关键词: 长纯合片段, 畜禽育种, 单核苷酸多态性, 近交评估, 候选基因鉴定

Abstract:

Runs of homozygosity (ROH) is a long tract of homozygous genotypes commonly found in individuals and populations, which generates on the offspring’s genome inherited identical haplotypes from each parent. ROH contains a wealth of genetic information about populations, which makes it a useful tool for providing information to study how populations change over time. Moreover, ROH can estimate the genetic relationships between individuals to minimize the inbreeding mating rates. In addition, ROH can expose harmful mutations in the genome. The frequencies, sizes and distributions of ROHs in the genome are influenced by natural and artificial selection, recombination, linkage disequilibrium, population history, mutation rate and inbreeding level. Recently, with the use of high-throughput genotype technology and the reduction of second-generation sequencing costs, livestock and poultry breeding have entered into the genomic era. The selection intensity of the elites in livestock and poultry significantly increase to improve their performances, but it will increase inbreeding and cause inbreeding depression as well. Based on ROH molecular information, it is more accurately to detect past and nearest in close relative mating. The ROH-based inbreeding coefficient (F_ROH) can obtain an individual's true inbreeding coefficient, i.e. the realized inbreeding coefficient, and the pedigree-based F_PED is the expectation value of inbreeding coefficient. In the absence of genealogical information, F_ROH can be used to infer information about a group's history and the inbreeding levels. Meanwhile, the selection reshapes ROH patterns in different regions of the genome. In addition, the selection can increase the homozygosities around the target point, and harmful mutations are thought to occur more frequently in the ROH region, which can be detected by ROH to reduce the risk of complex diseases. After long-term selection, one ROH appeared in multiple individuals’ genomes in the same population, resulting in ROH islands. It has confirmed the correlation between ROH and the selected genomic region. The candidate genes related to economic traits can be annotated on the ROH islands by means of biological information. In addition, ROH also provides a new perspective for assessing the genetic diversity in domestic animals. Genome-wide ROH detection on the population can used to investigate the genetic structure of this population, and F_ROH can evaluate the impact of inbreeding in the current breeding program, which can adjust breeding plans to protect the genetic diversity of varieties. Therefore, ROH has gradually become an important index to explore the historical population structure, the level of inbreeding, candidate gene identification. There are mainly two kinds of methods to identify ROH: observation genotype counting method and model-based analysis. Commonly used softwares include PLINK, GERMLINE, BEAGLE, GARLIC, etc. In practical applications, PLINK is the most common ROH detection tool. Since the SNP chip for cattle was firstly used in domestic animals, the cattle population was firstly conduct genome-wide ROH detection. Now, studies on ROH are becoming more popular in pigs, sheep and other domestic animals. This review mainly described the principle of ROH formation and its detection methods, as well as progress of its application in livestock and poultry, so as to provide reference for the genetic breeding of livestock and poultry.

Key words: runs of homozygosity, livestock and poultry breeding, single nucleotide polymorphism, inbreeding evaluation, candidate genes identification