Development and Characterization of Simple Sequence Repeat Markers Providing Genome-Wide Coverage and High Resolution in Maize

Simple sequence repeats (SSRs) have been widely used in maize genetics and breeding, because they are co-dominant, easy to score, and highly abundant. In this study, we used whole-genome sequences from 16 maize inbreds and 1 wild relative to determine SSR abundance and to develop a set of high-density polymorphic SSR markers. A total of 264 658 SSRs were identified across the 17 genomes, with an average of 135 693 SSRs per genome. Marker density was one SSR every of 15.48 kb. (C/G)n, (AT)n, (CAG/CTG)n, and (AAAT/ATTT)n were the most frequent motifs for mono, di-, tri-, and tetra-nucleotide SSRs, respectively. SSRs were most abundant in intergenic region and least frequent in untranslated regions, as revealed by comparing SSR distributions of three representative resequenced genomes. Comparing SSR sequences and e-polymerase chain reaction analysis among the 17 tested genomes created a new database, including 111 887 SSRs, that could be develop as polymorphic markers in silico. Among these markers, 58.00, 26.09, 7.20, 3.00, 3.93, and 1.78% of them had mono, di-, tri-, tetra-, penta-, and hexa-nucleotide motifs, respectively. Polymorphic information content for 35 573 polymorphic SSRs out of 111 887 loci varied from 0.05 to 0.83, with an average of 0.31 in the 17 tested genomes. Experimental validation of polymorphic SSR markers showed that over 70% of the primer pairs could generate the target bands with length polymorphism, and these markers would be very powerful when they are used for genetic populations derived from various types of maize germplasms that were sampled for this study.     

Genetic Diversity of Some Pear Cultivars and Genotypes Using Simple Sequence Repeat (SSR) Markers

The genetic diversity and relationships among 47 pear cultivars and genotypes (Pyrus spp.), including 4 Japanese pears (Pyrus pyrifolia), 40 European pears (Pyrus communis), 1 Chinese pear (Pyrus bretschneideri) as well as 2 wild relatives (Pyrus salicifolia and Pyrus mazandaranica) were studied using 28 microsatellite primer pairs. A total of 174 alleles were produced at the 28 SSR loci with their sizes ranging from 81 to 290?bp. The number of observed alleles for each locus ranged from 3 (TsuENH014 and TsuENH046) to 12 (NB103a), with an average of 6.21 alleles per locus. In some SSR loci, more than two alleles were amplified in some cultivars and genotypes, suggesting that duplication has occurred in those accessions. This information suggests that at least two genomic regions exist for these loci in the pear genome. The observed heterozygosity (H _o) values of amplified loci ranged from 0.17 (TsuENH006) to 0.97 (NB103a). Shannon's information index (I) value was observed to be highest (2.14) in the NB103a locus, while the TsuENH006 locus had the lowest value with an average of 1.37 among SSR loci. The Dice genetic similarity coefficient ranged from 0.29 (??Nijisseiki?? and P. mazandaranica) to 0.91 (??Chojuro?? and ??Nijisseiki??) among samples. UPGMA cluster analysis showed two major groups corresponding to the Japanese and European pears.     

Transmission of Fruit Quality Traits in Apricot (Prunus armeniaca L.) and Analysis of Linked Quantitative Trait Loci (QTLs) Using Simple Sequence Repeat (SSR) Markers

Twelve important pomological traits related to fruit quality were studied during 3 years in an F₁ apricot progeny of 160 seedlings derived from a cross between the Spanish selection ‘Z701-1’ and the South African cultivar ‘Palsteyn’. Results indicated quantitative transmission of most of the fruit quality traits studied. In addition, a clear influence of the genetic background of parents was observed. In some seedlings, values outside the range of the parent were observed due to the influence of this genetic background. No correlations were found among most agronomic traits in apricot during the 3 years of the study. However, high correlations between years were described for most of the evaluated traits, and the environment had limited influence on the expression of the trait. A genetic map was developed using 41 apricot and peach SSR markers. The map obtained showed eight linkage groups (corresponding to the eight chromosomes) covering a total distance of 369.3 cM and an average distance between markers of 9 cM. Fifty-four QTLs associated with different traits were identified, including: blooming date (linkage groups G1, G4 and G7); ripening time (G4 and G6); fruit development (G4 and G6); fruit weight (G1 and G4); stone weight (G1 and G7); flesh color (G1 and G6); pH (G1, G2 and G4); malic acid (G1, G2 and G4); and soluble solids content (G4 and G5). We have highlighted several QTLs in G4 that explain the variability in various traits related to fruit quality such as blooming date, ripening time, and soluble solids content. In addition, we have also highlighted an important QTL on G2 that explains much of the variation in levels of acidity.     

Differentiation of the American and Oriental Maydeae Accessions Using the Maize Simple Sequence Repeat (SSR) Markers

The present study evaluated the utility of maize microsatellite markers in genotype differentiation and analysis of genetic diversity among the Oriental Maydeae accessions (Coix aquatica and Chionachne koenigii) vis-à-vis the American Maydeae (maize, teosintes and maize-teosinte derivatives). Analysis of 27 microsatellite loci distributed throughout the maize genome led to the detection of 89 SSR alleles at average of 3.30 per locus. Polymorphism information content (PIC) values and observed genetic distances showed the existence of large variability among the various accessions. The maize SSR markers, particularly nc013, phi059, bnlg1523 and umc1014, were highly effective in differentiating the Oriental Maydeae accessions from the American Maydeae. Cluster analysis and Principal Component Analysis based on the SSR data clearly indicated significant genetic divergence between the Oriental Maydeae and the American Maydeae accessions, as well as between Coix aquatica and Chionachne koenigii. Molecular analyses would be valuable in gaining a better understanding of genera belonging to the Oriental Maydeae, the lesser known wild relatives of maize.     

38份晾晒烟种质资源遗传关系的SSR分析

利用SSR标记技术对38份晾晒烟种质资源的遗传关系进行了分析。从自己开发的近3000对烟草SSR引物中随机选出30对引物,在38份供试材料中共检测出173个等位基因,每对SSR引物可检测的等位基因数为2~11个,平均为5.77个。38份材料间遗传相似系数（GS）的变化范围为0.165-0.928,平均GS 为0.546。表明38份晾晒烟的遗传多样性丰富,遗传差异较大,亲缘关系较远。聚类分析表明,在L1（GS-0.165）处可将38个品种分为2大类,即晾晒烟类群和美国从烟草起源地收集的烟草（TI：Tobacco Instruction）类群;晾晒烟类群又可进一步分为4组,其聚类结果与所期望的结果基本一致。表明SSR是一种有效、稳定和可靠的分子标记,能较好地从分子水平上揭示烟草(尤其是晾晒烟)种质资源的遗传背景和亲缘关系。     

Transferability and Fine-Mapping of Genome-Wide Associated Loci for Adult Height across Human Populations

Human height is the prototypical polygenic quantitative trait. Recently, several genetic variants influencing adult height were identified, primarily in individuals of East Asian (Chinese Han or Korean) or European ancestry. Here, we examined 152 genetic variants representing 107 independent loci previously associated with adult height for transferability in a well-powered sample of 1,016 unrelated African Americans. When we tested just the reported variants originally identified as associated with adult height in individuals of East Asian or European ancestry, only 8.3% of these loci transferred (p-values≤0.05 under an additive genetic model with directionally consistent effects) to our African American sample. However, when we comprehensively evaluated all HapMap variants in linkage disequilibrium (r ²≥0.3) with the reported variants, the transferability rate increased to 54.1%. The transferability rate was 70.8% for associations originally reported as genome-wide significant and 38.0% for associations originally reported as suggestive. An additional 23 loci were significantly associated but failed to transfer because of directionally inconsistent effects. Six loci were associated with adult height in all three groups. Using differences in linkage disequilibrium patterns between HapMap CEU or CHB reference data and our African American sample, we fine-mapped these six loci, improving both the localization and the annotation of these transferable associations.     

Correlation of Simple Sequence Repeat (SSR) Variants in the Leader Sequence of the waxy Gene with Amylose Content of the Grain in Rice

Variation of two simple sequence repeats (SSRs) in the leader region of the waxy gene was analyzed in a sample of 74 accessions, including Oryza sativa L. ssp. indica, japonica and wild rice ( O.rufipogon) representing a wide distribution range of amylose content (AC) in cultivated rice. Eight alleles were detected in the (CT)n motif and two alleles were resolved in the (AATT)n motif. The distribution of the alleles of the two SSRs was quite uneven as detected by the (CT)n motif. The repeat numbers of the two SSR motifs, (CT)n and (AATT)n, appeared to be inversely related such that the total length of this region was maintained. AC of the varieties was highly correlated with the length of SSRs. Differences in AC among the various SSR genotypes were statistically highly significant as analyzed using genotypes of both SSR motifs. Although the SSR variation did not seem to have obvious function in the synthesis of the starch synthase encoded by the waxy gene, the almost perfect correlation between the two SSRs and AC level could be used for quality improvement in rice breeding programs.     

水稻蜡质基因引导区的两个SSR序列与直链淀粉含量的相关性(英文)

分析了蜡质基因引导区的两个简单重复序列 (SSR) (CT) n 和 (AATT) n 在 74份水稻材料中的多态性及其与直链淀粉含量 (AC)的关系。这些材料包括了籼稻 (OryzasativaL .ssp .indica)、粳稻 (O .sativassp .japonica)和普通野生稻 (O .rufipogon) ,其AC值覆盖了栽培稻AC分布的整个范围。以 (CT) n 作标记检测到 8个等位基因 ,粳稻品种趋于含有重复数目较多 (n≥ 16 )的等位基因 ,重复次数较少 (n≤ 14)的等位基因只出现在籼稻中。 (AATT)n检测到 2个等位基因 ,野生稻中少数植株表现出杂合性。分析表明AC与这两个SSR序列基因型高度相关 ,高AC (>2 2 .0 % )品种具有 (CT)重复次数较少 (n≤ 14)的等位基因 ;相反 ,除了糯米外 ,所有低或者中等AC的品种都有 (CT)重复数较多 (n≥ 16 )的等位基因。具有重复次数较多的 (AATT) 6等位基因的品种多为高AC ,具有重复次数较少的(AATT) 5等位基因的品种多为低或中等AC。不同SSR基因型品种间AC差异极显著。虽然目前还不能确定这两个SSR序列在直链淀粉合成中的直接功能 ,SSR变异与AC间近乎完全的相关性可作为分子标记直接用于水稻的品质改良。     

辽宁省近15年的部分水稻主栽品种的简单重复序列(SSR)多态性分析

应用简单重复序列(SSR)标记方法对辽宁省近15年的14个大面积种植的水稻品种进行遗传多样性分析的结果表明,17对引物共产生43个位点,其中多态性位点17个,平均每对SSR引物检测到2.53个,占位点总数的39.53%。用Nei’s公式计算水稻品种间的遗传距离,并以算术平均非加权聚类(UPGMA)法进行聚类分析并结合系谱分析结果表明,辽宁省近15年的水稻主栽品种遗传多样性不够丰富,多数品种间的亲缘关系较近,欲进一步提高产量还需拓宽遗传基础。     

Genetic diversity and population structure of the endangered conifer Taxus wallichiana var. mairei (Taxaceae) revealed by Simple Sequence Repeat (SSR) markers

Taxus wallichiana var. mairei is an endangered conifer with important medicinal value in southern China. Nuclear SSR markers were employed to assess genetic diversity and structure of 13 geographically disjunct populations. The present study revealed a moderate genetic diversity (H_E = 0.538) and low genetic differentiation (F_ST = 0.159). And most populations encountered in severe inbreeding and bottleneck effect. No significant genetic structure was detected by IBD and Structure analysis, which was supported by AMOVA analysis. The present results could be ascribed to an earlier period of more pronounced gene flow when the species had a more continuous distribution. However, the 13 studied populations were divided into four clusters based on the UPGMA dendrogram; these clusters were almost congruent with their geographical distributions. Vital areas such as southern mountains of Sichuan basin, Nanling Mts. and the margin of this yew's distribution range had a high priority for conservation.     

小麦SSR和EST-SSR引物对无芒雀麦的通用性分析

无芒雀麦(Bromus inermis Leyss.)具有营养价值高、产量大、利用季节长、耐寒耐旱、适应性强等优良品质。为了解小麦SSR和EST-SSR引物在亲缘植物无芒雀麦中的通用性,本研究选用位于普通小麦7个部分同源群的203对SSR引物和46对EST-SSR引物对无芒雀麦基因组DNA进行了扩增。结果显示:有137对(67.49%)SSR和30对(65.22%)EST-SSR引物对无芒雀麦可以有效扩增,平均扩增条带数分别为2.8和2.5,即小麦SSR和EST-SSR引物在无芒雀麦中具有较高的通用性;研究还发现,来自小麦B基因组和第5同源群染色体的引物在无芒雀麦中的有效扩增比率和平均扩增条带数最低。据此推断,小麦B基因组和第5同源群染色体可能与无芒雀麦基因组的亲缘关系较远。该研究对开发无芒雀麦基因组的特异分子标记、进行遗传多样性分析和功能基因定位等具有一定的参考价值。     

Inheritance of Flowering Time in Apricot (<Emphasis Type="Italic">Prunus armeniaca</Emphasis> L.) and Analysis of Linked Quantitative Trait Loci (QTLs) using Simple Sequence Repeat (SSR) Markers

Time of flowering was studied during 3 years in a BC1 apricot progeny of 73 seedlings derived from a cross between the F1 selection “Z506-07” (“Orange Red” × “Currot”) and the Spanish cultivar “Currot”. Results indicated a quantitative inheritance of flowering time in apricot with an influence of juvenility and environmental conditions (chill accumulation) on the evaluation and expression of this trait. Genetic maps consisting of 11 linkage groups for both parents representing the eight chromosomes of apricot were developed using 46 apricot and peach simple sequence repeat (SSR-microsatellites) markers and were used for the identification of quantitative trait loci (QTL). QTL analysis for flowering time allowed the identification of one significant QTL on the linkage group 5 (G5) of “Z506-07”, and explaining most of the phenotypic variation. Two microsatellite loci (UDAp-423r and AMPA-105) were found to be tightly linked to this important agronomic trait. Finally, we discuss the stability of the QTL described during the 3 years of the study and the development of efficient marker-assisted selection strategies applied to apricot and other Prunus breeding programs.     

Genome-Wide Characterization and Linkage Mapping of Simple Sequence Repeats in Mei (Prunus mume Sieb. et Zucc.)

Because of its popularity as an ornamental plant in East Asia, mei (Prunus mume Sieb. et Zucc.) has received increasing attention in genetic and genomic research with the recent shotgun sequencing of its genome. Here, we performed the genome-wide characterization of simple sequence repeats (SSRs) in the mei genome and detected a total of 188,149 SSRs occurring at a frequency of 794 SSR/Mb. Mononucleotide repeats were the most common type of SSR in genomic regions, followed by di- and tetranucleotide repeats. Most of the SSRs in coding sequences (CDS) were composed of tri- or hexanucleotide repeat motifs, but mononucleotide repeats were always the most common in intergenic regions. Genome-wide comparison of SSR patterns among the mei, strawberry (Fragaria vesca), and apple (Malus×domestica) genomes showed mei to have the highest density of SSRs, slightly higher than that of strawberry (608 SSR/Mb) and almost twice as high as that of apple (398 SSR/Mb). Mononucleotide repeats were the dominant SSR motifs in the three Rosaceae species. Using 144 SSR markers, we constructed a 670 cM-long linkage map of mei delimited into eight linkage groups (LGs), with an average marker distance of 5 cM. Seventy one scaffolds covering about 27.9% of the assembled mei genome were anchored to the genetic map, depending on which the macro-colinearity between the mei genome and Prunus T×E reference map was identified. The framework map of mei constructed provides a first step into subsequent high-resolution genetic mapping and marker-assisted selection for this ornamental species.     

Characterization of Novel Minisatellite Repeat Loci in Atlantic Salmon (Salmo salar) and Their Phylogenetic Distribution

We present here the sequence and characterization of various minisatellite-like tandem repeat loci isolated from the genome of Atlantic salmon (Salmo salar). Their diversity of sequence and lack of core motifs common to minisatellites of other species suggest the presence of numerous and previously unidentified simple sequence repeat families in this salmonid. Evidence for their ubiquity was provided by screening of a salmon genomic library. Southern blot analysis of the phylogenetic distribution of a subset of the minisatellites found one sequence to be pervasive among vertebrates, others present only in Salmoninae or Salmonidae species, and one amplified only in Atlantic salmon. There is evidence for the positioning of microsatellite and minisatellite arrays in close proximity at many loci. Furthermore, one tandem repeat appears to have been inserted into the transposase coding region of a copy of the Tc1 transposon-like element recently identified in salmonids. Received: 9 October 1996 / Accepted: 20 May 1997     

Length Polymorphisms of Simple Sequence Repeat DNA in Soybean

The objective of this work was to ascertain the presence and degree of simple sequence repeat (SSR) DNA length polymorphism in the soybean [Glycine max (L.) Merr.]. A search of GenBank revealed no (CA)n or (GT)n SSRs with n greater than 8 in soybean. In contrast, 5 (AT)n and 1 (ATT)n SSRs with n ranging from 14 to 27 were detected. Polymerase chain reaction (PCR) primers to regions flanking the six SSR loci were used in PCR amplification of DNA from 43 homozygous soybean genotypes. At three loci, amplification produced one PCR product per genotype and revealed 6, 7 and 8 product length variants (alleles) at the three loci, respectively. F1 hybrids between parents carrying different alleles produced two PCR products identical to the two parents. Codominant segregation of alleles among F2 progeny was demonstrated at each locus. A soybean DNA library was screened for the presence of (CA/GT)n SSRs. Sequencing of positive clones revealed that the longest such SSR was (CA)9. Thus, (CA)n SSRs with n of 15 or more are apparently much less common in soybean than in the human genome. In contrast to humans, (CA)n SSRs will probably not provide an abundant source of genetic markers in soybean. However, the apparent abundance of long (AT)n sequences should allow this SSR to serve as a source of highly polymorphic genetic markers in soybean.