应用SSR分子标记分析国外种质对我国小麦品种的遗传贡献

利用363对SSR标记分析了在我国小麦生产和育种中发挥了重要作用的11份国外引进品种和33份选育品种的遗传组成,旨在揭示国外种质对我国小麦品种改良的遗传贡献,指导种质资源引进和利用。国外种质包含了选育品种所发现等位变异的76.3%。与不同时期小麦品种等位基因多样性比较发现,国外种质的平均等位变异数最多(3.92),20世纪60年代(2.86)和70年代(3.01)基本一致,80年代有所升高(3.46)。品种间遗传距离比较与品种等位基因多样性结果相吻合。比较引进和选育品种在SSR位点的等位变异频率变化,发现至少在33个SSR位点,国外种质等位变异在我国小麦育种中被优先选择(该等位变异在引进和选育品种的分布频率均高于70%),其中一些位点已知与产量、生育期和抗病等性状密切相关。表明引进品种在以上基因组区域对我国小麦品种具有非常高的遗传贡献。     

应用SSR分子标记分析国外种质对我国小麦品种的遗传贡献

利用363对SSR标记分析了在我国小麦生产和育种中发挥了重要作用的11份国外引进品种和33份选育品种的遗传组成,旨在揭示国外种质对我国小麦品种改良的遗传贡献,指导种质资源引进和利用。国外种质包含了选育品种所发现等位变异的76.3%。与不同时期小麦品种等位基因多样性比较发现,国外种质的平均等位变异数最多(3.92),20世纪60年代(2.86)和70年代(3.01)基本一致,80年代有所升高(3.46)。品种间遗传距离比较与品种等位基因多样性结果相吻合。比较引进和选育品种在SSR位点的等位变异频率变化,发现至少在33个SSR位点,国外种质等位变异在我国小麦育种中被优先选择(该等位变异在引进和选育品种的分布频率均高于70%),其中一些位点已知与产量、生育期和抗病等性状密切相关。表明引进品种在以上基因组区域对我国小麦品种具有非常高的遗传贡献。     

小麦骨干亲本临汾5064单元型区段的遗传解析

利用分子标记解析骨干亲本临汾5064单元型区段在其衍生后代中的遗传规律, 可以为小麦分子育种提供依据。在临汾5064及其21个衍生品种(系)中, 395个SSR标记共检测出895个等位变异, 不同位点的等位变异为1~8个, 平均2.27个, 平均多态性指数为0.25。临汾5064及衍生后代中146个位点具有相同等位变异, 遗传贡献超过80%的位点有30个。实验结果表明, 临汾5064对衍生子一代和子二代的遗传贡献率分别为65.30%和64.24%, 且未随着世代的增加而明显下降。所有衍生后代与亲本完全相同的单元型区段有16个, 贡献率大于80%的染色体区段分布在所有染色体上。关联分析发现这些单元型区段存在重要农艺性状的QTL簇, 几乎都与重要农艺性状显著相关, 表明这些区段在育种过程中受到强烈选择。     

我国分子育种迎来高通量时代——记中玉金标记分子标记实验室

<正>近年来,随着生物技术迅猛发展,我国育种家利用高通量测序、分子标记等等先进的生物技术和信息技术手段,架起了种质基因资源信息衔接庞大数据的桥梁,建立起常规育种与生物育种相结合的平台,大幅度提高了育种效率,使育种工作实现了由"经验"向"科学"的根本性转变。为了让分子标记技术和基因组测序技术带动我国种业的发展,中玉金标记(北京)生物技术     

主要麻类作物基因组学与遗传改良:现状与展望

随着测序技术的发展,主要麻类作物(黄麻、红麻、苎麻、亚麻和工业大麻)参考基因组从2011年至2020年陆续完成测序,这标志着麻类作物科学已经进入基因组时代。文章首先详细概述主要麻类作物基因组测序。其次,评述了基于基因组学的麻类作物重要应用价值基因挖掘。基于参考基因组和转录组测序,大量关于纤维发育、响应非生物胁迫的候选基因被挖掘,以促进麻类作物纤维的物种特性和“不与粮食争好地”的逆境农业。同时不同麻类作物特异性状候选基因陆续被报道,如红麻雄性不育、亚麻种子含油量和大麻大麻素相关候选基因等。再次,麻类作物基因组测序完成为基于组学的麻类作物遗传改良提供可能:有助于麻类作物种质资源形成和演化机制研究,系统解析纤维产量、纤维品质、抗病耐逆等农艺性状形成的分子基础;有助于建立高通量基因型-表型数据库,挖掘优异基因资源与创制新种质;有助于创新并集成分子标记辅助选择、基因组选择、转基因等技术,建立高效的快速育种技术体系。宜选育高产高效、抗逆抗病、适宜轻简化机械化、优质专用的多用途麻类作物新品种,以满足麻类作物相关产业的市场需求,适应麻类作物生产方式。尽管已经获得重要基因以及位点的信息,但如何高效率利用已有基因资源对麻类作物进行遗传改良仍需面临一系列挑战,如成熟稳定的遗传转化体系、麻类作物基因编辑体系构建及基因组选择育种等。     

我国科学家获得首个染色体级别橡胶树参考基因组图谱

正由云南省热带作物科学研究所特聘研究员、中国科学院昆明植物研究所研究员、热带作物种质资源与基因组学云南省创新团队首席科学家高立志教授带领的云南省热带作物科学研究所、中国科学院昆明植物研究所和华南农业大学基因组学与生物信息学研究中心的联合研究团队,历经6年,在国际上首次获得了达到染色体级别的高质量巴西橡胶树优良品种GT1的参考基因组序列,并揭示大戟植物基因组的染色体进化、胶乳生物合成与橡胶树的驯化。该研究为橡胶树的高产、抗病、抗旱、抗寒等重要经济性状的基因组选择育种与优异基因资源的发掘利用提供了染色体级别的高质量橡胶树参考基因组图谱。     

基于重测序的陆地棉InDel标记开发与评价

碱基插入/缺失(InDel)是基因组中丰富的遗传变异形式。InDel以其密度高、易于基因型分型等优点成为分子标记开发的理想来源。本研究利用262份陆地棉品系重测序数据鉴定的InDel位点,在全基因组范围内设计了3206个InDel标记并挑选均匀分布的320个标记进行验证。320个标记筛选出87个多态性标记,多态性率为26.88%。利用多态性标记对不同地理来源的262份陆地棉种质资源进行基因分型,共检测到160个等位位点;多态性信息含量(PIC)为0.0836～0.3750,平均值为0.3073;基因多样性指数变异范围为0.0874～0.5000,平均值为0.3876,表明我国陆地棉遗传基础相对狭窄。群体结构分析将262份陆地棉品系大致划分为2个亚群,聚类分析和主成分分析的结果与之基本一致。采用混合线性模型(Mixed linear model)对6个纤维品质性状的关联分析检测到65个关联位点(P 0.01),各位点对表型变异贡献率为2.57%～8.12%。本研究旨在利用重测序数据开发全基因组范围的可用于凝胶检测的InDel标记,为棉花种质资源研究和分子标记辅助选择育种提供便捷工具。     

引进陆地棉种质材料纤维品质及农艺性状关联分析

引进陆地棉(Gossypium hirsutum)种质材料的性状-标记关联分析是发掘其优异基因并在分子标记辅助育种中使用的科学依据。本研究利用199个SSR标记和42个In Del标记对94份国外陆地棉种质材料和27份新疆本地品种的纤维品质和农艺学性状进行全基因组关联分析。遗传结构和Neighbor-Join聚类分析将陆地棉种质群体划分为2个亚群,连锁不平衡分析发现有9.42%的位点组合存在LD(p0.01,r2≥0.05);基于混合线性模型的关联分析结果显示,能够同时在2个播期检测到的与6个纤维品质性状、4个产量性状和4个农艺性状显著关联的标记位点分别有18个、10个和5个,平均表型变异解释率分别为6.06%(1.17%~13.86%)、4.62%(1.18%~15.28%)和6.75%(1.87%~9.98%)。上述关联位点中共检测到188个等位变异,其中表型效应值大于0.6的优异等位变异有12个。研究结果可进一步用于分子辅助育种,并为基因精细定位提供参考资料。     

SNPS在大豆等作物遗传及改良中的应用

单核苷酸多态性(singlenucleotidepolymorphism,SNP)是指DNA序列上的单个碱基变异,它具有分布广、多态信息量大、易于检测和统计分析等优点,被称为继RFLP和微卫星标记后的第三代基因遗传标记。单核苷酸多态性是等位基因间序列差异最为普遍的类型,可作为一种高通量的遗传标记。已建立PCR扩增目标序列及其产物测序和电子SNP(eSNP)等多种发现和检测SNP的方法。大豆等作物也已开展了SNP分析。一些栽培作物种质的多样件不断减少,其结果连锁不平衡(linkagedise鄄quilibrium,LD)增加,这有利于目的基因座上SNP单元型(haplotype)与表型的相关性分析。SNP已在作物基因作图及其整合、分子标记辅助育种和功能基因组学等领域展示了广泛的应用价值。     

基于测序技术的红花基因组学研究进展

红花(Carthamus tinctorius L.)是药食同源的经济作物,富含丰富的营养物质与药用活性成分,可用于活血通经,去瘀止痛等。对经闭,难产,产后瘀血作痛,痈肿,跌打损伤有一定的治疗效果。随着人们对红花经济价值的重视,红花的应用愈发广泛,与日常生活联系日益密切。如今,迫切需要破解红花全基因组,为红花种质资源筛选、优良性状选育等提供理论依据。基因测序技术是研究红花基因组学的重要手段,在红花种质资源评价、遗传多样性分析、目标基因筛选、基因定位和分离等方面发挥重要作用。本研究综述了红花测序技术研究进展情况,着重介绍了三代测序技术,同时阐述了组装技术的研究进展,以及分子标记在红花基因组学的应用。这些可为红花遗传连锁图谱构建、关键基因定位、物种起源机制、分子标记辅助育种(MMAB)等提供参考。     

中国小麦品种抗赤霉病基因Fhb1的鉴定与溯源

提高赤霉病抗性已成为我国小麦主产区的重要育种目标之一。Fhb1是抗性最强且最稳定的抗赤霉病基因, 阐明其在我国小麦育种中的应用及传递路径, 对抗赤霉病育种有重要意义。本研究通过分析229份小麦品种(系) Fhb1区段内PFT (pore-forming toxin-like)、HC (HCBT-like defense response protein)和His (histidine-rich calcium-binding protein)基因的多样性与赤霉病抗性的关系, 发现PFT-I/His-I为抗病单倍型。基因检测和系谱分析表明, 中国小麦品种所含Fhb1至少有2个来源, 分别为苏麦3号和宁麦9号, 并以后者为主。本研究开发的诊断性标记PFT-CAPS和His-InDel可有效用于Fhb1的分子标记辅助育种。     

中国作物分子育种现状与发展前景

近年来,随着基因组测序等多种技术实现突破,基因组学、表型组学等多门“组学”及生物信息学得到迅猛发展,作物育种理论和技术也发生了重大变革。以分子标记育种、转基因育种、分子设计育种为代表的现代作物分子育种技术逐渐成为了全世界作物育种的主流,在我国也正在成为作物遗传改良的重要手段。本文在界定分子育种的基础上,简要分析了中国作物分子育种研究现状和面临的问题,探讨了未来我国作物分子育种的发展策略。     

谷子近缘野生种的亲缘关系及其利用研究

谷子在约1万年前由青狗尾草驯化而来,我国是谷子的起源中心。谷子所属的狗尾草属在全世界约有125个种,其中中国有15个种,从二倍体到八倍体均有。目前利用染色体原位杂交技术鉴定出狗尾草属6个基因组,利用分子标记分析发现狗尾草属是多起源的,与其多样性的基因组一致。系统演化分析发现,青狗尾草和谷子亲缘关系最近,其次是法式狗尾草和轮生狗尾草;基因组比较分析发现, S. adhaerans的B基因组和S. grisebachii的C基因组与谷子和青狗尾草的A基因具有相对近的亲缘关系,而其他基因组和谷子亲缘较远。在野生资源的利用方面,谷子育种工作者已成功将近缘野生种自然发生的抗除草剂基因转育到谷子中,培育成功了可化学除草的新品种并在生产上利用。本文对谷子野生种的分类、基因组构成、系统进化关系和遗传育种的研究进展进行了综述,重点讨论了谷子近缘野生种在谷子起源与驯化、遗传育种中起到的作用,并对谷子近缘野生种在谷子驯化及育种中的进一步利用做了展望。     

Using molecular markers for detecting domestication, improvement, and adaptation genes

Development of statistical tests to detect selection (strictly speaking, departures from the neutral equilibrium model) has been an active area of research in population genetics over the last 15 years. With the advent of dense genome sequencing of many domesticated crops, some of this machinery (which heretofore has been largely restricted to human genetics and evolutionary biology) is starting to be applied in the search for genes under recent selection in crop species. We review the population genetics of signatures of selection and formal tests of selection, with discussions as to how these apply in the search for domestication and improvement genes in crops and for adaptation genes in their wild relatives. Plant domestication has specific features, such as complex demography, selfing, and selection of alleles starting at intermediate frequencies, that compromise many of the standard tests, and hence the full power of tests for selection has yet to be realized.     

High level of natural variation in a groundnut (Arachis hypogaea L.) germplasm collection assayed by selected informative SSR markers

The ability to identify genetic variation is indispensable for effective management and use of genetic resources in crop breeding. Genetic variation among 189 groundnut ( Arachis hypogaea L.) accessions comprising landraces, cultivars, a mutant, advanced breeding lines and others (unknown genetic background) representing 29 countries and 10 geographical regions was assessed at 25 microsatellite or simple sequence repeat loci. A high number of alleles (265) were detected in the range of 3 (Ah1TC6G09) to 20 (Ah1TC11H06) with an average of 10.6 alleles per locus. The polymorphism information content value at these loci varied from 0.38 (Ah1TC6G09) to 0.88 (Ah1TC11H06) with an average of 0.70. A total of 59 unique alleles and 127 rare alleles were detected at almost all the loci assayed. Cluster analysis grouped 189 accessions into four clusters. In general, genotypes of South America and South Asia showed high level of diversity. Extraordinary level of natural genetic variation reported here provides opportunities to the groundnut community to make better decisions and define suitable strategies for harnessing the genetic variation in groundnut breeding.     

Chickpea molecular breeding: New tools and concepts

Summary Chickpea is a cool season grain legume of exceptionally high nutritive value and most versatile food use. It is mostly grown under rain fed conditions in arid and semi-arid areas around the world. Despite growing demand and high yield potential, chickpea yield is unstable and productivity is stagnant at unacceptably low levels. Major yield increases could be achieved by development and use of cultivars that resist/tolerate abiotic and biotic stresses. In recent years the wide use of early maturing cultivars that escape drought stress led to significant increases in chickpea productivity. In the Mediterranean region, yield could be increased by shifting the sowing date from spring to winter. However, this is hampered by the sensitivity of the crop to low temperatures and the fungal pathogen Ascochyta rabiei. Drought, pod borer (Helicoverpa spp.) and the fungus Fusarium oxysporum additionally reduce harvests there and in other parts of the world. Tolerance to rising salinity will be a future advantage in many regions. Therefore, chickpea breeding focuses on increasing yield by pyramiding genes for resistance/tolerance to the fungi, to pod borer, salinity, cold and drought into elite germplasm. Progress in breeding necessitates a better understanding of the genetics underlying these traits. Marker-assisted selection (MAS) would allow a better targeting of the desired genes. Genetic mapping in chickpea, for a long time hampered by the little variability in chickpea’s genome, is today facilitated by highly polymorphic, co-dominant microsatellite-based markers. Their application for the genetic mapping of traits led to inter-laboratory comparable maps. This paper reviews the current situation of chickpea genome mapping, tagging of genes for ascochyta blight, fusarium wilt resistance and other traits, and requirements for MAS. Conventional breeding strategies to tolerate/avoid drought and chilling effects at flowering time, essential for changing from spring to winter sowing, are described. Recent approaches and future prospects for functional genomics of chickpea are discussed.     

Identification of two types of differentiation in cultivated rice (Oryza sativa L.) detected by polymorphism of isozymes and hybrid sterility

Magnitudes of genetic variation within each of major varietal groups of cultivated rice were surveyed in terms of isozyme polymorphism and allelic differentiation of hybrid sterility loci, both of which are considered to have litt le selective value. Allelic differences for 20 isozyme loci were examined in a total of 337 accessions, including Indica and Japonica rices. Aus cultivars from India, Javanica cultivars and both landraces and cultivars from China. Eleven out of the 20 isozyme loci were polymorphic. The Aus cultivars contained more alleles per locus than others. The hybrid sterilities in the crosses among Chinese cultivars, Indica and Japonica cultivars were mainly controlled by locus S-5, whereas the hybrid sterilities of Aus cultivars, when they were crossed to Indica, Japonica or Javanica cultivars, were found to be controlled by allelic interaction at hybrid sterility loci S-5, S-7, S-9 and S-15. Also in terms of the number of alleles at S-5 and S-7, Aus cultivars contained more alleles than others. While the Aus group showed an extreme diversity for both hybrid sterility alleles and isozymes, modern cultivars from the south of YangZi River in China were classified into Indica type and those from the north were into Japonica, which were almost the same as those in Japan. On the basis of the measured polymorphism the Indica-Japonica differentiation was explained by founder effects, i.e., through selection and distribution of two original sources each with a unique set of markers. Contrastingly, the continuous and pronounced diversity in the Aus group was attributed to the absence of such a process. The intermediate groups in Yunnan province and Tai-hu Lake region of China are considered to be isolated from such founder effects, retaining an intermediate diversity in terms of isozymes and hybrid sterility genes. Since hybrid sterility hampers the exchange of genes between cultivars of different groups, the understanding of its genetic basis will be important in rice breeding, particularly in hybrid rice breeding. This revised version was published online in July 2006 with corrections to the Cover Date.     

Breeding for provitamin A biofortification of maize (Zea mays L.)

Vitamin A deficiency is widely prevailing in children and women of developing countries. Deficiency of vitamin A causes night blindness, growth retardation, xerophthalmia and increases the susceptibility against epidemic diseases. Among different interventions of overcoming malnutrition, biofortification is the most acceptable and preferred intervention among researchers, growers and consumers. Maize is grown and consumed in those regions where vitamin A deficiency is most prevalent; thus, targeting this crop for provitamin A biofortification is the most appropriate solution. Different breeding strategies including diversity analysis, introduction and stability analysis of exotic germplasm, hybridization, heterosis breeding, mutagenesis and marker‐assisted selection are practised for exploring maize germplasm and development of provitamin A‐enriched cultivars. Genome‐wide association selection and development of transgenic maize genotypes are also being practised, whereas RNA interference and genome editing tools could also be used as potential strategies for provitamin A biofortification of maize genotypes. The use of these breeding strategies for provitamin A biofortification of maize is comprehensively reviewed to provide a working outline for maize breeders.     

小麦抗麦红吸浆虫基因标记的开发与验证

麦红吸浆虫(SitodiplosismosellanaGéhin)严重影响小麦产量和品质,选育和使用抗虫品种是降低虫害损失最安全有效的途径,利用抗虫性连锁或功能标记对提高小麦抗虫分子育种效率具有重要意义。在前期从转录组数据中挖掘到抗虫性主效QTL (QSm.hbau-4A) 6个相关差异基因的基础上,依据这些基因序列中存在的InDel和SNP,分别开发了2个EST标记和6个KASP标记,并在抗虫性不同的一套重组近交系(RIL)和一套小麦品种中进行了标记的有效性验证。所开发的8个标记在抗、感虫小麦亲本间均表现出较好的多态性,在RIL株系中的检测有效率均达到90%左右;除E10-10外,这些标记在供试高抗(56.3%～86.7%)和高感(85.7%～100.0%)小麦品种中的检测有效率均较高,可用于小麦种质资源的抗虫性筛选。同时发现, 11个具备所有抗虫标记位点的抗虫小麦品种,多为审定时间较早或已停止使用的品种,这使得结合标记辅助选择等手段鉴定和创新小麦抗虫种质资源的工作日益紧迫。     

二十一世纪水稻育种新战略Ⅱ．利用远缘杂交和多倍体双重优势进行超级稻育种

本文论述了远缘杂交和多倍体化结合利用基因组间和多倍本杂种优势，开创水稻育种新途径的策略。纵观水稻育种的历史，无论是常规杂交育种，还是杂交稻育种，其研究战略都是建立在有性生殖和二倍体基础上的，归根结底，都是利用栽培稻同一基因组（A基因组）内优良基因的重组以及从野生稻向栽培稻引入少数优良基因。从作物进化趋势看，水稻是二倍体，基因组小、DNA含量低、染色体小，增加基因组数，提高倍性水平，利用异源多倍体杂种优势将是水稻育种新途径。针对同源四倍体水稻结实率低的关键问题，可采取拉大亲缘关系距离、减少多价体形成，应用广亲和、无融合生殖基因等措施，从遗传机理上提高多倍体水稻结实率。按三步实施战略：一、选用极端类型籼粳稻、爪哇稻，诱导亚种间杂种多倍体；二、诱导亚洲栽培稻和非洲栽培稻以及非洲野生稻种间杂种多倍体；三、诱导AA基因组的栽培稻与其它不同基因组野生稻（BB、CC、BBCC、CCDD、DD、EE、FF、GG、HHJJ）的种间多倍体。在实施过程中发挥一特殊基因材料的特殊作用，如广亲和基因对于克服籼粳杂种一代不育性、特别是雌败育的作用，无融合生殖缺乏减数分裂发生和受精过程对于克服染色体配对分离而导致的杂种败育的作用，以及类似于小麦中存在的抑制部分同源染色体配对的Ph基因对于防止水稻异源多倍体的基因组间部分同源性配对形成多价体、染色体桥、落后染色体等现象的作用，为选育异源多倍体水稻、无融合生殖水稻提供可靠保证。近三年的实践已经初获良好的结果，利用无融合生殖水稻品系籼粳交，亚洲稻与美洲稻杂交已获得杂种优势明显、结实率高达85％的优良多倍体株系，为实现这一育种新战略打下了良好基础。