金针菇种质资源5个农艺性状与SSR标记的关联分析

金针菇(Flammulina velutipes)是一种重要的商业化栽培食用菌,为挖掘控制金针菇重要农艺性状的基因组区段,本研究以90份金针菇种质资源为实验材料,测定其原基期、菌柄直径、菌柄长度、菌盖直径和单瓶产量5个农艺性状,利用全基因组序列开发的95份多态简单重复序列(simple sequence repeat,SSR)标记对供试材料进行基因组扫描,在分析实验材料的群体结构和连锁不平衡基础上,采用一般线性模型方法对5个农艺性状进行关联分析。结果表明,各供试材料的5个农艺性状均有极显著差异。95份多态SSR标记共检测到582个等位变异,平均每个位点的等位变异数为6.13个。标记多态信息含量(polymorphism information content,PIC)变化范围为0.204~0.818,平均为0.542。群体遗传结构分析将供试材料分为8个亚群体,群体内SSR位点间存在较高的连锁不平衡(linkage disequilibrium,LD),不平衡程度D’值大于0.5的组合数占总组合数的33.01%。关联分析检测出28个标记与5个性状显著相关,其中原基期的关联标记有2个,菌柄直径的关联标记有12个,菌柄长度的关联标记有3个,菌盖直径的关联标记有9个,单瓶产量的关联标记有5个。关联SSR标记对表型变异解释率的变幅为5.11%~23.55%。研究表明,所选金针菇种质资源群体的遗传多样性以及连锁不平衡程度较高,适用于关联分析研究。本研究结果对金针菇核心种质资源库构建以及分子标记辅助育种具有参考价值。     

全基因组关联分析在水稻遗传育种中的应用

关联分析是解析作物表型多样性遗传基础的有效工具,也是挖掘有利等位基因的重要手段,在作物遗传育种中发挥着越来越重要的作用。随着挖掘覆盖全基因组的单核苷酸多态性(Single nucleotide polymorphisms,SNP)标记技术的不断改进,基于连锁不平衡(Linkage disequilibrium,LD)的全基因组关联分析为研究作物的农艺、品质、产量和抗性等复杂性状提供了新途径。本文在系统介绍全基因组关联分析方法的基础上,详尽总结了其在水稻遗传育种中的研究进展,并探讨了其存在的潜在问题及解决途径。     

关联分析及其在植物中的应用

关联分析是新近开始在植物数量性状研究和植物育种中应用的一种分析方法。它以连锁不平衡为基础鉴定某一群体内性状与遗传标记或候选基因间的关系,是对分子育种中QTL分析的补充和提高。本文在介绍连锁不平衡的定义和度量方法的基础上,讨论连锁不平衡程度和群体结构对关联分析的影响,综述了关联分析在植物方面的研究进展,并最后讨论了关联分析在植物数量性状和分子育种研究中可能的应用。     

全基因组关联分析(GWAS)在作物农艺性状研究中的应用

全基因组关联分析(genome-wide association study,GWAS)是近年发展起来的用于研究复杂性状的一种有效方法。迄今,国内外学者已运用GWAS方法对一些农作物的重要农艺性状开展了研究。研究不仅丰富了分子标记,而且为揭示复杂农艺性状的分子机理提供了新思路。本文介绍了全基因组关联分析的流程及原理,就其在作物农艺性状研究中的应用进行了总结,并提出了目前面临的问题及改进措施。     

短季棉早熟及相关性状的QTL定位北大核心CSCD

短季棉育种是缓解我国当前粮棉争地矛盾、实现粮棉双丰收的有效途径。研究短季棉早熟及相关性状的遗传,寻找与其相关基因紧密连锁的分子标记对于短季棉育种具有重要意义。以百棉2号×TM-1组合构建的F2为作图群体,利用SSR标记构建遗传连锁图,采用复合区间作图法对短季棉早熟及相关性状在F2群体中进行QTL定位,构建了一张含152个SSR标记、40个连锁群、总长1010.3cM、覆盖棉花基因组的22.6%、标记间平均距离为5.91cM的短季棉分子标记遗传连锁图谱,得到的40个连锁群已定位到相应的21条染色体上,为短季棉分子遗传图谱进一步饱和奠定了良好的基础;检测出22个控制早熟及相关性状的QTL,其中检测到的主效QTL可用于短季棉标记辅助选择育种。     

黄瓜叶面积主效QTL小叶2基因(ll2)的遗传定位

叶片面积影响光合作用效率,是农作物产量的重要构成性状之一。野生黄瓜(Cucumis sativus var.hardwickii)的叶片较小,经过人工驯化后的栽培黄瓜(Cucumis sativus var.sativus)的叶片面积扩大了2~3倍。前人研究已经将控制黄瓜叶面积的主效基因之一ll(little leaf)定位在第6号染色体上。本研究以黄瓜小叶品系XF-24(P1)、大叶品系DF-32(P2)杂交产生的205个单株的F2群体为研究材料,用SAS软件对成熟期调查的各单株相同节位的叶面积进行正态性检验,结果服从正态分布,符合数量性状的遗传特征。为了有效地加快研究进程,在双亲测序情况下,采用插入缺失位点(insertion and deletion,InDel)标记进行基因定位。研究结合双亲全基因组测序数据,生物信息学分析得出双亲序列之间的InDel位点,用Primer Premier 5.0软件在所有染色体上均匀设计88对InDel标记引物,扩增采用分离群体分组混合分析法(bulked segregant analysis,BSA)组建大叶、小叶基因池,池间有多态的引物再进一步扩增F2群体DNA,筛选到7个与黄瓜叶面积基因ll2连锁的分子标记,位于黄瓜第7号染色体上,分别是InDel-1、InDel-2、InDel-3、InDel-4、InDel-5、InDel-6、InDel-7。建立遗传连锁图谱并进行区间作图寻找QTL位点,结果显示,遗传连锁图谱包含以上7个InDel标记,连锁区间为22.1 cM,包括1个控制黄瓜叶片大小的主效QTL位点ll2(little leaf 2),位于标记InDel-2与InDel-4之间,这两个标记之间物理距离为1.24 Mb。与前人的研究结果相比,定位区间更小且是7号染色体上首次发现的黄瓜叶面积QTL位点。截止目前,在黄瓜6号、7号染色体共发现了2个黄瓜叶面积主效QTL位点,分别是ll和ll2,表明黄瓜叶面积遗传机制复杂。叶面积主效QTL ll2的遗传定位,对于控制黄瓜叶片面积的遗传机制和分子机理研究以及分子标记辅助育种具有重要的意义。     

作物数量性状位点研究进展及其育种应用

农作物中产量、品质、抗性等重要性状大多属于数量性状,因此对于数量性状位点(quantitative trait locus,QTL)的探索一直是植物分子生物学领域的研究重点。近年来,越来越多农作物重要性状的QTL被定位乃至克隆。同时,随着高通量测序技术的不断成熟,一些超高密度遗传图谱的构建和全基因组关联分析(genome wide association study,GWAS)的应用使得植物功能基因组学进入了一个飞速发展的时期。这为作物QTL的大规模挖掘、克隆以及复杂数量性状的遗传改良提供了良好的契机。本文从QTL的定位、克隆以及在育种中的应用几个方面,对近年来农作物QTL的研究策略和研究进展进行了较为详细的综述和探讨。     

高粱千粒重全基因组关联分析和候选基因预测

千粒重是作物产量构成的三要素之一。增加粒重是提高作物产量的重要途径。为阐明高梁千粒重的遗传机理,本试验以主要来自于我国16个高粱种植省份的242份高粱品种(系)组成的关联群体为研究材料,借助覆盖全基因组的2 015 850个高质量SNPs标记,采用多位点分析软件mrMLM 4.0 R软件包中的mrMLM、FASTmrMLM、FASTmrEMMA、ISIS EM-BLASSO、pLARmEB、pKWmEB 6种模型,对2018—2020年贵州贵阳、浙江杭州、海南乐东、海南陵水3年4点7个环境的高梁千粒重进行全基因组关联分析。结果表明,7个环境的高梁千粒重均表现连续正态分布,呈现明显的数量性状遗传特性,变异范围于10~50 g之间。利用6个模型共检测到323个与千粒重显著关联的数量性状核苷酸位点(QTNs),这些位点不均匀地分布在10条染色体上。单个QTN可解释0.4%~26.6%的表型变异。不同模型检测到的位点数目不同,FASTmrMLM模型最多,然后依次是pKWmEB模型、pLARmEB模型、mrMLM模型、ISIS EM-BLASSO模型和FASTmrEMMA模型。合并共同QTNs后得到96个显著影响千粒重的QTNs,其中4个QTNs与前人报道的高粱基因位点重叠,另有4个QTNs包含与水稻中克隆的粒重相关基因qGW7/GL7、BG2、OsARF4、RSR1、TGW6等同源的基因。本研究结果为探究高粱千粒重性状分子遗传机理和高粱分子设计育种提供了科学依据。     

分子标记技术在杉木研究中的应用

综述了分子标记技术在杉木种质资源鉴定、群体遗传多样性研究、遗传连锁图谱构建和数量性状位点(QTL)定位及分子标记辅助选择育种等方面的应用进展,指出目前该方面研究存在的问题,并展望了分子标记技术在杉木研究中的应用前景     

利用BSA-Seq方法快速定位作物农艺性状QTL/基因概述

为了利用生物学技术和手段来解决农业问题,让基因组测序技术、转基因及基因编辑等现代分子生物学技术为农业遗传育种服务,实现常规育种与分子设计育种的紧密结合,加速作物精准育种进程,近年颇受学术界关注。现梳理了一些分子生物学专用名词概念,概述了目前在正向遗传学研究中如何利用极端表型材料基于全基因组测序的BSA-Seq方法(MutMap法、MutMap+法、MutMap-Gap法、QTL-seq法)快速定位重要农艺性状的QTL/基因,为快速定位和克隆候选基因提供新思路。     

枣遗传图谱构建研究进展

枣遗传图谱是枣树分子辅助育种的重要工具之一。高质量的枣遗传图谱在遗传演化分析、QTLs基因定位等研究中发挥了重要作用。为开展图位克隆重要农艺性状基因、加快枣育种进程,本文简要概述了目前国内外枣遗传图谱的研究进展,包括设计亲本组合、真实子代鉴定、构建作图群体、遗传图谱构建和相关QTL定位研究等方面,进一步探讨前人研究存在的问题并提出相关解决措施,为开展筛选农艺状候选基因和枣分子辅助育种研究奠定了理论基础。     

Collection and characterization of yellow endosperm sorghums from West Africa for biofortification

Sorghum is a good candidate crop for breeding to increase provitamin A, i.e., biofortification. Yellow endosperm sorghums contain carotenoids, including precursors of vitamin A, and sorghum is a major staple crop in areas of Asia and Africa where vitamin A deficiency is prevalent. Our objective was to collect and characterize yellow endosperm sorghums as a potential new source of genetic diversity to increase provitamin A content. A set of 164 landraces were collected from southern Niger and northern Nigeria. The most important use of these cultivars was as food. The endosperm exhibited a significant variation in yellow intensity. Lutein, zeaxanthin and β-carotene were the most abundant carotenoids in the ten landraces with the most intense yellow color. Cluster analysis, principal coordinate analysis and population differentiation test revealed that this set of 164 landraces represent a new genetic pool that might increase the genetic diversity of yellow endosperm sorghums in applied breeding programs.     

Genome-wide association study to identify chromosomal regions related to panicle architecture in rice (Oryza sativa)

Panicle architecture directly affects the grain yield of rice; meanwhile, crop domestication has increased the complexity of rice panicle size and branching pattern. Genome-wide association study (GWAS) was performed to investigate the genetic basis underlying panicle architecture using 183 rice accessions from around the world and a 7 K SNP array. Phenotyping was conducted at Texas A&M AgriLife Research Center in Beaumont, TX. GWAS was performed using MLM (Q?+?K) model using GAPIT software. At p-value?<?0.001, a total of 49 GWAS QTLs controlling various panicle architecture traits were mapped. Considering the recurring and linked SNPs across the panicle architecture traits, 42 independent QTL regions were identified. Among these, 27 QTL regions co-localized with known genes or previously reported QTLs or significant SNP markers, while 15 were potentially novel QTL regions. The results of our study offer useful information on genetic bases controlling panicle architecture in rice, which could be further validated and utilized for designing markers for use in markers assisted selection (MAS) in rice breeding programs.

     

Population genetic analysis of hyacinth bean (<Emphasis Type="Italic">Lablab purpureus</Emphasis> (L.) Sweet,Leguminosae) indicates an East African origin and variation in drought tolerance

Population genetic studies are effective ways of researching the origin of, and genetic variation within, crop species, with a view to breeding for increased tolerances or novel traits. This is particularly important now that we are facing climate change and an increasing global population. Lablab purpureus (L.) Sweet (hyacinth bean) is an underutilised legume that has the potential of being an important crop species in the future due to its enhanced environmental tolerances relative to other legumes. It is farmed extensively, but locally, throughout Africa and Asia, however limited research and development of the crop has been undertaken so far, hence an investigation into its origin and diversity is warranted. Our microsatellite analysis suggests an East African origin of Lablab because of the genetic similarities between East African lines and the wild subspecies, subsp. uncinatus. The East African lines were also more genetically diverse. Two chloroplast DNA haplotypes were resolved and Africa was the only continent where both were present, again suggesting an African origin followed by the dissemination of lines outside of Africa coupled with a reduction in genetic diversity. Variation in tolerance to drought was recorded, with some lines able to tolerate 14 days without watering. In sum, we propose an East African origin of Lablab and have identified potential adaptive diversity for future crop breeding attempts.     

The use of genetic resources in crop improvement: Lessons from China

The use of crop genetic resources in improvement programmes should be the ultimate objective of all undertakings in the field of germplasm resources. The present situation and future direction of the use of crop germplasm in China was assessed from responses to a questionnaire distributed to 165 plant breeders and curators nationwide. The general opinions for the limiting factors of germplasm utilization were also evaluated. Responses from the questionnaire indicated that the use of germplasm in breeding programmes is much more important than the direct use of germplasm in crop production as cultivars released. Among different types of crop genetic resources, released varieties and breeding lines contribute more to crop breeding. Wild relatives and genetic stocks, however, are expected to play a greater role in the future. Landraces will remain important in improvement. Limited useful germplasm available to breeders is the basic reason for the insufficient use of germplasm in crop breeding at present. The complex reasons which affect the availability of useful germplasm involve the research level, links between breeder and curator and others. To counter these, we propose some suggestions and measures which can be implemented in the near future.     

Identifying QTLs and Epistasis in Structured Plant Populations Using Adaptive Mixed LASSO

Association analysis in important crop species has generated heightened interest for its potential in dissecting complex traits by utilizing diverse mapping populations. However, the mixed linear model approach is currently limited to single marker analysis, which is not suitable for studying multiple QTL effects, epistasis and gene by environment interactions. In this paper, we propose the adaptive mixed LASSO method that can incorporate a large number of predictors (genetic markers, epistatic effects, environmental covariates, and gene by environment interactions) while simultaneously accounting for the population structure. We show that the adaptive mixed LASSO estimator possesses the oracle property of adaptive LASSO. Algorithms are developed to iteratively estimate the regression coefficients and variance components. Our results demonstrate that the adaptive mixed LASSO method is very promising in modeling multiple genetic effects when a large number of markers are available and the population structure cannot be ignored. It is expected to be a powerful tool for studying the architecture of complex traits in important plant species. Supplemental materials for this article are available from the journal website.     

植物氮素吸收利用相关NPF基因家族研究进展

氮(N)是植物生长发育需要量最大的矿质营养元素,也是作物产量的限制因子。硝态氮(NO₃^--N)是植物吸收利用氮素的主要形态之一。目前,植物中已报道4个基因家族(NPF、NRT2、CLC和SLAC1/SLAH)参与硝态氮的吸收和利用,其中NPF基因家族成员数量众多且功能多样化,近年来获得较多关注和深入研究。模式植物拟南芥和主要粮食作物水稻、玉米和小麦中,分别含有53、93、79和331个NPF基因。拟南芥NPF家族中已有超过一半成员(31/53)的生物学功能被解析,粮食作物水稻中NPF基因功能亦有较多报道。研究表明,NPF基因广泛参与了植物对氮素的吸收及其调控、转运、分配/再分配等过程,一些成员对于改良和提高作物氮素利用率(nitrogen use efficiency, NUE)具有重要作用。因此,从氮素进入植物体及其在植物体内流动的层面出发,发掘具有重要功能的候选NPF基因,对于解析植物利用氮素的分子机制及其遗传改良具有重要意义。本文综述了模式植物拟南芥以及粮食作物中已报道的NPF基因在氮素吸收和利用中的生物学功能。目前粮食作物玉米中仅有4...     

Genetic diversity and relationship of Guinea yam (<Emphasis Type="Italic">Dioscorea cayenensis</Emphasis> Lam.–<Emphasis Type="Italic">D. rotundata</Emphasis> Poir. complex) germplasm in Benin (West Africa) using microsatellite markers

Guinea yam (Dioscorea cayenensis–D. rotundata complex) is an important tuber crop that highly contributes to food security and poverty alleviation in Benin. The knowledge and understanding of the extent of genetic variation of Guinea yam germplasm is important for planning of the genetic conservation, and the utilisation of this resource. The objective of this study was to assess the genetic diversity and relationships of 64 yam landraces whose dried chips are considered as resistant to insect attacks using 41 simple sequence repeat. Among these primers, 13 were found to be polymorphic, giving 113 polymorphic alleles. The number of alleles per locus ranged from 4 (Ym50) to 13 (Ym29), with an average of 8.69. Unique allele was observed with some landraces (Singou and Tchakatchaka) and can be considered as unique gene and use in yam breeding program. The mean polymorphic information content values for all markers used was 0.76 and ranged between 0.58 and 0.91 in loci YM3 and YM32 respectively. The genetic distance of yam landraces ranged from 0.45 (Yasoubagarou) to 0.04 (Assinapeira and Alahina), indicating that the yam germplasm has a high degree of genetic diversity supported by an averagely observed heterozygosity of 0.78. Cluster analysis using unweighted pair group method with arithmetic average grouped the 64 yam landraces into two distinct clusters. This tendency was also observed in the principal coordinate analysis. The analysis of molecular variance revealed that 96 % of the variation was found within the population and only 4 % between the populations. Genetic diversity and relationship assessments among the 64 yam landraces of Benin could provide useful information for efficient use of these materials, especially for genetic improvement.