Identification Of Genetic Structure Research Articles

Recapitulating whole genome based population genetic structure for Indian wild tigers through an ancestry informative marker panel.

Identification of genetic structure within wildlife populations have implications in their conservation and management. Accurately inferring population genetic structure requires whole-genome data across the geographical range of the species, which can be resource-intensive. A cheaper strategy is to employ a subset of markers that can efficiently recapitulate the population genetic structure inferred by the whole genome data. Such ancestry informative markers (AIMs), have rarely been developed for endangered species such as tigers utilizing single nucleotide polymorphisms (SNPs). Here, we first identify the population structure of the Indian tiger using whole-genome sequences and then develop an AIMs panel with a minimum number of SNPs that can recapitulate this structure. We identified four population clusters of Indian tigers with North-East, North-West, and South Indian tigers forming three separate groups, and Terai and Central Indian tigers forming a single cluster. To evaluate the robustness of our AIMs, we applied it to a separate dataset of tigers from across India. Out of 92 SNPs present in our AIMs panel, 49 were present in the new dataset. These 49 SNPs were sufficient to recapitulate the population genetic structure obtained from the whole genome data. To the best of our knowledge, this is the first-ever SNP-based AIMs panel for big cats, which can be used as a cost-effective alternative to whole-genome sequencing for detecting the biogeographical origin of Indian tigers. Our study can be used as a guideline for developing an AIMs panel for the management of other endangered species where obtaining whole genome sequences are difficult.

Genetic characterization of three fertility genes in Egyptian sheep and goat breeds

One of the effective approaches for genetic improvement of productivity traits in farm animals is markerassisted selection (MAS) depending on the genetic markers that are associated with superior productivity traits. The improvement of fertility trait is one of the main targets in small ruminant breeding programs. This work aimed to identify RFLPs and SNPs variations among three fertility genes in Egyptian sheep and goat breeds. RFLP analysis of the amplified fragments at 462-bp from exon 1 of GDF9 using HpaII endonuclease showed the presence of two genotypes GG and AG. Depending on the presence of the restriction site of TaqI endonuclease (T^CGA) in the 348-bp amplified fragment from exon 5 of GPR54 gene, the results showed the presence of two alleles, C and T with three genotypes, viz. CC, TT and CT. The PCR amplified fragments of 190-bp from FecB gene were digested with AvaII restriction enzyme and the results showed that all tested animals had the same homozygous non-carrier genotype (++). It was concluded that the identification of genetic structure and nucleotide sequences of GDF9, GPR54 and FecB genes is considered the first step towards the genetic improvements of fertility trait in Egyptian small ruminants where these genes are associated with different fertility traits parameter like ovulation rate, ovarian follicular development, puberty and litter size in small ruminant breeds.

Genetic structure identification and assessment of interrelationships between Brassica and allied genera using newly developed genic-SSRs of Indian Mustard (Brassica juncea L.)

Brassica and allied genera are valuable sources of edible oils, vegetables, condiments and other products. They also find utility for specific applications as renewable industrial or fuel oils. Wild and weedy species of these genera are precious genetic resources of agronomic and economic traits. Scientists have developed a large number of genomic resources for cultivated species of Brassica. However, members of allied genera including wild and weedy species have remained mainly neglected. In this study, we tested the cross-transferability of 460 genic-SSRs, out of the 4108 genic-SSRs developed in our earlier study in Brassica juncea, to 21 accessions representing 19 species from eight different genera of the family Brassicaceae. A total of 200 genic-SSRs yielded single amplicons of which 150 exhibited cross-transferability. Cross-taxa allelic distribution analysis of the cross-transferable genic-SSRs highlighted preferential accumulation of 15 private alleles in cultivated Brassicas with distinct niche-specific roles. One hundred twenty-one genic-SSRs were found to be polymorphic with polymorphism information content values ranging from 0.09 to 0.66. The cross-transferable genic-SSRs were employed to identify population structure, Nei’s genetic distance-based clustering, and principal coordinate analysis. The results convincingly demonstrated the efficacy of cross-transferable genic-SSRs in delineating taxonomic status of species of Brassica and allied genera and thus could be efficiently used in more extensive marker-based studies.

Polyclonal uses of T‐cell receptor (TCR)α and β genes for cytotoxic T lymphocytes in human metastatic melanoma: possible involvement of TCRα in tumor‐cell recognition

Identification of genetic structure and diversity of T-cell receptor (TCR)alpha and beta genes for cytotoxic T lymphocytes (CTLs) infiltrating human cancers is important for the better understanding of molecular mechanisms of host defense at tumor sites. cDNAs of TCR alpha and beta genes of 22 different melanoma-specific CTL clones established from the tumor-infiltrating lymphocytes of 2 patients were sequenced for analysis of their genetic structure and diversity. V alpha 7.2-J alpha 10-C alpha was found in 4 of 22 clones, 2 of which also used the same beta-chain. The other 20 clones showed different combinations of alpha and beta use. At deduced amino-acid levels, 7 of 9 clones from one patient used a threonine residue at the 26th position in the complementarity-determining region (CDR)1 of TCR alpha. Eight of 13 clones used a threonine at the 99th or a serine residue at the 100th position in CDR3 of TCR alpha CTL clones with the same or different TCR alpha showed the same or different patterns of cytotoxicity, respectively. These results suggest that CTLs usually do not demonstrate clonal expansion at tumor sites of metastatic melanoma's but rather that polyclonal T cells capable of binding to multiple melanoma determinants through CDR3 of TCR alpha accumulate in the tumor.