Population Structure and Genetic Diversity within Peach latent mosaic viroid Field Isolates from Peach Showing three Symptoms

To gain insight into the molecular basis of field isolates inducing the symptoms of leaf yellowing, discolouration along leaf sides and leaf mosaic, six isolates from peach showing the three different symptoms in the field were studied by single-strand conformation polymorphism analysis and nucleotide sequence analysis. Results revealed that each Peach latent mosaic viroid (PLMVd) isolate is composed of a population of genetically related variants (haplotypes), one being predominant with frequencies from 32% to 57%, and most of others having a low frequency of 4–5%. Each predominant haplotype was sequenced, as well as some non-predominant haplotypes selected randomly for comparative purposes. In each isolate, sequence alignment among the predominant and non-predominant haplotypes demonstrated that the predominant haplotype had the least variation with others among them, and its sequence was identical to the consensus sequence, which inflected that the predominant haplotype displayed a wide representative of sequence for others in a PLMVd isolate. The similarities and genetic distance between the predominant sequences from peach showing the same symptoms were higher and smaller, respectively, than that with different symptoms; they were more than 98.8% and <1%, respectively, between the predominant sequences with same symptomatic source, and were <98.5% and more than 1%, respectively, between the predominant sequences with different symptomatic source. Some particular variations were indicated for these isolates, and it revealed that the isolates with the symptom of discolouration along leaf sides on their source peach trees had a G or U in position 169 nt, and the isolates with the symptom of leaf yellowing had U and C in 115 and 116 nt, respectively, and the isolates with the symptom of leaf mosaic showed diversity at (3 nt: delete C; 5 nt: A and 54 nt: U).     

Effect of swine lymphocyte antigen haplotypes on birth and weaning weights in pigs

Birth weights of 708 live piglets and weaning weights of 566 piglets were used to investigate the effect of the swine lymphocyte antigen (SLA) complex on these traits in Large White pigs. Piglets were from litters of a long-term selection experiment to measure response for selection to increase litter size. SLA haplotypes were determined using conventional class I antisera. A total of 14 haplotypes were detected. The effect of SLA haplotype on birth and weaning weights was investigated using a statistical model that included the effects of experimental group, sire, dam, sex and SLA haplotype. Results indicated that SLA class I haplotype 13.1.3 increased birth weights (P less than 0.10) and significantly increased weaning weights (P less than 0.01). This effect of haplotype 13.1.3 on weaning weight was 605 +/- 215 g (0.3 standard deviations). SLA class I homozygosity did not appear to affect birth and weaning weights. These results suggest that the SLA complex plays an important role in early growth in the pig and that further study of SLA effects on growth and reproduction are warranted.     

Founder effects explain the distribution of the HLAA1-B17 but not the absence of theA1-B8 haplotypes in India

The HLA system may play an important role in natural selection processes through its involvement in immune response and because of the HLA association of some diseases. Linkage disequilibrium in the HLA system poses many interesting questions. India. a melting pot of races and cultures in sympatric isolation, provides an ideal opportunity to study these aspects. Linkage disequilibrium and haplotype data are valuable in the comparison of various populations. An analysis of the available HLA A-B haplotype data for the Indian population documents the heterogeneous nature of the latter: each endogamous caste group, major group or even regional group has its characteristic haplotype profile. The haplotypeA1-B17 is present in most Indian populations butA10-B8 occurs mostly in North India: this may be a consequence of founder effects. The haplotypeAl-B8 a typical Caucasian haplotype, is absent in the Indian subcontinent: this may be due to the selective disadvantageA1-B8 confers in the Indian environment. The different regional and caste groups of India possessing diverse haplolype combinations provide an ideal opportunity to evaluate the selective values of these haplotypes and to study human immunogenetics.     

Comparative analysis of the tuberculosis susceptibility genetic make-up in Tuvinians and Russians

Polymorphisms of the tuberculosis (TB) susceptibility genes SLC11A1, VDR, IL12B, IL1B, and IL1RN were studied, for the first time in Russia, in Tuvinians from the Tyva Republic and ethnic Russians from Tomsk. Compared with Russians, Tuvinians had significantly higher frequencies of potentially pathological alleles SLC11A1*543N (0.139 vs. 0.043, P = 4.6 · 10^?5), IL12B*1188C (0.378 vs. 0.174, P = 1.1 · 10^?8), VDR*b (0.825 vs. 0.532, P = 3.2 · 10^?16), IL1B*(+3953A1) (0.865 vs. 0.806, P = 0.035), and IL1RN*A1 (0.849 vs. 0.786, P = 0.030). However, none of the alleles was associated with TB in Tuvinians. Compared with healthy subjects, Russian patients with TB had higher frequencies of alleles IL1RN*A2 (0.258 vs. 0.186, P = 0.024), SLC11A1*274T (0.251 vs. 0.164, P = 0.009), IL12B*1188C (0.240 vs. 0.174, P = 0.044), and IL1B*(+3953A2) (0.259 vs. 0.194, P = 0.044). The structure of linkage disequilibrium in pairs of alleles differed between Tuvinians and Russians. In total, the results suggest ethnic specificity of the distribution and pathogenetic significance of the alleles of the TB susceptibility genes.     

Locus‐specific ancestry to detect recent response to selection in admixed Swiss Fleckvieh cattle

Identification of selection signatures is one of the current endeavors of evolutionary genetics. Admixed populations may be used to infer post‐admixture selection. We calculated local ancestry for Swiss Fleckvieh, a composite of Simmental (SI) and Red Holstein Friesian (RHF), to infer such signals. Illumina Bovine SNP50 BeadChip data for 300 admixed, 88 SI and 97 RHF bulls were used. The average RHF ancestry across the whole genome was 0.70. To identify regions with high deviation from average, we considered two significance thresholds, based on a permutation test and extreme deviation from normal distribution. Regions on chromosomes 13 (46.3–47.3 Mb) and 18 (18.7–25.9 Mb) passed both thresholds in the direction of increased SI. Extended haplotype homozygosity within (iHS) and between (Rsb) populations was calculated to explore additional patterns of pre‐ and post‐admixture selection signals. The Rsb score of admixed and SI was significant in a wide region of chromosome 18 (6.6–24.6 Mb) overlapped with one area of strong local ancestry deviation. FTO, with pleiotropic effect on milk and fertility, NOD2 on dairy and NKD1 and SALL1 on fertility traits are located there. Genetic differentiation of RHF and SI (F_st), an alternative indicator of pre‐admixture selection in pure populations, was calculated. No considerable overlap of peaks of local ancestry deviations and F_st was observed. We found two regions with significant signatures of post‐admixture selection in this very young composite, applying comparatively stringent significance thresholds. The signals cover relatively large genomic areas and did not allow pinpointing of the gene(s) responsible for the apparent shift in ancestry proportions.