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Lu Y.-F.,China Agricultural University | Lu Y.-F.,Nanyang Normal University | Li H.-W.,China Agricultural University | Li H.-W.,National Engineering Laboratory for Animal Breeding | And 4 more authors.
Journal of Integrative Agriculture | Year: 2013

Maintenance and management of genetic diversity of farm animal genetic resources (AnGR) is very important for biological, socioeconomical and cultural significance. The core concern of conservation for farm AnGR is the retention of genetic diversity of conserved populations in a long-term perspective. However, numerous factors may affect evolution of genetic diversity of a conserved population. Among those factors, the genetic architecture of conserved populations is little considered in current conservation strategies. In this study, we investigated the dynamic changes of genetic diversity of conserved populations with two scenarios on initial genetic architectures by computer simulation in which thirty polymorphic microsatellite loci were chosen to represent genetic architecture of the populations with observed heterozygosity (Ho) and expected heterozygosity (He), observed and mean effective number of alleles (Ao and Ae), number of polymorphic loci (NP) and the percentage of polymorphic loci (PP), number of rare alleles (RA) and number of non-rich polymorphic loci (NRP) as the estimates of genetic diversity. The two scenarios on genetic architecture were taken into account, namely, one conserved population with same allele frequency (AS) and another one with actual allele frequency (AA). The results showed that the magnitude of loss of genetic diversity is associated with genetic architecture of initial conserved population, the amplitude of genetic diversity decline in the context AS was more narrow extent than those in context AA, the ranges of decline of Ho and Ao were about 4 and 2 times in AA compared with that in AS, respectively, the occurrence of first monomorphic locus and the time of change of measure NP in scenario AA is 20 generations and 23 generations earlier than that in scenario AS, respectively. Additionally, we found that NRP, a novel measure proposed by our research group, was a proper estimate for monitoring the evolution of genetic diversity in a closed conserved population. Our study suggested that current managements of conserved populations should emphasize on initial genetic architecture in order to make an effective and feasible conservation scheme. © 2013 Chinese Academy of Agricultural Sciences.

Jiang L.,National Engineering Laboratory for Animal Breeding | Liu X.,National Engineering Laboratory for Animal Breeding | Yang J.,National Engineering Laboratory for Animal Breeding | Wang H.,National Engineering Laboratory for Animal Breeding | And 6 more authors.
BMC Genomics | Year: 2014

Background: Genome wide association study (GWAS) has been proven to be a powerful tool for detecting genomic variants associated with complex traits. However, the specific genes and causal variants underlying these traits remain unclear. Results: Here, we used target-enrichment strategy coupled with next generation sequencing technique to study target regions which were found to be associated with milk production traits in dairy cattle in our previous GWAS. Among the large amount of novel variants detected by targeted resequencing, we selected 200 SNPs for further association study in a population consisting of 2634 cows. Sixty six SNPs distributed in 53 genes were identified to be associated significantly with on milk production traits. Of the 53 genes, 26 were consistent with our previous GWAS results. We further chose 20 significant genes to analyze their mRNA expression in different tissues of lactating cows, of which 15 were specificly highly expressed in mammary gland. Conclusions: Our study illustrates the potential for identifying causal mutations for milk production traits using target-enrichment resequencing and extends the results of GWAS by discovering new and potentially functional mutations. © Jiang et al.; licensee BioMed Central Ltd.

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