Genetic linkage map construction for white jute (Corchorus capsularis L.) using SRAP,ISSR and RAPD markers

White jute (Corchorus capsularis) and dark jute (Corchorus olitorius) are two important cultivated crops that are used for natural fibre production. Some genetic maps have been developed for dark jute, but the genetic map information for white jute (C. capsularis) is limited. In this study, a linkage map comprising 44 sequence‐related amplified polymorphisms (SRAPs), 57 intersimple sequence repeats (ISSRs) and 18 randomly amplified polymorphic DNA (RAPD) covering 2185.7 cM with a mean density of 18.7 cM per locus was constructed in an F₂ population consisting of 185 individuals derived from a cross between two diverse genotypes of ‘Xinxuan No. 1’ and ‘Qiongyueqing’ in white jute. These markers were evenly distributed in the linkage groups without any clustering. This genetic linkage map construction will facilitate the mapping of agronomic traits and marker‐assisted selection breeding in white jute.     

Molecular Diversity and Association Analysis of Drought and Salt Tolerance in Gossypium hirsutum L. Germplasm

Association mapping is a useful tool for the detection of genes selected during plant domestication based on their linkage disequilibrium (LD). This study was carried out to estimate genetic diversity, population structure and the extent of LD to develop an association framework in order to identify genetic variations associated with drought and salt tolerance traits. 106 microsatellite marker primer pairs were used in 323 Gossypium hirsutum germplasms which were grown in the drought shed and salt pond for evaluation. Polymorphism (PIC=0.53) was found, and three groups were detected (K=3) with the second likelihood ΔK using STRUCTURE software. LD decay rates were estimated to be 13-15 cM at r2 0.20. Significant associations between polymorphic markers and drought and salt tolerance traits were observed using the general linear model (GLM) and mixed linear model (MLM) (P 0.01). The results also demonstrated that association mapping within the population structure as well as stratification existing in cotton germplasm resources could complement and enhance quantitative trait loci (QTLs) information for marker-assisted selection.     

黄瓜重要性状相关分子标记研究进展

综述了不同分子标记技术在黄瓜重要病害（白粉病、霜霉病、枯萎病、黑星病、炭疽病、病毒病）、果实品质（苦味、果瘤、果色、果实光泽及果实形状）、生殖发育（性别分化和单性结实）及营养生长（叶色、植株高度及侧枝）等重要性状中的研究进展,旨在为今后黄瓜育种提供理论依据和基础。最后,讨论了目前黄瓜分子标记技术在黄瓜育种研究中相对薄弱的原因,并对今后黄瓜育种前景进行了展望。     

Kazusa Marker DataBase: a database for genomics,genetics, and molecular breeding in plants

In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.     

Comparative genomics of Brassicaceae crops

The family Brassicaceae is one of the major groups of the plant kingdom and comprises diverse species of great economic, agronomic and scientific importance, including the model plant Arabidopsis. The sequencing of the Arabidopsis genome has revolutionized our knowledge in the field of plant biology and provides a foundation in genomics and comparative biology. Genomic resources have been utilized in Brassica for diversity analyses, construction of genetic maps and identification of agronomic traits. In Brassicaceae, comparative sequence analysis across the species has been utilized to understand genome structure, evolution and the detection of conserved genomic segments. In this review, we focus on the progress made in genetic resource development, genome sequencing and comparative mapping in Brassica and related species. The utilization of genomic resources and next-generation sequencing approaches in improvement of Brassica crops is also discussed.     

Rapid genotyping with DNA micro-arrays for high-density linkage mapping and QTL mapping in common buckwheat (Fagopyrum esculentum Moench)

For genetic studies and genomics-assisted breeding, particularly of minor crops, a genotyping system that does not require a priori genomic information is preferable. Here, we demonstrated the potential of a novel array-based genotyping system for the rapid construction of high-density linkage map and quantitative trait loci (QTL) mapping. By using the system, we successfully constructed an accurate, high-density linkage map for common buckwheat (Fagopyrum esculentum Moench); the map was composed of 756 loci and included 8,884 markers. The number of linkage groups converged to eight, which is the basic number of chromosomes in common buckwheat. The sizes of the linkage groups of the P1 and P2 maps were 773.8 and 800.4 cM, respectively. The average interval between adjacent loci was 2.13 cM. The linkage map constructed here will be useful for the analysis of other common buckwheat populations. We also performed QTL mapping for main stem length and detected four QTL. It took 37 days to process 178 samples from DNA extraction to genotyping, indicating the system enables genotyping of genome-wide markers for a few hundred buckwheat plants before the plants mature. The novel system will be useful for genomics-assisted breeding in minor crops without a priori genomic information.     

水产动物遗传图谱的构建和 QTL 定位研究进展

改革开放三十年来,我国水产养殖业取得了举世瞩目的成就,产量约占世界水产养殖总产量的70％,养殖对象也由四大家鱼不断向各名特优鱼扩展。但由于我国水产养殖行业与国外相比发展较晚,基础研究较为薄弱,加之育种过程中缺乏科学的规范和标准,苗种总体质量不高,种质资源退化较为严重,出现生长速度慢、抗病力低、成活率低等现象。在如今养殖环境每况愈下和高密度养殖的条件下,很容易爆发大规模死亡。因此,水产动物的良种选育成为了制约我国渔业经济进一步发展的瓶颈。为了解决这个棘手的问题,我国遗传学家对良种选育工作开展了广泛而深入的研究。早期的选育工作将主要精力集中于遗传参数的估计以制定相应的选择策略［1‐2］,尽管在育种实践过程中取得了不少的成就,但亦有其缺陷：（1）从本质上讲是将控制数量性状的多微效基因作为一个整体来研究,因此终究只能是一种数率统计和概率推断,无法将控制性状的基因分离出来,更无法从基因水平上阐明性状差异产生的原因;（2）由于基因型到表型的过程中伴有遗传信息的改变,所以通过表型值进行选育往往不能达到很好的效果,甚至可能出现很大的偏差。因此,QTL 定位应运而生,它的理论基础也是将数量性状看成是多个微效基因共同作用的结果,所不同的是,它可以通过高密度遗传图谱的构建和连锁概率分析,将影响性状的各主效基因分离开来并定位于某一区间,进一步精细定位后,通过图位克隆或候选基因等方法实现目的基因的分离克隆,这就从分子水平上解决了数量性状的遗传本质问题,并且完成了从结构基因组研究向功能基因组研究的过渡。除此之外,对 QTL 的选择是直接对基因型的选择,排除了环境因素对选择所造成的影响,精确度大大提高,并可以对个体进行早期选择,使育种周期大大缩短。由于遗传图谱构建和QTL定位对于基因组研究及育种实践的重要性,国内外科研人员对许多水产动物都开展了相关研究［3‐33］。当然,Q T L的成功定位必须依赖于高质量、高饱和度的的遗传图谱。至目前为止,有近20种海淡水养殖动物公布了遗传连锁图谱,虹鳟（On‐corhynchus mykiss ）、罗非鱼（ Tilapia）、大西洋鲑（Salmo salar）等都建立了中高密度的遗传图谱,为其基因组研究和育种工作打下了坚实的基础。     

辣椒种内遗传图谱的构建及主要农艺性状的QTL分析

以一年生辣椒（Capsicum annuum L.）‘Perennial’、‘83-58’为亲本构建的包含128个株系的F6代重组自交系为作图群体,构建了一个包含有18个连锁群的遗传图谱。该遗传图谱共有131个标记,其中SSR标记105个,CAPS标记23个,SCAR标记1个,果实辣味（pun）和果柄着生方向（up）2个形态标记。该图谱全长633.71 cM,标记间的平均距离为4.8 cM,连锁群的长度为7.07 ~ 75.16 cM,平均长度为35.21 cM,每个连锁群上的标记数为3 ~ 17个。对群体进行10个主要农艺性状调查,利用基于完备区间作图方法（Inclusive Composite Interval Mapping）的QTL IciMapping V3.2软件（http：//www. isbreeding. net/）选择加性效应模型ICIM-ADD进行QTL定位,在重组自交系（RIL）群体中共检测到株高、伸展度、始花节位、叶长、叶宽、侧枝长度、果形、果形指数、心室数和果实横径等10个性状的20个QTL位点。     

Refined mapping of quantitative trait loci for somatic cell score on BTA02 in the German Holstein

The aim of this study was to more precisely map a previously reported quantitative trait locus (QTL) affecting somatic cell score on Bos taurus autosome 2 by increasing the number of markers fourfold, analysing more families and exploiting within‐population linkage disequilibrium (LD). A granddaughter design of 10 German Holstein grandsire families with 1121 progeny tested sons was used. Twenty‐six markers with an average marker spacing of 3.14 cM were genotyped along 81.6 cM. Linkage analysis (LA) was performed using variance‐component methodology. The incorporation of LD was first done using variance‐component methods followed by regression on marker alleles. LA revealed genome‐wide significance (LOD > 3) at 15 contiguous marker‐intervals, with the maximum test‐statistic between DIK2862 and BMS778 and a 1‐lod drop‐off interval of 38 cM. While the variance‐component methods could not detect any LD, two individual markers with a significant effect (ILSTS098, p < 0.05; BMS778, p < 0.01) were found by regression analysis. Compared with previous results QTL‐localisation was substantially narrowed; further fine‐mapping should focus on the close vicinity of BMS778.     

大豆重组自交系群体NJRIKY遗传图谱的加密及其应用效果

作物基因组研究,包括基因或数量性状位点(QTL)定位、图位克隆以及物理图谱构建等,首先必须建立具有丰富标记信息的高密度遗传连锁图谱。由科丰1号和南农1138-2杂交组合衍生的重组自交系群体NJRIKY已经构建了4张大豆遗传连锁图谱,但由于遗传信息和标记数目不够充分,在基因和QTL作图时仍然存在精确度和准确度问题。为增加NJRIKY图谱密度,本研究在967对SSR引物中获得了401个多态性SSR标记。结合其他分子数据,使用作图软件Mapmaker/Exp3.0b,获得一张含有553个遗传标记,25个连锁群,总长2071.6cM,平均图距3.70cM的新遗传连锁图谱,其中SSR标记316个,RFLP标记197个,EST标记39个,形态标记1个。连锁群上大于20cM的标记间隔由原来42个减少到2个。原图谱的3个SMV抗性基因定位于D1b连锁群末端的开放区间上且仅与一个RFLP标记连锁,利用加密图谱对Rsc-3、Rsc-7、Rsc-9、Rsc-13、Rsa、Rn1和Rn3等7个SMV抗性基因重定位,全部位于D1b连锁群,与相邻分子标记距离均小于6cM,其中Rsc-9、Rn1、Rsa的距离小于1cM,Rsc-13与EST标记GMKF168a共分离。对本群体农艺性状进行QTL重定位,获得8个性状相关的42个主效QTL,其中20个QTL遗传贡献率大于10%,与原图谱比较,新定位的各QTL的标记区间明显缩短,与相邻标记的连锁更加紧密。