Abstract
Dianzhong cattle is a classic Chinese indigenous cattle breed with historical records dating back to 200 BC. But with its genomic differences having not been clearly elucidated, the quest for genomic characterization will be an essential step towards understanding the genomic basis of productivity and adaptation to survival under Chinese farming systems. Here we compared 10 Dianzhong cattle (four newly sequenced and six downloaded) with 29 published genomes of three underlying ancestral populations (Chinese zebu, Indian zebu, and Yanbian cattle) to characterize the genomic variations of Dianzhong cattle. Dianzhong cattle has a high nucleotide diversity (0.0034), second only to Chinese zebu. Together with analyses of linkage disequilibrium decay and runs of homozygosity, Dianzhong cattle displayed higher genomic diversity and weaker artificial selection compared with Yanbian cattle. From a selective sweep analysis by four methods (Fst, π-ratio, XP-CLR, and XP-EHH), the positive selective signals were mainly manifested in candidate genes and pathways related to heat resistance, growth and development, fat deposition, and male reproduction. Missense mutations were detected in candidate genes, SDS (c.944C > A and p.Ala315Glu), PDGFD (c.473A > G and p.Lys158Arg), and DDX4 (rs460251486, rs722912933, and rs517668236), which related to heat resistance, fat deposition, and spermatogenesis, respectively. Our findings unravel, at the genome-wide level, the unique diversity of Dianzhong cattle while emphasizing the opportunities for improvement of livestock productivity in further breeding programs.
Highlights
Domestic cattle generally refers to two subspecies, Bos taurus and Bos taurus indicus
The analyses of unique single-nucleotide polymorphism (SNP) and non-synonymous SNPs displayed that the genetic diversity of Dianzhong cattle was second only to Chinese zebu (Supplementary Figure S1)
The nucleotide diversity ranking calculated in this study (Chinese zebu > Dianzhong cattle > Indian zebu > Yanbian cattle) was basically consistent with the earlier results (Chen et al, 2018)
Summary
Domestic cattle generally refers to two subspecies, Bos taurus and Bos taurus indicus. They were domesticated in the Fertile Crescent (∼10,000 years ago) and the Indus Valley (∼8,000 years ago), respectively (Utsunomiya et al, 2019). These two subspecies can be interbred without barriers, unlike other bovine subspecies (buffalo, American bison, etc.) that have reproductive isolation (Wu et al, 2018). Dianzhong cattle is one of the most widely distributed indigenous breeds in Yunnan. It has a long history of breeding, with historical records dating back to 200 BC (China National Commission of Animal Genetic Resources, 2011). Blind hybridization as well as the lack of breed conservation planning caused the threat of breed degradation in Dianzhong cattle
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