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. 2022 Aug 25;17(8):e0271718.
doi: 10.1371/journal.pone.0271718. eCollection 2022.

Genomic inbreeding and runs of homozygosity analysis of indigenous cattle populations in southern China

Yuqiang Liu  1   2 , Guoyao Zhao  1 , Xiaojue Lin  2 , Jiahao Zhang  2 , Guanyu Hou  3 , Luepei Zhang  1 , Dewu Liu  2 , Yaokun Li  2 , Junya Li  1 , Lingyang Xu  1
Affiliations

Genomic inbreeding and runs of homozygosity analysis of indigenous cattle populations in southern China

Yuqiang Liu et al. PLoS One. .

Abstract

Runs of homozygosity (ROH) are continuous homozygous segments from the common ancestor of parents. Evaluating ROH pattern can help to understand inbreeding level and genetic basis of important traits. In this study, three representative cattle populations including Leiqiong cattle (LQC), Lufeng cattle (LFC) and Hainan cattle (HNC) were genotyped using the Illumina BovineHD SNPs array (770K) to assess ROH pattern at genome wide level. Totally, we identified 26,537 ROH with an average of 153 ROH per individual. The sizes of ROH ranged from 0.5 to 53.26Mb, and the average length was 1.03Mb. The average of FROH ranged from 0.10 (LQC) to 0.15 (HNC). Moreover, we identified 34 ROH islands (with frequency > 0.5) across genome. Based on these regions, we observed several breed-specific candidate genes related to adaptive traits. Several common genes related to immunity (TMEM173, MZB1 and SIL1), and heat stress (DNAJC18) were identified in all three populations. Three genes related to immunity (UGP2), development (PURA) and reproduction (VPS54) were detected in both HNC and LQC. Notably, we identified several breed-specific genes related to sperm development (BRDT and SPAG6) and heat stress (TAF7) in HNC, and immunity (CDC23 and NME5) and development (WNT87) in LFC. Our findings provided valuable insights into understanding the genomic homozygosity pattern and promoting the conservation of genetic resources of Chinese indigenous cattle.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. The distributions of ROH statistics per individual for indigenous cattle populations in southern China.
(A) Violin plot of the total length of ROH events per individual. (B) Violin plot the total number of ROH events per individual. LQC: Leiqiong cattle; LFC: Lufeng cattle; HNC: Hainan cattle.
Fig 2
Fig 2. Total length and number of ROH for three size classes including Small (0.5 to 1 Mb), Medium (1 to 5 Mb) and Large (>5 Mb).
(A) The total number of ROH for size classes. (B) The total length of ROH for three size classes. LQC: Leiqiong cattle; LFC: Lufeng cattle; HNC: Hainan cattle.
Fig 3
Fig 3. The distributions of inbreeding coefficient.
(A) The distributions of FHOM across populations. (B) The distributions of FROH across populations. (C)The distributions of FGRM across populations. FHOM: inbreeding coefficient based on the proportion of homozygous SNP, FROH: inbreeding coefficient based on the proportion of the genome covered by runs of homozygosity, FGRM: inbreeding coefficient based on the genomic relationship matrix.
Fig 4
Fig 4. Line plot of inbreeding coefficient for each chromosome among the three populations.
Fig 5
Fig 5. The distribution of ROH across autosomes in the three populations.
The x-axis represents the genomic coordinate, and the y-axis displays the frequency of overlapping ROH among individuals. (A) LFC; (B) HNC; (C) LQC.
Fig 6
Fig 6. Candidate genes identified for the three populations overlapping with ROH islands.
(A) The Venn diagram of the identified genes for three populations when the threshold frequency of ROH islands is set to 0.3. (B) The Venn diagram of the identified genes for three populations when the threshold frequency of ROH islands is set to 0.5.
See this image and copyright information in PMC

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