| In order to understand the status of germplasm resources of Qingtian paddy field carp(Cyprinus carpio var.qingtianensis)and the genetic differences between the three groups of Qingtian paddy field carp、blunt snout bream(Megalobrama amblycephala)and their hybrid,and then explore the genetic characteristics of the distant hybrid offspring with Qingtian paddy field carp as the mother and blunt snout bream as the father,so as to provide a basis for distant hybridization and molecular breeding of Qingtian paddy field carp.In this paper,the population of hybrids and their parents obtained by distant hybridization of Qingtian paddy field carp and blunt snout bream in Qingtian County,Lishui City,Zhejiang Province,China,was used to analyze the morphological differences of the population,and the genetic structure and genetic diversity of the population were studied by using 2b-RADseq technology to type SNP markers,and the genome-wide association analysis of the population based on morphological differences and SNP molecular markers was analyzed.The main conclusions are as follows:1.Morphological study of Qingtian paddy field carp、blunt snout bream and hybridBased on traditional morphological data and framework data,multivariate statistical analysis was performed on the morphology of 14 biological groups of Qingtian paddy field carp(♀),blunt snout bream(♂)and hybrid.One-way ANOVA showed that there were no significant differences between the number of caudal scales and ventral fin bars in hybrid and the parent(P>0.05),and the pectoral and caudal fin stripes of hybrid were significantly different from those of the mother Qingtian paddy field carp(P<0.05),and there was no significant difference in the remaining 12 personality traits(P>0.05),which were significantly different from the paternal blunt snout bream in the caudal scales,There were no significant differences between the 4personality traits of pectoral fin stripes,ventral fin stripes and caudal fin stripes(P>0.05),and the remaining 10 personality traits had significant differences(P<0.05).The average HI of the quantifiable trait indicates that the hybrid is more similar to the Qingtian paddy field carp.Six biological traits with significant differences(P<0.01)were screened out by discriminant and principal component analysis: D7-9/full length(X22),D3-6/full length(X14),D5-8/full length(X18),snout length/full length(X3),eye diameter/full length(X7)and body length/full length(X1),and the categorical discriminant functions Y1 and Y2 were obtained,which could effectively distinguish the two groups of hybrid and Qingtian paddy field carp.The first and second principal components of the morphology of hybrid and blunt snout bream can separate the two biological groups,reflecting the difference in tail and back,respectively.The cluster analysis plot showed that the bream and the hybrid offspring were far apart,and the morphological differences between the two groups were large.The first and second principal components of the morphological principal components of hybrid and Qingtian paddy field carp could not separate the two biological groups,indicating that the morphological differences between the offspring and the mother of the hybrid were small.2.Population genetics of Qingtian paddy field carp、blunt snout bream and hybridIn this study,the genetic structure and genetic diversity of the hybrid with Qingtian paddy field carp and blunt snout bream were analyzed based on 2b-RADseq.The results showed that 58099 SNP genetic markers were identified between hybrid and Qingtian paddy field carp population,and the conversion and inversion ratio was1.523.The Ho,He,Fig,Pi and Ne of the two groups of Qingtian paddy field carp and hybrid were 0.156/0.200,0.167/0.174,0.141/0.137,0.174/0.182 and 1.256/1.316,respectively.Except for the polymorphic information content,the other genetic diversity indexes of Qingtian paddy field carp were lower than those of hybrid.Phylogenetic tree analysis divided 30 biological individuals into 2 branches,one group of Qingtian paddy field carp and the rest of the hybrid were grouped,STRUCTURE analysis and PCA analysis also divided 30 biological individuals into 2subgroups,Qingtian paddy field carp and hybrid each as a subgroup.The proportion of homozygous sites in Qingtian paddy field carp was smaller than that of hybrid,but the proportion of heterozygous sites was greater than that of hybrid.A total of 34564 SNP genetic markers were identified in the hybrid and blunt snout bream populations with a conversion and reversal ratio of 1.774.The Ho,He,Fig,Pi and Ne of the two groups of blunt snout bream and hybrid were 0.048/0.358,0.047/0.573,0.041/0.276,0.050/0.375 and 1.070/1.674,respectively.The genetic diversity indexes of blunt snout bream were lower than those of the hybrid.Phylogenetic tree analysis divided30 biological individuals into 2 branches,one cluster into a group of blunt snout bream,and the rest of the hybrid into one,STRUCTURE analysis and PCA analysis also divided 30 biological individuals into 2 subgroups,and the group blunt snout bream and hybrid were each a subgroup.The proportion of homozygous sites is greater than that of hybrid,but the proportion of heterozygous sites is smaller than that of hybrid enetic differentiation between the hybrid and the Qingtian paddy field carp population,and the population of the group blunt snout bream had a high degree of genetic differentiation,which was consistent with the genetic distance comparison results.In summary,there is a large genetic differentiation between the hybrid and the parent population,but the genetic difference with the paternal group blunt snout bream is greater,and after distant hybridization,the hybrid and the parent population have been significantly differentiated in the genome,and this distant hybrid is relatively successful.3.Genome-wide association analysis of differential traits between Qingtian paddy field carp、blunt snout bream and hybridAccording to the results of multivariate statistical analysis of the morphology of hybrid and Qingtian paddy field carp and Lumphead blunt snout bream,two personality traits with significant differences between hybrid and their parents were selected,respectively,X24 and X25,and X12 and X14 of Qingtian paddy field carp,and a total of 3 SNP sites with significant differences in X24,0 X25,63 X12 and X14 were detected by GWAS analysis of 4 different traits,and a total of 50 kp regions were detected above and below the genome position of SNP sites.X24 had 3 candidates,X12 had 63,and X14 had 7 candidate genes.After analysis and summary,LOC109063082,LOC109096762 and LOC122148208,three significantly related genes,are closely related to the MAPK signal pathway,which is involved in a series of physiological activities such as cell growth,development,differentiation and apoptosis,and may be the key to cause the difference in the traits of hybrid and Qingtian paddy field carp X12(D3-4).These three genes need further verification to explore the genetic differences between hybrid and Qingtian paddy field carp. |
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