Current genetic conservation of Chinese indigenous horses revealed with Y-chromosomal and mitochondrial DNA polymorphisms

Abstract

To investigate the genetic diversity of Chinese indigenous horses and determine the genetic status of extant horse breeds, novel Y chromosomal microsatellite markers and known Y chromosomal SNPs and mtDNA loop sequences, were employed to study the genetic diversity levels of 13 Chinese indigenous horse populations and four introduced breeds. Sixteen Y-chromosomal microsatellite markers, including seven newly identified loci, were used in the genotyping. The results showed that 4 out of the 16 loci were highly polymorphic in Chinese indigenous horse populations, in which the polymorphisms of 3 loci, ECAYP12, ECAYP13, and ECAYCAU3, were first reported in the present study. The polymorphic Y chromosomal microsatellite markers result in 19 haplotypes in the studied horses and formed 24 paternal lines when merged with the 14 Y chromosomal SNPs reported previously. The haplotypes CHT18 and SS24 harboring AMELY gene mutation were the ancestral haplotypes, and other haplotypes were derived from them by one or more mutation steps. The horse populations in mountainous and remote areas of southwestern China have the most ancient paternal lines, which suggests that ancient paternal lines preserved in local populations attributed to less human interventions. Our results also showed that the northern local breeds had higher mtDNA diversity than the southern ones in China. The frequency of haplogroup B, F, and G of mtDNA in Chinese indigenous horses has declined in recent years, and some breeds are in endangered status mainly due to small population sizes. Urgent actions should be taken to conserve the genetic diversity of the indigenous horse populations, especially the rare paternal lines. Our findings help to elucidate the genetic diversity and evolutionary history of Chinese domestic horses, which will facilitate the conservation of the indigenous horses in the future.

Unlocking Horse Y Chromosome Diversity

“…These haplotype distributions highlight the replacement of autochthonous Y chromosomes with the import of stallions belonging to three paternal lines (ancestral line, Neapolitan/Oriental and Thoroughbred wave) for the improvement of native breeds. Contrary to these findings, Chinese indigenous horse populations seem to have preserved their genetic diversity because they have not been subjected to intensive selection, thus presenting a particular genetic pattern and unique MSY haplotype variants [ 133 , 135 , 138 , 141 , 142 ]. A recent study focused on a large sample of Chinese horses filled the known gap in the worldwide context by adding information on the Asian populations not previously analysed [ 142 ].…”

“…In 2017, Librado and colleagues analysed the genomes of 14 horses lived from Bronze to Iron Ages, confirming the presence of a large genetic diversity in the early stages of domestication [ 117 ]. Recently, the presence of the most ancient paternal lines in Chinese native horses was confirmed through the analysis of 16 Y-chromosomal microsatellite markers, thus reporting for the first time seven novel microsatellite loci [ 135 ], in addition to those previously detected [ 130 , 132 , 136 ]. Among them, four were highly polymorphic only in Chinese local populations and the analysis of the genetic relationships between all the 268 male horses analysed allowed for the identification of 19 Y-chromosomal haplotypes.…”

“…Among them, four were highly polymorphic only in Chinese local populations and the analysis of the genetic relationships between all the 268 male horses analysed allowed for the identification of 19 Y-chromosomal haplotypes. Three indigenous breeds (Debao pony, Guizhou and Jinjiang) living in the isolated regions of southwestern China, showed haplotypes distant from those arbored by other Chinese indigenous and introduced horses, thus suggesting a highly paternal diversity preserved in this geographic area [ 135 ]. In the last twenty years, many modern horse breeds from different geographic areas were analysed for the Y chromosome by employing different sequencing technologies ( Table S2 ).…”

Whole-Genome Sequence Analysis Reveals the Origin of the Chakouyi Horse

“…In the Ming Dynasty (A.D.1368–1644), a market for exchanging tea for horses was established in Tianzhu County, and horses from Inner-Mongolia and the Qinghai–Tibet Plateau were gathered in the place, which facilitated gene exchange between the introduced horses and the local horses [ 22 ]. Our previous study with Y chromosomal microsatellites also indicated that the Mongolian horse, the Chakouyi horse, and the Tibetan horse have close genetic links [ 3 ]. The Kazak horse is an ancient indigenous breed distributed in Xinjiang Province along the Silk Road.…”

“…Previous studies on Chinese indigenous horses with mtDNA showed that the haplotype diversity of Chakouyi horses was relatively high compared with other Chinese indigenous horse breeds (CHBs), which indicated that there are plentiful maternal lines in Chakouyi horses [ 2 ]. Analysis with Y-chromosomal microsatellite DNA revealed that the Chakouyi horse has a close genetic link with the Mongolian horse [ 3 ]. Another study with whole genome SNP array indicated that the Chakouyi horse is one of the most likely ancestors of the Jinjiang horse, an indigenous horse breed from the southeastern coasts of China [ 4 ].…”