Characteristics Of Genome Structure In Horse×Donkey Hybrids

As the hybrids of horse and donkey,hinny and mule belongs to interspecific hybrids and Distant Hybridized Progenies.Compared with the inbred hybrids,the distant hybrid has not only the genetic characteristics of parents,but also has recombination characteristics.There are some differences in appearance and physiological characteristics of reciprocal-cross hybrid(hinny and mule),such as mule is taller than hinny,tail is longer,ears are shorter and muscle strength is stronger in mule than those in hinny.There are some heterosis in mule and hinny,such as strong resistance to disease,rough feeding and longevity.The purpose of this study is to obtain the correlation between the genome structural characteristics and heterosis by analyzing the genetic variation of mule and donkey genomes,and try to explain the differences of physiological characteristics between mule and donkey on a genome-wide scale.The results are as follows:1.A total of 380 Gb clean bases were generated after genome sequencing for two hinnies and mules,89.9-104 Gb clean bases in each individual.The average GC content of four hybrids was 43.54%.In average,97.91% and 92.30% of clean reads in hybrids were aligned to horse genome and donkey genome when they were as the reference genome,respectively.Among them,86.89% and 85.89% of clean readswere uniquely mapped.Because the genome size of hinny and mule are unknown,the sequencing depth are about 27.5× and 27.6× when the genome size of horse and donkey is taken as reference.The average percentage of hybrid genome aligned to horse and donkey reference genome were 49.08% and 50.93%,respectively.The content of donkey genome in mule is 1.85% higher than that of horse genome.2.When horse genome was as the reference genome,we identified 29,515,796,29,515,095,29,565,310,29,398,065 SNPs,2,95,8398,2,944,246,2,945,901,2,935,480 INDELs,and 12,270,9,078,10,783,10,955 CNVR in hinny-1,hinny-2,mule-1 and mule-2,respectively.SNP and INDEL density and CNVR enrichment on horse chromosomes in hinnes and mules were calculated.The results showed that SNP and INDEL density were the highest on chr12 and 31,and the lowest on chromosome X.The highest CNVR enrichment chromosome was chr 12,and chr17 was the lowest.There are 365,1378 and 484 hinny-specific SNP,INDEL and CNVR releted genes,and 365,1,376,417 mule specific SNP,INDEL and CNVR related genes,respectively.Hinny-mule shared SNP,INDEL and CNCR related genes were9990,9989 and 1282.We performed a functional annotation clustering analysis of these genes to identify gene function.The result was that genes were mainly enriched in metabolic and immune related pathways,genes enriched in longevity related pathways were also found.3.When donkey genome was as the reference genome,28,973,545,29,103,121,29,024,024 and 28,899,727 SNPs,3,009,808,3,019,841,3,006,103 and 2,986,902 INDELs,27486,24377,27010 and 24518 CNVR were identified in hinny-1,hinny-2,mule-1 and mule-2,respectively.There are 1,225,1,709,1,009 hinny-specific SNP,INDEL and CNVR releted genes,and 1,224,1,661,1,143 mule specific SNP,INDEL and CNVR related genes,respectively.Hinny-mule shared SNP,INDEL and CNCR related genes were 9990,9989 and 1282.The result of functional annotation clustering was that genes were also mainly enriched in metabolic and immune related pathways,and several genes enriched in longvity pathways.4.we identified 293,321,388 和 502 CTXR in hinny-1,hinny-2,mule-1 and mule-2.The highest CTX enrichment was found on chr 3.CTX related genes include10 horse genes and 15 donkey genes shared between four individual was performed functional annotionin and they enriched in metabolic related pathways.5.All the genetic variation and CTX related genes were collected and co-expression network of different expression genes(DEGs)in hinny specific variant and mule specific variant genes were carried out.We found that the key genes in co-expression network were related to metabolic related pathways.GAPDH and ALDOA was participated in glycolysis / gluconeogenesis,and ALDOA is an glycolysis enzyme,which contributes to biological process related to muscle maintenance and striated muscle contraction.APOA1 was important for lipid metabolism,CXCL1 was related to immunity.Genetic variation and CTX genes releted to metabolism,immunity and longevity may be associated with coarse feeding tolerance,strong resistance and longevity.The genome variation in hinny and mule enriches the genomic data ofequine,and provides theoretical basis for the genomic research of Distant Hybridized Progenies.