical and Comparative Genomics of Brassica under Altered Ca Supply Identifies Arabidopsis Ca-Transporter Orthologs

Although Ca transport in plants is highly complex, the overexpression of vacuolar Ca²⁺ transporters in crops is a promising new technology to improve dietary Ca supplies through biofortification. Here, we sought to identify novel targets for increasing plant Ca accumulation using genetical and comparative genomics. Expression quantitative trait locus (eQTL) mapping to 1895 cis- and 8015 trans-loci were identified in shoots of an inbred mapping population of Brassica rapa (IMB211 × R500); 23 cis- and 948 trans-eQTLs responded specifically to altered Ca supply. eQTLs were screened for functional significance using a large database of shoot Ca concentration phenotypes of Arabidopsis thaliana. From 31 Arabidopsis gene identifiers tagged to robust shoot Ca concentration phenotypes, 21 mapped to 27 B. rapa eQTLs, including orthologs of the Ca²⁺ transporters At-CAX1 and At-ACA8. Two of three independent missense mutants of BraA.cax1a, isolated previously by targeting induced local lesions in genomes, have allele-specific shoot Ca concentration phenotypes compared with their segregating wild types. BraA.CAX1a is a promising target for altering the Ca composition of Brassica, consistent with prior knowledge from Arabidopsis. We conclude that multiple-environment eQTL analysis of complex crop genomes combined with comparative genomics is a powerful technique for novel gene identification/prioritization.     

芥菜型油菜和白菜型油菜种间杂种遗传分析

种间杂交是一种拓宽栽培作物遗传基础和转移优良性状的重要手段,已经广泛地用于作物品质的改良。本研究通过芥菜型油菜（Brassica juncea L.）和白菜型油菜（Brassica rapa L.）种间杂交,将芥菜型油菜的有利性状转移到白菜型油菜中,创造新型白菜型油菜,以改良白菜型油菜的农艺性状、提高抗逆性和拓宽其遗传基础。研究结果表明：以芥菜型油菜作母本、白菜型油菜作父本的杂交组合较易获得杂交种子,杂种F1植株营养生长具有较明显的杂种优势,但花粉完全不育;以白菜型油菜回交获得的BC1植株间表型差异明显,平均花粉可染率为34.8%,介于 0~84%之间,群体自交不亲和;BC1F1和BC2群体变异广泛,出现自交亲和植株和黄籽植株,平均花粉可染率分别为79.7%和79.1%。     

西藏白菜型油菜遗传多样性的RAPD分析

通过利用22个10bp随机引物对来自西藏高原地区107份白菜型油菜种质资源材料的PAPD分析,探讨了西藏白菜型油菜品种之间的遗传分化关系,结果表明：（1）供试的107份材料共产生236条谱带,其中210条谱带有多态性,占88．98％,说明白菜型油菜在西藏高原地区具有较丰富的遗传多样性;（2）根据引物扩增出的DNA指纹图谱,运用UPGMA分析法,在遗传距离为0．078处,可将供试的107份白菜型油菜划分为11个类群,发现来自于同一地区或气候相似区的品种往往聚在一起,表明西藏高原白菜型油菜品种的相似性与其原产地的地理,气候背景密切相关,并在此基础上,结合西藏高原农业发展历史,气候背景以及地形地貌特点和植物地理学,植物区系学,植物进化论等方面的综合分析,提出西藏高原是世界白菜型油菜起源地的观点。     

Genetic relationships within Brassica rapa as inferred from AFLP fingerprints

Amplified fragment length polymorphism (AFLP) markers were employed to assess the genetic diversity amongst two large collections of Brassica rapa accessions. Collection A consisted of 161 B. rapa accessions representing different morphotypes among the cultivated B. rapa, including traditional and modern cultivars and breeding materials from geographical locations from all over the world and two Brassica napus accessions. Collection B consisted of 96 accessions, representing mainly leafy vegetable types cultivated in China. On the basis of the AFLP data obtained, we constructed phenetic trees using mega 2.1 software. The level of polymorphism was very high, and it was evident that the amount of genetic variation present within the groups was often comparable to the variation between the different cultivar groups. Cluster analysis revealed groups, often with low bootstrap values, which coincided with cultivar groups. The most interesting information revealed by the phenetic trees was that different morphotypes are often more related to other morphotypes from the same region (East Asia vs. Europe) than to similar morphotypes from different regions, suggesting either an independent origin and or a long and separate domestication and breeding history in both regions.     

心脏发育的基因调控

心脏发育是一个复杂的过程.在脊椎动物和无脊椎动物果蝇中驱动早期心脏分化的基因具有惊人的相似性.以果蝇、斑马鱼、小鼠等作为模式动物,以心脏的发育过程为主线,探讨了心脏发育的基因调控的研究进展.     

Genetic diversity of allozymes in turnip (Brassica rapa L. var. rapa) from the Nordic area

Genetic diversity and relationships based on isozymes were studied in 31 accessions of turnip (Brassica rapa L. var. rapa). The material included varieties, elite stocks, landraces and older turnip of slash-and-burn type from the Nordic area. A total of 9 isozyme loci and 26 alleles were studied. The isozyme systems were ACO, DIA, GPI, GOT, PGM, PGD and SKD. The level of heterozygosity was reduced in the landraces, but it was high for the variety group 'Ostersundom'. Turnip has a higher genetic variation than other crops within B. rapa and than in other species with the same breeding system. The genetic diversity showed that 18.7% of the genetic variation was within the accessions, and the total H tau value was 0.358. Gpi-I and Pgd-I showed the lowest variation compared with the other loci. The cluster analysis revealed five clusters, with one main cluster including 25 of the 31 accessions. The dendrogram indicated that the variety group 'Ostersundom' clustered together whereas the variety group 'Bortfelder' was associated with country of origin. The landraces were spread in different clusters. The 'slash-and-burn' type of turnip belonged to two groups.     

An Improved Brassica rapa Genetic Linkage Map and Locus-specific Variations in a Doubled Haploid Population

In this study, we describe the construction of an improved Chinese cabbage genetic linkage map by integrating simple sequence repeats (SSRs) and insertion/deletion polymorphisms (InDels) into a previously published map of a doubled haploid (DH) population. The population was derived from a cross between the Chinese cabbage line BY (Brassica rapa ssp. pekinensis) and a European turnip line MM (Brassica rapa L. ssp. rapifera). A total of 629 markers were aligned to ten linkage groups, with a total map length of 1,173.8 cM, and an average distance between markers of 1.87 cm. Of the 126 SSRs and 133 InDels mapped, 46 and 34 were novel, respectively. A comparison of the linkage map with the B. rapa genome showed that more than 93 % of the markers, including 112 SSRs and 129 InDels, could be anchored unambiguously to a specific location on one of the ten chromosomes. In most cases, the order of markers on the linkage map and physical map was similar; however, the majority of linkage groups contained a number of markers whose positions were either transposed or had moved slightly forwards or backwards. During microspore culture, it was observed that 11 SSRs and one InDel showed either variation in size, or the appearance of new marker bands in the DH lines. As a first step to addressing this SSR/InDel marker instability, six SSR and one InDel loci were sequenced, which revealed that the size variation was due mainly to changes in repeat-motif number or to the insertion/deletion of new fragments of DNA.     

Anthocyanin biosynthetic genes in Brassica rapa

Background

Anthocyanins are a group of flavonoid compounds. As a group of important secondary metabolites, they perform several key biological functions in plants. Anthocyanins also play beneficial health roles as potentially protective factors against cancer and heart disease. To elucidate the anthocyanin biosynthetic pathway in Brassica rapa, we conducted comparative genomic analyses between Arabidopsis thaliana and B. rapa on a genome-wide level.

Results

In total, we identified 73 genes in B. rapa as orthologs of 41 anthocyanin biosynthetic genes in A. thaliana. In B. rapa, the anthocyanin biosynthetic genes (ABGs) have expanded and most genes exist in more than one copy. The anthocyanin biosynthetic structural genes have expanded through whole genome and tandem duplication in B. rapa. More structural genes located upstream of the anthocyanin biosynthetic pathway have been retained than downstream. More negative regulatory genes are retained in the anthocyanin biosynthesis regulatory system of B. rapa.

Conclusions

These results will promote an understanding of the genetic mechanism of anthocyanin biosynthesis, as well as help the improvement of the nutritional quality of B. rapa through the breeding of high anthocyanin content varieties.

Electronic supplementary material

The online version of this article (doi: 10.1186/1471-2164-15-426) contains supplementary material, which is available to authorized users.     

Destiny of a transgene escape from Brassica napus into Brassica rapa

Transgenic Brassica napus can be easily crossed with wild Brassica rapa. The spread of the transgene to wild species has aroused the general concern about its effect on ecological and agricultural systems. This paper was designated, by means of population genetics, to study the fate of a transgene escape from B. napus to B. rapa. Three models were proposed to survey the change in gene frequency during successive backcross processes by considering selection pressures against aneuploids, against herbicide-susceptible individuals, and by considering A-C intergenomic recombination and the effect of genetic drift. The transmission rate of an A-chromosome gene through an individual to the next generation was 50%, irrespective of the chromosome number; while that of a C-chromosome transgene varied from 8.7% to 39.9%, depending on the chromosome number of the individual used in the backcross. Without spraying herbicide, the frequency of an A-chromosome gene was 50% in the BC(1) generation, and decreased by 50% with the advance of each backcross generation; that of a C-chromosome gene was around 39.9% in BC(1), 7.7% in BC(2), 1.2% in BC(3) and 0.1% in the BC(4) generation. Under the selection pressure against herbicide-susceptible individuals, the frequency of a transgene reached a stable value of about 5.5% within six generations of successive backcrossings. The effect of genetic drift and intergenomic exchange on gene transmission rate was discussed. It is suggested that the transgene integrated on a C-chromosome (or better on a cytoplasm genome) is safer than that on an A-chromosome. The transgenic cultivars should be cultivated rotationally by year(s) with other non-transgenic varieties in order to reduce the transfer of the transgene to wild B. rapa species.     

Genetic variation and selection response in model breeding populations of Brassica rapa following a diversity bottleneck

Domestication and breeding share a common feature of population bottlenecks followed by significant genetic gain. To date, no crop models for investigating the evolution of genetic variance, selection response, and population diversity following bottlenecks have been developed. We developed a model artificial selection system in the laboratory using rapid-cycling Brassica rapa. Responses to 10 cycles of recurrent selection for cotyledon size were compared across a broad population founded with 200 individuals, three bottleneck populations initiated with two individuals each, and unselected controls. Additive genetic variance and heritability were significantly larger in the bottleneck populations prior to selection and this corresponded to a heightened response of bottleneck populations during the first three cycles. However, the overall response was ultimately greater and more sustained in the broad population. AFLP marker analyses revealed the pattern and extent of population subdivision were unaffected by a bottleneck even though the diversity retained in a selection population was significantly limited. Rapid gain in genetically more uniform bottlenecked populations, particularly in the short term, may offer an explanation for why domesticators and breeders have realized significant selection progress over relatively short time periods.     

芸薹属植物基因组学研究进展

芸薹属是十字花科植物300多个属中最为重要的一个属,是我国栽培面积最大的蔬菜作物。拟南芥和芸薹属在十字花科中两者的亲缘关系最近,通过它们之间的比较作图,两者之间的共线性被大量发现。模式植物拟南芥全基因组测序已经完成,这为芸薹属作物的基因组研究提供了便利条件。芸薹属作物的功能基因组学能够进一步明确不同发育时期基因的功能,为解释芸薹属的进化提供基因证据。就芸薹属植物在比较基因组学、功能基因组学最新进展,特别是芸薹属与模式植物拟南芥在基因组之间的相互关系进行了综述。     

白菜型油菜自交亲和性变异分析

对不同来源的85份白菜型油菜品种的自交亲和指数研究表明,白菜型油菜的自交亲和性存在较大幅度的变异,自交亲和指数在0．00～9．28之间,这种变异不仅存在于品种间,而且存在于品种内不同个体间。85份参试材料中,自交亲和指数小于1的有50个品种;35个品种自交亲和指数大于1,自交亲和指数在1．00～9．28之间,其中亲和指数大于4的材料有28、44、45、55x、75、119、123、139号品种等。依据自交亲和指数,可将参试材料分为4种类型:高自交亲和类型(自交亲和指数>4．00);自交亲和类型(自交亲和指数1．00～3．99);自交不亲和类型(0．00< 自交亲和指数<1．00);高自交不亲和类型(自交亲和指数=0．00)。自交亲和性因地区而异,一般西部地区的品种自交亲和性高于其它地区的品种。     

Glucosinolate biosynthetic genes in Brassica rapa

Glucosinolates (GS) are a group of amino acid-derived secondary metabolites found throughout the Cruciferae family. Glucosinolates and their degradation products play important roles in pathogen and insect interactions, as well as in human health. In order to elucidate the glucosinolate biosynthetic pathway in Brassica rapa, we conducted comparative genomic analyses of Arabidopsis thaliana and B. rapa on a genome-wide level. We identified 102 putative genes in B. rapa as the orthologs of 52 GS genes in A. thaliana. All but one gene was successfully mapped on 10 chromosomes. Most GS genes exist in more than one copy in B. rapa. A high co-linearity in the glucosinolate biosynthetic pathway between A. thaliana and B. rapa was also established. The homologous GS genes in B. rapa and A. thaliana share 59-91% nucleotide sequence identity and 93% of the GS genes exhibit synteny between B. rapa and A. thaliana. Moreover, the structure and arrangement of the B. rapa GS (BrGS) genes correspond with the known evolutionary divergence of B. rapa, and may help explain the profiles and accumulation of GS in B. rapa.     

芜菁SSR引物的开发及多态性分析

目的:用于芜菁的简单序列重复(SSR)标记数量有限,初步探索多态性较好SSR的结构特性,开发更多的SSR引物,有助于芜菁的研究。方法:开发680对新的SSR引物,以2个芜菁品种为模板进行多态性扩增,筛选出多态性较好的引物。结果:565(83.1%)对引物在2种芜菁之间能够有效扩增,有多态性的引物有141对(20.7%);SSR的长度与其多态性水平之间没有直接的线性关系,但SSR基序碱基数与重复次数和多态性水平之间存在一定的联系,即3碱基为基序、7次重复的SSR多态性较好。结论:SSR的类型与引物的多态性之间有一定的联系。     

芸薹属植物比较基因组学研究进展

芸薹属(Brassica)植物是双子叶植物比较基因组学研究的重点对象。经过十几年的研究, 芸薹属植物比较基因组学研究已取得很大进展。宏观共线性和微观共线性两个层次的研究均发现, 芸薹属植物之间以及芸薹属和拟南芥之间都存在广泛的共线性, 表明拟南芥信息在芸薹属中具有重要应用价值。芸薹属作物基因组内存在着多个拷贝的共线性区域, 支持二倍体芸薹属作物起源于多倍体祖先的假设。