基于简化基因组测序的娄门鸭遗传多样性评价

doi:10.11843/j.issn.0366-6964.2022.06.008

摘要/Abstract

摘要： 旨在通过分析娄门鸭保种群体的遗传多样性和群体结构来评估保种效果。本研究在娄门鸭保种群中随机选择同一世代163只90日龄的健康个体(39公，124母)，翅静脉采血后提取基因组DNA，利用简化基因组测序技术检测全基因组范围内的单核苷酸多态性(SNPs); 利用R软件计算个体水平的多态信息含量(PIC)、固定指数(Fix-index)、香农信息指数(SHI)、基因多样性指数(Nei)、有效等位基因数(Ne)以及本研究自创的相对多态信息含量(rPIC)等6个遗传多样性指标，并比较分析了不同染色体水平的遗传多样性指标; 同时利用admixture软件分析群体遗传结构，gcta软件分析群体主成分和个体间的亲缘关系，并分析连续性纯合片段(runs of homozygosity，ROH)以及基因组近交系数F_ROH，评估保种效果。结果显示，163只娄门鸭个体共检测到622 205个SNPs位点，质控过滤后得到374 455个高质量SNPs位点，其中50.70%的位点分布在NC_040046、NC_040047、NC_040048和NC_040049四个染色体中。娄门鸭群体PIC、Nei、Ne、SHI和rPIC指标值分别为0.154 1、0.192 9、1.336、0.296 9和0.410 9，对于SNPs而言，该群体38.80%的SNPs位点属于高度多态性位点，遗传多样性较为丰富; Fix-index值为0.320 8，说明娄门鸭群体出现了分化，这与遗传结构、PCA和亲缘关系分析将娄门鸭群体划分为3个群体的结果一致。PIC、Nei、Ne和SHI四个指标分别在不同染色体上的分布规律均一致，且4个指标两两相关性均达到0.97以上，而Fix-index与其他4个指标的相关性较低，在0.23以下，说明可以选择Fix-index以及PIC等少数指标来评估娄门鸭群体的遗传多样性。163只娄门鸭个体共检测到2 966条ROH，ROH片段长度主要集中在0~2 Mb区间; 基于ROH得到的基因组近交系数F_ROH在公、母鸭中分别为0.027 5和0.043 3，说明娄门鸭保种群近交程度较低; 具体到染色体水平，NC_040068、NC_040074染色体的F_ROH值分别达到0.352 4和0.319 3。结果提示，娄门鸭保种群的遗传多样性较丰富，群体基因组近交系数较低，但个别染色体的近交系数较高，且群体出现了部分分化。后续保种中可以将遗传结构分析得到的3个分化的亚群个体之间进行适当的非随机交配，消除目前的群体分化现象，并重点监测染色体近交系数较高的基因组区域，避免个别染色体近交系数上升过快。

关键词: 鸭, 遗传多样性, 群体结构, ROH, 近交系数

Abstract: This study aimed to explore the genetic diversity and population structure of Loumen duck conservation population and evaluate the conservation effect. In this study, a total of 163 healthy 90-day-old Loumen ducks (39 males and 124 females) of the same generation were randomly selected from the Loumen duck conservation population, and genomic DNA was extracted after wing-vein blood collection to detect genome-wide single nucleotide polymorphisms (SNPs) using reduced-representation genome sequencing techniques. Six genetic diversity indexes, including polymorphism information content (PIC), fixation index (Fix-index), Shannon information index (SHI), gene diversity index (Nei), effective number of alleles (Ne) and relative PIC (rPIC), were calculated by R software, and the genetic diversity indexes at different chromosome levels were compared. At the same time, admixture software was used to analyze the population genetic structure, and gcta software was used to analyze the principal component analysis (PCA) and genetic relationship, and the runs of homozygosity (ROH) and genomic inbreeding coefficient F_ROH were analyzed to evaluate the conservation effect. The results showed that 622 205 SNPs were detected in 163 Loumen ducks, and 374 455 high-quality SNPs were obtained after quality control filtration, of which 50.70% were distributed in 4 chromosomes of NC_ 040046, NC_ 040047, NC_ 040048 and NC_ 040049. The PIC, Nei, Ne, SHI and rPIC values of Loumen duck population were 0.154 1, 0.192 9, 1.336, 0.296 9 and 0.410 9, respectively. For SNPs, 38.80% of the loci in this population belonged to highly polymorphic loci and had rich genetic diversity. Fix-index value was 0.320 8, indicating that the Loumen duck population had differentiated, which was consistent with the result that the Loumen duck population was divided into 3 populations by genetic structure, PCA and kinship analysis. All the distribution patterns of PIC, Nei, Ne and SHI on different chromosomes were consistent, and the correlation coefficients of the 4 indexes was more than 0.97, while the correlation between Fix-index and the other 4 indexes was lower than 0.23, indicating that a few indexes such as Fix-index and PIC could be selected to evaluate the genetic diversity of Loumen duck population. A total of 2 966 ROH fragments were detected in 163 Loumen ducks, and the length was mainly concentrated in the range of 0-2 Mb. The genomic inbreeding coefficients F_ROH obtained based on ROH were 0.027 5 and 0.043 3 in male and female ducks, respectively, indicating that the inbreeding degree of the conserved population of Loumen duck was low. At the chromosome level, the F_ROH values of chromosome NC_040068 and NC_040074 were 0.352 4 and 0.319 3, respectively. Loumen duck conservation population has rich genetic diversity and low population genomic inbreeding coefficient, but the inbreeding coefficient of individual chromosomes is high, and the population has partial differentiation. Therefore, appropriate non-random mating between individuals of the 3 differentiated subpopulations obtained from genetic structure analysis can be used in subsequent conservation to eliminate the current population differentiation, and the genomic regions with high inbreeding coefficient shall be monitored to avoid the rapid increase of inbreeding coefficient of special chromosomes.

Key words: duck, genetic diversity, population structure, ROH, inbreeding coefficient

中图分类号:

S834.2

刘宏祥, 沈永杰, 张丽华, 章双杰, 王靖, 朱杰, 陈瑜哲, 朱春红, 宋卫涛, 张丹, 陶志云, 徐文娟, 刘红林, 李慧芳. 基于简化基因组测序的娄门鸭遗传多样性评价[J]. 畜牧兽医学报, 2022, 53(6): 1735-1748.

LIU Hongxiang, SHEN Yongjie, ZHANG Lihua, ZHANG Shuangjie, WANG Jing, ZHU Jie, CHEN Yuzhe, ZHU Chunhong, SONG Weitao, ZHANG Dan, TAO Zhiyun, XU Wenjuan, LIU Honglin, LI Huifang. Genetic Diversity Evaluation of Loumen Duck Based on Reduced-Representation Genome Sequencing[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(6): 1735-1748.

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