Microsatellite Polymorphism

Simple sequence repeat (SSR) is currently the most preferred molecular marker system owing to their highly desirable properties viz., abundance, hyper-variability, and suitability for high-throughput analysis. Hence, in present study an attempt was made to mine and analyze microsatellite dynamics in whole genome of Fusarium oxysporum f. sp. lycopersici. The distribution pattern of different SSR motifs provides the evidence of greater accumulation of tetra-nucleotide (3837) repeats followed by tri-nucleotide (3367) repeats. Maximum frequency distribution in coding region was shown by mono-nucleotide SSR motifs (34.8%), where as minimum frequency is observed for penta-nucleotide SSR (0.87%). Highest relative abundance (1023 SSR/Mb) and density of SSRs (114.46 bp/Mb) were observed on chromosome 1, while least density of SSR motifs was recorded on chromosome 11 (7.40 bp/Mb) and 12 (7.41 bp/Mb), respectively. Maximum trinucleotide (34.24%) motifs code for glutamic acid (GAA) while GT/CT were the most frequent repeat of dinucleotide SSRs. Most common and highly repeated SSR motifs were identified as (A)64, (T)48, (GT)24, (GAA)31, (TTTC)24, (TTTCT)28 and (AACCAG)27. Overall, the generated information may serve as baseline information for developing SSR markers that could find applications in genomic analysis of F. oxysporum f. sp. lycopersici for better understanding of evolution, diversity analysis, population genetics, race identification and acquisition of new virulence.

Expressed sequence tags (ESTs) from turmeric (Curcuma longa L.) were used for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). A total of 231 microsatellite repeats were detected from 12,593 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs accounts to one SSR per 17.96 kb of EST. Mononucleotides were the most abundant class of microsatellite repeat in turmeric ESTs followed by trinucleotides. A robust set of 17 polymorphic EST–SSRs were developed and used for evaluating 20 turmeric accessions. The number of alleles detected ranged from 3 to 8 per loci. The developed markers were also evaluated in 13 related species of C. longa confirming high rate (100%) of cross species transferability. The polymorphic microsatellite markers generated from this study could be used for genetic diversity analysis and resolving the taxonomic confusion prevailing in the genus.

A single locus system of 6 microsatellite markers was evaluated for paternity testing. A nonradioactive method based on peroxidase labeling of a DNA probe was used to estimate the allele frequency of markers D1S216, D3S1217, D7S480, D9S157, D13S153, and D16S422 by genotyping 1134-1698 chromosomes. The number of detected alleles were 22, 15, 23, 10, 16, and 19, respectively, and the allele frequency varied from 0.001 to 0.317. The genotype of 87 families, consisting of mother, father, and child was determined. The probability that a random individual will give a positive paternity was evaluated. We conclude that the markers can be reliably typed and give sufficient and reliable information for paternity testing.

An efficient method for crossing green foxtail (Setaria viridis) is currently lacking. S. viridis is considered to be the new model plant for the study of C4 system in monocots and so an effective crossing protocol is urgently needed. S. viridis is a small grass with C4-NADP (ME) type of photosynthesis and has the advantage of having small genome of about 515 Mb, small plant stature, short life cycle, multiple tillers, and profuse seed set, and hence is an ideal model species for research. The objectives of this project were to develop efficient methods of emasculation and pollination, and to speed up generation advancement. We assessed the response of S. viridis flowers to hot water treatment (48°C) and to different concentrations of gibberellic acid, abscisic acid, maleic hydrazide (MH), and kinetin. We found that 500 μM of MH was effective in the emasculation of S. viridis, whilst still retaining the receptivity of the stigma to pollination. We also report effective ways to accel...

Intraspecific variation in sociosexual behavior has typically been investigated in the context of its relationship with environmental factors, but neurogenetic factors can also influence sociosexual behavior. In laboratory studies of prairie voles (Microtus ochrogaster), length polymorphism of microsatellite DNA within the gene (avpr1a) encoding the vasopressin 1a receptor is correlated with variation in male sociosexual behavior. However, field studies of prairie voles have found the relationship between male avpr1a microsatellite allele length and sociosexual behavior to be more ambiguous, possibly because most males had alleles of intermediate length. We tested the hypothesis that avpr1a microsatellite allele length mediates male sociosexual behavior in field settings by releasing voles into field enclosures where every male possessed two avpr1a microsatellite alleles at least one standard error longer or shorter than the mean length in their population of origin. Voles from an Illinois and Kansas population were examined separately as social monogamy appears more prevalent in the Illinois population. Illinois males with long avpr1a microsatellite alleles had smaller home ranges and overlapped a greater proportion of the home range of the female that they overlapped the most. Kansas males showed the opposite pattern. Illinois, but not Kansas, males with long avpr1a microsatellite alleles sired offspring with more females and sired more litters. Our results support the hypothesis that genetic variation associated with the avpr1a gene plays a role in mediating male prairie vole sociosexual behavior in nature. However, the relationship between specific male behaviors and male avpr1a microsatellite allele length sometimes differed significantly between Kansas and Illinois voles, suggesting relationships between specific male sociosexual behaviors and polymorphism associated with the avpr1a locus are complex, possibly involving specific nucleotide sequences or other population-specific genetic differences.

The indigenous groups of Sarawak that are well-known for diverse ethnicity featuring different cultures, languages and lifestyles, are among the earliest resident of Malaysian Borneo. The high survivorship of these early inhabitants had triggered an interest on their ability to develop immune or defense mechanisms towards the environment. Beta defensin is one of the well-studied adaptive immune functional gene of human. Beta defensins gene family plays a major role in innate and adaptive immune systems that are located in a cluster of at least seven genes on chromosome 8p23.1 with highly variable copy number. The ability of the indigenous people populating new settlements has been linked to their resistance or susceptibility towards certain disease which is influenced by the effectiveness of beta defensins adaptability. Hence, investigation on the distribution of beta defensins copy number variable gene in ethnics of Sarawak was conducted by investigating two microsatellite regions within the gene cluster. The result from 78 respondents comprising of the Iban, Bidayuh, Selako, Bugis and Jawa on the immediate copy number typing range from 2 to 8 copies. Interestingly, the copy numbers are not unique to the ethnics. They show a broad overview of shared copy number typing between them. All the sampled ethnics showed an agreement of copy number typing with modal copy of four based on EPEV1 and EPEV3 except for the Selako population. Pearson’s correlation shows excellent agreement between the samples with R2 =1. The differences in copy number typing between populations were mostly due to genetic drift within the population. Natural selection had caused small populations to develop defence mechanisms and adaptability towards the environment. Furthermore, intercultural marriage within small populations has discouraged gene flow and limits genetic drift which later becomes a mechanism of evolution for beta defensins copy number gene. This study highlights the diversity and distribution of beta defensins copy number variable gene between ethnics and localities. These may serve as the basis for our understanding of the evolution of the beta defensins gene within ethnicities and their ability in expansion of population due to resistant towards the environmental stress and natural selection.

Keywords: Indigenous people, beta defensins, immune defence, copy number, microsatellites assay, environment.

Expressed sequence tags (ESTs) from turmeric (Curcuma longa L.) were used for the screening of type and frequency of Class I (hypervariable) simple sequence repeats (SSRs). A total of 231 microsatellite repeats were detected from 12,593 EST sequences of turmeric after redundancy elimination. The average density of Class I SSRs accounts to one SSR per 17.96 kb of EST. Mononucleotides were the most abundant class of microsatellite repeat in turmeric ESTs followed by trinucleotides. A robust set of 17 polymorphic EST–SSRs were developed and used for evaluating 20 turmeric accessions. The number of alleles detected ranged from 3 to 8 per loci. The developed markers were also evaluated in 13 related species of C. longa confirming high rate (100%) of cross species transferability. The polymorphic microsatellite markers generated from this study could be used for genetic diversity analysis and resolving the taxonomic confusion prevailing in the genus.

Although a high number of microsatellite markers are available for livestock species allowing high density
genome coverage and mapping traits, few characterised microsatellite markers are available for dromedary camel
(Camelus dromedarius). Recently, 9 polymorphic tetranucleotide microsatellite markers have been reported for alpaca.
These microsatellites were tested for cross-species amplification in dromedary camel. Four were successfully amplified
giving sharp and specific bands whereas the remaining 5 showed either no amplification or multiple unspecific
amplification products. Polymorphism of the 4 markers which amplified (PCTD17, P132, P135, and P193) was evaluated
in a group of 34 unrelated Tunisian dromedary camels. All markers proved to be polymorphic in analysed panel.
Allele numbers varied from 7 (locus P132) to 13 (locus PCTD17) and deviation from Hardy–Weinberg equilibrium
was observed in the four loci. A multiplex PCR reaction was optimised for the amplification of the loci P132, P135
and P193. The tested markers in this work will be useful for the analysis of the genetic diversity of dromedary camel
populations.