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61.
Characterization of trinucleotide SSR motifs in wheat 总被引:21,自引:0,他引:21
Song QJ Fickus EW Cregan PB 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2002,104(2-3):286-293
Length differences among trinucleotide-based microsatellite alleles can be more easily detected and frequently produce fewer
”stutter bands” as compared to dinucleotide-based microsatellite markers. Our objective was to determine which trinucleotide
motif(s) would be the most-polymorphic and abundant source of trinucleotide microsatellite markers in wheat (Triticum aestivum L.). Four genomic libraries of cultivar ’Chinese Spring’ were screened with nine trinucleotide probes. Based on the screening
of 28550 clones, the occurrences of (CTT/GAA)
n
, (GGA/CCT)
n
, (TAA/ATT)
n
, (CAA/GTT)
n
, (GGT/CCA)
n
, (CAT/GTA)
n
, (CGA/GCT)
n
, (CTA/GAT)
n
, and (CGT/GCA)
n
repeats were estimated to be 5.4×104, 3.5×104, 3.2×104, 1.2×104, 6.3×103, 4.9×103, 4.5×103, 4.5×103 and 3.6×103, i.e., once every 293 kbp, 456 kbp, 500 kbp, 1.3 Mbp, 2.6 Mbp, 3.2 Mbp, 3.6 Mbp, 3.6 Mbp and 4.5 Mbp in the wheat genome,
respectively. Of 236 clones selected for sequencing, 38 (93%) (TAA/ATT)
n
, 30 (43%) (CTT/GAA)
n
, 16 (59%) (CAA/GTT)
n
, 3 (27%) (CAT/GTA)
n
and 2 (4%) (GGA/CCT)
n
clones contained microsatellites with eight or more perfect repeats. From these data, 29, 27 and 16 PCR primer sets were
designed and tested to the (TAA/ATT)
n
, (CTT/GAA)
n
and (CAA/GTT)
n
microsatellites, respectively. A total of 12 (41.4%) primers designed to (TAA/ATT)
n
, four (14.8%) to (CTT/GAA)
n
, and two (12.5%) to (CAA/GTT)
n
resulted in polymorphic markers. The results indicated that (TAA/ATT)
n
microsatellites would provide the most-abundant and the most-polymorphic source of trinucleotide microsatellite markers in
wheat.
Received: 17 February 2001 / Accepted: 31 May 2001 相似文献
62.
Mapping of QTL associated with waterlogging tolerance during the seedling stage in maize 总被引:7,自引:0,他引:7
BACKGROUND AND AIMS: Soil waterlogging is a major environmental stress that suppresses maize (Zea mays) growth and yield. To identify quantitative trait loci (QTL) associated with waterlogging tolerance at the maize seedling stage, a F2 population consisting of 288 F(2:3) lines was created from a cross between two maize genotypes, 'HZ32' (waterlogging-tolerant) and 'K12' (waterlogging-sensitive). METHODS: The F2 population was genotyped and a base-map of 1710.5 cM length was constructed with an average marker space of 11.5 cM based on 177 SSR (simple sequence repeat) markers. QTL associated with root length, root dry weight, plant height, shoot dry weight, total dry weight and waterlogging tolerance coefficient were identified via composite interval mapping (CIM) under waterlogging and control conditions in 2004 (EXP.1) and 2005 (EXP.2), respectively. KEY RESULTS AND CONCLUSIONS: Twenty-five and thirty-four QTL were detected in EXP.1 and EXP.2, respectively. The effects of each QTL were moderate, ranging from 3.9 to 37.3 %. Several major QTL determining shoot dry weight, root dry weight, total dry weight, plant height and their waterlogging tolerance coefficient each mapped on chromosomes 4 and 9. These QTL were detected consistently in both experiments. Secondary QTL influencing tolerance were also identified and located on chromosomes 1, 2, 3, 6, 7 and 10. These QTL were specific to particular traits or environments. Although the detected regions need to be mapped more precisely, the findings and QTL found in this study may provide useful information for marker-assisted selection (MAS) and further genetic studies on maize waterlogging tolerance. 相似文献
63.
64.
65.
66.
The abundance and inherent potential for variations in simple sequence repeats (SSRs) or microsatellites resulted in valuable source for genetic markers in
eukaryotes. We describe the organization and abundance of SSRs in fungus Fusarium graminearum (causative agent for Fusarium head blight or head
scab of wheat). We identified 1705 SSRs of various nucleotide repeat motifs in the sequence database of F. graminearum. It is observed that
mononucleotide repeats (62%) were most abundant followed by di- (20%) and trinucleotide repeats (14%). It is noted that tetra-, penta- and
hexanucleotide repeats accounted for only 4% of SSRs. The estimated frequency of Class I SSRs (perfect repeats ≥20 nucleotides) was one SSR per 124.5
kb, whereas the frequency of Class II (perfect repeats >10 nucleotides and ≫20 nucleotides) was one SSR per 25.6 kb. The dynamics of SSRs will be a
powerful tool for taxonomic, phylogenetic, genome mapping and population genetic studies as SSR based markers show high levels of allelic variation,
codominant inheritance and ease of analysis. 相似文献
67.
Takashi Sayama Tae-Young Hwang Kunihiko Komatsu Yoshitake Takada Masakazu Takahashi Shin Kato Hiroko Sasama Ayako Higashi Yumi Nakamoto Hideyuki Funatsuki Masao Ishimoto 《DNA research》2011,18(2):107-115
Among commonly applied molecular markers, simple sequence repeats (SSRs, or microsatellites) possess advantages such as a high level of polymorphism and codominant pattern of inheritance at individual loci. To facilitate systematic and rapid genetic mapping in soybean, we designed a genotyping panel comprised 304 SSR markers selected for allelic diversity and chromosomal location so as to provide wide coverage. Most primer pairs for the markers in the panel were redesigned to yield amplicons of 80–600 bp in multiplex polymerase chain reaction (PCR) and fluorescence-based sequencer analysis, and they were labelled with one of four different fluorescent dyes. Multiplex PCR with sets of six to eight primer pairs per reaction generated allelic data for 283 of the 304 SSR loci in three different mapping populations, with the loci mapping to the same positions as previously determined. Four SSRs on each chromosome were analysed for allelic diversity in 87 diverse soybean germplasms with four-plex PCR. These 80 loci showed an average allele number and polymorphic information content value of 14.8 and 0.78, respectively. The high level of polymorphism, ease of analysis, and high accuracy of the SSR genotyping panel should render it widely applicable to soybean genetics and breeding. 相似文献
68.
利用覆盖玉米全基因组的22对SSR引物,对180份玉米自交系的亲缘关系进行分子评价.结果显示:22对SSR引物共检测到129个等位基因,每一位点平均等位基因数5.9,变幅2~13;平均基因多样性指数和平均多态性信息含量分别为0.583和0.528.基于模型的群体结构分析将所有材料分为5个类群,与国内自交系划分的杂种优势... 相似文献
69.
Qi-Yue Zhou Hui-Xia Cai Zi-Han Liu Lang-Xing Yuan Lei Yang Tuo Yang Bo Li Pan Li 《Plant Diversity》2022,44(6):542
Wenchengia alternifolia (Lamiaceae), the sole species of the genus Wenchengia is extremely rare and is currently listed as Critically Endangered (CR) on the IUCN Red List. The species had long been considered endemic to Hainan Island, China and was once believed to be extinct until a small remnant population was rediscovered at the type locality in 2010. Four more populations were later found on Hainan and in Vietnam. In order to develop genomic resources for further studies on population genetics and conservation biology of this rare species, we identified infraspecific molecular markers in the present study, using genome skimming data of five individuals collected from two populations on Hainan Island and three populations in Vietnam respectively. The length of plastome of the five individuals varied from 152,961 bp to 150,204 bp, and exhibited a typical angiosperm quadripartite structure. Six plastid hotspot regions with the Pi > 0.01 (trnH-psbA, psbA-trnK, rpl22, ndhE, ndhG-ndhI and rps15-ycf1), 1621 polymorphic gSSRs, as well as 1657 candidate SNPs in 237 variant nuclear genes were identified, thereby providing important information for further genetic studies. 相似文献
70.
陕棉抗病种质及其衍生品种的遗传多样性与群体结构研究 总被引:1,自引:0,他引:1
通过72个分布于棉花全基因组的SSR标记,对54份陕棉抗病种质及其衍生品种的遗传多样性与群体结构进行了分析。结果表明:(1)54份陕棉种质间的遗传相似系数在0.733 3~0.987 2之间,其中材料间相似系数≤0.90的占11.1%,相似系数≥0.95的占55.6%,相似系数在0.90~0.95的占33.3%。(2)72个SSR标记等位基因变异的多态性信息含量(PIC值)在0.04~0.68,平均为0.33。(3)基于遗传距离的UPGMA聚类分析显示,在遗传相似系数为0.877时将54个品种分为5类,第Ⅰ类44个品种,第Ⅲ类7个品种,第Ⅱ、Ⅳ、Ⅴ类各1个品种。(4)基于数学模型的聚类和群体结构分析显示,54份种质归属于4个组群。研究认为,54份材料间遗传相似系数较大,遗传基础比较狭窄,多样性很低。 相似文献