Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.)

A transcript map has been constructed by the development and integration of genic molecular markers (GMMs) including single nucleotide polymorphism (SNP), genic microsatellite or simple sequence repeat (SSR) and intron spanning region (ISR)-based markers, on an inter-specific mapping population of chickpea, the third food legume crop of the world and the first food legume crop of India. For SNP discovery through allele re-sequencing, primer pairs were designed for 688 genes/expressed sequence tags (ESTs) of chickpea and 657 genes/ESTs of closely related species of chickpea. High-quality sequence data obtained for 220 candidate genic regions on 2–20 genotypes representing 9 Cicer species provided 1,893 SNPs with an average frequency of 1/35.83 bp and 0.34 PIC (polymorphism information content) value. On an average 2.9 haplotypes were present in 220 candidate genic regions with an average haplotype diversity of 0.6326. SNP2CAPS analysis of 220 sequence alignments, as mentioned above, provided a total of 192 CAPS candidates. Experimental analysis of these 192 CAPS candidates together with 87 CAPS candidates identified earlier through in silico mining of ESTs provided scorable amplification in 173 (62.01%) cases of which predicted assays were validated in 143 (82.66%) cases (CGMM). Alignments of chickpea unigenes with Medicago truncatula genome were used to develop 121 intron spanning region (CISR) markers of which 87 yielded scorable products. In addition, optimization of 77 EST-derived SSR (ICCeM) markers provided 51 scorable markers. Screening of easily assayable 281 markers including 143 CGMMs, 87 CISRs and 51 ICCeMs on 5 parental genotypes of three mapping populations identified 104 polymorphic markers including 90 markers on the inter-specific mapping population. Sixty-two of these GMMs together with 218 earlier published markers (including 64 GMM loci) and 20 other unpublished markers could be integrated into this genetic map. A genetic map developed here, therefore, has a total of 300 loci including 126 GMM loci and spans 766.56 cM, with an average inter-marker distance of 2.55 cM. In summary, this is the first report on the development of large-scale genic markers including development of easily assayable markers and a transcript map of chickpea. These resources should be useful not only for genome analysis and genetics and breeding applications of chickpea, but also for comparative legume genomics

An overview of the toxic effect of potential human carcinogen Microcystin-LR on testis

The worldwide occurrence of cyanobacterial blooms due to water eutrophication evokes extreme concerns. These blooms produce cyanotoxins which are hazardous to living organisms. So far among these toxins, Microcystin-LR (MC-LR) is the most toxic and the most frequently encountered toxin produced by the cyanobacteria in the contaminated aquatic environment. Microcystin-LR is a potential carcinogen for animals and humans, and the International Agency for Research on Cancer has classified Microcystin-LR as a possible human carcinogen. After liver, testis has been considered as one of the most important target organs of Microcystin-LR toxicity. Microcystin-LR crosses the blood–testis barrier and interferes with DNA damage repair pathway and also increases expression of the proto-oncogenes, genes involved in the response to DNA damage, cell cycle arrest, and apoptosis in testis. Toxicity of MC-LR disrupts the motility and morphology of sperm and also affects the hormone levels of male reproductive system. MC-LR treated mice exhibit oxidative stress in testis through the alteration of antioxidant enzyme activity and also affect the histopathology of male reproductive system. In the present review, an attempt has been made to comprehensively address the impact of MC-LR toxicity on testis

Design and Characterization of DNA Aptamer for Breast Tumor Marker by an Advantageous Method

ABSTRACT: Aptamers are agents able to bind tightly and selectively to disease markers, offering great potential for applications in disease diagnosis and therapy. Functionally they are ssDNA or RNA oligonucleotides which are highly specific and selective to their target along with highest affinity. We have selected DNA aptamer against breast tumor marker (CA 15-3) by using a modified SELEX methodology. For the selection round CA 15-3 were immobilized on magnetic beads and to check the affinity of selected aptamers for their target fluorescent labeled aptamers were used. Aptamers were selected from an initial library containing 25 base long variable regions for their ability to bind to the CA 15-3. After 12 rounds of the selection and amplification we found 90% pool of DNA sequences which are able to bind with CA 15-3. These aptamers were cloned, sequenced and labeled by fluorescent molecule. The binding affinity of these aptamers (K D value) was quantified by using FAM labeled aptamers. Our results aim to develop new diagnostic assays against breast tumor marker for the early diagnosis of breast cancer