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1

Electronic Resource

Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.) (1997)

Chen, X. ; Temnykh, S. ; Xu, Y. ; [et al.]

Springer

Theoretical and applied genetics 95 (1997), S. 553-567

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ISSN: 1432-2242

Keywords: Key words Microsatellite ; Simple sequence repeats (SSR) ; Simple sequence length polymorphism(SSLP) ; Linkage map ; Molecular map ; Rice (Oryza sativa)

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract Ninety-four newly developed microsatellite markers were integrated into existing RFLP framework maps of four rice populations, including two doubled haploid, a recombinant inbred, and an interspecific backcross population. These simple sequence repeats (SSR) were predominantly poly(GA) motifs, targetted because of their abundance in rice. They were isolated from a previously described sheared library and a newly constructed enzyme-digested library. Differences in the average length of poly(GA) tracts were observed for clones isolated from the two libraries. The length of GA motifs averaged 21 repeat units for clones isolated from the Tsp-509-digested library, while motifs averaged 17 units for clones from the sheared library. There was no evidence of clustering of microsatellite markers near centromeres or telomeres. Mapping of the 94 newly developed markers as well as of 27 previously reported microsatellites provided genome-wide coverage of the 12 chromosomes, with an average distance of 1 SSLP (simple sequence repeat polymorphism) per 16–20 cM.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s001220050596

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2

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Integrated map of AFLP, SSLP and RFLP markers using a recombinant inbred population of rice (Oryza sativa L.) (1998)

Cho, Y. G. ; McCouch, S. R. ; Kuiper, M. ; [et al.]

Springer

Theoretical and applied genetics 97 (1998), S. 370-380

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ISSN: 1432-2242

Keywords: Key words Amplified fragment length polymorphism (AFLP) ; Simple-sequence length polymorphism (SSLP) ; Restriction fragment length polymorphism (RFLP) ; Rice (Oryza sativa L.) ; Molecular map

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract A molecular map of rice consisting of 231 amplified fragment length polymorphisms (AFLPs), 212 restriction fragment length polymorphisms (RFLPs), 86 simple-sequence length polymorphisms (SSLPs), five isozyme loci, and two morphological mutant loci [phenol staining of grain (Ph), semi-dwarf habit (sd-1)] has been constructed using an F11 recombinant inbred (RI) population. The mapping population consisted of 164 RI lines and was developed via single-seed descent from an intercross between the genetically divergent parents Milyang 23 (M) (tongil type) and Gihobyeo (G) ( japonica type). A subset of previously mapped RFLP and SSLP markers were used to construct the map framework. The AFLP markers were derived from ten EcoRI(+2) and MseI(+3) primer combinations. All marker types were well distributed throughout the 12 chromosomes. The integrated map covered 1814 cM, with an average interval size of 3.4 cM. The MG map is a cornerstone of the Korean Rice Genome Research Program (KRGRP) and is being continuously refined through the addition of partially sequenced cDNA markers derived from an immature-seed cDNA library developed in Korea, and microsatellite markers developed at Cornell. The population is also being used for quantitative trait locus (QTL) analysis and as the basis for marker-assisted variety development.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s001220050907

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3

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The semidwarf gene, sd-1, of rice (Oryza sativa L.). I. Linkage with the esterase locus, Estl-2 (1994)

Cho, Y. G. ; Eun, M. Y. ; Kim, Y. K. ; [et al.]

Springer

Theoretical and applied genetics 89 (1994), S. 49-53

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ISSN: 1432-2242

Keywords: Rice ; Semidwarf gene ; Isozyme marker Esterase ; Isoelectric focusing

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract The linkage relationship between the semidwarf gene (sd-1) and the isozyme locus EstI-2 was elucidated using segregating populations derived from crosses between several semidwarf testers and tall rice varieties. Bimodal distributions for culm length were observed in F2 populations of three cross combinations, including Shiokari/Shiokari (sd-1), Taichung 65 (A,Pn,Pau)/Taichung 65 (sd-1), and Milyang 23/Kasalath. Taking the valley of the distribution curves as the dividing point, two height classes were apparent with a segregation ratio of 3 tall∶1 short, demonstrating this character to be under the control of a single recessive gene. An inheritance study of esterase isozymes, based on isoelectric focusing (IEF), showed that the EstI-2 locus had two active allozymes of monomeric structure and one null form, which were designated “a”, “b”, and “n”, respectively (Eun et al. 1990). Semidwarf testers such as Shiokari (sd-1), Taichung 65 (sd-1) and Milyang 23 have an active allozyme designated as EstI-2aa, while the tall parents, Shiokari and Taichung 65 (A,Pn,Pau), have the active allozyme, EstI-2bb, and Kasalath has a null form of the allozyme, EstI-2nn. By dividing F2 populations based on EstI-2 allozyme patterns, culmlength distributions exhibited trimodal curves. Most of the short plants had the homozygous EstI-2aa pattern of the short parents, most of the tall plants had the homozygous pattern, EstI-2bb or EstI-2nn, and most of the intermediate plants had the heterozygous EstI-2ab or EstI-2an banding pattern. Einkage analysis indicated that sd-1 and EstI-2 were tightly linked. These findings were also confirmed by segregation analyses in F3 progenies. No recombinants among 171 F3 families from the Shiokari/Shiokari (sd-1) combination, five recombinants among 267 F3 families from Taichung 65 (A,Pn,Pau)/Taichung 65(sd-1), and only two recombinants out of 237 F3 families from Milyang 23/Kasalath, were found. The recombination values were 0, 1.87 and 0.8%, respectively.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00226981

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4

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The semidwarf gene, sd-1, of rice (Oryza sativa L.). II. Molecular mapping and marker-assisted selection (1994)

Cho, Y. G. ; Eun, M. Y. ; McCouch, S. R. ; [et al.]

Springer

Theoretical and applied genetics 89 (1994), S. 54-59

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ISSN: 1432-2242

Keywords: Rice ; Semidwarf gene (sd-1) ; RFLP ; Molecular marker ; Marker-assisted selection

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract To establish the location of the semidwarf gene, sd-1, the anthocyanin activator (A), purple node (Pn), purple auricle (Pau), and the isozyme locus, EstI-2, in relation to DNA markers on the molecular linkage map of rice, 20 RFLP markers, previously mapped to the central region of chromosome 1 (McCouch et al. 1988), were mapped onto an F2 population derived from the cross Taichung 65 (A,Pn,Pau)/Taichung 65 (sd-1). sd-1 and EstI-2 were determined to be linked most tightly to RFLP markers RG 109 and RG 220, which cosegregated with each other. The distance between these RFLP markers and sd-1 was estimated to be 0.8 cM, based on an observed recombination value of 0.8%. The order of genes and markers in this region of chromosome 1 was determined to be sd-1 — (EstI-2 — RG220 — RG109) — RG381 — A — Pn — Pau. To test the efficacy of selection for sd-1 based on these linked markers, 50-day-old F2 seedlings derived from another cross, Milyang 23/Gihobyeo, were analyzed for marker genotype. At this age, the semidwarf character could not be clearly detected based on phenotype. In addition, plant height was normally distributed in this population, making it difficult to unambiguously identify plants carrying sd-1. Thirteen seedlings homozygous for the sd-1-associated allele at EstI-2, RG220 and RG109, and 13 seedlings homozygous for the Sd-1-associated allele at all three marker loci were selected for further genetic analysis. At 20 days after heading, the culm lengths of these 26 plants were measured and the expected phenotype was confirmed in every case. These 26 plants were then selfed for four generations and F6 lines were again evaluated to determine whether any recombination among the three molecular markers, or between these markers and the sd-1 gene, could be detected. No recombinants were identified, confirming the tight linkage of these loci and the usefulness of genotypic selection for this recessive semidwarf character prior to the time when it can be evaluated based on phenotype.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00226982

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5

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Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.) (2000)

Cho, Y. G. ; Ishii, T. ; Temnykh, S. ; [et al.]

Springer

Theoretical and applied genetics 100 (2000), S. 713-722

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ISSN: 1432-2242

Keywords: Key words Allelic diversity ; Simple sequence repeat (SSR) ; Microsatellite marker ; Rice (Oryza sativa L.)

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract The growing number of rice microsatellite markers warrants a comprehensive comparison of allelic variability between the markers developed using different methods, with various sequence repeat motifs, and from coding and non-coding portions of the genome. We have performed such a comparison over a set of 323 microsatellite markers; 194 were derived from genomic library screening and 129 were derived from the analysis of rice-expressed sequence tags (ESTs) available in public DNA databases. We have evaluated the frequency of polymorphism between parental pairs of six inter- subspecific crosses and one inter-specific cross widely used for mapping in rice. Microsatellites derived from genomic libraries detected a higher level of polymorphism than those derived from ESTs contained in the GenBank database (83.8% versus 54.0%). Similarly, the other measures of genetic variability [the number of alleles per locus, polymorphism information content (PIC), and allele size ranges] were all higher in genomic library-derived microsatellites than in their EST-database counterparts. The highest overall degree of genetic diversity was seen in GA-containing microsatellites of genomic library origin, while the most conserved markers contained CCG- or CAG-trinucleotide motifs and were developed from GenBank sequences. Preferential location of specific motifs in coding versus non-coding regions of known genes was related to observed levels of microsatellite diversity. A strong positive correlation was observed between the maximum length of a microsatellite motif and the standard deviation of the molecular-weight of amplified fragments. The reliability of molecular weight standard deviation (SDmw) as an indicator of genetic variability of microsatellite loci is discussed.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s001220051343

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6

Electronic Resource

Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.) (2000)

Temnykh, S. ; Park, William D. ; Ayres, Nicola ; [et al.]

Springer

Theoretical and applied genetics 100 (2000), S. 697-712

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ISSN: 1432-2242

Keywords: Key words Microsatellite markers ; Genetic map ; Allelic diversity ; Genome organization ; Rice (Oryza sativa L.)

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract In order to enhance the resolution of an existing genetic map of rice, and to obtain a comprehensive picture of marker utility and genomic distribution of microsatellites in this important grain species, rice DNA sequences containing simple sequence repeats (SSRs) were extracted from several small-insert genomic libraries and from the database. One hundred and eighty eight new microsatellite markers were developed and evaluated for allelic diversity. The new simple sequence length polymorphisms (SSLPs) were incorporated into the existing map previously containing 124 SSR loci. The 312 microsatellite markers reported here provide whole-genome coverage with an average density of one SSLP per 6 cM. In this study, 26 SSLP markers were identified in published sequences of known genes, 65 were developed based on partial cDNA sequences available in GenBank, and 97 were isolated from genomic libraries. Microsatellite markers with different SSR motifs are relatively uniformly distributed along rice chromosomes regardless of whether they were derived from genomic clones or cDNA sequences. However, the distribution of polymorphism detected by these markers varies between different regions of the genome.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/s001220051342

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7

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Construction of a gene expression profile of a human fetal liver by single-pass cDNA sequencing (1995)

Choi, S. S. ; Yun, J. W. ; Choi, E. K. ; [et al.]

Springer

Mammalian genome 6 (1995), S. 653-657

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ISSN: 1432-1777

Source: Springer Online Journal Archives 1860-2000

Topics: Biology , Medicine

Notes: Abstract We have obtained an overall gene expression profile of a human fetal liver by sequencing the 5′ ends of random cDNA clones from an unbiased cDNA library. As a result, many novel genes that might be related to liver growth and hemopoiesis have been identified. Poly (A)+ RNA was purified from the liver of a human fetus obtained at the 22nd week of gestation, and a directional library was constructed with oligo d(T)-primed cDNAs synthesized without any normalizing procedures. The 5′ end of each randomly chosen clone was sequenced by the dideoxy-chain termination methods, and each sequence was used for homology search in the public databases such as GenBank, SWISS-PROT, and PIR. Of 1231 random cDNA clones analyzed, 697 clones representing 204 different transcripts (57%), were identical to previously known human genes. The spectrum of the genes in this category reflected well the physiological characteristics of the fetal liver, a combination of hepatic and hemopoietic functions. About 4% of the clones represented novel gene transcripts with significant homologies to known genes of human or other organisms. These included several genes that are known to be involved in cellular differentiation and/or proliferation. About 25% of the clones had no statistically significant match to any known genes. In summary, we have identified 546 different gene transcripts consisting of 204 known human genes, 42 homologous genes, and 300 unknown genes. Thus, this approach appears to be a highly efficient way to identify novel genes of biological interest.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00352374

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