反转录转座子标记及在作物遗传育种中的应用

反转录转座子通过RNA中间体进行反转录而转座,广泛分布于各种植物基因组中,拷贝数多,异质性高,在种内和种间表现出较高的序列差异性和丰富的插入多态性。针对这些特点,开发出了几种基于反转录转座子的分子标记,如SSAP、RIVPI、RAP、REMAP和RBIP等。由于反转录转座子标记能揭示出丰富的多态性,因而在遗传多样性和系谱研究、遗传连锁图谱构建及性状基因定位等方面得到了应用。随着分离技术的不断改进,获取序列信息更加容易,反转录转座子作为分子标记用于作物遗传育种将具有广阔前景。     

QTL复合区间作图中标记筛选的效率及其影响因素研究

高效地筛选标记 ,是复合区间作图方法定位QTLs的基础。筛选出的主效标记和互作标记 ,除了用作控制背景遗传效应外 ,在定位具有上位性效应的QTLs时 ,还将用于构筑两维搜索区间。因而 ,标记筛选的效率将直接影响QTL定位的功效和精度。通过对不同方法筛选标记的效率进行模拟研究 ,发现回归方法明显优于随机效应预测方法 ,同归方法中又以前向选择法简单有效。普通遗传力和基因型×环境互作遗传力的增加都能提高标记筛选效率 ,前者对主效应较大的QTLs影响明显 ,后者对主效应较小的QTLs作用较大。过多过密的标记会降低标记筛选效率 ,其中密度增加对标记筛选的负作用更为突出。为了缓解标记筛选效率制约QTL定位功效的缺陷 ,可以用多环境下筛选出的标记共同构建两维搜索区间     

Comparison of genetic and physical maps of group 7 chromosomes from Triticum aestivum L.

We present a high density physical map of homoeologous group 7 chromosomes from Triticum aestivum L. using a series of 54 deletion lines, 6 random amplified polymorphic DNA (RAPD) markers and 91 cDNA or genomic DNA clones from wheat, barley and oat. So far, 51 chromosome segments have been distinguished by molecular markers, and 54 homoeoloci have been allocated among chromosomes 7A, 7B and 7D. The linear order of molecular markers along the chromosomes is almost identical in the A- B- and D-genome of wheat. In addition, there is colinearity between the physical and genetic maps of chromosomes 7A, 7B and 7D from T. aestivum, indicating gene synteny among the Triticeae. However, comparison of the physical map of chromosome 7D from T. aestivum with the genetic map from Triticum tauschii some markers have been shown to be physically allocated with distortion in more distal chromosome regions. The integration of genetic and physical maps could assist in estimating the frequency and distribution of recombination in defined regions along the chromosome. Physical distance did not correlate with genetic distance. A dense map facilitates the detection of multiple rearrangements. We present the first evidence for an interstitial inversion either on chromosome arm 7AS or 7DS of Chinese Spring. Molecularly tagged chromosome regions (MTCRs) provide landmarks for long-range mapping of DNA fragments.     

偏分离分子标记的作图方法

对取自MAPMAKER软件小鼠F_2群体(含333个体)的5个RFLP连锁标记数据作了共显性分子标记偏分离的分析。先确定选择类型的方程组(配子或合子),随后采用Newton-Raphson迭代法估算标记间的重组值。在构建分子标记遗传图谱时,如果两个相邻标记均存在偏分离,最好采用纳入偏分离因子的估算方法。在估计F_2群体标记间偏分离重组距离上,用连续x~2检测方法比传统x~2检测更为准确。     

不同作图群体对显隐性分子标记位点的作图效率

根据位点组合和位点的有效性,发展了一种对使用３种不同的作用图群体作图显隐性分子标记的作图效率评价方法,应用该方法所评价的结果是,双单倍体（ＤＨ）群体的作图效率最高,自交群体（Ｆ２群体）与回交群体的作图效率相同,因此使用双单倍体群体作图不仅所用费用低,而且作图速度快,但只有在极少数植物中能获得双单倍体群体,对于那些不能获得双单倍体的动植物物种而言,可使用自交群体或回交群体作图。如果作高密度的分子标记     

Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers

Sweetpotato genomic research is minimal compared to most other major crops despite its worldwide importance as a food crop. The development of a genetic linkage map in sweetpotato will provide valuable information about the genomic organization of this important species that can be used by breeders to accelerate the introgression of desired traits into breeding lines. We developed a mapping population consisting of 240 individuals of a cross between ‘Tanzania’, a cream-fleshed African landrace, and ‘Beauregard’, an orange-fleshed US sweetpotato cultivar. The genetic linkage map of this population was constructed using Amplified Fragment Length Polymorphism (AFLP) markers. A total of 1944 (‘Tanzania’) and 1751 (‘Beauregard’) AFLP markers, of which 1511 and 1303 were single-dose markers respectively, were scored. Framework maps consisting of 86 and 90 linkage groups for ‘Tanzania’ and ‘Beauregard’ respectively, were developed using a combination of JoinMap 3.0 and MAPMAKER/EXP 3.0. A total of 947 single-dose markers were placed in the final framework linkage map for ‘Tanzania’. The linkage map size was estimated as 5792 cM, with an average distance between markers of 4.5 cM. A total of 726 single-dose markers were placed in the final framework map for ‘Beauregard’. The linkage map length was estimated as 5276 cM, with an average distance between markers of 4.8 cM. Duplex and triple-dose markers were used to identify the corresponding homologous groups in the maps. Our research supports the hypothesis that sweetpotato is an autopolyploid. Distorted segregation in some markers of different dosages in this study suggests that some preferential pairing occurs in sweetpotato. However, strict allopolyploid inheritance in sweetpotato can be ruled out due to the observed segregation ratios of the markers, and the proportion of simplex to multiple-dose markers. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. This paper is a portion of a dissertation submitted by Jim C. Cervantes-Flores.     

High-resolution mapping of loci conferring resistance to sugarcane mosaic virus in maize using RFLP, SSR, and AFLP markers

Sugarcane mosaic virus (SCMV) is one of the most important virus diseases of maize in Europe. Genetic analysis on backcross five (BC5) progeny derived from the cross FAP1360A (resistant) × F7 (susceptible) confirmed that at least two dominant genes, Scm1 and Scm2, are required for resistance to SCMV in the progeny of this cross. With the aid of RFLP and SSR marker analyses, Scm1 was mapped in the region of 8.7 cM – between the nucleolus organizer region (nor) and RFLP marker bnl6.29 on the short arm of chromosome 6, while Scm2 was mapped to an interval of 26.8 cM flanked by the RFLP markers umc92 and umc102 near the centromere region of chromosome 3. Both chromosome regions were further enriched for AFLP markers by successful application of a bulked segregant analysis to this oligogenic trait. A total of 23 linked AFLP markers were identified, clustered in chromosome regions adjacent to either Scm1 or Scm2. Seven AFLP markers linked to Scm1 resided within the nor-bnl6.29 interval, and one of them, E3M8-1, showed no recombination with Scm1. Three AFLP markers linked to Scm2 are located between umc92 and umc102. Received: 13 October 1998 / Accepted: 18 January 1999     

Physical mapping of RFLP markers on four chromosome arms in maize using terminal deficiencies

Terminal deficiencies (TDs) generated by the r-XI deletion system in maize were used to physically map RFLP markers on the short arm of chromosome 2 (2S) and the long arm of chromosome 6 (6L), chromosome 8 (8L), and chromosome 10 (10L). Five TDs on 2S, 8 on 6L, 10 on 8L, and 20 on 10L were isolated using the recessive morphological markers lg1, py1, j1(gl18), and sr2, respectively, for selection. Two exceptional TDs on 2S and 8L also have a second breakpoint on the long arm of chromosome 2 (2L) and 8L, respectively. The physical mapping of RFLP probes in relation to TD breakpoints was done by Southern hybridization. The five TDs on 2S divide chromosome 2 into four regions, all of which are distinguishable by RFLP markers. Likewise, three remaining chromosome arms are divided by TDs into RFLP-marked regions: 8 TDs divide 6L into five regions, 10 TDs divided 8L into seven regions, and 20 TDs divide 10L into three regions. The linear order of the physical map of 6L and 8L is consistent with that of the genetic maps, but that of 2L and 10L is not. Four groups of markers on 2S as well as 2L, and two on 10L are in reverse order in the physical map compared with the genetic maps. Other intriguing results are that breakpoints of TDs on 6L and 8L are distributed throughout the selected region, but most of those on 2L and 10L cluster in a region near the centromere; a single TD arose after fertilization. Received: 17 March 1997 / Accepted: 26 June 1997     

Model fitting and model testing in the method of joint mapping of quantitative trait loci

A previous paper proposed a new method of QTL mapping called joint mapping (JM). Some problems have been found in model fitting and model testing due to the neglect of the correlations among different observations of the dependent variable in this model. The present paper reports a method of solving the problems. The coefficient of correlation between two observations of the dependent variable is derived. A generalized least square (GLS) approach is developed for model fitting and a strategy and procedure of model testing based on a chi-square test is suggested. A simulated example is given. The example shows that the JM method is quite efficient in mapping multiple linked QTLs.     

Genetic Analysis and Fine Mapping of Two Genes for Grain Shape and Weight in Rice

To identity genetic loci controlling grain weight, an elite indica rice variety, Baodali, with large grains was Identified and used in this study. Its derived F2, F3 and BC2F2 with another japonica dee variety Zhonghua 11 were used as mapping populations. Unkage analyses demonstrated that two genes controlling grain weight, designated as GW3 and GW6, were mapped to chromosome 3 and chromosome 6, respectively. Fine mapping delimited GW3 to a 122 kb physical distance between two sequence tagged site markers (WGW16 and WGW19) containing 16 open reading frames annotated by The Institute for Ganomic Research (http://www.tigr.org). GW6 was further mapped between two simple sequence repeat markers (RM7179 and RM3187). These results are useful for both marker assisted selection of grain weight, and for further cloning of GW genes, which will contribute to the dissection of the molecular mechanism underlying grain weight in rice.     

Genetic Analysis and Fine Mapping of Two Genes for Grain Shape and Weight in Rice

To identify genetic loci controlling grain weight, an elite indica rice variety, Baodali, with large grains was identified and used in this study. Its derived F2, F3 and BC2 F2 with another japonica rice variety Zhonghua 11 were used as mapping populations. Linkage analyses demonstrated that two genes controlling grain weight, designated as GW3 and GW6, were mapped to chromosome 3 and chromosome 6, respectively. Fine mapping delimited GW3 to a 122 kb physical distance between two sequence tagged site markers （WGWt6 and WGW19） containing 16 open reading frames annotated by The Institute for Genomic Research （http：//www.tigr.org）. GW6 was further mapped between two simple sequence repeat markers （RM7179 and RM3187）. These results are useful for both marker assisted selection of grain weight, and for further cloning of GW genes, which will contribute to the dissection of the molecular mechanism underlying grain weight in rice.     

葡萄雄性不育基因的初步定位

为了对葡萄雄性不育基因进行定位研究,以可育葡萄‘魏可’(Vitis vinifera L.)为亲本构建的自交群体88株为试验材料,运用分离群体分组混合分析法(bulked segregant analysis,BSA),构建了可育株和不育株基因池,结合SSR技术对葡萄雄性不育基因进行定位研究和生物信息学分析。该研究筛选到2个与葡萄雄性不育基因连锁的SSR标记VVMD34和VVIB23,且位于该基因两侧,遗传距离分别为3.5cM和1.9cM。2个标记间物理距离为1 134kb,在该区域总共预测到了111个候选基因。该研究对葡萄雄性不育基因的精细定位及分子标记辅助育种奠定了良好的基础。     

分子标记在绿豆遗传连锁图谱构建和基因定位研究中的应用

绿豆(Vigna radiata(L.)Wilczek)作为一种医食两用作物,不仅是重要的食物资源,在改善土壤环境、提高农民收入等方面也发挥着重要作用。然而,相对于大宗作物而言,绿豆基础研究薄弱,基因组研究更是落后。近年来,分子标记技术迅速发展,在绿豆基因组学研究中发挥了重要的作用。国内外利用分子标记技术已构建了超过20张绿豆遗传连锁图谱。一些优良基因尤其是与抗性相关的基因被鉴定或精细定位,为绿豆分子标记辅助选择打下基础,加快了抗性新品种的培育进程。本研究通过对分子标记技术在绿豆遗传连锁图谱构建、重要功能基因的定位等方面的应用进行综述,以期为绿豆遗传育种研究及功能基因组学分析提供参考。     

利用商品猪群定位猪耳型QTL

由 19头杂种公猪 [皮特兰× (皮特兰×汉普夏 ) ]、5 2头杂种母猪 [Leicoma× (大约克×长白 ) ]及其 332头后代组成的商品群作为参考家系 ,选择 172个微卫星标记和 3个 1类标记 (RYR1、PRKAG3、PIT1)对参考家系的个体进行遗传标记分型 ,构建了猪的整个基因组微卫星连锁图谱。按照线性评分的方法 (竖耳 :1分 ;垂耳 :- 1分 ;半垂耳 :0分 )测定猪的耳型表型值。耳型测定值的平均值为 0 .2 3,标准差为 0 .82。应用最小二乘回归方法对耳型的QTL进行定位 ,结果仅在 6号染色体的末端 (Sw1881和Sw32 2 )之间以 1%基因组显著性水平检测出 1个耳型基因位点 ,而在其他染色体上即使 10 %染色体显著性水平上也没有发现QTL。     

Rapid isolation of CA microsatellites from the tilapia genome

We have developed (CA)n microsatellite markers for the cichlid fish, Oreochromis niloticus using a variation of the hybrid capture method. The resulting genomic library was highly enriched in repetitive DNA with 96% of clones containing CA repeats. The number of repeats ranged from four to 45 with an average of 19. Two-thirds of the sequenced clones had 12 or more repeats and sufficient flanking sequence to design primers. The resulting markers were tested in an F2 cross of O. niloticus x O. aureus. Nearly 90% of the markers amplified in this cross and 74% of these were informative. This work demonstrates the importance of minimizing the number of polymerase chain reaction (PCR) amplification cycles before and after the enrichment steps to reduce PCR recombination and the generation of chimaeric clones.     

A simple and rapid method for calculating identity-by-descent matrices using multiple markers

A fast, partly recursive deterministic method for calculating Identity-by-Descent (IBD) probabilities was developed with the objective of using IBD in Quantitative Trait Locus (QTL) mapping. The method combined a recursive method for a single marker locus with a method to estimate IBD between sibs using multiple markers. Simulated data was used to compare the deterministic method developed in the present paper with a stochastic method (LOKI) for precision in estimating IBD probabilities and performance in the task of QTL detection with the variance component approach. This comparison was made in a variety of situations by varying family size and degree of polymorphism among marker loci. The following were observed for the deterministic method relative to MCMC: (i) it was an order of magnitude faster; (ii) its estimates of IBD probabilities were found to agree closely, even though it does not extract information when haplotypes are not known with certainty; (iii) the shape of the profile for the QTL test statistic as a function of location was similar, although the magnitude of the test statistic was slightly smaller; and (iv) the estimates of QTL variance was similar. It was concluded that the method proposed provided a rapid means of calculating the IBD matrix with only a small loss in precision, making it an attractive alternative to the use of stochastic MCMC methods. Furthermore, developments in marker technology providing denser maps would enhance the relative advantage of this method.     

棉花'晋 A'细胞质雄性不育恢复基因定位

用晋A衍生不育系与恢复系组配的分离群体进行遗传与定位分析,晋A恢复基因在F2和BC1的分离比例分别符合3∶1和1∶1,证明恢复基因由1对显性基因控制.用9个SSR标记和4个STS标记构建长度为82.1 cM的连锁群,恢复基因Rf定位在第19染色体(D08),与最近的标记CM042和CIR179分别相距5.4 cM和10.3 cM.以晋A衍生的7个不育系、4个保持系和10个恢复系对标记进行验证,分别扩增出同样的特异带型,说明与晋A恢复基因紧密连锁的标记可以直接用于晋A恢复系的分子标记辅助选择.     

一个新的水稻白化转绿突变体的生理特性和基因定位

秋丰M来源于粳稻秋丰的自然白化转绿突变株。其主要特征为前三叶白化带绿,第四叶及以后叶片均为淡绿色,抽穗时,秋丰M的颖壳和前三叶一样仍出现带绿的白化现象。不同生长时期对野生型和突变型水稻叶片色素含量测定的结果与田间观察结果一致,秋丰M确实存在着一个叶色显著变化的过程。主要农艺性状的比较结果表明,秋丰与秋丰M除穗颈长和千粒重达到极显著差异外,其他农艺性状均无明显差异。遗传分析发现该突变性状受一对隐性核基因控制。以209株培矮64S×秋丰M F_2的隐性突变个体为定位群体,将突变基因定位在水稻第2染色体长臂上,位于 SSR 标记RM475和RM2-22之间,其遗传距离分别为17.3 cM和2.9 cM,并将该基因命名为gra_(t)。     

水稻野生种质优异基因分子标记定位和利用的研究进展

野生稻由于长期处于野生状态,经受了各种灾害和不良环境的自然选择,抗逆性较强,是天然的基因库,保存着栽培稻不具有或已经消失了的特异基因。挖掘野生稻特异基因的研究日益受到重视。本文总结了近3年来在野生稻特异性状基因定位、克隆和育种利用方面的研究进展。 Abstract:Wild rice has adapted to weather and unfavorable environments under natural selection.It has been well recognized as a natural gene bank that conserves a lot of specific genes presently not available for extinct in the cultivated rice.There is an urgent need to explore these specific genes.The present paper summarized current researches in molecular mapping and cloning of useful genes from wild rice,and their potential application in breeding.     

Rice molecular genetic map using RFLPs and its applications

In the past decade, notable progress has been made in rice molecular genetic mapping using genomic or cDNA clones. A total of over 3000 DNA markers, mainly with RFLPs, have been mapped on the rice genome. In addition, many studies related to tagging of genes of interest, gene isolation by map-based cloning and comparative mapping between cereal genomes have advanced along with the development of a high-density molecular genetic map. Thus rice is considered a pivotal plant among cereal crops and, in addition to Arabidopsis, is a model plant in genome analysis. In this article, the current status of the construction of rice molecular genetic maps and their applications are reviewed.