Whole-genome resequencing reveals diversity, global and local ancestry proportions in Yunling cattle

Yunling cattle, a three-breed cross consisting of 1/2 Brahman cattle, 1/4 Murray Grey cattle and 1/4 Yunnan Yellow cattle, has advantage of rapid growth, good meat quality, enhanced tolerance towards a hot and humid climate, tick resistance and crude feed forbearance. Here, we investigated the genetic diversity, global and local ancestry proportions by sequencing the genomes of 131 Yungling cattle and 31 Brahman cattle (for control). Furthermore, we used 35 published genomes of ancestry breeds (including Angus cattle [ancestry of Murray Grey], Wannan cattle [ancestry of Yunnan Yellow cattle: Wenshan and Dianzhong], Wenshan and Dianzhong cattle) to characterize the formation process of Yunling cattle. The highest nucleotide diversity was found in the Wannan cattle, followed by Wenshan, Dianzhong, Brahman, Yunling and Angus cattle. The results of LD decay in each breed was largely consistent with the results of nucleotide diversity, except for the faster decay in Angus cattle out of a smaller effective population size and a strong bottleneck during the breed formation. The population-structure analysis revealed that the cross-breed Yunling cattle harboured the ancestry with Angus (0.44), Brahman (0.48) and Wannan cattle (0.08). Subsequently, we used RFmix to infer local ancestry in Yunling cattle and then performed chi-squared test to obtain the segments whose proportions of a certain ancestry were excessive compared with the whole-genome level, leading to 391 Angus, 49 Brahman and 2,312 Wannan segments. Gene annotation and KEGG enrichment analysis revealed that the excessive Angus, Brahman and Wannan segments might contribute to the rapid growth, immune resistance and indigenous adaptation, respectively, in Yunling cattle. Our results help understand ancestry components and formation process in Yunling cattle and will provide an opportunity for selective breeding by molecular approaches in future.