水稻DH群体的分子连锁图谱及基因组分析

利用扩大的籼粳杂交来源（窄叶青８号×京系１７）的水稻（ＯｒｙｚａｓａｔｉｖａＬ．）加倍单倍体（ＤＨ）群体,构建了包含４４４个位点的分子连锁图谱,覆盖水稻基因组１９６２ｃＭ（ｃｅｎｔｉＭｏｒｇｏｎ）,标记间的平均图距小于５ｃＭ。此图谱包括２７６个ＲＦＬＰ标记、３４个ＲＡＰＤ标记、８９个微卫星标记、１０个ＡＦＬＰ标记、２６个端粒重复相关序列（ＴＡＳ）标记以及９个同工酶标记。该遗传图谱与其它的水稻高密度遗传图谱具有较高的可比性,并有自己的特点,适于进行各种持续性的遗传学研究     

水稻双单倍体群体的分子标记图示基因型分析

利用窄叶青８号（籼稻）／京系１７（粳稻）花培产生的双单倍体群体建立了一个包含１６０个分子标记的遗传连锁图,在此基础上利用ＨＹＰＥＲＧＥＮＥ软件建立了５２个ＤＨ系的图示基因型,并对ＤＨ系的亲本基因组比率和染色体的交换重组频率进行了比较分析。结果表明本实验所用的ＤＨ群体没有显著偏离正态分布,籼粳稻杂交后代中植株的籼粳表现与同工酶、形态指数和基因组比率的分析结果一致,此外还发现ＤＨ群体中出现了大量的交换罕见染色体。利用图示基因型分析发现株高和分子标记ＲＺ９７８和ＲＧ４Ａ相关,生育期和ＲＲＫ０８－１、ＲＧ４７７和ＲＧ５１１相关。本文还就图示基因型分析技术在ＤＨ群体的遗传分析和选择育种中的应用进行了讨论．     

Construction of Rice RAPD Molecular Linkage Map

A rice (Oryza sativa L. ) molecular linkage map has been constructed form over 52 random amplified polymorphic DNA (RAPD) markers with the double haploid (DH) population. It covered a total genetic distance of over 898.4 cM (centimorgan) with 17.3 cM between markers and was complemental with RFLP linkage map.     

利用两个测序水稻品种构建微卫星连锁图谱

利用已完成基因组测序的两个水稻品种日本晴和931l的数据库成功开发出水稻微卫星新标记,并利用由90个单株组成的日本晴×9311 F2作图群体,构建了一张包含152个SSR标记位点、覆盖基因组总长度2 455.7 cM的连锁图谱,有46个SSR新标记为自主开发,该图谱标记间的平均遗传距离为16.16 cM;并将未能在Temnykh等人(2001)构建的图谱上定位的微卫星标记RM345和RM494定位在第6染色体上.通过与Temnykh等人(2001)和兰涛等人(2003)所构建的图谱从作图群体的类型和大小、标记的类型和数量、标记在染色体上的线性排列顺序等几个方面进行比较,所绘制的图谱其标记在染色体线性排列上与Temnykh等人绘制的图谱具有很高的一致性,达93.81%.     

利用双单倍体群体剖析水稻产量及其相关性状的遗传基础

主效QTL、上位性效应和它们与环境的互作(QE)都是数量性状的重要遗传因素。利用籼粳交珍汕97／武育粳2号F1植株上的花药进行组织培养得到的190个双单倍体群体和179个微卫星标记,通过两年两重复田间试验,采用混合线性模型方法分析了9个控制水稻产量及其相关性状的遗传效应,得到57个主效QTL,41对上位性互作,8对QTL与环境的互作和7对上位性效应与环境的互作。单个主效QTL解释这些性状1．3％～25．8％的表型方差。各性状QTL的累积表型贡献率达11．5％～66．8％。大多数性状之间具有显著的表型相关性,相关性较高的性状之间常具有较多共同或紧密连锁的QTL。结果表明,基因的多效性或紧密连锁可能是性状相关的重要遗传基础。     

大豆遗传图谱的构建和分析

利用大豆栽培品种科丰1号和南农1138－2杂交得到的重组近交系NJRIKY,通过RFLP,SSR,RAPD和AFLP4种分子标记的遗传连锁分析,构建了包含24个连锁群,由792个遗传标记组成的大豆较高密度连锁图谱,该图谱覆盖2320．7cM,平均图距2．9cM,SSR标记的多态性较高,在基因组中的位置相对稳定,可以作为锚定标记,有利于连锁群的归并和不同图谱的比较整合;而AFLP标记对于增加图谱密度效率较高,但其容易出现聚集现象,从而造成连锁群上有很大的空隙（gap),另外,在连锁群中有21．7％的分子标记出现偏分离,该图谱为基因定位,比较基因组学和重要农艺性状的QTL定位等研究打下了基础。     

粳稻SRAP分子标记遗传群的构建与分析

用超级稻品种‘沈农606’和普通粳稻‘丽江新团黑谷’为亲本杂交获得的102份F_2代单株,通过SRAP分子标记遗传分析,构建了包含14个连锁群,由129个多态性位点组成的水稻连锁图谱,此图谱覆盖基因组长度1671.5 cM,平均图距13.0 cM。连锁群上有17.2%的多态性位点表现偏分离,偏分离标记在连锁群上存在热点区域。     

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.     

用双单倍体群体构建水稻的分子连锁图

本研究以窄叶青８号（籼稻）×京系１７（粳稻）的Ｆ１花培株系──ＤＨ群体为基础建立了１个水稻的ＲＦＬＰ连锁框架图,该图含ＲＦＬＰ标记、同功酶标记等共１０８个位点,标记间的平均间距为８．６ｃＭ。该图谱与已发表的用其他群体构建的图谱有很高的可比性。利用该框架图定位了２个未知位点的同功酶标记基因和１个籼稻亲本的抗稻瘟病基因。研究表明,目前的群体可进一步扩大成为一个永久性的作图群体,并应用于水稻基因定位和基因组研究     

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 。     

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.     

水稻籼粳交DH群体苗期耐冷性基因的分子标记定位

水稻苗期低温冷害导致的烂秧现象是水稻生产中重要的限制因素之一。以一个水稻籼粳交(圭630／02428)DH群体为材料,在幼苗3叶1心时用10℃低温处理3d,随后恢复培养,以恢复培养5d后的秧苗成活率(％)为指标,鉴定该DH群体的苗期耐冷性。利用已构建的RFLP连锁图谱和基于混合线性模型的定位软件QTLMapper1.0对水稻苗期耐冷性进行QTL分析,检测到控制水稻苗期耐冷性的3个QTLs,分别位于第3、11、12染色体上,贡献率分别为7．9％、18．3％和24.4％,其增效等位基因均来自于亲本“02428”。同时检测到控制水稻苗期耐冷性的上位性互作位点8个,分散分布于第2、7、8、9、11染色体上,其中有2对互作的贡献率在15％左右,这2对互作的增效基因型均为来自2个亲本的重组基因型。苗期耐冷性在2个亲本间差异很大,在DH群体中呈现出连续变异,有明显的超亲分离。这些结果表明,水稻苗期耐冷性是受多基因控制的数量性状,基因的上位性互作是其重要的遗传基础之一。     

水稻粒簇生材料Cgr320的鉴定及遗传偏分离分析

籽粒簇生稻Cgr320为一类水稻突变材料,其性状表现为2~3朵颖花(籽粒)簇生在水稻主穗轴或枝梗顶部。为了进一步明确其簇生性状的遗传机制,本研究用Cgr320作父本分别与武运粳24和93-11配制了2个杂交组合,获得杂种F1、F2分离群体,对亲本、F1和F2群体的簇生性状进行了形态学观察和遗传连锁分析。结果表明,Cgr320其他农艺性状与普通栽培稻差异不显著。簇生性状在F1植株表现为野生型,在F2群体中出现严重偏离孟德尔(3∶1)遗传分离,卡方测验值X2(3∶1)为7.71和144.87。随机选取第1、2、3、4、5、6、7、8、9、10、11和12染色体上RM493、RM3762、RM1338、RM3217、RM249、RM20155、RM3325、RM22418、RM6797、RM1146、RM7557和RM27706等12对微卫星标记对武运粳24/Cgr320 22个F2隐性(簇生)单株进行遗传连锁分析,发现12个标记所扩增的22个F2隐性单株基因型都极显著偏向武运粳24,卡方检验值X2(1∶2∶1)大于X2(0.05,2)临界值5.991,控制cgr320簇生性状基因存在严重偏分离遗传,这种遗传现象必将误导我们判定控制籽粒簇生基因所在的连锁群。本研究结果将为水稻基因定位研究提供参考信息。     

Construction of a Microsatellite Linkage Map with Two Sequenced Rice Varieties

Based on the successful development of new microsatellite markers from the data of two whole-sequenced rice varieties, japonica variety Nipponbare and indica variety 9311, an F₂ population of 90 lines, which was derived from a single cross between Nipponbare and 9311, was applied to construct a genetic linkage framework map. The map covered 2 455.7 cM of total genomic length, and consisted of 152 simple sequence repeats (SSRs) loci including 46 pairs of new SSR primers developed by our research institute. The average genetic distance between two markers was 16.16 cM. In addition, markers RM345 and RM494, which have not been mapped on the Temnykh's map et al. (2001) were anchored on the sixth chromosome of this map. We compared this research with maps of Temnykh et al.(2001) and LAN et al. (2003) regarding the aspects of type and size of population, type and quantity of markers, and the marker arrangement order on chromosome, etc. Results indicated that the similarity of marker linear alignment was 93.81% between this map and T-map, Finally, the important significance of using sequenced rice varieties to construct linkage map was also discussed.     

玉米F2群体分子标记偏分离的遗传分析

以优良玉米杂交组合 (综 3× 87 1)的F2 群体为材料 ,构建了包含 15 0个SSR标记和 2 4个RFLP标记的玉米分子标记连锁图。通过对 174个分子标记的分析 ,发现有 4 9个分子标记表现偏分离 (P <0 0 5 ) ,占总标记数的2 8 2 %。这些偏分离标记有 11个偏向父本综 3,占 2 2 5 % ;12个偏向母本 87 1,占 2 4 5 % ;2 5个偏向杂合体 ,占5 1 0 %。还有 1个标记同时偏向双亲。同时在 9条不同的染色体上发现 14个偏分离的热点区域 ,其中 4个与已经定位的配子体基因的位置相近 ,由此表明配子体基因是导致偏分离的部分原因。所发现的SDR6 1和SDR7 2似乎是两个新的偏分离热点区域。进一步讨论了引起偏分离的原因 ,以及偏分离标记对QTL定位的影响。对于单位点的QTL分析而言 ,偏分离标记一般不会影响QTL定位的位置和效应 ;对于两位点的上位性分析而言 ,则要求较少的偏分离标记和较大的群体     

RAPD标记构建家蚕分子连锁图

以大造、Ｃ１０８及其Ｆ２群体构建了１个家蚕的ＲＡＰＤ连锁框架图,该图含ＲＡＰＤ标记位点１８２个,来自大造的１０３个标记分属前２３个连锁群,来自Ｃ１０８的７９个标记分属后１６个连锁群,覆盖基因组的总长度为１１４８．３ｃＭ（ｃｅｎｔｉｍｏｒｇａｎ）,它能与本室用同一群体构建的ＳＡＤＦ图谱相整合,亦可与相应的ＲＦＬＰ图谱相互补充。     

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.     

RAPD和SSR两种标记构建的中国对虾遗传连锁图谱

利用RAPD和SSR分子标记结合拟测交策略,对中国对虾(Fenneropenaeuschinensis)“黄海1号”雌虾与野生雄虾作为亲本进行单对杂交产生的F1代,采用RAPD和SSR两种分子标记技术初步构建了中国对虾雌、雄遗传连锁图谱。对460个RAPD引物和44对SSR引物进行筛选,共选出61个RAPD引物和20对SSR引物,用于对父母本和82个F1个体进行遗传分析。共得到母本分离标记146个(RAPD标记128个,微卫星标记18个)和父本分离标记127个(RAPD标记109个,微卫星标记18个)。雌性图谱包括8个连锁群、9个三联体和14个连锁对,标记间平均间隔为11·28cM,图谱共覆盖1173cM,覆盖率为59·36%;雄性图谱包括10个连锁群、12个三联体和7个连锁对,标记间平均间隔为12·05cM,图谱共覆盖1144·6cM,覆盖率为62·01%。中国对虾遗传图谱的构建为其分子标记辅助育种、比较基因组作图及数量性状位点的定位与克隆奠定了基础。     

Localization of the rice stripe disease resistance gene, Stv-bi, by graphical genotyping and linkage analyses with molecular markers

 We used graphical genotyping and linkage analyses with molecular markers to determine the chromosomal location of the rice stripe disease resistance gene, Stv-b ⁱ . The stripe resistance gene from the indica rice (Oryza sativa) cv ‘Modan’ was introgressed into several Japanese rice varieties. We found 4 RFLP markers in ‘Modan’, five susceptible parental rice varieties (‘Norin No. 8’, ‘Sachihikari’, ‘Kanto No. 98’, ‘Hokuriku No.103’ and ‘Koganebare’) and four resistant progeny varieties (‘St. No. 1’, ‘Aichi No. 6’, ‘Aoisora’ and ‘Asanohikari’). Graphical genotyping of the resistant progeny revealed a chromosomal segment ascribable to ‘Modan’ and associated with stripe resistance. The chromosomal segment from ‘Modan’ was located at 35.85 cM on chromosome 11. Linkage analysis using 120 F₂ individuals from a cross between ‘Koshihikari’ (susceptible) and ‘Asanohikari’ (resistant) revealed another 8 RFLP markers in the same chromosome. We performed a bioassay for rice stripe resistance in F₃ lines of the F₂ individuals using infective small brown planthoppers and identified an 1.8-cM segment harboring the rice stripe disease resistance gene, Stv-b ⁱ , between XNpb220 and XNpb257/ XNpb254. Furthermore, Stv-b ⁱ was linked by 0.0 cM to a RFLP marker, ST10, which was developed on the basis of the results of RAPD analysis. These DNA markers near the Stv-b ⁱ locus may be useful in marker-assisted selection and map-based cloning of the Stv-b ⁱ gene. Received: 26 September 1997 / Accepted: 4 November 1997     

用微卫星标记构建两系稻培矮64s/E32的分子遗传连锁图 Construction of a Microsatellite Linkage Map in a DH Population

用两系杂交稻强优组合培矮64s/E32的一个加倍单倍体（DH）群体,共86个株系,构建了水稻的SSR标记遗传连锁图。选用美国康耐尔大学公布的302对SSR引物,共有127对在两个亲本间检测到多态性,比率为4205%。建成的水稻染色体的图谱（记为PEMAP）共包含122个SSLP标记座位,总长度为1213.4 cM。PEMAP与Temnykh等发表的图谱（记为CUMAP）具有很高的可比性,绝大多数标记都被定位于相同的染色体上,且排列顺序一致。该DH群体的偏分离情况较严重,122个标记座位中有34个发生显著偏分离,比例达27.8%。值得注意的是,在第1、3、10、11染色体上的标记全部偏向培矮64s,第4、6、7、8、9染色体上的标记则全部偏向E32。 Abstract:A doubled haploid population (DH) consisting of 86 lines derived by anther culture of Peiai64s/E32,a two-line hybrid rice variety with high heterosis,was used to construct a microsatellite or SSLP linkage map of rice chromosomes.A total of 302 PCR primers for SSLP analysis on these chromosomes were chosen from a map published by Cornell University (designated CUMAP) and 127 (42.05%) of them were found polymorphic between the two parents.Those polymorphic PCR primers were used for population genotyping.The map (designated PEMAP) comprises 122 microsatellite maker loci,covering a total length of 1213.4 cM.The PEMAP is highly comparable with the CUMAP.Most of the markers were mapped onto the same chromosomes and aligned in the same order.Serious segregation distortion was observed in this DH population,with 34 (27.8%) markers showing significant deviation.It is noted that all markers on chromosomes 1,3,10 and 11 were biased to Peiai64s,while those on chromosomes 4,6,7,8 and 9 were opposite.