Assessment of Autozygosity Derived From Runs of Homozygosity in Jinhua Pigs Disclosed by Sequencing Data.

Jinhua pig, a well-known Chinese indigenous breed, has evolved as a pig breed with excellent meat quality, greater disease resistance, and higher prolificacy. The reduction in the number of Jinhua pigs over the past years has raised concerns about inbreeding. Runs of homozygosity (ROH) along the genome have been applied to quantify individual autozygosity to improve the understanding of inbreeding depression and identify genes associated with traits of interest. Here, we investigated the occurrence and distribution of ROH using next-generation sequencing data to characterize autozygosity in 202 Jinhua pigs, as well as to identify the genomic regions with high ROH frequencies within individuals. The average inbreeding coefficient, based on ROH longer than 1 Mb, was 0.168 ± 0.052. In total, 18,690 ROH were identified in all individuals, among which shorter segments (1-5 Mb) predominated. Individual ROH autosome coverage ranged from 5.32 to 29.14% in the Jinhua population. On average, approximately 16.8% of the whole genome was covered by ROH segments, with the lowest coverage on SSC11 and the highest coverage on SSC17. A total of 824 SNPs (about 0.5%) and 11 ROH island regions were identified (occurring in over 45% of the samples). Genes associated with reproduction (HOXA3, HOXA7, HOXA10, and HOXA11), meat quality (MYOD1, LPIN3, and CTNNBL1), appetite (NUCB2) and disease resistance traits (MUC4, MUC13, MUC20, LMLN, ITGB5, HEG1, SLC12A8, and MYLK) were identified in ROH islands. Moreover, several quantitative trait loci for ham weight and ham fat thickness were detected. Genes in ROH islands suggested, at least partially, a selection for economic traits and environmental adaptation, and should be subject of future investigation. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the pig genome.

An Efficient Genotyping Method in Chicken Based on Genome Reducing and Sequencing.

Single nucleotide polymorphisms (SNPs) are essential for identifying the genetic mechanisms of complex traits. In the present study, we applied genotyping by genome reducing and sequencing (GGRS) method to construct a 252-plex sequencing library for SNP discovery and genotyping in chicken. The library was successfully sequenced on an Illumina HiSeq 2500 sequencer with a paired-end pattern; approximately 400 million raw reads were generated, and an average of approximately 1.4 million good reads per sample were generated. A total of 91,767 SNPs were identified after strict filtering, and all of the 252 samples and all of the chromosomes were well represented. Compared with the Illumina 60K chicken SNP chip data, approximately 34,131 more SNPs were identified using GGRS, and a higher SNP density was found using GGRS, which could be beneficial for downstream analysis. Using the GGRS method, more than 3528 samples can be sequenced simultaneously, and the cost is reduced to $18 per sample. To the best of our knowledge, this study describes the first report of such highly multiplexed sequencing in chicken, indicating potential applications for genome-wide association and genomic selection in chicken.

Genotyping by genome reducing and sequencing for outbred animals.

Next-generation sequencing (NGS) approaches are widely used in genome-wide genetic marker discovery and genotyping. However, current NGS approaches are not easy to apply to general outbred populations (human and some major farm animals) for SNP identification because of the high level of heterogeneity and phase ambiguity in the haplotype. Here, we reported a new method for SNP genotyping, called genotyping by genome reducing and sequencing (GGRS) to genotype outbred species. Through an improved procedure for library preparation and a marker discovery and genotyping pipeline, the GGRS approach can genotype outbred species cost-effectively and high-reproducibly. We also evaluated the efficiency and accuracy of our approach for high-density SNP discovery and genotyping in a large genome pig species (2.8 Gb), for which more than 70,000 single nucleotide polymorphisms (SNPs) can be identified for an expenditure of only $80 (USD)/sample.

Application of multivariate statistical techniques in the assessment of water quality in the Southwest New Territories and Kowloon, Hong Kong.

The application of different multivariate statistical techniques for the interpretation of a complex data matrix obtained during 2000-2007 from the watercourses in the Southwest New Territories and Kowloon, Hong Kong was presented in this study. The data set consisted of the analytical results of 23 parameters measured monthly at 16 different sampling sites. Hierarchical cluster analysis grouped the 12 months into two periods and the 16 sampling sites into three groups based on similarity in water quality characteristics. Discriminant analysis (DA) provided better results both temporally and spatially. DA also offered an important data reduction as it only used four parameters for temporal analysis, affording 84.2% correct assignations, and eight parameters for spatial analysis, affording 96.1% correct assignations. Principal component analysis/factor analysis identified four latent factors standing for organic pollution, industrial pollution, nonpoint pollution, and fecal pollution, respectively. KN1, KN4, KN5, and KN7 were greatly affected by organic pollution, industrial pollution, and nonpoint pollution. The main pollution sources of TN1 and TN2 were organic pollution and nonpoint pollution, respectively. Industrial pollution had high effect on TN3, TN4, TN5, and TN6.

Qualitative analysis and quantitative simulation on Yin-Huang water salinization mechanism in Bei-Da-Gang Reservoir.

Yellow River water transfer for Tianjin is important in solving the water shortage in Tianjin, which facilitate economic development and social progress for many years. Fresh water drawn from Yellow River (i.e., Yin-Huang water) becomes saltier and saltier when being stored in the Bei-Da-Gang reservoir. We qualitatively analyze the water salinization mechanism based on mass transfer theory. The main factors are salinity transfer of saline soil, evaporation concentrating, and the agitation of wind. A simulative experimental pond and an evaporation pond were built beside the Bei-Da-Gang reservoir to quantitatively investigate the water salinization based on water and solute balance in the simulative pond. 80% of increased [Cl-] is due to the salinity transfer of the saline soil and the other 20% is due to evaporation concentrating, so the former is the most important factor. We found that the salinization of Yin-Huang water can be described with a zero-dimension linear model.