Mapping Quantitative Trait Loci Controlling Endosperm Traits with Molecular Marker

Based on the genetic models for triploid endosperm traits and on the methods for mapping diploid quantitative traits loci (QTLs), the genetic constitutions, components of means and genetic variances of QTL controlling endosperm traits under flanking marker genotypes of different generations were presented. From these results, a multiple linear regression method for mapping QTL underlying endosperm traits in cereals was proposed, which used the means of endosperm traits under flanking marker genotypes as a dependent variable, the coefficient of additive effect (d) and dominance effect (h1 and/or h2) of a putative QTL in a given interval as independent variables. This method can work at any position in a genome covered by markers and increase the estimation precision of QTL location and their effects by eliminating the interference of other relative QTLs. This method can also be easily used in other uneven data such as markers and quantitative traits detected or measured in plants and tissues different either in generations or at chromosomal ploidy levels, and in endosperm traits controlled by complicated genetic models considering the effects produced by genotypes of both maternal plants and seeds on them.

Analysis of SSR loci and development of SSR primers in Eucalyptus

In this study,28,691 genome sequences and16,566 expressed sequence tags(ESTs) of Eucalyptus were derived from the Gen Bank database.A total of 2292 SSR loci were sought out from 1785 effective sequences.Through analyses of SSR loci information,the SSR motif length was negatively correlated with the abundance of the SSRs.In the EST sequences of Eucalyptus,triplet repeat motifs were the most abundant,and dinucleotide repeats motifs had the highest frequencies.Subsequently,395 pairs of primers were designed based on the SSR loci.Using optimized SSR-PCR conditions,340 pairs of primers were successfully screened,with a success rate of 86.1%.By construction of a maximum likelihood phylogenetic tree of six eucalypt species,represented by five species of the genus Eucalyptus and one of the genus Corymbia,the genetic relationships of Eucalyptus urophylla and E.camaldulensis suggested by this tree was found to differ from that suggested by traditional morphological taxonomy.The results provide insights for evaluating geneticdiversity of Eucalyptus and analysis of Eucalyptus phylogenetics using SSR markers.

Rice molecular markers and genetic mapping:Current status and prospects

Dramatic changes in climatic conditions that supplement the biotic and abiotic stresses pose severe threat to the sustainable rice production and have made it a difficult task for rice molecular breeders to enhance production and productivity under these stress factors. The main focus of rice molecular breeders is to understand the fundamentals of molecular pathways involved in complex agronomic traits to increase the yield. The availability of complete rice genome sequence and recent improvements in rice genomics research has made it possible to detect and map accurately a large number of genes by using linkage to DNA markers. Linkage mapping is an effective approach to identify the genetic markers which are co-segregating with target traits within the family. The ideas of genetic diversity, quantitative trait locus（QTL） mapping, and marker-assisted selection（MAS） are evolving into more efficient concepts of linkage disequilibrium（LD） also called association mapping and genomic selection（GS）, respectively. The use of cost-effective DNA markers derived from the fine mapped position of the genes for important agronomic traits will provide opportunities for breeders to develop high-yielding, stress-resistant, and better quality rice cultivars. Here we focus on the progress of molecular marker technologies, their application in genetic mapping and evolution of association mapping techniques in rice.

Physio-Biochemical and Genetic Exploration for Submergence Tolerance in Rice (<i>Oryza sativa</i>L.) Landraces with Special References to <i>Sub</i>1 Loci

In the present study a group of four indigenous and less popular rice genotypes (Meghi, Panibhasha, Jabra and Sholey) reported by growers as submergence tolerant lines from flood prone areas of south Bengal were explored through study of nodal anatomy, physio-biochemical screening under submergence and genotyping with submergence tolerance linked rice microsatellite loci (RM loci). To identify the different allelic forms of different Sub1 compnents (Sub1A, Sub1B and Sub1C) among the studied lines, the genomic DNA of individual genotypes was amplified with three ethylene response factor like genes from Sub1 loci, located on rice chromosome 9. From the different physio-biochemical experiments performed in this investigation, it has been shown that Meghi and Jabra are the two probable potent genotypes which share common properties of both submergence tolerant and deep water nature whereas rest two genotypes (Sholey and Panibhasha) behave like typical deep water rice. The submergence tolerance property of Meghi was also confirmed from submergence tolerance linked SSR based genotyping by sharing with FR13A for some common alleles as reflected in fingerprint derived dendrogram. The rest of the genotypes shared a number of alleles and were included in a separate cluster. The common behaviour of Meghi and FR13A under submergence was also confirmed from genetic study of Sub1 loci through sharing of some common alleles for three Sub1 components (Sub1A, Sub1B and Sub1C loci). One SSR loci (RM 285) was identified as a potent molecular marker for submergence tolerance breeding programme involving these two selected rice lines (Meghi and Jabra) as donor plant through marker assisted selection.

Detecting mislabeling and identifying unique progeny in Acacia mapping population using SNP markers

Acacia hybrids offer a great potential for paper industry in Southeast Asia due to their fast growth and ability to grow on abandoned or marginal lands. Breeding Acacia hybrids with desirable traits can be achieved through marker assisted selection(MAS) breeding. To develop a MAS program requires development of linkage maps and QTL analysis. Two mapping populations were developed through interspecific hybridization for linkage mapping and QTL analysis. All seeds per pod were cultured initially to improve hybrid yield as quality and density of linkage mapping is affected by the size of the mapping population. Progenies from two mapping populations were field planted for phenotypic and genotypic evaluation at three locations in Malaysia,(1) Forest Research Institute Malaysia field station at Segamat, Johor,(2) Borneo Tree Seeds and Seedlings Supplies Sdn, Bhd.(BTS) field trial site at Bintulu, Sarawak, and(3) Asiaprima RCF field trial site at Lancang, Pahang. During field planting, mislabeling was reported at Segamat, Johor, and a similar problem was suspected for Bintulu, Sarawak. Early screening with two isozymes effectively selected hybrid progenies, and these hybrids were subsequently further confirmed by using species-specific SNPs. During field planting, clonal mislabeling was reported and later confirmed by using a small set of STMS markers. A large set of SNPs were also used to screen all ramets in both populations. A total of 65.36% mislabeled ramets were encountered in the wood density population and 60.34% in the fibre length mapping population. No interpopulation pollen contamination was detected because all ramets found their match within the same population in question.However, mislabeling was detected among ramets of the same population. Mislabeled individuals were identified and grouped as they originated from 93 pods for wood density and 53 pods for fibre length mapping populations.On average 2 meiotically unique seeds per pod(179 seeds/93 pods) for wood density and 3 meiotically unique seeds per pod(174 seeds/53 pods) for fibre length mapping population were found. A single step statistical method was used to evaluate the most informative set of SNPs that could subsequently be used for routine checks for mislabeling in multi-location field trials and for labelling superior clones to protect breeder’s rights. A preliminary set of SNPs with a high degree of informativeness was selected for the mislabeling analysis in conjunction with an assignment test. Two subsets were successfully identified,i.e., 51 SNPs for wood density and 64 SNPs for fibre length mapping populations to identify all mislabeled ramets which had been previously identified. Mislabeling seems to be a common problem due to the complexity involved in the production of mapping populations. Therefore, checking for mislabeling is imperative for breeding activities and for analyses such as linkage mapping in which a correlation between genotypic and phenotypic data is determined.

Malate dehydrogenase in plants: Its genetics, structure, localization and use as a marker

This article is an overview of literature data on the structure, properties, functions and genetic control of the enzyme malate dehydrogenase (MDH) in plants. In most of the plant entities studied, this enzyme is highly polymorphic, which means that malate dehydrogenase has multiple molecular forms. It has been found that MDH polymorphism in each species is genetically determined by several loci with multiple alleles. A readily identifiable phenotypic manifestation and a high activity of malate dehydrogenase in diverse organs and tissues make this enzyme a reliable and convenient genetic marker, which can effectively be used in special, ecological and population genetics.

The Power of Integrative Approaches to Develop Markers for Maize Molecular Breeding

Recent advances in genomics and bioinformatics now offer real opportunities for dissecting complex traits into their component sub-traits, which will simplify the process of developing the tools necessary to

小麦茎基腐病抗性位点研究进展

对小麦茎基腐病(FCR)抗性位点研究进行综述。目前,在小麦所有的21条染色体上定位了140个抗性QTL,含10个抗性基因,虽然报道的抗性位点很多,但主效位点不明确,严重影响小麦FCR抗性改良进程。分析了小麦FCR抗性位点研究中的主要问题,提出了统一抗性鉴定标准、增强成株期抗性研究等建议,以明确抗FCR主效位点/基因并开发分子标记,通过分子标记辅助选择促进FCR抗性改良进程。

茄子果皮转录组SSR位点分析及标记开发

以茄子(Solanum melongena L.)果皮样品转录组的36568条转录本为试材,采用MISA(MicroSAtellite)软件进行SSR位点搜索,研究SSR位点的分布频率和特征,同时利用Primer 3.0软件对检索出的SSR位点设计引物,验证引物有效性,以期为茄子的种质鉴定、亲缘关系分析、分子标记辅助育种及遗传图谱构建等提供参考依据。结果表明:在转录本中共检测出9775个SSR位点,分布于6289条转录本上,平均5.49 kb存在1个SSR位点,发生频率26.73%。SSR位点特征分析显示,单核苷酸为优势重复基元类型,占SSR位点总数的47.67%;A/T基元是数量最多的重复基元,占总数的46.13%;97.91%的重复基元的重复次数在5~25,92.21%的SSR重复序列长度分布在10~30 bp。对所有SSR位点进行引物设计,共获得6619对EST-SSR引物。随机选择27对EST-SSR引物在12个茄子自交系中进行PCR扩增,引物有效性为92.59%,多态率为33.33%。

基于线粒体12S基因分析福建省棘胸蛙不同地理种群遗传多样性

棘胸蛙Quasipaa spinosa为福建省特色分布的大型蛙类,被列入三有保护动物之列,开发新的辨别福建省内棘胸蛙不同地理种群的快速方法对于该物种的保护极为重要。通过选取福建省内14个地区的野生棘胸蛙样本,提取其DNA并通过PCR扩增出线粒体12S rRNA基因,然后进行一代测序,基于获得的12S rRNA基因序列构建了进化树。结果表明:福建省内的棘胸蛙可以分成两大类种群,武夷山、建阳、顺昌、将乐、明溪、永安、华安、德化和新罗聚为一类(西部群体),武夷山、政和、屏南、宁德、福鼎、永泰、德化、新罗和福安聚为另一类(东部群体),其中,武夷山、德化、新罗在两个大类均有分布。为了更快地基于12S rRNA基因区分两个群体,筛选了这两大类种群的12S rRNA基因的SNP位点,并利用竞争性等位基因特异性PCR(KASP,Kompetitive Allele-Specific PCR)方法,开发了一种针对这两个群体的特异性SNP快速分型方法,结果显示所开发的KASP检测体系能准确区分福建省野生棘胸蛙的两个支系。该结果可为深入了解福建省内棘胸蛙的种群分化、有效鉴别不同地理种群,以及为种质资源保护和育种工作提供科学依据。

基于简化基因组测序宽鳍鱲的微卫星分子标记及遗传多样性分析

【目的】建立基于简化基因组测序(2b-RAD)宽鳍鱲(Zacco platypus)的微卫星分子标记,并进行遗传多样性分析,为有效开展宽鳍鱲品种间遗传多样性分析和分子育种,挖掘和利用宽鳍鱲种质资源提供参考。【方法】利用限制性内切酶EcoRⅠ打断基因组DNA,每个样本分别进行物理打碎,选取300~700 bp插入片段文库,利用Illumina HiSeq PE150测序平台进行双末端(Paired-End)测序获得海量遗传多态性标签序列。【结果】2b-RAD筛选宽鳍鱲的微卫星位点得到两端各留100 bp作为引物的SSR数量为41018个,带有引物片段的SSR数量为1522个,片段引物的设计率为37.1%,构建的文库质量较高,测序深度达高准确度下的分型标准。在筛选的64个微卫星位点中,有14个位点(21.88%)具有多态性,由于存在无效等位基因,有3个位点(Zpla08、Zpla09和Zpla10)显著偏离Hardy-Weinberg平衡(P<0.05),因此选用其中的11个微卫星位点分析宽鳍鱲群体遗传多样性。基于11个微卫星DNA位点的分析表明,宽鳍鱲7个群体的平均等位基因数(N_(A))为3.66,平均Shannon;s信息指数(I)为0.689,平均观测杂合度(H_(O))为0.315,平均期望杂合度(H_(E))为0.354,平均多态信息含量(PIC)为0.409。【结论】基于简化基因组测序(2b-RAD)开发宽鳍鱲的微卫星分子标记可用于评估野生宽鳍鱲种群的遗传多样性、遗传结构和物种鉴定。宽鳍鱲基因组DNA 14个微卫星位点中有11个微卫星位点具有中高多态性,3个位点(Zpla08、Zpla09、Zpla10)偏离Hardy-Weinberg平衡,在群体遗传研究中应慎用。

高粱×苏丹草后代群体农艺及产量性状QTL初步定位

为进一步探究高粱籽粒和茎秆产量的遗传规律,运用粒用高粱忻粱52和苏丹草TS 185作为亲本进行杂交并得到F_(2)及F_(2)∶3群体,利用115对多态性引物对430份F_(2)群体使用区间作图法构建遗传连锁图谱,以LOD值等于3作为阈值。结果表明,分蘖数、叶片数、茎粗、穗长、株高、茎秆鲜质量、整株鲜质量、着壳率、穗质量、千粒质量、单穗粒质量、单穗粒数12个农艺性状共检测到86个QTL。在1号染色体sam17164—sam15397区间定位到茎秆鲜质量的QTL;在2号染色体Xcup64—Xcup26区间定位到分蘖数的QTL,Xtxp019—sam01138区间定位到叶片的QTL,Xcup26—Xtxp080区间定位到茎秆鲜质量的QTL;在3号染色体sam44791—sam33751区间定位到穗长的QTL;在7号染色体sam39622—sam43980区间定位到着壳率的QTL;在8号染色体sam10491—sam17740区间定位到整株鲜质量的QTL;在10号染色体sam710901b—sam59778区间定位到分蘖数的QTL,以上这些都是新检测到的位点。

有利基因和有利的基因互作能够提高籼粳杂种育性

利用一套籼粳交DH系与两份具有广亲和性的水稻光（温）敏核不育系测交，构建两个测交F_1群体，同时用92个多型性的RFLP标记分析了杂交亲本和另外30个不同类型的籼、粳品种（对照组）的基因型。利用对照组舢或粳表型与分子标记的关联性，检测出41个与籼粳分化高度相关的RFLP标记。结果表明，87．8％的这种标记参与了对杂种优势显著或极显著的影响，表明在水稻的演化过程中，参与适应性进化的基因与控制经济产量的QTLs存在平行进化关系。进一步分析表明，杂种F_1育性是一个影响籼粳杂种产量优势的主要因子，而F_1育性同时受分化标记位点内和位点间基因互作的重要影响，提出了解释籼粳杂种育性现象的新模式。

21个野生、培育及地方猪种免疫及生化遗传标记基因位点的遗传分化研究

分析了亚、欧、美、非21个野生、培育及地方猪种4个免疫遗传标记基因位点（E、F、G、L系统）和3个生化遗传标记基因位点（Cp、Am和Tf）的遗传多态性，认为E、Fa、TfC基因在亚洲猪种与欧美猪种间存在着显著差异，是亚洲猪种3个重要的遗传标记基因。根据Fa基因频率在亚、欧、美、非猪种的变化规律分析了其基因流向特点，证明欧美猪的育种过程中利用了中国地方猪种的血缘。计算了所测猪种间的Net’s标准遗传距离，聚类分析发现2个欧洲地方猪种的遗传距离最近，非洲Barodawochnick猪则相距很远，其他猪种的聚类结果与各自的育种历史和地理分布相符，可以认为免疫及生化遗传标记是进行猪种间的遗传分化和品种间的遗传距离分析的有效手段。

两种供氮水平下水稻穗长QTLs的检测

在水稻 (IR6 4× Azucena) DH群体中应用分子标记连锁图 ,对不同供氮水平下的穗长性状进行 QTL区间作图分析。在高氮水平下检测到控制穗长的 QTL s 2个 ,分别位于第 1和第 4染色体上 ;在低氮水平下检测到 5个穗长 QTL s,其中 3个分别位于第 1、4和 6染色体上 ,2个位于第 3染色体的不同部位 ,说明穗长 QTL与供氮水平之间可能存在交互效应。基于这种互作效应及研究中观察到的两供试亲本对低氮胁迫的耐性差异 ,推测仅在低氮水平下检测到的穗长 QTLs可能跟水稻对低氮胁迫耐性有一定的关联。

微卫星DNA在分子遗传标记研究中的应用

随着种群遗传学的发展 ,分子遗传标记特别是微卫星标记已经成为研究种群遗传的有力工具。本文就微卫星遗传标记的研究背景、技术应用以及优势与不足等方面进行了综述。

杂交水稻中超显性效应的分析

本文提出亚群体分析法 ,在二个衍生于杂交稻推广组合的F2 群体中 ,挑选均匀分布于连锁图谱的DNA标记作为固定因子 ,分别根据每个固定因子的基因型将F2 群体分成三类亚群体 :母本型 (I型 )、父本型 (II型 )和杂合型 (III型 )。在大量III型亚群体中 ,杂合度与产量和穗数呈显著正相关。在表现这种相关性的III型亚群体内分析产量QTL和穗数QTL,发现超显性作用是研究组合杂种优势的主要遗传基础。

玉米抗纹枯病QTL定位

以玉米自交系R15（抗）×掖478（感）的229个F2单株为作图群体,构建了包含146个SSR标记位点的遗传连锁图谱,全长1666 cM,平均图距11.4 cM.通过麦粒嵌入法对F2：4群体进行人工接种纹枯病菌,并以相对病斑高为病级划分标准鉴定了玉米纹枯病的抗性.用复合区间作图法分析抗病QTL及遗传效应,共检测到9个抗性QTL,分布于第1、2、3、4、5、6和10条染色体上,单个QTL可解释表型方差的3.72%～7.19%,其中有2个QTL位于染色体6.01抗病基因簇附近.

普通小麦多酚氧化酶活性的QTL分析

多酚氧化酶 (polyphenoloxidase ,PPO)是引起面团 (片 )颜色褐变的主要原因。利用 12 2对SSR引物、4对贮藏蛋白STS引物和 10对AFLP引物组合 ,分析了中优 95 0 7×CA96 32的 71个DH系的基因型 ,构建了由 173个位点组成的遗传连锁图 ,在小麦 2 1个连锁群上覆盖 2 881cM。将该群体种植于 3个环境 ,采用复合区间作图法 (CIM)进行了PPO活性的QTL分析。结果表明 ,控制籽粒PPO活性的主效QTL有 2个 ,分别位于染色体 2AL和 2DL上 ,贡献率分别为 37 9%～5 0 0 %和 2 5 0 %～ 2 9 1%。所有QTL都来自高PPO活性亲本中优 95 0 7。讨论了通过遗传途径降低PPO活性及利用分子标记辅助育种的可能性。

数量性状基因作图精度的主要影响因子

采用计算机模拟数据和数量性状基因作图的双侧标记基因型均值回归方法 ,研究了分子标记密度、性状遗传力和样本容量 3因素对 F2 群体数量性状基因图谱构建的影响。结果表明 :( 1)在 QTL被发现的能力上 ,适当大 (标记间距 15c M)的标记密度较有利于 QTL的检测 ,过大或过小均不利 ;随着遗传力提高和样本容量变大发现 QTL的能力提高 ,但效率下降。为此可以给出一定保证度下的最适标记密度和样本容量 ,以减少试验成本。如 QTL的遗传力 10 %、标记间距 15c M,则样本容量 30 0就可保证 QTL的发现能力达 80 %以上。 ( 2 )在 QTL位置和效应估计上 ,只要标记间距不过大 (如 50c M) ,一般来说 ,一旦 QTL能被检测到 ,则其位置和效应的估计也较准确 ,其位置估计值的 95%置信区间绝大多数在 2 0 c