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) represen...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.展开更多
A simple and efficient method was presented for isolating microsatellite DNA markers from peanut (Arachis hypogaea L.) genome. The genomic DNA was converted into pre-amplified AFLP fragments and hybridized with biotin...A simple and efficient method was presented for isolating microsatellite DNA markers from peanut (Arachis hypogaea L.) genome. The genomic DNA was converted into pre-amplified AFLP fragments and hybridized with biotin-labeled SSR probes. Then the hybrid mixture was used to incubate with magnetic beads coated with streptavidin. After washing to remove the non-SSR fragments, the eluted single-strand DNA, which was cloned and sequenced, was largely enriched for microsatellites. Primers can then be designed according to the sequence flanking the repeat motifs and used for polymorphism analysis. The whole experiment can be completed within one week and can be employed as a reliable option for any molecular laboratory to develop SSR markers.展开更多
Microsatellite DNA or simple sequence repeats (SSRs) can be derived from expressed se- quence tags (ESTs). These markers are important for gene mapping as well as marker-assisted selection (MAS). To develop EST-SSRs f...Microsatellite DNA or simple sequence repeats (SSRs) can be derived from expressed se- quence tags (ESTs). These markers are important for gene mapping as well as marker-assisted selection (MAS). To develop EST-SSRs for cotton gene map- ping, we selected and characterized functional markers in Gossypium raimondii, which consisted of 58906 non-redundant EST sequences from NCBI. Among them there were 2620 microsatellite se- quences containing 2818 EST-SSRs, which amoun- ted to 4.45% of the non-redundant starting sequence population. This incidence was equivalent to one EST-SSR in every 14.8 kb of G. raimondii genetic material. Among the different motifs ranging from 1 to 6 bp, trinucleotide repeats were most abundant (38.31%), followed by dinucleotide repeats (24.09%) and mononucleotide repeats (23.35%). Among all identified motif types, A/T had the highest frequency (18.67%), followed by AT/TA (14.83%). Among the compound motifs, tandem trinucleotides occurred with the highest frequency (48.65%). In all, we identi- fied 1554 EST-SSRs primer pair sequences. 300 of them were randomly selected to screen the poly- morphisms between the mapping parents G· hirsutum acc. TM-1 and G· barbadense cv. Hai7124, to con- struct linkage groups in cultivated allotetraploid cot- ton. Among them, 129 (43%) primer pairs were found to have polymorphisms. Using these EST-SSRs we can compare EST-SSR distributions among different cotton species and various chromosomal locations.展开更多
文摘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.
文摘A simple and efficient method was presented for isolating microsatellite DNA markers from peanut (Arachis hypogaea L.) genome. The genomic DNA was converted into pre-amplified AFLP fragments and hybridized with biotin-labeled SSR probes. Then the hybrid mixture was used to incubate with magnetic beads coated with streptavidin. After washing to remove the non-SSR fragments, the eluted single-strand DNA, which was cloned and sequenced, was largely enriched for microsatellites. Primers can then be designed according to the sequence flanking the repeat motifs and used for polymorphism analysis. The whole experiment can be completed within one week and can be employed as a reliable option for any molecular laboratory to develop SSR markers.
基金supported in part by the National Natural Science Foundation of China(Grant Nos.30471104&30270806)Programs for Changjiang Scholars and Innovative Research Team in University and for New Century Excellent Talents in Ministry of Education(Grant No.NCET-04-0500)+1 种基金Program for Excellent Talents in Jiangsu Province(Grant No.BK2003414)Jiangsu High-Tech Project(Grant No.BG2004305).
文摘Microsatellite DNA or simple sequence repeats (SSRs) can be derived from expressed se- quence tags (ESTs). These markers are important for gene mapping as well as marker-assisted selection (MAS). To develop EST-SSRs for cotton gene map- ping, we selected and characterized functional markers in Gossypium raimondii, which consisted of 58906 non-redundant EST sequences from NCBI. Among them there were 2620 microsatellite se- quences containing 2818 EST-SSRs, which amoun- ted to 4.45% of the non-redundant starting sequence population. This incidence was equivalent to one EST-SSR in every 14.8 kb of G. raimondii genetic material. Among the different motifs ranging from 1 to 6 bp, trinucleotide repeats were most abundant (38.31%), followed by dinucleotide repeats (24.09%) and mononucleotide repeats (23.35%). Among all identified motif types, A/T had the highest frequency (18.67%), followed by AT/TA (14.83%). Among the compound motifs, tandem trinucleotides occurred with the highest frequency (48.65%). In all, we identi- fied 1554 EST-SSRs primer pair sequences. 300 of them were randomly selected to screen the poly- morphisms between the mapping parents G· hirsutum acc. TM-1 and G· barbadense cv. Hai7124, to con- struct linkage groups in cultivated allotetraploid cot- ton. Among them, 129 (43%) primer pairs were found to have polymorphisms. Using these EST-SSRs we can compare EST-SSR distributions among different cotton species and various chromosomal locations.
