Evaluation of the Conservation Effect in Penzhoushandi Conserved Population Based on SNP Chip

doi:10.7668/hbnxb.20192586

Abstract

Abstract:

The aim of this study was to better understand the Penzhoushandi pigs.The 50K SNP chip was used to analyze the SNPs in 152 healthy adult Penzhoushandi pigs conserved population.The proportion of polymorphism markers,expected heterozygosity and observed heterozygosity were calculated by Plink software and the effective size of conserved population was calculated by SNeP(V1.1)software.The IBS distance matrix was analysed by Plink software and the genomic relationship G matrix was analyzed by Gamatrix(V2)software.The Mega X(V10.0)software was used to analysis the family structure of conserved population.The numbers and length of ROHs and inbreeding coefficient based on ROHs of each sample were calculated by Plink software.The results showed that the proportion of polymorphism markers was 0.660 1 and the effective size of conserved population was 7.4.The expected heterozygosity and observed heterozygosity were 0.289 2 and 0.294 7.The average IBS genetic distance of whole group was(0.234 1±0.027 3),and the average IBS genetic distance of boars was(0.228 0±0.033 5).The whole conserved group could be divided into 5 families with boars and 1 family without boars. The size of boars in family A and D was relatively small. A total of 3 737 ROHs,gatherring in individuals with the most ROHs by 21-25(32.24%)numbers and 100-200 Mb length(42.11%),were founded in the Penzhoushandi pigs conserved population.The average inbreeding coefficient of conserved population was 0.085.In general,the genetic diversity of the Penzhoushandi pigs conserved population was relatively rich,but there was also existing a risk of inbreeding among some individuals. The families in the conserved population were relatively less,and the number of boars in some families was small. Thus,there was a risk of ancestry loss in this families. Therefore,selection and breeding measures should be strengthened or extra ancestry should be introduced to ensure the long-term preservation of the genetic diversity of Penzhoushandi pigs.

Key words: Penzhoushandi pigs, 50K SNP chip, Conserved population, Genetic structures, Conservation effect

LONG Xi, CHAI Jie, CHEN Li, PAN Hongmei, ZHANG Liang, CHEN Siqing, GUO Zongyi, ZHANG Tinghuan. Evaluation of the Conservation Effect in Penzhoushandi Conserved Population Based on SNP Chip[J]. Acta Agriculturae Boreali-Sinica, 2022, 37(S1): 358-365. doi: 10.7668/hbnxb.20192586.

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Figures/Tables 6

Fig.1 Visualization results of genetic relationship analysis based on IBS distance matrix Each small square represents the genetic distance value between two pairs from the first sample to the last one, the larger the value,the closer it is to red,that is,the larger the genetic distance between two individuals,vice versa.

Fig.2 Visualization results of genetic relationship analysis based on G matrix Each small square represents the value of the relationship between two pairs from the first sample to the last one, the larger the value,the closer it is to red,that is,the closer relationship between two individuals.

Fig.3 Cluster analysis results of boars in the Penzhoushandi pig sconserved population

Fig.4 Distribution of ROH number in Penzhoushandi pigs

Fig.5 Distribution of ROH length in Penzhoushandi pigs

Tab.1 Distribution ratio of inbreeding coefficient in Penzhoushandi pigs population

近交系数 Inbreeding coefficient	百分比/% Percentage
≥0.5	0
0.25~0.50	0
0.125~0.250	17.11
0.062 5~0.125 0	51.97
≤0.062 5	30.92

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