We have identified numerous Ancestral Haplotypes encoding a 14-Mb region of Bota C19. Three are frequent in Simmental, Angus and Wagyu and have been conserved since common progenitor populations. Others are more relevant to the differences between these 3 breeds including fat content and distribution in muscle. SREBF1 and Growth Hormone, which have been implicated in the production of healthy b...

Summary: Although the 1000 Genomes haplotypes are the most commonly used reference panel for imputation, medical sequencing projects are generating large alternate sets of sequenced samples. Imputation in African Americans using 3384 haplotypes from the Exome Sequencing Project, compared with 2184 haplotypes from 1000 Genomes Project, increased effective sample size by 8.3–11.4% for coding vari...

Based on mitochondrial 16S rRNA sequences, we suggest that the founder individuals of the introduced Greek population of Chamaeleo africanus originated in the Nile Delta region of Egypt. In Ch. chamaeleon, we discovered in the eastern Mediterranean new 16S rRNA haplotypes, being highly distinct from previously published western Mediterranean haplotypes. Eastern Mediterranean haplotypes were fou...

We propose to build a software system that will use probabilistic de Bruijn graphs for reconstruction of viral haplotypes without a reference genome. The haplotypes are assumed to arise through mutation and/or recombination processes. In the software system, when provided with a set of reads, the software developed should determine the number, sequences, and relative frequencies of the haplotypes.

We report discoveries of different haplotypes associated with the centromeres of three potato chromosomes, including haplotypes composed of long arrays of satellite repeats and haplotypes lacking the same repeats. These results are in favor of the hypothesis that satellite repeat-based centromeres may originate from neocentromeres that lack repeats.

We had investigated whether sequence variants within DKK3 gene are associated with the development of prostate cancer in a Korean study cohort. We evaluated the association between 53 single nucleotide polymorphisms (SNPs) in the DKK3 gene and prostate cancer risk as well as clinical characteristics (PSA, clinical stage, pathological stage and Gleason score) in Korean men (272 prostate cancer s...

Children's observed effortful control (EC) at 30, 42, and 54 months (n = 145) was predicted from the interaction between mothers' observed parenting with their 30-month-olds and three variants of the solute carrier family C6, member 3 (SLC6A3) dopamine transporter gene (single nucleotide polymorphisms in intron8 and intron13, and a 40 base pair variable number tandem repeat [VNTR] in the 3'-unt...

The t-complex is located on the proximal third of chromosome 17 in the house mouse. Naturally occurring variant forms of the t-complex, known as complete t-haplotypes, are found in wild mouse populations. The t-haplotypes contain at least four nonoverlapping inversions that suppress recombination with the wild-type chromosome, and lock into strong linkage disequilibrium loci affecting normal tr...

Eusideroxylon zwageri is a large tropical rainforest tree native to Indonesia, Malaysia, the Philippines, and Brunei. Because of its high economic value, illegal logging and overexploitation is threatening this species in several locations in Indonesia. In this study, in order to conserve genetic resources, we investigated the genetic structure of E. zwageri in Indonesia using chloroplast DNA s...

Cellular metabolism is regulated by enzyme complexes within the mitochondrion, the function of which are sensitive to the prevailing temperature. Such thermal sensitivity, coupled with the observation that population frequencies of mitochondrial haplotypes tend to associate with latitude, altitude, or climatic regions across species distributions, led to the hypothesis that thermal selection ha...