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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #336965

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: Ruminant-specific multiple duplication events of PRDM9 before speciation

Author
item PADHI, ABINASH - University Of Maryland
item SHEN, BOTONG - University Of Maryland
item JIANG, JICAI - University Of Maryland
item ZHOU, YANG - Northwest Agricultural & Forestry University
item Liu, Ge - George
item MA, LI - University Of Maryland

Submitted to: BMC Evolutionary Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/26/2017
Publication Date: 3/14/2017
Citation: Padhi, A., Shen, B., Jiang, J., Zhou, Y., Liu, G., Ma, L. 2017. Ruminant-specific multiple duplication events of PRDM9 before speciation. BMC Evolutionary Biology. 17:79.

Interpretive Summary: Understanding the genetic and evolutionary mechanisms of speciation genes like PRDM9 in ruminants is important. Using phylogenetic analyses, this study demonstrates that gene duplication, concerted evolution and positive selection are the likely forces that underlie the expansion of ruminant PRDM9 sub-family. These results fill our knowledge gaps about PRDM9 expansion and provide important insights into mammalian reproduction and fitness. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enable animal selection will benefit from this study.

Technical Abstract: Understanding the genetic and evolutionary mechanisms of speciation genes in sexually reproducing organisms would provide important insights into mammalian reproduction and fitness. PRDM9, a widely known speciation gene, has recently gained attention for its important role in meiotic recombination and hybrid incompatibility. The present study reports two gene duplication events of PRDM9 in ruminants: an inter-chromosomal duplication that occurred between chromosome 1 (chr1) and chromosome X (chrX), and an intra-chromosomal X-linked duplication, which resulted in two additional copies of PRDM9 in ruminants. Each gene copy present in all the three genera (Bos, Capra, and Ovis) and form a separate monophyletic group, thus indicating the duplication events were likely to have occurred before the speciation events of this group. Although inter-chromosomal duplication between autosomes is common, the observation of such duplication between chrX and chr1 is rare and may possibly have happened due to unequal crossing-overs millions of years ago when sex chromosomes were independently derived from a pair of ancestral autosomes. Two copies of the PRDM9 gene, one X-linked and one autosomal, are characterized by the presence of variable sized tandem-repeated C2H2 zinc fingers (ZFs) and evolved under strong positive selection and concerted evolution, supporting the notion of well-established Red Queen hypothesis. The other X-linked copy lost its ZFs and likely lost its function. Collectively, gene duplication, concerted evolution and positive selection are the likely forces that underlie the expansion of ruminant PRDM9 sub-family.