Acta Veterinaria et Zootechnica Sinica ›› 2022, Vol. 53 ›› Issue (6): 1735-1748.doi: 10.11843/j.issn.0366-6964.2022.06.008

• ANIMALGENETICS AND BREEDING • Previous Articles     Next Articles

Genetic Diversity Evaluation of Loumen Duck Based on Reduced-Representation Genome Sequencing

LIU Hongxiang1,3, SHEN Yongjie2, ZHANG Lihua2, ZHANG Shuangjie1, WANG Jing2, ZHU Jie2, CHEN Yuzhe2, ZHU Chunhong1, SONG Weitao1, ZHANG Dan1, TAO Zhiyun1, XU Wenjuan1, LIU Honglin3, LI Huifang1*   

  1. 1. Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China;
    2. Animal Husbandry and Veterinary Station of Kunshan City, Suzhou 215300, China;
    3. Nanjing Agricultural University, Nanjing 210095, China
  • Received:2021-10-21 Online:2022-06-23 Published:2022-06-25

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 FROH 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 FROH 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 FROH 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

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