Genome-Wide Runs of Homozygosity Revealed Selection Signatures in Bos indicus

Abstract

Genome-wide runs of homozygosity (ROH) are suitable for understanding population history, calculating genomic inbreeding, deciphering genetic architecture of complex traits and diseases as well as identifying genes linked with agro-economic traits. Autozygosity and ROH islands, genomic regions with elevated ROH frequencies, were characterized in 112 animals of seven Indian native cattle breeds (B. indicus) using BovineHD BeadChip. In total, 4138 ROH were detected. The average number of ROH per animal was maximum in draft breed, Kangayam (63.62 ± 22.71) and minimum in dairy breed, Sahiwal (24.62 ± 11.03). The mean ROH length was maximum in Vechur (6.97 Mb) and minimum in Hariana (4.04 Mb). Kangayam revealed the highest ROH based inbreeding (F_{ROH > 1Mb} = 0.113 ± 0.059), whereas Hariana (F_{ROH > 1Mb} = 0.042 ± 0.031) and Sahiwal (F_{ROH > 1Mb} = 0.043 ± 0.048) showed the lowest. The high standard deviation observed in each breed highlights a considerable variability in autozygosity. Out of the total autozygous segments observed in each breed except Vechur, > 80% were of short length (< 8 Mb) and contributed almost 50% of the genome proportion under ROH. However, in Vechur cattle, long ROH contributed 75% of the genome proportion under ROH. ROH patterns revealed Hariana and Sahiwal breeds as less consanguineous, while recent inbreeding was apparent in Vechur. Maximum autozygosity observed in Kangayam is attributable to both recent and ancient inbreeding. The ROH islands were harbouring higher proportion of QTLs for production traits (20.68% vs. 14.64%; P≤ 0.05) but lower for reproductive traits (11.49% vs. 15.76%; P≤ 0.05) in dairy breeds compared to draft breed. In draft cattle, genes associated with resistant to diseases/higher immunity (LYZL1, SVIL, and GPX4) and stress tolerant (CCT4) were identified in ROH islands; while in dairy breeds, for milk production (PTGFR, CSN1S1, CSN2, CSN1S2, and CSN3). Significant difference in ROH islands among large and short statured breeds was observed at chromosome 3 and 5 involving genes like PTGFR and HMGA2 responsible for milk production and stature, respectively. PCA analysis on consensus ROH regions revealed distinct clustering of dairy, draft and short stature cattle breeds.

Keywords: FROH; autozygosity; genomic inbreeding; runs of homozygosity islands; selection sweep.

Figure 1

The number of ROH per chromosome and percentage coverage. The bars exhibit the total number of ROH per chromosome identified in the 112 animals. The line shows the average percentage of ROH for every chromosome. To determine the percentage of ROH per chromosome, the mean ROH length was calculated by adding all ROH (in Mb) on a chromosome and then dividing by the number of animals that had ROH on that chromosome. The mean ROH length was then divided by the chromosome length (in Mb) and transformed to percentage. SW, Sahiwal; TP, Tharparkar; GR, Gir; HR, Hariana.

Figure 2

The total number of ROH and length of genome under ROH for each individual in a breed. SW, Sahiwal; TP, Tharparkar; GR, Gir; HR, Hariana; KG, Kangayam; OG, Ongole; VC, Vechur.

Figure 3

Individual value plot displaying proportion of autosome covered in runs of homozygosity (ROH) per animal. The crossed circle shows the median ROH value of each breed.

Figure 4

Breed-wise mean of sum of ROH. Within each ROH length category, the sum of ROH (in Mb) was calculated per animal and averaged breed-wise. Breeds from left to right are Sahiwal (SW), Tharparkar (TP), Gir (GR), Hariana (HR), Kangayam (KG), Ongole (OG), and Vechur (VC).