LEARNING The objectives of BIOS 781 are to present: OBJECTIVES: 1. basic population and quantitative genetic principles, including classical genetics, chromosomal theory of inheritance, and meiotic recombination 2. an exposure to QTL mapping methods of complex quantitative traits and linkage methods to detect co-segregation with disease 3. methods for assessing marker-disease linkage disequilibrium, including case-control approaches 4. methods for genome-wide association and stratification control.

Genetic Data Analysis

This is the oldest English language journal in genetics. Founded by W. Bateson and R. C. Punnett in 1910, the Journal of Genetics was later edited by J. B. S. Haldane; later, Haldane and his wife, Helen Spurway brought the journal with them to India. After his death in 1964, Mrs. Haldane continued publication of the journal, with Madhav Gadgil and H. Sharat Chandra (Indian Institute of Science, Bangalore) and Suresh Jayakar (Laboratorio de Genetica Biochimica ed Evoluzionistica, Pavia) as editors, until her own death in 1977. In 1985, with the permission of Haldane’s heirs, the Indian Academy of Sciences resumed publication of the journal. The journal retains its traditional interest in evolutionary research that is of relevance to geneticists, even if not explicitly genetic in nature.

The journal of genetics

Statistics of natural selection

The horse (Equus ferus caballus) is one of the earliest domesticated species and has played an important role in the development of human societies over the past 5,000 years. In this study, we characterized the genome of the Marwari horse, a rare breed with unique phenotypic characteristics, including inwardly turned ear tips. It is thought to have originated from the crossbreeding of local Indian ponies with Arabian horses beginning in the 12th century. We generated 101 Gb (~30 × coverage) of whole genome sequences from a Marwari horse using the Illumina HiSeq2000 sequencer. The sequences were mapped to the horse reference genome at a mapping rate of ~98% and with ~95% of the genome having at least 10 × coverage. A total of 5.9 million single nucleotide variations, 0.6 million small insertions or deletions, and 2,569 copy number variation blocks were identified. We confirmed a strong Arabian and Mongolian component in the Marwari genome. Novel variants from the Marwari sequences were annotated, and were found to be enriched in olfactory functions. Additionally, we suggest a potential functional genetic variant in the TSHZ1 gene (p.Ala344>Val) associated with the inward-turning ear tip shape of the Marwari horses. Here, we present an analysis of the Marwari horse genome. This is the first genomic data for an Asian breed, and is an invaluable resource for future studies of genetic variation associated with phenotypes and diseases in horses.

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Whole genome sequence and analysis of the Marwari horse breed and its genetic origin.

Main conclusionMetabolite profiling of tuber flesh and peel for selected colored potato varieties revealed cultivar and tissue specific profiles of anthocyanins and other polyphenols with variations in composition and concentration.Starchy tubers of Solanum tuberosum are a staple crop and food in many countries. Among cultivated potato varieties a huge biodiversity exists, including an increasing number of red and purple colored cultivars. This coloration relates to the accumulation of anthocyanins and is supposed to offer nutritional benefits possibly associated with the antioxidative capacity of anthocyanins. However, the anthocyanin composition and its relation to the overall polyphenol constitution in colored potato tubers have not been investigated closely. This study focuses on the phytochemical characterization of the phenolic composition of a variety of colored potato tubers, both for peel and flesh tissues. First, liquid chromatography (LC) separation coupled to UV and mass spectrometry (MS) detection of polyphenolic compounds of potato tubers from 57 cultivars was used to assign groups of potato cultivars differing in their anthocyanin and polyphenol profiles. Tissues from 19 selected cultivars were then analyzed by LC separation coupled to multiple reaction monitoring (MRM) to detect quantitative differences in anthocyanin and polyphenol composition. The measured intensities of 21 anthocyanins present in the analyzed potato cultivars and tissues could be correlated with the specific tuber coloration. Besides secondary metabolites well-known for potato tubers, the metabolic profiling led to the detection of two anthocyanins not described for potato tuber previously, which we tentatively annotated as pelargonidin feruloyl-xylosyl-glucosyl-galactoside and cyanidin 3-p-coumaroylrutinoside-5-glucoside. We detected significant correlations between some of the measured metabolites, as for example the negative correlation between the main anthocyanins of red and blue potato cultivars. Mainly hydroxylation and methylation patterns of the B-ring of dihydroflavonols, leading to the formation of specific anthocyanidin backbones, can be assigned to a distinct coloring of the potato cultivars and tuber tissues. However, basically the same glycosylation and acylation reactions occur regardless of the main anthocyanidin precursor present in the respective red and blue/purple tissue. Thus, the different anthocyanin profiles in red and blue potato cultivars likely relate to superior regulation of the expression and activities of hydroxylases and methyltransferases rather than to differences for downstream glycosyl- and acyltransferases. In this regard, the characterized potato cultivars represent a valuable resource for the molecular analysis of the genetic background and the regulation of anthocyanin side chain modification.

Metabolite profiling of red and blue potatoes revealed cultivar and tissue specific patterns for anthocyanins and other polyphenols (supplemental data files)

The high/low-amplitude anisotropic wave train events (HAE/LAE) in CR intensity have been investigated during the period 1981–1990, using the neutron monitoring data for different latitudes. In all, 21 HAE and 15 LAE cases have been studied. It has been observed that the phase of the diurnal anisotropy remains in the same co-rotational direction for the majority of the HAE/LAE cases. However, it has also been observed that the phase of the diurnal anisotropy changes to later hours in some of the HAE cases, whereas it changes to early hours in some of the LAE cases. Further, the amplitude of the semi-diurnal anisotropy for HAE/LAE cases remains statistically the same; however, the phase of the semi-diurnal anisotropy for HAE has been found to shift to later hours for all events. Furthermore, the HAE occur dominantly during the declining phase of solar activity, whereas LAE occur dominantly during the minimum solar activity period. The geomagnetic activity index-Ap has been observed to remain low during the period of each HAE/LAE. The possible phenomenon to cause the enhanced/low-amplitude daily variation has been proposed to appear on the back side of the Sun.

Effect of Interplanetary Turbulences Causing High/low Amplitude Anisotropic Wave Trains in Cr Intensity

Genetic diversity within the Marwari breed of horses was evaluated using 26 different microsatellite pairs with 48 DNA samples from unrelated horses. This molecular characterisation was undertaken to evaluate the problem of genetic bottlenecks also, if any, in this breed. The estimated mean (± s.e.) allelic diversity was 5.9 (± 2.24), with a total of 133 alleles. A high level of genetic variability within this breed was observed in terms of high values of mean (±s.e.) effective number of alleles (3.3 ± 1.27), observed heterozygosity (0.5306 ± 0.22), expected Levene’s heterozygosity (0.6612 ± 0.15), expected Nei’s heterozygosity (0.6535 ± 0.14), and polymorphism information content (0.6120 ± 0.03). Low values of Wright’s fixation index, FIS (0.2433 ± 0.05) indicated low levels of inbreeding. This basic study indicated the existence of substantial genetic diversity in the Marwari horse population. No significant genotypic linkage disequilibrium was detected across the population, suggesting no evidence of linkage between loci. A normal ‘L’ shaped distribution of mode-shift test, non-significant heterozygote excess on the basis of different models, as revealed from Sign, Standardized differences and Wilcoxon sign rank tests as well as non-significantM ratio value suggested that there was no recent bottleneck in the existing Marwari breed population, which is important information for equine breeders. This study also revealed that the Marwari breed can be differentiated from some other exotic breeds of horses on the basis of three microsatellite primers.

Genetic diversity and bottleneck studies in the Marwari horse breed.

Las poblaciones de las seis razas equinas registradas por laOficina Nacional India deRecursos Zoogeneticos han disminuido drasticamente a causa de la cria sin criterio y de su menor utilizacion. En este trabajo, se estudiaron 15 indices biometricos, junto con caracteristicas raciales tipicas, en 50 animales de cada raza, excepto en la raza Bhutia (35) para su caracterizacion fenotipica. En base a sus alzadas a la cruz, las razas Kathiawari y Marwari se clasificaron como �caballos�, mientras que las razas Zanskari, Manipuri, Bhutia y Spiti se clasificaron como �ponis�. La raza Marwari fue la de mayor alzada y la que era significativamente diferente a otras razas en la mayoria de los indices
biometricos. La raza Spiti fue la que presento una menor alzada entre las seis poblaciones de caballos y ponis estudiadas. Se observo un moderado dimorfismo sexual en algunos de los indices biometricos en las diferentes razas. En las razas Marwari y Kathiawari, tanto los sementales como las yeguas, pueden girar las orejas en un angulo de 180°, quedando las puntas de las orejas en el centro, siendo una caracteristica tipica de estas dos razas. Este trabajo tiene como objetivo proporcionar informacion de referencia para la identificacion y comparacion de las distintas razas de equidos de la India, con el proposito de sensibilizar a genetistas y criadores acerca de la importancia de producir ejemplares tipicos, de su conservacion y para la mejora de la gestion de estos valiosos recursos geneticos.

Phenotypic characterization of Indian equine breeds: a comparative study

Comparative genetic diversity analysis among six Indian breeds and English Thoroughbred horses

The genetic relationships of three Indian horse breeds-Marwari, Spiti, and Kathiawari were studied by genotyping 96 individuals with 20 polymorphic microsatellite markers. A total of 157 alleles were detected across 20 polymorphic loci. The Marwari population showed the highest allelic diversity (A = 5.7 and Ar = 5.14), followed by Spiti (A = 4.9 and Ar = 4.74) and Kathiawari (A = 4.1 and Ar = 3.82). The gene diversity was highest in the Spiti population (He = 0.67), followed by Marwari (He = 0.66) and Kathiawari (He = 0.59). Within population inbreeding estimates (f) in Marwari, Spiti and Kathiawari breeds were 0.18, 0.08, and 0.07, respectively, suggesting high level of inbreeding in these breeds. Analysis of bottleneck revealed evidence of recent bottleneck in Spiti and Kathiawari populations. Pair-wise Fst analysis, AMOVA and assignment tests demonstrated high genetic differentiation and low gene flow between populations. The information about genetic diversity and population structure will be useful for the future development of effective breeding management in order to preserve these Indian horse breeds.

Mamta Chauhan

Papers

Effect of Interplanetary Turbulences Causing High/low Amplitude Anisotropic Wave Trains in Cr Intensity

Genetic diversity and bottleneck studies in the Marwari horse breed.

Phenotypic characterization of Indian equine breeds: a comparative study

Comparative genetic diversity analysis among six Indian breeds and English Thoroughbred horses

Genetic diversity and population structure of three Indian horse breeds.