Assessment of genetic diversity in Dalbergia sissoo clones through RAPD profiling

We studied the genetic polymorphism among 29 clones of shisham （Dalbergia sissoo Roxb） belonging to different geographic regions using random amplified polymorphic DNA （RAPD） markers. Out of 30 primers used, only 20 primers generated polymorphism in amplified product. In total 232 bands were amplified with 20 primers, of which 192 （82%） were polymorphic with an average of 9.6 bands/primer. The resolving power （Rp） ranged from 2.14 （Primer 5） to 11.93 （Primer 4）. Primer 4 and Primer 3 possessed high Rp value. Polymorphism information content （PIC） ranged from 0.15 （Primer 5） to 0.37 （Primer 4）. Primer 4 amplified total 18 bands in 29 genotypes with PIC value of 0.37 hence; this set of primer was most informative. The similarity coefficient analysis revealed two clusters. The first cluster comprised of only 10 clones and the second major cluster comprised of 19 clones. The genetic similarity among 29 clones ranged from 25.86% （clone 10 and 235） to 100% （clone 19 and 59）, suggesting a wide genetic base in shisham clones.

A genetic diversity assessment of starch quality traits in rice landraces from the Taihu basin,China

There are nearly 1 000 rice landrace varieties in the Taihu basin, China. To assess the genetic diversity of the rice, 24 intragenic molecular markers（representing 17 starch synthesis-related genes） were investigated in 115 Taihu basin rice landraces and 87 improved cultivars simultaneously. The results show that the average genetic diversity and polymorphism information content values of the landraces were higher than those of improved cultivars. In total, 41 and 39 allele combinations（of the 17 genes） were derived from the landraces and improved cultivars, respectively; only two identical allele combinations were found bet ween the two rice variety sources. Cluster analysis, based on the molecular markers, revealed that the rice varieties could be subdivided into five groups and, within these, the japonica improved rice and japonica landrace rice varieties were in two separate groups. According to the quality reference criteria to classify the rice into grades, some of the landraces were found to perform we ll, in terms of starch quality. For example, according to NY /T595-2002 criteria from the Ministry of Agriculture of China, 25 and 33 landraces reached grade 1, in terms of their apparent amylose content and gel consistency. Th e varieties that had outstanding quality could be used as breeding materials for rice quality breeding programs in the future. Our study is useful for future applications, such as genetic diversity studies, the protection of rice variety and improvment of rice quality in breeding programs.

Development and characterization of SSR markers in Himalayan species Betula utilis

Betula utilis D.Don.is an important species of alpine Himalaya and forms the major treeline component of western Himalaya.The different populations of B.utilis are declining and are under high risk.In the present study,novel expressed sequence tag-simple sequence repeat(EST-SSR)primers were developed from expressed sequence tag(EST)data of different Betula species.Of the10,796 designed primers,the percentages of di-,tri-,tetra-,penta-,and hexa-repeats were 36%,35%,15%,5.5%and7.7%,respectively.For validation,50 primers were synthesized randomly and were characterized in 20 different B.utilis accessions from north-western Himalaya.Of these,45 primers amplified fragments in a range of 1-6.The 24 polymorphic primers produced 111 fragments in aggregate with 4.6 fragments on average.Polymorphism information content(PIC)ranged from 0.288 in marker BUMS-24 to 0.497 in BUMS-3 and BUMS-7,with an average of 0.447 among polymorphic markers.Dendrogram based on Jaccard’s similarity coefficient and UPGMA method showed that newly developed SSR markers distinguished twenty accessions of B.utilis into two groups.As no SSR markers were available in this species,the newly developed markers will foster molecular genetics research and conservation efforts for this species.

Genetic Analysis of Three Populations of Barbados Blackbelly Sheep at Microsatellite Loci

The phenotypic traits of high prolificacy, low fat on the rib eye muscle and high tolerance to internal parasites make the Barbados Blackbelly （BBB） sheep a valuable economic resource for small subsistence farmers on some Caribbean islands. However, the determination of what is a purebred BBB sheep has long been a contentious issue because of the subjectivity. It is therefore necessary to have a more reliable means of identifying what is a purebred BBB sheep for purposes of conservation and breed improvement. Three geographically isolated populations of BBB sheep were genetically analysed at 19 microsatellite loci. Eighteen of the microsatellites were found to be useful for genetic analysis of the BBB sheep, based on polymorphic information content （PIC） values （0.5 〈 PIC 〉 0.25）. One microsatellite was not useful for genetic analysis based on PIC （0.111）, however it is considered to be a locus of interest because it is fully inbred （f = 1） and homozygous in all of the populations analysed. The analysis also showed that the purebred population of BBB sheep can be distinguished from other populations by formation of distinct clusters when subjected to analysis of molecular variance （AMOVA） and the construction of a rooted consensus tree using the Neighbour-Joining method and pair-wise distances based on marker estimated kinships.

Construction of a Normalized Full-Length cDNA Library of Cephalopod Amphioctopus fangsiao and Development of Microsatellite Markers

Amphioctopus fangsiao is one of the most economically important species and has been considered to be a candidate for aquaculture. In order to facilitate its fine-scale genetic analyses, we constructed a normalized full-length library successfully and developed a set of microsatellite markers in this study. The normalized full-length library had a storage capacity of 6.9×105 independent clones. The recombination efficiency was 95% and the average size of inserted fragments was longer than 1000 bp. A total of 3440 high quality ESTs were obtained, which were assembled into 1803 unigenes. Of these unigenes, 450(25%) were assigned into 33 Gene Ontology terms, 576(31.9%) into 153 Kyoto Encyclopedia of Genes and Genomes pathways, and 275(15.3%) into 22 Clusters of Orthologous Groups. Seventy-six polymorphic microsatellite markers were identified. The number of alleles per locus ranged from 4 to 17, and the observed and expected heterozygosities varied between 0.167 and 0.967 and between 0.326 and 0.944, respectively. Twelve loci were significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction and no linkage disequilibrium was found between different loci. This study provided not only a useful resource for the isolation of the functional genes, but also a set of informative microsatellites for the assessment of population structure and conservation genetics of A. fangsiao.

Genetic Diversity of Indigenous Chicken (Gallus Gallus domesticus) from Ecozones of Egypt and Kingdom of Saudi Arabia

Genetic diversity of two chicken ecotypes from Ismailia-Egypt (ISM) and Taif-Saudi Arabia (TA) was evaluated using 39 microsatellites. DNA was extracted from blood of 25 chickens/ecotype. The number of alleles was 157 and 138, the number of alleles/locus averaged 4.2±2.2 and 3.6±1.6, and the highest number of private alleles was 9 and 5 for ISM and TA, respectively. Percentage of shared alleles between the two ecotypes was 45%. This panel of markers is reasonably informative as the mean polymorphic information content for ISM and TA was 0.47±0.21, and 0.41±0.2. Similar average of observed heterozygosity was attained for both ecotypes. Conversely, averages of expected heterozygosity differed between two ecotypes, 0.52±0.23 vs. 0.45±0.21 for ISM and TA. 8 and 12 loci have significantly deviated from HWE of ISM and TA. Estimate of genetic distance was 0.2 and FST index was 0.29. Results showed only 6% of genetic diversity is shared between these two ecotypes.

Sequence Information on Simple Sequence Repeats and Single Nucleotide Polymorphisms through Transcriptome Analysis of Mungbean

Mungbean （Vigna radiata （L.） Wilczek） is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptome sequencing. A total of 150 159 and 142 993 reads produced 5 254 and 6 374 large contigs （〉_500 bp） with an average length of 833 and 853 for Sunhwa and Jangan, respectively. Functional annotation to known sequences yielded 41.34% and 41.74% unigenes for Jangan and Sunhwa. A higher number of simple sequence repeat （SSR） motifs was identified in Jangan （1 630） compared with that of Sunhwa （1 334）. A similar SSR distribution pattern was observed in both varieties. A total of 8 249 single nucleotide polymorphisms （SNPs） and indels with 2 098 high-confidence candidates were identified in the two mungbean varieties. The average distance between individual SNPs was -860 bp. Our report demonstrates the utility of transcriptomic data for implementing a functional annotation and development of genetic markers. We also provide large resource sequence data for mungbean improvement programs.

High-throughput development of genome-wide locus-specific informative SSR markers in wheat

Dear Editor,Although simple sequence repeat（SSR）markers are not new,they are still useful and often used markers in molecular mapping and marker-assisted breeding,particularly in developing countries.However,locus-specific SSR markers could be more useful and informative in wheat breeding and genetic studies.In the present study,221,911 locus-specific SSR markers were designed.Verification of polymorphisms showed that the proportion of polymorphic markers increases with an increase in SSR size.