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Genetic structure and linkage disequilibrium in Korean rice germplasm
Jong-Wook Chung,Anupam Dixit,Gi-An Lee,Kyung-Ho Ma,Jae-Woong Yu,Jung-Ro Lee,Sok-Young Lee,Hee-Kyoung Kang,Nam-Jin Chung,Yong-Gu Cho,Kenneth L. McNally,Jae-Gyun Kwag,Seung-Geun Jong,Yong-Jin Park 한국작물학회 2008 한국작물학회 학술발표대회 논문집 Vol.2008 No.10
The present study was carried out to assess the genetic diversity, population structure and linkage disequilibrium in Korea. In model-based population, Korean rice germplasm were classified into four subpopulaton designated as indica cultivated, japonica cultivated, indica weedy, and japonica weedy were identified. Pair-wise estimates of FST indicated a different degree of differentiation between the four model-based populations with values ranging from 0.073 (between japonica cultivated and japonica weedy) and 0.474 (between japonica weedy and indica weedy). The indica weedy population appeared to be highly differentiated as compared to other populations. The indica cultivated have the highest gene diversity (0.58), followed by japonica cultivated (0.50), japonica weedy (0.42) and indica weedy (0.35). The total number of specific alleles in indica weedy and japonica weedy populations was 39 alleles (23 markers) and 55 alleles (22 markers), respectively. An average of LD (r2) value of indica weedy and japonica weedy type was higher than two other populations, both in inter- and intra-chromosome, indicating the possible reproductive and geographical isolations of sub-populations in cultivated rice fields.
MA, KYUNG-HO,JANG, DUK-HWAN,DIXIT, ANUPAM,CHUNG, JONG-WOOK,LEE, SOK-YOUNG,LEE, JUNG-RO,KANG, HEE-KYOUG,KIM, SEONG-MIN,PARK, YONG-JIN BLACKWELL 2007 MOLECULAR ECOLOGY NOTES Vol.7 No.6
<P>Abstract</P><P>The present study reports the development of 30 polymorphic microsatellite markers for zoysiagrass <I>Zoysia japonica</I> Steud. The 30 markers produced a total of 125 alleles with an average of 4.2 alleles per locus. Values for observed and expected heterozygosities ranged from 0.10 to 0.95 and from 0.15 to 0.81, respectively. At significance threshold (<I>P <</I> 0.05), 11 loci deviated from Hardy–Weinberg equilibrium, whereas significant linkage disequilibrium values were observed between 16 pairs of loci. These markers may provide information needed to select genetically diverse parents for developing breeding and mapping populations of zoysiagrass.</P>
Isolation and characterization of microsatellite markers in <i>Perilla frutescens</i> Brit
KWON, SOON-JAE,LEE, JU-KYONG,KIM, NAM-SOO,YU, JAE-WOONG,DIXIT, ANUPAM,CHO, EUN-GI,PARK, YONG-JIN Blackwell Science Ltd 2005 MOLECULAR ECOLOGY NOTES Vol.5 No.2
<P>Abstract</P><P>We isolated and characterized 13 polymorphic microsatellite primers from <I>Perilla frutescens</I> Brit. var. <I>frutescens</I> by using a modified method that involves one-way PCR amplification with single primer prior to enrichment with an ‘oligo hook’. The efficiency of this procedure for isolating unique microsatellite sequences was approximately 77%. The number of alleles per microsatellite locus ranged from three to 10 with an average of 6.5 alleles per locus while fragment size varied from 156 to 298 bp. The observed and expected heterozygosities ranged from 0.52 to 0.86 and 0.52 to 0.89, respectively. These newly isolated microsatellite markers are expected to provide valuable resources for different genetic studies currently underway in our <I>Perilla</I> genome research program.</P>
Characterization of new microsatellite markers in mung bean, <i>Vigna radiata</i> (L.)
GWAG, JAE-GYUN,CHUNG, JONG-WOOK,CHUNG, HUN-KI,LEE, JEONG-HEUI,MA, KYUNG-HO,DIXIT, ANUPAM,PARK, YONG-JIN,CHO, EUN-GI,KIM, TAE-SAN,LEE, SUK-HA BLACKWELL 2006 MOLECULAR ECOLOGY NOTES Vol.6 No.4
<P>Abstract</P><P>The present work reports the isolation and characterization of new polymorphic microsatellites in mung bean (<I>Vigna radiata</I> L.). Of 93 designed primer pairs, seven were found to amplify polymorphic microsatellite loci, which were then characterized using 34 mung bean accessions. The number of alleles ranged from two to five alleles per locus with an average of three alleles. Observed and expected heterozygosity values ranged from 0 to 0.088 and from 0.275 to 0.683, respectively. All seven loci showed significant deviations from Hardy–Weinberg equilibrium, whereas only one pairwise combination (GBssr-MB77 and GBssr-MB91) exhibited significant departure from linkage disequilibrium. These newly developed markers are currently being utilized for diversity assessment within the mung bean germplasm collection of the Korean Gene Bank.</P>