Reconstruction of the Major Maternal and Paternal Lineages in the Feral New Zealand Kaimanawa Horses

SIMPLE SUMMARY: New Zealand has the fourth largest feral horse population (Kaimanawa and Far North horses) in the world. The Kaimanawas (KHs) are feral horses descended from various domestic horse breeds released into the Kaimanawa ranges in the 19th and 20th centuries. Over time, the population size has fluctuated dramatically due to hunting, large-scale farming and forestry. Currently, the herd is managed by an annual round-up, limiting the number to 300 horses to protect the rare and unique native flora in this region. Here, we examined 96 KHs to investigate their genetic similarity with respect to other domestic horse breeds, using uniparental markers (mitochondrial DNA, Y-chromosome). Our results indicate that although six maternal and six paternal lineages contributed to the KH gene pool, the current population is dominated by few ancestral lineages, and possibly represents two KH sub-populations. We show that three horse breeds, namely Welsh ponies, Thoroughbred and Arabian horses had a major influence in the genetic-makeup of the extant KH population. Moreover, our results suggest that mitochondrial genetic diversity in KHs is closer to the Sable Island horses, and less than other feral horse populations around the world. Our current findings, combined with ongoing research will provide insight into the KH population-specific genetic variations and level of inbreeding. This will advance equine genomic research and improve the management strategies to conserve these treasured New Zealand horses. ABSTRACT: New Zealand has the fourth largest feral horse population in the world. The Kaimanawas (KHs) are feral horses descended from various domestic horse breeds released into the Kaimanawa ranges in the 19th and 20th centuries. Over time, the population size has fluctuated dramatically due to hunting, large-scale farming and forestry. Currently, the herd is managed by an annual round-up, limiting the number to 300 individuals to protect the native ecosystem. Here, we genotyped 96 KHs for uniparental markers (mitochondrial DNA, Y-chromosome) and assessed their genetic similarity with respect to other domestic horses. We show that at least six maternal and six paternal lineages contributed unequally to the KH gene pool, and today’s KH population possibly represents two sub-populations. Our results indicate that three horse breeds, namely Welsh ponies, Thoroughbreds and Arabian horses had a major influence in the genetic-makeup of the extant KH population. We show that mitochondrial genetic diversity in KHs (π = 0.00687 ± 0.00355) is closer to that of the Sable Island horses (π = 0.0034 ± 0.00301), and less than other feral horse populations around the world. Our current findings, combined with ongoing genomic research, will provide insight into the population-specific genetic variation and inbreeding among KHs. This will largely advance equine research and improve the management of future breeding programs of these treasured New Zealand horse.